The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit

NASA Astrophysics Data System (ADS)

Balabin, Roman M.

2011-10-01

High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).

Molecular structure and conformational composition of methyl chloroacetate: An electron-diffraction and ab initio molecular orbital investigation

NASA Astrophysics Data System (ADS)

Aarset, Kirsten; Boldermo, Kjell Gunnar; Hagen, Kolbjørn

2010-08-01

The molecular structure and conformational composition of methyl chloroacetate, H 2ClC sbnd C( dbnd O) sbnd O sbnd CH 3, have been determined by gas-phase electron-diffraction (GED), using results from ab initio molecular orbital calculations (HF, MP2 and MP3/6-311+G(d,p)) to obtain constraints on some of the structural parameters. The molecules exist in the gas-phase at 25 °C as a mixture of two stable conformers: syn with C sbnd Cl eclipsing C dbnd O and gauche with C sbnd H approximately eclipsing C dbnd O. In both of these conformers O sbnd CH 3 is also eclipsing C dbnd O. The experimentally observed conformational composition at 25 °C was 36(8)% syn and 64(8)% gauche (parenthesised values are 2 σ), corresponding to a free energy difference between conformers of ΔGexp° = 1.4(9) kJ/mol. The corresponding theoretical values obtained for Δ G° are 1.1 kJ/mol (HF), 2.3 kJ/mol (MP2), and 2.4 kJ/mol (MP3). The results for the principal distances ( rh1) and angles ( ∠h1) for the major gauche conformer obtained from the combined GED/ ab initio study (2 σ uncertainties) are r(CO sbnd CCl) = 1.502(9) Å, r(C sbnd H) = 1.084(6) Å (average value), r(C sbnd Cl) = 1.782(4) Å, r(C dbnd O) = 1.213(4) Å, r(CO sbnd O) = 1.346(4) Å, r(CH 3sbnd O) = 1.468(10) Å, ∠C sbnd C sbnd Cl = 110.0(6)°, ∠C sbnd C dbnd O = 124.7(6)°, ∠C sbnd C sbnd O = 108.3(10)°, ∠C sbnd O sbnd C = 115.9(8)°, ϕ(Cl sbnd C sbnd C dbnd O) = 111(2)°, ϕ(C sbnd O sbnd C dbnd O) = 3(3)°.

A Comparison of the ab Initio Calculated and Experimental Conformational Energies of Alkylcyclohexanes

NASA Astrophysics Data System (ADS)

Freeman, Fillmore; Tsegai, Zufan M.; Kasner, Marc L.; Hehre, Warren J.

2000-05-01

Ab initio 6-31G(d) and MP2/6-31G(d)//6-31G(d) methods were used to calculate the energies of the rotamers of the chair conformers of alkylcyclohexanes and trimethylsilylcyclohexane. The MP2/6-31G(d)//6-31G(d) calculated conformational energies ( ? or A values, in kcal/mol) of the alkylcyclohexanes (Me = 1.96; Et = 1.80; Pr = 1.73 iso-Pr = 1.60; t-Bu = 5.45; neo-pent = 1.32) and trimethylsilylcyclohexane (SiMe3 = 2.69) are similar to the experimental values. Plots of the calculated conformational energies for the alkylcyclohexanes and trimethylsilylcyclohexane versus their experimental values are linear (slope = 1.253 and r = .993 for 6-31G(d) and slope = 1.114 and r = .982 for MP2/6-31G(d)//6-31G(d)). The conformational energies are determined primarily by steric effects which include gauche (synclinal) interactions and repulsive nonbonded interactions in both the axial and equatorial conformers.

Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets.

PubMed

Manna, Debashree; Kesharwani, Manoj K; Sylvetsky, Nitai; Martin, Jan M L

2017-07-11

Benchmark ab initio energies for BEGDB and WATER27 data sets have been re-examined at the MP2 and CCSD(T) levels with both conventional and explicitly correlated (F12) approaches. The basis set convergence of both conventional and explicitly correlated methods has been investigated in detail, both with and without counterpoise corrections. For the MP2 and CCSD-MP2 contributions, rapid basis set convergence observed with explicitly correlated methods is compared to conventional methods. However, conventional, orbital-based calculations are preferred for the calculation of the (T) term, since it does not benefit from F12. CCSD(F12*) converges somewhat faster with the basis set than CCSD-F12b for the CCSD-MP2 term. The performance of various DFT methods is also evaluated for the BEGDB data set, and results show that Head-Gordon's ωB97X-V and ωB97M-V functionals outperform all other DFT functionals. Counterpoise-corrected DSD-PBEP86 and raw DSD-PBEPBE-NL also perform well and are close to MP2 results. In the WATER27 data set, the anionic (deprotonated) water clusters exhibit unacceptably slow basis set convergence with the regular cc-pVnZ-F12 basis sets, which have only diffuse s and p functions. To overcome this, we have constructed modified basis sets, denoted aug-cc-pVnZ-F12 or aVnZ-F12, which have been augmented with diffuse functions on the higher angular momenta. The calculated final dissociation energies of BEGDB and WATER27 data sets are available in the Supporting Information. Our best calculated dissociation energies can be reproduced through n-body expansion, provided one pushes to the basis set and electron correlation limit for the two-body term; for the three-body term, post-MP2 contributions (particularly CCSD-MP2) are important for capturing the three-body dispersion effects. Terms beyond four-body can be adequately captured at the MP2-F12 level.

The torsional energy profile of 1,2-diphenylethane: an ab initio study

NASA Astrophysics Data System (ADS)

Ivanov, Petko M.

1997-08-01

Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

PubMed

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

Ab initio calculations, structure, NBO and NCI analyses of Xsbnd H⋯π interactions

NASA Astrophysics Data System (ADS)

Wu, Qiyang; Su, He; Wang, Hongyan; Wang, Hui

2018-02-01

The performance of ab initio methods (MP2, DFT/B3LYP, random-phase approximation (RPA), CCSD(T) and QCISD(T)) in predicting interaction energy of Xsbnd H⋯π (Xsbnd H = HCCH, HCl, HF; π = C2H2, C2H4, C6H6) hydrogen complexes are assessed systematically. The CCSD(T)/CBS benchmarks of interaction energy are reported. It is found that RPA agrees well with CCSD(T)/CBS benchmarks and experimental results. CCSD(T) and QCISD(T) perform the best only when compared with CCSD(T)/CBS benchmarks, MP2 performs well only for experimental data. B3LYP provides the worst accuracy. Additionally, the equilibrium structure, interaction type of Xsbnd H⋯π hydrogen complexes are investigated by the natural bond orbital (NBO) and the non-covalent interaction index (NCI).

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data.

PubMed

Pitonák, Michal; Neogrády, Pavel; Cerný, Jirí; Grimme, Stefan; Hobza, Pavel

2009-01-12

Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.

An ab initio study of the molecular properties of the propyne water hydrogen-bonded complex

NASA Astrophysics Data System (ADS)

Lopes, Kelson C.; Araújo, Regiane C. M. U.; Rusu, Victor H.; Ramos, Mozart N.

2007-05-01

We have employed ab initio MP2 and DFT/B3LYP calculations with the 6-31++G(d,p) basis set to obtain structural, electronic and vibrational properties of the H-bonded complex between propyne and water. This study has revealed that H 2O can doubly complex with propyne forming a quasi five-membered ring. The first complexation occurs through the hydrogen bond between the acid hydrogen of H 2O and the C tbnd C triple bond, whereas the second complexation involves the oxygen atom of H 2O and the in-plane hydrogen atom of the methyl group in propyne. Our calculations have shown that the H-bond lengths between H⋯π and O⋯HC) are 2.419 and 2.707 Å, respectively, employing the DFT/B3LYP calculation whereas the corresponding MP2 values are 2.373 and 2.651 Å. The binding energies including both BSSE and ZPE corrections are -6.16 and -6.72 kJ mol -1, respectively, using the DFT/B3LYP and MP2 calculations. For example, the O-H stretching frequencies of water are decreased by -60 and -29 cm -1 using the DFT/B3LYP calculation, whereas the bending frequency is increased by +15 cm -1. As expected, the infrared intensities for the stretching modes are increased after complexation, especially involving the O-H b bond forming the hydrogen bond with the C tbnd C triple bond.

Intermolecular Potentials of Methane Assessed by Second Virial Coefficients, ab Initio Dimer Interaction Energies, and Aggregate Cohesive Energies.

PubMed

Ribeiro, Douglas S

2017-06-01

This study presents computations of three energy related properties for 26 previously published multisite intermolecular potentials of methane: MM2, MM3, MM2en, MM3en, MM2mc, MM3mc, MM3envir, RMK, OPLS all-atom, MUB-2, AMBER, BOYD, Williams, Sheikh, MG, Tsuzuki, E2-Gay, E4-Gay, MP4exp-6(iii), MP4exp-6(iv), Rowley-A, Rowley-B, TraPPE-EH, Ouyang, CLC, and Chao and three united atom potentials: Saager-Fischer (SF), OPLS united atom, and HFD. The three properties analyzed are the second virial coefficients for 14 temperature points in the range of 110 to 623.15 K, the interaction energies for 12 orientations of the methane dimer as a function of distance followed by a comparison to three ab initio data sets and the cohesive energy of the aggregate of 512 methane molecules. The latter computed energies are correlated to latent heat of evaporation of 11 potentials and are proposed as surrogate approximate parameters for ΔH vap for the studied potentials. The 10 best performing potentials are selected by rms order in each one of the properties and three of them are found to be present simultaneously in the three sets: Tsuzuki, MM3mc, and MM2mc. On the basis of the cohesive energy of the aggregate, a quantitative measure of the anisotropy of the potentials is proposed. The results are discussed on the basis of anisotropy, nonadditivity and ability of the potentials to reproduce ab initio data. It is concluded that the nonadditivity of the pair potentials holds and the available ab initio data did not lead to pair potentials that are cohesive enough to reproduce accurately the second virial coefficients.

G3(MP2)-CEP theory and applications for compounds containing atoms from representative first, second and third row elements of the periodic table.

PubMed

Pereira, Douglas Henrique; Rocha, Carlos Murilo Romero; Morgon, Nelson Henrique; Custodio, Rogério

2015-08-01

The compact effective potential (CEP) pseudopotential was adapted to the G3(MP2) theory, herein referred to as G3(MP2)-CEP, and applied to the calculation of enthalpies of formation, ionization energies, atomization energies, and electron and proton affinities for 446 species containing elements of the 1st, 2nd, and 3rd rows of the periodic table. A total mean absolute deviation of 1.67 kcal mol(-1) was achieved with G3(MP2)-CEP, compared with 1.47 kcal mol(-1) for G3(MP2). Electron affinities and enthalpies of formation are the properties exhibiting the lowest deviations with respect to the original G3(MP2) theory. The use of pseudopotentials and composite theories in the framework of the G3 theory is feasible and compatible with the all electron approach. Graphical Abstract Application of composite methods in high-level ab initio calculations.

A QUANTUM MECHANICAL STUDY OF THE PROTONATION AND COVALENT HYDRATION OF QUINAZOLINE IN THE PRESENCE OF METAL CATIONS

EPA Science Inventory

We have investigated the protonation and reversible covalent hydration of quinazoline in the presence of Li+, Na+, and Ca2+ ions using ab initio quantum mechanical calculations at the MP2/6-31G**//HF/6-31G*level of theory. Proton affinities, enthalpies of hydration at 298.15K (DH...

High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Soohaeng; Apra, Edoardo; Zeng, Xiao Cheng

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at the MP2 and CCSD(T) levels of theory and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17 the CCSD(T) calculations confirm the previously found at the MP2 level of theory "interior" arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum.

High-Level ab-initio Electronic Structure Calculations of Water Clusters (H2O)16 and (H2O)17 : a New Global Minimum for (H2O)16

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Soohaeng; Apra, Edoardo; Zeng, X.C.

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at both the MP2 and CCSD(T) levels of theory, and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17, the CCSD(T) calculations confirm the previously found at the MP2 level of theory interior arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum

Ionic liquids. Combination of combustion calorimetry with high-level quantum chemical calculations for deriving vaporization enthalpies.

PubMed

Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas; Schick, Christoph

2008-07-10

In this work, the molar enthalpies of formation of the ionic liquids [C2MIM][NO3] and [C4MIM][NO3] were measured by means of combustion calorimetry. The molar enthalpy of fusion of [C2MIM][NO3] was measured using differential scanning calorimetry. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for the ionic species using the G3MP2 theory. We have used a combination of traditional combustion calorimetry with modern high-level ab initio calculations in order to obtain the molar enthalpies of vaporization of a series of the ionic liquids under study.

Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study.

PubMed

Al-Otaibi, Jamelah S

2015-01-01

2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP). Møller-Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000-400 cm(-1)). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra. Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.

Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

NASA Astrophysics Data System (ADS)

Remko, Milan

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

Support vector machine regression (LS-SVM)--an alternative to artificial neural networks (ANNs) for the analysis of quantum chemistry data?

PubMed

Balabin, Roman M; Lomakina, Ekaterina I

2011-06-28

A multilayer feed-forward artificial neural network (MLP-ANN) with a single, hidden layer that contains a finite number of neurons can be regarded as a universal non-linear approximator. Today, the ANN method and linear regression (MLR) model are widely used for quantum chemistry (QC) data analysis (e.g., thermochemistry) to improve their accuracy (e.g., Gaussian G2-G4, B3LYP/B3-LYP, X1, or W1 theoretical methods). In this study, an alternative approach based on support vector machines (SVMs) is used, the least squares support vector machine (LS-SVM) regression. It has been applied to ab initio (first principle) and density functional theory (DFT) quantum chemistry data. So, QC + SVM methodology is an alternative to QC + ANN one. The task of the study was to estimate the Møller-Plesset (MPn) or DFT (B3LYP, BLYP, BMK) energies calculated with large basis sets (e.g., 6-311G(3df,3pd)) using smaller ones (6-311G, 6-311G*, 6-311G**) plus molecular descriptors. A molecular set (BRM-208) containing a total of 208 organic molecules was constructed and used for the LS-SVM training, cross-validation, and testing. MP2, MP3, MP4(DQ), MP4(SDQ), and MP4/MP4(SDTQ) ab initio methods were tested. Hartree-Fock (HF/SCF) results were also reported for comparison. Furthermore, constitutional (CD: total number of atoms and mole fractions of different atoms) and quantum-chemical (QD: HOMO-LUMO gap, dipole moment, average polarizability, and quadrupole moment) molecular descriptors were used for the building of the LS-SVM calibration model. Prediction accuracies (MADs) of 1.62 ± 0.51 and 0.85 ± 0.24 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) were reached for SVM-based approximations of ab initio and DFT energies, respectively. The LS-SVM model was more accurate than the MLR model. A comparison with the artificial neural network approach shows that the accuracy of the LS-SVM method is similar to the accuracy of ANN. The extrapolation and interpolation results show that LS-SVM is superior by almost an order of magnitude over the ANN method in terms of the stability, generality, and robustness of the final model. The LS-SVM model needs a much smaller numbers of samples (a much smaller sample set) to make accurate prediction results. Potential energy surface (PES) approximations for molecular dynamics (MD) studies are discussed as a promising application for the LS-SVM calibration approach. This journal is © the Owner Societies 2011

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Computation of geometries and frequencies of singlet and triplet nitromethane with density functional theory byusing gaussian type orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jursic, B.S.

1996-12-31

The results of the computational study of the structures, energies, dipole moments and IR spectra for a singlet and a triplet nitromethane are presented. Five different hybrids (BHandH, BHandHLYP, B3LYP, B3P86 and B3PW91), local (SVWN), and nonlocal (BLYP) DFT methods are used with various sizes of the gaussian type of basis set. The obtained results are compared to the HF, MP2, and MCSCF ab initio calculations, as well as, to the experimental results. Becke`s three functional based hybrid DFT methods outperform the following: the ab initio (HF, MP2 and MCSCF), the Becke`s half-and-half based DFT methods, and the local (SVWNmore » or LSDA) and nonlocal (BLYP) DFT methods. The computed nitromethane geometry, the dipole moment, the energy difference, and the IR frequency are in extraordinary agreement with the experimental results. Thus, we are recommending the B3LYP and the B3PW91 as the methods of choice when the computational study of small {open_quotes}difficult{close_quotes} molecules is considered.« less

Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

NASA Astrophysics Data System (ADS)

Autrey, Daniel; Choo, Jaebum; Laane, Jaan

2000-10-01

The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 on Mg 2+ sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations.

PubMed

Yoshioka, Akio; Fukuzawa, Kaori; Mochizuki, Yuji; Yamashita, Katsumi; Nakano, Tatsuya; Okiyama, Yoshio; Nobusawa, Eri; Nakajima, Katsuhisa; Tanaka, Shigenori

2011-09-01

Ab initio electronic-state calculations for influenza virus hemagglutinin (HA) trimer complexed with Fab antibody were performed on the basis of the fragment molecular orbital (FMO) method at the second and third-order Møller-Plesset (MP2 and MP3) perturbation levels. For the protein complex containing 2351 residues and 36,160 atoms, the inter-fragment interaction energies (IFIEs) were evaluated to illustrate the effective interactions between all the pairs of amino acid residues. By analyzing the calculated data on the IFIEs, we first discussed the interactions and their fluctuations between multiple domains contained in the trimer complex. Next, by combining the IFIE data between the Fab antibody and each residue in the HA antigen with experimental data on the hemadsorption activity of HA mutants, we proposed a protocol to predict probable mutations in HA. The proposed protocol based on the FMO-MP2.5 calculation can explain the historical facts concerning the actual mutations after the emergence of A/Hong Kong/1/68 influenza virus with subtype H3N2, and thus provides a useful methodology to enumerate those residue sites likely to mutate in the future. Copyright © 2011 Elsevier Inc. All rights reserved.

On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors.

PubMed

Bauzá, Antonio; Alkorta, Ibon; Frontera, Antonio; Elguero, José

2013-11-12

In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl(-) or Br(-)), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions, we have studied how the hybridization of the chalcogen atom influences the interaction energies.

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction.

PubMed

Siu, Chi-Kit; Liu, Zhi-Feng; Tse, John S

2002-09-11

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

PubMed

Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

2005-10-07

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

Ab initio SCF study of the barrier to internal rotation in simple amides. Part 3. Thioamides

NASA Astrophysics Data System (ADS)

Vassilev, Nikolay G.; Dimitrov, Valentin S.

2003-06-01

The free energies of activation for rotation about the thiocarbonyl C-N bond in X-C(S)N(CH 3) 2 (X=H, F, Cl, CH 3, CF 3) were calculated at the MP2(fc)/6-31+G*//6-31G* and MP2(fc)/6-311++G**//6-311++G** levels and compared with literature NMR gas-phase data. The results of calculations indicate that the nonbonded interactions in ground state (GS) are mainly responsible for the differences in the rotational barriers. For X=H, CH 3 and CF 3, the anti transition state (TS) is more stable; for the case X=Cl, the syn TS is more stable, while for the X=F, the two TS are energetically almost equivalent.

Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

NASA Astrophysics Data System (ADS)

Srivastava, Santosh K.; Singh, Vipin B.

2013-11-01

Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

Ab initio study of the barrier to internal rotation in simple amides. 1. N, N-dimethylformamide and N, N-dimethylcarbamic halogenides

NASA Astrophysics Data System (ADS)

Vassilev, Nikolay G.; Dimitrov, Valentin S.

1999-06-01

Free energies of activation for rotation about the amide C-N bond in X-C(O)N(CH 3) 2 (X=H, F, Cl and Br) were calculated at the MP2(fc)/6-31+G*//6-31G* and MP2(fc)/6-311++G**//6-311++G** levels and compared with NMR gas-phase data. The results of calculations indicate that the repulsion between X and methyl group in ground state and the repulsion between X or oxygen and nitrogen lone pair in transition states (TS) are largely responsible for the difference in the free energies of the studied amides. For X=H (DMF), the anti TS is more stable; for the cases X=Cl, Br, the syn TS is more stable, while for the case X=F the two transition states are energetically almost equivalent.

Evaluation of Density Functionals and Basis Sets for Carbohydrates

USDA-ARS?s Scientific Manuscript database

Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...

Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

NASA Astrophysics Data System (ADS)

Klein, Erik; Lukeš, Vladimír

2006-11-01

In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

High-level ab initio calculations for the four low-lying families of minima of (H2O)(20): 1. Estimates of MP2/CBS binding energies and comparison with empirical potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanourgakis, Georgios S.; Apra, Edoardo; Xantheas, Sotiris S.

2004-08-08

We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). Themore » energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.« less

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Ab initio correlated study of the Al13H- anion: Isomers, their kinetic stability and vertical detachment energies

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2012-01-01

We report correlated ab initio calculations for the Al13H- cluster anion isomers, their kinetic stability and vertical detachment energies (VDEs). Of the two most energetically favored anion structures involving H atom in terminal and threefold bridged sites of the icosahedral Al13-, the higher energy ‘threefold bridged' isomer is shown to be of low kinetic stability. Our results are consistent with the recent photoelectron spectroscopy (PE) study of Grubisic et al. who observed two distinct Al13H- isomers, one of them identified as ‘metastable'. The VDE energies computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level for the ‘terminal' and ‘threefold bridged' Al13H- isomers of 3.21 and 2.32 eV are in good agreement with those determined in the PE study.

Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods

NASA Astrophysics Data System (ADS)

Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.

1997-08-01

We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.

Probing the Properties of Polynuclear Superhalogens without Halogen Ligand via ab Initio Calculations: A Case Study on Double-Bridged [Mg2 (CN)5 ](-1) Anions.

PubMed

Li, Jin-Feng; Li, Miao-Miao; Bai, Hongcun; Sun, Yin-Yin; Li, Jian-Li; Yin, Bing

2015-12-01

An ab initio study of the superhalogen properties of eighteen binuclear double-bridged [Mg2 (CN)5 ](-1) clusters is reported herein by using various theoretical methods. High-level CCSD(T) results indicate that all the clusters possess strong superhalogen properties owing to their high vertical electron detachment energies (VDEs), which exceed 6.8 eV (highest: 8.15 eV). The outer valence Green's function method provides inaccurate relative VDE values; hence, this method is not suitable for this kind of polynuclear superhalogens. Both the HF and MP2 results are generally consistent with the CCSD(T) level regarding the relative VDE values and-especially interesting-the average values of the HF and MP2 VDEs are extremely close to the CCSD(T) results. The distributions of the extra electrons of the anions are mainly aggregated into the terminal CN units. These distributions are apparently different from those of previously reported triple-bridged isomers and may be the reason for the decreased VDE values of the clusters. In addition, comparisons of the VDEs of binuclear and mononuclear superhalogens as well as studies of the thermodynamic stabilities with respect to the detachment of various CN(-1) ligands are also performed. These results confirm that polynuclear structures with pseudohalogen ligands can be considered as probable new superhalogens with enhanced properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization.

PubMed

Salim, Michael A; Willow, Soohaeng Yoo; Hirata, So

2016-05-28

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials is taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born-Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization

NASA Astrophysics Data System (ADS)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So

2016-05-01

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials is taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born-Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So, E-mail: sohirata@illinois.edu

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D{sub 2}O ice greater than that of H{sub 2}O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials ismore » taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born–Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.« less

Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

NASA Astrophysics Data System (ADS)

Georgieva, Miglena K.

2004-03-01

The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

PubMed Central

Maulitz, Andreas H.; Lightstone, Felice C.; Zheng, Ya-Jun; Bruice, Thomas C.

1997-01-01

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF/6–31+G(d), MP2/6–31+G(d), and MP4/6–31+G(d) levels of theory. The central barriers (calculated from the initial ion–molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen. PMID:9192609

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data.

PubMed

Durig, Douglas T; Durig, M S; Durig, James R

2005-05-01

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.

Effect of tautomerism on Au-6-mercaptopurine nanocluster stability

NASA Astrophysics Data System (ADS)

Rashidpour, Neda; Kashid, Vikas; Shah, Vaishali

2013-02-01

We have investigated the stability of conjugated nanoparticles of Au-6-Mercaptopurine (6-MP) using ab initio density functional theory. We have studied the conjugation of the 6 tautomers of 6-MP via the different atomic sites with the gold nanoparticles. Our results show that the least stable tautomer has the strongest adsorption with the Au nanoparticles whereas the most stable tautomer has the weakest adsorption. We will discuss our results to explain the experimentally observed increased plasma half life time of the conjugated drug in vitro.

Ab initio/GIAO-CCSD(T) (13)C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6H13(+) and C7H15(+).

PubMed

Olah, George A; Prakash, G K Surya; Rasul, Golam

2016-01-05

The rearrangement pathways of the equilibrating tertiary carbocations, 2,3-dimethyl-2-butyl cation (C6H13(+), 1), 2,3,3-trimethyl-2-butyl cation (C7H15(+), 5) and 2,3-dimethyl-2-pentyl cation (C7H15(+), 8 and 9) were investigated using the ab initio/GIAO-CCSD(T) (13)C NMR method. Comparing the calculated and experimental (13)C NMR chemical shifts of a series of carbocations indicates that excellent prediction of δ(13)C could be achieved through scaling. In the case of symmetrical equilibrating cations (1 and 5) the Wagner-Meerwein 1,2-hydride and 1,2-methide shifts, respectively, produce the same structure. This indicates that the overall (13)C NMR chemical shifts are conserved and independent of temperature. However, in the case of unsymmetrical equilibrating cations (8 and 9) the Wagner-Meerwein shift produces different tertiary structures, which have slightly different thermodynamic stabilities and, thus, different spectra. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level structure 8 is only 90 calories/mol more stable than structure 9. Based on computed (13)C NMR chemical shift calculations, mole fractions of these isomers were determined by assuming the observed chemical shifts are due to the weighted average of the chemical shifts of the static ions. © 2015 Wiley Periodicals, Inc.

An ab initio MO study on the hydrolysis of methyl chloride with explicit consideration of 13 water molecules

NASA Astrophysics Data System (ADS)

Yamataka, Hiroshi; Aida, Misako

1998-06-01

Ab initio MO calculations (HF/3-21G, HF/6-31G, HF/6-31+G* and MP2/6-31+G*) were carried out on the hydrolysis of CH 3Cl in which up to 13 water solvent molecules were explicitly considered. For n⩾3, three important stationary points ( cmp1, TS, and cmp2) were detected in the course of the reaction. The calculations for the n=13 system at the HF/6-31+G* level reproduced the experimental activation enthalpy and the secondary deuterium kinetic isotope effect. The two reacting bond lengths in the transition state are 1.975 Å (O-C) and 2.500 Å (C-Cl), and CH 3Cl is surrounded by 13 water molecules without any apparent vacant space. The proton transfer from the attacking water to the water cluster occurs after TS is reached.

Theoretical and experimental studies of the structure and vibrational spectra of NTO

NASA Astrophysics Data System (ADS)

Sorescu, Dan C.; Sutton, Teressa R. L.; Thompson, Donald L.; Beardall, David; Wight, Charles A.

1996-10-01

The structure and vibrational spectra of the high explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) have been determined by ab initio molecular orbital calculations at the Hartree-Fock and second-order Møller-Plesset levels and by density functional theory (B3LYP). Experimental frequencies for the molecule have been determined from infrared spectra of pure NTO films and NTO molecules isolated in an argon matrix at 21 K. A force field for gas phase NTO has been obtained based on calculated results at the MP2/6-311G∗∗ level. In addition, a force field for solid state NTO has been constructed using the experimental vibrational frequencies for NTO films and scaled ab initio vibrational frequencies. Differences between the solid state and gas phase results indicate that the environment and preparation procedure exert a marked influence on the spectral characteristics of the NTO molecule.

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

On the origin of the gauche effect. A quantum chemical study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Engkvist, O.; Karlström, G.; Widmark, P.-O.

1997-01-01

The conformational equilibrium of 1,2-difluoroethane has been investigated using ab initio quantum chemical calculations at the SCF, MP2 and CCSD(T) levels, with ANO basis sets. The relative stability of the gauche-conformation of 1,2-difluoroethane is found to be a consequence of the nodal structure of the singly occupied orbital in the CFH 2 radical. It is also shown that the nodal structure of the singly occupied orbitals in the CFH biradical can explain the stability of the cis conformation of 1,2-difluoroethene.

PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling

PubMed Central

Siddharthan, Rahul

2008-01-01

PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we widen the scope of the program, addressing two major problems in computational regulatory genomics. First, PhyloGibbs-MP can localise predictions to small, undetermined regions of a large input sequence, thus effectively predicting cis-regulatory modules (CRMs) ab initio while simultaneously predicting binding sites in those modules—tasks that are usually done by two separate programs. PhyloGibbs-MP's performance at such ab initio CRM prediction is comparable with or superior to dedicated module-prediction software that use prior knowledge of previously characterised transcription factors. Second, PhyloGibbs-MP can predict motifs that differentiate between two (or more) different groups of regulatory regions, that is, motifs that occur preferentially in one group over the others. While other “discriminative motif-finders” have been published in the literature, PhyloGibbs-MP's implementation has some unique features and flexibility. Benchmarks on synthetic and actual genomic data show that this algorithm is successful at enhancing predictions of differentiating sites and suppressing predictions of common sites and compares with or outperforms other discriminative motif-finders on actual genomic data. Additional enhancements include significant performance and speed improvements, the ability to use “informative priors” on known transcription factors, and the ability to output annotations in a format that can be visualised with the Generic Genome Browser. In stand-alone motif-finding, PhyloGibbs-MP remains competitive, outperforming PhyloGibbs-1.0 and other programs on benchmark data. PMID:18769735

An ab initio benchmark study of the H + CO --> HCO reaction

NASA Technical Reports Server (NTRS)

Woon, D. E.

1996-01-01

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies.

PubMed

Escorihuela, Jorge; Das, Anita; Looijen, Wilhelmus J E; van Delft, Floris L; Aquino, Adelia J A; Lischka, Hans; Zuilhof, Han

2018-01-05

Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne-1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH ⧧ ) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH ⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3-8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches.

Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies

PubMed Central

2017-01-01

Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne–1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH⧧) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3–8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches. PMID:29260879

Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate.

PubMed

Durig, James R; Zheng, Chao

2007-11-01

Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental quantities when available. These results are compared to the corresponding quantities of some similar molecules.

Ionization potential and electron affinity for six common explosive compounds by DFT, MP2, and CBS-QB3

DOE PAGES

Cooper, Jason K.; Grant, Christian D.; Zhang, Jin Z.

2012-07-20

The vertical and adiabatic ionization potential (IP V and IP A) and vertical electron affinity (EA V) for six explosives (RDX, HMX, TNT, PETN, HMTD, and TATP) have been studied by ab initio computational methods. The IPV was calculated using MP2 and CBS-QB3 while the IP A was calculated with B3LYP, CAM-B3LYP, ω B97XD, B2PLYP, and MP2. RDX and TNT IP A’s were also reported using CBS -QB3. Excluding results by CBS-QB3, B3LYP and B2PLYPD provided superior and more consistent results for calculating the IP. The EA V were calculated using the same methods however B3LYP performed the worst inmore » this case with MP2 and B2PLYPD predicting values closest to those made by CBS-QB3, which was used a reference due to lacking experimental data. Basis set effects were evaluated using 6- 31+G(d,p), 6-311+G(d,p), and 6-311+(3df,2p) for both IP and EA. 6-31+G(d,p) gave satisfactory results for calculating both IP however 6-311+G(3df,2p) had improved results in calculating the EA. The four nitro containing compounds had exothermic reduction potentials while the peroxides were unfavorable. Additionally, it was seen that RDX, HMX, TATP and HMTD were unstable in their reduced forms. Results are aimed to assist detection and screening methods.« less

Microwave Spectroscopic Investigations of the C-H\\cdotsπ Containing Complexes CH_2F_2\\cdotsPROPYNE and CH_2ClF\\cdotsPROPYNE

NASA Astrophysics Data System (ADS)

Peebles, Rebecca A.; Peebles, Sean A.; Christenholz, Cori L.; Ernst, Anthony A.; Dhahir, Yasser J.

2013-06-01

The spectra of the CH_2F_2\\cdotspropyne and CH_2ClF\\cdotspropyne complexes have been studied by chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy and by ab initio calculations at the MP2/6-311++G(2d,2p) level. Both complexes contain C-H\\cdotsπ contacts, with the halogen atoms angled towards the methyl group end of the propyne. While CH_2F_2\\cdotspropyne has C_s symmetry, CH_2ClF\\cdotspropyne has C_1 symmetry, with the fluorine and chlorine atoms straddling the propyne. Investigation of four single ^{13}C and the DC≡CCH_3 isotopologues in CH_2F_2\\cdotspropyne has allowed a detailed structural determination, while only the ^{35}Cl and ^{37}Cl isotopologues have so far been assigned for CH_2ClF\\cdotspropyne. Experimental data will be compared with ab initio results and with the analogous acetylene complexes, both of which have C_s symmetry structures, with double C-H\\cdotsπ interactions.

Analysis of vibrational spectra of 3-halo-1-propanols CH(2)XCH(2)CH(2)OH (X is Cl and Br).

PubMed

Badawi, Hassan M; Förner, Wolfgang

2008-12-01

The conformational stability and the three rotor internal rotations in 3-chloro- and 3-bromo-1-propanols were investigated by DFT-B3LYP/6-311+G and ab initio MP2/6-311+G, MP3/6-311+G and MP4(SDTQ)//MP3/6-311+G levels of theory. On the calculated potential energy surface twelve distinct minima were located all of which were not predicted to have imaginary frequencies at the B3LYP level of theory. The calculated lowest energy minimum in the potential curves of both molecules was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with earlier microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the two 3-halo-1-propanols were calculated at the B3LYP/6-311+G level of calculation and found to correspond to an equilibrium mixture of about 32% Ggt, 18% Ggg1, 13% Tgt, 8% Tgg and 8% Gtt conformations for 3-chloro-1-propanol and 34% Ggt, 15% Tgt, 13% Ggg1, 9% Tgg and 7% Gtt conformations for 3-bromo-1-propanol at 298.15K. The nature of the high energy conformations was verified by carrying out solvent experiments using formamide ( epsilon=109.5) and MP3 and MP4//MP3 calculations. The vibrational frequencies of each molecule in its three most stable forms were computed at the B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecules.

Density functional Gaussian-type-orbital approach to theoretical study of nitric oxide dimers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jursic, B.S.; Zdravkovski, Z.

Structure and total energies of the cis NO dimer, the trans NO dimer, and the NO monomer were calculated by ab initio methods (UHF, UMP2, and MP3) and density functional theory methods (LSDA and BLYP) with different basis sets [from 3-21G* to 6-311++(3df,3pd)]. The system is especially hard to model because two NO molecules are weakly associated in a dimer that has very long N-N bond. The results obtained by different methods are compared and the necessity of correlational methods for studying these systems is discussed.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

A theoretical study of hydrogen- and lithium-bonded complexes of F-H∕Li and Cl-H∕Li with NF3, NH3, and NH2(CH3).

PubMed

McDowell, Sean A C; St Hill, Janine A S

2011-10-28

Hydrogen- and lithium-bonded complexes of A-H∕Li (A = F, Cl) with the amine analogues NF(3), NH(3), and NH(2)(CH(3)) were studied at the MP2∕6-311++G(d,p) level of theory. Bond extensions and redshifts were obtained for the H-bonded complexes, while bond extensions and blueshifts were obtained for the Li-bonded species. The variation of these and other properties with the basicity of the amines was investigated and rationalized by comparing the ab initio results with predictions from a model derived from perturbation theory.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

A computational and spectroscopic study of the gas-phase conformers of adrenaline

NASA Astrophysics Data System (ADS)

Çarçabal, P.; Snoek, L. C.; van Mourik, T.

The conformational landscapes of the neurotransmitter l-adrenaline (l-epinephrine) and its diastereoisomer pseudo-adrenaline, isolated in the gas phase and un-protonated, have been investigated by using a combination of mass-selected ultraviolet and infrared holeburn spectroscopy, following laser desorption of the sample into a pulsed supersonic argon jet, and DFT and ab initio computation (at the B3LYP/6-31+G*, MP2/6-31+G* and MP2/aug-cc-pVDZ levels of theory). Both for adrenaline and its diastereoisomer, pseudo-adrenaline, one dominant molecular conformation, very similar to the one seen in noradrenaline, has been observed. It could be assigned to an extended side-chain structure (AG1a) stabilized by an OH → N intramolecular hydrogen bond. An intramolecular hydrogen bond is also formed between the neighbouring hydroxyl groups on the catechol ring. The presence of further conformers for both diastereoisomers could not be excluded, but overlapping electronic spectra and low ion signals prevented further assignments.

Raman mapping and in situ SERS spectroelectrochemical studies of 6-mercaptopurine SAMs on the gold electrode.

PubMed

Yang, Haifeng; Liu, Yanli; Liu, Zhimin; Yang, Yu; Jiang, Jianhui; Zhang, Zongrang; Shen, Guoli; Yu, Ruqin

2005-02-24

The self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) were formed at the roughened polycrystalline gold surfaces in acid and alkaline media. The time-dependent Raman mapping spectral analysis in conjunction with the quantum calculations for the vibrational modes using ab initio BLYP/6-31G method suggested that both of the resulted 6MP SAMs adopted the same adsorption mode through the S atom of pyrimidine moiety and the N7 atom of the imidazole moiety anchoring the gold surface in a vertical way. The in situ surface-enhanced Raman scattering spectroelectrochemical experiment was conducted to examine the stability of the SAMs at various bias potentials. It was found that the detaching process of the 6MP SAMs from the surface involved one electron reduction as the voltage was applied at ca. 0.7 V vs a standard calomel electrode.

Accurate Vibrational-Rotational Parameters and Infrared Intensities of 1-Bromo-1-fluoroethene: A Joint Experimental Analysis and Ab Initio Study.

PubMed

Pietropolli Charmet, Andrea; Stoppa, Paolo; Giorgianni, Santi; Bloino, Julien; Tasinato, Nicola; Carnimeo, Ivan; Biczysko, Malgorzata; Puzzarini, Cristina

2017-05-04

The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC═CH 2 , 1,1-C 2 H 2 BrF) were investigated in the range 300-6500 cm -1 , and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD(T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra.

Gas-phase Conformational Analysis of (R,R)-Tartaric Acid, its Diamide, N,N,N',N'- Tetramethyldiamide and Model Compounds

NASA Astrophysics Data System (ADS)

Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek

A review over most recent ab initio studies carried out at both RHF and MP2 levels on (R,R)-tartaric acid (TA), its diamide (DA), tetramethyldiamide (TMDA) and on three prototypic model systems (each of them constitutes a half of the respective parental molecule), i.e. 2-hydroxyacetic acid (HA), 2-hydroxyacetamide (HD) and 2-hydroxy-N,N-dimethylacetamide (HMD) is presented. (R,R)-tartaric acid and the derivatives have been completely optimized at RHF/6-31G* level and subsequently single-point energies of all conformers have been calculated with the use of second order perturbation theory according to the scheme: MP2/6-31G*//RHF/6-31G*. In the complete optimization of the model molecules at RHF level we have employed relatively large basis sets, augmented with polarisation and diffuse functions, namely 3-21G, 6-31G*, 6-31++G** and 6-311++G**. Electronic correlation has been included with the largest basis set used in this study, i.e. MP2/6-311++G**//RHF/6-311++G** single-point energy calculations have been performed. General confomational preferences of tartaric acid derivatives have been analysed as well as an attempt has been made to define main factors affecting the conformational behaviour of these molecules in the isolated state, in particular, the role and stability of intramolecular hydrogen bonding. In the case of the model compounds, our study principally concerned the conformational preferences and hydrogen bonding structure within the [alpha]-hydroxy-X moiety, where X=COOH, CONH2, CON(CH3)2.

Calculation of boron-isotope fractionation between B(OH) 3(aq) and B(OH)4-(aq)

NASA Astrophysics Data System (ADS)

Rustad, James R.; Bylaska, Eric J.; Jackson, Virgil E.; Dixon, David A.

2010-05-01

Density functional and correlated molecular orbital calculations (MP2) are carried out on B(OH) 3· nH 2O clusters ( n = 0, 6, 32), and B(OH)4-· nH 2O ( n = 0, 8, 11, 32) to estimate the equilibrium distribution of 10B and 11B isotopes between boric acid and borate in aqueous solution. For the large 32-water clusters, multiple conformations are generated from ab initio molecular dynamics simulations to account for the effect of solvent fluctuations on the isotopic fractionation. We provide an extrapolated value of the equilibrium constant α34 for the isotope exchange reaction 10B(OH) 3(aq) + 11B(OH)4- (aq) = 11B(OH) 3(aq) + 11B(OH)4- (aq) of 1.026-1.028 near the MP2 complete basis set limit with 32 explicit waters of solvation. With some exchange-correlation functionals we find potentially important contributions from a tetrahedral neutral B(OH) 3·H 2O Lewis acid-base complex. The extrapolations presented here suggest that DFT calculations give a value for 10 3ln α34 about 15% higher than the MP2 calculations.

Homogeneous and heterogeneous noncovalent dimers of formaldehyde and thioformaldehyde: structures, energetics, and vibrational frequencies.

PubMed

Van Dornshuld, Eric; Holy, Christina M; Tschumper, Gregory S

2014-05-08

This work provides the first characterization of five stationary points of the homogeneous thioformaldehyde dimer, (CH2S)2, and seven stationary points of the heterogeneous formaldehyde/thioformaldehyde dimer, CH2O/CH2S, with correlated ab initio electronic structure methods. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with second-order Møller-Plesset perturbation theory (MP2) and 13 different density functionals in conjunction with triple-ζ basis sets augmented with diffuse and multiple sets of polarization functions. The MP2 results indicate that the three stationary points of (CH2S)2 and four of CH2O/CH2S are minima, in contrast to two stationary points of the formaldehyde dimer, (CH2O)2. Single-point energies were also computed using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods and basis sets as large as heavy-aug-cc-pVTZ. The (CH2O)2 and CH2O/CH2S MP2 and MP2-F12 binding energies deviated from the CCSD(T)-F12 binding energies by no more than 0.2 and 0.4 kcal mol(-1), respectively. The (CH2O)2 and CH2O/CH2S global minimum is the same at every level of theory. However, the MP2 methods overbind (CH2S)2 by as much as 1.1 kcal mol(-1), effectively altering the energetic ordering of the thioformaldehyde dimer minima relative to the CCSD(T)-F12 energies. The CCSD(T)-F12 binding energies of the (CH2O)2 and CH2O/CH2S stationary points are quite similar, with the former ranging from around -2.4 to -4.6 kcal mol(-1) and the latter from about -1.1 to -4.4 kcal mol(-1). Corresponding (CH2S)2 stationary points have appreciably smaller CCSD(T)-F12 binding energies ranging from ca. -1.1 to -3.4 kcal mol(-1). The vibrational frequency shifts upon dimerization are also reported for each minimum on the MP2 potential energy surfaces.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

NASA Astrophysics Data System (ADS)

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-10-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

PubMed

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T; Dannenberg, J J

2012-10-07

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

PubMed Central

Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

2012-01-01

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

PubMed

Moon, Jiwon; Kim, Joonghan

2016-09-29

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

Ab initio molecular orbital calculations on HBr - 2 Geometry, frequencies, and enthalpy changes

NASA Astrophysics Data System (ADS)

Ikuta, Shigeru; Saitoh, Toshikazu; Nomura, Okio

1990-08-01

HBr-2 has D∞h symmetry at both the second-order (MP2) and third-order (MP3) Møller-Plesset perturbation levels of theory with the extended basis sets, whereas the Hartree-Fock level of theory predicts that it has C∞v symmetry. A potential energy map is calculated with the MP2 method as a function of two parameters, i.e., the distance of two Br atoms and the displacement of H from the center of them. Two-dimensional vibration analysis is performed by using this potential energy map. The calculated ν1 is 200 cm-1 and the ν3 is 837 cm-1 in HBr-2, and those in DBr-2 are 199 and 569 cm-1, respectively. Thus the ratio of the asymmetric vibration (ν3)H/(ν3)D is 1.47, being somewhat greater than the value of √2 expected for a harmonic oscillator. The enthalpy changes (ΔH°) in the reaction of Br- with an HBr molecule are determined by both the MP3 total energy changes and the thermal energy changes between the reactants and the product. The calculated enthalpy change of -21.2 kcal/mol is in good agreement with the experimental one (-21 kcal/mol) recently observed by Caldwell and Kebarle. These calculated data on HBr-2, which will provide us with a useful guide for future measurements of gas-phase vibrational spectra, are compared with those on HCl-2 and HF-2.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

PubMed

Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

Ab initio investigation of structure, stability, thermal behavior, bonding, and infrared spectra of ionized water cluster (H2O)6+

NASA Astrophysics Data System (ADS)

Liu, Lei; Hu, Cui-E.; Tang, Mei; Chen, Xiang-Rong; Cai, Ling-Cang

2016-10-01

The low-lying isomers of cationic water cluster (H2O)6+ have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6+ and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level. The interaction energies using the complete basis set limits at MP2 level are also reported. The relationships between their structure arrangement and their energies are discussed. Based on the results of thermal simulation, structural change from a four-numbered ring to a tree-like structure occurs at T ≈ 45 K, and the relative population of six lowest-free-energy isomers is found to exceed 4% at some point within the studied temperature range. Studies reveal that, among these six isomers, two new-found isomers constitute 10% of isomer population at 180 K, and the experimental spectra can be better explained with inclusions of the two isomers. The molecular orbitals for six representative cationic water clusters are also studied. Through topological and reduced density gradient analysis, we investigated the structural characteristics and the bonding strengths of these water cluster radical cations.

On the role of the termolecular reactions 2O2 + H2 → 2HO2 and 2O2 + H2 → H + HO2 + O2 in formation of the first radicals in hydrogen combustion: ab initio predictions of energy barriers.

PubMed

Monge-Palacios, M; Rafatijo, Homayoon

2017-01-18

We have investigated the role of termolecular reactions in the early chemistry of hydrogen combustion. We performed molecular chemical dynamics simulations using ReaxFF in LAMMPS to identify potential initial reactions for a 1 : 4 mixture of H 2  : O 2 in the NVT ensemble at density 276.3 kg m -3 and ∼3000 K (∼4000 atm) and ∼4000 K (∼5000 atm), and then characterized the saddle points for those reactions using ab initio methods: CCSD(T) = FC/cc-pVTZ//MP2/6-31G, CCSD(T) = FULL/aug-cc-pVTZ//CCSD = FC/cc-pVTZ and CASSCF MP2/6-31G//MP2/6-31G. The main initial reaction is H 2 + O 2 → H + HO 2 , frequently occurring in the presence of a second O 2 as a third body; that is, 2O 2 + H 2 → H + HO 2 + O 2 . The second most frequent reaction is 2O 2 + H 2 → 2HO 2 . We found three saddle points on the triplet PES of these termolecular reactions: one for 2O 2 + H 2 → H + HO 2 + O 2 and two for 2O 2 + H 2 → 2HO 2 . In the latter case, one has a symmetric structure consistent with simultaneous formation of two HO 2 and the other corresponds to a bimolecular reaction between O 2 and H 2 that is "interrupted" by a second O 2 before going to completion. The classical barrier height of the symmetric saddle point for 2O 2 + H 2 → 2HO 2 is 49.8 kcal mol -1 . The barrier to H 2 + O 2 → H + HO 2 is 58.9 kcal mol -1 . The termolecular reaction will be competitive with H 2 + O 2 → H + HO 2 only at sufficiently high pressures.

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trendsmore » derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.« less

Microwave Spectroscopic Study of the Atmospheric Oxidation Product m-TOLUIC Acid and its Monohydrate

NASA Astrophysics Data System (ADS)

Al-Jabiri, Mohamad; Schnitzler, Elijah G.; Seifert, Nathan A.; Jäger, Wolfgang

2017-06-01

m-Toluic acid is a photo-oxidation product of m-xylene, a chemical byproduct of the oil and gas industry, and is a common component of secondary atmospheric aerosol. Organic acids, such as m-toluic acid, are also thought to play an important role in the initial steps of aerosol formation, which involves formation of hydrogen bonded clusters with molecular species, such as water, ammonia, and sulfuric acid. Somewhat surprisingly, the rotational spectrum of the m-toluic acid monomer has not been studied before. We have identified four stable conformers using ab initio calculations at the MP2/6-311++G(2df,2pd) level of theory. The two lowest energy conformers are rather close in energy and their rotational spectra were measured using a Balle-Flygare type microwave spectrometer. The structures and barriers to methyl internal rotation were determined. We have identified four isomers of the monohydrate of m-toluic acid using ab initio calculations. Measurements of the microwave spectra of the two lowest energy isomers are underway with a newly constructed chirped pulse microwave Fourier transform spectrometer in the frequency range from 2 to 6 GHz. The spectra and analyses will be presented.

Experimental evidence for blue-shifted hydrogen bonding in the fluoroform-hydrogen chloride complex: a matrix-isolation infrared and ab initio study.

PubMed

Gopi, R; Ramanathan, N; Sundararajan, K

2014-07-24

The 1:1 hydrogen-bonded complex of fluoroform and hydrogen chloride was studied using matrix-isolation infrared spectroscopy and ab initio computations. Using B3LYP and MP2 levels of theory with 6-311++G(d,p) and aug-cc-pVDZ basis sets, the structures of the complexes and their energies were computed. For the 1:1 CHF3-HCl complexes, ab initio computations showed two minima, one cyclic and the other acyclic. The cyclic complex was found to have C-H · · · Cl and C-F · · · H interactions, where CHF3 and HCl sub-molecules act as proton donor and proton acceptor, respectively. The second minimum corresponded to an acyclic complex stabilized only by the C-F · · · H interaction, in which CHF3 is the proton acceptor. Experimentally, we could trap the 1:1 CHF3-HCl cyclic complex in an argon matrix, where a blue-shift in the C-H stretching mode of the CHF3 sub-molecule was observed. To understand the nature of the interactions, Atoms in Molecules and Natural Bond Orbital analyses were carried out to unravel the reasons for blue-shifting of the C-H stretching frequency in these complexes.

Thermodynamic properties of {Delta}H{sub f 298}{degree}, S{sub 298}{degree}, and C{sub p}(T) for 2-fluoro-2-methylpropane, {Delta}H{sub f 298}{degree} of fluorinated ethanes, and group additivity for fluoroalkanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Takahiro; Bozzelli, J.W.

1999-09-09

G2(MP2) composite calculations are performed to obtain thermodynamic properties ({Delta}H{sub f 298}{degree}, S{sub 298}{degree} and C{sub p}(T)'s) of 2-fluoro-2-methylpropane. {Delta}H{sub f 298}{degree} is calculated from the G2(MP2) calculated enthalpy of reaction ({Delta}H{sub rxn 298}{degree}) and use of isodesmic reactions. Standard entropy (S{sub 298}{degree} in cal/(mol{center{underscore}dot}K)) and heat capacities (C{sub p}(T)'s in cal/(mol{center{underscore}dot}K)) are calculated using the rigid-rotor--harmonic-oscillator approximation with direct integration over energy levels of the intermolecular rotation potential energy curve. These thermodynamic properties are used to estimate data for the C/C3/F group. Enthalpies of formation ({Delta}H{sub f 298}{degree} in kcal/mol) for 1,2-difluoroethane ({minus}102.7), 1,1,2-trifluoroethane ({minus}156.9), 1,1,2,2- and 1,1,1,2-tetrafluoroethane (209.6more » and 213.3), and pentafluoroethane ({minus}264.1), are calculated using total energies obtained from G2(MP2) composite ab initio methods. Isodesmic reactions with existing literature values of {Delta}H{sub f 298}{degree} for ethane, 1-fluoroethane, 1,1-difjuoroethane and 1,1,1-trifluoroethane are used. Fluorine/fluorine interaction terms, F/F, 2F/F, 3F/F, 2F/2F, and 3F/2F, where ``/'' indicates interaction for alkane compounds, for {Delta}H{sub f 298}{degree} are reevaluated based on {Delta}H{sub f 298}{degree} of the above five fluoroethanes. Thermodynamic properties ({Delta}H{sub f 298}{degree}, S{sub 298}{degree} and C{sub p}(T)'s (300 {le} T/K {le} 1500)) for fluorinated carbon groups, C/C3F, C/C2/F/H, C/C2/F2, are calculated using data from ab initio methods and existing literature data. Fluorine-methyl (alkyl) group additivity corrections for gauche interactions are also evaluated.« less

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Microwave Spectra and AB Initio Studies of the Ne-Acetone Complex

NASA Astrophysics Data System (ADS)

Gao, Jiao; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang

2015-06-01

Microwave spectra of the neon-acetone van der Waals complex were measured using a cavity-based molecular beam Fourier-transform microwave spectrometer in the region from 5 to 18 GHz. Both 20Ne and 22Ne containing isotopologues were studied and both c- and weaker a-type rotational transitions were observed. The transitions are split into multiplets due to the internal rotation of two methyl groups in acetone. Electronic structure calculations were done at the MP2 level of theory with the 6-311++g (2d, p) basis set for all atoms and the internal rotation barrier height of the methyl groups was determined to be about 2.8 kJ/mol. The ab initio rotational constants were the basis for our spectroscopic searches, but the multiplet structures and floppiness of the complex made the quantum number assignment very difficult. The assignment was finally achieved with the aid of constructing closed frequency loops and predicting internal rotation splittings using the XIAM code. Analyses of the spectra yielded rotational and centrifugal distortion constants, as well as internal rotation parameters, which were interpreted in terms of structure and internal dynamics of the complex. H. Hartwig and H. Dreizler, Z. Naturforsch. A 51, 923 (1996).

Quantum chemical study of the structure, spectroscopy and reactivity of NO+.(H2O)n=1-5 clusters

NASA Astrophysics Data System (ADS)

Linton, Kirsty A.; Wright, Timothy G.; Besley, Nicholas A.

2018-03-01

Quantum chemical methods including Møller-Plesset perturbation (MP2) theory and density functional theory (DFT) have been used to study the structure, spectroscopy and reactivity of NO+.(H2O)n=1-5 clusters. MP2/6-311++G** calculations are shown to describe the structure and spectroscopy of the clusters well. DFT calculations with exchange-correlation functionals with a low fraction of Hartree-Fock exchange give a binding energy of NO+.(H2O) that is too high and incorrectly predict the lowest energy structure of NO+.(H2O)2, and this error may be associated with a delocalization of charge onto the water molecule directly binding to NO+. Ab initio molecular dynamics (AIMD) simulations were performed to study the NO+.(H2O)5 H+.(H2O)4 + HONO reaction to investigate the formation of HONO from NO+.(H2O)5. Whether an intracluster reaction to form HONO is observed depends on the level of electronic structure theory used. Of note is that methods that accurately describe the relative energies of the product and reactant clusters did not show reactions on the timescales studied. This suggests that in the upper atmosphere the reaction may occur owing to the energy present in the NO+.(H2O)5 complex following its formation. This article is part of the theme issue `Modern theoretical chemistry'.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2017-04-01

An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases.

PubMed

Alkorta, Ibon; Blanco, Fernando; Solimannejad, Mohammad; Elguero, Jose

2008-10-30

A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.

Improved assignments of the vibrational fundamental modes of ortho -, meta -, and para -xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, we report high quality quantitative vapor-phase infrared spectra of all three isomers over the 540-6500 cm -1 range. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C 2v symmetry for ortho-xylene, andmore » two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have C s and C 2 symmetry, and for para-xylene these conformers have C 2v or C 2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, we made an arbitrary choice to discuss the C s conformer for meta-xylene and the C 2v conformer for para-xylene. We report integrated band intensities for all isomers. Using the quantitative infrared data, we determine the global warming potential values of each isomer and discuss potential bands for atmospheric monitoring.« less

Improved assignments of the vibrational fundamental modes of ortho-, meta-, and para-xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

NASA Astrophysics Data System (ADS)

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.; Nguyen, Kiet T.; Williams, Stephen D.; Johnson, Timothy J.

2017-12-01

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, high quality quantitative vapor-phase infrared spectra of all three isomers over the 6500 - 540 cm-1 range are reported. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C2v symmetry for ortho-xylene, and two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have Cs and C2 symmetry, and for para-xylene these conformers have C2v or C2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, an arbitrary choice to discuss the Cs conformer for meta-xylene and the C2v conformer for para-xylene is made. Integrated band intensities for all isomers are reported. Using the quantitative infrared data, the global warming potential values of each isomer are determined. Potential bands for atmospheric monitoring are also discussed.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

Modulating of the pnicogen-bonding by a H⋯π interaction: An ab initio study.

PubMed

Esrafili, Mehdi D; Sadr-Mousavi, Asma

2017-08-01

An ab initio study of the cooperativity in XH 2 P⋯NCH⋯Z and XH 2 P⋯CNH⋯Z complexes (X=F, Cl, Br, CN, NC; Z=C 2 H 2 ,C 6 H 6 ) connected by pnicogen-bonding and H⋯π interactions is carried out by means of MP2 computational method. A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes considered, a favorable cooperativity is observed, especially in X=F and CN complexes. However, for a given X or Z, the amount of cooperativity effects in XH 2 P⋯CNH⋯Z complexes are more important than XH 2 P⋯NCH⋯Z counterparts. Besides, the influence of a H⋯π interaction on a P⋯N (C) bond is more pronounced than that of a P⋯N (C) bond on a H⋯π bond. The quantum theory of atoms in molecules shows that ternary complexes have increased electron densities at their bond critical points relative to the corresponding binary systems. The results also indicate that the strength of the P⋯N(C) and H⋯π interactions increases in the presence of the solvent. Copyright © 2017 Elsevier Inc. All rights reserved.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Spectroscopic determination of the water pair potential

NASA Astrophysics Data System (ADS)

Fellers, Raymond Scott, II

This thesis details the first experimental determination of a water pair potential via nonlinear least squares fit of high precision microwave and far-IR vibration- rotation-tunneling (VRT) data. Provided is a review of the theory of intermolecular forces, methods of determining these forces by ab initio theory, and a survey of analytical forms that are parameterized to model such forces. Also reviewed are important features of water dimer VRT spectra, in particular the characteristic tunneling splittings due to hydrogen bond rearrangements, and how these features are related to the anisotropy of the water dimer potential energy surface (PES). Comparisons are made between high level ab initio calculations of the water dimer PES and a number of well known water pair potentials. The importance of the intramolecular degrees of freedom in the parameterization of a new PES is studied through a systematic series of ab initio calculations. These results suggest that a reasonably accurate pair potential can be constructed with the constraint of rigid monomers. ÅThe computation of the VRT states of the water dimer in a fully-coupled six-dimensional Hamiltonian by the split Wigner pseudospectral (SWPS) method is presented. Discussed in detail is the performance of the code and recent improvements of the algorithm which significantly decrease the execution time over an earlier implementation. The VRT states of several potentials are calculated and compared to experiment. It is shown that none of these potentials can reproduce the water dimer tunneling splittings with quantitative accuracy. The SWPS code is embedded in a non-linear least squares fitting routine and is used to fit a potential to 22 microwave and far-IR transitions. The resulting PES, VRT- 1(R,P), is derived from the ab initio/semiempirical ASPW (Anisotropic Site Potential for Water) potential which includes multipole expansions for the electrostatic, dispersion, exchange- repulsion, and induction terms. Induction is iterated to first-order. VRT-1(R,P) reproduces VRT spectra and temperature dependent second virial coefficients to high accuracy. The dimer equilibrium and zero-point binding energies (De and D0) are 4.91 kcal mol and 3.46 kcal/mol, respectively, which are in agreement with the best theoretical estimates. The dimer equilibrium structure [ROO = 2.924 Å, θ a = 48.5°, and θd = 50.2°] agrees with large basis set MP2 calculations. Additionally, the trimer equilibrium structure [ROO = 2.756 Å and D e=15.6 kcal/mol] and tetramer equilibrium structure [R OO = 2.783 Å and De = 25.9 kcal/mol] are also very close to second-order Möller-Plesset (MP2) calculations. The hydrogen bond rearrangement pathways of the dimer PES are determined by the eigenvector following method. The two lowest energy rearrangement barriers, corresponding to the acceptor switching and interchange motions, are 157 cm-1 and 207 cm-1, respectively, which is in excellent agreement with ab initio predictions of 158 cm -1 and 199 cm-1, respectively

Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

PubMed

Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

2014-04-23

We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

On the Interaction between Carbon Dioxide and Nanomaterials with High Accuracy ab initio and DFT Calculations

NASA Astrophysics Data System (ADS)

Vogiatzis, Konstantinos D.; Mavrandonakis, Antreas; Klopper, Wim; Froudakis, George

2009-08-01

The separation, capture and storage of carbon dioxide from the flue gas is an environmental and economical problem of significant importance. Zeolites and activated carbons have been used from the industries in order to reduce the emissions of CO2. A new family of materials, the metal-organic frameworks (MOFs), has been recently proposed as an efficient substitute of the abovementioned materials. In particular, materials based on zinc complexes with imidazo-like aromatic compounds which builds frameworks similar with those of Zeolites (Zeolite-Imidazolium Frameworks, ZIFs), have the potential for efficient separation of CO2 from CO and CH4. [1]. Weak interactions between carbon dioxide and heterocyclic aromatic compounds are being examined with high accuracy ab initio methods. CO2 has zero dipole moment but a significant quadrupole moment enables it to operate as a weak acid or weak base, according to his environment. Nitrogen-containing aromatic compounds act as electron donors, while CO2 acts as an electron acceptor. Electrostatic interactions induce a non-permanent dipole moment on CO2 and the complex is stabilized by in-plane hydrogen bonds between the charged oxygens of CO2 and nearby hydrogen of the aromatic molecule. In addition, dispersion forces from the electron correlation contribute to the interaction energy. By using explicitly correlated methods (MP2-F12/aug-cc-pVTZ) [2] and by adding the contribution from the triples excitations, calculated with a smaller basis (6-311++G**), we reach to an approximate CCSD(T) complete basis set result. [3] Extrapolation schemes were used in order to reach the MP2 basis set limit and compare it with the CCSD(T)/CBS result. Those results are in excellent agreement with the explicitly correlated MP2-F12. In addition, our complexes are being investigated with DFT methods that calculate separately the dispersion energy (DFT-D) [4] and modified MP2 which scaling of spin pair correlation [5]. DFT-D results are in good agreement with CCSD(T)/CBS results, providing us a computational cheap method with high accuracy. The quantization of the interaction is examined by changing the aromaticity of the heterocyclic molecules and by talking into account the electron correlation. [6] The electron density of the nitrogen that binds CO2 is gradually decreasing by substituting carbons with nitrogens in pyridine (pyrimidine, pyrazine, triazine), leading to lower binding energy.

Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry (Briefing Charts)

DTIC Science & Technology

2015-06-28

HMX RDX  Recent Works  See Geith et al...Propellants, Explosives, Pyrotechnics, 29, 3 (2004)  ∆Hcomb(DNB) = (5195 ± 300) kJ kg-1 (bomb calorimetry and MP2/cc-pVTZ ∆Hf) cf HMX 9435 & RDX 9560 kJ...kg-1  Vd = 8660 ms-1, cf HMX 9100 & RDX 8750 ms-1  See Geith et al., Combust and Flame, 139, 358 (2004)  Recent synthesis (known since 1898 by

Chirality recognition in the glycidol···propylene oxide complex: a rotational spectroscopic study.

PubMed

Thomas, Javix; Sunahori, Fumie X; Borho, Nicole; Xu, Yunjie

2011-04-11

Chirality recognition in the hydrogen-bonded glycidol···propylene oxide complex has been studied by using rotational spectroscopy and ab initio calculations. An extensive conformational search has been performed for this binary adduct at the MP2/6-311++G(d,p) level of theory and a total of 28 homo- and heterochiral conformers were identified. The eight binary conformers, built of the two dominant glycidol monomeric conformers, g-G+ and g+G-, were predicted to be the most stable ones. Jet-cooled rotational spectra of six out of the eight conformers were observed and unambiguously assigned for the first time. The experimental stability ordering has been obtained and compared with the ab initio predictions. The relative stability of the two dominant glycidol monomeric conformers is reversed in some cases when binding to propylene oxide. The contributions of monomeric energy, deformation energy, and binary intermolecular interaction energy to the relative stability of the binary conformers are discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A theoretical study of the H-abstraction reactions from HOI by moist air radiolytic products (H, OH, and O (3P)) and iodine atoms (2P(3/2)).

PubMed

Hammaecher, Catherine; Canneaux, Sébastien; Louis, Florent; Cantrel, Laurent

2011-06-23

The rate constants of the reactions of HOI molecules with H, OH, O ((3)P), and I ((2)P(3/2)) atoms have been estimated over the temperature range 300-2500 K using four different levels of theory. Geometry optimizations and vibrational frequency calculations are performed using MP2 methods combined with two basis sets (cc-pVTZ and 6-311G(d,p)). Single-point energy calculations are performed with the highly correlated ab initio coupled cluster method in the space of single, double, and triple (pertubatively) electron excitations CCSD(T) using the cc-pVTZ, cc-pVQZ, 6-311+G(3df,2p), and 6-311++G(3df,3pd) basis sets. Reaction enthalpies at 0 K were calculated at the CCSD(T)/cc-pVnZ//MP2/cc-pVTZ (n = T and Q), CCSD(T)/6-311+G(3df,2p)//MP2/6-311G(d,p), and CCSD(T)/6-311++G(3df,3pd)//MP2/6-311G(d,p) levels of theory and compared to the experimental values taken from the literature. Canonical transition-state theory with an Eckart tunneling correction is used to predict the rate constants as a function of temperature. The computational procedure has been used to predict rate constants for H-abstraction elementary reactions because there are actually no literature data to which the calculated rate constants can be directly compared. The final objective is to implement kinetics of gaseous reactions in the ASTEC (accident source term evaluation code) program to improve speciation of fission products, which can be transported along the reactor coolant system (RCS) of a pressurized water reactor (PWR) in the case of a severe accident.

Ab Initio Theoretical Studies on the Kinetics of Hydrogen Abstraction Type Reactions of Hydroxyl Radicals with CH3CCl2F and CH3CClF2

NASA Astrophysics Data System (ADS)

Saheb, Vahid; Maleki, Samira

2018-03-01

The hydrogen abstraction reactions from CH3Cl2F (R-141b) and CH3CClF2 (R-142b) by OH radicals are studied theoretically by semi-classical transition state theory. The stationary points for the reactions are located by using KMLYP density functional method along with 6-311++G(2 d,2 p) basis set and MP2 method along with 6-311+G( d, p) basis set. Single-point energy calculations are performed by the CBS-Q and G4 combination methods on the geometries optimized at the KMLYP/6-311++G(2 d,2 p) level of theory. Vibrational anharmonicity coefficients, x ij , which are needed for semi-classical transition state theory calculations, are computed at the KMLYP/6-311++G(2 d,2 p) and MP2/6-311+G( d, p) levels of theory. The computed barrier heights are slightly sensitive to the quantum-chemical method. Thermal rate coefficients are computed over the temperature range from 200 to 2000 K and they are shown to be in accordance with available experimental data. On the basis of the computed rate coefficients, the tropospheric lifetime of the CH3CCl2F and CH3CClF2 are estimated to be about 6.5 and 12.0 years, respectively.

Ab initio calculations of anharmonic vibrational spectroscopy for hydrogen fluoride (HF)n (n = 3, 4) and mixed hydrogen fluoride/water (HF)n(H2O)n (n = 1, 2, 4) clusters

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Gerber, R. Benny

2002-01-01

Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)n, with n = 3, 4 and mixed clusters of hydrogen fluoride with water (HF)n(H2O)n where n = 1, 2. For the (HF)4(H2O)4 complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)n, good agreement is found with experimental data. This agreement shows that the Moller-Plesset (MP2) potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)n(H2O)n experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments.

Ab Initio Calculations of Anharmonic Vibrational Spectroscopy for Hydrogen Fluoride (HF)n (n=3,4) and Mixed Hydrogen Fluoride/Water (HF)n(H20)n (n=1,2,4) Clusters

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Gerber, R. Benny; Kwak, Dochan (Technical Monitor)

2001-01-01

Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)n with n=3,4 and mixed clusters of hydrogen fluoride with water (HF)n(H2O)n where n=1,2. For the (HF)4(H2O)4 complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)n, good agreement is found with experimental data. This agreement shows that the MP2 potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)n(H2O)n experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments.

Quantum chemical study of the structure, spectroscopy and reactivity of NO+.(H2O) n=1-5 clusters.

PubMed

Linton, Kirsty A; Wright, Timothy G; Besley, Nicholas A

2018-03-13

Quantum chemical methods including Møller-Plesset perturbation (MP2) theory and density functional theory (DFT) have been used to study the structure, spectroscopy and reactivity of NO + (H 2 O) n =1-5 clusters. MP2/6-311++G** calculations are shown to describe the structure and spectroscopy of the clusters well. DFT calculations with exchange-correlation functionals with a low fraction of Hartree-Fock exchange give a binding energy of NO + (H 2 O) that is too high and incorrectly predict the lowest energy structure of NO + (H 2 O) 2 , and this error may be associated with a delocalization of charge onto the water molecule directly binding to NO + Ab initio molecular dynamics (AIMD) simulations were performed to study the NO + (H 2 O) 5 [Formula: see text] H + (H 2 O) 4 + HONO reaction to investigate the formation of HONO from NO + (H 2 O) 5 Whether an intracluster reaction to form HONO is observed depends on the level of electronic structure theory used. Of note is that methods that accurately describe the relative energies of the product and reactant clusters did not show reactions on the timescales studied. This suggests that in the upper atmosphere the reaction may occur owing to the energy present in the NO + (H 2 O) 5 complex following its formation.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

Quantum chemical ab initio prediction of proton exchange barriers between CH{sub 4} and different H-zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, Christian; Sauer, Joachim, E-mail: js@chemie.hu-berlin.de

2015-09-14

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, thismore » difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.« less

Spectra and structure of silicon containing compounds. XXXII. Raman and infrared spectra, conformational stability, vibrational assignment and ab initio calculations of n-propylsilane-d0 and Si-d3.

PubMed

Durig, James R; Pan, Chunhua; Guirgis, Gamil A

2003-03-15

The infrared (3100-40 cm(-1)) and Raman (3100-20 cm(-1)) spectra of gaseous and solid n-propylsilane, CH(3)CH(2)CH(2)SiH(3) and the Si-d(3) isotopomer, CH(3)CH(2)CH(2)SiD(3), have been recorded. Additionally, the Raman spectra of the liquids have been recorded and qualitative depolarization values obtained. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of n-propylsilane dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 220+/-22 cm(-1) (2.63+/-0.26 kJ mol(-1)) with the anti conformer the more stable form. A similar value of 234+/-23 cm(-1) (2.80+/-0.28 kJ mol(-1)) was obtained for deltaH for the Si-d(3) isotopomer. At ambient temperature it is estimated that there is 30+/-2% of the gauche conformer present. The potential function governing the conformation interchange has been estimated from the far infrared spectral data, the enthalpy difference, and the dihedral angle of the gauche conformer, which is compared to the one predicted from ab initio MP2/6-31G(d) calculations. The barriers to conformational interchange are: 942, 970 and 716 cm(-1) for the anti to gauche, gauche to gauche, and gauche to anti conformers, respectively. Relatively complete vibrational assignments are proposed for both the n-propylsilane-d(0) and Si-d(3) molecules based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios, and normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities and depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311 + G(d,p) and 6-311 + G(2d,2p) basis sets. From the isolated Si-H stretching frequency from the Si-d(2) isotopomer the r(0) distances of 1.484 and 1.485 A have been determined for the SiH(s) and SiH(a) bonds, respectively, for the anti conformer, and 1.486 A for the SiH bond for the gauche conformer. Utilizing previously reported microwave rotational constants for the anti conformer and the determined SiH distances along with ab initio predicted parameters 'adjusted r(0)' parameters have been obtained for the anti conformer. The results are discussed and compared to those obtained for some similar molecules. Copyright 2002 Elsevier Science B.V.

Spectra and structure of silicon containing compounds. XXXII. Raman and infrared spectra, conformational stability, vibrational assignment and ab initio calculations of n-propylsilane-d 0 and Si-d 3

NASA Astrophysics Data System (ADS)

Durig, James R.; Pan, Chunhua; Guirgis, Gamil A.

2003-03-01

The infrared (3100-40 cm -1) and Raman (3100-20 cm -1) spectra of gaseous and solid n-propylsilane, CH 3CH 2CH 2SiH 3 and the Si-d 3 isotopomer, CH 3CH 2CH 2SiD 3, have been recorded. Additionally, the Raman spectra of the liquids have been recorded and qualitative depolarization values obtained. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 °C) studies of the infrared spectra of n-propylsilane dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 220±22 cm -1 (2.63±0.26 kJ mol -1) with the anti conformer the more stable form. A similar value of 234±23 cm -1 (2.80±0.28 kJ mol -1) was obtained for Δ H for the Si-d 3 isotopomer. At ambient temperature it is estimated that there is 30±2% of the gauche conformer present. The potential function governing the conformation interchange has been estimated from the far infrared spectral data, the enthalpy difference, and the dihedral angle of the gauche conformer, which is compared to the one predicted from ab initio MP2/6-31G(d) calculations. The barriers to conformational interchange are: 942, 970 and 716 cm -1 for the anti to gauche, gauche to gauche, and gauche to anti conformers, respectively. Relatively complete vibrational assignments are proposed for both the n-propylsilane-d 0 and Si-d 3 molecules based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios, and normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities and depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311+G(d,p) and 6-311+G(2d,2p) basis sets. From the isolated SiH stretching frequency from the Si-d 2 isotopomer the r0 distances of 1.484 and 1.485 Å have been determined for the SiH s and SiH a bonds, respectively, for the anti conformer, and 1.486 Å for the SiH bond for the gauche conformer. Utilizing previously reported microwave rotational constants for the anti conformer and the determined SiH distances along with ab initio predicted parameters 'adjusted r0' parameters have been obtained for the anti conformer. The results are discussed and compared to those obtained for some similar molecules.

Experimental and theoretical studies on the structure and spectroscopic properties of (E)-1-(2-aminophenyl)-3-(pyridine-4-yl) prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Cruz Ortiz, Andrés Felipe; Sánchez López, Alberto; García Ríos, Alejandro; Cuenú Cabezas, Fernando; Rozo Correa, Ciro Eduardo

2015-10-01

(E)-1-(2-aminophenyl)-3-(pyridine-4-yl)prop-2-en-1-one (or simply 2-aminochalcone) was synthetized and characterized by elemental analysis, FT-IR, NMR, MS and XRD. Molecular geometry optimization, vibrational harmonic frequencies, 1H and 13C NMR chemical shifts were calculated by ab initio (HF and MP2) and density functional theory (DFT) methods, with B3LYP and B3PW91 functionals, using GAUSSIAN 09 program package without any constraint on the geometry. With VEDA software vibrational frequencies were assigned in terms of the potential energy distribution. A detailed interpretation of the FT-IR, NMR and XRD, experimental and calculated, is reported. The HOMO and LUMO energy gap that reflects the chemical activity of the molecule were also studied by DFT and above basis set. All theoretical results correspond to a great extent to experimental ones.

Organic carbonates: experiment and ab initio calculations for prediction of thermochemical properties.

PubMed

Verevkin, Sergey P; Emel'yanenko, Vladimir N; Kozlova, Svetlana A

2008-10-23

This work has been undertaken in order to obtain data on thermodynamic properties of organic carbonates and to revise the group-additivity values necessary for predicting their standard enthalpies of formation and enthalpies of vaporization. The standard molar enthalpies of formation of dibenzyl carbonate, tert-butyl phenyl carbonate, and diphenyl carbonate were measured using combustion calorimetry. Molar enthalpies of vaporization of these compounds were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. Molar enthalpy of sublimation of diphenyl carbonate was measured in the same way. Ab initio calculations of molar enthalpies of formation of organic carbonates have been performed using the G3MP2 method, and results are in excellent agreement with the available experiment. Then the group-contribution method has been developed to predict values of the enthalpies of formation and enthalpies of vaporization of organic carbonates.

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

PubMed

Wang, Zhi-Xiang; Duan, Yong

2004-11-15

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

PubMed

Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

2013-04-02

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling of a Tröger’s tweezer and its complexation properties

NASA Astrophysics Data System (ADS)

Parchaňský, Václav; Matějka, Pavel; Dolenský, Bohumil; Havlík, Martin; Bouř, Petr

2009-09-01

Molecular tweezers attracted attention because of their potential to selectively bind important chemicals, which can be utilized in medicine or in pollution treatment. In this study, the aromatic binding properties of a recently synthesized tweezer based on the Tröger's base and its complex with nitrobenzene are investigated ab initio, using the DFT and MP2 computations. The predicted geometries and energies of the complex with nitrobenzene are well comparable with the experimental data. The B3LYP and BPW91 functionals did not provide a stable binding, in contrast to the observation. Only addition of the empirical Grimme correction for the van der Waals forces, not present in conventional DFT, yielded results consistent with the experiment, MP2 computations, and similar benchmark models. The correction also caused minor improvements of the Raman and infrared spectra, but not in the entire region of vibrational frequencies. The results suggest that the role of the electrostatic interaction in the investigated complex is minor and the interaction stabilization is driven by the contact area between the polarizable aromatic systems. The vdW-DFT method thus provides an efficient tool for the rational synthesis of the complexes.

Quantum chemistry and TST study of the mechanism and kinetics of the butadiene and isoprene reactions with mercapto radicals

NASA Astrophysics Data System (ADS)

Francisco-Márquez, Misaela; Alvarez-Idaboy, J. Raul; Galano, Annia; Vivier-Bunge, Annik

2008-03-01

The reactions of isoprene and butadiene with SH rad radicals have been investigated by density functional theory and ab initio molecular orbital theories. We report the thermodynamics and kinetics of four different pathways, involving addition of SH rad radicals to all double-bonded carbon atoms. Calculations have been performed on all stationary points using BHandHLYP functional, Moller-Plesset perturbation theory to second-order (MP2) and the composite CBS-QB3 method at the MP2 optimized geometries and frequencies. Pre-reactive complexes have been identified. The apparent activation energies are negative for SH rad addition at the terminal carbon atoms and are slightly smaller than those for OH rad addition at the same positions. The calculated overall rate coefficient for butadiene + SH rad reaction at 298 K is in excellent agreement with the only available experimentally measured value. Activation energies and overall rate coefficients at different temperatures are predicted for the first time for butadiene + SH rad and isoprene + SH rad reactions. The reactions of butadiene and isoprene with SH rad radicals were found to be about four times faster than with OH rad radicals.

RDX geometries, excited states, and revised energy ordering of conformers via MP2 and CCSD(T) methodologies: insights into decomposition mechanism.

PubMed

Molt, Robert W; Watson, Thomas; Lotrich, Victor F; Bartlett, Rodney J

2011-02-10

The geometries, harmonic frequencies, elec-tronic excitation levels, and energetic orderings of various conformers of RDX have been computed at the ab initio MP2 and CCSD(T) levels, providing more reliable results than have been previously obtained. We observe that the various local minimum-energy conformers are all competitive for being the absolute minimum and that, at reasonable temperatures, several conformers will appreciably contribute to the population of RDX. As a result, we have concluded that any mechanistic study to investigate thermal decomposition can reasonably begin from any one of the cyclohexane conformers of RDX. As such, it is necessary to consider the transition states for each RDX conformer to gauge what the activation energy is. Homolytic bond dissociation has long been speculated to be critical to detonation; we report here the most accurate estimates of homolytic BDEs yet calculated, likely to be accurate within 3 kcal mol(-1). The differences in energy for homolytic BDEs among all the possible RDR conformers are again small, such that most all of the conformers can reasonably be speculated as the next step in the mechanism starting from the RDR radical.

Probing Vitamine C, Aspirin and Paracetamol in the Gas Phase: High Resolution Rotational Studies

NASA Astrophysics Data System (ADS)

Mata, S.; Cabezas, C.; Varela, M.; Pena, I.; Nino, A.; López, J. C.; Alonso, J. L.; Grabow, J.-U.

2011-06-01

A solid sample of Vitamin C (m.p. 190°C) vaporized by laser ablation has been investigated in gas phase and characterized through their rotational spectra. Two spectroscopy techniques has been used to obtain the spectra: a new design of broadband chirped pulse Fourier transform microwave spectroscopy with in-phase/quadrature-phase-modulation passage-acquired-coherence technique (IMPACT) and conventional laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW). Up to now, two low-energy conformer have been observed and their rotational constants determined. Ab initio calculations at the MP2/6-311++G (d,p) level of theory predicted rotational constants which helped us to identify these conformers unequivocally. Among the molecules to benefit from the LA-MB-FTMW technique there are common important drugs never observed in the gas phase through rotational spectroscopy. We present here the results on acetyl salicylic acid and acetaminophen (m.p. 136°C), commonly known as aspirin and paracetamol respectively. We have observed two stable conformers of aspirin and two for paracetamol. The internal rotation barrier of the methyl group in aspirin has been determined for both conformers from the analysis of the A-E splittings due to the coupling of internal and overall rotation. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11,617-627 (2009)and references therein

Can Carbamates Undergo Radical Oxidation in the Soil Environment? A Case Study on Carbaryl and Carbofuran.

PubMed

Ćwieląg-Piasecka, Irmina; Witwicki, Maciej; Jerzykiewicz, Maria; Jezierska, Julia

2017-12-19

Radical oxidation of carbamate insecticides, namely carbaryl and carbofuran, was investigated with spectroscopic (electron paramagnetic resonance [EPR] and UV-vis) and theoretical (density functional theory [DFT] and ab initio orbital-optimized spin-component scaled MP2 [OO-SCS-MP2]) methods. The two carbamates were subjected to reaction with • OH, persistent DPPH • and galvinoxyl radical, as well as indigenous radicals of humic acids. The influence of fulvic acids on carbamate oxidation was also tested. The results obtained with EPR and UV-vis spectroscopy indicate that carbamates can undergo direct reactions with various radical species, oxidizing themselves into radicals in the process. Hence, they are prone to participate in the prolongation step of the radical chain reactions occurring in the soil environment. Theoretical calculations revealed that from the thermodynamic point of view hydrogen atom transfer is the preferred mechanism in the reactions of the two carbamates with the radicals. The activity of carbofuran was determined experimentally (using pseudo-first-order kinetics) and theoretically to be noticeably higher in comparison with carbaryl and comparable with gallic acid. The findings of this study suggest that the radicals present in soil can play an important role in natural remediation mechanisms of carbamates.

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.

2010-09-01

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O dbnd C sbnd O sbnd H) and the non-planar Tgcpp ( cisoid O dbnd C sbnd O sbnd H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding O⋯H interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar + CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation ofmore » the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar + CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.« less

Carbon dioxide capture using covalent organic frameworks (COFs) type material-a theoretical investigation.

PubMed

Dash, Bibek

2018-04-26

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO 2 capture. In this study, first principle calculations were performed for CO 2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO 2 and nitrogen gas. Binding energies (BEs) of CO 2 and N 2 molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO 2 and N 2 interactions was studied using quantum calculations.

Matrix-isolation and ab initio study of HKrCCCl and HXeCCCl

NASA Astrophysics Data System (ADS)

Zhu, Cheng; Räsänen, Markku; Khriachtchev, Leonid

2015-12-01

We report on two new noble-gas molecules, HKrCCCl and HXeCCCl, prepared in low-temperature Kr and Xe matrices. These molecules are made by UV photolysis of HCCCl in the matrices and subsequent thermal annealing. The HCCCl precursor is produced by microwave discharge of a mixture of a matrix gas with trichloroethylene (HClC=CCl2). The assignments of the new noble-gas molecules are supported by deuteration experiments and quantum chemical calculations at the MP2(full) and CCSD(T) levels of theory with the def2-TZVPPD basis set. No evidence of ClXeCCH, which is computationally reliably stable, is found in the experiments. ClKrCCH as well as the Ar compounds HArCCCl and ClArCCH are not observed either, which is in agreement with the calculations.

Far-Infrared and Raman Spectra and The Ring-Twisting Potential Energy Function of 1,3-Cyclohexadiene

NASA Astrophysics Data System (ADS)

Autrey, Daniel; Choo, Jaebum; Laane, Jaan

2001-10-01

The nu19 (A2) ring-twisting vibration of 1,3-cyclohexadiene has been analyzed from the vapor-phase Raman and infrared spectra. The Raman spectrum shows nine ring-twisting transitions in the 116 - 199 cm-1 region. The far-infrared spectrum confirms five of these transitions, despite the fact that the vibration is infrared forbidden in the C2v (planar) approximation. Other Raman and infrared combination bands verify the assignments and provide information on the vibrational coupling. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function, which has a barrier to planarity of 1132 cm-1 and energy minima corresponding to twisting angles of 9.1º and 30.1º. Ab initio calculations were also carried out using Moller-Plesset perturbation theory (MP2) with a large number of different basis sets. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range and calculated vibrational frequencies in excellent agreement with the experimental values.

On the isotropic Raman spectrum of Ar2 and how to benchmark ab initio calculations of small atomic clusters: Paradox lost.

PubMed

Chrysos, Michael; Dixneuf, Sophie; Rachet, Florent

2015-07-14

This is the long-overdue answer to the discrepancies observed between theory and experiment in Ar2 regarding both the isotropic Raman spectrum and the second refractivity virial coefficient, BR [Gaye et al., Phys. Rev. A 55, 3484 (1997)]. At the origin of this progress is the advent (posterior to 1997) of advanced computational methods for weakly interconnected neutral species at close separations. Here, we report agreement between the previously taken Raman measurements and quantum lineshapes now computed with the employ of large-scale CCSD or smartly constructed MP2 induced-polarizability data. By using these measurements as a benchmark tool, we assess the degree of performance of various other ab initio computed data for the mean polarizability α, and we show that an excellent agreement with the most recently measured value of BR is reached. We propose an even more refined model for α, which is solution of the inverse-scattering problem and whose lineshape matches exactly the measured spectrum over the entire frequency-shift range probed.

The equilibrium molecular structures of cross-conjugated alkenes with particular reference to [3]- and [4]-dendralene from ab initio studies of various conformers

NASA Astrophysics Data System (ADS)

Palmer, Michael H.; Blair-Fish, John A.; Sherwood, Paul

1997-07-01

A study of the equilibrium structures and relative energies for the conformers of 3-methylenepenta-1,4-diene (MPD) and bis(3,4-methylene)-1,5-hexadiene (MHD) have been obtained by SCF and MP2 correlated methods; a double zeta+polarisation basis set (DZP) was used. Both planar and non-planar forms were evaluated for a variety of point groups. The force constants for each conformer were obtained, in order to determine whether the minima were saddle points rather than genuine minima owing to the constraints of molecular symmetry. For both molecules, all the non-planar forms studied were of lower energy than the best planar-forms. Indeed the planar structures are all saddle-points between the interconverting pairs of non-planar forms, as shown by one or more negative vibration frequencies for the planar molecules. The relative energies and structures of the different conformers of MPD and MHD are almost identical between the SCF and MP2 series, the MP2 calculations merely leading to slight extensions of the C=C bonds, minor changes in dihedral angles, and small changes otherwise. Because of the H⋯H interactions, all the planar forms showed considerable in-plane angle bending, and small but consistent H-C bond compressions were also obtained in the most hindered cases. The lowest energy conformer of MPD is a gauche-trans conformer, with symmetry C 1, but a second conformer of trans-trans type and C 2 symmetry lies only 6 kJ mol -1 above. The C 2 non-planar conformer of MHD containing (basically) trans-butadiene units is the lowest energy by a significant amount, but several trans-cis and cis-cis conformers were all identified as potential species for gas phase mixtures.

New insight into the structure, internal rotation barrier and vibrational analysis of 2-fluorostyrene

NASA Astrophysics Data System (ADS)

Tuttolomondo, María Eugenia; Navarro, Amparo; Peña, Tomás; Fernández-Liencres, María Paz; Granadino-Roldán, José Manuel; Parker, Stewart F.; Fernández-Gómez, Manuel

2009-06-01

The molecular structure of 2-fluorostyrene has been optimized at ab initio (MP2 and CCSD) and DFT levels (B3LYP, mPW1PW91) with different basis sets (6-31G ∗, 6-311++G ∗∗, cc-pVDZ). B3LYP predicts planar structures for both cis and trans conformers, the latter being more stable than the former. mPW1PW91, MP2 and CCSD calculations yield a quasi-planar conformation in agreement with XRD and microwave data. The vinyl-phenyl torsion barrier of 2-fluorostyrene has been calculated at B3LYP, mPW1PW91, MP2 and CCSD levels with 6-31G ∗ basis set as well as at MP2/cc-pVDZ level. Results have been compared with experimental data from the vibronic spectrum of the jet-cooled compound through a deconvolution of the total electronic potential energy by a sixfold Fourier-type expansion. As a result, MP2/cc-pVDZ shows the best performance as regards the torsional barrier height for the trans form. The effects governing the torsion barriers and preferred conformations have been analyzed at mPW1PW91/6-31G ∗ and MP2/cc-pVDZ levels. To achieve this, two different schemes, i.e. the total electron energy and the natural bond orbital, NBO, partition schemes have been used. The Atoms-in-Molecules (AIM) theory has been applied to the cis and trans conformers in order to detect intramolecular contacts. Furthermore, a twofold aimed analysis of the vibrational spectrum has been performed. First, to obtain a complete assignment nonexistent so far and second, to confirm the being of the predicted cis and trans forms in the liquid and solid states. New records of infrared and Raman spectra, and for the first time, the inelastic neutron scattering (INS) spectrum have been used. Moreover, the mPW1PW91/6-31G ∗ harmonic force field has been scaled using a multiple scaling (SQM) force field procedure. To achieve this, the initial scale factors were refined in order to get the best possible fitting between the calculated and experimental frequencies attaining to a final rms deviation of 5 cm -1.

Ab initio electron correlated studies on the intracluster reaction of NO+ (H2O)(n) → H3O+ (H2O)(n-2) (HONO) (n = 4 and 5).

PubMed

Asada, Toshio; Nagaoka, Masataka; Koseki, Shiro

2011-01-28

Hydrated nitrosonium ion clusters NO(+)(H(2)O)(n) (n = 4 and 5) were investigated by using MP2/aug-cc-pVTZ level of theory to clarify isomeric reaction pathways for formation of HONO and fully hydrated hydride ions. We found some new isomers and transition state structures in each hydration number, whose lowest activation energies of the intracluster reactions were found to be 4.1 and 3.4 kcal mol(-1) for n = 4 and n = 5, respectively. These thermodynamic properties and full quantum mechanical molecular dynamics simulation suggest that product isomers with HONO and fully hydrated hydride ions can be obtained at n = 4 and n = 5 in terms of excess hydration binding energies which can overcome these activation barriers.

Thermal decomposition pathways of ethane

NASA Astrophysics Data System (ADS)

Gordon, Mark S.; Truong, Thanh N.; Pople, John A.

1986-10-01

The alternate thermal decomposition pathways for ethane in its ground state have been investigated, using ab initio electronic structure calculations. Single-point energies were obtained at the full MP4/6-311 G ∗∗ level, using 6-31 G ∗ geometries for reactant, products, and transition states. The thermodynamically favored products are ethylene and molecular hydrogen, but a very large barrier (130 kcal/mol) is found for the direct 1,2-elimination of hydrogen. When calculated barriers are taken into account, the lowest-energy process is the homolytic cleavage of the C-C bond to form two methyl radicals.

An ab initio/Rice-Ramsperger-Kassel-Marcus study of the hydrogen-abstraction reactions of methyl ethers, H(3)COCH(3-x)(CH(3))(x), x = 0-2, by OH; mechanism and kinetics.

PubMed

Zhou, Chong-Wen; Simmie, John M; Curran, Henry J

2010-07-14

A theoretical study of the mechanism and kinetics of the H-abstraction reaction from dimethyl (DME), ethylmethyl (EME) and iso-propylmethyl (IPME) ethers by the OH radical has been carried out using the high-level methods CCSD(T)/CBS, G3 and G3MP2BH&H. The computationally less-expensive methods of G3 and G3MP2BH&H yield results for DME within 0.2-0.6 and 0.7-0.9 kcal mol(-1), respectively, of the coupled cluster, CCSD(T), values extrapolated to the basis set limit. So the G3 and G3MP2BH&H methods can be confidently used for the reactions of the higher ethers. A distinction is made between the two different kinds of H-atoms, classified as in/out-of the symmetry plane, and it is found that abstraction from the out-of-plane H-atoms proceeds through a stepwise mechanism involving the formation of a reactant complex in the entrance channel and product complex in the exit channel. The in-plane H-atom abstractions take place through a more direct mechanism and are less competitive. Rate constants of the three reactions have been calculated in the temperature range of 500-3000 K using the Variflex code, based on the weak collision, master equation/microcanonical variational RRKM theory including tunneling corrections. The computed total rate constants (cm(3) mol(-1) s(-1)) have been fitted as follows: k(DME) = 2.74 xT(3.94) exp (1534.2/T), k(EME) = 20.93 xT(3.61) exp (2060.1/T) and k(IPME) = 0.55 xT(3.93) exp (2826.1/T). Expressions of the group rate constants for the three different carbon sites are also provided.

Hemi bonds and noncovalent interactions in the cational systems (XH2P: SHY)+

NASA Astrophysics Data System (ADS)

Li, Xiang; Li, An Yong

2016-08-01

Quantum chemistry ab initio MP2 and CCSD calculations were performed to investigate the P⋯S hemi bonds and noncovalent interactions in the radical cational systems (H3P:SH2)+, (FH2P:SH2)+ and (H3P:SHF)+. The hydride dimer (H3P:SH2)+ has a P⋯S hemi bonding structure and a H-bonding structure, (FH2P:SH2)+ has two hemi bonding structures and a proton-transferred H-bonding structure, (H3P:SHF)+ has two hemi bonding structures and three noncovalent structures. It is remarkable that these hemi bonds also have characters of pnicogen and chalcogen bonds. The binding energy, stability and bonding nature of the hemi bonds were presented.

The gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide from combustion calorimetry, vapor pressure measurements, and ab initio calculations.

PubMed

Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas

2007-04-04

Ionic liquids are attracting growing interest as alternatives to conventional molecular solvents. Experimental values of vapor pressure, enthalpy of vaporization, and enthalpy of formation of ionic liquids are the key thermodynamic quantities, which are required for the validation and development of the molecular modeling and ab initio methods toward this new class of solvents. In this work, the molar enthalpy of formation of the liquid 1-butyl-3-methylimidazolium dicyanamide, 206.2 +/- 2.5 kJ.mol-1, was measured by means of combustion calorimetry. The molar enthalpy of vaporization of 1-butyl-3-methylimidazolium dicyanamide, 157.2 +/- 1.1 kJ.mol-1, was obtained from the temperature dependence of the vapor pressure measured using the transpiration method. The latter method has been checked with measurements of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, where data are available from the effusion technique. The first experimental determination of the gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide, 363.4 +/- 2.7 kJ.mol-1, from thermochemical measurements (combustion and transpiration) is presented. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for 1-butyl-3-methylimidazolium dicyanamide using the G3MP2 theory. Excellent agreement with experimental results has been observed. The method developed opens a new way to obtain thermodynamic properties of ionic liquids which have not been available so far.

Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions.

PubMed

Bauzá, Antonio; Seth, Saikat Kumar; Frontera, Antonio

2018-04-05

Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP). A charge density analysis using the Bader's theory of "atoms in molecules" is carried out to characterize the interactions and to analyze their strengthening or weakening depending on the variation of charge density at critical points. The importance of electrostatic effects on the mutual influence of the interaction is studied by means of molecular electrostatic potential calculations. By taking advantage of these computational tools, the present study examines interplay of these interactions. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparative semiempirical and ab initio study of the structural and chemical properties of uric acid and its anions

NASA Astrophysics Data System (ADS)

Altarsha, Muhannad; Monard, Gérald; Castro, Bertrand

Semiempirical, density functional theory (DFT), and ab initio calculations have been performed to assess the relative stabilities of 15 possible tautomer forms of neutral uric acid, and of the different urate mono- and dianion forms. These methods have also been used to compute ionization potentials (IPs) for uric acid and its derived anions. Overall, we have found that semiempirical calculations, in particular PM3, perform well as compared with B3LYP or MP2 computations toward these different structural and chemical properties of uric acid: the triketo form of uric acid is the most stable tautomer form of neutral uric acid. Three other tautomer forms are relatively close in energy, within the range 2-6 kcal/mol above the triketo form, with a mean energy deviation of only 1.3 kcal/mol between PM3 and DFT or ab initio results; the monoanion form of uric acid obtained by abstracting one proton in position 3 (denoted UAN3-) is the most stable form among all four possible urate monoanions both in gas phase and in solution; the dianion form of uric acid obtained by abstracting two protons, respectively, in positions 3 and 9 of uric acid (denoted UAN3-N9-) is the most stable urate dianion form both in gas phase and in solution. However, these two most stable species do not have the lowest IPs in solution: among monoanions and dianions, respectively, the species with the lowest IPs are UAN7- and UAN7-N9-.

Theoretical Calculation of Jet Fuel Thermochemistry. 1; Tetrahydrodicylopentadiene (JP10) Thermochemistry Using the CBS-QB3 and G3(MP2)//B3LYP Methods

NASA Technical Reports Server (NTRS)

Zehe, Michael J.; Jaffe, Richard L.

2010-01-01

High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.

Electron ionization and dissociation of aliphatic amino acids

NASA Astrophysics Data System (ADS)

Papp, P.; Shchukin, P.; Kočíšek, J.; Matejčík, Š.

2012-09-01

We present experimental and theoretical study of electron ionization and dissociative ionization to the gas phase amino acids valine, leucine, and isoleucine. A crossed electron/molecular beams technique equipped with quadrupole mass analyzer has been applied to measure mass spectra and ion efficiency curves for formation of particular ions. From experimental data the ionization energies of the molecules and the appearance energies of the fragment ions were determined. Ab initio calculations (Density Functional Theory and G3MP2 methods) were performed in order to calculate the fragmentation paths and interpret the experimental data. The experimental ionization energies of parent molecules [P]+ 8.91 ± 0.05, 8.85 ± 0.05, and 8.79 ± 0.05 eV and G3MP2 ionization energies (adiabatic) of 8.89, 8.88, and 8.81 eV were determined for valine, leucine, and isoleucine, respectively, as well as the experimental and theoretical threshold energies for dissociative ionization channels. The comparison of experimental data with calculations resulted in identification of the ions as well as the neutral fragments formed in the dissociative reactions. Around 15 mass/charge ratio fragments were identified from the mass spectra by comparison of experimental appearance energies with calculated reaction enthalpies for particular dissociative reactions.

High-Level Ab Initio Calculations of Intermolecular Interactions: Heavy Main-Group Element π-Interactions.

PubMed

Krasowska, Małgorzata; Schneider, Wolfgang B; Mehring, Michael; Auer, Alexander A

2018-05-02

This work reports high-level ab initio calculations and a detailed analysis on the nature of intermolecular interactions of heavy main-group element compounds and π systems. For this purpose we have chosen a set of benchmark molecules of the form MR 3 , in which M=As, Sb, or Bi, and R=CH 3 , OCH 3 , or Cl. Several methods for the description of weak intermolecular interactions are benchmarked including DFT-D, DFT-SAPT, MP2, and high-level coupled cluster methods in the DLPNO-CCSD(T) approximation. Using local energy decomposition (LED) and an analysis of the electron density, details of the nature of this interaction are unraveled. The results yield insight into the nature of dispersion and donor-acceptor interactions in this type of system, including systematic trends in the periodic table, and also provide a benchmark for dispersion interactions in heavy main-group element compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of molecular structure of succinic acid in a very complex conformational landscape: Gas-phase electron diffraction (GED) and ab initio studies

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Abaev, Maxim A.; Rykov, Anatolii N.; Shishkov, Igor F.

2011-06-01

The molecular structure of succinic acid has been investigated by the gas-phase electron diffraction (GED) method for the first time. According to predictions of MP2/cc-pVTZ calculations, the molecule has 18 stable conformers with the C sbnd C sbnd C sbnd C chain in the gauche ( G) or anti ( A) configuration, and four of them, I ( G), II ( A), III ( G) and IV ( A) belonging to the C 2, C 2h, C 1 and C 1 point groups, respectively, with relative energies ΔE ZPE within 2.2 kcal/mol can be present at the experimental temperature of 445 K in noticeable amounts. The ratio of the conformers I:II:III:IV = 45(15):20(15):10(assumed):25(15) (in %) has been determined in the GED analysis guided by theoretical predictions. To take into account vibrational effects, the corrections Δ( r e - r a) to the experimental r a bond lengths were calculated from the MP2/cc-pVTZ quadratic and cubic force constants. The obtained equilibrium structural parameters of the dominant conformer I are the following (bond lengths in Å, angles in degrees): r e(C sp3sbnd C sp3) = 1.508(3), r e(C sp3sbnd C sp2) = 1.499(2), r e(C sbnd O) = 1.343(2), r e(C dbnd O) = 1.202(1), e(C sbnd C sbnd C) = 111.8(4), e(C sbnd C sbnd O) = 112.0(4), e(O sbnd C dbnd O) = 123.0(1), τ(C sbnd C sbnd C sbnd C) = 69.9(11). Yielding the best agreement with the GED structure, the MP2/cc-pVQZ approximation overestimates the C sbnd O and C dbnd O bond lengths by ca. 0.005(2) Å.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greene, Samuel M., E-mail: samuel.greene@chem.ox.ac.uk; Shan, Xiao, E-mail: xiao.shan@chem.ox.ac.uk; Clary, David C., E-mail: david.clary@chem.ox.ac.u

Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives aremore » obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.« less

Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

PubMed

Szostak, Roman; Aubé, Jeffrey; Szostak, Michal

2015-08-21

Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

Ab initio study of charge transfer between lithium and aromatic hydrocarbons. Can the results be directly transferred to the lithium-graphene interaction?

PubMed

Sadlej-Sosnowska, N

2014-08-28

We have used electronic density calculations to study neutral complexes of Li with aromatic hydrocarbons. The charge transferred between a Li atom and benzene, coronene, circumcoronene, and circumcircumcoronene has been studied by ab initio methods (at the HF and MP2 level). Toward this aim, the method of integrating electron density in two cuboid fragments of space was applied. One of the fragments was constructed so that it enclosed the bulk of the electron density of lithium; the second, the bulk of the electron density of hydrocarbon. It was found that for each complex two conformations were identified: the most stable with a greater vertical Li-hydrocarbon distance, on the order of 2.5 Å, and another of higher energy with a corresponding distance less than 2 Å. In all cases the transfer of a fractional number, 0.1-0.3 electrons, between Li and hydrocarbon was found; however, the direction of the transfer was not the same in all complexes investigated. The structures of complexes of the first configuration could be represented as Li(σ-)···AH(σ+), whereas the opposite direction of charge transfer was found for complexes of the second configuration, with higher energy. The directions of the dipole moments in the complexes supported these conclusions because they directly measure the redistribution of electron density in a complex with respect to substrates.

Internal rotation in halogenated toluenes: Rotational spectrum of 2,3-difluorotoluene

NASA Astrophysics Data System (ADS)

Nair, K. P. Rajappan; Herbers, Sven; Grabow, Jens-Uwe; Lesarri, Alberto

2018-07-01

The microwave rotational spectrum of 2,3-difluorotoluene has been studied by pulsed supersonic jet using Fourier transform microwave spectroscopy. The tunneling splitting due to the methyl internal rotation in the ground torsional state could be unambiguously identified and the three-fold (V3) potential barrier hindering the internal rotation of the methyl top was determined as 2518.70(15) J/mol. The ground-state rotational parameters for the parent and seven 13C isotopic species in natural abundance were determined with high accuracy, including all quartic centrifugal distortion constants. The molecular structure was derived using the substitution (rs) method. From the rotational constants of the different isotopic species the rs structure as well as the r0 structure was determined. Supporting ab initio (MP2) and DFT (B3LYP) calculations provided comparative values for the potential barrier and molecular parameters.

Matrix-isolation and ab initio study of HKrCCCl and HXeCCCl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Cheng; Räsänen, Markku; Khriachtchev, Leonid, E-mail: leonid.khriachtchev@helsinki.fi

2015-12-28

We report on two new noble-gas molecules, HKrCCCl and HXeCCCl, prepared in low-temperature Kr and Xe matrices. These molecules are made by UV photolysis of HCCCl in the matrices and subsequent thermal annealing. The HCCCl precursor is produced by microwave discharge of a mixture of a matrix gas with trichloroethylene (HClC=CCl{sub 2}). The assignments of the new noble-gas molecules are supported by deuteration experiments and quantum chemical calculations at the MP2(full) and CCSD(T) levels of theory with the def2-TZVPPD basis set. No evidence of ClXeCCH, which is computationally reliably stable, is found in the experiments. ClKrCCH as well as themore » Ar compounds HArCCCl and ClArCCH are not observed either, which is in agreement with the calculations.« less

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study.

PubMed

Szczepaniak, Marek; Moc, Jerzy

2015-11-05

D-Erythrose is a C4 monosaccharide with a biological and potential astrobiological relevance. We have investigated low-energy structures of d-erythrose and their interconversion in the gas phase with the highest-level calculations up-to-date. We have identified a number of structurally distinct furanose and open-chain isomers and predicted α ↔ α and β ↔ β furanose interconversion pathways involving the O-H rotamers. We have estimated relative Gibbs free energies of the erythrose species based on the CCSD(T)/aug-cc-pVTZ electronic energies and MP2/aug-cc-pVTZ vibrational frequencies. By using natural bond orbital theory we have also quantified a stabilization of erythrose conformers and interconversion transition states by intramolecular H-bonds.

Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic-Aromatic Side Chain Interactions in Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdes, Haydee; Pluhackova, Kristyna; Hobza, Pavel

The performance of a wide range of quantum chemical calculations for the ab initio study of realistic model systems of aromatic-aromatic side chain interactions in proteins (in particular those π-π interactions occurring between adjacent residues along the protein sequence) is here assessed on the phenylalanyl-glycyl-phenylalanine (FGF) tripeptide. Energies and geometries obtained at different levels of theory are compared with CCSD(T)/CBS benchmark energies and RI-MP2/cc-pVTZ benchmark geometries, respectively. Consequently, a protocol of calculation alternative to the very expensive CCSD(T)/CBS is proposed. In addition to this, the preferred orientation of the Phe aromatic side chains is discussed and compared with previous resultsmore » on the topic.« less

Structures and vibrational spectra of pinacol.. 1. Infrared and matrix infrared spectra of monomeric pinacol. Ab initio calculations on conformers and vibrational frequencies

NASA Astrophysics Data System (ADS)

Dahlqvist, Martti; Hotokka, Matti; Räsänen, Markku

1998-04-01

The infrared spectra of monomeric pinacol molecules (2,3-dimethyl-2,3-butanediol; (CH 3) 2C(OH)C(OH)(CH 3) 2) have been recorded in the gas phase and dilute nonpolar solutions, and in an argon matrix. The vibrational data are consistent with the intramolecularly hydrogen-bonded G-type (gauche with respect to the central C-C bond) conformers and there is no evidence for the T-type (trans with respect to the central C-C bond) conformers, which have been observed in the condensed phases. This was confirmed by studying the infrared region 835-815 cm -1, which was found to be the most indicative to show spectral changes within the type of the conformers. In this region the band of the T-type conformers (assigned to the hybridized asymmetric vibration of the central CC and CO stretching modes) disappears when going from the condensed phases to phases, where pinacol molecules are monomeric. Ab initio HF/6-311G** (MP2/6-311G**) calculations support the experimental findings; the calculated relative energies for the tGg', gGg', g'Gg', tTt, and gTg' conformers are 0.0 (0.0), 3.4 (3.4), 5.1 (5.9), 7.9 (11.3), and 12.0 (14.0) kJ mol -1, respectively. Consequently, only the G-type conformers are sufficiently populated to give rise to observable spectral lines. Both experimental findings and theoretical calculations demonstrated that the bands in the argon matrix spectrum of pinacol are due to the most stable tGg' conformer. Although the ab initio calculations predict that also the gGg' and g'Gg' conformers are present in the gas phase and in dilute nonpolar solutions their existence could not be confirmed experimentally. Hence, we conclude that the conformation sensitive bands may coincide in the spectra. The HF/6-311G** ab initio calculations for vibrational frequencies of pinacol are consistent with this conclusion, suggesting only small differences between the wavenumbers of the G-type conformers. Pinacol does not show infrared-induced photorotamerization in the low-temperature argon matrix. This is due to the high energy barrier to internal rotation around the central C-C bond as demonstrated by ab initio calculations. Assignments of the vibrational bands were made with the aid of computer animations of the ab initio calculated harmonic vibrations, common group frequencies, and analogy conclusions from related compounds. The deuterium derivatives [(CD 3) 2C(OH)C(OH)(CD 3) 2 and (CH 3) 2C(OD)C(OD)(CH 3) 2] of pinacol were also utilized even though their spectra were recorded only in the condensed phases.

Acid base chemistry of luteolin and its methyl-ether derivatives: A DFT and ab initio investigation

NASA Astrophysics Data System (ADS)

Amat, Anna; De Angelis, Filippo; Sgamellotti, Antonio; Fantacci, Simona

2008-09-01

The acid-base chemistry of luteolin, a flavonoid with important pharmacological and dyeing properties, and of the related methyl ether derivatives have been investigated by DFT and MP2 methods, testing different computational setups. We calculate the pK's of all the possible deprotonation sites, for which no experimental assignment could be achieved. The calculated pK's deliver a different acidity order for the two most acidic deprotonation sites between luteolin and its methyl ether derivatives, due to intramolecular hydrogen bonding in luteolin. A lowest p Ka of 6.19 is computed for luteolin, in good agreement with available experimental data.

A spectroscopic and computational investigation of the conformational structural changes induced by hydrogen bonding networks in the glycidol-water complex.

PubMed

Conrad, A R; Teumelsan, N H; Wang, P E; Tubergen, M J

2010-01-14

Rotational spectra were recorded in natural abundance for the (13)C isotopomers of two conformers of glycidol. Moments of inertia from the (13)C isotopomers were used to calculate the substitution coordinates and C-C bond lengths of two glycidol monomer conformations. The structures of seven different conformational minima were found from ab initio (MP2/6-311++G(d,p)) optimizations of glycidol-water. The rotational spectrum of glycidol-water was recorded using microwave spectroscopy, and the rotational constants were determined to be A = 3902.331 (11) MHz, B = 2763.176 (3) MHz, and C = 1966.863 (3) MHz. Rotational spectra were also recorded for glycidol-H(2)(18)O, glycidol-D(b)OH, and glycidol-d(O)-D(2)O. The rotational spectra were assigned to the lowest-energy ab initio structure, and the structure was improved by fitting to the experimental moments of inertia. The best-fit structure shows evidence for structural changes in glycidol to accommodate formation of the intermolecular hydrogen bonding network: the O-C-C-O torsional angle in glycidol was found to increase from 40.8 degrees for the monomer to 49.9 degrees in the water complex.

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study

NASA Astrophysics Data System (ADS)

Stepanenko, Tetyana; Lapinski, Leszek; Nowak, Maciej J.; Kwiatkowski, Józef S.; Leszczynski, Jerzy

2001-02-01

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N 2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G( d, p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G( d, p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.

Theoretical studies of UO(2)(OH)(H(2)O)(n) (+), UO(2)(OH)(2)(H(2)O)(n), NpO(2)(OH)(H(2)O)(n), and PuO(2)(OH)(H(2)O)(n) (+) (n

PubMed

Cao, Zhiji; Balasubramanian, K

2009-10-28

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.

Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

PubMed

Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

2012-01-28

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. © 2012 American Institute of Physics

Thermodynamic Calculations for Molecules with Asymmetric Internal Rotors. II. Application to the 1,2-Dihaloethanes

PubMed Central

Wong, Bryan M.; Fadri, Maria M.; Raman, Sumathy

2012-01-01

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables. PMID:17663439

Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1,2-dihaloethanes.

PubMed

Wong, Bryan M; Fadri, Maria M; Raman, Sumathy

2008-02-01

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables. (c) 2007 Wiley Periodicals, Inc.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Thermochemical and kinetic analyses on oxidation of isobutenyl radical and 2-hydroperoxymethyl-2-propenyl radical.

PubMed

Zheng, X L; Sun, H Y; Law, C K

2005-10-13

In recognition of the importance of the isobutene oxidation reaction in the preignition chemistry associated with engine knock, the thermochemistry, chemical reaction pathways, and reaction kinetics of the isobutenyl radical oxidation at low to intermediate temperature range were computationally studied, focusing on both the first and the second O2 addition to the isobutenyl radical. The geometries of reactants, important intermediates, transition states, and products in the isobutenyl radical oxidation system were optimized at the B3LYP/6-311G(d,p) and MP2(full)/6-31G(d) levels, and the thermochemical properties were determined on the basis of ab initio, density functional theory, and statistical mechanics. Enthalpies of formation for several important intermediates were calculated using isodesmic reactions at the DFT and the CBS-QB3 levels. The kinetic analysis of the first O2 addition to the isobutenyl radical was performed using enthalpies at the CBS-QB3 and G3(MP2) levels. The reaction forms a chemically activated isobutenyl peroxy adduct which can be stabilized, dissociate back to reactants, cyclize to cyclic peroxide-alkyl radicals, and isomerize to the 2-hydroperoxymethyl-2-propenyl radical that further undergoes another O2 addition. The reaction channels for isomerization and cyclization and further dissociation on this second O2 addition were analyzed using enthalpies at the DFT level with energy corrections based on similar reaction channels for the first O2 addition. The high-pressure limit rate constants for each reaction channel were determined as functions of temperature by the canonical transition state theory for further kinetic model development.

Theoretical study of the gas-phase reactions of iodine atoms ((2)P(3/2)) with H(2), H(2)O, HI, and OH.

PubMed

Canneaux, Sébastien; Xerri, Bertrand; Louis, Florent; Cantrel, Laurent

2010-09-02

The rate constants of the reactions of iodine atoms with H(2), H(2)O, HI, and OH have been estimated using 39, 21, 13, and 39 different levels of theory, respectively, and have been compared to the available literature values over the temperature range of 250-2500 K. The aim of this methodological work is to demonstrate that standard theoretical methods are adequate to obtain quantitative rate constants for the reactions involving iodine-containing species. Geometry optimizations and vibrational frequency calculations are performed using three methods (MP2, MPW1K, and BHandHLYP) combined with three basis sets (cc-pVTZ, cc-pVQZ, and 6-311G(d,p)). Single-point energy calculations are performed with the highly correlated ab initio coupled cluster method in the space of single, double, and triple (pertubatively) electron excitations CCSD(T) using the cc-pVnZ (n = T, Q, and 5), aug-cc-pVnZ (n = T, Q, and 5), 6-311G(d,p), 6-311+G(3df,2p), and 6-311++G(3df,3pd) basis sets. Canonical transition state theory with a simple Wigner tunneling correction is used to predict the rate constants as a function of temperature. CCSD(T)/cc-pVnZ//MP2/cc-pVTZ (n = T and Q), CCSD(T)/6-311+G(3df,2p)//MP2/6-311G(d,p), and CCSD(T)/6-311++G(3df,3pd)//MP2/6-311G(d,p) levels of theory provide accurate kinetic rate constants when compared to available literature data. The use of the CCSD(T)/cc-pVQZ//MP2/cc-pVTZ and CCSD(T)/6-311++G(3df,3pd) levels of theory allows one to obtain a better agreement with the literature data for all reactions with the exception of the I + H(2) reaction R(1) . This computational procedure has been also used to predict rate constants for some reactions where no available experimental data exist. The use of quantum chemistry tools could be therefore extended to other elements and next applied to develop kinetic networks involving various fission products, steam, and hydrogen in the absence of literature data. The final objective is to implement the kinetics of gaseous reactions in the ASTEC (Accident Source Term Evaluation Code) code to improve speciation of fission transport, which can be transported along the Reactor Coolant System (RCS) of a Pressurized Water Reactor (PWR) in case of a severe accident.

Lanthanide complex coordination polyhedron geometry prediction accuracies of ab initio effective core potential calculations.

PubMed

Freire, Ricardo O; Rocha, Gerd B; Simas, Alfredo M

2006-03-01

lanthanide coordination compounds efficiently and accurately is central for the design of new ligands capable of forming stable and highly luminescent complexes. Accordingly, we present in this paper a report on the capability of various ab initio effective core potential calculations in reproducing the coordination polyhedron geometries of lanthanide complexes. Starting with all combinations of HF, B3LYP and MP2(Full) with STO-3G, 3-21G, 6-31G, 6-31G* and 6-31+G basis sets for [Eu(H2O)9]3+ and closing with more manageable calculations for the larger complexes, we computed the fully predicted ab initio geometries for a total of 80 calculations on 52 complexes of Sm(III), Eu(III), Gd(III), Tb(III), Dy(III), Ho(III), Er(III) and Tm(III), the largest containing 164 atoms. Our results indicate that RHF/STO-3G/ECP appears to be the most efficient model chemistry in terms of coordination polyhedron crystallographic geometry predictions from isolated lanthanide complex ion calculations. Moreover, both augmenting the basis set and/or including electron correlation generally enlarged the deviations and aggravated the quality of the predicted coordination polyhedron crystallographic geometry. Our results further indicate that Cosentino et al.'s suggestion of using RHF/3-21G/ECP geometries appears to be indeed a more robust, but not necessarily, more accurate recommendation to be adopted for the general lanthanide complex case. [Figure: see text].

Vibrational energies for HFCO using a neural network sum of exponentials potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pradhan, Ekadashi; Brown, Alex, E-mail: alex.brown@ualberta.ca

2016-05-07

A six-dimensional potential energy surface (PES) for formyl fluoride (HFCO) is fit in a sum-of-products form using neural network exponential fitting functions. The ab initio data upon which the fit is based were computed at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12]/cc-pVTZ-F12 level of theory. The PES fit is accurate (RMSE = 10 cm{sup −1}) up to 10 000 cm{sup −1} above the zero point energy and covers most of the experimentally measured IR data. The PES is validated by computing vibrational energies for both HFCO and deuterated formyl fluoride (DFCO) using block improved relaxationmore » with the multi-configuration time dependent Hartree approach. The frequencies of the fundamental modes, and all other vibrational states up to 5000 cm{sup −1} above the zero-point energy, are more accurate than those obtained from the previous MP2-based PES. The vibrational frequencies obtained on the PES are compared to anharmonic frequencies at the MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory obtained using second-order vibrational perturbation theory. The new PES will be useful for quantum dynamics simulations for both HFCO and DFCO, e.g., studies of intramolecular vibrational redistribution leading to unimolecular dissociation and its laser control.« less

Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

NASA Astrophysics Data System (ADS)

Kristyán, Sándor

1997-11-01

In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: experimental and theoretical investigations

NASA Astrophysics Data System (ADS)

Allaf, Abdul. W.; Kassem, M.; Alibrahim, M.; Boustani, Ihsan

1999-03-01

An attempt was made to observe the gas-phase infrared spectrum of Phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by an on-line process using phosphorus (III) oxychloride, OPCl as precursor passed over heated AgCN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands centered at 2165 and 1385 cm -1. These bands are assigned to, ν1 (CN stretch) and ν2 (OP stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Møller-Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension.

PubMed

Greene, Samuel M; Shan, Xiao; Clary, David C

2016-06-28

Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

PubMed

Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

2005-12-01

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

Vibrational Spectroscopy of Ions and Radicals Present in the Interstellar Medium and in Planetary Atmospheres: A Theoretical Study

NASA Technical Reports Server (NTRS)

Chaban, Galina M.

2004-01-01

Anharmonic vibrational frequencies and intensities are calculated for OH(H2O)n and H(H2O)n radicals (that form on icy particles of the interstellar medium), HCO radical (the main intermediate in the synthesis of organic molecules in space), NH2(-) and C2H(-) anions, H5(+) cation, and other systems relevant to interstellar chemistry. In addition to pure ions and radicals, their complexes with water are studied to assess the effects of water environment on infrared spectra. The calculations are performed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. Fundamental, overtone, and combination excitations are computed. The results are in good agreement with available experimental data and provide reliable predictions for vibrational excitations not yet measured in laboratory experiments. The data should be useful for interpretation of astronomically observed spectra and identification of ions and radicals present in the interstellar medium and in planetary atmospheres.

Structure and vibrational spectra of pyridine betaine hydrochloride

NASA Astrophysics Data System (ADS)

Szafran, Mirosław; Koput, Jacek; Baran, Jan; Głowiak, Tadeusz

1997-12-01

The crystal structure of pyridine betaine hydrochloride (PBET·HCl) was determined by X-ray diffraction to be monoclinic, space group {P2 1}/{c} with a = 8.533(2) Å, b = 9.548(2) Å, c = 10.781(2) Å, β = 107.228(3)° and Z = 4. Betaine is protonated and the carboxyl group forms a hydrogen bond with the chloride ion: O·Cl - distance is 2.928(3) Å. The interaction of pyridine betaine (PBET) with HCl was examined by ab initio self-consistent field (SCF), second-order Møller-Plesset (MP2) and density functional theory (DFT) methods using the 6-31G(d,p) basis set. Two minima are located in the potential surface at the SCF level (PBETH +·Cl - and PBET·HCl, with the latter being 1.2 kcal mol -1 lower in energy) and only one minimum (PBET·HCl) at the MP2 and DFT levels. The molecular parameters of PBETH +·Cl -, computed by the SCF method, reproduce the corresponding experimental data. The computed vibrational frequencies of PBETH +·Cl - resemble correctly the experimental vibrational spectrum in the solid state. The root-mean-square (r.m.s.) deviations between the experimental and calculated SCF frequencies are 65 cm -1 for all bands and 15 cm -1 without the νClH band. All measured IR bands were interpreted in terms of the calculated vibrational models.

Multiple Hydrogen Bond Tethers for Grazing Formic Acid in Its Complexes with Phenylacetylene.

PubMed

Karir, Ginny; Kumar, Gaurav; Kar, Bishnu Prasad; Viswanathan, K S

2018-03-01

Complexes of phenylacetylene (PhAc) and formic acid (FA) present an interesting picture, where the two submolecules are tethered, sometimes multiply, by hydrogen bonds. The multiple tentacles adopted by PhAc-FA complexes stem from the fact that both submolecules can, in the same complex, serve as proton acceptors and/or proton donors. The acetylenic and phenyl π systems of PhAc can serve as proton acceptors, while the ≡C-H or -C-H of the phenyl ring can act as a proton donor. Likewise, FA also is amphiprotic. Hence, more than 10 hydrogen-bonded structures, involving O-H···π, C-H···π, and C-H···O contacts, were indicated by our computations, some with multiple tentacles. Interestingly, despite the multiple contacts in the complexes, the barrier between some of the structures is small, and hence, FA grazes around PhAc, even while being tethered to it, with hydrogen bonds. We used matrix isolation infrared spectroscopy to experimentally study the PhAc-FA complexes, with which we located global and a few local minima, involving primarily an O-H···π interaction. Experiments were corroborated by ab initio computations, which were performed using MP2 and M06-2X methods, with 6-311++G (d,p) and aug-cc-pVDZ basis sets. Single-point energy calculations were also done at MP2/CBS and CCSD(T)/CBS levels. The nature, strength, and origin of these noncovalent interactions were studied using AIM, NBO, and LMO-EDA analysis.

The application of midbond basis sets in efficient and accurate ab initio calculations on electron-deficient systems

NASA Astrophysics Data System (ADS)

Choi, Chu Hwan

2002-09-01

Ab initio chemistry has shown great promise in reproducing experimental results and in its predictive power. The many complicated computational models and methods seem impenetrable to an inexperienced scientist, and the reliability of the results is not easily interpreted. The application of midbond orbitals is used to determine a general method for use in calculating weak intermolecular interactions, especially those involving electron-deficient systems. Using the criteria of consistency, flexibility, accuracy and efficiency we propose a supermolecular method of calculation using the full counterpoise (CP) method of Boys and Bernardi, coupled with Moller-Plesset (MP) perturbation theory as an efficient electron-correlative method. We also advocate the use of the highly efficient and reliable correlation-consistent polarized valence basis sets of Dunning. To these basis sets, we add a general set of midbond orbitals and demonstrate greatly enhanced efficiency in the calculation. The H2-H2 dimer is taken as a benchmark test case for our method, and details of the computation are elaborated. Our method reproduces with great accuracy the dissociation energies of other previous theoretical studies. The added efficiency of extending the basis sets with conventional means is compared with the performance of our midbond-extended basis sets. The improvement found with midbond functions is notably superior in every case tested. Finally, a novel application of midbond functions to the BH5 complex is presented. The system is an unusual van der Waals complex. The interaction potential curves are presented for several standard basis sets and midbond-enhanced basis sets, as well as for two popular, alternative correlation methods. We report that MP theory appears to be superior to coupled-cluster (CC) in speed, while it is more stable than B3LYP, a widely-used density functional theory (DFT). Application of our general method yields excellent results for the midbond basis sets. Again they prove superior to conventional extended basis sets. Based on these results, we recommend our general approach as a highly efficient, accurate method for calculating weakly interacting systems.

Quantum chemical investigation of attractive non-covalent interactions between halomethanes and rare gases.

PubMed

McAllister, Linda J; Bruce, Duncan W; Karadakov, Peter B

2012-11-01

The interaction between rare gas atoms and trifluoromethylhalides and iodomethane is investigated using ab initio and density functional theory (DFT) methods: MP2, CCSD, B3LYP, M06, M06-L, M06-2X, M06-HF, X3LYP, PBE, B97-D, B3LYP-D3, and M06-L-D3, in combination with the aug-cc-pVTZ and aug-cc-pVTZ-PP basis sets. A weakly attractive interaction is observed for all complexes, whose strength increases as the rare gas and halogen bond donor become more polarizable, and as the group bound to the halogen bond donor becomes more electron-withdrawing. The separation between iodine and krypton in the complex CF(3)I···Kr, calculated at the MP2 and B3LYP-D3 levels of theory, agrees very well with recent experimental results (Stephens, S. L.; Walker, N. R.; Legon, A. C. J. Chem. Phys. 2011, 135, 224309). Analysis of the ability of theoretical methods to account for the dispersion interaction present in these complexes leads to the conclusion that MP2 and B3LYP-D3, which produce very similar results, are the better performing methods, followed by B97-D and the M06 suite of functionals; the popular B3LYP as well as X3LYP perform poorly and significantly underestimate the interaction strength. The orbitals responsible for the interaction are identified through Edmiston-Ruedenberg localization; it is shown that, by combining the key orbitals, it is possible to observe a molecular orbital picture of a σ-hole interaction.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Photochemistry of formaldoxime−nitrous acid complexes in an argon matrix: identification of formaldoxime nitrite.

PubMed

Golec, Barbara; Bil, Andrzej; Mielke, Zofia

2009-08-27

We have studied the structure and photochemistry of the formaldoxime−nitrous acid system (CH2NOH−HONO) by help of FTIR matrix isolation spectroscopy and ab initio methods. The MP2/6-311++G(2d,2p) calculations show stability of six isomeric CH2NOH···HONO complexes. The FTIR spectra evidence formation of two hydrogen bonded complexes in an argon matrix whose structures are determined by comparison of the experimental spectra with the calculated ones for the six stable complexes. In the matrix there is present the most stable cyclic complex with two O−H···N bonds; a strong bond is formed between the OH group of HONO and the N atom of CH2NOH and the weaker one between the OH group of CH2NOH and the N atom of HONO. In the other complex present in the matrix the OH group of formaldoxime is attached to the OH group of HONO forming an O−H···O bond. The irradiation of the CH2NOH···HONO complexes with the filtered output of the mercury lamp (λ > 345 nm) leads to the formation of formaldoxime nitrite, CH2NONO, and its two isomeric complexes with water. The main product is the CH2NONO···H2O complex in which water is hydrogen bonded to the N atom of the C═N group. The identity of the photoproducts is confirmed by both FTIR spectroscopy and MP2 or QCISD(full) calculations with the 6-311++G(2d,2p) basis set. The intermediate in this reaction is iminoxyl radical that is formed by abstraction of hydrogen atom from formaldoxime OH group by an OH radical originating from HONO photolysis.

Effect of Methyl Substitution on the N-H···O Interaction in Complexes of Pyrrole with Water, Methanol, and Dimethyl Ether: Matrix Isolation Infrared Spectroscopy and ab Initio Computational Studies.

PubMed

Sarkar, Shubhra; Ramanathan, N; Sundararajan, K

2018-03-08

Hydrogen-bonded interactions of pyrrole with water and methanol have been studied using matrix isolation infrared spectroscopy and compared with the calculation performed on dimethyl ether. Computations carried out at MP2/aug-cc-pVDZ level of theory yielded two minima for the pyrrole-water and pyrrole-methanol complexes. The global and local minima correspond to the N-H···O and O-H···π complexes, respectively, where the N-H group of pyrrole interacts with oxygen of water/methanol and O-H of water and methanol interacts with the π cloud of pyrrole. Computations performed on the pyrrole-dimethyl ether gave only N-H···O type complex. From the experimental vibrational wavenumber shifts in the N-H stretching and N-H bending modes of pyrrole, as well as in the O-H stretching modes of water and methanol, the 1:1 N-H···O complexes were discerned. The strength of the N-H···O hydrogen bond and the corresponding shift in the N-H stretching vibrational wavenumbers increases in the order pyrrole-water < pyrrole-methanol < pyrrole-dimethyl ether, where a proton is successively replaced by a methyl group. Apart from the 1:1 complexes, higher clusters of 2:1 and 1:2 pyrrole-water and pyrrole-methanol complexes were also generated in N 2 matrix. Atoms in molecules and natural bond orbital analyses were carried out at the MP2/aug-cc-pVDZ level to understand the nature of interaction in the 1:1 pyrrole-water, pyrrole-methanol and pyrrole-dimethyl ether complexes.

Vibrational spectroscopy of (SO4(2-)).(H2O)n clusters, n=1-5: harmonic and anharmonic calculations and experiment.

PubMed

Miller, Yifat; Chaban, Galina M; Zhou, Jia; Asmis, Knut R; Neumark, Daniel M; Gerber, R Benny

2007-09-07

The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n

Ab initio studies on the solvation, electronic structures and intracluster reactions in M(+)L(n), with M(+)=magnesium and calcium singly-charged ions, L=water, methanol, ammonia, and n=1-6, and the elimination of a hydrogen atom in H atom in hydrated sodium clusters

NASA Astrophysics Data System (ADS)

Chan, Ka Wai

The solvation and electronic structures of M+Ln, with M+ = Mg+ and Cat, L = H2O, CH 3OH and NH3, n=1-6 were investigated by ab initio calculations using G03 package and density functional theory based ab initio molecular dynamics (AIMD) simulations with projector augmented-wave (PAW) method and a planewave basis set using Vienna Ab initio Simulation Package (VASP). Furthermore, ab initio studies on the intracluster reactions of Mg+ and Ca+ ions with different solvent molecules, H2O, CH3OH and NH3, were also done using G03 package. Finally, the elimination of a H atom in Na(H2O)n was studied. Such studies on the interactions and reactivity in gas clusters can provide insights into their analogies existing in condense phase. Interactions of Mg+ and Ca+ ions in different solvent molecules, H2O, CH3OH and NH3, were calculated with B3LYP and MP2 methods with basis sets 6-31+g** and 6-311+g**. A systematic comparison on the structures and reactivities of these clusters should provide a better understanding on the interplay of the ion-solvent, solvent-solvent, and electron-solvent interactions. It can provide a better understanding on the structures and bonding of complexes having analogies to those existing in condense phase. For Mg+(CH3OH)n and Ca+(CH 3OH)n, both H-elimination from OH/CH bond and CH3-elimination were investigated. H-elimination from O---H bond becomes more accessible for large cluster due to the diffusion of electron density to O---H bond. Studies on the H-elimination in Mg+(NH3)n and H-elimination from C---H bond in Mg+(CH3OH) n show that the reaction barriers flatten above 20 kcal/mol as n reaches 4 and above. These calculation results prove that the source of loss of H atom in ground state Mg+(CH3OH)n should be through the O---H bond rather than through the C---H bond. Compared to Mg+(CH3OH)n, the reaction barriers for H-elimination in Mg+(NH3)n is much larger, which is in consistent with the experimental observation of little H-elimination for Mg+(NH3)n unless it's photo-excited. The examination of neutral Na(H2O)n clusters, n=4~15 for H-elimination was carried out. The reaction profile for H-elimination was obtained by energy minimization at constrained O---H distance which was successively increased. There was a general trend of decreasing reaction barrier, as the cluster size grows. In contrast to Mg+(H 2O)n, the expected switch-off of H-elimination as in Mg +(H2O)n cannot be observed.

Theoretical Study of Decomposition Pathways for HArF and HKrF

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Lundell, Jan; Gerber, R. Benny; Kwak, Donchan (Technical Monitor)

2002-01-01

To provide theoretical insights into the stability and dynamics of the new rare gas compounds HArF and HKrF, reaction paths for decomposition processes HRgF to Rg + HF and HRgF to H + Rg + F (Rg = Ar, Kr) are calculated using ab initio electronic structure methods. The bending channels, HRgF to Rg + HF, are described by single-configurational MP2 and CCSD(T) electronic structure methods, while the linear decomposition paths, HRgF to H + Rg + F, require the use of multi-configurational wave functions that include dynamic correlation and are size extensive. HArF and HKrF molecules are found to be energetically stable with respect to atomic dissociation products (H + Rg + F) and separated by substantial energy barriers from Rg + HF products, which ensure their kinetic stability. The results are compatible with experimental data on these systems.

Torsion-wagging tunneling and vibrational states in hydrazine determined from its ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Łodyga, Wiesław; Makarewicz, Jan

2012-05-01

Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.

Mid-infrared signatures of hydroxyl containing water clusters: Infrared laser Stark spectroscopy of OH–H{sub 2}O and OH(D{sub 2}O){sub n} (n = 1-3)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, Federico J.; INFIQC, Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón, X5000HUA Córdoba; Brice, Joseph T.

2015-10-28

Small water clusters containing a single hydroxyl radical are synthesized in liquid helium droplets. The OH–H{sub 2}O and OH(D{sub 2}O){sub n} clusters (n = 1-3) are probed with infrared laser spectroscopy in the vicinity of the hydroxyl radical OH stretch vibration. Experimental band origins are qualitatively consistent with ab initio calculations of the global minimum structures; however, frequency shifts from isolated OH are significantly over-predicted by both B3LYP and MP2 methods. An effective Hamiltonian that accounts for partial quenching of electronic angular momentum is used to analyze Stark spectra of the OH–H{sub 2}O and OH–D{sub 2}O binary complexes, revealing amore » 3.70(5) D permanent electric dipole moment. Computations of the dipole moment are in good agreement with experiment when large-amplitude vibrational averaging is taken into account. Polarization spectroscopy is employed to characterize two vibrational bands assigned to OH(D{sub 2}O){sub 2}, revealing two nearly isoenergetic cyclic isomers that differ in the orientation of the non-hydrogen-bonded deuterium atoms relative to the plane of the three oxygen atoms. The dipole moments for these clusters are determined to be approximately 2.5 and 1.8 D for “up-up” and “up-down” structures, respectively. Hydroxyl stretching bands of larger clusters containing three or more D{sub 2}O molecules are observed shifted approximately 300 cm{sup −1} to the red of the isolated OH radical. Pressure dependence studies and ab initio calculations imply the presence of multiple cyclic isomers of OH(D{sub 2}O){sub 3}.« less

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Vibrational spectroscopy of (SO42-).(H2O)n clusters, n=1-5: Harmonic and anharmonic calculations and experiment

NASA Astrophysics Data System (ADS)

Miller, Yifat; Chaban, Galina M.; Zhou, Jia; Asmis, Knut R.; Neumark, Daniel M.; Benny Gerber, R.

2007-09-01

The vibrational spectroscopy of (SO42-)•(H2O)n is studied by theoretical calculations for n =1-5, and the results are compared with experiments for n =3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850cm-1, is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n =2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO42-)•(H2O)5: The global minimum of the potential energy corresponds to a Cs structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-)•(HSO4-)•(H2O)n, for n ⩽5.

Millimeter Wave Spectrum of the Weakly Bound Complex CH2═CHCN·H2O: Structure, Dynamics, and Implications for Astronomical Search.

PubMed

Calabrese, Camilla; Vigorito, Annalisa; Maris, Assimo; Mariotti, Sergio; Fathi, Pantea; Geppert, Wolf D; Melandri, Sonia

2015-12-03

The weakly bound 1:1 complex between acrylonitrile (CH2═CHCN) and water has been characterized spectroscopically in the millimeter wave range (59.6-74.4 GHz) using a Free Jet Absorption Millimeter Wave spectrometer. Precise values of the rotational and quartic centrifugal distortion constants have been obtained from the measured frequencies of the normal and isotopically substituted water moiety (DOH, DOD, H(18)OH). Structural parameters have been estimated from the rotational constants and their differences among isotopologues: the complex has a planar structure with the two subunits held together by a O-H···N (2.331(3) Å) and a C-H···O (2.508(4) Å) interaction. The ab initio intermolecular binding energy, obtained at the counterpoise corrected MP2/aug-cc-pVTZ level of calculation, is De = 24.4 kJ mol(-1).

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Specific formation of negative ions from leucine and isoleucine molecules

NASA Astrophysics Data System (ADS)

Papp, Peter; Shchukin, Pavel; Matejčík, Štefan

2010-01-01

Dissociative electron attachment (DEA) to gas phase leucine (Leu) and isoleucine (Ile) molecules was studied using experimental and quantum-chemical methods. The relative partial cross sections for DEA have been measured using crossed electron/molecular beams technique. Supporting ab initio calculations of the structure, energies of neutral molecules, fragments, and negative ions have been carried out at G3MP2 and B3LYP levels in order to interpret the experimental data. Leu and Ile exhibit several common features. The negative ionic fragments from both molecules are formed in the electron energy range from 0 to approximately 14 eV via three resonances (1.2, 5.5, and 8 eV). The relative partial cross sections for DEA Leu and Ile are very similar. The dominant negative ions formed were closed shell negative ions (M-H)- (m/z=130) formed preferentially via low electron energy resonance of 1.23 eV. Additional negative ions with m/z=115, 114, 113, 112, 84, 82, 74, 45, 26, and 17 have been detected.

De(side chain) model of epothilone: bioconformer interconversions DFT study.

PubMed

Rusinska-Roszak, Danuta; Lozynski, Marek

2009-07-01

Using ab initio methods, we have studied conformations of the de(sidechain)de(dioxy)difluoroepothilone model to quantify the effect of stability change between the exo and endo conformers of the epoxy ring. The DFT minimization of the macrolactone ring reveals four low energy conformers, although MP2 predicted five stable structures. The model tested with DFT hybride functional (B3LYP/6-31+G(d,p)) exhibits the global minimum for one of the exo forms (C), experimentally observed in the solid state, but unexpectedly with the MP2 electron correlation method for the virtual endo form (W). Using the QST3 technique, several pathways were found for the conversion of the low energy conformers to the other low energy exo representatives, as well as within the endo analog subset. The potential energy relationships obtained for several exo forms suggest a high conformational mobility between three, experimentally observed, conformers. The high rotational barrier, however, excludes direct equilibrium with experimental EC-derived endo form S. The highest calculated transition state for the conversion of the most stable exo M interligand to the endo S form is approximately a 28 kcal/mol above the energy of the former. The two-step interconversion of the exo H conformer to the endo S requires at least 28 kcal/mol. Surprisingly, we found that the transition state energy of the H form to the virtual endo W has the acceptable value of about 9 kcal/mol and the next energy barrier for free interconversion of endo W to endo S is 13 kcal/mol.

Energetic studies and phase diagram of thioxanthene.

PubMed

Freitas, Vera L S; Monte, Manuel J S; Santos, Luís M N B F; Gomes, José R B; Ribeiro da Silva, Maria D M C

2009-11-19

The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 +/- 4.1 kJ x mol(-1)) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p degrees = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 +/- 0.8 kJ x mol(-1)), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p degrees = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 +/- 4.2 kJ x mol(-1). Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data.

Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory.

PubMed

Krasnoshchekov, Sergey V; Vogt, Natalja; Stepanov, Nikolay F

2015-06-25

The numerical-analytic implementation of the operator version of the canonical Van Vleck second-order vibrational perturbation theory (CVPT2) is employed for a purely ab initio prediction and interpretation of the infrared (IR) and Raman anharmonic spectra of a medium-size molecule of the diketo tautomer of uracil (2,4(1H,3H)-pyrimidinedione), which has high biological importance as one of the four RNA nucleobases. A nonempirical, semidiagonal quartic potential energy surface (PES) expressed in normal coordinates was evaluated at the MP2/cc-pVTZ level of theory. The quality of the PES was improved by replacing the harmonic frequencies with the "best" estimated CCSD(T)-based values taken from the literature. The theoretical method is enhanced by an accurate treatment of multiple Fermi and Darling-Dennison resonances with evaluation of the corresponding resonance constants W and K (CVPT2+WK method). A prediction of the anharmonic frequencies as well as IR and Raman intensities was used for a detailed interpretation of the experimental spectra of uracil. Very good agreement between predicted and observed vibrational frequencies has been achieved (RMSD ∼4.5 cm(-1)). The model employed gave a theoretically robust treatment of the multiple resonances in the 1680-1790 cm(-1) region. Our new analysis gives the most reliable reassignments of IR and Raman spectra of uracil available to date.

Combined experimental and theoretical study of the benzocaine/Ar van der Waals system in supersonic expansions.

PubMed

León, Iker; Aguado, Edurne; Lesarri, Alberto; Fernández, José A; Castaño, Fernando

2009-02-12

The electronic spectra of Benzocaine x Ar(n), n = 0-4 were obtained using two-color resonance enhanced multiphoton ionization; the 1:1 and 1:2 clusters were investigated by ultraviolet/ultraviolet hole burning, stimulated emission pumping, and other laser spectroscopies. A single isomer was found for the 1:1 cluster, while two isomers of the 1:2 cluster were found: one with the two Ar atoms on the same side of the chromophore, and the other with the two Ar atoms sitting on opposite sides of the chromophore. The observed shifts point to the existence of a single isomer for the 1:3 and 1:4 species. Dissociation energies for the neutral ground and first excited electronic state and the ion ground electronic state of the complexes have been determined by the fragmentation threshold method and by ab initio calculations conducted at the MP2 level with 6-31++g(2d, p), 6-311++g(2d, p) and AUG-cc-pVTZ basis sets. The results are compared with those obtained for other similar systems.

Theoretical study on the spectroscopic properties of CO3(*-).nH2O clusters: extrapolation to bulk.

PubMed

Pathak, Arup K; Mukherjee, Tulsi; Maity, Dilip K

2008-10-24

Vertical detachment energies (VDE) and UV/Vis absorption spectra of hydrated carbonate radical anion clusters, CO(3)(*-).nH(2)O (n=1-8), are determined by means of ab initio electronic structure theory. The VDE values of the hydrated clusters are calculated with second-order Moller-Plesset perturbation (MP2) and coupled cluster theory using the 6-311++G(d,p) set of basis functions. The bulk VDE value of an aqueous carbonate radical anion solution is predicted to be 10.6 eV from the calculated weighted average VDE values of the CO(3)(*-).nH(2)O clusters. UV/Vis absorption spectra of the hydrated clusters are calculated by means of time-dependent density functional theory using the Becke three-parameter nonlocal exchange and the Lee-Yang-Parr nonlocal correlation functional (B3LYP). The simulated UV/Vis spectrum of the CO(3)(*-).8H(2)O cluster is in excellent agreement with the reported experimental spectrum for CO(3)(*-) (aq), obtained based on pulse radiolysis experiments.

Investigation of hydrogen bonding and self-association in neat HCONH 2 and the binary mixture (HCONH 2+CH 3OH) by concentration dependent Raman study and ab initio calculations

NASA Astrophysics Data System (ADS)

Ojha, Animesh K.; Srivastava, Sunil K.; Koster, J.; Shukla, M. K.; Leszczynski, J.; Asthana, B. P.; Kiefer, W.

2004-02-01

Raman spectra of neat formamide (HCONH 2) and its binary mixture (HCONH 2+CH 3OH) with hydrogen donor solvent, methanol (CH 3OH) were investigated using a sensitive scanning multichannel detection scheme, which is simultaneously more precise also, especially when the observed Raman line profile has multiple component bands. The spectra in the two regions, namely 1200-1500 and 1500-1800 cm -1 were recorded with varying mole fractions of the reference molecule, HCONH 2, from 0.1 to 0.9. The spectra in the region 1200-1500 cm -1 show a broad band at ˜1312 cm -1, which shows a peculiar concentration dependence, and a relatively sharp peak at ˜1392 cm -1, whose peak position is not influenced by concentration. The spectra in the region 1500-1800 cm -1 also show two peaks, one at ˜1593 cm -1 and the other one at ˜1668 cm -1 which are assigned to NH 2 bending and ν(CO) stretching vibrations, respectively. Both these Raman bands show an appreciable upshift of ˜15-20 cm -1 and the one at ˜1668 cm -1 has also a distinct asymmetry towards higher wavenumber. The optimized geometries and vibrational wavenumbers of various normal modes for neat formamide as well as its hydrogen-bonded complexes were also calculated using ab initio theory at the MP2 level. The results have been used to understand and explain the concentration dependent changes in the spectral features in terms of hydrogen bonding and self-association.

Relaxation of structural parameters and potential coefficients of nonrigid molecules. General symmetry properties and application to ab initio study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Ha, T.-K.; Günthard, H. H.

1989-07-01

Structural parameters like bond length, bond angles, etc. and harmonic and anharmonic potential coefficients of molecules with internal rotation, inversion or puckering modes are generally assumed to vary with the large amplitude internal coordinates in a concerted manner (relaxation). Taking the coordinate vectors of the nuclear configuration of semirigid molecules with relaxation (SRMRs) as functions of relaxing structural parameters and finite amplitude internal coordinate, the isometric group of SRMRs is discussed and the irreducible representations of the latter are shown to classify into engendered and nonengendered ones. On this basis a concept of equivalent sets of nuclei SRMRs is introduced and an analytical expression is derived which defines the most general functional form of relaxation increments of all common types of structural parameters compatible with isometric symmetry. This formula is shown to be a close analog of an analytical expression defining the transformations induced by the isometric group of infinitesimal internal coordinates associated with typical structural parameters. Furthermore analogous formulae are given for the most general form of the relaxation of harmonic potential coefficients as a function of finite internal coordinates. The general relations are illustrated by ab initio calculations for 1,2-difluoroethane at the MP4/DZP//HF/4-31G* level for twelve values of the dihedral angle including complete structure optimization. The potential to internal rotation is found to be in essential agreement with experimentally derived data. For a complete set of ab initio structural parameters the associated relaxation increments are represented as Fourier series, which are shown to confirm the form predicted by the general formula and the isometric group of 1,2-difluoroethane. Depending on type of the structural parameters (bond length, bond angles, etc.), the associated relaxation increments appear to follow some simple rules. Similarly a complete set of harmonic potential coefficients derived from the ab initio calculations will be analyzed in terms of Fourier series and shown to conform to the symmetry requirements of the symmetry group. Relaxation of potential coefficients is found to amount to up to ≈5% for some types of diagonal and nondiagonal terms and to reflect certain "topological" rules similar to regularities of harmonic potential constants of quasi-rigid molecules found in empirical determinations of valence force fields.

New mechanism for autocatalytic decomposition of H2CO3 in the vapor phase.

PubMed

Ghoshal, Sourav; Hazra, Montu K

2014-04-03

In this article, we present high level ab initio calculations investigating the energetics of a new autocatalytic decomposition mechanism for carbonic acid (H2CO3) in the vapor phase. The calculation have been performed at the MP2 level of theory in conjunction with aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(3df,3pd) basis sets as well as at the CCSD(T)/aug-cc-pVTZ level. The present study suggests that this new decomposition mechanism is effectively a near-barrierless process at room temperature and makes vapor phase of H2CO3 unstable even in the absence of water molecules. Our calculation at the MP2/aug-cc-pVTZ level predicts that the effective barrier, defined as the difference between the zero-point vibrational energy (ZPE) corrected energy of the transition state and the total energy of the isolated starting reactants in terms of bimolecular encounters, is nearly zero for the autocatalytic decomposition mechanism. The results at the CCSD(T)/aug-cc-pVTZ level of calculations suggest that the effective barrier, as defined above, is sensitive to some extent to the levels of calculations used, nevertheless, we find that the effective barrier height predicted at the CCSD(T)/aug-cc-pVTZ level is very small or in other words the autocatalytic decomposition mechanism presented in this work is a near-barrierless process as mentioned above. Thus, we suggest that this new autocatalytic decomposition mechanism has to be considered as the primary mechanism for the decomposition of carbonic acid, especially at its source, where the vapor phase concentration of H2CO3 molecules reaches its highest levels.

Methylphenidate side effects in advanced cancer: a retrospective analysis.

PubMed

Lasheen, Wael; Walsh, Declan; Mahmoud, Fade; Davis, Mellar P; Rivera, Nilo; Khoshknabi, Dilara Seyidova

2010-02-01

Methylphenidate (MP) is often recommended for symptom control in advanced cancer. Little is known about its side effects in frail adults. To evaluate MP-associated symptoms or side effects (S/E). Data was collected from 2 published prospective cohort series and a phase 2 study of MP for symptom control in advanced cancer. All 3 reports had identical dosing schedules and symptom assessments. Initial MP doses were 10 mg/d (5 mg at 8 AM and at 12 noon) titrated up to a maximum of 30 mg/d. Depression, fatigue, and symptoms identified as possible MP S/E were evaluated for presence (prevalence) and for severity (using categorical scales) before MP (day 0) and on days 3, 5, and 7 thereafter. The categorical scale used was none, mild, moderate, and severe. 62 patients were enrolled. Fifty completed 7 days of MP with a median age of 69 (range 30-90) years. Thirty-five received MP 10 mg/day. Most (96%) had improvement in depression and/or fatigue. Among the 62 patients, new symptom prevalence throughout the study was agitation (16%), insomnia (16%), dry mouth (15%), nausea (10%), tremors (6%), anorexia (5%), headache (3%), palpitations (2%), and vomiting (2%). Patients could have more than 1 symptom simultaneously. Seven (11%) withdrew due to MP S/E. Some symptoms present before MP showed significant improvement during MP therapy. (1) Treatment with MP (10-20 mg/d) in advanced cancer is well tolerated. (2) S/E symptoms with MP appeared to improve spontaneously despite continued MP therapy. (3) Depression and fatigue improved at doses lower than those recommended in other clinical conditions. (4) MP improved depression and fatigue, and some secondary symptoms associated with them. Methylphenidate (MP) appears safe when used in the treatment of depression and fatigue in advanced cancer.

Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

PubMed

Varadwaj, Pradeep Risikrishna

2010-05-01

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density rho ( c ), the Laplacian of electron charge density nabla(2)rho(c), and the total energy density (H ( c )) at the critical points between the interatomic regions that the interaction N...H is indeed electrostatic in origin (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) < 0) and HX ((rho(c) > 0, nabla(2)rho(c) < 0 and H(c) < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E((2)), caused by charge transfer mechanism shows that the interaction N...H is n(N) --> BD*(HX) delocalization.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

Nature and position of functional group on thiopurine substrates influence activity of xanthine oxidase--enzymatic reaction pathways of 6-mercaptopurine and 2-mercaptopurine are different.

PubMed

Tamta, Hemlata; Kalra, Sukirti; Thilagavathi, Ramasamy; Chakraborti, Asit K; Mukhopadhyay, Anup K

2007-02-01

Xanthine oxidase-catalyzed hydroxylation reactions of the anticancer drug 6-mercaptopurine (6-MP) and its analog 2-mercaptopurine (2-MP) as well as 6-thioxanthine (6-TX) and 2-thioxanthine (2-TX) have been studied using UV-spectroscopy, high pressure liquid chromatography, photodiode array, and liquid chromatography-based mass spectral analysis. It is shown that 6-MP and 2-MP are oxidatively hydroxylated through different pathways. Enzymatic hydroxylation of 6-MP forms 6-thiouric acid in two steps involving 6-TX as the intermediate, whereas 2-MP is converted to 8-hydroxy-2-mercaptopurine as the expected end product in one step. Surprisingly, in contrast to the other thiopurines, enzymatic hydroxylation of 2-MP showed a unique hyperchromic effect at 264 nm as the reaction proceeded. However, when 2-TX is used as the substrate, it is hydroxylated to 2-thiouric acid. The enzymatic hydroxylation of 2-MP is considerably faster than that of 6-MP, while 6-TX and 2-TX show similar rates under identical reaction conditions. The reason why 2-MP is a better substrate than 6-MP and how the chemical nature and position of the functional groups present on the thiopurine substrates influence xanthine oxidase activity are discussed.

Ab initio study of the structural properties of ascorbic acid (vitamin C)

NASA Astrophysics Data System (ADS)

Allen, Reeshemah N.; Shukla, M. K.; Reed, Demarcio; Leszczynski, Jerzy

Geometries of the neutral and ionic tautomeric species of ascorbic acid were optimized at the density functional theory (DFT) level using the B3LYP functional. The radical species were evaluated using the unrestricted B3LYP method. Single-point energy calculations were also performed using the Møller-Plesset (MP2) and unrestricted MP2 (UMP2) methods for the closed-shell and open-shell systems, respectively. The effects of aqueous solution were evaluated using the conducting polarized continuum model (CPCM) and polarized continuum model (PCM). The geometries of most stable radicals in the respective groups were also optimized in the water solution using the CPCM model at the UB3LYP level. All calculation were performed using the 6-311++G(d,p) basis set. The nature of stationary points on the gas phase potential energy surfaces (PESs) was evaluated using vibrational frequency calculations; all geometries characterize local minima. The species obtained by the deprotonation of the O3 site is the most stable monoanion of ascorbic acid. For the radical species, the structure obtained by the dehydrogenation of the O3 site is the most stable monoradical. Among the radical anions, the species obtained by the deprotonation of the O3 site and subsequent dehydrogenation of the O2 site is the most stable in the gas phase and in an aqueous medium. The computed isotropic hyperfine coupling constants of this species were found to be in good agreement with the experimental data. Our investigation also supports the earlier findings that the oxidized species of ascorbic acid in water solution by the OH? radical is radical anion of the AAO?3O-2 form. The spin densities and molecular electrostatic potentials are also discussed.

The Conformational Landscape of L-Threonine Matrix Isolation Infrared and {AB-INITIO Studies

NASA Astrophysics Data System (ADS)

Dubey, Pankaj; Mukhopadhyay, Anamika; Viswanathan, K. S.

2017-06-01

Amino acids, containing hydroxy side chains such as L-threonine and tyrosine play an important role in molecular recognition, such as in the docking of propofol, which is a commonly used anaesthetic. A rich conformational landscape of these amino acids makes them interesting candidates in the study of intra and intermolecular interactions. In this work, the conformational landscape of L-threonine was studied, as it can be expected to serve as a basis for understanding structure and functions of polypeptides and other biomolecules. The matrix isolation technique (MI) coupled with a high temperature effusive molecular beam (EMB) nozzle was used to trap conformers of amino acid, which were then characterized using FTIR spectroscopy. The usefulness of MI-EMB-FTIR spectroscopy is that it can trap structures corresponding to the local minima along with the global minimum and hence allows for a better exploration of the potential energy surface. A major challenge in conformational analysis of amino acids using matrix isolation FTIR arises from its non-volatile nature. A home built heating system which was mounted close to the cryotip, was used to evaporate the non-volatile amino acids. Our infrared spectra show that three conformations were trapped in the matrix. Experimental results were supported by {ab-initio calculations performed using the CCSD(T), MP2 and M06-2X methods together with 6-311++G(d,p) and aug/cc-pVDZ basis sets. The side chains of the amino acids appeared to have an influence on the preferential stabilisation of a particular backbone structure of amino acids. Factors such as entropy, anomeric effect and intramolecular H-bonding were also found to play an important role in determining conformal preferences, which will be discussed.

Synthesis and characterization of a series of Group 4 phenoxy-thiol derivatives

DOE PAGES

Boyle, Timothy J.; Neville, Michael L.; Parkes, Marie V.

2016-02-11

In this study, a series of Group 4 phenoxy-thiols were developed from the reaction products of a series of metal tert-butoxides ([M(OBu t) 4]) with four equivalents of 4-mercaptophenol (H-4MP). The products were found by single crystal X-ray diffraction to adopt the general structure [(HOBu t)(4MP) 3M(μ-4MP)] 2 [where M = Ti (1), Zr (2), Hf (3)] from toluene and [(py) 2M(4MP)] where M = Ti (4), Zr (5) and [(py)(4MP) 3Hf(μ-4MP)] 2 (6) from pyridine (py). Varying the [Ti(OR) 4] precursors (OR = iso-propoxide (OPr i) or neo-pentoxide (ONep)) in toluene led to [(HOR)(4MP) 3Ti(μ-4MP)] 2 (OR = OPrmore » i (7), ONep (8)), which were structurally similar to 1. Lower stoichiometric reactions in toluene led to partial substitution by the 4MP ligands yielding [H][Ti(μ-4MP)(4MP)(ONep) 3] 2 (9). Independent of the stoichiometry, all of the Ti derivatives were found to be red in color, whereas the heavier congeners were colorless. Attempts to understand this phenomenon led to investigation with a series of varied –SH substituted phenols. From the reaction of H-2MP and H-3MP (2-mercaptophenol and 3-mercaptophenol, respectively), the isolated products had identical arrangements: [(ONep) 2(2MP)Ti(μ,η2-2MP)] 2 (10) and [(HOR)(3MP)M(μ-3MP)] 2 (M/OR = Ti/ONep (11); Zr/OBu t (12)) with a similar red color. Based on the simulated and observed UV–Vis spectra, it was reasoned that the color was generated due to a ligand-to-metal charge transfer for Ti that was not available for the larger congeners.« less

An Ultra-High Field Study of Cerebellar Pathology in Early Relapsing-Remitting Multiple Sclerosis Using MP2RAGE.

PubMed

Fartaria, Mário João; OʼBrien, Kieran; Şorega, Alexandra; Bonnier, Guillaume; Roche, Alexis; Falkovskiy, Pavel; Krueger, Gunnar; Kober, Tobias; Bach Cuadra, Meritxell; Granziera, Cristina

2017-05-01

The aim of this study was to study focal cerebellar pathology in early stages of multiple sclerosis (MS) using ultra-high-field magnetization-prepared 2 inversion-contrast rapid gradient-echo (7T MP2RAGE). Twenty early-stage relapsing-remitting MS patients underwent an MP2RAGE acquisition at 7 T magnetic resonance imaging (MRI) (images acquired at 2 different resolutions: 0.58 × 0.58 × 0.58 mm, 7T_0.58, and 0.75 × 0.75 × 0.90 mm, 7T_0.75) and 3 T MRI (1.0 × 1.0 × 1.2 mm, 3T_1.0). Total cerebellar lesion load and volume and mean cerebellar lesion volume were compared across images using a Wilcoxon signed-rank test. Mean T1 relaxation times in lesions and normal-appearing tissue as well as contrast-to-noise ratio (CNR) measurements were also compared using a Wilcoxon signed-rank test. A multivariate analysis was applied to assess the contribution of MRI metrics to clinical performance in MS patients. Both 7T_0.58 and 7T_0.75 MP2RAGE showed significantly higher lesion load compared with 3T_1.0 MP2RAGE (P < 0.001). Plaques that were judged as leukocortical in 7T_0.75 and 3T_1.0 MP2RAGEs were instead identified as WM lesions in 7T_0.58 MP2RAGE. Cortical lesion CNR was significantly higher in MP2RAGEs at 7 T than at 3 T. Total lesion load as well as total and mean lesion volume obtained at both 7 T and 3 T MP2RAGE significantly predicted attention (P < 0.05, adjusted R = 0.5), verbal fluency (P < 0.01, adjusted R = 0.6), and motor performance (P = 0.01, adjusted R = 0.7). This study demonstrates the value of 7 T MP2RAGE to study the cerebellum in early MS patients. 7T_0.58 MP2RAGE provides a more accurate anatomical description of white and gray matter pathology compared with 7T_0.75 and 3T_1.0 MP2RAGE, likely due to the improved spatial resolution, lower partial volume effects, and higher CNR.

Chirped-Pulse and Cavity Based Fourier Transform Microwave Spectroscopy of the Methyl Lactate-Ammonia Adduct

NASA Astrophysics Data System (ADS)

Thomas, Javix; Sukhorukov, Oleksandr; Jaeger, Wolfgang; Xu, Yunjie

2012-06-01

The hydrogen bonded complex of ammonia with methyl lactate, a chiral alpha-hydroxyester, has been studied using rotational spectroscopy and high level ab initio calculations. Previous studies showed that methyl lactate can exist in a number of conformers. However, only the most stable one which has an intramolecular hydrogen bonded ring formed with its alcoholic hydroxyl and its carbonyl oxygen atom was detected experimentally An extensive ab initio search has been performed to locate all possible low energy conformers of the methyl lactate-ammonia contact pair. Five lowest energy conformers have been identified at the MP2/6-311++G(d,p) level. The lowest energy conformer favors an insertion arrangement, where ammonia is inserted into the existing intramolecular hydrogen bonded ring in the most stable methyl lactate conformer. Broadband scans for the rotational spectra of possible binary conformers have been carried out using a chirped-pulse Fourier transform microwave (FTMW) instrument. The most stable binary adduct was identified and assigned. The final frequency measurements have been done with a cavity based FTMW instrument. The spectrum observed shows complicated fine and hyperfine splitting patterns, likely due to the internal rotations of the methyl groups of methyl lactate and that of ammonia, as well as the 14N quadrupolar nucleus. The binary adduct with 15NH3 has also been studied to simplify the splitting pattern and to aid the assignments of the extensive splittings. The isotopic data and the fine and hyperfine structures will be discussed in terms of internal rotation dynamics and geometry of the hydrogen bonded adduct.

Modeling the weak hydrogen bonding of pyrrole and dichloromethane through Raman and DFT study.

PubMed

Singh, Dheeraj Kumar; Asthana, Birendra Pratap; Srivastava, Sunil Kumar

2012-08-01

Raman spectra of neat pyrrole (C(4)H(5)N) and its binary mixtures with dichloromethane (CH(2)Cl(2), DCM) with varying mole fractions of C(4)H(5)N from 0.1 to 0.9 were recorded in order to monitor the influence of molecular interaction on spectral features of selected vibrational bands of pyrrole in the region 600-1600 cm(-1). Only 1369 cm(-1) vibrational band of pyrrole shows a significant change in its peak position in going from neat pyrrole to the complexes. The 1369 cm(-1) band shows (∼6 cm(-1)) blue shift upon dilution and the corresponding linewidth shows the maximum shift at C = 0.5 mole fraction of pyrrole upon dilution which clearly indicates that the concentration fluctuation model plays major role. Quantum chemical calculation using density functional theory (DFT) and ab-initio (MP2 and HF) methods were performed employing high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat pyrrole and its complexes with DCM in gas phase. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. In order to account for the solvent effect on vibrational features and changes in optimized structural parameters of pyrrole, polarizable continuum model (PCM) (bulk solvations) and PCM (specific plus bulk solvations) calculations were performed. Two possible configurations of pyrrole + DCM complex have been predicted by B3LYP and HF methods, whereas the MP2 method gave only single configuration in which H atom of DCM is bonded to π ring of the pyrrole molecule. This affects significantly the ring vibrations of pyrrole molecule, which was also observed in our experimental results.

Hydrogen bonding in microsolvation: photoelectron imaging and theoretical studies on Au(x)(-)-(H2O)(n) and Au(x)(-)-(CH3OH)(n) (x = 1, 2; n = 1, 2) complexes.

PubMed

Wu, Xia; Tan, Kai; Tang, Zichao; Lu, Xin

2014-03-14

We have combined photoelectron velocity-map imaging (VMI) spectroscopy and theoretical calculations to elucidate the geometry and energy properties of Aux(-)(Solv)n clusters with x = 1, 2; n = 1, 2; and Solv = H2O and CH3OH. Besides the blue-shifted vertical electron detachment energies (VDEs) of the complexes Au1,2(-)(Solv)n with the increase of the solvation number (n), we independently probed two distinct Au(-)(CH3OH)2 isomers, which combined with MP2/aug-cc-pVTZ(pp) calculations represent a competition between O···H-O hydrogen bonds (HBs) and Au···H-O nonconventional hydrogen bonds (NHBs). Complementary calculations provide the total binding energies of the low-energy isomers. Moreover, the relationship between the total binding energies and total VDEshift is discussed. We found that the Au1,2(-) anions exhibit halide-analogous behavior in microsolvation. These findings also demonstrate that photoelectron velocity map imaging spectroscopy with the aid of the ab initio calculations is an effective tool for investigating weak-interaction complexes.

Conformational stability from temperature-dependent fourier transform infrared spectra of noble gas solutions, r0 structural parameters, and barriers to internal rotation for ethylamine.

PubMed

Durig, James R; Zheng, Chao; Gounev, Todor K; Herrebout, Wouter A; van der Veken, Benjamin J

2006-05-04

Variable temperature (-55 to -145 degrees C) studies of the infrared spectra (3500 to 100 cm(-1)) of ethylamine, CH(3)CH(2)NH(2), dissolved in liquid krypton and/or xenon have been recorded. From these data, the enthalpy differences have been determined to be 54 +/- 4 cm(-1) (0.65 +/- 0.05 kJ/mol), with the trans conformer (methyl group relative to the lone pair of electrons on nitrogen) being the more stable form. It is estimated that there is 61 +/- 1% of the doubly degenerate gauche form present at ambient temperature. The conformational energetics have been calculated with the Møller-Plesset perturbation method to the second order (MP2(full)) and the fourth order (MP4(SDTQ)) as well as with density functional theory by the B3LYP method utilizing a variety of basis sets. Basis sets with diffuse functions lead to incorrect prediction of the conformational stability. On the basis of the frequencies of the torsional transitions along with the determined experimental enthalpy difference and gauche dihedral angle, the potential function governing conformational interchange has been obtained, and the determined Fourier cosine coefficients are V(1) = -207 +/- 48, V(2) = 320 +/- 67, V(3) = 1072 +/- 25, V(4) = 55 +/- 11, and V(5) = -96 +/- 28 cm(-1), with a trans-to-gauche barrier of 1286 cm(-1), and a gauche-to-gauche barrier of 715 cm(-1). The 3-fold methyl rotational barriers have been determined to be 1241 +/- 4 and 1281 +/- 10 cm(-1) for the gauche and trans conformers, respectively. By utilizing the previously reported microwave rotational constants combined with the structural parameters predicted at the MP2(full)/6-311+ G(d,p) level, adjusted r(0) structural parameters have been obtained. A complete vibrational assignment is given for the trans conformer, which is supported by normal coordinate calculations utilizing scaled force constants from ab initio B3LYP/6-311++G(3df,3pd) calculations. Proposed assignments are also made for the fundamentals of the gauche conformer. The results of these spectroscopic and theoretical studies are discussed and compared to the corresponding results for similar molecules.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saeed, Noha M.; El-Demerdash, Ebtehal; Abdel-Rahman, Hanaa M.

Methyl palmitate (MP) and ethyl palmitate (EP) are naturally occurring fatty acid esters reported as inflammatory cell inhibitors. In the current study, the potential anti-inflammatory activity of MP and EP was evaluated in different experimental rat models. Results showed that MP and EP caused reduction of carrageenan-induced rat paw edema in addition to diminishing prostaglandin E2 (PGE2) level in the inflammatory exudates. In lipopolysaccharide (LPS)-induced endotoxemia in rats, MP and EP reduced plasma levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). MP and EP decreased NF-κB expression in liver and lung tissues and ameliorated histopathological changes caused by LPS.more » Topical application of MP and EP reduced ear edema induced by croton oil in rats. In the same animal model, MP and EP reduced neutrophil infiltration, as indicated by decreased myeloperoxidase (MPO) activity. In conclusion, this study demonstrates the effectiveness of MP and EP in combating inflammation in several experimental models. -- Highlights: ► Efficacy of MP and EP in combating inflammation was displayed in several models. ► MP and EP reduced carrageenan-induced rat paw edema and prostaglandin E2 level. ► MP and EP decreased TNF-α and IL-6 levels in experimental endotoxemia. ► MP and EP reduced NF-κB expression and histological changes in rat liver and lung. ► MP and EP reduced croton oil-induced ear edema and neutrophil infiltration.« less

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Experimental and ab initio studies of the reactive processes in gas phase i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH collisions with potassium ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, E.; Lucas, J. M.; Andrés, J. de

2014-10-28

Collisions between potassium ions and neutral i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH, all in their electronic ground state, have been studied in the 0.10–10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K{sup +} + i-C{sub 3}H{sub 7}Br collisions KHBr{sup +} formation was observed and quantified, while the analogous KH{sub 2}O{sup +} formation in K{sup +} + i-C{sub 3}H{sub 7}OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C{sub 3}H{sub 7}{sup +} and either KBr or KOH, respectively, have been observed. For all these processes, absolutemore » cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr{sup +} formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.« less

Mechanistic and kinetic study of the CH3CO + O2 reaction.

PubMed

Hou, Hua; Li, Aixiao; Hu, Hongyi; Li, Yuzhen; Li, Hui; Wang, Baoshan

2005-06-08

Potential-energy surface of the CH3CO + O2 reaction has been calculated by ab initio quantum chemistry methods. The geometries were optimized using the second-order Moller-Plesset theory (MP2) with the 6-311G(d,p) basis set and the coupled-cluster theory with single and double excitations (CCSD) with the correlation consistent polarized valence double zeta (cc-pVDZ) basis set. The relative energies were calculated using the Gaussian-3 second-order Moller-Plesset theory with the CCSD/cc-pVDZ geometries. Multireference self-consistent-field and MP2 methods were also employed using the 6-311G(d,p) and 6-311++G(3df,2p) basis sets. Both addition/elimination and direct abstraction mechanisms have been investigated. It was revealed that acetylperoxy radical [CH3C(O)OO] is the initial adduct and the formation of OH and alpha-lactone [CH2CO2(1A')] is the only energetically accessible decomposition channel. The other channels, e.g., abstraction, HO2 + CH2CO, O + CH3CO2, CO + CH3O2, and CO2 + CH3O, are negligible. Multichannel Rice-Ramsperger-Kassel-Marcus theory and transition state theory (E-resolved) were employed to calculate the overall and individual rate coefficients and the temperature and pressure dependences. Fairly good agreement between theory and experiments has been obtained without any adjustable parameters. It was concluded that at pressures below 3 Torr, OH and CH2CO2(1A') are the major nascent products of the oxidation of acetyl radicals, although CH2CO2(1A') might either undergo unimolecular decomposition to form the final products of CH2O + CO or react with OH and Cl to generate H2O and HCl. The acetylperoxy radicals formed by collisional stabilization are the major products at the elevated pressures. In atmosphere, the yield of acetylperoxy is nearly unity and the contribution of OH is only marginal.

Conformational Studies of 1-OCTYNE from Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Maturo, Mark P.; Obenchain, Daniel A.; Melchreit, Robert; Cooke, S. A.; Novick, Stewart E.

2017-06-01

Alkanes of the form CH_3(CH_2)_nCH_3 generally favor ground state geometries that have co-planar carbon atoms. In this study, we have looked at a long chain hydrocarbon with a terminal carbon-carbon triple bond, viz., 1-octyne. Guided by the results of the 1-hexyne studies, three possible low energy conformers were studied which we reference as anti-anti (AA, straight chain), anti-gauche (AG, terminal methyl group is gauche), and gauche-anti (GA, ethyl group is gauche). An initial broadband chirp-pulse was performed between 7-13 GHz and a total of sixty-eight transitions were fit. Additional measurements on a Balle Flygare cavity instrument yielded an additional seventy-three lines belonging to three of the conformers. Transitions for all 8 of the singly substituted ^{13}C isotopologues, in natural abundance, have also been observed for the AA conformer. Ab-initio optimizations at the MP2/6-311++g(2d,2p) level of theory and basis set for these three conformers will be compared to experimental rotational constants. Structure determinations of the AA conformer will also be discussed. Atticks, K.; Bohn, R. K.; Michaels H. H. Int'l J. of Quantum Chem. 2001, 85, 514-519; Utzat, K.; Bohn, R. K.; Michaels H. H. J. Mol. Struct. 2007, 841, 22-27

A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

NASA Astrophysics Data System (ADS)

Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

2009-07-01

Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH⋯N and NH⋯O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1, respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

Experimental evidence for the blue-shifted hydrogen-bonded complexes of CHF3 with π-electron donors.

PubMed

Gopi, R; Ramanathan, N; Sundararajan, K

2017-06-15

Blue-shifted hydrogen-bonded complexes of fluoroform (CHF 3 ) with benzene (C 6 H 6 ) and acetylene (C 2 H 2 ) have been investigated using matrix isolation infrared spectroscopy and ab initio computations. For CHF 3 -C 6 H 6 complex, calculations performed at the B3LYP and MP2 levels of theory using 6-311++G (d,p) and aug-cc-pVDZ basis sets discerned two minima corresponding to a 1:1 hydrogen-bonded complex. The global minimum correlated to a structure, where the interaction is between the hydrogen of CHF 3 and the π-electrons of C 6 H 6 and a weak local minimum was stabilized through H…F interaction. For the CHF 3 -C 2 H 2 complex, computation performed at MP2/aug-cc-pVDZ level of theory yielded two minima, corresponding to the cyclic C-H…π complex A (global) and a linear C-H…F (n-σ) complex B (local). Experimentally a blue-shift of 32.3cm -1 and 7.7cm -1 was observed in the ν 1 C-H stretching mode of CHF 3 sub-molecule in Ar matrix for the 1:1 C-H…π complexes of CHF 3 with C 6 H 6 and C 2 H 2 respectively. Natural bond orbital (NBO), Atoms-in-molecule (AIM) and energy decomposition (EDA) analyses were carried out to explain the blue-shifting and the nature of the interaction in these complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

Ab initio theoretical study of dipole-bound anions of molecular complexes: (HF)3- and (HF)4- anions

NASA Astrophysics Data System (ADS)

Ramaekers, Riet; Smith, Dayle M. A.; Smets, Johan; Adamowicz, Ludwik

1997-12-01

Ab initio calculations have been performed to determine structures and vertical electron detachment energy (VDE) of the hydrogen fluoride trimer and tetramer anions, (HF)3- and (HF)4-. In these systems the excess electron is bound by the dipole field of the complex. It was determined that, unlike the neutral complexes which prefer the cyclic structures, the equilibrium geometries of the anions have "zig-zag" shapes. For both complexes the predicted VDEs are positive [210 meV and 363 meV for (HF)3- and (HF)4-, respectively], indicating that the anions are stable systems with respect to the vertical electron detachment. These results were obtained at the coupled-cluster level of theory with single, double and triple excitations [CCSD(T) method; the triple-excitation contribution in this method is calculated approximately using the perturbation approach] with the anion geometries obtained using the second-order Møller-Plesset perturbation theory (MP2) method. The same approach was also used to determine the adiabatic electron affinities (AEA) of (HF)3 and (HF)4. In addition to the electronic contribution, we also calculated the contributions (using the harmonic approximation) resulting from different zero-point vibration energies of the neutral and anionic clusters. The calculations predicted that while the AEA of (HF)3 is positive (44 meV), the AEA for (HF)4 is marginally negative (-16 meV). This suggests that the (HF)3- anion should be a stable system, while the (HF)4- is probably metastable.

Shelf-life of minimally processed lettuce and cabbage treated with gaseous chlorine dioxide and cysteine.

PubMed

Gómez-López, Vicente M; Ragaert, Peter; Jeyachchandran, Visvalingam; Debevere, Johan; Devlieghere, Frank

2008-01-15

Gaseous ClO2 was evaluated for effectiveness in prolonging the shelf-life of minimally processed (MP) lettuce and MP cabbage, previously immersed in a cysteine solution in order to inhibit browning occurring during ClO2 treatment. Each vegetable was shredded, washed, and separated in two portions, one to be treated with ClO2 gas and the other to remain untreated as reference sample. The batch to be treated with ClO2 gas was immersed for 1 min in a 0.5% solution of HCl.L-cysteine monohydrate. Then both batches were spun dried. MP vegetables were decontaminated in a cabinet at 90-91% relative humidity and 22-25 degrees C up to 10 min, including 30 s of ClO2 injection into the cabinet. The ClO2 concentration rose to 1.74 mg/L (MP lettuce) and 1.29 mg/L (MP cabbage). Then samples were stored under modified atmosphere at 7 degrees C for shelf-life studies. Changes in O2 and CO2 headspace concentrations, microbiological quality (aerobic plate count (APC), psychrotrophs, lactic acid bacteria, and yeasts), sensory quality, and pH were followed during storage. The respiration rate of the minimally processed vegetables was significantly increased by the ClO2 gas treatment only in the case of MP cabbage (P<0.05). The gas treatment reduced initially APC and psychrotroph count of MP lettuce and APC, psychrotroph counts, yeast counts and pH of MP cabbage (P<0.05). ClO2 treatment did not cause initially any significant (P<0.05) sensorial alteration, except for a weak off-odour in MP lettuce. Interestingly, no browning was observed after treating, which can be accounted to the use of L-cysteine. Although an initial microbiological reduction was observed due to ClO2 gas treatment, APC and psychrotroph counts reached in the samples treated with ClO2 higher levels than in those non-treated with ClO2 before the third day of the shelf-life study. Untreated and treated samples of MP lettuce were sensorial unacceptable due to bad overall visual quality after 4 days, while treated and untreated MP cabbage remained sensorial acceptable during the 9 days of the study. L-cysteine reduced (P<0.05) the decontamination efficacy of ClO2 when applied to MP cabbage but not in the case of MP lettuce. Gaseous ClO2 failed to prolong the shelf-life of MP lettuce and MP cabbage, the reason for the enhanced growth of microorganisms in decontaminated samples should be investigated. Nonetheless, our results prove that it is possible to inhibit browning caused by ClO2.

Unraveling Synaptic GCaMP Signals: Differential Excitability and Clearance Mechanisms Underlying Distinct Ca2+ Dynamics in Tonic and Phasic Excitatory, and Aminergic Modulatory Motor Terminals in Drosophila

PubMed Central

Xing, Xiaomin

2018-01-01

Abstract GCaMP is an optogenetic Ca2+ sensor widely used for monitoring neuronal activities but the precise physiological implications of GCaMP signals remain to be further delineated among functionally distinct synapses. The Drosophila neuromuscular junction (NMJ), a powerful genetic system for studying synaptic function and plasticity, consists of tonic and phasic glutamatergic and modulatory aminergic motor terminals of distinct properties. We report a first simultaneous imaging and electric recording study to directly contrast the frequency characteristics of GCaMP signals of the three synapses for physiological implications. Different GCaMP variants were applied in genetic and pharmacological perturbation experiments to examine the Ca2+ influx and clearance processes underlying the GCaMP signal. Distinct mutational and drug effects on GCaMP signals indicate differential roles of Na+ and K+ channels, encoded by genes including paralytic (para), Shaker (Sh), Shab, and ether-a-go-go (eag), in excitability control of different motor terminals. Moreover, the Ca2+ handling properties reflected by the characteristic frequency dependence of the synaptic GCaMP signals were determined to a large extent by differential capacity of mitochondria-powered Ca2+ clearance mechanisms. Simultaneous focal recordings of synaptic activities further revealed that GCaMPs were ineffective in tracking the rapid dynamics of Ca2+ influx that triggers transmitter release, especially during low-frequency activities, but more adequately reflected cytosolic residual Ca2+ accumulation, a major factor governing activity-dependent synaptic plasticity. These results highlight the vast range of GCaMP response patterns in functionally distinct synaptic types and provide relevant information for establishing basic guidelines for the physiological interpretations of presynaptic GCaMP signals from in situ imaging studies. PMID:29464198

Structure and dynamics of cyclic amides: The rotational spectrum of 1,3-dimethyl-2-imidazolidinone

NASA Astrophysics Data System (ADS)

Vigorito, Annalisa; Paoloni, Lorenzo; Calabrese, Camilla; Evangelisti, Luca; Favero, Laura B.; Melandri, Sonia; Maris, Assimo

2017-12-01

The structure and the internal dynamics of the lactam 1,3-dimethyl-2-imidazolidinone, also known as N,N‧-dimethylethyleneurea, have been investigated through the analysis of its free-jet absorption rotational spectrum. One conformer has been assigned. The pure μb-type spectrum, recorded in the 59.6-74.4 GHz frequency range entails an inertial defect Δc = -16.39 uÅ2, indicating that the molecule has C2 symmetry with a twisted arrangement of the ring. The methyl internal rotation barrier V3 = 7.181 (3) kJ mol-1 and the 14N diagonal nuclear quadrupole coupling constants χaa = 2.14 (14) and (χbb-χcc) = 7.26 (6) MHz were determined from the analysis of the hyperfine structure. They are in good agreement with the ab initio MP2/6-311++G(d,p) calculations which also estimate the electric dipole moment value as 3.9 D.

Oxidation of dimethyl-ether and ethylene in the atmosphere and combustion environment and thermodynamic studies on hydrofluorocarbons usingab initio calculation methods

NASA Astrophysics Data System (ADS)

Yamada, Takahiro

1999-08-01

Reaction pathways and kinetics are analyzed on CH3OC.H2 unimolecular decay and on the complete CH3OC.H2 + O2 reaction system using thermodynamic properties DHdegf 298,Sdeg 298, and Cp(T) 300 <= T/K <= 1500) derived by two ab initio calculation methods, CBS-q and G2. These are used to determine thermodynamic properties of reactants, intermediate radicals and transition state (TS) compounds. Quantum Rice-Ramsperger-Kassel (QRRK) analysis is used to calculate energy dependent rate constants, k(E), and master equation is used to account for collisional stabilization. Comparison of calculated fall-off with experiment indicates that the CBS-q and G2 calculated Ea,rxn for the rate controlling transition state (β-scission reaction to CH 2O + C.H2OOH) needs to be lowered by factor of 3.3 kcal/mol and 4.0 kcal/mol respectively in order to match the data of Sehested et al. Experimental results on dimethyl-ether pyrolysis and oxidation reaction systems are compared with a detailed reaction mechanism model. The computer code CHEMKIN II is used for numerical integration. Overall agreement of the model data with experimental data is very good. Reaction pathways are analyzed and kinetics are determined on formation and reactions of the adduct resulting from OH addition to ethylene using the above ab initio methods. Hydrogen atom tunneling is included by use of Eckart formalism. Rate constants are compared with experimentally determined product branching ratios (C.H2CH 2OH stabilization: CH2O + CH3: CH3CHO + H). ab initio calculations are performed to estimate thermodynamic properties of nine fluorinated ethane compounds (fluoroethane to hexafluoroethane), eight fluoropropane (1-fluoropropane, 1,1- and 1,2- difluoropropane, 1,1,1- and 1,1,2-trifluoropropane, 1,1,1,2- and 1,1,2,2-tetrafluoropropane and 1,1,1,2,2- pentafluoropropane), and 2-fluoro,2-methylpropane. Standard entropies and heat capacities are calculated using the rigid-rotor-harmonic-oscillator approximation with direct integration over energy levels of the intramolecular rotation potential energy curve. Enthalpies of formation are estimated using G2MP2 total energies and isodesmic reactions. Thermodynamic properties for fluorinated carbon groups C/C/F/H2, C/C/F2/H, C/C/F3, C/C2/F/H, C/C2/F2 and C/C3/F for fluorinated alkane compounds, CD/F/H and CD/F2 for fluorinated alkene compounds and CT/F for fluorinated alkyne compounds are estimated. Fluorine-fluorine interaction terms F/F, 2F/F, 3F/F, 2F/2F, 3F/2F and 3F/3F for alkane compounds, F//F, 2F//F and 2F/2F for alkene compounds, and F///F for alkyne compound are also estimated.

Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects.

PubMed

Rivelino, Roberto

2008-01-17

Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.

High Temperature Induced Anthocyanin Inhibition and Active Degradation in Malus profusion

PubMed Central

Rehman, Rana Naveed Ur; You, Yaohua; Zhang, Lei; Goudia, Bachir Daoura; Khan, Abdul Rehman; Li, Pengmin; Ma, Fangwang

2017-01-01

The red fleshed fruits of Malus profusion represent gradual color loss during high temperature in summer, potentially due to active degradation of anthocyanin. The objective of this study was to examine both physiological and molecular evidence of anthocyanin degradation. Malus crabapple fruits were exposed to either room temperature (RT = 18 ± 2°C: 25 ± 2°C) or high temperature (HT = 33 ± 2°C: 25 ± 2°C) regimens (12 h: 12 h) under hypoxic (2%) or normoxic (21%) oxygen levels. The results showed that the concentration of cyanidin 3-galactoside (cy-3-gal) was dramatically reduced following HT treatments due to a significant down-regulation of anthocyanin biosynthetic genes (MpCHS, MpDFR, MpLDOX, MpUFGT, and MpMYB10). Among other repressor MYBs, MpMYB15 expression was high following HT treatment of the fruit. HT led to the generation of a substantial concentration of H2O2 due to enhanced activities of superoxide dismutase (SOD), methane dicarboxylic aldehyde (MDA) content and cell sap pH value. Similarly, transcript levels of MpVHA-B1 and MpVHA-B2 were reduced which are involved in the vacuolar transportation of anthocyanin. The enzymatic degradation of anthocyanin was eventually enhanced coupled with the oxidative activities of peroxidase (POD) and H2O2. Conversely, the RT treatments potentially enhanced anthocyanin content by stabilizing physiological attributes (such as MDA, H2O2, and pH, among others) and sustaining sufficient biosynthetic gene expression levels. Quantitative real-time PCR analysis indicated that the transcription of MpPOD1, MpPOD8 and MpPOD9 genes in fruit tissues was up-regulated due to HT treatment and that hypoxic conditions seems more compatible with the responsible POD isoenzymes involved in active anthocyanin degradation. The results of the current study could be useful for understanding as well as elucidating the physiological phenomenon and molecular signaling cascade underlying active anthocyanin degradation in Malus crops. PMID:28848597

Protective effect of polysaccharide from maca (Lepidium meyenii) on Hep-G2 cells and alcoholic liver oxidative injury in mice.

PubMed

Zhang, Lijun; Zhao, Qingsheng; Wang, Liwei; Zhao, Mingxia; Zhao, Bing

2017-06-01

To study the characterization and hepatoprotective activity of polysaccharide from maca (Lepidium meyenii), the main polysaccharide from maca (MP-1) was obtained by DEAE-52 cellulose column. The average molecular weight of MP-1 was 1067.3kDa and the polysaccharide purity was 91.63%. In order to assess the antioxidant activities of MP-1, four kinds of methods were used, including scavenging hydroxyl radical, DPPH, superoxide anion radical, and FRAP, and the results indicated high antioxidant activities. Furthermore, hepatoprotective activity of MP-1 was studied both in vitro and vivo. In vitro, the alcohol induced Hep-G2 cells model was established to evaluate the protective effect of MP-1, which demonstrated MP-1 can alleviate alcohol damage in Hep-G2 cells. In vivo, the Institute　of　Cancer　Researcch (ICR) mice were used to evaluate hepatoprotecive effects of MP-1 on alcoholic liver disease (ALD). Supplement with MP-1 supressed the triglyceride level both in serum and in hepatic tissue. In addition, MP-1 ameliorated serous transaminases increase induced by alcohol, including aspartate transaminase, alanine aminotransferase, and γ-glutamyl transpeptidase. Moreover, MP-1 also dramatically increased the superoxide dismutase, glutathione peroxidase, and glutathione s-transferase levels in alcoholic mice. Meantime, histopathologic results MP-1 lighten inflammation induced by alcohol. These results indicate that MP-1 possesses hepatoprotective activity against hepatic injury induced by alcohol. Copyright © 2017 Elsevier B.V. All rights reserved.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks

NASA Astrophysics Data System (ADS)

McGibbon, Robert T.; Taube, Andrew G.; Donchev, Alexander G.; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L.; Shaw, David E.

2017-10-01

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol-1 (root-mean-square error 0.09 kcal mol-1), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks.

PubMed

McGibbon, Robert T; Taube, Andrew G; Donchev, Alexander G; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L; Shaw, David E

2017-10-28

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol -1 (root-mean-square error 0.09 kcal mol -1 ), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Characterization of the programmed cell death induced by metabolic products of Alternaria alternata in tobacco BY-2 cells.

PubMed

Cheng, Dan-Dan; Jia, Yu-Jiao; Gao, Hui-Yuan; Zhang, Li-Tao; Zhang, Zi-Shan; Xue, Zhong-Cai; Meng, Qing-Wei

2011-02-01

Alternaria alternata has received considerable attention in current literature and most of the studies are focused on its pathogenic effects on plant chloroplasts, but little is known about the characteristics of programmed cell death (PCD) induced by metabolic products (MP) of A. alternata, the effects of the MP on mitochondrial respiration and its relation to PCD. The purpose of this study was to explore the mechanism of MP-induced PCD in non-green tobacco BY-2 cells and to explore the role of mitochondrial inhibitory processes in the PCD of tobacco BY-2 cells. MP treatment led to significant cell death that was proven to be PCD by the concurrent cytoplasm shrinkage, chromatin condensation and DNA laddering observed in the cells. Moreover, MP treatment resulted in the overproduction of reactive oxygen species (ROS), rapid ATP depletion and a respiratory decline in the tobacco BY-2 cells. It was concluded that the direct inhibition of the mitochondrial electron transport chain (ETC), alternative pathway (AOX) capacity and catalase (CAT) activity by the MP might be the main contributors to the MP-induced ROS burst observed in tobacco BY-2 cells. The addition of adenosine together with the MP significantly inhibited ATP depletion without preventing PCD; however, when the cells were treated with the MP plus CAT, ROS overproduction was blocked and PCD did not occur. The data presented here demonstrate that the ROS burst played an important role in MP-induced PCD in the tobacco BY-2 cells.

Four Structures of Tartaric Acid Revealed in the Gas Phase

NASA Astrophysics Data System (ADS)

Cortijo, Vanessa; Díez, Verónica; Alonso, Elena R.; Mata, Santiago; Alonso, José L.

2017-06-01

The tartaric acid, one of the most important organic compounds, has been transferred into the gas phase by laser ablation of its natural crystalline form (m.p.174°C) and probed in a supersonic expansion by chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW). Four stable structures, two with an extended (trans) disposition of the carbon chain and two with a bent (gauche) disposition, have been unequivocally identified on the basis of the experimental rotational constants in conjunction with ab initio predictions. The intramolecular interactions that govern the conformational preferences are dominated by cooperative O-H...O=C type and O-H?O hydrogen bonds extended along the entire molecule. The observation of only μc- type spectra for one "trans" and one "gauche" conformers, support the existence of a C2 symmetry for each structure.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

PubMed Central

Kasavajhala, Koushik; Bikkina, Swetha; Patil, Indrajit; MacKerell, Alexander D.; Priyakumar, U. Deva

2015-01-01

Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution. PMID:25668757

Phenothiazine-anthraquinone donor-acceptor molecules: synthesis, electronic properties and DFT-TDDFT computational study.

PubMed

Zhang, Wen-Wei; Mao, Wei-Li; Hu, Yun-Xia; Tian, Zi-Qi; Wang, Zhi-Lin; Meng, Qing-Jin

2009-09-17

Two donor-acceptor molecules with different pi-electron conjugative units, 1-((10-methyl-10H-phenothiazin-3-yl)ethynyl)anthracene-9,10-dione (AqMp) and 1,1'-(10-methyl-10H-phenothiazine-3,7-diyl)bis(ethyne-2,1-diyl)dianthracene-9,10-dione (Aq2Mp), have been synthesized and investigated for their photochemical and electrochemical properties. Density functional theory (DFT) calculations provide insights into their molecular geometry, electronic structures, and properties. These studies satisfactorily explain the electrochemistry of the two compounds and indicate that larger conjugative effect leads to smaller HOMO-LUMO gap (Eg) in Aq2Mp. Both compounds show ICT and pi --> pi* transitions in the UV-visible range in solution, and Aq2Mp has a bathochromic shift and shows higher oscillator strength of the absorption, which has been verified by time-dependent DFT (TDDFT) calculations. The differences between AqMp and Aq2Mp indicate that the structural and conjugative effects have great influence on the electronic properties of the molecules.

40 CFR 86.145-82 - Calculations; particulate emissions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... final reported test results for the mass particulate (Mp) in grams/mile shall be computed as follows. Mp = 0.43(Mp1 + Mp2)/(Dct + Ds) + 0.57(Mp3 + Mp2)/(Dht = Ds) where: (1) Mp1 = Mass of particulate...) for determination.) (2) Mp2 = Mass of particulate determined from the “stabilized” phase of the cold...

40 CFR 86.145-82 - Calculations; particulate emissions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... final reported test results for the mass particulate (Mp) in grams/mile shall be computed as follows. Mp = 0.43(Mp1 + Mp2)/(Dct + Ds) + 0.57(Mp3 + Mp2)/(Dht = Ds) where: (1) Mp1 = Mass of particulate...) for determination.) (2) Mp2 = Mass of particulate determined from the “stabilized” phase of the cold...

Layered crystal structure, conformational and vibrational properties of 2,2,2-trichloroethoxysulfonamide: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Gil, Diego M.; Piro, Oscar E.; Echeverría, Gustavo A.; Tuttolomondo, María E.; Altabef, Aída Ben

2013-12-01

The molecular structure of 2,2,2-trichloroethoxysulfonamide, CCl3CH2OSO2NH2, has been determined in the solid state by X-ray diffraction data and in the gas phase by ab initio (MP2) and DFT calculations. The substance crystallizes in the monoclinic P21/c space group with a = 9.969(3) Å, b = 22.914(6) Å, c = 7.349(2) Å, β = 91.06(3)°, and Z = 8 molecules per unit cell. There are two independent, but closely related molecular conformers in the crystal asymmetric unit. They only differ in the angular orientation of the sulfonamide (sbnd SO2NH2) group. The conformers are arranged in the lattice as center-symmetric Nsbnd H⋯O(sulf)-bonded dimers. Neighboring dimers are linked through further Nsbnd H⋯O(sulf) bonds giving rise to a crystal layered structure. The solid state infrared and Raman spectra have been recorded and the observed bands assigned to the molecular vibration modes. Also, the thermal behavior of the substance was investigated by TG-DT analysis. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond (NBO) analysis.

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

PubMed

Markova, Nadezhda; Pejov, Ljupco; Stoyanova, Nina; Enchev, Venelin

2017-05-01

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute-solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the 'bare' finite solute-solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in 'bulk' solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar - 11.74 kcal mol -1 for guanosine and 11.16 kcal mol -1 for acyclovir, and the respective rate constants (k = 1.5 × 10 1 s -1 , guanosine and k = 4.09 × 10 1 s -1 , acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.

Calciuric effects of protein and potassium bicarbonate but not of sodium chloride or phosphate can be detected acutely in adult women and men.

PubMed

Whiting, S J; Anderson, D J; Weeks, S J

1997-05-01

An acute load test was used to test the influence of dietary factors on urinary calcium excretion. In study 1, 10 fasting premenopausal women consumed test meals providing a moderate amount of protein (MP; 23 g), MP plus 23 mmol KHCO3 (MP+K), MP plus 23 mmol NaCl (MP+Na), and a high amount of protein (HP; 53 g), HP plus 70 mmol KHCO3 (HP+K), and HP plus 70 mmol NaCl (HP+Na). Protein was casein:lactalbumin (80:20), except for the treatments with added sodium chloride, to which only casein was added. In study 2, the effects of HP and HP plus 50 mmol KHCO3 (HP+K) were compared with those of MP or MP plus 7.5 mmol phosphate (MP+Pi), equaling the additional phosphate of HP, in 10 adult men. Subjects completed all treatments in random order. In study 1, the peak of calcium excretion was at 3 h for all treatments, except for HP+K, which indicated an acute hypocalciuric effect of potassium. Unexpectedly, there was no hypercalciuric effect of adding sodium chloride, nor was urine sodium increased. In study 2, calcium excretion was significantly higher with HP than with MP+Pi but not with MP at 3 h, indicating an acute hypercalciuric effect of protein alone. A hypocalciuric effect of potassium (HP+K compared with HP) but not of phosphate (MP compared with MP+Pi) was seen. An acute load test measuring changes 3 h postload was appropriate for examining the calciuric effects of protein and potassium bicarbonate, but not those of sodium chloride or phosphate in adults.

Accelerating MP2C dispersion corrections for dimers and molecular crystals

NASA Astrophysics Data System (ADS)

Huang, Yuanhang; Shao, Yihan; Beran, Gregory J. O.

2013-06-01

The MP2C dispersion correction of Pitonak and Hesselmann [J. Chem. Theory Comput. 6, 168 (2010)], 10.1021/ct9005882 substantially improves the performance of second-order Møller-Plesset perturbation theory for non-covalent interactions, albeit with non-trivial computational cost. Here, the MP2C correction is computed in a monomer-centered basis instead of a dimer-centered one. When applied to a single dimer MP2 calculation, this change accelerates the MP2C dispersion correction several-fold while introducing only trivial new errors. More significantly, in the context of fragment-based molecular crystal studies, combination of the new monomer basis algorithm and the periodic symmetry of the crystal reduces the cost of computing the dispersion correction by two orders of magnitude. This speed-up reduces the MP2C dispersion correction calculation from a significant computational expense to a negligible one in crystals like aspirin or oxalyl dihydrazide, without compromising accuracy.

Actions of 2-methylpiperidine (MP) and its interactions with (-)-nicotine (N) in the dog and rat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sloan, J.W.; Martin, W.R.; Bostwick, M.

1986-03-01

(+/-)-MP is a highly specific drug for enhancing the binding of (+/-)-(/sup 3/H)N in the rat brain P/sub 2/ preparation. Competition studies employing (+/-)-(/sup 3/H)N as the labelled ligand show that this activity resides in the (+) isomer. Saturation studies employing (+/-)-(/sup 3/H)MP indicate that it binds to a very high affinity site which is presumed to be an up-regulatory site. Studies were conducted where (+/-)-MP was injected through an implanted cannula into the 4th ventricle of intact beagle-type dogs. (+/-)-MP, like low doses of (+)-N, another drug which has specificity in enhancing the binding of (+/-)-, and (-)- andmore » (+)-(/sup 3/H)N, produced EEG synchronization and miosis. (-)-N produced analgesia where as (+/-)-MP produced hyperalgesia. In the urethane-pentobarbital anethetized rats, the i.v. infusion of (+)-MP (600 ..mu..g/kg/min for 10 min), had no effect on heart rate, blood pressure or respiration. Pretreatment with (+)-MP delayed and decreased the bradycardia, vasodepression, and enhanced tidal volume produced by (-)-N infusion (60 ..mu..g/kg/min). These data show that the pharmacologic actions of MP are different from (-)-N and hexamethonium and that MP, which enhances the binding of (+/-)- and (-)-(/sup 3/H)N at the high affinity site, appears to exert opposite effects to and antagonistic effects against (-)-N.« less

Preparation and Evaluation of a Modified Mohs Paste Mixed with Zinc Oxide 10% Topical Oil-Based Ointment.

PubMed

Tsuruta, Minako; Miyoshi, Takanori; Tsuruyama, Moeko; Matsumoto, Saori; Yamashina, Takuya; Irie, Kenji; Matsuo, Naomi; Itonaga, Tomomi; Hiraki, Yoichi; Kawamata, Yosei

2018-05-01

The skin fixative used in Mohs chemosurgery contains zinc chloride and is referred to as Mohs paste (MP). However, MP shows a remarkable change in rheological characteristics after its preparation. To prepare an MP with stable rheological characteristics, we prepared a modified MP (mMP) using zinc oxide 10% single ointment (Zn _ointment ), which is an oil-based ointment. We evaluated mMP by determining its rheological characteristics, depth of tissue fixation, and observation of the tissue surface after treatment. The viscosity of mMP increased after three months. However, the treatment-dependent viscosity of mMP could be obtained by mixing with glycerin. The viscosity and spreadability of mMP _3mth , which was three months after preparation, were 1992.0 ± 376.5 Pa·s and 2.1 ± 0.1 cm, respectively. In contrast, the viscosity and spreadability of MP mixed with glycerin were 436.9 ± 0.0 Pa·s and 2.8 ± 0.0 cm, respectively. The fixed invasion depth of MP was significantly higher than that of mMP (p < 0.05). This study of a mixture of MP and Zn _ointment showed that the viscosity of mMP could be adjusted with glycerin. Also, the tissue fixation of mMP progressed slowly compared with that of MP. This finding suggests that mMP is effective and safe for Mohs treatment.

Mercaptopurine Ingestion Habits, Red Cell Thioguanine Nucleotide Levels, and Relapse Risk in Children With Acute Lymphoblastic Leukemia: A Report From the Children’s Oncology Group Study AALL03N1

PubMed Central

Landier, Wendy; Hageman, Lindsey; Chen, Yanjun; Kornegay, Nancy; Evans, William E.; Bostrom, Bruce C.; Casillas, Jacqueline; Dickens, David S.; Angiolillo, Anne L.; Lew, Glen; Maloney, Kelly W.; Mascarenhas, Leo; Ritchey, A. Kim; Termuhlen, Amanda M.; Carroll, William L.; Relling, Mary V.; Wong, F. Lennie

2017-01-01

Purpose Children with acute lymphoblastic leukemia (ALL) are generally instructed to take mercaptopurine (6-MP) in the evening and without food or dairy products. This study examines the association between 6-MP ingestion habits and 6-MP adherence, red cell thioguanine nucleotide (TGN) levels, and risk of relapse in children with TMPT wild-type genotype. Methods Participants included 441 children with ALL receiving oral 6-MP for maintenance. Adherence was monitored over 48,086 patient-days using the Medication Event Monitoring System; nonadherence was defined as adherence rate < 95%. 6-MP ingestion habits examined included: takes 6-MP with versus never with food, takes 6-MP with versus never with dairy, and takes 6-MP in the evening versus morning versus varying times. Results Median age at study was 6 years (range, 2 to 20 years); 43.8% were nonadherent. Certain 6-MP ingestion habits were associated with nonadherence (taking 6-MP with dairy [odds ratio (OR), 1.9; 95% CI, 1.3 to 2.9; P = .003] and at varying times [OR, 3.4; 95% CI, 1.8 to 6.3; P = .0001]). After adjusting for adherence and other prognosticators, there was no association between 6-MP ingestion habits and relapse risk (6-MP with food: hazard ratio [HR], 0.7; 95% CI, 0.3 to 1.9; P = .5; with dairy: HR, 0.3; 95% CI, 0.07 to 1.5; P = .2; taken in evening/night: HR, 1.1; 95% CI, 0.2 to 7.8; P = .9; at varying times: HR, 0.3; 95% CI, 0.04 to 2.7; P = .3). Among adherent patients, there was no association between red cell TGN levels and taking 6-MP with food versus without (206.1 ± 107.1 v 220.6 ± 121.6; P = .5), with dairy versus without (220.1 ± 87.8 v 216.3 ± 121.3; P =.7), or in the evening/night versus morning/midday versus varying times (218.8 ± 119.7 v 195.5 ± 82.3 v 174.8 ± 93.4; P = .6). Conclusion Commonly practiced restrictions surrounding 6-MP ingestion might not influence outcome but may hinder adherence. Future recommendations regarding 6-MP intake during maintenance therapy for childhood ALL should aim to simplify administration. PMID:28339328

Mercaptopurine Ingestion Habits, Red Cell Thioguanine Nucleotide Levels, and Relapse Risk in Children With Acute Lymphoblastic Leukemia: A Report From the Children's Oncology Group Study AALL03N1.

PubMed

Landier, Wendy; Hageman, Lindsey; Chen, Yanjun; Kornegay, Nancy; Evans, William E; Bostrom, Bruce C; Casillas, Jacqueline; Dickens, David S; Angiolillo, Anne L; Lew, Glen; Maloney, Kelly W; Mascarenhas, Leo; Ritchey, A Kim; Termuhlen, Amanda M; Carroll, William L; Relling, Mary V; Wong, F Lennie; Bhatia, Smita

2017-05-20

Purpose Children with acute lymphoblastic leukemia (ALL) are generally instructed to take mercaptopurine (6-MP) in the evening and without food or dairy products. This study examines the association between 6-MP ingestion habits and 6-MP adherence, red cell thioguanine nucleotide (TGN) levels, and risk of relapse in children with TMPT wild-type genotype. Methods Participants included 441 children with ALL receiving oral 6-MP for maintenance. Adherence was monitored over 48,086 patient-days using the Medication Event Monitoring System; nonadherence was defined as adherence rate < 95%. 6-MP ingestion habits examined included: takes 6-MP with versus never with food, takes 6-MP with versus never with dairy, and takes 6-MP in the evening versus morning versus varying times. Results Median age at study was 6 years (range, 2 to 20 years); 43.8% were nonadherent. Certain 6-MP ingestion habits were associated with nonadherence (taking 6-MP with dairy [odds ratio (OR), 1.9; 95% CI, 1.3 to 2.9; P = .003] and at varying times [OR, 3.4; 95% CI, 1.8 to 6.3; P = .0001]). After adjusting for adherence and other prognosticators, there was no association between 6-MP ingestion habits and relapse risk (6-MP with food: hazard ratio [HR], 0.7; 95% CI, 0.3 to 1.9; P = .5; with dairy: HR, 0.3; 95% CI, 0.07 to 1.5; P = .2; taken in evening/night: HR, 1.1; 95% CI, 0.2 to 7.8; P = .9; at varying times: HR, 0.3; 95% CI, 0.04 to 2.7; P = .3). Among adherent patients, there was no association between red cell TGN levels and taking 6-MP with food versus without (206.1 ± 107.1 v 220.6 ± 121.6; P = .5), with dairy versus without (220.1 ± 87.8 v 216.3 ± 121.3; P =.7), or in the evening/night versus morning/midday versus varying times (218.8 ± 119.7 v 195.5 ± 82.3 v 174.8 ± 93.4; P = .6). Conclusion Commonly practiced restrictions surrounding 6-MP ingestion might not influence outcome but may hinder adherence. Future recommendations regarding 6-MP intake during maintenance therapy for childhood ALL should aim to simplify administration.

Machine Learning Force Field Parameters from Ab Initio Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ying; Li, Hui; Pickard, Frank C.

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor duringmore » the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.« less

Effect of dietary copper on the copper content of urine, parotid saliva, and sweat in humans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turnlund, J.R.

Eleven young men were confined to a metabolic research unit to study the effect of the level of dietary copper (Cu) on Cu metabolism. They were fed a constant diet containing the following three levels of dietary Cu: adequate Cu (1.68 mg/d) for 24 days (MP1), low Cu (0.785 mg/d) for 42 days (MP2), and high Cu (7.53 mg/d) for 24 days (MP3). Urine was collected throughout the study and Cu was determined in 6-day pools from the beginning of the study, the end of each MP, and the midpoint of MP2. Parotid saliva was collected near the end ofmore » each MP. Sweat was collected from the upper arm and ancillary area of three subjects for 2-day periods near the end of each MP. Urinary Cu averaged 0.34, 0.34 and 0.33 {mu}mol/d for MP 1, 2, and 3, respectively. Individual averages ranged from 0.16 to 0.39 {mu}mol/d. Parotid saliva Cu averaged 13.4, 13.0, and 12.0 nmol/L for MP 1, 2 and 3, respectively. Individual averages ranged from 6.9 to 17.8 nmol/L. Sweat Cu levels were very low and did not appear to be affected by dietary Cu. The limited data suggest that sweat losses would have little effect on Cu balance. Neither urinary nor salivary Cu was affected by dietary Cu or related to indices of Cu status (serum Cu, ceruloplasmin, or erythrocyte superoxide dismutase). Urinary and salivary Cu differed significantly among individuals. Results suggest that urinary, salivary, and sweat Cu do not play a role in regulating Cu retention or affect Cu status of humans.« less

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.

PubMed

Kóna, Juraj

2008-01-21

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.

Molecular dynamics investigations of ozone on an ab initio potential energy surface with the utilization of pattern-recognition neural network for accurate determination of product formation.

PubMed

Le, Hung M; Dinh, Thach S; Le, Hieu V

2011-10-13

The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very low dissociation probability up to 2.4 eV of internal energy during the investigating period (5 ps), which suggests that dissociation does not occur directly from the singlet ground-state, but it involves the excited triplet-state as an intermediate step and requires more reaction time to occur.

High-dimensional fitting of sparse datasets of CCSD(T) electronic energies and MP2 dipole moments, illustrated for the formic acid dimer and its complex IR spectrum

NASA Astrophysics Data System (ADS)

Qu, Chen; Bowman, Joel M.

2018-06-01

We present high-level, coupled-mode calculations of the infrared spectrum of the cyclic formic acid dimer. The calculations make use of full-dimensional, ab initio potential energy and dipole moment surfaces. The potential is a linear least-squares fit to 13 475 CCSD(T)-F12a/haTZ (haTZ means aug-cc-pVTZ basis set for O and C, and cc-pVTZ for H) energies, and the dipole moment surface is a fit to the dipole components, calculated at the MP2/haTZ level of theory. The variables of both fits are all (45) internuclear distances (actually Morse variables). The potential, which is fully permutationally invariant, is the one published recently and the dipole moment surface is newly reported here. Details of the fits, especially the dipole moment, and the database of configurations are given. The infrared spectrum of the dimer is calculated by solving the nuclear Schrödinger equation using a vibrational self-consistent field and virtual-state configuration interaction method, with subsets of the 24 normal modes, up to 15 modes. The calculations indicate strong mode-coupling in the C—H and O—H stretching region of the spectrum. Comparisons are made with experiments and the complexity of the experimental spectrum in the C—H and O—H stretching region is successfully reproduced.

Evidence for phosphorus bonding in phosphorus trichloride-methanol adduct: a matrix isolation infrared and ab initio computational study.

PubMed

Joshi, Prasad Ramesh; Ramanathan, N; Sundararajan, K; Sankaran, K

2015-04-09

The weak interaction between PCl3 and CH3OH was investigated using matrix isolation infrared spectroscopy and ab initio computations. In a nitrogen matrix at low temperature, the noncovalent adduct was generated and characterized using Fourier transform infrared spectroscopy. Computations were performed at B3LYP/6-311++G(d,p), B3LYP/aug-cc-pVDZ, and MP2/6-311++G(d,p) levels of theory to optimize the possible geometries of PCl3-CH3OH adducts. Computations revealed two minima on the potential energy surface, of which, the global minimum is stabilized by a noncovalent P···O interaction, known as a pnictogen bonding (phosphorus bonding or P-bonding). The local minimum corresponded to a cyclic adduct, stabilized by the conventional hydrogen bonding (Cl···H-O and Cl···H-C interactions). Experimentally, 1:1 P-bonded PCl3-CH3OH adduct in nitrogen matrix was identified, where shifts in the P-Cl modes of PCl3, O-C, and O-H modes of CH3OH submolecules were observed. The observed vibrational frequencies of the P-bonded adduct in a nitrogen matrix agreed well with the computed frequencies. Furthermore, computations also predicted that the P-bonded adduct is stronger than H-bonded adduct by ∼1.56 kcal/mol. Atoms in molecules and natural bond orbital analyses were performed to understand the nature of interactions and effect of charge transfer interaction on the stability of the adducts.

Systemic Exposure to Thiopurines and Risk of Relapse in Children With Acute Lymphoblastic Leukemia: A Children's Oncology Group Study.

PubMed

Bhatia, Smita; Landier, Wendy; Hageman, Lindsey; Chen, Yanjun; Kim, Heeyoung; Sun, Can-Lan; Kornegay, Nancy; Evans, William E; Angiolillo, Anne L; Bostrom, Bruce; Casillas, Jacqueline; Lew, Glen; Maloney, Kelly W; Mascarenhas, Leo; Ritchey, A Kim; Termuhlen, Amanda M; Carroll, William L; Wong, F Lennie; Relling, Mary V

2015-06-01

Variability in prescribed doses of 6-mercaptopurine (6MP) and lack of adherence to a 6MP treatment regimen could result in intra-individual variability in systemic exposure to 6MP (measured as erythrocyte thioguanine nucleotide [TGN] levels) in children with acute lymphoblastic leukemia (ALL). The effect on relapse risk of this variability is unknown. To determine the effect of high intra-individual variability of 6MP systemic exposure on relapse risk in children with ALL. We used a prospective longitudinal design (Children's Oncology Group study [COG-AALL03N1]) to monitor 6MP and disease relapse in 742 children with ALL in ambulatory care settings of 94 participating institutions from May 30, 2005, to September 9, 2011. All participants met the following eligibility criteria: (1) diagnosis of ALL at 21 years or younger; (2) first continuous remission in progress at the time of study entry; (3) receiving self-, parent-, or caregiver-administered oral 6MP during maintenance therapy; and (4) completion of at least 6 months of maintenance therapy at the time of study enrollment. The median patient age at diagnosis was 5 years; 68% were boys; and 43% had National Cancer Institute-based high-risk disease. Daily 6MP regimen adherence was measured over 68 716 person-days using an electronic system that recorded the date and time of each 6MP bottle opening; adherence rate was defined as the ratio of days that a 6MP bottle was opened to days thata 6MP bottle was prescribed. Average monthly 6MP dose intensity was measured over 120 439 person-days by dividing the number of 6MP doses actually prescribed by the number of planned protocol doses (75 mg/m2/d). Monthly erythrocyte TGN levels (pmol/8 × 108 erythrocytes) were measured over 6 consecutive months per patient (n = 3944 measurements). Using intra-individual coefficients of variation (CV%), patients were classified as having stable (CV% <85th percentile) vs varying (CV% ≥85th percentile) indices. Median follow-up time was 6.7 years from the time of diagnosis. Adjusting for clinical prognosticators, we found that patients with 6MP nonadherence (mean adherence rate <95%) were at a 2.7-fold increased risk of relapse (95% CI, 1.3-5.6; P = .01) compared with patients with a mean adherence rate of 95% or greater. Among adherers, high intra-individual variability in TGN levels contributed to increased relapse risk (hazard ratio, 4.4; 95% CI, 1.2-15.7; P = .02). Furthermore, adherers with varying TGN levels had varying 6MP dose intensity (odds ratio [OR], 4.5; 95% CI, 1.5-13.4; P = .01) and 6MP drug interruptions (OR, 10.2; 95% CI, 2.2-48.3; P = .003). These findings emphasize the need to maximize 6MP regimen adherence and maintain steady thiopurine exposure to minimize relapse in children with ALL.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

Classification and discrimination of pediatric patients undergoing open heart surgery with and without methylprednisolone treatment by cytomics

NASA Astrophysics Data System (ADS)

Bocsi, Jozsef; Mittag, Anja; Pierzchalski, Arkadiusz; Osmancik, Pavel; Dähnert, Ingo; Tárnok, Attila

2011-02-01

Introduction: Methylprednisolone (MP) is frequently preoperatively administered in children undergoing open heart surgery. The aim of this medication is to inhibit overshooting immune responses. Earlier studies demonstrated cellular and humoral immunological changes in pediatric patients undergoing heart surgeries with and without MP administration. Here in a retrospective study we investigated the modulation of the cellular immune response by MP. The aim was to identify suitable parameters characterizing MP effects by cluster analysis. Methods: Blood samples were analysed from two aged matched groups with surgical correction of septum defects. Group without MP treatment consisted of 10 patients; MP was administered on 21 patients (median dose: 11mg/kg) before cardiopulmonary bypass (CPB). EDTA anticoagulated blood was obtained 24 h preoperatively, after anesthesia, at CPB begin and end (CPB2), 4h, 24h, 48h after surgery, at discharge and at out-patient followup (8.2; 3.3-12.2 month after surgery; median and IQR). Flow cytometry showed the biggest MP relevant changes at CPB2 and 4h postoperatively. They were used for clustering analysis. Classification was made by discriminant analysis and cluster analysis by means of Genes@work software. Results & conclusion: 146 parameters were obtained from analysis. Cross-validation revealed several parameters being able to discriminate between MP groups and to identify immune modulation. MP administration resulted in a delayed activation of monocytes, increased ratio of neutrophils, reduced T-lymphocytes counts. Cluster analysis demonstrated that classification of patients is possible based on the identified cytomics parameters. Further investigation of these parameters might help to understand the MP effects in pediatric open heart surgery.

High resolution FTIR spectroscopic study of the ν4 band of CH 3CHF 2 enclosed in a flow of cold N 2 gas

NASA Astrophysics Data System (ADS)

Appadoo, Dominique R. T.; Robertson, Evan G.; McNaughton, Don

2003-01-01

An enclosive flow cooling (EFC) cell has been constructed, and coupled to a Brüker IFS 120HR high resolution Fourier transform spectrometer to record rotationally cold absorption spectra of gases of atmospheric interest at high spectral resolution. The new system has been characterized using N 2O, revealing that rotational temperatures as cold as 110 K are readily attainable using liquid nitrogen as a cryogen. Infrared spectra of the ν4 band of 1,1-difluoroethane (R152a), CH 3CHF 2, cooled in the EFC cell have been measured at a resolution of 0.0019 cm-1. Eight hundred and twenty rovibrational transitions of the weak ν4 band with 2⩽ J'⩽46 and Kc'⩽16 were assigned and fitted to Watson's A-reduced Hamiltonian. The ν4 CH 3 symmetric deformation ( a/c-type) was found to be coupled to the ν13 asymmetric deformation ( b-type) via an a-axis Coriolis interaction. In the ensuing analysis, values of spectroscopic constants were obtained for both the ν4 and dark ν13 states. Supporting ab initio calculations up to the MP2/TZV+(3 df,3 p) level are presented.

Hydrolysis and Sulfation Pattern Effects on Release of Bioactive Bone Morphogenetic Protein-2 from Heparin-Based Microparticles.

PubMed

Tellier, Liane E; Miller, Tobias; McDevitt, Todd C; Temenoff, Johnna S

2015-10-28

Glycosaminoglycans (GAGs) such as heparin are promising materials for growth factor delivery due to their ability to efficiently bind positively charged growth factors including bone morphogenetic protein-2 (BMP-2) through their negatively charged sulfate groups. Therefore, the goal of this study was to examine BMP-2 release from heparin-based microparticles (MPs) after first, incorporating a hydrolytically degradable crosslinker and varying heparin content within MPs to alter MP degradation and second, altering the sulfation pattern of heparin within MPs to vary BMP-2 binding and release. Using varied MP formulations, it was found that the time course of MP degradation for 1 wt% heparin MPs was ~4 days slower than 10 wt% heparin MPs, indicating that MP degradation was dependent on heparin content. After incubating 100 ng BMP-2 with 0.1 mg MPs, most MP formulations loaded BMP-2 with ~50% efficiency and significantly more BMP-2 release (60% of loaded BMP-2) was observed from more sulfated heparin MPs (MPs with ~100% and 80% of native sulfation). Similarly, BMP-2 bioactivity in more sulfated heparin MP groups was at least four-fold higher than soluble BMP-2 and less sulfated heparin MP groups, as determined by an established C2C12 cell alkaline phosphatase (ALP) assay. Ultimately, the two most sulfated 10 wt% heparin MP formulations were able to efficiently load and release BMP-2 while enhancing BMP-2 bioactivity, making them promising candidates for future growth factor delivery applications.

High-dose methotrexate-based immuno-chemotherapy for elderly primary CNS lymphoma patients (PRIMAIN study).

PubMed

Fritsch, K; Kasenda, B; Schorb, E; Hau, P; Bloehdorn, J; Möhle, R; Löw, S; Binder, M; Atta, J; Keller, U; Wolf, H-H; Krause, S W; Heß, G; Naumann, R; Sasse, S; Hirt, C; Lamprecht, M; Martens, U; Morgner, A; Panse, J; Frickhofen, N; Röth, A; Hader, C; Deckert, M; Fricker, H; Ihorst, G; Finke, J; Illerhaus, G

2017-04-01

To investigate immuno-chemotherapy for elderly immuno-competent patients (⩾65 years) with newly diagnosed primary central nervous system lymphoma, we conducted a multicentre single-arm trial. One cycle consisted of rituximab (375 mg/m 2 , days 1, 15, 29), high-dose methotrexate (3 g/m 2 days 2, 16, 30), procarbazine (60 mg/m 2 days 2-11) and lomustine (110 mg/m 2 , day 2)-R-MPL protocol. Owing to infectious complications, we omitted lomustine during the study and consecutive patients were treated with the R-MP protocol. Three cycles were scheduled and repeated on day 43. Subsequently, patients commenced 4 weekly maintenance treatment with procarbazine (100 mg for 5 days). Primary end point was complete remission (CR) after 3 cycles. We included 107 patients (69 treated with R-MPL and 38 with R-MP). In all, 38/107 patients achieved CR (35.5%) and 15 (14.0%) achieved partial remission. R-MP was associated with a lower CR rate (31.6%) compared with R-MPL (37.7%), but respective 2-year progression-free survival (All 37.3%; R-MP 34.9%; R-MPL 38.8%) and overall survival (All 47.0%; R-MP 47.7%; R-MPL 46.0%) rates were similar. R-MP was associated with less ⩾grade 3 toxicities compared with R-MPL (71.1% vs 87.0%). R-MP is more feasible while still associated with similar efficacy compared with R-MPL and warrants further improvement in future studies.

Correlation between capillary oxygen saturation and small intestinal wall thickness in the equine colic patient

PubMed Central

Mirle, Elisabeth; Wogatzki, Anna; Kunzmann, Robert; Schoenfelder, Axel M; Litzke, Lutz F

2017-01-01

The surgical evaluation of haemorrhagic infarcted intestine and the decision for or against bowel resection require a lot of experience and are subjective. The aim of this prospective, clinical study was to examine the correlation between oxygen saturation and small intestinal wall (IW) thickness, using two objective methods. In 22 colicky horses, the blood flow, oxygen saturation and relative amount of haemoglobin were measured intraoperatively via laser Doppler and white light spectroscopy (O2C, oxygen to see, LEA Medizintechnik) at six measuring points (MPs) in small and large intestines. Furthermore, the IW thickness was measured ultrasonographically. Nine of 22 horses had an increased small IW thickness greater than 4 mm (Freeman 2002, Scharner and others 2002, le Jeune and Whitcomb 2014) at measuring point 1 (MP1) (strangulated segment), four horses had a thickened bowel wall at measuring point 3 (MP3) (poststenotic) and one at measuring point 2 (MP2). The oxygen saturation was 0 at MP1 in six horses, at MP3 in two horses and at MP2 (prestenotic) in one. Oxygen saturation and small IW thickness were independent of each other at MP1 and MP2. At MP3, the two parameters were negatively correlated. In summary, it is not possible to draw conclusions about oxygen saturation based on IW thickness. PMID:28761667

Correlation between capillary oxygen saturation and small intestinal wall thickness in the equine colic patient.

PubMed

Mirle, Elisabeth; Wogatzki, Anna; Kunzmann, Robert; Schoenfelder, Axel M; Litzke, Lutz F

2017-01-01

The surgical evaluation of haemorrhagic infarcted intestine and the decision for or against bowel resection require a lot of experience and are subjective. The aim of this prospective, clinical study was to examine the correlation between oxygen saturation and small intestinal wall (IW) thickness, using two objective methods. In 22 colicky horses, the blood flow, oxygen saturation and relative amount of haemoglobin were measured intraoperatively via laser Doppler and white light spectroscopy (O2C, oxygen to see, LEA Medizintechnik) at six measuring points (MPs) in small and large intestines. Furthermore, the IW thickness was measured ultrasonographically. Nine of 22 horses had an increased small IW thickness greater than 4 mm (Freeman 2002, Scharner and others 2002, le Jeune and Whitcomb 2014) at measuring point 1 (MP1) (strangulated segment), four horses had a thickened bowel wall at measuring point 3 (MP3) (poststenotic) and one at measuring point 2 (MP2). The oxygen saturation was 0 at MP1 in six horses, at MP3 in two horses and at MP2 (prestenotic) in one. Oxygen saturation and small IW thickness were independent of each other at MP1 and MP2. At MP3, the two parameters were negatively correlated. In summary, it is not possible to draw conclusions about oxygen saturation based on IW thickness.

Ammonia-water cation and ammonia dimer cation.

PubMed

Kim, Hahn; Lee, Han Myoung

2009-06-25

We have investigated the structure, interaction energy, electronic properties, and IR spectra of the ammonia-water cation (NH(3)H(2)O)(+) using density functional theory (DFT) and high-level ab initio theory. The ammonia-water cation has three minimum-energy structures of (a) H(2)NH(+)...OH(2), (b) H(3)N(+)...OH(2), and (c) H(3)NH(+)...OH. The lowest-energy structure is (a), followed by (c) and (b). The ammonia dimer cation has two minimum-energy structures [the lowest H(3)NH(+)...NH(2) structure and the second lowest (H(3)N...NH(3))(+) structure]. The minimum transition barrier for the interconversion between (a), (b), and (c) is approximately 6 kcal/mol. Most DFT calculations with various functionals, except a few cases, overstabilize the N...O and N...N binding, predicting different structures from Moller-Plesset second-order perturbation (MP2) theory and the most reliable complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. Thus, the validity test of the DFT functionals for these ionized molecular systems would be of importance.

Orbital-Optimized MP3 and MP2.5 with Density-Fitting and Cholesky Decomposition Approximations.

PubMed

Bozkaya, Uğur

2016-03-08

Efficient implementations of the orbital-optimized MP3 and MP2.5 methods with the density-fitting (DF-OMP3 and DF-OMP2.5) and Cholesky decomposition (CD-OMP3 and CD-OMP2.5) approaches are presented. The DF/CD-OMP3 and DF/CD-OMP2.5 methods are applied to a set of alkanes to compare the computational cost with the conventional orbital-optimized MP3 (OMP3) [Bozkaya J. Chem. Phys. 2011, 135, 224103] and the orbital-optimized MP2.5 (OMP2.5) [Bozkaya and Sherrill J. Chem. Phys. 2014, 141, 204105]. Our results demonstrate that the DF-OMP3 and DF-OMP2.5 methods provide considerably lower computational costs than OMP3 and OMP2.5. Further application results show that the orbital-optimized methods are very helpful for the study of open-shell noncovalent interactions, aromatic bond dissociation energies, and hydrogen transfer reactions. We conclude that the DF-OMP3 and DF-OMP2.5 methods are very promising for molecular systems with challenging electronic structures.

Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

2006-09-20

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. Themore » structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.« less

Determining the amount of rumen-protected methionine supplement that corresponds to the optimal levels of methionine in metabolizable protein for maximizing milk protein production and profit on dairy farms.

PubMed

Cho, J; Overton, T R; Schwab, C G; Tauer, L W

2007-10-01

The profitability of feeding rumen-protected Met (RPMet) sources to produce milk protein was estimated using a 2-step procedure: First, the effect of Met in metabolizable protein (MP) on milk protein production was estimated by using a quadratic Box-Cox functional form. Then, using these estimation results, the amounts of RPMet supplement that corresponded to the optimal levels of Met in MP for maximizing milk protein production and profit on dairy farms were determined. The data used in this study were modified from data used to determine the optimal level of Met in MP for lactating cows in the Nutrient Requirements of Dairy Cattle (NRC, 2001). The data used in this study differ from that in the NRC (2001) data in 2 ways. First, because dairy feed generally contains 1.80 to 1.90% Met in MP, this study adjusts the reference production value (RPV) from 2.06 to 1.80 or 1.90%. Consequently, the milk protein production response is also modified to an RPV of 1.80 or 1.90% Met in MP. Second, because this study is especially interested in how much additional Met, beyond the 1.80 or 1.90% already contained in the basal diet, is required to maximize farm profits, the data used are limited to concentrations of Met in MP above 1.80 or 1.90%. This allowed us to calculate any additional cost to farmers based solely on the price of an RPMet supplement and eliminated the need to estimate the dollar value of each gram of Met already contained in the basal diet. Results indicated that the optimal level of Met in MP for maximizing milk protein production was 2.40 and 2.42%, where the RPV was 1.80 and 1.90%, respectively. These optimal levels were almost identical to the recommended level of Met in MP of 2.40% in the NRC (2001). The amounts of RPMet required to increase the percentage of Met in MP from each RPV to 2.40 and 2.42% were 21.6 and 18.5 g/d, respectively. On the other hand, the optimal levels of Met in MP for maximizing profit were 2.32 and 2.34%, respectively. The amounts of RPMet required to increase the percentage of Met in MP from each RPV to 2.32 and 2.34% were 18.7 and 15.6 g/d, respectively. In each case, the additional daily profit per cow was estimated to be $0.38 and $0.29. These additional profit estimates were $0.02 higher than the additional profit estimates for maximizing milk protein production.

The distorted tropane of scopoline.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Basterretxea, Francisco J; Fernández, José A; Castaño, Fernando

2013-06-24

The structural isomerization of scopine into scopoline (oscine) has been observed in a supersonic jet expansion using microwave spectroscopy. The rotational spectrum evidences a single structure in the gas phase, providing a first description of the (three-ring) structurally distorted tropane in scopoline. The absence of rotational signatures of any scopine conformation suggests a practically quantitative isomerization at the vaporization temperatures of the experiment (ca. 90 °C). The determined rotational parameters of scopoline reveal the structural consequences of the intramolecular cyclation of scopine, which breaks the original epoxy group and creates a new ether bridge and a 7β-hydroxytropane configuration. The hydroxy group further stabilizes the molecule by an O-H⋅⋅⋅N intramolecular hydrogen bond, which, in turn, forces the N-methyl group to the less stable axial form. Supporting ab initio (MP2) and DFT (B3LYP, M06-2X) calculations are included. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of the gas-phase structure and rotational barrier of trimethylsilyl trifluoromethanesulfonate and comparison with covalent sulfonates

NASA Astrophysics Data System (ADS)

Defonsi Lestard, María E.; Tuttolomondo, María E.; Varetti, Eduardo L.; Wann, Derek A.; Robertson, Heather E.; Rankin, David W. H.; Altabef, Aida Ben

2010-12-01

The molecular structure of trimethylsilyl trifluoromethanesulfonate, CF 3SO 2OSi(CH 3) 3, has been determined in the gas phase from electron-diffraction data supplemented by ab initio (MP2) and DFT calculations using 6-31G(d), 6-311++G(d,p) and 6-311G++(3df,3pd) basis sets. Both experimental and theoretical data indicate that only one gauche conformer is possible by rotating about the O-S bond. The anomeric effect is a fundamental stereoelectronic interaction and presents a profound influence on the electronic geometry. We have investigated the origin of the anomeric effect by means of NBO and AIM analysis. A natural bond orbital analysis showed that the lpπ[O bonded to Si)] → σ *[C-S] hyperconjugative interaction favors the gauche conformation. In addition, comparison of the structural and stereoelectronic properties of the title molecule with those of silyl trifluoromethanesulfonate and methyl trifluoromethanesulfonate has been carried out.

Blurred digital mammography images: an analysis of technical recall and observer detection performance.

PubMed

Ma, Wang Kei; Borgen, Rita; Kelly, Judith; Millington, Sara; Hilton, Beverley; Aspin, Rob; Lança, Carla; Hogg, Peter

2017-03-01

Blurred images in full-field digital mammography are a problem in the UK Breast Screening Programme. Technical recalls may be due to blurring not being seen on lower resolution monitors used for review. This study assesses the visual detection of blurring on a 2.3-MP monitor and a 5-MP report grade monitor and proposes an observer standard for the visual detection of blurring on a 5-MP reporting grade monitor. 28 observers assessed 120 images for blurring; 20 images had no blurring present, whereas 100 images had blurring imposed through mathematical simulation at 0.2, 0.4, 0.6, 0.8 and 1.0 mm levels of motion. Technical recall rate for both monitors and angular size at each level of motion were calculated. χ 2 tests were used to test whether significant differences in blurring detection existed between 2.3- and 5-MP monitors. The technical recall rate for 2.3- and 5-MP monitors are 20.3% and 9.1%, respectively. The angular size for 0.2- to 1-mm motion varied from 55 to 275 arc s. The minimum amount of motion for visual detection of blurring in this study is 0.4 mm. For 0.2-mm simulated motion, there was no significant difference [χ 2 (1, N = 1095) = 1.61, p = 0.20] in blurring detection between the 2.3- and 5-MP monitors. According to this study, monitors ≤2.3 MP are not suitable for technical review of full-field digital mammography images for the detection of blur. Advances in knowledge: This research proposes the first observer standard for the visual detection of blurring.

Blurred digital mammography images: an analysis of technical recall and observer detection performance

PubMed Central

Borgen, Rita; Kelly, Judith; Millington, Sara; Hilton, Beverley; Aspin, Rob; Lança, Carla; Hogg, Peter

2017-01-01

Objective: Blurred images in full-field digital mammography are a problem in the UK Breast Screening Programme. Technical recalls may be due to blurring not being seen on lower resolution monitors used for review. This study assesses the visual detection of blurring on a 2.3-MP monitor and a 5-MP report grade monitor and proposes an observer standard for the visual detection of blurring on a 5-MP reporting grade monitor. Methods: 28 observers assessed 120 images for blurring; 20 images had no blurring present, whereas 100 images had blurring imposed through mathematical simulation at 0.2, 0.4, 0.6, 0.8 and 1.0 mm levels of motion. Technical recall rate for both monitors and angular size at each level of motion were calculated. χ2 tests were used to test whether significant differences in blurring detection existed between 2.3- and 5-MP monitors. Results: The technical recall rate for 2.3- and 5-MP monitors are 20.3% and 9.1%, respectively. The angular size for 0.2- to 1-mm motion varied from 55 to 275 arc s. The minimum amount of motion for visual detection of blurring in this study is 0.4 mm. For 0.2-mm simulated motion, there was no significant difference [χ2 (1, N = 1095) = 1.61, p = 0.20] in blurring detection between the 2.3- and 5-MP monitors. Conclusion: According to this study, monitors ≤2.3 MP are not suitable for technical review of full-field digital mammography images for the detection of blur. Advances in knowledge: This research proposes the first observer standard for the visual detection of blurring. PMID:28134567

Improved human islet preparations using Glucocorticoid and Exendin-4

PubMed Central

Miki, Atsushi.; Ricordi, Camillo.; Yamamoto, Toshiyuki.; Sakuma, Yasunaru.; Misawa, Ryosuke.; Mita, Atsuyoshi.; Inverardi, Luca.; Alejandro, Rodolfo; Ichii, Hirohito.

2014-01-01

Objectives The effects of Glucocorticoid during culture on human islet cells have been controversial. Exendin-4 (EX) enhances the insulin secretion and significantly improves clinical outcomes in islet cell transplantation. In this study, we examined the effects of Glucocorticoids and exendin-4 on human islet cells during pre-transplant culture. Methods Methylprednisolone (MP) and/or EX were added to the standard culture medium for clinical islet cell transplantation. Islets were cultured for 24 hours with three different conditions (Control: no additives, MP alone, MP+EX). Beta cell fractional viability, cellular composition, multiple cytokine/chemokine production, multiple phosphorylation proteins and glucose induced insulin secretion were evaluated. Results Viable beta cell survival in MP and MP+EX group was significantly higher than in the control group. EX prevented MP induced reduction of insulin secretion. MP supplementation to the culture medium decreased cytokine and chemokine production. Moreover, Erk1/2 phosphorylation was significantly increased by MP and MP+EX. Conclusions Glucocorticoid supplementation into culture media significantly decreased the cytokine/chemokine production and increased the Erk1/2 phosphorylation, resulting in the improvement of human beta cell survival. In addition, EX maintained the insulin secretion suppressed by MP. The supplementation of MP and EX together could be a useful strategy to create suitable human islets for transplantation. PMID:25036907

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Cell-derived microparticles promote coagulation after moderate exercise.

PubMed

Sossdorf, Maik; Otto, Gordon P; Claus, Ralf A; Gabriel, Holger H W; Lösche, Wolfgang

2011-07-01

Cell-derived procoagulant microparticles (MP) might be able to contribute to exercise-induced changes in blood hemostasis. This study aimed to examine (i) the concentration and procoagulant activity of cell-derived MP after a moderate endurance exercise and (ii) the differences in the release, clearance, and activity of MP before and after exercise between trained and untrained individuals. All subjects performed a single bout of physical exercise on a bicycle ergometer for 90 min at 80% of their individual anaerobic threshold. MP were identified and quantified by flow cytometry measurements. Procoagulant activity of MP was measured by a prothrombinase activity assay as well as tissue factor-induced fibrin formation in MP-containing plasma. At baseline, no differences were observed for the absolute number and procoagulant activities of MP between trained and untrained subjects. However, trained individuals had a lower number of tissue factor-positive monocyte-derived MP compared with untrained individuals. In trained subjects, exercise induced a significant increase in the number of MP derived from platelets, monocytes, and endothelial cells, with maximum values at 45 min after exercise and returned to basal levels at 2 h after exercise. Untrained subjects revealed a similar increase in platelet-derived MP, but their level was still increased at 2 h after exercise, indicating a reduced clearance compared with trained individuals. Procoagulant activities of MP were increased immediately after exercise and remained elevated up to 2 h after exercise. We conclude that increased levels of MP were found in healthy individuals after an acute bout of exercise, that the amount of circulating MP contributes to an exercise-induced increase of hemostatic potential, and that there were differences in kinetic and dynamic characteristics between trained and untrained individuals.

Sun light mediated synthesis of gold nanoparticles as carrier for 6-mercaptopurine: Preparation, characterization and toxicity studies in zebrafish embryo model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganeshkumar, Moorthy; Sastry, Thotapalli Parvathaleswara; Sathish Kumar, Muniram

2012-09-15

Highlights: ► Gold nanoparticles prepared using eco-friendly method with good in vitro stability. ► Can be used as drug delivery system. ► Did not show any toxicity in zebrafish embryo. ► More toxic to cancer cells when compared to N-Au-Mp and Mp. -- Abstract: The objective of this study is to synthesize green chemistry based gold nanoparticles by sun light irradiation method. The prepared gold nanoparticles (AuNPs) were modified using folic acid and then coupled with 6-mercaptopurine. These modified nanoparticles were used as a tool for targeted drug delivery to treat laryngeal cancer. In the present study, novel bionanocomposites containingmore » nutrient agar coated gold nano particles (N-AuNPs) coupled with 6-mercaptopurine (drug) (N-AuNPs-Mp), folic acid (ligand) (N-AuNPs-Mp-Fa) and rhodamine (dye) (N-AuNPs-Rd), a fluorescent agent, were prepared and characterized by IR, UV, TEM, Particle size analysis and in vitro stability. The toxicity and fluorescence of N-Au was studied using zebrafish embryo model. The in vitro cytotoxicity of free Mp, N-Au-Mp and N-Au-Mp-Fa against HEp-2 cells was compared and found that the amount of Mp required to achieve 50% of growth of inhibition (IC{sub 50}) was much lower in N-Au-Mp-Fa than in free Mp and N-Au-Mp.« less

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

Methylprednisolone does not inhibit the release of growth hormone after intravenous injection of a novel growth hormone secretagogue in rats.

PubMed

Malmlöf, K; Johansen, P B; Haahr, P M; Wilken, M; Oxlund, H

1999-12-01

The present study was undertaken to study the growth hormone-releasing properties and growth-promoting effect of a GH secretagogue ipamorelin (IPA) in rats given the synthetic glucocorticoid methylprednisolone (MP). In a first experiment, rats received either saline or MP (5.0 mg/kg) for 8 days. Treatment with MP significantly (P< 0.001) decreased body weight gain, but the acute response to either IPA or growth hormone releasing hormone (GHRH) in terms of plasma GH was not changed. In a second experiment, venous catheters were surgically implanted. On the next day, rats were randomly allocated to receive saline alone, MP alone (5.0 mg/kg) or MP plus IPA in doses of 0.4 or 1.6 mg/kg/day for 10 days. IPA was administered intravenously four times a day.MP treatment significantly (P< 0.05) retarded recovery from surgery in terms of body weight. Thus, saline treated animals lost 4.0 +/- 3.5 g over the entire experimental period, whereas animals receiving MP lost 13. 6 +/- 2.9 g. When IPA was given together with MP, losses in body weight were significantly (P< 0.05) reduced to 2.3 +/- 2.0 and 1.6 +/- 2.0 g in animals given the high and low dose of IPA, respectively. In parallel with this IGF-I levels increased. In conclusion, this work shows that MP does not disrupt the response of the GH-IGF-I axis to an exogenous stimulus like IPA, and repeated stimulation leads to increases in IGF-I and of body weight gain. Copyright 1999 Harcourt Publishers Ltd.

6-Mercaptopurine reverses experimental vasospasm and alleviates the production of endothelins in NO-independent mechanism-a laboratory study.

PubMed

Chang, Chih-Zen; Wu, Shu-Chuan; Kwan, Aij-Lie; Lin, Chih-Long; Hwang, Shiuh-Lin

2011-04-01

Increased endothelin-1 (ET-1) production and diminished nitric oxide synthase (NOS) bioavailability has been observed in aneurysmal subarachnoid hemorrhage (SAH). The authors previously found that 6-mercaptopurine (6-mp) is effective in preventing and reversing arterial narrowing in a rodent SAH model. This present study is of interest to examine the effect of 6-mp on ET-1/endothelial nitric oxide synthase (eNOS) in this animal model. A rodent double hemorrhage SAH model was employed. Animals were randomly assigned to six groups (sham, SAH only, vehicle, 0.5, 1.0 and 2 mg kg(-1) day(-1) 6-mp treatment). Monoclonal CD45 immunostaining was utilized to evaluate monocytes and microglia. The level of pro-inflammatory cytokines, such as IL-1, IL-6 and TNF-α(RT-PCR), and ET-1 (ELISA) was measured. The basilar arteries (BAs) were harvested and sliced, and their cross-sectional areas were determined. Radiolabeled NOS assay kit was applied to detect eNOS. Morphologically, convolution of internal elastic lamina, endothelial cells distortion, and necrotic smooth muscle were prevalently present in the basilar artery of SAH groups, which was absent in the 1 and 2 mg kg(-1) day(-1) 6-mp plus SAH group or the healthy controls. Significant vasospasm was noted in the vehicle group (lumen patency, 54.6%, p ≤ 0.01 compared with the sham group), but it was less prominent in the 2 mg kg(-1) day(-1) 6-mp treatment group (lumen patency, 87.6%, p < 0.05). In addition, administration with 2 mg kg(-1) day(-1) 6-mp reduced cytokine levels by 11%, 47%, and 34% for IL-1, IL-6, and TNF-α, respectively, and increased ET-1 levels were found in all the animals subject to SAH (SAH only, SAH plus vehicle, SAH plus 0.5 and 1.0 mg kg(-1) day(-1) 6-mp) except in the 2 mg kg(-1) day(-1) 6-mp SAH group, when compared with the healthy controls (no SAH). Meanwhile, treatment with 6-mp did not induce the levels of expressed eNOS in BAs in the 6-mp groups (0.5, 1.0, and 2 mg kg(-1) day(-1) 6-mp plus SAH) when compared with that in the SAH groups (p > 0.1). In summary, treatment with 6-mp decreased the release of pro-inflammatory cytokines and diminished experimental vasospasm. This study offered first evidence that 6-mp dose-dependently reduces the level of ET-1 in a NO-independent mechanism, which corresponds to its antivasospastic effect in the condition of chronic vasospasm.

Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation.

PubMed

Bozkaya, Uğur

2018-03-15

Efficient implementations of analytic gradients for the orbital-optimized MP3 and MP2.5 and their standard versions with the density-fitting approximation, which are denoted as DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5, are presented. The DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5 methods are applied to a set of alkanes and noncovalent interaction complexes to compare the computational cost with the conventional MP3, MP2.5, OMP3, and OMP2.5. Our results demonstrate that density-fitted perturbation theory (DF-MP) methods considered substantially reduce the computational cost compared to conventional MP methods. The efficiency of our DF-MP methods arise from the reduced input/output (I/O) time and the acceleration of gradient related terms, such as computations of particle density and generalized Fock matrices (PDMs and GFM), solution of the Z-vector equation, back-transformations of PDMs and GFM, and evaluation of analytic gradients in the atomic orbital basis. Further, application results show that errors introduced by the DF approach are negligible. Mean absolute errors for bond lengths of a molecular set, with the cc-pCVQZ basis set, is 0.0001-0.0002 Å. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Thermosensitive block copolymer [(PNIPAM)-b-(Glycine)] thin film as protective layer for drug loaded mesoporous silica nanoparticles

NASA Astrophysics Data System (ADS)

Amgoth, Chander; Joshi, Suman

2017-10-01

Synthesis and characterization of [(PNIPAM)-b-(Gly)] and mesoporous silica nanoparticles (MP-SiO2 NPs) were carried out separately and used to develop [(PNIPAM)-b-(Gly)]-(MP-SiO2 NPs). The synthesized MP-SiO2 NPs were meso porous in nature. The size of SiO2 NPs is in the range of ~180-250 nm (in diameter) with an average pore size of 2.8 nm within the particles. Interestingly, these mesoporous SiO2 NPs were loaded with anticancer drug (ITM-imatinib mesylate) fallow by the incubation for 24 h at RT. However, ITM loaded MP-SiO2 NPs were capped or covered with synthesized [(PNIPAM)-b-(Gly)] thin film. Here, thin film acts as protective layer for drug loaded MP-SiO2 NPs, with that leakage of drug molecules throughout its transport pathway can be avoided. Significantly, thermosensitive [(PNIPAM)-b-(Gly)] polymer thin film depletes at body temperature (~37 °C) and drug molecules come out from the pores of SiO2 NPs. However, developed [(PNIPAM)-b-(Gly)]-(MP-SiO2 NPs) is compatible and used for cell inhibition studies. After 24 h treatment, drug ITM released from [(PNIPAM)-b-(Gly)]-(MP-SiO2 NPs) shows significant (>90%) inhibition on leukemia blood cancer (K562) cells.

Thermochemistry and kinetics for 2-butanone-1-yl radical (CH2·C(═O)CH2CH3) reactions with O2.

PubMed

Sebbar, N; Bozzelli, J W; Bockhorn, H

2014-01-09

Thermochemistry of reactants, intermediates, transition state structures, and products along with kinetics on the association of CH2·C(═O)CH2CH3 (2-butanone-1-yl) with O2 and dissociation of the peroxy adduct isomers are studied. Thermochemical properties are determined using ab initio (G3MP2B3 and G3) composite methods along with density functional theory (B3LYP/6-311g(d,p)). Entropy and heat capacity contributions versus temperature are determined from structures, vibration frequencies, and internal rotor potentials. The CH2·C(═O)CH2CH3 radical + O2 association results in a chemically activated peroxy radical with 27 kcal mol(-1) excess of energy. The chemically activated adduct can react to stabilized peroxy or hydroperoxide alkyl radical adducts, further react to lactones plus hydroxyl radical, or form olefinic ketones and a hydroperoxy radical. Kinetic parameters are determined from the G3 composite methods derived thermochemical parameters, and quantum Rice-Ramsperger-Kassel (QRRK) analysis to calculate k(E) with master equation analysis to evaluate falloff in the chemically activated and dissociation reactions. One new, not previously reported, peroxy chemistry reaction is presented. It has a low barrier path and involves a concerted reaction resulting in olefin formation, H2O elimination, and an alkoxy radical.

Benchmarking singlet and triplet excitation energies of molecular semiconductors for singlet fission: Tuning the amount of HF exchange and adjusting local correlation to obtain accurate functionals for singlet-triplet gaps

NASA Astrophysics Data System (ADS)

Brückner, Charlotte; Engels, Bernd

2017-01-01

Vertical and adiabatic singlet and triplet excitation energies of molecular p-type semiconductors calculated with various DFT functionals and wave-function based approaches are benchmarked against MS-CASPT2/cc-pVTZ reference values. A special focus lies on the singlet-triplet gaps that are very important in the process of singlet fission. Singlet fission has the potential to boost device efficiencies of organic solar cells, but the scope of existing singlet-fission compounds is still limited. A computational prescreening of candidate molecules could enlarge it; yet it requires efficient methods accurately predicting singlet and triplet excitation energies. Different DFT formulations (Tamm-Dancoff approximation, linear response time-dependent DFT, Δ-SCF) and spin scaling schemes along with several ab initio methods (CC2, ADC(2)/MP2, CIS(D), CIS) are evaluated. While wave-function based methods yield rather reliable singlet-triplet gaps, many DFT functionals are shown to systematically underestimate triplet excitation energies. To gain insight, the impact of exact exchange and correlation is in detail addressed.

Tautomerism of monochalcogenosilanoic acids CH3Si(＝O)XH (X D S, Se, Te) in the gas phase and in the polar and aprotic solution: An ab initio computational investigation

NASA Astrophysics Data System (ADS)

Li, Qiang-Gen; Deng, Chao; Ren, Yi; Wong, Ning-Bew; Chu, San-Yan; Wang, Xin

Computational investigations by an ab initio molecular orbital method (HF and MP2) with the 6-311+G(d,p) and 6-311++G(2df, 2pd) basis sets on the tautomerism of three monochalcogenosilanoic acids CH3Si(＝O)XH (X D S, Se, and Te) in the gas phase and a polar and aprotic solution tetrahydrofuran (THF) was undertaken. Calculated results show that the silanol forms CH3Si(＝X)OH are much more stable than the silanone forms CH3Si(＝O)XH in the gas-phase, which is different from the monochalcogenocarboxylic acids, where the keto forms CH3C(＝O)XH are dominant. This situation may be attributed to the fact that the Si＝O and O＝H single bonds in the silanol forms are stronger than the Si＝X and X＝H single bonds in the silanone forms, respectively, even though the Si＝X (X D S, Se, and Te) double bonds are much weaker than the Si＝O double bondE These results indicate that the stability of the monochalcogenosilanoic acid tautomers is not determined by the double bond energies, contrary to the earlier explanation based on the incorrect assumption that the Si＝S double bond is stronger than the S＝O double bond for the tautomeric equilibrium of RSi(＝O)SH (R＝H, F, Cl, CH3, OH, NH2) to shift towards the thione forms [RSi(＝S)OH]. The binding with CH3OCH3 enhances the preference of the silanol form in the tautomeric equilibrium, and meanwhile significantly lowers the tautomeric barriers by more than 34 kJ/mol in THF solution.0

Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions.

PubMed

Soydaş, Emine; Bozkaya, Uğur

2015-04-14

An assessment of orbital-optimized MP2.5 (OMP2.5) [ Bozkaya, U.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 204105 ] for thermochemistry and kinetics is presented. The OMP2.5 method is applied to closed- and open-shell reaction energies, barrier heights, and aromatic bond dissociation energies. The performance of OMP2.5 is compared with that of the MP2, OMP2, MP2.5, MP3, OMP3, CCSD, and CCSD(T) methods. For most of the test sets, the OMP2.5 method performs better than MP2.5 and CCSD, and provides accurate results. For barrier heights of radical reactions and aromatic bond dissociation energies OMP2.5-MP2.5, OMP2-MP2, and OMP3-MP3 differences become obvious. Especially, for aromatic bond dissociation energies, standard perturbation theory (MP) approaches dramatically fail, providing mean absolute errors (MAEs) of 22.5 (MP2), 17.7 (MP2.5), and 12.8 (MP3) kcal mol(-1), while the MAE values of the orbital-optimized counterparts are 2.7, 2.4, and 2.4 kcal mol(-1), respectively. Hence, there are 5-8-folds reductions in errors when optimized orbitals are employed. Our results demonstrate that standard MP approaches dramatically fail when the reference wave function suffers from the spin-contamination problem. On the other hand, the OMP2.5 method can reduce spin-contamination in the unrestricted Hartree-Fock (UHF) initial guess orbitals. For overall evaluation, we conclude that the OMP2.5 method is very helpful not only for challenging open-shell systems and transition-states but also for closed-shell molecules. Hence, one may prefer OMP2.5 over MP2.5 and CCSD as an O(N(6)) method, where N is the number of basis functions, for thermochemistry and kinetics. The cost of the OMP2.5 method is comparable with that of CCSD for energy computations. However, for analytic gradient computations, the OMP2.5 method is only half as expensive as CCSD.

The mechanism of action of lymphokines. IX. The enzymatic basis of hydrogen peroxide production by lymphokine-activated macrophages.

PubMed

Freund, M; Pick, E

1986-08-15

The purpose of this study was to elucidate the biochemical basis of the enhanced hydrogen peroxide (H2O2) production by guinea pig peritoneal macrophages (MP) cultured in lymphokine (LK)-containing medium. The markedly augmented H2O2 generation by these cells, demonstrable by the horseradish peroxidase (HRP)-catalyzed oxidation of phenol red, is distinguished by its lack of dependence on a second stimulus. We demonstrate that H2O2 production is truly spontaneous and is not caused by a stimulant present among the H2O2 assay reagents. The principal candidate for such a role was HRP type II (a mixture of five isoenzymes) that was reported to be capable of eliciting an oxidative burst in MP. Four distinct HRP isoenzymes that were found incapable of provoking an oxidative response were nevertheless adequate for demonstrating H2O2 production by LK-activated MP. Blocking the MP receptor for mannose by the addition of mannan to the assay system resulted in enhanced detection of H2O2 by low concentrations of HRP type II and by three out of four HRP isoenzymes. Treatment of MP with LK-containing medium for 72 hr did not result in a significant change in the activity of cellular superoxide dismutase (SOD) compared with MP cultured for the same length of time in control medium. By using the specific inhibitor of copper, zinc-containing SOD, sodium diethyldithiocarbamate (DDC), and the universal SOD inhibitor, sodium nitroprusside, we found that the predominant enzyme in guinea pig peritoneal MP is probably manganese-containing SOD. Incubation of LK-activated MP with nitroprusside resulted in almost total inhibition of H2O2 production and a simultaneous switch to superoxide (O2-) liberation. Similar exposure to DDC had no effect. These data indicate that H2O2 produced by LK-activated MP is derived exclusively by enzymatic dismutation of O2- mediated by a manganese-containing SOD. The increase in spontaneous H2O2 production induced by LK is therefore secondary to augmented O2- production that occurs at a cellular location where O2- is accessible to SOD. The enzymatic basis of the enhanced oxygen radical production was investigated by determining the kinetic parameters of the O2- -forming NADPH oxidase of resting LK-treated MP in a cellfree system in which O-2 production was induced by sodium dodecyl sulfate. The Km for NADPH and the Vmax of the enzyme of LK-treated MP were not different from those of the enzyme of MP incubated in control medium. We conclude that LK treatment of MP does not modulate the NADPH oxidase itself but, most likely, a process related to activation of the enzyme.

Effect of increasing dietary metabolizable protein on nitrogen efficiency in Holstein dairy cows

PubMed Central

Imran, Muhammad; Pasha, Talat Naseer; Shahid, Muhammad Qamer; Babar, Imran; Naveed ul Haque, Muhammad

2017-01-01

Objective The objective of the study was to determine the effects of increasing levels of metabolizable protein (MP) on lactation performance and nitrogen (N) efficiencies in lactating dairy cows. Methods Nine multiparous cows in mid lactation [113±25 days in milk] received three treatments in a 3×3 Latin square design with a period length of 21 days. The treatments were three diets, designed to provide similar energy and increasing supply of MP (g/d) (2,371 [low], 2,561 [medium], and 2,711 [high] with corresponding crude protein levels [%]) 15.2, 18.4, and 20.9, respectively. Results Increasing MP supplies did not modify dry matter intake, however, it increased milk protein, fat, and lactose yield linearly. Similarly, fat corrected milk increased linearly (9.3%) due to an increase in both milk yield (5.2%) and milk fat content (7.8%). No effects were observed on milk protein and lactose contents across the treatments. Milk nitrogen efficiency (MNE) decreased from 0.26 to 0.20; whereas, the metabolic efficiency of MP decreased from 0.70 to 0.60 in low to high MP supplies, respectively. The concentration of blood urea nitrogen (BUN) increased linearly in response to increasing MP supplies. Conclusion Increasing MP supplies resulted in increased milk protein yield; however, a higher BUN and low MNE indicated an efficient utilization of dietary protein at low MP supplies. PMID:28002937

The Manchester-Fothergill procedure versus vaginal hysterectomy with uterosacral ligament suspension: a matched historical cohort study.

PubMed

Tolstrup, Cæcilie Krogsgaard; Husby, Karen Ruben; Lose, Gunnar; Kopp, Tine Iskov; Viborg, Petra Hall; Kesmodel, Ulrik Schiøler; Klarskov, Niels

2018-03-01

This study compares vaginal hysterectomy with uterosacral ligament suspension (VH) with the Manchester-Fothergill procedure (MP) for treating pelvic organ prolapse (POP) in the apical compartment. Our matched historical cohort study is based on data from four Danish databases and the corresponding electronic medical records. Patients with POP surgically treated with VH (n = 295) or the MP (n = 295) in between 2010 and 2014 were matched for age and preoperative POP stage in the apical compartment. The main outcome was recurrent or de novo POP in any compartment. Secondary outcomes were recurrent or de novo POP in each compartment and complications. The risk of recurrent or de novo POP in any compartment was higher after VH (18.3%) compared with the MP (7.8%) (Hazard ratio, HR = 2.5, 95% confidence interval (CI): 1.3-4.8). Recurrence in the apical compartment occurred in 5.1% after VH vs. 0.3% after the MP (hazard ratio (HR) = 10.0, 95% confidence interval (CI) 1.3-78.1). In the anterior compartment, rates of recurrent or de novo POP were 11.2% after VH vs. 4.1% after the MP (HR = 3.5, 95% CI 1.4-8.7) and in the posterior compartment 12.9% vs. 4.7% (HR = 2.6, 95% CI 1.3-5.4), respectively. There were more perioperative complications (2.7 vs. 0%, p = 0.007) and postoperative intra-abdominal bleeding (2 vs. 0%, p = 0.03) after VH. This study shows that the MP is superior to VH; if there is no other indication for hysterectomy, the MP should be preferred to VH for surgical treatment of POP in the apical compartment.

Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

2010-10-14

A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low excitation energies largely below the dissociation limit as well as a negligible IVR contribution.

Assessment of G3(MP2)//B3 theory including a pseudopotential for molecules containing first-, second-, and third-row representative elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rocha, Carlos Murilo Romero; Morgon, Nelson Henrique; Custodio, Rogério, E-mail: roger@iqm.unicamp.br

2013-11-14

G3(MP2)//B3 theory was modified to incorporate compact effective potential (CEP) pseudopotentials, providing a theoretical alternative referred to as G3(MP2)//B3-CEP for calculations involving first-, second-, and third-row representative elements. The G3/05 test set was used as a standard to evaluate the accuracy of the calculated properties. G3(MP2)//B3-CEP theory was applied to the study of 247 standard enthalpies of formation, 104 ionization energies, 63 electron affinities, 10 proton affinities, and 22 atomization energies, comprising 446 experimental energies. The mean absolute deviations compared with the experimental data for all thermochemical results presented an accuracy of 1.4 kcal mol{sup −1} for G3(MP2)//B3 and 1.6more » kcal mol{sup −1} for G3(MP2)//B3-CEP. Approximately 75% and 70% of the calculated properties are found with accuracy between ±2 kcal mol{sup −1} for G3(MP2)//B3 and G3(MP2)//B3-CEP, respectively. Considering a confidence interval of 95%, the results may oscillate between ±4.2 kcal mol{sup −1} and ±4.6 kcal mol{sup −1}, respectively. The overall statistical behavior indicates that the calculations using pseudopotential present similar behavior with the all-electron theory. Of equal importance to the accuracy is the CPU time, which was reduced by between 10% and 40%.« less

Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure-activity relationships/tendencies in other 6'-derivatives.

PubMed

El-Sayed, Ahmed A; Tamara Molina, A; Álvarez-Ros, M C; Alcolea Palafox, M

2015-01-01

A comprehensive theoretical conformational analysis of the anti-HIV Nikavir prodrug was carried out; this prodrug has noticeable advantage over the approved drug AZT. The whole conformational parameters (χ, α, β, γ, δ, ϕ, P and νmax) were analysed as well as the NBO natural atomic charges. The calculations were carried out by means of DFT/B3LYP and ab initio MP2 methods with full relaxation of all geometrical parameters. The search located at least 67 stable structures, 4 of which were within a 1 kcal/mol electronic energy range of the global minimum. By MP2 it corresponds to the calculated values of the exocyclic torsional angles χ=-108.0°, β=14.5°, γ=76.7° and ε=71.5°. The results obtained are in accordance to those found in related anti-HIV nucleoside analogues. Comparisons of the conformers with those determined in the common anti-HIV drug AZT were carried out. A detailed analysis of the lowest vibrations (<200 cm(-1)) in the best conformer of Nikavir was carried out. The most stable hydrated cluster of this conformer with 20 explicit water molecules was determined. Calculations in five of its 6'-derivatives were performed to identify structural trends that might correlate with the anti-HIV activity of these compounds. Ten structure-activity relationships/tendencies were established that can help for the design of new drugs. Several recommendations for this design were expressed.

6-mercaptopurine dosage and pharmacokinetics influence the degree of bone marrow toxicity following high-dose methotrexate in children with acute lymphoblastic leukemia.

PubMed

Schmiegelow, K; Bretton-Meyer, U

2001-01-01

Through inhibition of purine de novo synthesis and enhancement of 6-mercaptopurine (6MP) bioavailability high-dose methotrexate (HDM) may increase the incorporation into DNA of 6-thioguanine nucleotides (6TGN), the cytoxic metabolites of 6MP. Thus, coadministration of 6MP could increase myelotoxicity following HDM. Twenty-one children with standard risk (SR) and 25 with intermediate risk (IR) acute lymphoblastic leukemia (ALL) were studied. During consolidation therapy they received either three courses of HDM at 2 week intervals without concurrent oral 6MP (SR-ALL) or four courses of HDM given at 2 week intervals with 25 mg/m2 of oral 6MP daily (IR-ALL). During the first year of maintenance with oral 6MP (75 mg/m2/day) and oral MTX (20 mg/m2/week) they all received five courses of HDM at 8 week intervals. In all cases, HDM consisted of 5,000 mg of MTX/m2 given over 24 h with intraspinal MTX and leucovorin rescue. Erythrocyte levels of 6TGN (E-6TGN) and methotrexate (E-MTX) were, on average, measured every second week during maintenance therapy. When SR consolidation (6MP: 0 mg), IR consolidation (6MP: 25 mg/m2), and SR/IR maintenance therapy (6MP: 75 mg/m2) were compared, white cell and absolute neutrophil count (ANC) nadir, lymphocyte count nadir, thrombocyte count nadir, and hemoglobin nadir after HDM decreased significantly with increasing doses of oral 6MP. Three percent of the HDM courses given without oral 6MP (SR consolidation) were followed by an ANC nadir <0.5 x 10(9)/l compared to 50% of the HDM courses given during SR/IR maintenance therapy. Similarly, only 13% of the HDM courses given as SR-ALL consolidation induced a thrombocyte count nadir <100 x 10(9)/l compared to 58% of the HDM courses given during maintenance therapy. The best-fit model to predict the ANC nadir following HDM during maintenance therapy included the dose of 6MP prior to HDM (beta = -0.017, P= 0.001), the average ANC level during maintenance therapy (beta = 0.82, P = 0.004), and E-6TGN (beta = -0.0029, P= 0.02). The best-fit model to predict the thrombocyte nadir following HDM during maintenance therapy included only mPLATE (beta = 0.0057, P = 0.046). In conclusion, the study indicates that reductions of the dose of concurrently given oral 6MP could be one way of reducing the risk of significant myelotoxicity following HDM during maintenance therapy of childhood ALL.

Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

PubMed

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

2013-01-15

Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.

PubMed

Lemke, Kono H

2017-06-21

This study presents results for the binding energy and geometry of the H 2 S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of D e , E ZPE , D o , and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of D e are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance r SS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H 2 S dimer geometry and binding energy. As regards the structure of (H 2 S) 2 , MPn, CCSD, and CCSD(T) level values of r SS , obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy D e are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies D e with E ZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields D o = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Effects of a Single Water Molecule on the Reaction Barrier of Interstellar CO2 Formation Reaction.

PubMed

Tachikawa, Hiroto; Kawabata, Hiroshi

2016-08-25

The mechanism by which CO2 is formed in the interstellar space remains a mystery. The most likely reaction is collision between CO and OH; however, previous theoretical works have shown that the activation barrier for CO2 formation is high enough to prevent the reaction at the low thermal conditions of space (∼10 K). The effects of single water molecule on the reaction barrier of CO2 formation from reaction between CO and OH have been investigated here by means of ab initio calculation. The barrier height along the lowest-energy pathway in the reaction between CO and OH in the absence of the H2O molecule was calculated to be 2.3 kcal/mol when CCSD(T) energy corrections are combined with the MP2 basis set limit. In the case of the hydrated (H2O-CO-OH) system, the inclusion of a single H2O molecule into the system significantly decreased the barrier height to 0.2 kcal/mol. This suggests that CO2 can be formed when CO and OH react in the presence of H2O, even under thermal conditions as low as 10 K.

Conformation and hydrogen bonding in 4-Aminobutanol

NASA Astrophysics Data System (ADS)

Khalil, Andrew S.; Duguay, Taylor M.; Lavrich, Richard J.

2017-06-01

Rotational spectra of the most abundant and four 13C isotopomers of 4-aminobutanol have been recorded in natural abundance using a Fourier-transform microwave spectrometer. For the most abundant isotopomer, 56 hyperfine components from the fifteen a- and b-type transitions measured were fit to the quadupole coupling constants, χaa = -3.843(3) MHz, χbb = 1.971(3) MHz. Rotational and centrifugal distortion constants determined from fits of the resulting unsplit line centers to the Watson A-reduction Hamiltonian are A = 4484.893(3) MHz, B = 2830.721(1) MHz, C = 1942.9710(3) MHz, ΔJ = 0.98(3) kHz, ΔJK = 1.4(1) kHz, ΔK = - 2.6(5) kHz, δJ = 0.27(1) kHz, and δK = 1.7(1) kHz. Between nine and eleven rotational transitions were measured for the 13C isotopes and rotational constants were determined by fixing the distortion constants to the values found for the normal isotope. The five sets of moments of inertia were used to determine the 4-aminobutanol substitution structure as well to perform a least-squares fit of the lowest energy ab initio structure. The heavy atom coordinates determined from these two methods are in excellent agreement. The conformation of 4-aminobutanol is stabilized by an intramolecular hydrogen bond from the alcohol proton to amino nitrogen with a resulting hydrogen bond distance of 1.891 Å. The experimental structure is consistent with the lowest energy ab initio [MP2/6-311++G(d,p)] structure.

Mycelial development preceding basidioma formation in Moniliophthora perniciosa is associated to chitin, sugar and nutrient metabolism alterations involving autophagy.

PubMed

Gomes, Dayane Santos; Lopes, Maíza Alves; Menezes, Sara Pereira; Ribeiro, Lidiane Figueredo; Dias, Cristiano Villela; Andrade, Bruno Silva; de Jesus, Raildo Mota; Pires, Acassia Benjamin Leal; Goes-Neto, Aristóteles; Micheli, Fabienne

2016-01-01

We identified and characterized two chitinases, named MpCHIT1 and MpCHIT2, from the fungus Moniliophthora perniciosa - the etiologic agent of witches' broom disease in cacao tree (Theobroma cacao L.) - during its development, mainly in the mycelia phases preceding the basidioma formation. The expression of MpCHIT1 and MpCHIT2, together with MpCHS and MpATG8 (chitin synthase and autophagy genes, respectively), was analyzed during the M. perniciosa growth and development on bran-based solid medium as well as in liquid medium containing H2O2 or rapamycin (oxidative and nutritional related-autophagy stress agents, respectively). In order to link the expression of chitin metabolism-related genes to nutritional composition influencing fungus development, we also quantified total and reduced sugars, as well as macro- and micronutrients in the bran-based solid medium. The expression analysis showed that the MpCHS expression increased through mycelial development and then decreased in the primordium and basidioma phases, while the expression of MpCHIT1 and MpCHIT2 was higher in basidioma and primordium phases, respectively. Moreover, the expression pattern of MpCHIT1 and MpCHIT2 is distinct, the second correlated with the MpATG8 expression pattern and possibly with autophagy process, while the first may be related to the basidioma formation. The quantification of total and reduced sugars, as well as macro- and micronutrients supported the idea that the cell wall restructuration due to MpCHS, MpCHIT1 and MpCHIT2 is related to stress and fungal nutrient reallocation, allowing the formation and development of the basidioma. Experiments involving M. perniciosa growth on liquid medium containing H2O2 or rapamycin showed that MpCHIT1 and MpCHIT2 were over-expressed in response to oxidative but also to nutritional related-autophagy stresses. Interestingly, the expression level of MpCHS, MpCHIT1 and MpCHIT2 in presence of rapamycin is similar to the one observed in the primordium and basidioma from bran-based solid medium. The analysis of the overall data allowed designing a general scheme of chitin metabolism and autophagy during M. perniciosa development, focusing on the mycelium phases as crucial and environmentally influenced steps preceding the primordium and basidioma formation. These data support the idea that the nutritional environment of M. perniciosa influences its development and life cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

[Preliminary results of noncontact temperature measuring using an infrared thermometer on the tarsus pf swine with osteoarthrosis tarsi deformans].

PubMed

Sabec, D; Lazar, P

1990-01-01

The surface temperature on tarsus of 54 performance tested boars of about 60 kg of Swedish Landrace was measured by means of infra-red thermometer at three measuring points (MP1, MP2 and MP3). MP1 was situated above the tuberculum of os metatarsale III or, as visualised in 21 slaughtered boars, above pathoanatomical alterations of osteoarthrosis tarsi deformans (OATD). MP2 was located directly medially and MP3 laterally from MP1. A clear palpatory symptom was found only with 10 boars, while all 21 slaughtered boars showed different morphological lesions of OATD. The average temperature at MP1 was 35.69 degrees C and was significantly higher (P = .01) than at MP2 (35.34) and MP3 (35.30). The temperature differences between MP1 and MP2 or MP3 were statistically reliable. Boars, who had a clear palpatory symptoms at tuberculum, showed an average temperature at MT1 of 36.27 degrees C, which was higher (P = .0114) than of those with an unclear palpatory symptom (35.64 degrees C). The results show that the temperature differences are the consequence of OATD.

Sequence variations in RepMP2/3 and RepMP4 elements reveal intragenomic homologous DNA recombination events in Mycoplasma pneumoniae.

PubMed

Spuesens, Emiel B M; Oduber, Minoushka; Hoogenboezem, Theo; Sluijter, Marcel; Hartwig, Nico G; van Rossum, Annemarie M C; Vink, Cornelis

2009-07-01

The gene encoding major adhesin protein P1 of Mycoplasma pneumoniae, MPN141, contains two DNA sequence stretches, designated RepMP2/3 and RepMP4, which display variation among strains. This variation allows strains to be differentiated into two major P1 genotypes (1 and 2) and several variants. Interestingly, multiple versions of the RepMP2/3 and RepMP4 elements exist at other sites within the bacterial genome. Because these versions are closely related in sequence, but not identical, it has been hypothesized that they have the capacity to recombine with their counterparts within MPN141, and thereby serve as a source of sequence variation of the P1 protein. In order to determine the variation within the RepMP2/3 and RepMP4 elements, both within the bacterial genome and among strains, we analysed the DNA sequences of all RepMP2/3 and RepMP4 elements within the genomes of 23 M. pneumoniae strains. Our data demonstrate that: (i) recombination is likely to have occurred between two RepMP2/3 elements in four of the strains, and (ii) all previously described P1 genotypes can be explained by inter-RepMP recombination events. Moreover, the difference between the two major P1 genotypes was reflected in all RepMP elements, such that subtype 1 and 2 strains can be differentiated on the basis of sequence variation in each RepMP element. This implies that subtype 1 and subtype 2 strains represent evolutionarily diverged strain lineages. Finally, a classification scheme is proposed in which the P1 genotype of M. pneumoniae isolates can be described in a sequence-based, universal fashion.

Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature

NASA Astrophysics Data System (ADS)

Dick, Jeffrey M.; Evans, Katy A.; Holman, Alex I.; Jaraula, Caroline M. B.; Grice, Kliti

2013-12-01

Estimates of standard molal Gibbs energy (ΔGf°) and enthalpy (ΔHf°) of formation, entropy (S°), heat capacity (CP°) and volume (V°) at 25 °C and 1 bar of aqueous phenanthrene (P) and 1-, 2-, 3-, 4- and 9-methylphenanthrene (1-MP, 2-MP, 3-MP, 4-MP, 9-MP) were made by combining reported standard-state properties of the crystalline compounds, solubilities and enthalpies of phenanthrene and 1-MP, and relative Gibbs energies, enthalpies and entropies of aqueous MP isomers from published quantum chemical simulations. The calculated properties are consistent with greater stabilities of the β isomers (2-MP and 3-MP) relative to the α isomers (1-MP and 9-MP) at 25 °C. However, the metastable equilibrium values of the abundance ratios 2-MP/1-MP (MPR) and (2-MP + 3-MP)/(1-MP + 9-MP) (MPI-3) decrease with temperature, becoming <1 at ∼375-455 °C. The thermodynamic model is consistent with observations of reversals of these organic maturity parameters at high temperature in hydrothermal and metamorphic settings. Application of the model to data reported for the Paleoproterozoic Here’s Your Chance (HYC) Pb-Zn-Ag ore deposit (McArthur River, Northern Territory, Australia) indicates a likely effect of high-temperature equilibration on reported values of MPR and MPI-3, but this finding is contingent on the location within the deposit. If metastable equilibrium holds, a third aromatic maturity ratio, 1.5 × (2-MP + 3-MP)/(P + 1-MP + 9-MP) (MPI-1), can be used as a proxy for oxidation potential. Values of logaH2aq determined from data reported for HYC and for a sequence of deeply buried source rocks are indicative of more reducing conditions at a given temperature than those inferred from data reported for two sets of samples exposed to contact or regional metamorphism. These results are limiting-case scenarios for the modeled systems that do not account for effects of non-ideal mixing or kinetics, or external sources or transport of the organic matter. Nevertheless, quantifying the temperature dependence of equilibrium constants of organic reactions enables the utilization of organic maturity parameters as relative geothermometers at temperatures higher than the nominal limits of the oil window.

Divalent carbon(0) chemistry, part 1: Parent compounds.

PubMed

Tonner, Ralf; Frenking, Gernot

2008-01-01

Quantum-chemical calculations with DFT (BP86) and ab initio methods [MP2, SCS-MP2, CCSD(T)] have been carried out for the molecules C(PH(3))(2) (1), C(PMe(3))(2) (2), C(PPh(3))(2) (3), C(PPh(3))(CO) (4), C(CO)(2) (5), C(NHC(H))(2) (6), C(NHC(Me))(2) (7) (Me(2)N)(2)C=C=C(NMe(2))(2) (8), and NHC (9), where NHC=N-heterocyclic carbene and NHC(Me)=N-methyl-substituted NHC. The electronic structure in 1-9 was analyzed with charge- and energy-partitioning methods. The results show that the bonding situations in L(2)C compounds 1-8 can be interpreted in terms of donor-acceptor interactions between closed-shell ligands L and a carbon atom which has two lone-pair orbitals L-->C<--L. This holds particularly for the carbodiphosphoranes 1-3 where L=PR(3), which therefore are classified as divalent carbon(0) compounds. The NBO analysis suggests that the best Lewis structures for the carbodicarbenes 6 and 7 where L is a NHC ligand have C==C==C double bonds as in the tetraaminoallene 8. However, the Lewis structures of 6-8, in which two lone-pair orbitals at the central carbon atom are enforced, have only a slightly higher residual density. Visual inspection of the frontier orbitals of the latter species reveals their pronounced lone-pair character, which suggests that even the quasi-linear tetraaminoallene 8 is a "masked" divalent carbon(0) compound. This explains the very shallow bending potential of 8. The same conclusion is drawn for phosphoranylketene 4 and for carbon suboxide (5), which according to the bonding analysis have hidden double-lone-pair character. The AIM analysis and the EDA calculations support the assignment of carbodiphosphoranes as divalent carbon(0) compounds, while NHC 9 is characterized as a divalent carbon(II) compound. The L-->C((1)D) donor-acceptor bonds are roughly twice as strong as the respective L-->BH(3) bond.

Brain kinetics of methylphenidate (Ritalin) enantiomers after oral administration.

PubMed

Ding, Yu-Shin; Gatley, S John; Thanos, Panayotis K; Shea, Colleen; Garza, Victor; Xu, Youwen; Carter, Pauline; King, Payton; Warner, Don; Taintor, Nicholas B; Park, Daniel J; Pyatt, Bea; Fowler, Joanna S; Volkow, Nora D

2004-09-01

Methylphenidate (MP) (Ritalin) is widely used for the treatment of attention deficit hyperactivity disorder (ADHD). It is a chiral drug, marketed as the racemic mixture of d- and l-threo enantiomers. Our previous studies (PET and microdialysis) in humans, baboons, and rats confirm the notion that pharmacological specificity of MP resides predominantly in the d-isomer. A recent report that intraperitoneally (i.p.) administered l-threo-MP displayed potent, dose-dependent inhibition of cocaine- or apomorphine-induced locomotion in rats, raises the question of whether l-threo-MP has a similar effect when given orally. It has been speculated that l-threo-MP is poorly absorbed in humans when it is given orally because of rapid presystemic metabolism. To investigate whether l-threo-MP or its metabolites can be delivered to the brain when it is given orally, and whether l-threo-MP is pharmacologically active. PET and MicroPET studies were carried out in baboons and rats using orally delivered C-11-labeled d- and l-threo-MP ([methyl-(11)C]d-threo-MP and [methyl-(11)C]l-threo-MP). In addition, we assessed the effects of i.p. l-threo-MP on spontaneous and cocaine-stimulated locomotor activity in mice. There was a higher global uptake of carbon-11 in both baboon and rat brain for oral [(11)C]l-threo-MP than for oral [(11)C]d-threo-MP. Analysis of the chemical form of radioactivity in rat brain after [(11)C]d-threo-MP indicated mainly unchanged tracer, whereas with [(11)C]l-threo-MP, it was mainly a labeled metabolite. The possibility that this labeled metabolite might be [(11)C]methanol or [(11)C]CO(2), derived from demethylation, was excluded by ex vivo studies in rats. When l-threo-MP was given i.p. to mice at a dose of 3 mg/kg, it neither stimulated locomotor activity nor inhibited the increased locomotor activity due to cocaine administration. These results suggest that, in animal models, l-threo-MP or its metabolite(s) is (are) absorbed from the gastrointestinal tract and enters the brain after oral administration, but that l-threo-MP may not be pharmacologically active. These results are pertinent to the question of whether l-threo-MP contributes to the behavioral and side effect profile of MP during treatment of ADHD. Copyright 2004 Wiley-Liss, Inc.

Electronic Structure of Ethynyl Substituted Cyclobutadienes

NASA Astrophysics Data System (ADS)

Emmert, Frank Lee Emmert, III; Thompson, Stephanie J.; Slipchenko, Lyudmila V.

2011-06-01

We investigated the effects of ethynyl substitution on the electronic structure of cyclobutadiene. These species are involved in Bergman Cyclization reactionsand are possible intermediates in the formation of fullerenes and graphite sheets. Prediction of the electronic energy of cyclobutadiene is challenging for single-reference ab initio methods such as HF, MP2 or DFT because of Jahn-Teller distortions and the diradical character of the singlet state. We determined the vertical and adiabatic singlet-triplet energy splittings, the natural charges and spin densities in substituted cyclobutadienes, using the equations of motion spin flip coupled cluster with single and double excitations (EOM-SF-CCSD) method that accurately describes diradical states. The adiabatic singlet-triplet gaps decrease upon substituent addition, but the singlet state is always lower in energy. However, we found that the results are affected by spin-contamination of the reference state and deteriorate when an unrestricted HF reference is employed. O. L. Chapman, C. L. McIntosh, J. Pacansky, "Cyclobutadiene" J. Am. Chem. Soc. 1973, 95, (2), 614-617. N. S. Goroff, "Mechanism of Fullerene Formation." Acc. Chem. Res. 1996, 29, (2), 77-83. L.V. Slipchenko and A.I. Krylov, "Singlet-triplet gaps in diradicals by the Spin-Flip approach: A benchmark study", J. Chem. Phys. 2002, 117, 4694-4708.

Survey of college students' MP3 listening: Habits, safety issues, attitudes, and education.

PubMed

Hoover, Alicia; Krishnamurti, Sridhar

2010-06-01

To survey listening habits and attitudes of typical college students who use MP3 players and to investigate possible safety issues related to MP3 player listening. College students who were frequent MP3 player users (N = 428) filled out a 30-item online survey. Specific areas probed by the present survey included frequency and duration of MP3 player use, MP3 player volume levels used, types of earphones used, typical environments in which MP3 player was worn, specific activities related to safety while listening to MP3 players, and attitudes toward MP3 player use. The majority of listeners wore MP3 players for less than 2 hr daily at safe volume levels. About one third of respondents reported being distracted while wearing an MP3 player, and more than one third of listeners experienced soreness in their ears after a listening session. About one third of respondents reported occasionally using their MP3 players at maximum volume levels. Listeners indicated willingness to (a) reduce volume levels, (b) decrease listening duration, and (c) buy specialized earphones to conserve their hearing. The study found concerns regarding the occasional use of MP3 players at full volume and reduced environmental awareness among some college student users.

Assessment of the overlap metric in the context of RI-MP2 and atomic batched tensor decomposed MP2

NASA Astrophysics Data System (ADS)

Schmitz, Gunnar; Christiansen, Ove

2018-06-01

The resolution-of-the-identity approximation (RI) is a standard tool to accelerate the evaluation of two electron repulsion integrals. However introducing further approximations on top of for example RI-MP2, makes it important to check again the made choices. Usually the so called Coulomb metric is used. An alternative is the less accurate overlap metric, which has the benefit of a faster decay with distance. We encountered both choices in our atomic batched tensor decomposed MP2 (AB-MP2) and went with the Coulomb metric for the safe choice. In this work we re-investigate the choice of Coulomb and overlap metric for RI-MP2 and AB-MP2.

Abstraction kinetics of H-atom by OH radical from pinonaldehyde (C10H16O2): ab initio and transition-state theory calculations.

PubMed

Dash, Manas Ranjan; Rajakumar, B

2012-06-21

The kinetics and abstraction rate coefficients of hydroxyl radical (OH) reaction with pinonaldehyde were computed using G3(MP2) theory and transition-state theory (TST) between 200 and 400 K. Structures of the reactants, reaction complexes (RCs), product complexes (PCs), transition states (TSs), and products were optimized at the MP2(FULL)/6-31G* level of theory. Fifteen transition states were identified for the title reaction and confirmed by intrinsic reaction coordinate (IRC) calculations. The contributions of all the individual hydrogens in the substrate molecule to the total reaction are computed. The quantum mechanical tunneling effect was computed using Wigner's and Eckart's methods (both symmetrical and unsymmetrical methods). The reaction exhibits a negative temperature dependent rate coefficient, k(T) = (1.97 ± 0.34) × 10(-13) exp[(1587 ± 48)/T] cm(3) molecule(-1) s(-1), k(T) = (3.02 ± 0.56) × 10(-13) exp[(1534 ± 52/T] cm(3) molecule(-1) s(-1), and k(T) = (4.71 ± 1.85) × 10(-14) exp[(2042 ± 110)/T] cm(3) molecule(-1) s(-1) with Wigner's, Eckart's symmetrical, and Eckart's unsymmetrical tunneling corrections, respectively. Theoretically calculated rate coefficients are found to be in good agreement with the experimentally measured ones and other theoretical results. It is shown that hydrogen abstraction from -CHO position is the major channel, whereas H-abstraction from -COCH(3) is negligible. The atmospheric lifetime of pinonaldehyde is computed to be few hours and found to be in excellent agreement with the experimentally estimated ones.

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 2 : I\\0x2010 205 NB speed flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various speed flow plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2; I-2...

Renal damage induced by the pesticide methyl parathion in male Wistar rats.

PubMed

Fuentes-Delgado, Victor Hugo; Martínez-Saldaña, María Consolación; Rodríguez-Vázquez, María Luisa; Reyes-Romero, Miguel Arturo; Reyes-Sánchez, José Luis; Jaramillo-Juárez, Fernando

2018-01-01

Little information is apparently available regarding the nephrotoxic effects induced by pesticides. The aim of this study was to examine the influence of low doses of methyl parathion (MP) on the structure and function of the kidney of male Wistar rats. A corn oil (vehicle) was administered to control rats, whereas treated rats received MP at 0.56 mg/kg orally (1/25 of LD 50 ), every third day, for 8 weeks. At the end of each week following MP exposure, creatinine and glucose levels were measured in plasma, while glucose, inorganic phosphate, total proteins, albumin, and activity of γ-glutamyltranspeptidase (GGT) were determined in urine. Kidney histological study was also performed. Compared with control rats, MP significantly increased plasma glucose and creatinine levels accompanied by decreased urinary flow rate and elevated urinary excretion rates of glucose, phosphate, and albumin. Further, the activity of GGT in urine was increased significantly. The proximal cells exhibited cytoplasmic vacuolization, positive periodic acid Schiff inclusions, and brush border edge loss after 2 or 4 weeks following MP treatment. Finally, renal cortex samples were obtained at 2, 4, 6, and 8 weeks of MP treatment, and the concentrations of reduced glutathione (GSH) and glutathione peroxidase (GPx) activity were measured. The mRNA expression levels of BAX and tumor necrosis factor-α (TNF-α) were also determined (RT-PCR). MP significantly decreased renal GSH levels, increased GPx activity, as well as downregulated the mRNA expression of TNF-α and BAX. Densitometry analysis showed a significant reduction in TNF-α and BAX mRNA expression levels at 2 and 4 weeks following MP treatment. Low doses of MP produced structural and functional damage to the proximal tubules of male rat kidney.

Melicope ptelefolia leaf extracts exhibit antioxidant activity and exert anti-proliferative effect with apoptosis induction on four different cancer cell lines.

PubMed

Kabir, Mohammad Faujul; Mohd Ali, Johari; Abolmaesoomi, Mitra; Hashim, Onn Haji

2017-05-05

Melicope ptelefolia is a well-known herb in a number of Asian countries. It is often used as vegetable salad and traditional medicine to address various ailments. However, not many studies have been currently done to evaluate the medicinal benefits of M. ptelefolia (MP). The present study reports antioxidant, anti-proliferative, and apoptosis induction activities of MP leaf extracts. Young MP leaves were dried, powdered and extracted sequentially using hexane (HX), ethyl acetate (EA), methanol (MeOH) and water (W). Antioxidant activity was evaluated using ferric reducing antioxidant power (FRAP), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) radicals scavenging and cellular antioxidant activity (CAA) assays. Anti-proliferative activity was evaluated through cell viability assay, using the following four human cancer cell lines: breast (HCC1937, MDA-MB-231), colorectal (HCT116) and liver (HepG2). The anti-proliferative activity was further confirmed through cell cycle and apoptosis assays, including annexin-V/7-aminoactinomycin D staining and measurements of caspase enzymes activation and inhibition. Overall, MP-HX extract exhibited the highest antioxidant potential, with IC 50 values of 267.73 ± 5.58 and 327.40 ± 3.80 μg/mL for ABTS and DPPH radical-scavenging assays, respectively. MP-HX demonstrated the highest CAA activity in Hs27 cells, with EC 50 of 11.30 ± 0.68 μg/mL, while MP-EA showed EC 50 value of 37.32 ± 0.68 μg/mL. MP-HX and MP-EA showed promising anti-proliferative activity towards the four cancer cell lines, with IC 50 values that were mostly below 100 μg/mL. MP-HX showed the most notable anti-proliferative activity against MDA-MB-231 (IC 50  = 57.81 ± 3.49 μg/mL) and HCT116 (IC 50  = 58.04 ± 0.96 μg/mL) while MP-EA showed strongest anti-proliferative activity in HCT116 (IC 50  = 64.69 ± 0.72 μg/mL). The anticancer potential of MP-HX and MP-EA were also demonstrated by their ability to induce caspase-dependent apoptotic cell death in all of the cancer cell lines tested. Cell cycle analysis suggested that both the MP-HX and MP-EA extracts were able to disrupt the cell cycle in most of the cancer cell lines. MP-HX and MP-EA extracts demonstrated notable antioxidant, anti-proliferative, apoptosis induction and cancer cell cycle inhibition activities. These findings reflect the promising potentials of MP to be a source of novel phytochemical(s) with health promoting benefits that are also valuable for nutraceutical industry and cancer therapy.

High hydrostatic pressure processing reduces the glycemic index of fresh mango puree in healthy subjects.

PubMed

Elizondo-Montemayor, Leticia; Hernández-Brenes, Carmen; Ramos-Parra, Perla A; Moreno-Sánchez, Diana; Nieblas, Bianca; Rosas-Pérez, Aratza M; Lamadrid-Zertuche, Ana C

2015-04-01

Dietary guidelines recommend the daily consumption of fruits; however, healthy and type 2 diabetes mellitus (T2DM) subjects receive conflicting messages regarding ingestion of fruits, such as mango, because of its sugar content. We investigated the effects of high hydrostatic pressure (HHP) processing of fresh mango puree (MP) on the glycemic indexes (GIs) and postprandial glycemic responses of 38 healthy Mexican subjects in a randomized cross-over clinical trial. Physicochemical characterization of MP included sugar profiles by HPLC-ELSD, starch, fibers, moisture, viscosity, swelling capacity and solubility properties of alcohol insoluble residue (AIR). The mean GI for HHP-MP was significantly lower (32.7 ± 13.4) than that of unprocessed-MP (42.7 ± 19.5). A significantly higher proportion of subjects showed a low GI following the consumption of HHP-MP compared to unprocessed-MP and none of them showed a high GI for the HHP-MP, compared to a significantly higher proportion for the unprocessed-MP. The viscosity and AIR solubility values of HHP-MP samples were significantly higher, which influenced glucose peaking later (Tmax) at 45 minutes and induced 20% lower AUC values than unprocessed-MP, corresponding to greater retardation indexes. The study findings support data stating that low GI fruits are appropriate for glycemic control and that mango may be included as part of healthy subjects' diets and potentially T2DM subjects' diets. Furthermore, HHP processing of mango may offer additional benefits for glycemic control, as its performance regarding GI, AUC and Tmax was significantly better than that of the unprocessed-MP. To our knowledge, this is the first report on the impact of this commercial non-thermal pasteurization technology on glucose metabolism.

Purification and biochemical characterization of a novel ecto-apyrase, MP67, from Mimosa pudica.

PubMed

Okuhata, Riku; Takishima, Takeshi; Nishimura, Naoaki; Ueda, Shogo; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2011-09-01

We have previously reported the presence of an apyrase in Mimosa pudica. However, only limited information is available for this enzyme. Thus, in this study, the apyrase was purified to homogeneity. The purified enzyme had a molecular mass of around 67 kD and was able to hydrolyze both nucleotide triphosphate and nucleotide diphosphate as substrates. The ratio of ATP to ADP hydrolysis velocity of the purified protein was 0.01 in the presence of calcium ion, showing extremely high substrate specificity toward ADP. Thus, we designated this novel apyrase as MP67. A cDNA clone of MP67 was obtained using primers designed from the amino acid sequence of trypsin-digested fragments of the protein. In addition, rapid amplification of cDNA ends-polymerase chain reaction was performed to clone a conventional apyrase (MpAPY2). Comparison of the deduced amino acid sequences showed that MP67 is similar to ecto-apyrases; however, it was distinct from conventional apyrase based on phylogenetic classification. MP67 and MpAPY2 were expressed in Escherichia coli, and the recombinant proteins were purified. The recombinant MP67 showed high substrate specificity toward ADP rather than ATP. A polyclonal antibody raised against the recombinant MP67 was used to examine the tissue distribution and localization of native MP67 in the plant. The results showed that MP67 was ubiquitously distributed in various tissues, most abundantly in leaves, and was localized to plasma membranes. Thus, MP67 is a novel ecto-apyrase with extremely high substrate specificity for ADP.

Purification and Biochemical Characterization of a Novel Ecto-Apyrase, MP67, from Mimosa pudica1[C][W][OA

PubMed Central

Okuhata, Riku; Takishima, Takeshi; Nishimura, Naoaki; Ueda, Shogo; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2011-01-01

We have previously reported the presence of an apyrase in Mimosa pudica. However, only limited information is available for this enzyme. Thus, in this study, the apyrase was purified to homogeneity. The purified enzyme had a molecular mass of around 67 kD and was able to hydrolyze both nucleotide triphosphate and nucleotide diphosphate as substrates. The ratio of ATP to ADP hydrolysis velocity of the purified protein was 0.01 in the presence of calcium ion, showing extremely high substrate specificity toward ADP. Thus, we designated this novel apyrase as MP67. A cDNA clone of MP67 was obtained using primers designed from the amino acid sequence of trypsin-digested fragments of the protein. In addition, rapid amplification of cDNA ends-polymerase chain reaction was performed to clone a conventional apyrase (MpAPY2). Comparison of the deduced amino acid sequences showed that MP67 is similar to ecto-apyrases; however, it was distinct from conventional apyrase based on phylogenetic classification. MP67 and MpAPY2 were expressed in Escherichia coli, and the recombinant proteins were purified. The recombinant MP67 showed high substrate specificity toward ADP rather than ATP. A polyclonal antibody raised against the recombinant MP67 was used to examine the tissue distribution and localization of native MP67 in the plant. The results showed that MP67 was ubiquitously distributed in various tissues, most abundantly in leaves, and was localized to plasma membranes. Thus, MP67 is a novel ecto-apyrase with extremely high substrate specificity for ADP. PMID:21788364

Analysis of Levodopa Content in Commercial Mucuna pruriens Products Using High-Performance Liquid Chromatography with Fluorescence Detection.

PubMed

Soumyanath, Amala; Denne, Tanya; Hiller, Amie; Ramachandran, Shaila; Shinto, Lynne

2018-02-01

Mucuna pruriens (MP) seeds contain levodopa (up to 2% by weight) and have been used in traditional Indian medicine to treat an illness named "Kampavata," now understood to be Parkinson's disease (PD). Studies have shown MP to be beneficial, and even superior, to levodopa alone in treating PD symptoms. Commercial products containing MP are readily available from online and retail sources to patients and physicians. Products often contain extracts of MP seeds, with significantly higher levodopa content than the seeds. However, MP products have limited regulatory controls with respect to quality and content of active ingredient. The aim of this study was to apply a quantitative method to determine levodopa content in readily available MP products that might be used by patients or in research studies. Levodopa present in six commercial MP products was quantified by solvent extraction followed by reversed-phase high-performance liquid chromatography (HPLC) coupled to fluorescence detection (FD). Certificates of analysis (COA) were obtained, from manufacturers of MP products, to assess the existence and implementation of specifications for levodopa content. HPLC-FD analysis revealed that the levodopa content of the six commercial MP products varied from 6% to 141% of individual label claims. No product contained levodopa within normal pharmacopeial limits of 90%-110% label claim. The maximum daily dose of levodopa delivered by the products varied from 14.4 to 720 mg/day. COAs were inconsistent in specifications for and verification of levodopa content. The commercial products tested varied widely in levodopa content, sometimes deviating widely from the label claim. These deficiencies could impact efficacy and safety of MP products used by PD patients and compromise the results of scientific studies on MP products. The HPLC-FD method described in this study could be utilized by both manufacturers and scientific researchers to verify levodopa content of MP products.

The PDE10A inhibitor MP-10 and haloperidol produce distinct gene expression profiles in the striatum and influence cataleptic behavior in rodents.

PubMed

Gentzel, Renee C; Toolan, Dawn; Roberts, Rhonda; Koser, Amy Jo; Kandebo, Monika; Hershey, James; Renger, John J; Uslaner, Jason; Smith, Sean M

2015-12-01

Phosphodiesterase 10A (PDE10A) has garnered attention as a potential therapeutic target for schizophrenia due to its prominent striatal expression and ability to modulate striatal signaling. The present study used the selective PDE10A inhibitor MP-10 and the dopamine D2 antagonist haloperidol to compare effects of PDE10A inhibition and dopamine D2 blockade on striatopallidal (D2) and striatonigral (D1) pathway activation. Our studies confirmed that administration of MP-10 significantly elevates expression of the immediate early genes (IEG) c-fos, egr-1, and arc in rat striatum. Furthermore, we demonstrated that MP-10 induced egr-1 expression was distributed evenly between enkephalin-containing D2-neurons and substance P-containing D1-neurons. In contrast, haloperidol (3 mg/kg) selectively activated egr-1 expression in enkephalin neurons. Co-administration of MP-10 and haloperidol (0.5 mg/kg) increased IEG expression to a greater extent than either compound alone. Similarly, in a rat catalepsy assay, administration of haloperidol (0.5 mg/kg) or MP-10 (3-30 mg/kg) did not produce cataleptic behavior when dosed alone, but co-administration of haloperidol with MP-10 (3 and 10 mg/kg) induced cataleptic behaviors. Interestingly, co-administration of haloperidol with a high dose of MP-10 (30 mg/kg) failed to produce cataleptic behavior. These findings are important for understanding the neural circuits involved in catalepsy and suggest that the behavioral effects produced by PDE10A inhibitors may be influenced by concomitant medication and the level of PDE10A inhibition achieved by the dose of the inhibitor. Copyright © 2015. Published by Elsevier Ltd.

A performance comparison of the Cray-2 and the Cray X-MP

NASA Technical Reports Server (NTRS)

Schmickley, Ronald; Bailey, David H.

1986-01-01

A suite of thirteen large Fortran benchmark codes were run on Cray-2 and Cray X-MP supercomputers. These codes were a mix of compute-intensive scientific application programs (mostly Computational Fluid Dynamics) and some special vectorized computation exercise programs. For the general class of programs tested on the Cray-2, most of which were not specially tuned for speed, the floating point operation rates varied under a variety of system load configurations from 40 percent up to 125 percent of X-MP performance rates. It is concluded that the Cray-2, in the original system configuration studied (without memory pseudo-banking) will run untuned Fortran code, on average, about 70 percent of X-MP speeds.

Carbon-oxygen clusters as hypothetical high energy-density materials

NASA Astrophysics Data System (ADS)

Evangelisti, Stefano

1997-05-01

An an initio investigation on the hypothetical systems C nO n ( n = 2, 3, 4) is presented. Calculations have been performed at SCF and MP2 level, using a [3s2p1 d] basis set on each atom. At this level of approximation, two metastable structures have been found. They are C 2O 2 with C 2v symmetry (an irregular tetrahedron) and C 4O 4 with T d symmetry (two regular tetrahedra copenetrating each other). On the other hand, the search of local minima with C nv structures has failed for n = 3, 4. For the two metastable structures also larger basis sets have been used, up to [4s3p2d1f] (in the case of C 4O 4, at SCF level only). The computed energy release of the dissociation reaction (C nO n → n CO) of the two metastable structures is very high (about 100 kcal per mole of CO produced). It is of the same magnitude of the energy computed for the corresponding isoelectronic structures N 4 and N 8. If these or similar CO-clusters could be synthesized, these systems are candidates to be high energy-density materials (HEDM).

ONIOM Investigation of the Second-Order Nonlinear Optical Responses of Fluorescent Proteins.

PubMed

de Wergifosse, Marc; Botek, Edith; De Meulenaere, Evelien; Clays, Koen; Champagne, Benoît

2018-05-17

The first hyperpolarizability (β) of six fluorescent proteins (FPs), namely, enhanced green fluorescent protein, enhanced yellow fluorescent protein, SHardonnay, ZsYellow, DsRed, and mCherry, has been calculated to unravel the structure-property relationships on their second-order nonlinear optical properties, owing to their potential for multidimensional biomedical imaging. The ONIOM scheme has been employed and several of its refinements have been addressed to incorporate efficiently the effects of the microenvironment on the nonlinear optical responses of the FP chromophore that is embedded in a protective β-barrel protein cage. In the ONIOM scheme, the system is decomposed into several layers (here two) treated at different levels of approximation (method1/method2), from the most elaborated method (method1) for its core (called the high layer) to the most approximate one (method2) for the outer surrounding (called the low layer). We observe that a small high layer can already account for the variations of β as a function of the nature of the FP, provided the low layer is treated at an ab initio level to describe properly the effects of key H-bonds. Then, for semiquantitative reproduction of the experimental values obtained from hyper-Rayleigh scattering experiments, it is necessary to incorporate electron correlation as described at the second-order Møller-Plesset perturbation theory (MP2) level as well as implicit solvent effects accounted for using the polarizable continuum model (PCM). This led us to define the MP2/6-31+G(d):HF/6-31+G(d)/IEFPCM scheme as an efficient ONIOM approach and the MP2/6-31+G(d):HF/6-31G(d)/IEFPCM as a better compromise between accuracy and computational needs. Using these methods, we demonstrate that many parameters play a role on the β response of FPs, including the length of the π-conjugated segment, the variation of the bond length alternation, and the presence of π-stacking interactions. Then, noticing the small diversity of the FP chromophores, these results highlight the key role of the β-barrel and surrounding residues on β, not only because they can locally break the noncentrosymmetry vital to a β response but also because it can impose geometrical constraints on the chromophore.

Low energy isomers of (H{sub 2}O){sub 25} from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in, E-mail: sotiris.xantheas@pnnl.gov; Rakshit, Avijit

2014-10-28

We report new global minimum candidate structures for the (H{sub 2}O){sub 25} cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2more » level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H{sub 2}O){sub 25} cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.« less

MpAMT1;2 from Marchantia polymorpha is a High-Affinity, Plasma Membrane Ammonium Transporter.

PubMed

Guo, Hanqing; Wang, Nu; McDonald, Tami R; Reinders, Anke; Ward, John M

2018-05-01

Plant ammonium transporters in the AMT/MEP/Rh (ammonium transporter/methylammonium and ammonium permease/Rhesus factor) superfamily have only been previously characterized in flowering plants (angiosperms). Plant AMT1s are electrogenic, while plant AMT2s are electroneutral, and MEP and Rh transporters in other organisms are electroneutral. We analyzed the transport function of MpAMT1;2 from the basal land plant Marchantia polymorpha, a liverwort. MpAMT1;2 was shown to localize to the plasma membrane in Marchantia gametophyte thallus by stable transformation using a C-terminal citrine fusion. MpAMT1;2 expression was studied using quantitative real-time PCR and shown to be higher when plants were N deficient and lower when plants were grown on media containing ammonium, nitrate or the amino acid glutamine. Expression in Xenopus oocytes and analysis by electrophysiology revealed that MpAMT1;2 is an electrogenic ammonium transporter with a very high affinity for ammonium (7 µM at pH 5.6 and a membrane potential of -137 mV). A conserved inhibitory phosphorylation site identified in angiosperm AMT1s is also present in all AMT1s in Marchantia. Here we show that a phosphomimetic mutation T475D in MpAMT1;2 completely inhibits ammonium transport activity. The results indicate that MpAMT1;2 may be important for ammonium uptake into cells in the Marchantia thallus.

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 10 : OR\\0x2010217 NB ramp flow & ML speed-flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ramp flow and ML speed-flow plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2....

Prescription Drug Abuse - Multiple Languages

MedlinePlus

... Spanish) PDF The basics - Opioids, part 1 - English MP3 The basics - Opioids, part 1 - español (Spanish) MP3 The basics - Opioids, part 1 - English MP4 The ... español (Spanish) PDF Pain - Opioids, part 2 - English MP3 Pain - Opioids, part 2 - español (Spanish) MP3 Pain - ...

Comparative pharmacokinetics of (S)-MP3950, a novel 5-HT4 receptor agonist, in normal and atropine-induced gastrointestinal motility disorders rats.

PubMed

Wang, Binjie; Sun, Xiaoyang; Wang, Shixiao; Guo, Ping; Li, Shujuan; Zhang, Meiyu; Zhao, Longshan; Chen, Xiaohui

2018-08-01

1. (S)-MP3950 is the (S)-enantiomer of active metabolite of mosapride, which exhibits higher 5-HT 4 receptor agonistic effect than mosapride. It shows promise to become a novel drug candidate for the treatment of gastrointestinal motility disorders (GMDs). However, the pharmacokinetic behavior of (S)-MP3950 in the pathological state of GMDs remains unclear. Herein, we investigated the comparative pharmacokinetics of (S)-MP3950 in normal and GMDs rats. 2. The comparative pharmacokinetics of (S)-MP3950 in normal and atropine-induced GMD rats were studied by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The validated UPLC-MS/MS method was successfully applied to investigate the pharmacokinetic profiles of (S)-MP3950 in normal and atropine-induced GMDs rats. Results showed that comparing to normal rats, C max reduced by 73.8%, AUC 0-t decreased by 57.6% and AUC 0-∞ declined by 56.8% in model rats. Additionally, the elimination half-life (t 1/2 ) and T max were prolonged slightly. 3. The pharmacokinetic results demonstrated that the atropine-induced GMDs reduced the absorption of (S)-MP3950. The pharmacokinetics research in the pathological state might provide more useful information for further study of novel gastric motility candidates.

Improvement of aqueous solubility and rectal absorption of 6-mercaptopurine by addition of sodium benzoate.

PubMed

Takeichi, Y; Kimura, T

1994-10-01

The solubility of 6-mercaptopurine (6-MP) in water increased as the concentration of sodium benzoate or sodium hippurate in the solution increased. The solubility of 6-MP in 20% (w/v) sodium benzoate or sodium hippurate solution was about 6-fold larger than that of 6-MP alone. The stability constant of the soluble complex of 6-MP with sodium benzoate was estimated to be 2-8 M-1 from (1) phase-solubility study and (2) analysis of chemical shifts observed in 1H-NMR. Partition of 6-MP from the saturated solution to n-octanol was also greatly increased by the addition of sodium benzoate or sodium hippurate, the degree being less in the latter. Administration of 6-MP with 20% (w/v) sodium benzoate to rat rectum resulted in enhanced absorption and the area under the plasma concentration-time curve was comparable to that obtained by intravenous administration (bioavailability = 100%), while the bioavailability after intrarectal administration of 6-MP with 20% (w/v) sodium hippurate was only 9%. The reason for the difference was discussed.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

NASA Astrophysics Data System (ADS)

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-01

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution time/parallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f , (e.g. Verlet algorithm) is available to propagate the system from time ti (trajectory positions and velocities xi = (ri; vi)) to time ti+1 (xi+1) by xi+1 = fi(xi), the dynamics problem spanning an interval from t0 : : : tM can be transformed into a root finding problem, F(X) = [xi - f (x(i-1)]i=1;M = 0, for the trajectory variables. The root finding problem is solved using amore » variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton optimization schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed and the effectiveness of various approaches to solving the root finding problem are tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl+4H2O AIMD simulation at the MP2 level. The maximum speedup obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow TCP/IP networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl+4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. By using these algorithms we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 seconds per time step to 6.9 seconds per time step.« less

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

PubMed

Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Hydration behavior of magnesium potassium phosphate cement and stability analysis of its hydration products through thermodynamic modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Tao; Chen, Huisu; Li, Xiangyu

Magnesium potassium phosphate cement (MKPC) is normally applied in civil engineering because of its short setting time and superior mechanical properties. This study investigates the hydration behavior and hydration products of MKPC influenced by molar ratio between magnesia and phosphate (M/P ratio) through thermodynamic method. Results show that the composition of ultimate hydration products are controlled by concentration of KH{sub 2}PO{sub 4} and MgO, activity of water and pH value of solution. When M/P ratio is lower than 0.64, the hydration product is MgHPO{sub 4}·3H{sub 2}O; When M/P ratio is between 0.64 and 0.67, the hydration products are MgHPO{sub 4}·3H{submore » 2}O and Mg{sub 2}KH(PO{sub 4}){sub 2}·15H{sub 2}O. When M/P ratio is between 0.67 and 1.00, hydration products are Mg{sub 2}KH(PO{sub 4}){sub 2}·15H{sub 2}O and KMgPO{sub 4}·6H{sub 2}O; When M/P ratio is higher than 1.00, the hydration product is KMgPO{sub 4}·6H{sub 2}O together with unreacted MgO. This study also investigated the effect of additives, namely B(OH){sub 3}, H{sub 3}PO{sub 4}, K{sub 2}HPO{sub 4} and KH{sub 2}PO{sub 4}. - Highlights: • A database particularly for MKPC system at 25°C, 0.1 MPa was established and verified. • The pH value corresponding to specific M/P ratio in MKPC system is successfully predicted at 25°C, 0.1 MPa. • The composition of hydration products influenced by M/P ratio and some additives is successfully predicted at 25°C, 0.1 MPa.« less

Morphology and kinetics of the formation of polyamide benzimidazole in N-methylpyrrolidone

NASA Astrophysics Data System (ADS)

Khanchich, O. A.; Larionov, V. B.; Biryukov, A. L.

2018-02-01

Polymerization-optical methods were used to study the supermolecular structure in the gelation of systems based on polyamidobenzimidazole (PABI) in N-methylpyrrolidone (N-MP) and the kinetics of phase transformations during polymer coagulation from a the solution. It was found that the use of N-MP leads to the appearance in the PABI-N-MP-H2O system of spherulites having a structure characteristic of LC structures. It is shown that the alternation of metastable structures upon gelation of the PABY - N-MP-H2O system is consistent with the appearance of the LC phase of the cholesteric type.

The accuracy of quantum chemical methods for large noncovalent complexes

PubMed Central

Pitoňák, Michal; Řezáč, Jan; Pulay, Peter

2013-01-01

We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable “accuracy/cost” ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent. PMID:24098094

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Azathioprine suppresses the mixed lymphocyte reaction of patients with Lesch-Nyhan syndrome.

PubMed Central

Szawlowski, P W; Al-Safi, S A; Dooley, T; Maddocks, J L

1985-01-01

The mixed lymphocyte reaction of Lesch-Nyhan patients (HGPRT deficient) was used to study the immunosuppressive effects of azathioprine and 6-mercaptopurine (6-MP). Mitogen stimulated lymphocytes of these patients are highly resistant to azathioprine and 6-MP. When both stimulator and responder lymphocytes in the MLR were HGPRT deficient, azathioprine (36 microM) was much more inhibitory than 6-MP (100 microM). Azathioprine produced inhibition of 98.2% and 78.5% compared with the values of 63.9% and 30.6% for 6-MP. The difference in inhibitory activity between azathioprine and 6-MP was reduced when normal stimulator lymphocytes were cultured with HGPRT deficient responder lymphocytes in the MLR. These results provide very strong evidence that the nucleotide metabolites of azathioprine and 6-MP are unnecessary for immunosuppression. They also suggest that azathioprine and 6-MP interfere with antigenic triggering of the MLR. PMID:2934083

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

NASA Astrophysics Data System (ADS)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 8 : OR\\0x2010217 NB ML speed\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML speed-occupancy plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-21...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 7 : OR\\0x2010217 NB ML speed\\0x2010flow plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML speed-flow plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-217 NB,...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 9 : OR\\0x2010217 NB ML flow\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various ML flow occupancy plots: OR-217 NB, 72nd MP 6.61; OR-217 NB, 99W-EB MP 5.9; OR-217 NB, 99W-WB MP 5.85; OR-217 NB, Greenburg MP 4.65; OR-217 NB, Scholls MP 3.85; OR-217 NB, Denney MP 2.68; OR-217 NB, Allen MP 2.16; OR-217...

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.

PubMed

Pitonák, M; Neogrády, P; Hobza, P

2010-02-14

Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.

Structural evolution of the [(CO2)n(H2O)]- cluster anions: quantifying the effect of hydration on the excess charge accommodation motif.

PubMed

Muraoka, Azusa; Inokuchi, Yoshiya; Hammer, Nathan I; Shin, Joong-Won; Johnson, Mark A; Nagata, Takashi

2009-08-06

The [(CO2)n(H2O)]- cluster anions are studied using infrared photodissociation (IPD) spectroscopy in the 2800-3800 cm(-1) range. The observed IPD spectra display a drastic change in the vibrational band features at n = 4, indicating a sharp discontinuity in the structural evolution of the monohydrated cluster anions. The n = 2 and 3 spectra are composed of a series of sharp bands around 3600 cm(-1), which are assignable to the stretching vibrations of H2O bound to C2O4- in a double ionic hydrogen-bonding (DIHB) configuration, as was previously discussed (J. Chem. Phys. 2005, 122, 094303). In the n > or = 4 spectrum, a pair of intense bands additionally appears at approximately 3300 cm(-1). With the aid of ab initio calculations at the MP2/6-31+G* level, the 3300 cm(-1) bands are assigned to the bending overtone and the hydrogen-bonded OH vibration of H2O bound to CO2- via a single O-H...O linkage. Thus, the structures of [(CO2)n(H2O)]- evolve with cluster size such that DIHB to C2O4- is favored in the smaller clusters with n = 2 and 3 whereas CO2- is preferentially stabilized via the formation of a single ionic hydrogen-bonding (SIHB) configuration in the larger clusters with n > or = 4.

Mechanical perturbation-induced ethylene releases apical dominance in Pharbitis nil by restricting shoot growth

NASA Technical Reports Server (NTRS)

Prasad, T. K.; Cline, M. G.

1985-01-01

Mechanical perturbation (MP, rubbing) or internodes of Pharbitis nil shoots initiates release of lateral buds (LB) from apical dominance within 48 h. Evidence is presented which suggests that MP promotion of LB outgrowth is mediated by ethylene-induced restriction of main shoot growth. Ethylene production in the internodes is stimulated by MP within 2 h. Effects of MP are mimicked by treatments with 1-aminocyclopropane-1-carboxylic acid (ACC) and are negated by the inhibitors of ethylene production or action, aminoethoxy vinylglycine (AVG) and AgNO3. The fact that effects of MP, ACC, and ethylene inhibitors are observed to occur on main shoot growth at least 24 h before they are observed to occur on LB growth suggests a possible cause and effect relationship. MP also causes an increase in internode diameter. MP stimulation of ethylene production appears to be mediated by ACC synthase. The results of this study and our previous studies suggest that apical dominance may be released by any mechanism which induces ethylene restriction of main shoot growth.

Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study.

PubMed

Kołaski, Maciej; Zakharenko, Aleksey A; Karthikeyan, S; Kim, Kwang S

2011-10-11

We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The -OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (ΔEe/ΔE0) interaction energies and the enthalpies/free energies (ΔHr/ΔGr at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (HmXOn where X = B/N/P/Cl/Br/I, m = 1-3, and n = 0-4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X(+)···O(-) electrostatic interactions are important.

Structure, vibrational spectrum, and ring puckering barrier of cyclobutane.

PubMed

Blake, Thomas A; Xantheas, Sotiris S

2006-09-07

We present the results of high level ab initio calculations for the structure, harmonic and anharmonic spectroscopic constants, and ring puckering barrier of cyclobutane (C4H8) in an effort to establish the minimum theoretical requirements needed for their accurate description. We have found that accurate estimates for the barrier between the minimum (D(2d)) and transition state (D(4h)) configurations require both higher levels of electron correlation [MP4, CCSD(T)] and orbital basis sets of quadruple-zeta quality or larger. By performing CCSD(T) calculations with basis sets as large as cc-pV5Z, we were able to obtain, for the first time, a value for the puckering barrier that lies within 10 cm(-1) (or 2%) from experiment, whereas the best previously calculated values were in errors exceeding 40% of experiment. Our best estimate of 498 cm(-1) for the puckering barrier is within 10 cm(-1) of the experimental value proposed originally, but it lies approximately 50 cm(-1) higher than the revisited value, which was obtained more recently using different assumptions regarding the coupling between the various modes. It is therefore suggested that revisiting the analysis of the experimental data might be warranted. Our best computed values (at the CCSD(T)/aug-cc-pVTZ level of theory) for the equilibrium structural parameters of C4H8 are r(C-C) = 1.554 A, r(C-H(alpha)) = 1.093 A, r(C-H(beta)) = 1.091 A, phi(C-C-C) = 88.1 degrees , alpha(H(alpha)-C-H(beta)) = 109.15 degrees , and theta = 29.68 degrees for the puckering angle. We have found that the puckering angle theta is more sensitive to the level of electron correlation than to the size of the basis set for a given method. We furthermore present anharmonic calculations that are based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structure. We have found that the anharmonic calculations predict the experimentally measured fundamental band origins within 1% (< or =30 cm(-1)) for most vibrations. The results of the current study can serve as a guide for future calculations on the substituted four-member ring hydrocarbon compounds. To this end we present a method for estimating the puckering barrier height at higher levels of electron correlation [MP4, CCSD(T)] from the MP2 results that can be used in chemically similar compounds.

A comparative study of the infrared and Raman spectra of aniline and o-, m-, p-phenylenediamine isomers.

PubMed

Badawi, Hassan M; Förner, Wolfgang; Ali, Shaikh A

2013-08-01

The structural stabilities of o-, m- and p-phenylenediamine (PDA) isomers were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311G(**) basis set. From the calculations the three isomers were predicted to exist predominantly in an anti (transoid) structure. In the o-isomer, the syn (cisoid) form is calculated to turn to the anti (transoid) form with the two HNCC torsional angles of about 44 and 10° and the NH2 inversion barrier of 3-4 kcal/mol. The CCNH torsional angles in the m-PDA and p-PDA isomers were calculated to be about 25-26° as compared to 20° in aniline. A comparison of the Raman spectra of the three PDA-s with those of aniline shows the high sensitivity of the ring breathing mode to the nature of substituents in the aniline ring. The vibrational wavenumbers were computed at the DFT-B3LYP for aniline and the o-, m- and p-PDA isomers for the purpose of comparison. Complete vibrational assignments were made on the basis of normal coordinate analyses and potential energy distributions for aniline and the o-, m- and p-PDA molecules. Copyright © 2013 Elsevier B.V. All rights reserved.

Alkaline hydrolysis of ethylene phosphate: an ab initio study by supermolecule model and polarizable continuum approach.

PubMed

Xia, Futing; Zhu, Hua

2011-09-01

The alkaline hydrolysis reaction of ethylene phosphate (EP) has been investigated using a supermolecule model, in which several explicit water molecules are included. The structures and single-point energies for all of the stationary points are calculated in the gas phase and in solution at the B3LYP/6-31++G(df,p) and MP2/6-311++G(df,2p) levels. The effect of water bulk solvent is introduced by the polarizable continuum model (PCM). Water attack and hydroxide attack pathways are taken into account for the alkaline hydrolysis of EP. An associative mechanism is observed for both of the two pathways with a kinetically insignificant intermediate. The water attack pathway involves a water molecule attacking and a proton transfer from the attacking water to the hydroxide in the first step, followed by an endocyclic bond cleavage to the leaving group. While in the first step of the hydroxide attack pathway the nucleophile is the hydroxide anion. The calculated barriers in aqueous solution for the water attack and hydroxide attack pathways are all about 22 kcal/mol. The excellent agreement between the calculated and observed values demonstrates that both of the two pathways are possible for the alkaline hydrolysis of EP. Copyright © 2011 Wiley Periodicals, Inc.

Effect of TiO 2 particle size and layer thickness on mesoscopic perovskite solar cells

DOE PAGES

Lee, Dong Geon; Kim, Min-cheol; Kim, Byeong Jo; ...

2017-11-16

Mesoporous TiO 2 (mp-TiO 2) layers are commonly used as electron transport layers in perovskite solar cells, which help to extract electrons from the perovskite light-absorbing layer and transport them to the electrodes. We investigated the effects of the layer thickness of mp-TiO 2 and particle size of TiO 2 on photovoltaic properties, in terms of the surface area of the mp-layer and the interfacial areas of the TiO 2 nanoparticles in the mp-layer. Various mp-TiO 2 layers with thicknesses of 150, 250, and 400 nm and particle sizes of 25 nm and 41 nm were prepared to compare themore » photovoltaic properties of such layer-containing perovskite solar cells. Time-resolved photoluminescence decay and impedance studies showed that interfacial resistance as well as perovskite-to-TiO 2 charge injection are important factors affecting photovoltaic performance. The deterioration of the photovoltaic parameters with increasing TiO 2/TiO 2 interfacial area also confirms that the interfacial series resistance that arises from these connections should be reduced to enhance the performance of mesoscopic perovskite solar cells.« less

Effect of TiO 2 particle size and layer thickness on mesoscopic perovskite solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Dong Geon; Kim, Min-cheol; Kim, Byeong Jo

Mesoporous TiO 2 (mp-TiO 2) layers are commonly used as electron transport layers in perovskite solar cells, which help to extract electrons from the perovskite light-absorbing layer and transport them to the electrodes. We investigated the effects of the layer thickness of mp-TiO 2 and particle size of TiO 2 on photovoltaic properties, in terms of the surface area of the mp-layer and the interfacial areas of the TiO 2 nanoparticles in the mp-layer. Various mp-TiO 2 layers with thicknesses of 150, 250, and 400 nm and particle sizes of 25 nm and 41 nm were prepared to compare themore » photovoltaic properties of such layer-containing perovskite solar cells. Time-resolved photoluminescence decay and impedance studies showed that interfacial resistance as well as perovskite-to-TiO 2 charge injection are important factors affecting photovoltaic performance. The deterioration of the photovoltaic parameters with increasing TiO 2/TiO 2 interfacial area also confirms that the interfacial series resistance that arises from these connections should be reduced to enhance the performance of mesoscopic perovskite solar cells.« less

Synthesis of Potential Prophylactic Agents Against Cyanide Intoxication

DTIC Science & Technology

1993-05-06

34/21) S 2,6-C 2 Ad 72 mp 139" CsH3C12NO 163 (lie mp 139.5-140.5") 6 4-OMe A 45 Mp 73-79e CH 7N0% (lit t mp 73-741) 7 2-OMe A 50 Mp 66" C*HNO 126 (litf...Form. Found cation. Compd. No. Reactants Yield, % Mp, *C (cation.anion) %C %H %N anion Part A. 1 -Alkoxypyridinium salts. 14 2,3-Mes, 87 120-122 CH ...111 + 4(C6H6CVs O, 28.62 3.22 4.40 ..... (MeO)2SO2 _OSO 2 CH s ) is 4-OMe,6 + 78 46-48 CSH 121NO 2 34.18 4.30 4.91 154, 126 Ed (CsH12NO2-) 34.02

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

PubMed

Lonsdale, Richard; Hoyle, Simon; Grey, Daniel T; Ridder, Lars; Mulholland, Adrian J

2012-02-28

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.

Diagnostic accuracy of frozen-section analysis of cancer-containing bladder transurethral resection specimens for the presence of muscularis propria invasion.

PubMed

Goyal, Rajen; Zhu, Bing; Parimi, Vamsi; Lin, Xiaoqi; Rohan, Stephen M

2014-07-01

Frozen section (FS) consultation is generally an accurate diagnostic modality. At our institution, we are frequently asked to assess transurethral resection specimens (TURBT) at FS for muscularis propria (MP) invasion by carcinoma. This study documents our experience in evaluating cancer-containing TURBT specimens at FS for MP invasion. 32 TURBT sent for FS from 2008-2010 were identified. The FS and permanent section (PS) diagnoses were reviewed. Cases excluded from the calculation of test performance included: (1) cases without cancer on FS or PS slides, (2) FS diagnosis deferred, (3) cases without MP on FS and subsequent PS slides. Sensitivity (SEN), specificity (SPEC), positive predictive value (PPV), and negative predictive value (NPV) for identifying MP invasion at FS were calculated. In 6 cases, no cancer was present in FS or PS slides (18%). The FS diagnosis was deferred on 3 cases (9%). In one case (3%) MP was not present in the FS or the subsequent PS slides. Of the remaining 22 cases, 2 false positive and 6 false negative diagnoses of MP invasion were identified. The test performance for FS assessment of MP invasion in TURB were SEN=33%, SPEC=84%, PPV=60%, and NPV=64%. Identifying MP invasion on PS can be difficult, and our results suggest that this is more difficult at FS. Though this study is based on small numbers, our results point to the conclusion that examination of TURBT specimens for MP invasion is best done on PS. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Spectra and structure of organophosphorus compounds. LI. IR and Raman spectra, conformational stability, barriers to internal rotation, vibrational assignment, and ab initio calculations of n-propylphosphine

NASA Astrophysics Data System (ADS)

Durig, J. R.; Gounev, T. K.; Lee, M. S.; Little, T. S.

1994-10-01

The Raman (3100 to 50 cm -1) and IR (3100 to 50 cm -1) spectra of gaseous and solid n-propylphosphine, C 3H 7PH 2, and the corresponding P- d2 isotopomer have been recorded. Additionally, the Raman spectra of the liquids have been obtained with qualitative depolarization ratios. From these data, all five possible conformers have been identified in the fluid states and the trans-trans conformer is shown to be the most stable rotamer in both the gaseous and liquid states and it is the only conformer present in the solid. The first trans refers to the orientation of the lone pair to the ethylene group (rotation around the PC bond) whereas the second trans refers to the orientation of the methyl group relative to the PC bond (rotation around the -CH 2CH 2 bond). The next most stable conformer is the gauche-trans rotamer where the enthalpy difference has been determined from variable-temperature Raman studies to be 140 ± 5 cm -1 (400 ± 14 cal mol -1) for the vapor and 351 ± 20 cm -1 (1004 ± 57 cal mol -1) for the liquid. The other three conformers have nearly the same stabilities but significantly higher energies than the two more stable rotamers. From the far-IR data and relative conformer stabilities, some of the coefficients of the potential function governing conformer interconversion are estimated. A complete vibrational assignment is proposed for the trans-trans conformer and for the fundamentals for most of the heavy atom motions for the other conformers. The conformational stabilities, barriers to internal rotation, and fundamental vibrational frequencies which have been determined experimentally are compared to those obtained from ab initio calculations employing the RHF/3-21G* and/or RHF/6-31G* basis sets. Additionally, the conformational stabilities and structural parameters have been determined with the 6-31G* basis set with electron correlation at the MP2 level. These results are compared with the corresponding quantities for some similar molecules.

Unexpected Decrease in Milk Production after Fenbendazole Treatment of Dairy Cows during Early Grazing Season

PubMed Central

Ravinet, Nadine; Chartier, Christophe; Bareille, Nathalie; Lehebel, Anne; Ponnau, Adeline; Brisseau, Nadine; Chauvin, Alain

2016-01-01

Gastrointestinal nematodes (GIN) infection can impair milk production (MP) in dairy cows. To investigate whether MP would be optimized by spring targeted-selective anthelmintic treatment in grazing cows, we assessed (1) the effect on MP of an anthelmintic treatment applied 1.5 to 2 months after turn-out, and (2) herd and individual indicators associated with the post-treatment MP response. A randomized controlled clinical trial was conducted in 13 dairy farms (578 cows) in western France in spring 2012. In each herd, lactating cows of the treatment group received fenbendazole orally, control cows remained untreated. Daily cow MP was recorded from 2 weeks before until 15 weeks after treatment. Individual serum pepsinogen and anti-Ostertagia antibody levels (expressed as ODR), faecal egg count and bulk tank milk (BTM) Ostertagia ODR were measured at treatment time. Anthelmintic treatment applied during the previous housing period was recorded for each cow. In each herd, information regarding heifers’ grazing and anthelmintic treatment history was collected to assess the Time of Effective Contact (TEC, in months) with GIN infective larvae before the first calving. The effect of treatment on weekly MP averages and its relationships with herd and individual indicators were studied using linear mixed models with two nested random effects (cow within herd). Unexpectedly, spring treatment had a significant detrimental effect on MP (-0.92 kg/cow/day on average). This negative MP response was particularly marked in high producing cows, in cows not treated during the previous housing period or with high pepsinogen levels, and in cows from herds with a high TEC or a high BTM ODR. This post-treatment decrease in MP may be associated with immuno-inflammatory mechanisms. Until further studies can assess whether this unexpected result can be generalized, non-persistent treatment of immunized adult dairy cows against GIN should not be recommended in early grazing season. PMID:26808824

Unexpected Decrease in Milk Production after Fenbendazole Treatment of Dairy Cows during Early Grazing Season.

PubMed

Ravinet, Nadine; Chartier, Christophe; Bareille, Nathalie; Lehebel, Anne; Ponnau, Adeline; Brisseau, Nadine; Chauvin, Alain

2016-01-01

Gastrointestinal nematodes (GIN) infection can impair milk production (MP) in dairy cows. To investigate whether MP would be optimized by spring targeted-selective anthelmintic treatment in grazing cows, we assessed (1) the effect on MP of an anthelmintic treatment applied 1.5 to 2 months after turn-out, and (2) herd and individual indicators associated with the post-treatment MP response. A randomized controlled clinical trial was conducted in 13 dairy farms (578 cows) in western France in spring 2012. In each herd, lactating cows of the treatment group received fenbendazole orally, control cows remained untreated. Daily cow MP was recorded from 2 weeks before until 15 weeks after treatment. Individual serum pepsinogen and anti-Ostertagia antibody levels (expressed as ODR), faecal egg count and bulk tank milk (BTM) Ostertagia ODR were measured at treatment time. Anthelmintic treatment applied during the previous housing period was recorded for each cow. In each herd, information regarding heifers' grazing and anthelmintic treatment history was collected to assess the Time of Effective Contact (TEC, in months) with GIN infective larvae before the first calving. The effect of treatment on weekly MP averages and its relationships with herd and individual indicators were studied using linear mixed models with two nested random effects (cow within herd). Unexpectedly, spring treatment had a significant detrimental effect on MP (-0.92 kg/cow/day on average). This negative MP response was particularly marked in high producing cows, in cows not treated during the previous housing period or with high pepsinogen levels, and in cows from herds with a high TEC or a high BTM ODR. This post-treatment decrease in MP may be associated with immuno-inflammatory mechanisms. Until further studies can assess whether this unexpected result can be generalized, non-persistent treatment of immunized adult dairy cows against GIN should not be recommended in early grazing season.

α-Methylprednisolone conjugated cyclodextrin polymer-based nanoparticles for rheumatoid arthritis therapy

PubMed Central

Hwang, Jungyeon; Rodgers, Kathleen; Oliver, James C; Schluep, Thomas

2008-01-01

A glycinate derivative of α-methylprednisolone (MP) was prepared and conjugated to a linear cyclodextrin polymer (CDP) with a loading of 12.4% w/w. The polymer conjugate (CDP-MP) self-assembled into nanoparticles with a size of 27 nm. Release kinetics of MP from the polymer conjugate showed a half-life (t1/2) of 50 h in phosphate buffer solution (PBS) and 19 h in human plasma. In vitro, the proliferation of human lymphocytes was suppressed to a similar extent but with a delayed effect when CDP-MP was compared with free MP. In vivo, CDP-MP was administered intravenously to mice with collagen-induced arthritis and compared with free MP. CDP-MP was administered weekly for six weeks (0.07, 0.7, and 7 mg/kg/week) and MP was administered daily for six weeks (0.01, 0.1, and 1 mg/kg/day). Body weight changes were minimal in all animals. After 28 days, a significant decrease in arthritis score was observed in animals treated weekly with an intermediate or high dose of CDP-MP. Additionally, dorsoplantar swelling was reduced to baseline in animals treated with CDP-MP at the intermediate and high dose level. Histological evaluation showed a reduction in synovitis, pannus formation and disruption of architecture at the highest dose level of CDP-MP. MP administered daily at equivalent cumulative doses showed minimal efficacy in this model. This study demonstrates that conjugation of MP to a cyclodextrin-polymer may improve its efficacy, leading to lower doses and less frequent administration for a safer and more convenient management of rheumatoid arthritis. PMID:18990945

A method to assess the migration properties of cell-derived microparticles within a living tissue.

PubMed

Hoang, Thang Q; Rampon, Christine; Freyssinet, Jean-Marie; Vriz, Sophie; Kerbiriou-Nabias, Danièle

2011-09-01

Cells undergoing activation or apoptosis exhibit plasma membrane changes, leading to the formation of shed vesicles (microparticles, MP). Although their effects on recipient cells in vitro, and their ability to support inflammatory or thrombotic events in the circulation have been studied, the spreading of such vesicles in tissues is still elusive. Our aim was to set up a method to examine the behavior of these vesicles in vivo. We examined the persistence of green-fluorescent microparticles (fMP), prepared after Ca2+ ionophore activation (iono-fMP) or apoptogenic treatment (eto-fMP) of human Jurkat T lymphoblastic or non-hematopoietic embryonic kidney (HEK) cell lines, following injection in zebrafish embryos 2h after egg fertilization. One hour post-injection, iono-fMP issued from both cell types formed a fluorescent dispersal in the intercellular space of embryos. In contrast, eto-fMP or MP deprived of sialic acid at their membrane, gathered together at the site of injection. We propose a method characterizing the abilities of MP to spread in the intercellular space. We showed that MP produced by apoptosis of T cells and those deprived of sialic acid at their membrane do not diffuse within the living cells. On the contrary, MP shed upon calcium induced activation of T and HEK cells, diffuse at a distance and spread in the intercellular space. The fate of injected MP relies on the type of induction rather than the cell species and results provide a model to test the ability of vesicles to interact locally or to spread outside of the site of production. Copyright © 2011 Elsevier B.V. All rights reserved.

Laplace-transformed atomic orbital-based Møller–Plesset perturbation theory for relativistic two-component Hamiltonians

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helmich-Paris, Benjamin, E-mail: b.helmichparis@vu.nl; Visscher, Lucas, E-mail: l.visscher@vu.nl; Repisky, Michal, E-mail: michal.repisky@uit.no

2016-07-07

We present a formulation of Laplace-transformed atomic orbital-based second-order Møller–Plesset perturbation theory (MP2) energies for two-component Hamiltonians in the Kramers-restricted formalism. This low-order scaling technique can be used to enable correlated relativistic calculations for large molecular systems. We show that the working equations to compute the relativistic MP2 energy differ by merely a change of algebra (quaternion instead of real) from their non-relativistic counterparts. With a proof-of-principle implementation we study the effect of the nuclear charge on the magnitude of half-transformed integrals and show that for light elements spin-free and spin-orbit MP2 energies are almost identical. Furthermore, we investigate themore » effect of separation of charge distributions on the Coulomb and exchange energy contributions, which show the same long-range decay with the inter-electronic/atomic distance as for non-relativistic MP2. A linearly scaling implementation is possible if the proper distance behavior is introduced to the quaternion Schwarz-type estimates as for non-relativistic MP2.« less

Pharmacokinetics and Safety of MP-376 (Levofloxacin Inhalation Solution) in Cystic Fibrosis Subjects▿

PubMed Central

Geller, David E.; Flume, Patrick A.; Griffith, David C.; Morgan, Elizabeth; White, Dan; Loutit, Jeffery S.; Dudley, Michael N.

2011-01-01

The pharmacokinetics and tolerability of nebulized MP-376 (levofloxacin inhalation solution [Aeroquin]) were determined in cystic fibrosis (CF) subjects. Ten CF subjects received single 180-mg doses of two formulations of MP-376, followed by a multiple-dose phase of 240 mg once daily for 7 days. Serum and expectorated-sputum samples were assayed for levofloxacin content. Safety was evaluated following the single- and multiple-dose study phases. Nebulized MP-376 produced high concentrations of levofloxacin in sputum. The mean maximum plasma concentration (Cmax) ranged between 2,563 and 2,932 mg/liter for 180-mg doses of the 50- and 100-mg/ml formulations, respectively. After 7 days of dosing, the mean Cmax for the 240-mg dose was 4,691 mg/liter. The mean serum levofloxacin Cmax ranged between 0.95 and 1.28 for the 180-mg doses and was 1.71 for the 240-mg dose. MP-376 was well tolerated. Nebulized MP-376 produces high sputum and low serum levofloxacin concentrations. The pharmacokinetics, safety, and tolerability were similar for the two formulations. MP-376 240 mg (100 mg/ml) is being advanced into late-stage clinical development. PMID:21444699

Incidence of tinnitus in mp3 player users.

PubMed

Figueiredo, Ricardo Rodrigues; Azevedo, Andreia Aparecida de; Oliveira, Patrícia Mello de; Amorim, Sandro Pereira Vasconcellos; Rios, Artur Guedes; Baptista, Vanderlei

2011-06-01

Exposure to loud noise is one of the main causes of tinnitus. To analyze the incidence of tinnitus in mp3 player users and non-users. One hundred subjects aged from 15 to 30 years were enrolled, 54 of them were regular mp3 player users and 46 were not. Patients with continuous tinnitus for at least 6 months completed the Tinnitus Handicap Inventory (THI) and were tested with high frequency audiometry and transient-evoked otoacoustic emissions (TAOE). A cross-sectional cohort study. The incidence of tinnitus in non-users was about 8 %; in mp3 player users it was about 28 %, a statistically significant difference. Hearing thresholds at 8 kHz were significantly higher in tinnitus patients that used mp3 portable players.TAOE were reduced at 2 kHz in the users group. No statistically significant difference was found in the THI scores between the two groups. Tinnitus was more frequent in teenagers and young adults who regularly listen to mp3 music in players. Moreover, the incidence of tinnitus among mp3 player users was associated with higher hearing thresholds at 8 kHz and lower TOAE at 2 kHz.

Ion Bernstein instability dependence on the proton-to-electron mass ratio: Linear dispersion theory

NASA Astrophysics Data System (ADS)

Min, Kyungguk; Liu, Kaijun

2016-07-01

Fast magnetosonic waves, which have as their source ion Bernstein instabilities driven by tenuous ring-like proton velocity distributions, are frequently observed in the inner magnetosphere. One major difficulty in the simulation of these waves is that they are excited in a wide frequency range with discrete harmonic nature and require time-consuming computations. To overcome this difficulty, recent simulation studies assumed a reduced proton-to-electron mass ratio, mp/me, and a reduced light-to-Alfvén speed ratio, c/vA, to reduce the number of unstable modes and, therefore, computational costs. Although these studies argued that the physics of wave-particle interactions would essentially remain the same, detailed investigation of the effect of this reduced system on the excited waves has not been done. In this study, we investigate how the complex frequency, ω = ωr+iγ, of the ion Bernstein modes varies with mp/me for a sufficiently large c/vA (such that ωpe2/Ωe2≡(me/mp)(c/vA)2≫1) using linear dispersion theory assuming two different types of energetic proton velocity distributions, namely, ring and shell. The results show that low- and high-frequency harmonic modes respond differently to the change of mp/me. For the low harmonic modes (i.e., ωr˜Ωp), both ωr/Ωp and γ/Ωp are roughly independent of mp/me, where Ωp is the proton cyclotron frequency. For the high harmonic modes (i.e., Ωp≪ωr≲ωlh, where ωlh is the lower hybrid frequency), γ/ωlh (at fixed ωr/ωlh) stays independent of mp/me when the parallel wave number, k∥, is sufficiently large and becomes inversely proportional to (mp/me)1/4 when k∥ goes to zero. On the other hand, the frequency range of the unstable modes normalized to ωlh remains independent of mp/me, regardless of k∥.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodríguez Guilbe, María M.; Protein Research and Development Center, University of Puerto Rico; Alfaro Malavé, Elisa C.

The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, thismore » protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.« less

Reactive oxygen species and autophagy play a role in survival and differentiation of the phytopathogen Moniliophthora perniciosa.

PubMed

Pungartnik, C; Melo, S C O; Basso, T S; Macena, W G; Cascardo, J C M; Brendel, M

2009-01-01

The hemibiotrophic basidiomycete Moniliophthora perniciosa causes "witches' broom disease" in cacao (Theobroma cacao). During plant infection, M. perniciosa changes from mono to dikaryotic life form, an event which could be triggered by changes in plant nutritional offer and plant defense molecules, i.e., from high to low content of glycerol and hydrogen peroxide. We have recently shown that in vitro glycerol induces oxidative stress resistance in dikaryotic M. perniciosa. In order to understand under which conditions in parasite-plant interaction M. perniciosa changes from intercellular monokaryotic to intracellular dikaryotic growth phase we studied the role of glycerol on mutagen-induced oxidative stress resistance of basidiospores and monokaryotic hyphae; we also studied the role of H(2)O(2) as a signaling molecule for in vitro dikaryotization and whether changes in nutritional offer by the plant could be compensated by inducible fungal autophagy. Mono-/dikaryotic glycerol or glucose-grown cells and basidiospores were exposed to the oxidative stress-inducing mutagens H(2)O(2) and Paraquat as well as to pre-dominantly DNA damaging 4-nitroquinoline-1-oxide and UVC irradiation. Basidiospores showed highest resistance to all treatments and glycerol-grown monokaryotic hyphae were more resistant than dikaryotic hyphae. Monokaryotic cells exposed to 1microM of H(2)O(2) in glycerol-media induced formation of clamp connections within 2 days while 1mM H(2)O(2) did not within a week in the same medium; no clamp connections were formed in H(2)O(2)-containing glucose media within a week. Lower concentrations of H(2)O(2) and glycerol, when occurring in parallel, are shown to be two signals for dikaryotization in vitro and may be also during the course of infection. Q-PCR studies of glycerol-grown dikaryotic cells exposed to oxidative stress (10mM H(2)O(2)) showed high expression of MpSOD2 and transient induction of ABC cytoplasmic membrane transporter gene MpYOR1 and autophagy-related gene MpATG8. Expression of a second ABC transporter gene MpSNQ2 was 14-fold induced after H(2)O(2) exposure in glucose as compared to glycerol-grown hyphae while MpYOR1 did not show strong variation of expression under similar conditions. Glucose-grown dikaryotic cells showed elevated expression of MpATG8, especially after exposure to H(2)O(2) and 4-nitroquinoline-1-oxide. During different stages preceding basidiocarp formation MpATG8 and the two catalase-encoding genes MpCTA1 and MpCTT1 were expressed continuously. We have compiled our results and literature data in a model graph, which compares the in vitro and in planta development and differentiation of M. perniciosa with the help of physiological and morphological landmarks.

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Oral 6-mercaptopurine versus oral 6-thioguanine and veno-occlusive disease in children with standard-risk acute lymphoblastic leukemia: report of the Children's Oncology Group CCG-1952 clinical trial

PubMed Central

Matloub, Yousif; Broxson, Emmett; La, Mei; Yanofsky, Rochelle; Sather, Harland; Hutchinson, Ray; Heerema, Nyla A.; Sorrell, April D.; Masterson, Margaret; Bleyer, Archie; Gaynon, Paul S.

2010-01-01

The Children's Cancer Group 1952 (CCG-1952) clinical trial studied the substitution of oral 6-thioguanine (TG) for 6-mercaptopurine (MP) and triple intrathecal therapy (ITT) for intrathecal methotrexate (IT-MTX) in the treatment of standard-risk acute lymphoblastic leukemia. After remission induction, 2027 patients were randomized to receive MP (n = 1010) or TG (n = 1017) and IT-MTX (n = 1018) or ITT (n = 1009). The results of the thiopurine comparison are as follows. The estimated 7-year event-free survival (EFS) for subjects randomized to TG was 84.1% (± 1.8%) and to MP was 79.0% (± 2.1%; P = .004 log rank), although overall survival was 91.9% (± 1.4%) and 91.2% (± 1.5%), respectively (P = .6 log rank). The TG starting dose was reduced from 60 to 50 mg/m2 per day after recognition of hepatic veno-occlusive disease (VOD). A total of 257 patients on TG (25%) developed VOD or disproportionate thrombocytopenia and switched to MP. Once portal hypertension occurred, all subjects on TG were changed to MP. The benefit of randomization to TG over MP, as measured by EFS, was evident primarily in boys who began TG at 60 mg/m2 (relative hazard rate [RHR] 0.65, P = .002). The toxicities of TG preclude its protracted use as given in this study. This study is registered at http://clinicaltrials.gov as NCT00002744. PMID:20124218

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Application of a BOSS – Gaussian Interface for QM/MM Simulations of Henry and Methyl Transfer Reactions

PubMed Central

Vilseck, Jonah Z.; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L.

2015-01-01

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with quantum mechanics alone. For several decades, semi-empirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the inter-program communication. The BOSS–Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS–Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations employing semiempirical methods. PMID:26311531

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

PubMed

Vilseck, Jonah Z; Kostal, Jakub; Tirado-Rives, Julian; Jorgensen, William L

2015-10-15

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods. © 2015 Wiley Periodicals, Inc.

Circulating microparticle levels are reduced in patients with ARDS.

PubMed

Shaver, Ciara M; Woods, Justin; Clune, Jennifer K; Grove, Brandon S; Wickersham, Nancy E; McNeil, J Brennan; Shemancik, Gregory; Ware, Lorraine B; Bastarache, Julie A

2017-05-25

It is unclear how to identify which patients at risk for acute respiratory distress syndrome (ARDS) will develop this condition during critical illness. Elevated microparticle (MP) concentrations in the airspace during ARDS are associated with activation of coagulation and in vitro studies have demonstrated that MPs contribute to acute lung injury, but the significance of MPs in the circulation during ARDS has not been well studied. The goal of the present study was to test the hypothesis that elevated levels of circulating MPs could prospectively identify critically ill patients who will develop ARDS and that elevated circulating MPs are associated with poor clinical outcomes. A total of 280 patients with platelet-poor plasma samples from the prospective Validating Acute Lung Injury biomarkers for Diagnosis (VALID) cohort study were selected for this analysis. Demographics and clinical data were obtained by chart review. MP concentrations in plasma were measured at study enrollment on intensive care unit (ICU) day 2 and on ICU day 4 by MP capture assay. Activation of coagulation was measured by plasma recalcification (clot) times. ARDS developed in 90 of 280 patients (32%) in the study. Elevated plasma MP concentrations were associated with reduced risk of developing ARDS (odds ratio (OR) 0.70 per 10 μM increase in MP concentration, 95% CI 0.50-0.98, p = 0.042), but had no significant effect on hospital mortality. MP concentration was greatest in patients with sepsis, pneumonia, or aspiration as compared with those with trauma or receiving multiple blood transfusions. MP levels did not significantly change over time. The inverse association of MP levels with ARDS development was most striking in patients with sepsis. After controlling for age, presence of sepsis, and severity of illness, higher MP concentrations were independently associated with a reduced risk of developing ARDS (OR 0.69, 95% CI 0.49-0.98, p = 0.038). MP concentration was associated with reduced plasma recalcification time. Elevated levels of circulating MPs are independently associated with a reduced risk of ARDS in critically ill patients. Whether this is due to MP effects on systemic coagulation warrants further investigation.

Multipoint to multipoint routing and wavelength assignment in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Qin, Panke; Wu, Jingru; Li, Xudong; Tang, Yongli

2018-01-01

In multi-point to multi-point (MP2MP) routing and wavelength assignment (RWA) problems, researchers usually assume the optical networks to be a single domain. However, the optical networks develop toward to multi-domain and larger scale in practice. In this context, multi-core shared tree (MST)-based MP2MP RWA are introduced problems including optimal multicast domain sequence selection, core nodes belonging in which domains and so on. In this letter, we focus on MST-based MP2MP RWA problems in multi-domain optical networks, mixed integer linear programming (MILP) formulations to optimally construct MP2MP multicast trees is presented. A heuristic algorithm base on network virtualization and weighted clustering algorithm (NV-WCA) is proposed. Simulation results show that, under different traffic patterns, the proposed algorithm achieves significant improvement on network resources occupation and multicast trees setup latency in contrast with the conventional algorithms which were proposed base on a single domain network environment.

Electric dipole (hyper)polarizabilities of selected X2Y2 and X3Y3 (X = Al, Ga, In and Y = P, As): III-V semiconductor clusters. An ab initio comparative study.

PubMed

Karamanis, Panaghiotis; Pouchan, Claude; Leszczynski, Jerzy

2008-12-25

A systematic ab initio comparative study of the (hyper)polarizabilities of selected III-V stoichiometric semiconductor clusters has been carried out. Our investigation focuses on the ground state structures of the dimers and on two dissimilar trimer configurations of aluminum, gallium, indium phosphide and arsenide. The basis set effect on both the polarizabilities and hyperpolarizabilities of the studied systems has been explicitly taken into account relying on the augmented correlation consistent aug-cc-pVnZ (n = D, T, Q, and 5) basis sets series. In addition, a rough estimation of the effects of the relativistic effects on the investigated properties is provided by extension of the study to include calculations performed with relativistic electron core potentials (or pseudopotentials). Electron correlation effects have been estimated utilizing methods of increasing predictive reliability, e.g., the Møller-Plesset many body perturbation theory and the couple cluster approach. Our results reveal that in the considered semiconductor species the Group III elements (Al, Ga, In) play a vital role on the values of their relative (hyper)polarizability. At all levels of theory employed the most hyperpolarizable clusters are the indium derivatives while the aluminum arsenide clusters also exhibit high, comparable hyperpolarizabilities. The less hyperpolarizable species are those composed of gallium and this is associated with the strong influence of the nuclear charge on the valence electrons of Ga due to the poor shielding that is provided by the semicore d electrons. In addition, the analysis of the electronic structure and the hyperpolarizability magnitudes reveals that clusters, in which their bonding is characterized by strong electron transfer from the electropositive to the electronegative atoms, are less hyperpolarizable than species in which the corresponding electron transfer is weaker. Lastly, from the methodological point of view our results point out that the hyperpolarizabilities of those species converge when an augmented triple-zeta quality basis set is used and, also, that the second order Møller-Plesset approximation (MP2) overestimates considerably their second hyperpolarizabilities with respect to the highest level of coupled cluster theory applied in this study (CCSD(T)).

Preferential inhibition of xanthine oxidase by 2-amino-6-hydroxy-8-mercaptopurine and 2-amino-6-purine thiol.

PubMed

Kalra, Sukirti; Jena, Gopabandhu; Tikoo, Kulbhushan; Mukhopadhyay, Anup Kumar

2007-05-18

The anticancer drug, 6-mercaptopurine (6MP) is subjected to metabolic clearance through xanthine oxidase (XOD) mediated hydroxylation, producing 6-thiouric acid (6TUA), which is excreted in urine. This reduces the effective amount of drug available for therapeutic efficacy. Co-administration of allopurinol, a suicide inhibitor of XOD, which blocks the hydroxylation of 6MP inadvertently enhances the 6MP blood level, counters this reduction. However, allopurinol also blocks the hydroxylation of hypoxanthine, xanthine (released from dead cancer cells) leading to their accumulation in the body causing biochemical complications such as xanthine nephropathy. This necessitates the use of a preferential XOD inhibitor that selectively inhibits 6MP transformation, but leaves xanthine metabolism unaffected. Here, we have characterized two such unique inhibitors namely, 2-amino-6-hydroxy-8-mercaptopurine (AHMP) and 2-amino-6-purinethiol (APT) on the basis of IC50 values, residual activity in bi-substrate simulative reaction and the kinetic parameters like Km, Ki, kcat. The IC50 values of AHMP for xanthine and 6MP as substrate are 17.71 +/- 0.29 microM and 0.54 +/- 0.01 microM, respectively and the IC50 values of APT for xanthine and 6MP as substrates are 16.38 +/- 0.21 microM and 2.57 +/- 0.08 microM, respectively. The Ki values of XOD using AHMP as inhibitor with xanthine and 6MP as substrate are 5.78 +/- 0.48 microM and 0.96 +/- 0.01 microM, respectively. The Ki values of XOD using APT as inhibitor with xanthine and 6MP as substrate are 6.61 +/- 0.28 microM and 1.30 +/- 0.09 microM. The corresponding Km values of XOD using xanthine and 6MP as substrate are 2.65 +/- 0.02 microM and 6.01 +/- 0.03 microM, respectively. The results suggest that the efficiency of substrate binding to XOD and its subsequent catalytic hydroxylation is much superior for xanthine in comparison to 6MP. In addition, the efficiency of the inhibitor binding to XOD is much more superior when 6MP is the substrate instead of xanthine. We further undertook the toxicological evaluation of these inhibitors in a single dose acute toxicity study in mice and our preliminary experimental results suggested that the inhibitors were equally non-toxic in the tested doses. We conclude that administration of either APT or AHMP along with the major anti-leukemic drug 6MP might serve as a good combination cancer chemotherapy regimen.

Anti-Inflammatory Effects of a Mytilus coruscus α-d-Glucan (MP-A) in Activated Macrophage Cells via TLR4/NF-κB/MAPK Pathway Inhibition

PubMed Central

Liu, Fuyan; Zhang, Xiaofeng; Li, Yuqiu; Chen, Qixin; Liu, Fei; Zhu, Xiqiang; Mei, Li; Song, Xinlei; Liu, Xia; Song, Zhigang; Zhang, Jinhua; Zhang, Wen; Ling, Peixue

2017-01-01

The hard-shelled mussel (Mytilus coruscus) has been used as Chinese traditional medicine for thousands of years; however, to date the ingredients responsible for the various beneficial health outcomes attributed to Mytilus coruscus are still unclear. An α-d-Glucan, called MP-A, was isolated from Mytilus coruscus, and observed to exert anti-inflammatory activity in THP-1 human macrophage cells. Specifically, we showed that MP-A treatment inhibited the production of inflammatory markers, including TNF-α, NO, and PGE2, inducible NOS (iNOS), and cyclooxygenase-2 (COX-2), in LPS-activated THP-1 cells. It was also shown to enhance phagocytosis in the analyzed cells, but to severely inhibit the phosphorylation of mitogen-activated protein kinases (MAPKs) and the nuclear translocation of NF-κB P65. Finally, MP-A was found to exhibit a high binding affinity for the cell surface receptor TLR4, but a low affinity for TLR2 and dectin-1, via surface plasmon resonance (SPR) analysis. The study indicates that MP-A suppresses LPS-induced TNF-α, NO and PEG2 production via TLR4/NF-κB/MAPK pathway inhibition, and suggests that MP-A may be a promising therapeutic candidate for diseases associated with TNF-α, NO, and/or PEG2 overproduction. PMID:28930149

Anti-Inflammatory Effects of a Mytilus coruscus α-d-Glucan (MP-A) in Activated Macrophage Cells via TLR4/NF-κB/MAPK Pathway Inhibition.

PubMed

Liu, Fuyan; Zhang, Xiaofeng; Li, Yuqiu; Chen, Qixin; Liu, Fei; Zhu, Xiqiang; Mei, Li; Song, Xinlei; Liu, Xia; Song, Zhigang; Zhang, Jinhua; Zhang, Wen; Ling, Peixue; Wang, Fengshan

2017-09-20

The hard-shelled mussel ( Mytilus coruscus ) has been used as Chinese traditional medicine for thousands of years; however, to date the ingredients responsible for the various beneficial health outcomes attributed to Mytilus coruscus are still unclear. An α-d-Glucan, called MP-A, was isolated from Mytilus coruscus , and observed to exert anti-inflammatory activity in THP-1 human macrophage cells. Specifically, we showed that MP-A treatment inhibited the production of inflammatory markers, including TNF-α, NO, and PGE2, inducible NOS (iNOS), and cyclooxygenase-2 (COX-2), in LPS-activated THP-1 cells. It was also shown to enhance phagocytosis in the analyzed cells, but to severely inhibit the phosphorylation of mitogen-activated protein kinases (MAPKs) and the nuclear translocation of NF-κB P65. Finally, MP-A was found to exhibit a high binding affinity for the cell surface receptor TLR4, but a low affinity for TLR2 and dectin-1, via surface plasmon resonance (SPR) analysis. The study indicates that MP-A suppresses LPS-induced TNF-α, NO and PEG2 production via TLR4/NF-κB/MAPK pathway inhibition, and suggests that MP-A may be a promising therapeutic candidate for diseases associated with TNF-α, NO, and/or PEG2 overproduction.

Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo Temperature Basin Paving and Molecular Tailoring Approaches benchmarked by full MP2 calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahu, Nityananda; Gadre, Shridhar R.; Bandyopadhyay, Pradipta

We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving (MCTBP) sampling of the cluster’s Potential Energy Surface (PES) with the Effective Fragment Potential (EFP), subsequent geometry optimization using the Molecular Tailoring fragmentation Approach (MTA) and final refinement at the second order Møller Plesset perturbation (MP2) level of theory. The MTA geometry optimizations usedmore » between 14 and 18 main fragments with maximum sizes between 11 and 14 water molecules and average size of 10 water molecules, whose energies and gradients were computed at the MP2 level. The MTA-MP2 optimized geometries were found to be quite close (within < 0.5 kcal/mol) to the ones obtained from the MP2 optimization of the whole cluster. The grafting of the MTA-MP2 energies yields electronic energies that are within < 5×10-4 a.u. from the MP2 results for the whole cluster while preserving their energy order. The MTA-MP2 method was also found to reproduce the MP2 harmonic vibrational frequencies in both the HOH bending and the OH stretching regions.« less

Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi™ Processor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Jacquelin, Mathias; De Jong, Wibe A.

2017-10-20

Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting and promising target for these algorithms, as they can provide the computational power that is needed to solve interesting problems in chemistry. In this paper, we describe the efforts of refactoring the existing AIMD plane-wave method of NWChem from an MPI-only implementation to a scalable, hybrid code that employs MPI and OpenMP tomore » exploit the capabilities of current and future many-core architectures. We describe the optimizations required to get close to optimal performance for the multiplication of the tall-and-skinny matrices that form the core of the computational algorithm. We present strong scaling results on the complete AIMD simulation for a test case that simulates 256 water molecules and that strong-scales well on a cluster of 1024 nodes of Intel Xeon Phi processors. We compare the performance obtained with a cluster of dual-socket Intel® Xeon® E5–2698v3 processors.« less

Magnetic biocatalysts of pectinase and cellulase: Synthesis and characterization of two preparations for application in grape juice clarification.

PubMed

Dal Magro, Lucas; Silveira, Vitória C C; de Menezes, Eliana Weber; Benvenutti, Edilson Valmir; Nicolodi, Sabrina; Hertz, Plinho F; Klein, Manuela P; Rodrigues, Rafael C

2018-04-07

In the present study, we prepared two different magnetic biocatalysts of pectinase and cellulase: carrier-free magnetic CLEAs (CLEA-MP*) and immobilization on glutaraldehyde-activated magnetite (Enz-Glu-MP*). The biocatalysts were compared to their magnetic properties, immobilization parameters, stability and grape juice clarification. Enz-Glu-MP* presented higher magnetic properties than CLEA-MP*, whereas this presented higher surface area and pore volume. The K M of the enzyme immobilized on Enz-Glu-MP* was 25.65mM, lower in comparison to the CLEA-MP* (33.83mM). On the other hand, CLEA-MP* was the most active and stable biocatalyst, presenting higher recovered activity (33.4% of cellulase), higher thermal stability (2.39 stabilization factor) and improved reusability (8cycles). The integration of magnetic technology with enzymatic immobilization emerges as a possibility to increase the recover and reuse of biocatalysts for application in juice technology. Copyright © 2018 Elsevier B.V. All rights reserved.

Musa paradisica RCI complements AtRCI and confers Na+ tolerance and K+ sensitivity in Arabidopsis.

PubMed

Liu, Bing; Feng, Dongru; Zhang, Bipei; Mu, Peiqiang; Zhang, Yang; He, Yanming; Qi, Kangbiao; Wang, Jinfa; Wang, Hongbin

2012-03-01

The mechanisms involved in Na⁺/K⁺ uptake and extrusion are important in plant salt tolerance. In this study, we investigated the physiological role of a plasma membrane (PM)-localized protein, MpRCI, from plantain in transgenic Arabidopsis under NaCl and KCl stress and determined its effect on PM fluidity and H⁺-ATPase activity. The MpRCI gene exhibited high homology to the AtRCI2 gene family in Arabidopsis and was therefore able to complement for loss of the yeast AtRCI2-related PMP3 gene. Results of phenotypic espial and atomic emission spectrophotometer (AES) assays indicated that MpRCI overexpression in the AtRCI2A knockout mutant with reduced shoot Na⁺ and increased K⁺ exhibited increased Na⁺-tolerance and K⁺-sensitivity under NaCl or KCl treatments, respectively. Furthermore, comparisons of PM fluidity and H⁺-ATPase activity in shoots, with expression or absence of MpRCI/AtRCI2A expression under NaCl or KCl stress, showed MpRCI maintained PM fluidity and H⁺-ATPase activity under stress conditions. Results suggest that MpRCI plays an essential role in Na⁺/K⁺ flux in plant cells. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

6-Mercaptopurine exerts an immunomodulatory and neuroprotective effect on permanent focal cerebral occlusion in rats.

PubMed

Chang, Chih-Zen; Kwan, Aij-Lie; Howng, Shen-Long

2010-08-01

A bursting cascade of inflammation imposes progressive neurological deterioration after experimental stroke has been demonstrated. In our study, 6-mercaptopurine (6-mp) has been successful in alleviating cerebral infarct in a rodent permanent middle cerebral artery occlusion (pMCAO) model. The present study was aimed to examine the effect of 6-mp on cytokine levels in experimental stroke. The rodent pMCAO model was employed. A dose of 2 mg/kg 6-mp or vehicle (0.1 mol/L PBS) was administered intraperitoneally 30 min after the induction of pMCAO. Neurological score, serum, and cerebrospinal fluid (CSF) cytokines such as IL-1beta, IL-6, and TNF-alpha and infarct volume were determined 48 h after pMCAO. Cerebral infarction volume was significantly decreased in animals treated with 6-mp (74.3%, p < 0.01), and the ratio of tissue edema was also decreased in 6-mp-treated groups (71%). Animals receiving 6-mp thus showed a significant decrease in IL-1 and TNF-alpha (18/43% and 48/64% in CSF/serum, respectively) when compared with the pMCAO groups (p < 0.01). This study demonstrates that 6-mp interposes the production of IL-1 and TNF-alpha in CSF and serum, attenuates ischemic brain injury, and thus alleviates neurological deficits in the pMCAO animals. These findings also offer first evidence that 6-mp may attenuate TNF-alpha-related neuron apoptosis and also support the notion that 6-mp and other anti-inflammatory agents could potentially have therapeutic uses in cases of cerebral infarct.

Concordance of macular pigment measurements obtained using customized heterochromatic flicker photometry, dual-wavelength autofluorescence, and single-wavelength reflectance.

PubMed

Dennison, Jessica L; Stack, Jim; Beatty, Stephen; Nolan, John M

2013-11-01

This study compares in vivo measurements of macular pigment (MP) obtained using customized heterochromatic flicker photometry (cHFP; Macular Metrics Densitometer(™)), dual-wavelength fundus autofluorescence (Heidelberg Spectralis(®) HRA + OCT MultiColor) and single-wavelength fundus reflectance (Zeiss Visucam(®) 200). MP was measured in one eye of 62 subjects on each device. Data from 49 subjects (79%) was suitable for analysis. Agreement between the Densitometer and Spectralis was investigated at various eccentricities using a variety of quantitative and graphical methods, including: Pearson correlation coefficient to measure degree of scatter (precision), accuracy coefficient, concordance correlation coefficient (ccc), paired t-test, scatter and Bland-Altman plots. The relationship between max MP from the Visucam and central MP from the Spectralis and Densitometer was investigated using regression methods. Agreement was strong between the Densitometer and Spectralis at all central eccentricities (e.g. at 0.25° eccentricity: accuracy = 0.97, precision = 0.90, ccc = 0.87). Regression analysis showed a very weak relationship between the Visucam and Densitometer (e.g. Visucam max on Densitometer central MP: R(2) = 0.008, p = 0.843). Regression analysis also demonstrated a weak relationship between MP measured by the Spectralis and Visucam (e.g. Visucam max on Spectralis central MP: R(2) = 0.047, p = 0.348). MP values obtained using the Heidelberg Spectralis are comparable to MP values obtained using the Densitometer. In contrast, MP values obtained using the Zeiss Visucam are not comparable with either the Densitometer or the Spectralis MP measuring devices. Taking cHFP as the current standard to which other MP measuring devices should be compared, the Spectralis is suitable for use in a clinical and research setting, whereas the Visucam is not. Copyright © 2013 Elsevier Ltd. All rights reserved.

Water adsorption on a copper formate paddlewheel model of CuBTC: A comparative MP2 and DFT study

NASA Astrophysics Data System (ADS)

Toda, Jordi; Fischer, Michael; Jorge, Miguel; Gomes, José R. B.

2013-11-01

Simultaneous adsorption of two water molecules on open metal sites of the HKUST-1 metal-organic framework (MOF), modeled with a Cu2(HCOO)4 cluster, was studied by means of density functional theory (DFT) and second-order Moller-Plesset (MP2) approaches together with correlation consistent basis sets. Experimental geometries and MP2 energetic data extrapolated to the complete basis set limit were used as benchmarks for testing the accuracy of several different exchange-correlation functionals in the correct description of the water-MOF interaction. M06-L and some LC-DFT methods arise as the most appropriate in terms of the quality of geometrical data, energetic data and computational resources needed.

Memantine-derived drugs as potential antitumor agents for the treatment of glioblastoma.

PubMed

Cacciatore, Ivana; Fornasari, Erika; Marinelli, Lisa; Eusepi, Piera; Ciulla, Michele; Ozdemir, Ozlem; Tatar, Abdulgani; Turkez, Hasan; Di Stefano, Antonio

2017-11-15

Glioblastoma is one of the most aggressive malignant primary brain cancer in adults. To date, surgery, radiotherapy and current pharmacological treatments are not sufficient to manage this pathology that has a high mortality rate (median survival 12-15months). Recently, anticancer multi-targeted compounds have attracted much attention with the aim to obtain new drugs able to hit different biological targets that are involved in the onset and progression of the disease. Here, we report the synthesis of novel memantine-derived drugs (MP1-10) and their potential antitumor activities in human U87MG glioblastoma cell line. MP1-10 were synthetized joining memantine, which is a NMDA antagonist, to different histone deacetylase inhibitors to obtain one molecule with improved therapeutic efficacy. Biological results indicated that MP1 and MP2 possessed more potent anti-proliferative effects on U87MG cells than MP3-10 in a dose-dependent manner. MP1 and MP2 induced significant cell death by apoptosis characterized by apoptotic morphological changes in Hoechst staining. Both drugs also exhibited non-genotoxic and only mild cytotoxic effects in human whole blood cells. However, only MP1, showing good chemico-physical properties (solubility, LogP) and enzymatic stabilities in gastric and intestinal fluids, can be considered a suitable candidate for in vivo pharmacokinetic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Work week duration, work-family balance and difficulties encountered by female and male physicians: results from the French SESMAT study.

PubMed

Estryn-Behar, M; Fry, C; Guetarni, K; Aune, I; Machet, G; Doppia, M A; Lassaunière, J M; Muster, D; Pelloux, P; Prudhomme, Ch

2011-01-01

France encounters difficulties attracting physicians to work in hospitals. Organisation at work and at home may be at the heart of the problem for female as well as for male physicians. A comprehensive questionnaire was filled out online by a representative sample of 1924 French hospital physicians. We conducted gender bivariate and multivariate analysis of the risk factors for burnout and intent to leave the profession(ITL). ITL was declared by 17.4% of physicians. According to 41.3% of female physicians (FP), their profession was an obstacle to having children (versus 19.3% for male physicians (MP)). Major factors linked with burnout were Effort/Reward imbalance (FP adjOR = 5.09, MP adjOR = 5.93), Work-family conflicts (FP adjOR = 2.97, MP adjOR = 3.04), and Low quality of teamwork (FP adjOR = 1.82, MP adjOR = 2.68). Major factors linked with ITL were Low quality of teamwork (FP adjOR = 4.49, MP adjOR = 3.03), Patient-related burnout (FP adjOR = 2.10, MP adjOR = 2.35) and General burnout (FP adjOR = 1.85, MP adjOR = 1.45). Excessive job demands are linked with burnout and with work-family conflicts, conducting to difficulties in organising one's life in order to have and raise children. Potential solutions include facilitating teamwork in order to reduce departure, which increase workload on those who stay increasing their work family conflict.

Orbital-optimized MP2.5 and its analytic gradients: Approaching CCSD(T) quality for noncovalent interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332; Sherrill, C. David

2014-11-28

Orbital-optimized MP2.5 [or simply “optimized MP2.5,” OMP2.5, for short] and its analytic energy gradients are presented. The cost of the presented method is as much as that of coupled-cluster singles and doubles (CCSD) [O(N{sup 6}) scaling] for energy computations. However, for analytic gradient computations the OMP2.5 method is only half as expensive as CCSD because there is no need to solve λ{sub 2}-amplitude equations for OMP2.5. The performance of the OMP2.5 method is compared with that of the standard second-order Møller–Plesset perturbation theory (MP2), MP2.5, CCSD, and coupled-cluster singles and doubles with perturbative triples (CCSD(T)) methods for equilibrium geometries, hydrogenmore » transfer reactions between radicals, and noncovalent interactions. For bond lengths of both closed and open-shell molecules, the OMP2.5 method improves upon MP2.5 and CCSD by 38%–43% and 31%–28%, respectively, with Dunning's cc-pCVQZ basis set. For complete basis set (CBS) predictions of hydrogen transfer reaction energies, the OMP2.5 method exhibits a substantially better performance than MP2.5, providing a mean absolute error of 1.1 kcal mol{sup −1}, which is more than 10 times lower than that of MP2.5 (11.8 kcal mol{sup −1}), and comparing to MP2 (14.6 kcal mol{sup −1}) there is a more than 12-fold reduction in errors. For noncovalent interaction energies (at CBS limits), the OMP2.5 method maintains the very good performance of MP2.5 for closed-shell systems, and for open-shell systems it significantly outperforms MP2.5 and CCSD, and approaches CCSD(T) quality. The MP2.5 errors decrease by a factor of 5 when the optimized orbitals are used for open-shell noncovalent interactions, and comparing to CCSD there is a more than 3-fold reduction in errors. Overall, the present application results indicate that the OMP2.5 method is very promising for open-shell noncovalent interactions and other chemical systems with difficult electronic structures.« less

Regulation of Vascular Tone, Angiogenesis and Cellular Bioenergetics by the 3-Mercaptopyruvate Sulfurtransferase/H2S Pathway: Functional Impairment by Hyperglycemia and Restoration by DL-α-Lipoic Acid.

PubMed

Coletta, Ciro; Módis, Katalin; Szczesny, Bartosz; Brunyánszki, Attila; Oláh, Gábor; Rios, Ester C S; Yanagi, Kazunori; Ahmad, Akbar; Papapetropoulos, Andreas; Szabo, Csaba

2015-02-18

Hydrogen sulfide (H2S), as a reducing agent and an antioxidant molecule, exerts protective effects against hyperglycemic stress in the vascular endothelium. The mitochondrial enzyme 3-mercaptopyruvate sulfurtransferase (3-MST) is an important biological source of H2S. We have recently demonstrated that 3-MST activity is inhibited by oxidative stress in vitro and speculated that this may have an adverse effect on cellular homeostasis. In the current study, given the importance of H2S as a vasorelaxant, angiogenesis stimulator and cellular bioenergetic mediator, we first determined whether the 3-MST/H2S system plays a physiological regulatory role in endothelial cells. Next, we tested whether a dysfunction of this pathway develops during the development of hyperglycemia and μmol/L to diabetes-associated vascular complications. Intraperitoneal (IP) 3-MP (1 mg/kg) raised plasma H2S levels in rats. 3-MP (10 1 mmol/L) promoted angiogenesis in vitro in bEnd3 microvascular endothelial cells and in vivo in a Matrigel assay in mice (0.3-1 mg/kg). In vitro studies with bEnd3 cell homogenates demonstrated that the 3-MP-induced increases in H2S production depended on enzymatic activity, although at higher concentrations (1-3 mmol/L) there was also evidence for an additional nonenzymatic H2S production by 3-MP. In vivo, 3-MP facilitated wound healing in rats, induced the relaxation of dermal microvessels and increased mitochondrial bioenergetic function. In vitro hyperglycemia or in vivo streptozotocin diabetes impaired angiogenesis, attenuated mitochondrial function and delayed wound healing; all of these responses were associated with an impairment of the proangiogenic and bioenergetic effects of 3-MP. The antioxidants DL-α-lipoic acid (LA) in vivo, or dihydrolipoic acid (DHLA) in vitro restored the ability of 3-MP to stimulate angiogenesis, cellular bioenergetics and wound healing in hyperglycemia and diabetes. We conclude that diabetes leads to an impairment of the 3-MST/H2S pathway, and speculate that this may contribute to the pathogenesis of hyperglycemic endothelial cell dysfunction. We also suggest that therapy with H2S donors, or treatment with the combination of 3-MP and lipoic acid may be beneficial in improving angiogenesis and bioenergetics in hyperglycemia.

Regulation of Vascular Tone, Angiogenesis and Cellular Bioenergetics by the 3-Mercaptopyruvate Sulfurtransferase/H2S Pathway: Functional Impairment by Hyperglycemia and Restoration by dl-α-Lipoic Acid

PubMed Central

Coletta, Ciro; Módis, Katalin; Szczesny, Bartosz; Brunyánszki, Attila; Oláh, Gábor; Rios, Ester CS; Yanagi, Kazunori; Ahmad, Akbar; Papapetropoulos, Andreas; Szabo, Csaba

2015-01-01

Hydrogen sulfide (H2S), as a reducing agent and an antioxidant molecule, exerts protective effects against hyperglycemic stress in the vascular endothelium. The mitochondrial enzyme 3-mercaptopyruvate sulfurtransferase (3-MST) is an important biological source of H2S. We have recently demonstrated that 3-MST activity is inhibited by oxidative stress in vitro and speculated that this may have an adverse effect on cellular homeostasis. In the current study, given the importance of H2S as a vasorelaxant, angiogenesis stimulator and cellular bioenergetic mediator, we first determined whether the 3-MST/H2S system plays a physiological regulatory role in endothelial cells. Next, we tested whether a dysfunction of this pathway develops during the development of hyperglycemia and μmol/L to diabetes-associated vascular complications. Intraperitoneal (IP) 3-MP (1 mg/kg) raised plasma H2S levels in rats. 3-MP (10 1 mmol/L) promoted angiogenesis in vitro in bEnd3 microvascular endothelial cells and in vivo in a Matrigel assay in mice (0.3–1 mg/kg). In vitro studies with bEnd3 cell homogenates demonstrated that the 3-MP-induced increases in H2S production depended on enzymatic activity, although at higher concentrations (1–3 mmol/L) there was also evidence for an additional nonenzymatic H2S production by 3-MP. In vivo, 3-MP facilitated wound healing in rats, induced the relaxation of dermal microvessels and increased mitochondrial bioenergetic function. In vitro hyperglycemia or in vivo streptozotocin diabetes impaired angiogenesis, attenuated mitochondrial function and delayed wound healing; all of these responses were associated with an impairment of the proangiogenic and bioenergetic effects of 3-MP. The antioxidants dl-α-lipoic acid (LA) in vivo, or dihydrolipoic acid (DHLA) in vitro restored the ability of 3-MP to stimulate angiogenesis, cellular bioenergetics and wound healing in hyperglycemia and diabetes. We conclude that diabetes leads to an impairment of the 3-MST/H2S pathway, and speculate that this may contribute to the pathogenesis of hyperglycemic endothelial cell dysfunction. We also suggest that therapy with H2S donors, or treatment with the combination of 3-MP and lipoic acid may be beneficial in improving angiogenesis and bioenergetics in hyperglycemia. PMID:25715337

Comparison of the neuroprotective potential of Mucuna pruriens seed extract with estrogen in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mice model.

PubMed

Yadav, Satyndra Kumar; Prakash, Jay; Chouhan, Shikha; Westfall, Susan; Verma, Mradul; Singh, Tryambak Deo; Singh, Surya Pratap

2014-01-01

Parkinson's disease (PD) is one of the most common neurodegenerative disease found in the aging population. Currently, many studies are being conducted to find a suitable and effective cure for PD, with an emphasis on the use of herbal plants. In Ayurveda, Mucuna pruriens (Mp), a leguminous plant, is used as an anti-inflammatory drug. In this study, the neuroprotective effect of an ethanolic extract of Mp seed is evaluated in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of PD and compared to estrogen, a well reported neuroprotective agent used for treating PD. Twenty-four Swiss albino mice were randomly divided into four groups: Control, MPTP, MPTP+Mp and MPTP+estrogen. The behavioural recovery in both Mp and estrogen treated mice was investigated using the rotarod, foot printing and hanging tests. The recovery of dopamine neurons in the substantia nigra (SN) region was estimated by tyrosine hydroxylase (TH), immunostaining. Additionally inducible nitric oxide synthase (iNOS) and glial fibrillary acidic protein (GFAP) immunoreactivity was evaluated to assess the level of oxidative damage and glial activation respectively. The levels of dopamine and its metabolite in the nigrostriatal region were measured by HPLC. Mp treatment restored all the deficits induced by MPTP more effectively than estrogen. Mp treatment recovered the number of TH-positive cells in both the SN region and the striatum while reducing the expression of iNOS and GFAP in the SN. Treatment with Mp significantly increased the levels of dopamine, DOPAC and homovanillic acid compared to MPTP intoxicated mice. Notably, the effect of Mp was greater than that elicited by estrogen. Mp down regulates NO production, neuroinflammation and microglial activation and all of these actions contribute to Mp's neuroprotective activity. These results suggest that Mp can be an effective treatment for neurodegenerative diseases, especially PD by decreasing oxidative stress and possibly by implementing neuronal and glial cell crosstalk. Copyright © 2013 Elsevier Ltd. All rights reserved.

Vitamin D Reduces Oxidative Stress-Induced Procaspase-3/ROCK1 Activation and MP Release by Placental Trophoblasts.

PubMed

Xu, Jie; Jia, Xiuyue; Gu, Yang; Lewis, David F; Gu, Xin; Wang, Yuping

2017-06-01

Increased microparticle (MP) shedding by placental trophoblasts contributes to maternal vascular inflammatory response and endothelial dysfunction in preeclampsia. Vitamin D has beneficial effects in pregnancy; however, its effect on trophoblast MP release has not been investigated. To investigate if vitamin D could protect trophoblasts from oxidative stress-induced MP release. Placental trophoblasts were isolated from uncomplicated and preeclamptic placentas. Effects of vitamin D on MP release induced by oxidative stress inducer CoCl2 were studied. Annexin V+ MPs were assessed by flow cytometry. Expression of caveolin-1, endothelial nitric oxide synthase (eNOS), procaspase-3, cleaved caspase-3, and Rho-associated coiled-coil protein kinase 1 (ROCK1) in trophoblasts and trophoblast-derived MPs were determined by Western blot. Trophoblasts from preeclamptic pregnancies released significantly more MPs than cells from uncomplicated pregnancies (P < 0.01). CoCl2-induced increase in MP release was associated with upregulation of caveolin-1 and downregulation of eNOS expression in trophoblasts (P < 0.05), which could be attenuated by 1,25(OH)2D3. Moreover, 1,25(OH)2D3 could also inhibit CoCl2-induced procaspase-3 cleavage and ROCK1 activation in trophoblasts. Consistently, CoCl2-induced upregulation of procaspase-3, cleaved caspase-3, and ROCK1 expression in trophoblast-derived MPs were also reduced in cells treated with 1,25(OH)2D3. Placental trophoblasts from preeclamptic pregnancies released more MP than cells from uncomplicated pregnancies. Oxidative stress-induced increase in MP shedding is associated with upregulation of caveolin-1 and downregulation of eNOS expression in placental trophoblasts. Inhibition of caspase-3 cleavage and ROCK1 activation, together with upregulation of eNOS expression, could be the potential cellular/molecular mechanism(s) of vitamin D protective effects on placental trophoblasts. Copyright © 2017 Endocrine Society

TcCYS4, a cystatin from cocoa, reduces necrosis triggered by MpNEP2 in tobacco plants.

PubMed

Santana, L S; Costa, M G C; Pirovani, N M; Almeida, A F; Alvim, F C; Pirovani, C P

2014-09-26

In Brazil, most cocoa bean production occurs in Southern Bahia. Witches' broom disease arrived in this area in 1989 and has since caused heavy losses in production. The disease is caused by the basidiomycete fungus Moniliophthora perniciosa, a hemibiotrophic fungus that produces the necrosis and ethylene-inducting protein (MpNEP2) during infection; this protein can activate cysteine proteases and induce programmed cell death. Cysteine proteases can be modulated by cystatin. In this study, we overexpressed TcCYS4, a cocoa cystatin, in tobacco plants and evaluated the effect on MpNEP2 in model plants. Tccys4 cDNA was cloned into the pCAMBIA 1390 vector and inserted into the tobacco plants via Agrobacterium tumefaciens. Transgene expression was analyzed by reverse transcription-quantitative PCR and Western blot analysis. Transcript and protein levels in Tcccys4:tobacco lines were 8.9- and 1.5-fold higher than in wild-type plants (wt). Tcccys4:tobacco lines showed no change in growth compared to wt plants. CO2 net assimilation (A) increased in Tcccys4:tobacco lines compared to wt plants. Only one line showed statistically significant stomatal conductance (gs) and transpiration rate (E) changes. MpNEP2 was infiltered into the foliar mesophyll of Tcccys4:tobacco lines and wt plants, and necrotic lesions were attenuated in lines highly expressing Tccys4. Our results suggest that cocoa cystatin TcCYS4 affects MpNEP2 activity related to the progression of programmed cell death in tobacco plants. This may occur through the action of cystatin to inhibit cysteine proteases activated by MpNEP2 in plant tissues. Further studies are necessary to examine cystatin in the Theobroma cacao-M. perniciosa pathosystem.

Assessment of symptomatic and neuroprotective efficacy of Mucuna pruriens seed extract in rodent model of Parkinson's disease.

PubMed

Kasture, Sanjay; Pontis, Silvia; Pinna, Annalisa; Schintu, Nicoletta; Spina, Liliana; Longoni, Rosanna; Simola, Nicola; Ballero, Mauro; Morelli, Micaela

2009-02-01

Mucuna pruriens (MP) has long been used in Indian traditional medicine as support in the treatment of Parkinson's disease. However, no systematic preclinical studies that aimed at evaluating the efficacy of this substance are available to date. This study undertook an extensive evaluation of the antiparkinsonian effects of an extract of MP seeds known to contain, among other components, 12.5% L: -dihydroxyphenylalanine (L: -DOPA), as compared to equivalent doses of L: -DOPA. Moreover, the neuroprotective efficacy of MP and its potential rewarding effects were evaluated. The results obtained reveal how an acute administration of MP extract at a dose of 16 mg/kg (containing 2 mg/kg of L: -DOPA) consistently antagonized the deficit in latency of step initiation and adjusting step induced by a unilateral 6-hydroxydopamine lesion, whereas L: -DOPA was equally effective only at the doses of 6 mg/kg. At the same dosage, MP significantly improved the placement of the forelimb in vibrissae-evoked forelimb placing, suggesting a significant antagonistic activity on both motor and sensory-motor deficits. The effects of MP extract were moreover investigated by means of the turning behavior test and in the induction of abnormal involuntary movements (AIMs) after either acute or subchronic administration. MP extract acutely induced a significantly higher contralateral turning behavior than L: -DOPA (6 mg/kg) when administered at a dose of 48 mg/kg containing 6 mg/kg of L: -DOPA. On subchronic administration, both MP extract (48 mg/kg) and L: -DOPA (6 mg/kg) induced sensitization of contralateral turning behavior; however, L: -DOPA alone induced a concomitant sensitization in AIMs suggesting that the dyskinetic potential of MP is lower than that of L: -DOPA. MP (48 mg/kg) was also effective in antagonizing tremulous jaw movements induced by tacrine, a validated test reproducing parkinsonian tremor. Furthermore, MP induced no compartment preference in the place preference test, indicating the lack of components characterized by rewarding effects in the extract. Finally, in a subchronic mice model of 1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine hydrochloride (MPTP)-induced dopamine neuron degeneration, MP extract did not prove capable of preventing either tyrosine hydroxylase decrease induced by MPTP or astroglial or microglial activation as assessed by means of GFAP and CD11b immunohistochemistry, supporting the absence of neuroprotective effects by MP. Characterization MP extract strongly supports its antiparkinsonian activity.

Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

NASA Astrophysics Data System (ADS)

Li, Jin-Feng; Sun, Yin-Yin; Bai, Hongcun; Li, Miao-Miao; Li, Jian-Li; Yin, Bing

2015-06-01

The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M2(CN)5]-1 (M = Ca, Be) clusters. At CCSD(T) level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE). The largest one is 9.70 eV for [Ca2(CN)5]-1 which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T), outer valence Green's function (OVGF) method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties.

A search for the optimal duration of treatment with 6-mercaptopurine for ulcerative colitis.

PubMed

Lobel, Efrat Z; Korelitz, Burton I; Xuereb, Mark A; Panagopoulos, Georgia

2004-03-01

6-mercaptopurine has proven to be effective in the treatment and maintenance of remission of ulcerative colitis (UC). The optimal duration of treatment with 6-MP is unknown. The intention of this study was to determine the best duration of treatment with 6-MP in terms of maintenance efficacy once remission has been achieved. We reviewed the records from the inflammatory bowel disease (IBD) center at Lenox Hill Hospital and one large IBD practice in New York City of 334 patients treated with 6-MP for UC. These patients were followed from 4 months to 28.7 yr. Sixty-one patients were treated with 6-MP for at least 6 months and had at least a 3-month disease-free interval off steroids while on the medication. These patients were divided into two groups: Group 1 continued 6-MP and group 2 discontinued the drug at various times for reasons other than relapse. Time to relapse was calculated for both groups. A Kaplan-Meier survival analysis was employed and differences between the two groups were analyzed using the log-rank test. The median time to relapse in group 2 was 24 wk and in group 1 was 58 wk (p < 0.05). There were no significant differences between the two groups in age, gender, extent of disease, use of concomitant 5-ASA products, dose of 6-MP during remission, duration of UC, and duration of treatment with 6-MP before remission was achieved. Discontinuation of treatment with 6-MP while UC is in remission leads to a higher relapse rate than maintenance on 6-MP. Therefore, we favor the indefinite treatment with 6-MP in most patients.

Apoptosis-inducing activity of HPLC fraction from Voacanga globosa (Blanco) Merr. on the human colon carcinoma cell.

PubMed

Acebedo, Alvin Resultay; Amor, Evangeline Cancio; Jacinto, Sonia Donaldo

2014-01-01

Voacanga globosa (Blanco), a plant endemic to the Philippines, is traditionally used especially by indigenous people of Bataan in the treatment of ulcers, wounds and tumorous growths. This study aimed to provide scientific evidence to therapeutic properties by determining cytotoxic and pro-apoptotic activity of HPLC fractions from leaves on HCT116 human colon carcinoma and A549 human lung carcinoma cell lines. Ethanolic extraction was performed on V globosa leaves followed by hexane and ethyl acetate partitioning. Silica gel column chromatography and high performance liquid chromatography (HPLC) produced MP1, MP2 and MP3 fractions. Cytotoxic activity of the fractions was determined through MTT assay against the cancer cell lines HCT116 and A549 and the non-cancer AA8 Chinese hamster ovarian cell line. Pro-apoptotic activities of the most active fractions were further assessed through DAPI staining, TUNEL assay and JC-1 mitochondrial membrane potential assay with HCT116 cells. While the MP1 fraction exerted no significant activity against all cell lines tested, MP2 and MP3 fractions demonstrated high toxicity against HCT116 and A549 cells. The MP3 fraction induced formation of apoptotic bodies, condensed DNA and other morphological changes consistent with apoptosis of HCT116 cells and TUNEL assay showed significant increase in DNA fragmentation over time. In these cells, the MP3 fraction also induced mitochondrial membrane destabilization, which is generally associated with the beginning of apoptosis. Phytochemical analysis demonstrated the presence only of saponins and terpenoids in the MP3 fraction. The results indicate that the MP3 fraction exerts cytotoxic activity on HCT116 cells via induction of apoptosis triggered by loss of mitochondrial membrane potential crucial for cell survival.

Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

NASA Astrophysics Data System (ADS)

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F.; Ingrosso, Francesca

2014-07-01

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F., E-mail: Manuel.Ruiz@univ-lorraine.fr

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering themore » potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.« less

Comparison of the effects of dietary single and multi-probiotics on growth, non-specific immune responses and disease resistance in starry flounder, Platichthys stellatus.

PubMed

Park, Youngjin; Moniruzzaman, Mohammad; Lee, Seunghan; Hong, Jeongwhui; Won, Seonghun; Lee, Jong Min; Yun, Hyeonho; Kim, Kang-Woong; Ko, Daegyun; Bai, Sungchul C

2016-12-01

An 8-week feeding trial was conducted to evaluate the effects of dietary probiotics on growth performance and non-specific immune responses in starry flounder, Platichthys stellatus. Fish averaging 46.5 ± 0.65 g (mean ± SD) were fed one of the six experimental diets; one control (Cont), and five other diets were prepared by supplementing single-probiotics 1 (Bacillus subtilis; SP 1 , 2 × 10 9  CFU kg -1 diet), single-probiotics 2 (Bacillus licheniformis; SP 2 , 2 × 10 9  CFU kg -1 diet), multi-probiotics 1 (Bacillus subtilis + Bacillus licheniformis; MP 1 , 2 × 10 9  CFU kg -1 diet), multi-probiotics 2 (commercial probiotics; Bacillus subtills + Bacillus licheniformis + Paenibacillus polymyxa + Aspergillus oryzae + Saccharomyces cerevisiae; MP 2 , 2 × 10 9  CFU kg -1 diet) and oxytetracycline (OTC) at 5 g OTC kg -1 diet. At the end of 8 weeks feeding trial, weight gain (WG) and specific growth rate (SGR) of fish fed SP 1 , MP 1 and MP 2 diets were significantly higher than those of fish fed control diet (P < 0.05). Superoxide dismutase (SOD) activity of fish fed MP 2 diet was significantly higher than those of fish fed OTC diet (P < 0.05). Nitro blue tetrazolium (NBT) activity and lysozyme activity of fish fed SP 1 , MP 1 and MP 2 diets were significantly higher than those of fish fed OTC diet (P < 0.05). However, there was no significant difference among fish fed SP 1 , SP 2 , MP 1 and MP 2 diets. During the Edwardsiella tarda challenge test, the first mortality occurred on day 2. After the 14 days challenge test, cumulative survival rate of fish fed MP 1 and MP 2 diets were significantly higher than those of fish fed control diet (P < 0.05). However, there was no significant difference among fish fed SP 1 , SP 2 , MP 1 , MP 2 and OTC diets in survival rate at the termination of the challenge test. Although there was little advantage in immunological parameters with fish fed MP diets, single and multi-probiotics were equally effective statistically. These results demonstrated that single or multi-probiotics had equal beneficial effect as an antibiotic replacer in terms of growth performance, non-specific immune responses and disease resistance in starry flounder. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison between Humphrey Field Analyzer and Micro Perimeter 1 in normal and glaucoma subjects.

PubMed

Ratra, Vineet; Ratra, Dhanashree; Gupta, Muneeswar; Vaitheeswaran, K

2012-05-01

To determine the correlation between fundus perimetry with Micro Perimeter 1 (MP1) and conventional automated static threshold perimetry using the Humphrey Field Analyzer (HFA) in healthy individuals and in subjects with glaucoma. In this study, we enrolled 45 eyes with glaucoma and 21 eyes of age-matched, healthy individuals. All subjects underwent complete ophthalmic examination. Differential light sensitivity was measured at 21 corresponding points in a rectangular test grid in both MP1 and HFA. Similar examination settings were used with Goldmann III stimulus, stimulus presentation time of 200 ms, and white background illumination (1.27 cd/m(2)). Statistical analysis was done with the SPSS 14 using linear regression and independent t-test. The mean light thresholds of 21 matching points in control group with MP1 and HFA were 14.97 ± 2.64 dB and 30.90 ± 2.08 dB, respectively. In subjects with glaucoma, the mean values were MP1: 11.73 ± 4.36 dB and HFA: 27.96 ± 5.41 dB. Mean difference of light thresholds among the two instruments was 15.86 ± 3.25 dB in normal subjects (P < 0.001) and 16.22 ± 2.77 dB in glaucoma subjects (P < 0.001). Pearson correlation analysis of the HFA and MP1 results for each test point location in both cases and control subjects showed significant positive correlation (controls, r = 0.439, P = 0.047; glaucoma subjects, r = 0.812, P < 0.001). There was no difference between nasal and temporal points but a slight vertical asymmetry was observed with MP1. There are significant and reproducible differences in the differential light threshold in MP1 and HFA in both normal and glaucoma subjects. We found a correction factor of 17.271 for comparison of MP1 with HFA. MP1 appeared to be more sensitive in predicting loss in glaucoma.

Morphological and glycan features of the camel oviduct epithelium.

PubMed

Accogli, Gianluca; Monaco, Davide; El Bahrawy, Khalid Ahmed; El-Sayed, Ashraf Abd El-Halim; Ciannarella, Francesca; Beneult, Benedicte; Lacalandra, Giovanni Michele; Desantis, Salvatore

2014-07-01

This study describes regional differences in the oviduct of the one-humped camel (Camelus dromedarius) during the growth phase (GP) and the mature phase (MP) of the follicular wave by means of morphometry, scanning electron microscopy (SEM) and glycohistochemistry investigations. Epithelium height significantly increased in the ampulla and decreased in the isthmus passing from the GP to the MP. Under SEM, non-ciliated cells displayed apical blebs (secretory) or short microvilli. Cilia glycocalyx expressed glycans terminating with sialic acid linked α2,6 to Gal/GalNAc (SNA affinity) throughout the oviducts of GP and MP and sialic acid linked α2,3 to Galβ1,3GalNAc (MAL II and KOH-sialidase (K-s)-PNA staining) throughout the MP oviducts. Non-ciliated cells displayed lectin-binding sites from the supra-nuclear cytoplasm to the luminal surface. Ampulla non-ciliated cells showed O-linked (mucin-type) sialoglycans (MAL II and K-s-PNA) during GP and MP and N-linked sialoglycans (SNA) during the MP. Isthmus non-ciliated cells expressed SNA reactivity in GP and MP, also K-s-PNA binders in MP, and MAL II and PNA affinity (Galβ1,3GalNAc) during GP. Galβ1,3GalNAc was sialilated in the non-ciliated cells of GP UTJ. Luminal surface lacked of Galβ1,3GalNAc in GP and MP, whereas it expressed α2,6- and α2,3-linked sialic acids. In GP intraluminal substance reacted with SNA, MAL II, K-s-PNA in ampulla and only with MAL II in the isthmus and UTJ. These results demonstrate that the morphology and the glycan pattern of the camel oviductal epithelium vary during the follicular wave and that could relate to the region-specific functions. Copyright © 2014 Elsevier GmbH. All rights reserved.

Purification, antitumor and immunomodulatory activity of polysaccharides from soybean residue fermented with Morchella esculenta.

PubMed

Li, Shuhong; Gao, Ang; Dong, Shuang; Chen, Ye; Sun, Shuang; Lei, Zhongfang; Zhang, Zhenya

2017-03-01

Crude polysaccharides (MPS) from soybean residue fermented with Morchella esculenta were extracted and purified by DEAE Sephadex A-50 chromatography and Sephadex G-100 size-exclusion chromatography in sequence. Three main fractions MP-1, MP-3 and MP-4 were obtained during the purification steps. The recovery rates based on MPS used were 26.2%, 29.1% and 18.7% for MP-1, MP-3 and MP-4 respectively. The monosaccharide composition, ultraviolet spectrum, infrared spectrum and NMR of the three fractions were analyzed. Furthermore, the influence of polysaccharides fractions upon activation of macrophage cells (RAW 264.7), antitumor activities of the human hepatocellular cell line (HepG-2) and human cervical carcinoma cells (Hela) in vitro were evaluated. The results indicated that the proliferation of MP-3 on RAW 264.7 was 313.57% at 25μg/mL, which is high while MP-1 had a higher growth inhibition effect on HepG-2 cells of 68.01% at concentration of 50μg/mL. The fractions of MP-1, MP-3 and MP-4 induced apoptosis in HepG-2 cells and Hela cells by arresting cell cycle progression at the G 0 /G 1 phase. These findings suggest that the purified polysaccharides fractions may be a potent candidate for human hepatocellular and cervical carcinoma treatment and prevention in functional foods and pharmacological fields. Copyright © 2016 Elsevier B.V. All rights reserved.

Lasagna-type arrays with halide-nitromethane cluster filling. The first recognition of the Hal(-)···HCH2NO2 (Hal = Cl, Br, I) hydrogen bonding.

PubMed

Gushchin, Pavel V; Kuznetsov, Maxim L; Wang, Qian; Karasik, Andrey A; Haukka, Matti; Starova, Galina L; Kukushkin, Vadim Yu

2012-06-21

The previously predicted ability of the methyl group of nitromethane to form hydrogen bonding with halides is now confirmed experimentally based on X-ray data of novel nitromethane solvates followed by theoretical ab initio calculations at the MP2 level of theory. The cationic (1,3,5-triazapentadiene)Pt(II) complexes [Pt{HN=C(NC(5)H(10))N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [1](Hal)(2) (Hal = Cl, Br, I), and [Pt{HN=C(NC(4)H(8)O)N(Ph)C(NH(2))=NPh}(2)](Cl)(2), [2](Cl)(2), were crystallized from MeNO(2)-containing systems providing nitromethane solvates studied by X-ray diffraction. In the crystal structure of [1][(Hal)(2)(MeNO(2))(2)] (Hal = Cl, Br, I) and [2][(Cl)(2)(MeNO(2))(2)], the solvated MeNO(2) molecules occupy vacant spaces between lasagna-type layers and connect to the Hal(-) ion through a weak hydrogen bridge via the H atom of the methyl thus forming, by means of the Hal(-)···HCH(2)NO(2) contact, the halide-nitromethane cluster "filling". The quantum-chemical calculations demonstrated that the short distance between the Hal(-) anion and the hydrogen atom of nitromethane in clusters [1][(Hal)(2)(MeNO(2))(2)] and [2][(Cl)(2)(MeNO(2))(2)] is not just a consequence of the packing effect but a result of the moderately strong hydrogen bonding.

Pyrrole multimers and pyrrole-acetylene hydrogen bonded complexes studied in N2 and para-H2 matrixes using matrix isolation infrared spectroscopy and ab initio computations

NASA Astrophysics Data System (ADS)

Sarkar, Shubhra; Ramanathan, N.; Gopi, R.; Sundararajan, K.

2017-12-01

Hydrogen bonded interaction of pyrrole multimer and acetylene-pyrrole complexes were studied in N2 and p-H2 matrixes. DFT computations showed T-shaped geometry for the pyrrole dimer and cyclic complex for the trimer and tetramer were the most stable structures, stabilized by Nsbnd H⋯π interactions. The experimental vibrational wavenumbers observed in N2 and p-H2 matrixes for the pyrrole multimers were correlated with the computed wavenumbers. Computations performed at MP2/aug-cc-pVDZ level of theory showed that C2H2 and C4H5N forms 1:1 hydrogen-bonded complexes stabilized by Csbnd H⋯π interaction (Complex A), Nsbnd H⋯π interaction (Complex B) and π⋯π interaction (Complex C), where the former complex is the global minimum and latter two complexes were the first and second local minima, respectively. Experimentally, 1:1 C2H2sbnd C4H5N complexes A (global minimum) and B (first local minimum) were identified from the shifts in the Nsbnd H stretching, Nsbnd H bending, Csbnd H bending region of pyrrole and Csbnd H asymmetric stretching and bending region of C2H2 in N2 and p-H2 matrixes. Computations were also performed for the higher complexes and found two minima corresponding to the 1:2 C2H2sbnd C4H5N and three minima for the 2:1 C2H2sbnd C4H5N complexes. Experimentally the global minimum 1:2 and 2:1 C2H2sbnd C4H5N complexes were identified in N2 and p-H2 matrixes.

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

Apheresis platelet concentrates contain platelet-derived and endothelial cell-derived microparticles.

PubMed

Rank, A; Nieuwland, R; Liebhardt, S; Iberer, M; Grützner, S; Toth, B; Pihusch, R

2011-02-01

Microparticles (MP) are membrane vesicles with thrombogenic and immunomodulatory properties. We determined MP subgroups from resting platelets, activated platelets and endothelial cells in donors and apheresis platelet concentrates (PC). MP were double stained with annexin V and CD61 (platelet-derived MP; PMP), P-selectin or CD63 (MP from activated platelets) and CD144 plus E-selectin (endothelial cell-derived MP; EMP) and detected by flow cytometry in platelet donors (n=36) and apheresis PC (n=11; Trima™). PC contained MP, mainly from resting platelets [93% (90-95)], and minor fractions of PMP from activated platelets [P-selectin(+) or CD63(+); 4·8% (3·2-7·7) and 2·6% (2·0-4·0)]. Compared to donors, levels of annexin V+ MP, PMP, P-selectin(+) and CD63(+) MP were 1·7-, 2·3-, 8·6- and 3·1-fold higher in PC (all P<0·05). During storage (1-5 days), levels of annexin V+ MP and PMP did not increase, although small increases in the fraction of P-selectin(+) or CD63(+) MP occurred (both P<0·05). PC also contained EMP, which were 2·6- to 3·7-fold enriched in PC compared to donors (P<0·05). Transfusion of apheresis PC also results in transfusion of HLA-carrying PMP and EMP. This might counteract the aim of reducing transfused HLA load by leucodepletion. The increases in PMP exposing P-selectin or CD63 reflect mild platelet activation during storage. We conclude that in leucodepleted platelet apheresis using fluidized particle bed technology, MP are harvested mainly from the donor by apheresis. Improvement in apheresis technology might reduce MP load. © 2010 The Author(s). Vox Sanguinis © 2010 International Society of Blood Transfusion.

Engineering mesenchymal stem cell spheroids by incorporation of mechanoregulator microparticles.

PubMed

Abbasi, Fatemeh; Ghanian, Mohammad Hossein; Baharvand, Hossein; Vahidi, Bahman; Eslaminejad, Mohamadreza Baghaban

2018-05-03

Mechanical forces throughout human mesenchymal stem cell (hMSC) spheroids (mesenspheres) play a predominant role in determining cellular functions of cell growth, proliferation, and differentiation through mechanotransductional mechanisms. Here, we introduce microparticle (MP) incorporation as a mechanical intervention method to alter tensional homeostasis of the mesensphere and explore MSC differentiation in response to MP stiffness. The microparticulate mechanoregulators with different elastic modulus (34 kPa, 0.6 MPa, and 2.2 MPa) were prepared by controlled crosslinking cell-sized microdroplets of polydimethylsiloxane (PDMS). Preparation of MP-MSC composite spheroids enabled us to study the possible effects of MPs through experimental and computational assays. Our results showed that MP incorporation selectively primed MSCs toward osteogenesis, yet hindered adipogenesis. Interestingly, this behavior depended on MP mechanics, as the spheroids that contained MPs with intermediate stiffness behaved similar to control MP-free mesenspheres with more tendencies toward chondrogenesis. However, by using the soft or stiff MPs, the MP-mesenspheres significantly showed signs of osteogenesis. This could be explained by the complex of forces which acted in the cell spheroid and, totally, provided a homeostasis situation. Incorporation of cell-sized polymer MPs as mechanoregulators of cell spheroids could be utilized as a new engineering toolkit for multicellular organoids in disease modeling and tissue engineering applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer

NASA Astrophysics Data System (ADS)

Hameed, Rabia; Khan, Afsar; van Mourik, Tanja

2018-05-01

B3LYP and MP2 calculations with the commonly-used 6-31+G(d) basis set predict qualitatively different structures for the Tyr-Gly conformer book1, which is the most stable conformer identified in a previous study. The structures differ mainly in the ψtyr Ramachandran angle (138° in the B3LYP structure and 120° in the MP2 structure). The causes for the discrepant structures are attributed to missing dispersion in the B3LYP calculations and large intramolecular BSSE in the MP2 calculations. The correct ψtyr value is estimated to be 130°. The MP2/6-31+G(d) profile identified an additional conformer, not present on the B3LYP surface, with a ψtyr value of 96° and a more folded structure. This minimum is, however, likely an artefact of large intramolecular BSSE values. We recommend the use of basis sets of at least quadruple-zeta quality in density functional theory (DFT), DFTaugmented with an empirical dispersion term (DFT-D) and second-order Møller-Plesset perturbation theory (MP2 ) calculations in cases where intramolecular BSSE is expected to be large.

Prolonged methylprednisolone therapy after the pulse treatment for patients with moderate-to-severe paraquat poisoning: A retrospective analysis.

PubMed

Gao, Jie; Feng, ShunYi; Wang, Jian; Yang, SiYuan; Li, Yong

2017-06-01

This retrospective study aims to evaluate the effect of prolonged methylprednisolone (MP) therapy on the mortality of patients with moderate-to-severe paraquat (PQ) poisoning after the pulse treatment.We performed a retrospective analysis of patients with acute moderate-to-severe PQ poisoning that were admitted to the emergency department from May 2012 to August 2016. Out of 138 patients, 60 were treated with pulse treatment (15 mg kg day MP for 3 days) and 78 were treated with prolonged MP therapy after pulse treatment (15 mg kg day MP for 3 days; afterward, the dosage was reduced in half every 2 days, and the MP therapy was terminated until 0.47 mg kg day). Kaplan-Meier method was used to compare the mortality between the 2 groups. Cox proportional hazard models were used to estimate the hazard ratios (HR) and 95% confidence intervals (CI).The mortality of the prolonged MP therapy after pulse treatment group was lower than that of the pulse group (47.4% vs 63.3%; log-rank tests, P  =  .003). According to the multivariate Cox analysis, the prolonged MP therapy after pulse treatment was significantly associated with a lower mortality risk (HR: 0.31, 95% CI: 0.19-0.52, P < .001) compared with the pulse group. In addition, the prolonged MP therapy after pulse treatment caused more incidences of leucopenia than the pulse treatment alone (25.6% vs 11.7%, P  =  .04).The prolonged MP therapy after pulse treatment can reduce the mortality of moderate-to-severe PQ poisoning patients.

Mechanism of action of a novel recombinant peptide, MP1102, against Clostridium perfringens type C.

PubMed

Zong, Lifen; Teng, Da; Wang, Xiumin; Mao, Ruoyu; Yang, Na; Hao, Ya; Wang, Jianhua

2016-06-01

This work is the first to report the antibacterial characteristics and antibacterial mechanisms of MP1102, which is a variant of NZ2114, against pathogenic Clostridium perfringens. MP1102 exhibited strong antimicrobial activity against C. perfringens strains CVCC 61, CVCC 1163, and CVCC 2032 at a low minimal inhibitory concentration (MIC) of 0.91 μM. MP1102 showed anti-C. perfringens activity over a wide pH range of 2.0 and 10.0, high thermal stability from 20 to 80 °C, and remarkable resistance to pepsin. The fractional inhibitory concentration index (FICI) indicated an additive or synergic effect between MP1102 and bacitracin zinc, nisin, vancomycin, virginiamycin, aureomycin, and ampicillin against C. perfringens (FICI = 0.3125-1.0). To further elucidate the antibacterial mechanism of MP1102, its effect on the C. perfringens CVCC 61 cell membrane and intracellular DNA was studied. Flow cytometry and scanning electron microscopy (SEM) indicated that MP1102 treatment resulted in the release of cellular contents by damaging the membrane. A DNA gel retardation and circular dichroism analysis demonstrated that MP1102 interacted with DNA and intercalated into the DNA base pairs. A cell cycle assay demonstrated that MP1102 affected cellular functions, such as DNA synthesis. These results suggested that MP1102 exhibited potential as a new antimicrobial agent against C. perfringens infections.

Oral administration of non-absorbable delayed release 6-mercaptopurine is locally active in the gut, exerts a systemic immune effect and alleviates Crohn’s disease with low rate of side effects: results of double blind Phase II clinical trial

PubMed Central

Israeli, E; Goldin, E; Fishman, S; Konikoff, F; Lavy, A; Chowers, Y; Melzer, E; Lahat, A; Mahamid, M; Shirin, H; Nussinson, E; Segol, O; Ya’acov, A Ben; Shabbat, Y; Ilan, Y

2015-01-01

Therapy for Crohn’s disease (CD) with thiopurines is limited by systemic side effects. A novel formulation of fixed-dose, delayed-release 6-mercaptopurine (DR-6MP) was developed, with local effect on the gut immune system and minimal absorption. The aim of this study was to evaluate the safety and efficacy of DR-6MP in patients with moderately severe CD compared to systemically delivered 6-mercaptopurine (Purinethol). Seventy CD patients were enrolled into a 12-week, double-blind controlled trial. The primary end-point was the percentage of subjects with clinical remission [Crohn’s Disease Activity Index (CDAI) < 150] or clinical response (100-point CDAI reduction). Twenty-six (56·5%) and 13 (54·2%) subjects from the DR-6MP and Purinethol cohorts, respectively, completed the study. DR-6MP had similar efficacy to Purinethol following 12 weeks of treatment. However, the time to maximal clinical response was 8 weeks for DR-6MP versus 12 weeks for Purinethol. A higher proportion of patients on DR-6MP showed clinical remission at week 8. A greater improvement in Inflammatory Bowel Disease Questionnaire (IBDQ) score was noted in the DR-6MP group. DR-6MP led to a decrease of CD62+ expression on T cells, implying a reduction of lymphocyte adhesion to site of inflammation. DR-6MP was safer than Purinethol, with significantly fewer adverse events (AEs). There was no evidence of drug-induced leucopenia in the DR-6MP group; the proportion of subjects who developed hepatotoxicity was lower for the DR-6MP. Non-absorbable DR-6MP is safe and biologically active in the gut. It is clinically effective, exerting a systemic immune response with low systemic bioavailability and a low incidence of side effects. PMID:25846055

Oral administration of non-absorbable delayed release 6-mercaptopurine is locally active in the gut, exerts a systemic immune effect and alleviates Crohn's disease with low rate of side effects: results of double blind Phase II clinical trial.

PubMed

Israeli, E; Goldin, E; Fishman, S; Konikoff, F; Lavy, A; Chowers, Y; Melzer, E; Lahat, A; Mahamid, M; Shirin, H; Nussinson, E; Segol, O; Ya'acov, A Ben; Shabbat, Y; Ilan, Y

2015-08-01

Therapy for Crohn's disease (CD) with thiopurines is limited by systemic side effects. A novel formulation of fixed-dose, delayed-release 6-mercaptopurine (DR-6MP) was developed, with local effect on the gut immune system and minimal absorption. The aim of this study was to evaluate the safety and efficacy of DR-6MP in patients with moderately severe CD compared to systemically delivered 6-mercaptopurine (Purinethol). Seventy CD patients were enrolled into a 12-week, double-blind controlled trial. The primary end-point was the percentage of subjects with clinical remission [Crohn's Disease Activity Index (CDAI) < 150] or clinical response (100-point CDAI reduction). Twenty-six (56·5%) and 13 (54·2%) subjects from the DR-6MP and Purinethol cohorts, respectively, completed the study. DR-6MP had similar efficacy to Purinethol following 12 weeks of treatment. However, the time to maximal clinical response was 8 weeks for DR-6MP versus 12 weeks for Purinethol. A higher proportion of patients on DR-6MP showed clinical remission at week 8. A greater improvement in Inflammatory Bowel Disease Questionnaire (IBDQ) score was noted in the DR-6MP group. DR-6MP led to a decrease of CD62(+) expression on T cells, implying a reduction of lymphocyte adhesion to site of inflammation. DR-6MP was safer than Purinethol, with significantly fewer adverse events (AEs). There was no evidence of drug-induced leucopenia in the DR-6MP group; the proportion of subjects who developed hepatotoxicity was lower for the DR-6MP. Non-absorbable DR-6MP is safe and biologically active in the gut. It is clinically effective, exerting a systemic immune response with low systemic bioavailability and a low incidence of side effects. © 2015 British Society for Immunology.

[Physiological and hygienic assessment of the impact of mobile phones with various radiation intensity on the functional state of brain of children and adolescents according to electroencephalographic data].

PubMed

Vyatleva, O A; Teksheva, L M; Kurgansky, A M

To test the effect of mobile phones (MP) of various radiation intensities on the functional state of the brain in children and adolescents, a sham-controlled EEG-study was conducted in a group of thirteen 6-13 years old children, including eight 6-10 years old children. The study showed that a 3-minute exposure to the MP causes the significant decline in alpha-band absolute power, which depends on the radiation intensity and the user’s age. Different from sham, an EEG-effect of MP with the energy flux density (EFD) about 100 mW/cm2 was registered both in total, and in a younger (6-10 yr) group. Its bilateral character, more prominent in the hemisphere that is ipsilateral to MP, indicates that this intensity of the radiation influences not only the superficial cortical areas of the ipsilateral hemisphere, but also the deep structures of the brain. MP with the EFD less than 1 mW/cm2 differed from sham by EEG-effect only in the group of children who are 6-10 years old. Its local, ipsilateral character indicates to the superficial influence of such intensity of the radiation on the cortex of the ipsilateral hemisphere. The results show that for the regulation of MP-radiation it’s necessary to consider age features of the brain’s response. The high significance of the EFD, as an index in the assessment of the impact of MP on the EEG of children, is shown. Since almost all schoolchildren are the users of mobile phones, the situation with the valuation of MP-effects on children of various ages, requires hygienic solution.

A novel 6-mercaptopurine oral liquid formulation for pediatric acute lymphoblastic leukemia patients - results of a randomized clinical trial.

PubMed

Hanff, Lidwien M; Mathot, Ron A A; Smeets, Oscar; Postma, Doerine J; Ramnarain, Satianand; Vermes, Andras; Pieters, Rob; Zwaan, C Michel

2014-08-01

Pediatric patients with acute lymphoblastic leukemia (ALL) are treated with oral 6-mercaptopurine (6MP) for nearly 2 years, but no pediatric formulation has been available. In this study, an oral 6MP liquid suitable for pediatric use was developed and tested in the target population. A randomized cross-over study was performed in 20 pediatric ALL patients (age 1.9 - 14.6 years), comparing pharmacokinetics and pharmacodynamics of a newly developed 6MP liquid formulation to 6MP capsules, both taken orally for 4 weeks. Based upon trough levels of the principal active metabolite,6-thioguanine nucleotides (6-TGN),a relative bioavailability of the liquid vs. capsules of 1.01 was found (90% CI 0.86 - 1.20), demonstrating bioequivalence. This was supported by the similarly observed 6MP dosages needed for leucocyte depletion, for both formulations (35 mg/day (range 10 - 115 mg)). 75% of the parents/patients (p = 0.005) preferred the oral liquid over the capsules because of the ease of administration. We conclude that the novel 6MP liquid is a promising treatment for ALL.

Mucuna pruriens in Parkinson disease: A double-blind, randomized, controlled, crossover study.

PubMed

Cilia, Roberto; Laguna, Janeth; Cassani, Erica; Cereda, Emanuele; Pozzi, Nicolò G; Isaias, Ioannis U; Contin, Manuela; Barichella, Michela; Pezzoli, Gianni

2017-08-01

To investigate whether Mucuna pruriens (MP), a levodopa-containing leguminous plant growing in all tropical areas worldwide, may be used as alternative source of levodopa for indigent individuals with Parkinson disease (PD) who cannot afford long-term therapy with marketed levodopa preparations. We investigated efficacy and safety of single-dose intake of MP powder from roasted seeds obtained without any pharmacologic processing. Eighteen patients with advanced PD received the following treatments, whose sequence was randomized: (1) dispersible levodopa at 3.5 mg/kg combined with the dopa-decarboxylase inhibitor benserazide (LD+DDCI; the reference treatment); (2) high-dose MP (MP-Hd; 17.5 mg/kg); (3) low-dose MP (MP-Ld; 12.5 mg/kg); (4) pharmaceutical preparation of LD without DDCI (LD-DDCI; 17.5 mg/kg); (5) MP plus benserazide (MP+DDCI; 3.5 mg/kg); (6) placebo. Efficacy outcomes were the change in motor response at 90 and 180 minutes and the duration of on state. Safety measures included any adverse event (AE), changes in blood pressure and heart rate, and the severity of dyskinesias. When compared to LD+DDCI, MP-Ld showed similar motor response with fewer dyskinesias and AEs, while MP-Hd induced greater motor improvement at 90 and 180 minutes, longer ON duration, and fewer dyskinesias. MP-Hd induced less AEs than LD+DDCI and LD-DDCI. No differences in cardiovascular response were recorded. Single-dose MP intake met all noninferiority efficacy and safety outcome measures in comparison to dispersible levodopa/benserazide. Clinical effects of high-dose MP were similar to levodopa alone at the same dose, with a more favorable tolerability profile. NCT02680977. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

The structure, stability, and infrared spectrum of B 2N, B 2N +, B 2N -, BO, B 2O and B 2N 2.

NASA Astrophysics Data System (ADS)

Martin, J. M. L.; François, J. P.; Gijbels, R.

1992-05-01

The structure, infrared spectrum, and heat of formation of B 2N, B 2N -, BO, and B 2O have been studied ab initio. B 2N is very stable; B 2O even more so. B 2N, B 2N -, B 2O, and probably B 2N + have symmetric linear ground-state structures; for B 2O, an asymmetric linear structure lies about 12 kcal/mol above the ground state. B 2N +, B 2N - and B 2O have intense asymmetric stretching frequencies, predicted near 870, 1590 and 1400 cm -1, respectively. Our predicted harmonic frequencies and isotopic shifts for B 2O confirm the recent experimental identification by Andrews and Burkholder. Absorptions at 1889.5 and 1998.5 cm -1 in noble-gas trapped boron nitride vapor belong the BNB and BNBN ( 3Π), respectively; a tentative assignment of 882.5 cm -1 to BNB + is proposed. Total atomization energies Σ De (Σ D0) are computed (accuracy ±2 kcal/mol) as: BO 193.1 (190.4), B 2O 292.5 (288.7), B 2N 225.0 (250.3) kcal/mol. The ionization potential and electron affinity of B 2N are predicted to be 8.62±0.1 and 3.34±0.1 eV. The MP4-level additivity approximations involved in G1 theory results in errors on the order of 1 kcal/mol in the Σ De values.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov; Weare, Jonathan Q., E-mail: weare@uchicago.edu; Weare, John H., E-mail: jweare@ucsd.edu

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for themore » trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.« less

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.

PubMed

Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L

2016-07-14

Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

Evaluation of work stress, turnover intention, work experience, and satisfaction with preceptors of new graduate nurses using a 10-minute preceptor model.

PubMed

Hu, Yi-Chun; Chen, Su-Ru; Chen, I-Hui; Shen, Hsi-Che; Lin, Yen-Kuang; Chang, Wen-Yin

2015-06-01

Preparing new graduate nurses (NGNs) to achieve standards of nursing competence is challenging; therefore, this study developed and evaluated the effects of a 10-minute preceptor (10MP) model for assisting NGNs in their professional development and increasing their retention in hospitals. A repeated-measures design study, with an intervention and a two-group comparison, was conducted. A total of 107 NGNs participated in the study. At day 7, work stress and work experience were moderately high for the NGNs in both the 10MP and traditional preceptor model (TPM) groups. The preceptorship program showed significant differences between groups (p = 0.001) regarding work stress at months 2 and 3 and work experience at months 1, 2, and 3. The 10MP group reported lower turnover intention and higher satisfaction with the preceptors than the TPM group. The 10MP model is effective at improving training outcomes and facilitating the professional development of NGNs. Copyright 2015, SLACK Incorporated.

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

PubMed Central

Rodríguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Akerboom, Jasper; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.

2008-01-01

Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way. PMID:18607093

Implementation of a 5-Minute Magnetic Resonance Imaging Screening Protocol for Prostate Cancer in Men With Elevated Prostate-Specific Antigen Before Biopsy.

PubMed

Weiss, Jakob; Martirosian, Petros; Notohamiprodjo, Mike; Kaufmann, Sascha; Othman, Ahmed E; Grosse, Ulrich; Nikolaou, Konstantin; Gatidis, Sergios

2018-03-01

The aims of this study were to establish a 5-minute magnetic resonance (MR) screening protocol for prostate cancer in men before biopsy and to evaluate effects on Prostate Imaging Reporting and Data System (PI-RADS) V2 scoring in comparison to a conventional, fully diagnostic multiparametric MR imaging (mpMRI) approach. Fifty-two patients with elevated prostate-specific antigen levels and without prior biopsy were prospectively included in this institutional review board-approved study. In all patients, an mpMRI protocol according to the PI-RADS recommendations was acquired on a 3 T MRI system. In addition, an accelerated diffusion-weighted imaging sequence was acquired using simultaneous multislice technique (DW-EPISMS). Two readers independently evaluated the images for the presence/absence of prostate cancer according to the PI-RADS criteria and for additional findings. In a first reading session, only the screening protocol consisting of axial T2-weighted and DW-EPISMS images was made available. In a subsequent reading session, the mpMRI protocol was assessed blinded to the results of the first reading, serving as reference standard. Both readers successfully established a final diagnosis according to the PI-RADS criteria in the screening and mpMRI protocol. Mean lesion size was 1.2 cm in the screening and 1.4 cm in the mpMRI protocol (P = 0.4) with 35% (18/52) of PI-RADS IV/V lesions. Diagnostic performance of the screening protocol was excellent with a sensitivity and specificity of 100% for both readers with no significant differences in comparison to the mpMRI standard (P = 1.0). In 3 patients, suspicious lymph nodes were reported as additional finding, which were equally detectable in the screening and mpMRI protocol. A 5-minute MR screening protocol for prostate cancer in men with elevated prostate-specific antigen levels before biopsy is applicable for clinical routine with similar diagnostic performance as the full diagnostic mpMRI approach.

Immunomodulation of Parkinson's disease using Mucuna pruriens (Mp).

PubMed

Rai, Sachchida Nand; Birla, Hareram; Zahra, Walia; Singh, Saumitra Sen; Singh, Surya Pratap

2017-11-01

Immune control is associated with nigrostriatal neuroprotection for Parkinson's disease (PD); though its direct cause and effect relationships have not yet been realized and modulating the immune system for therapeutic gain has been openly discussed. While the pathobiology of PD remains in study, neuroinflammation is thought to speed nigrostriatal degeneration. The neuroinflammatory cascade associated with PD begins with aggregation of misfolded or post-translationally modified α-synuclein (α-syn). Such aggregation results in neuronal cell death and the presence of chronically activated glia (microglia and astroglia), leading to the production of proinflammatory cytokines like tumor necrosis factor alpha (TNF-α), interleukin-1 beta (IL-1β), IL-6, and enzymes such as nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and cyclooxygenase-2 (COX-2). These changes in the glial phenotype can affect the central nervous system (CNS) microenvironment by producing a pro-inflammatory milieu that speeds PD pathogenesis. Mucuna pruriens (Mp) is the most popular drug in Ayurveda, the Indian system of medicine. Several reports have suggested that it possesses analgesic, anti-inflammatory, anti-neoplastic, anti-epileptic and anti-microbial activities. Mp contain L-DOPA and ursolic acid which has an anti-inflammatory property. There are very few literatures which show the immunomodulatory activity of Mp in PD, several researchers have tried to work on the immunomodulatory activity of Mp in some other diseases. The results of several studies show that Mp modulate the immune components like TNF-α, IL-6, IFN-λ, IL-1β, iNOS and IL-2 in the CNS. It also modulates the activity of the transcription factor NF-kB which plays an important role in the progression of the PD. Thus, by altering these cytokines or transcription factors, Mp protects or prevents the progression of PD. Thus in this review we try to explore the immunomodulatory activity of Mp in PD. Copyright © 2017 Elsevier B.V. All rights reserved.

Methylphenidate and the response to growth hormone treatment in short children born small for gestational age.

PubMed

Renes, Judith S; de Ridder, Maria A J; Breukhoven, Petra E; Lem, Annemieke J; Hokken-Koelega, Anita C S

2012-01-01

Growth hormone (GH) treatment has become a frequently applied growth promoting therapy in short children born small for gestational age (SGA). Children born SGA have a higher risk of developing attention deficit hyperactivity disorder (ADHD). Treatment of ADHD with methylphenidate (MP) has greatly increased in recent years, therefore more children are being treated with GH and MP simultaneously. Some studies have found an association between MP treatment and growth deceleration, but data are contradictory. To explore the effects of MP treatment on growth in GH-treated short SGA children Anthropometric measurements were performed in 78 GH-treated short SGA children (mean age 10.6 yr), 39 of whom were also treated with MP (SGA-GH/MP). The SGA-GH/MP group was compared to 39 SGA-GH treated subjects. They were matched for sex, age and height at start of GH, height SDS at start of MP treatment and target height SDS. Serum insulin-like growth factor-I (IGF-I) and IGF binding protein-3 (IGFBP-3) levels were yearly determined. Growth, serum IGF-I and IGFBP-3 levels during the first three years of treatment were analyzed using repeated measures regression analysis. The SGA-GH/MP group had a lower height gain during the first 3 years than the SGA-GH subjects, only significant between 6 and 12 months of MP treatment. After 3 years of MP treatment, the height gain was 0.2 SDS (± 0.1 SD) lower in the SGA-GH/MP group (P = 0.17). Adult height was not significantly different between the SGA-GH/MP and SGA-GH group (-1.9 SDS and -1.9 SDS respectively, P = 0.46). Moreover, during the first 3 years of MP treatment IGF-I and IGFBP-3 measurements were similar in both groups. MP has some negative effect on growth during the first years in short SGA children treated with GH, but adult height is not affected.

Can Motor Proficiency in Preschool Age Affect Physical Activity in Adolescence?

PubMed

Venetsanou, Fotini; Kambas, Antonis

2017-05-01

This study investigated if motor proficiency (MP) in preschool age associate with physical activity (PA) in adolescence. In 2004, the Bruininks-Oseretsky Test of Motor Proficiency-Short Form (BOTMP-SF) (7) was administered to 413 children, aged 4-6 years, who were classified to MP groups according to their BOTMP-SF total score (TS). In 2014, the PA of 106 former participants (47 boys, 59 girls) was measured with Omron pedometers. MP [three (high; above average; average)] × gender (two) ANOVA and Bonferroni tests were computed on average of steps/week. A significant interaction between the two factors was revealed (F = 15.27, p < .001, η 2 =.153), indicating that MP influenced male and female PA differently. Only in average MP group, males presented higher PA than females, whereas there were no differences between the two genders in the higher MP groups. Moreover, the only significant difference in PA among male groups was that between high and above average MP groups, while in females there were significant differences among all groups. High MP at preschool age positively associated with the PA in adolescence, especially in females. Emphasis on the development of proficient young movers might be beneficial for lifelong PA.

Preferential inhibition of xanthine oxidase by 2-amino-6-hydroxy-8-mercaptopurine and 2-amino-6-purine thiol

PubMed Central

Kalra, Sukirti; Jena, Gopabandhu; Tikoo, Kulbhushan; Mukhopadhyay, Anup Kumar

2007-01-01

Background The anticancer drug, 6-mercaptopurine (6MP) is subjected to metabolic clearance through xanthine oxidase (XOD) mediated hydroxylation, producing 6-thiouric acid (6TUA), which is excreted in urine. This reduces the effective amount of drug available for therapeutic efficacy. Co-administration of allopurinol, a suicide inhibitor of XOD, which blocks the hydroxylation of 6MP inadvertently enhances the 6MP blood level, counters this reduction. However, allopurinol also blocks the hydroxylation of hypoxanthine, xanthine (released from dead cancer cells) leading to their accumulation in the body causing biochemical complications such as xanthine nephropathy. This necessitates the use of a preferential XOD inhibitor that selectively inhibits 6MP transformation, but leaves xanthine metabolism unaffected. Results Here, we have characterized two such unique inhibitors namely, 2-amino-6-hydroxy-8-mercaptopurine (AHMP) and 2-amino-6-purinethiol (APT) on the basis of IC50 values, residual activity in bi-substrate simulative reaction and the kinetic parameters like Km, Ki, kcat. The IC50 values of AHMP for xanthine and 6MP as substrate are 17.71 ± 0.29 μM and 0.54 ± 0.01 μM, respectively and the IC50 values of APT for xanthine and 6MP as substrates are 16.38 ± 0.21 μM and 2.57 ± 0.08 μM, respectively. The Ki values of XOD using AHMP as inhibitor with xanthine and 6MP as substrate are 5.78 ± 0.48 μM and 0.96 ± 0.01 μM, respectively. The Ki values of XOD using APT as inhibitor with xanthine and 6MP as substrate are 6.61 ± 0.28 μM and 1.30 ± 0.09 μM. The corresponding Km values of XOD using xanthine and 6MP as substrate are 2.65 ± 0.02 μM and 6.01 ± 0.03 μM, respectively. The results suggest that the efficiency of substrate binding to XOD and its subsequent catalytic hydroxylation is much superior for xanthine in comparison to 6MP. In addition, the efficiency of the inhibitor binding to XOD is much more superior when 6MP is the substrate instead of xanthine. We further undertook the toxicological evaluation of these inhibitors in a single dose acute toxicity study in mice and our preliminary experimental results suggested that the inhibitors were equally non-toxic in the tested doses. Conclusion We conclude that administration of either APT or AHMP along with the major anti-leukemic drug 6MP might serve as a good combination cancer chemotherapy regimen. PMID:17511860

The Dominant-Negative Inhibition of Double-Stranded RNA-Dependent Protein Kinase PKR Increases the Efficacy of Rift Valley Fever Virus MP-12 Vaccine

PubMed Central

Lihoradova, Olga; Kalveram, Birte; Indran, Sabarish V.; Lokugamage, Nandadeva; Juelich, Terry L.; Hill, Terence E.; Tseng, Chien-Te K.; Gong, Bin; Fukushi, Shuetsu; Morikawa, Shigeru; Freiberg, Alexander N.

2012-01-01

Rift Valley fever virus (RVFV), belonging to the genus Phlebovirus, family Bunyaviridae, is endemic to sub-Saharan Africa and causes a high rate of abortion in ruminants and hemorrhagic fever, encephalitis, or blindness in humans. MP-12 is the only RVFV strain excluded from the select-agent rule and handled at a biosafety level 2 (BSL2) laboratory. MP-12 encodes a functional major virulence factor, the NSs protein, which contributes to its residual virulence in pregnant ewes. We found that 100% of mice subcutaneously vaccinated with recombinant MP-12 (rMP12)-murine PKRN167 (mPKRN167), which encodes a dominant-negative form of mouse double-stranded RNA (dsRNA)-dependent protein kinase (PKR) in place of NSs, were protected from wild-type (wt) RVFV challenge, while 72% of mice vaccinated with MP-12 were protected after challenge. rMP12-mPKRN167 induced alpha interferon (IFN-α) in sera, accumulated RVFV antigens in dendritic cells at the local draining lymph nodes, and developed high levels of neutralizing antibodies, while parental MP-12 induced neither IFN-α nor viral-antigen accumulation at the draining lymph node yet induced a high level of neutralizing antibodies. The present study suggests that the expression of a dominant-negative PKR increases the immunogenicity and efficacy of live-attenuated RVFV vaccine, which will lead to rational design of safe and highly immunogenic RVFV vaccines for livestock and humans. PMID:22573861

Genetic Instability of Breast Cancer Cells Induced by Aberrant Expression of hMpS1

DTIC Science & Technology

2004-09-01

and function of the mitotic spindle is dependent on the MpS1 protein kinase. The components of mitotic spindle checkpoints were first identified in...yeast and their homologs of higher organisms were then identified and characterized. These include Bubl, Bub2, Bub3, Madl, Mad2, Mad3 and MpS1 . MpS 1...spindle checkpoint and centrosome duplication (1-6). Although several recent reports demonstrated that vertebrate MpS1 proteins regulate the spindle

The efficacy of low dose azathioprine/6-mercaptopurine in patients with inflammatory bowel disease.

PubMed

Kim, Dong Uk; Kim, Young-Ho; Kim, Beom Jin; Chang, Dong Kyung; Son, Hee Jung; Rhee, Poong-Lyul; Kim, Jae J; Rhee, Jong Chul

2009-01-01

Azathioprine (AZA) and 6-mercaptopurine (6-MP) have been widely used in patients with ulcerative colitis (UC) and Crohn's disease (CD). However, some patients cannot tolerate standard doses (2-2.5 mg/kg for AZA or 1-1.5 mg/kg for 6-MP) due to side effects such as leukopenialneutropenia. The aim of this study was to evaluate the efficacy of low dose AZA/6-MP compared to the standard dose. From 1995 to 2005, 122 patients with UC or CD treated with AZA/6-MP at Samsung Medical Center in Korea were enrolled. We divided these patients into 2 groups (standard dose group versus low dose group) according to the maintenance dose. Among the 122 patients, 17 received the standard dose and 105 received a low dose. The mean maintenance doses were 2.25 mg/kg for the standard dose group and 1.35mg/kg for the low dose group. The clinical outcomes of remission induction, maintenance of remission and relapse rate showed no significant difference in comparisons between these two groups. Low dose AZA/6-MP was as effective as the standard dose for remission induction and maintenance of remission in patients with UC and CD. For patients that develop leukopenia/neutropenia during dose escalation, maintenance therapy with low dose AZA/6-MP should be considered.

Effects of excess metabolizable protein on ovarian function and circulating amino acids of beef cows: 2. Excessive supply in varying concentrations from corn gluten meal.

PubMed

Geppert, T C; Meyer, A M; Perry, G A; Gunn, P J

2017-04-01

In the dairy industry, excess dietary CP is consistently correlated with decreased conception rates. However, amount of excess CP effects on reproductive function in beef cattle is largely undefined. The objective of this experiment was to determine the effects of excess metabolizable protein (MP) supplementation from a moderately abundant rumen undegradable protein (RUP) source (corn gluten meal: 62% RUP) on ovarian function and circulating amino acid (AA) concentrations in beef cows consuming low quality forage. Non-pregnant, non-lactating beef cows (n=16) were allocated by age, BW and body condition score (BCS) to 1 of 2 isocaloric supplements designed to maintain BW for 60 days. Cows had ad libitum access to corn stalks and were individually offered a corn gluten meal-based supplement daily at 125% (MP125) or 150% (MP150) of National Research Council (NRC) MP requirements. After a 20-day supplement adaptation period, cows were synchronized for ovulation. After 10 days of synchronization, follicular growth was reset with gonadotropin releasing hormone. Daily thereafter, transrectal ultrasonography was performed to diagram ovarian follicular waves, and blood samples were collected for hormone, metabolite and AA analyses. After 7 days of observation of estrus, corpus luteum (CL) size was determined via ultrasound. Data were analyzed using the MIXED procedures of SAS. No differences (P⩾0.21) in BW and BCS existed throughout the study; however, plasma urea N at ovulation was greater (P=0.04) in MP150. Preovulatory ovarian follicle size at dominance, duration of dominance, size at spontaneous luteolysis, length of proestrus and wavelength were not different (P⩾0.11) between treatments. However, ovulatory follicles were larger (P=0.04) and average antral follicle count was greater (P=0.01) in MP150 than MP125. Estradiol concentration and ratio of estradiol to ovulatory follicle volume were not different due to treatment (P⩾0.25). While CL volume 7 days post-estrus was greater (P<0.01) in MP150 than MP125, circulating progesterone 7 days post-estrus and ratio of progesterone to CL volume were not different (P⩾0.21). Total AA were not different (P⩾0.76) at study initiation or completion; however, as a percent of total AA, branched-chain AA at ovulation were greater (P=0.02) in MP150. In conclusion, supplementation of CP at 150% of NRC MP requirements from a moderately undegradable protein source may enhance growth of the ovulatory follicle and subsequent CL compared with MP supplementation at 125% of NRC MP requirements.

Formation by yeast of 2-furanmethanethiol and ethyl 2-mercaptopropionate aroma compounds in Japanese soy sauce.

PubMed

Meng, Qi; Hatakeyama, Makoto; Sugawara, Etsuko

2014-01-01

Two aroma compounds of volatile thiols, 2-furanmethanethiol (2FM) and ethyl 2-mercaptopropionate (ET2MP), were formed in five types of Japanese soy sauce during fermentation by yeast. The concentrations of 2FM and ET2MP in the soy sauce samples increased during alcoholic fermentation. The concentrations of 2FM and ET2MP were higher in the soy sauce fermented by Zygosaccharomyces rouxii than in that fermented by Candida versatilis. The enantiomers of ET2MP were separated by gas chromatography in a capillary column. The average enantiomeric ratio of ET2MP in the soy sauce was approximately 1:1. 2FM was formed by yeast in a medium prepared from cysteine and furfural, and cysteine is considered the key precursor of 2FM by yeast in soy sauce.

Alterations in pain response are partially reversed by methylphenidate (Ritalin) in adults with attention deficit hyperactivity disorder (ADHD).

PubMed

Treister, Roi; Eisenberg, Elon; Demeter, Naor; Pud, Dorit

2015-01-01

Attention deficit hyperactivity disorder (ADHD) is characterized by dysregulation of sensory processing and neurobiology of dopamine. Although cumulative evidence suggests that dopamine is involved in pain processing, pain perception in ADHD subjects and the effect of dopamine agonists such as methylphenidate (MP, Ritalin) on it have rarely been studied. The aims of this study were to (1) psychophysically assess sensitivity to pain in ADHD subjects as compared to controls and (2) examine the effects of MP on pain response in ADHD subjects. Thirty subjects with ADHD and 30 age- and gender-matched controls participated in a preliminary trial. Pain threshold, intensity, and tolerance in response to cold pain stimulation were measured for both groups (ADHD with no treatment). In addition, the ADHD group was reassessed following a single dose of MP treatment. The ADHD subjects "without MP" in comparison with controls displayed significantly shorter cold pain threshold (2.8 ± 2.1 vs. 5.8 ± 2.5 seconds, respectively, P < 0.001) and cold tolerance (21.8 ± 22.3 vs. 62.8 ± 59.8 seconds, respectively P < 0.001). No differences in pain intensities between the groups were found. Following MP treatment, both cold threshold and tolerance in the ADHD subjects increased significantly compared to those with no treatment (3.6 ± 2.5 seconds, P = 0.011, and 46.4 ± 53.3 seconds, P < 0.001, respectively). These results suggest that adults with ADHD are more sensitive to pain compared with controls and that MP may exert antinociceptive properties in these subjects. Randomized, controlled trials are warranted to verify these findings. © 2013 World Institute of Pain.

VizieR Online Data Catalog: ChaMP X-ray point source catalog (Kim+, 2007)

NASA Astrophysics Data System (ADS)

Kim, M.; Kim, D.-W.; Wilkes, B. J.; Green, P. J.; Kim, E.; Anderson, C. S.; Barkhouse, W. A.; Evans, N. R.; Ivezic, Z.; Karovska, M.; Kashyap, V. L.; Lee, M. G.; Maksym, P.; Mossman, A. E.; Silverman, J. D.; Tananbaum, H. D.

2009-01-01

We present the Chandra Multiwavelength Project (ChaMP) X-ray point source catalog with ~6800 X-ray sources detected in 149 Chandra observations covering ~10deg2. The full ChaMP catalog sample is 7 times larger than the initial published ChaMP catalog. The exposure time of the fields in our sample ranges from 0.9 to 124ks, corresponding to a deepest X-ray flux limit of f0.5-8.0=9x10-16ergs/cm2/s. The ChaMP X-ray data have been uniformly reduced and analyzed with ChaMP-specific pipelines and then carefully validated by visual inspection. The ChaMP catalog includes X-ray photometric data in eight different energy bands as well as X-ray spectral hardness ratios and colors. To best utilize the ChaMP catalog, we also present the source reliability, detection probability, and positional uncertainty. (10 data files).

Hemato - Immunological and biochemical parameters, skin antibacterial activity, and survival in rainbow trout (Oncorhynchus mykiss) following the diet supplemented with Mentha piperita against Yersinia ruckeri.

PubMed

Adel, Milad; Pourgholam, Reza; Zorriehzahra, Jalil; Ghiasi, Maryam

2016-08-01

This study was aimed to assess the potential effects of Mentha piperita on the hemato - immunological and biochemical parameters, skin antibacterial activity and protection against Yersinia ruckeri infection in rainbow trout Oncorhynchus mykiss. Fish were divided into 4 groups before being fed diets supplemented with 0, 1, 2 and 3% of Mentha piperita (MP) plant extract for 8 weeks. Dose-dependent increases immune (both in skin mucus and blood serum) and hematological parameters (number of red and white cells, hematocrit and hemoglobin contents), as well as in respiratory burst activity, total protein, albumin, and neutrophil levels in fish fed supplemented diets compared to the control fish. Furthermore, dietary MP plant extract supplements have no significant effect on blood biochemical parameters and enzymatic activities of liver determined in serum of rainbow trout. After 8 weeks the cessation of feeding with MP plant extract, survival rates of 54.4%, 63.6% and 75.2% were recorded in groups which received 1, 2 and 3% of MP plant extract of feed, respectively, compared to 34.6% survivals in the control. This study underlying several positive effects of dietary administration of MP plant extract to farmed fish. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mucuna pruriens (L.) DC chemo sensitize human breast cancer cells via downregulation of prolactin-mediated JAK2/STAT5A signaling.

PubMed

Sinha, Sonam; Sharma, Sonal; Vora, Jaykant; Shah, Heta; Srivastava, Anshu; Shrivastava, Neeta

2018-05-10

Mucuna pruriens (L.) DC (MP) is an ancient Indian medicinal plant traditionally used to treat Parkinson's disease. L-Dopa (LD), precursor of dopamine is abundantly found in the seeds of MP. L-dopa is a natural inhibitor of prolactin (PRL) hormone which is required to maintain lactation in women but it's over production (hyperprolactinemia) plays critical role in advancement of breast cancer. We aim to examine the pharmacological effect of LD and MP on this hyperprolactinemia associated breast cancer and related signaling for effective management of the disease. We also investigated chemo-sensitizing effect of MP on hyperprolactinemia-mediated cisplatin resistance. Methanolic seed extract of MP were prepared and analysed using HPLC. Effect of LD and MP on the cellular viability of breast cancer cells (T47D, MCF-7, MDA-MB-468 and MDA-MB-231) were evaluated using MTT assay. Further, effect of LD and MP on colony forming potential, DNA damage, cell cycle distribution and apoptosis was determined using agar/agarose method, comet assay and annexin and PI method followed by FACS analysis. To reveal the molecular mechanism involved in the anti-cancer activity of MP, transcriptional and translational level analysis of the key proteins involved in the PRL-mediated signaling, was performed using RT-PCR and western blot analysis. The effect of MP extract on PRL-mediated signaling was validated using dopaminergic agonist bromocriptine. MP extract and cisplatin was given in different combination with appropriate controls to check their effect on chemo-resistivity of breast cancer cells. Our results demonstrated that MP seed extract has the potential to inhibit cellular proliferation of PRL expressing T47D and MCF-7 breast cancer cells via induction of DNA damage, G1 phase of cell cycle arrest and apoptosis more effectively as compare to LD. Further, MP-mediated anti-cancerous effect was associated with the downregulation of PRL expression, further suppressing the JAK2/STAT5A/Cyclin D1 signaling pathway which has been validated using dopaminergic agonist bromocriptine. Cancer-related hyperprolactinemia confers cisplatin resistance, we observed that MP via PRL inhibition, enhances cisplatin efficacy after their combinatorial treatment in breast cancer cells. Collectively, our study suggests that MP could be recommended as dietary supplement along with the chemotherapeutic agents against breast cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolutionarily Conserved Regulatory Mechanisms of Abscisic Acid Signaling in Land Plants: Characterization of ABSCISIC ACID INSENSITIVE1-Like Type 2C Protein Phosphatase in the Liverwort Marchantia polymorpha1[C][OA

PubMed Central

Tougane, Ken; Komatsu, Kenji; Bhyan, Salma Begum; Sakata, Yoichi; Ishizaki, Kimitsune; Yamato, Katsuyuki T.; Kohchi, Takayuki; Takezawa, Daisuke

2010-01-01

Abscisic acid (ABA) is postulated to be a ubiquitous hormone that plays a central role in seed development and responses to environmental stresses of vascular plants. However, in liverworts (Marchantiophyta), which represent the oldest extant lineage of land plants, the role of ABA has been least emphasized; thus, very little information is available on the molecular mechanisms underlying ABA responses. In this study, we isolated and characterized MpABI1, an ortholog of ABSCISIC ACID INSENSITIVE1 (ABI1), from the liverwort Marchantia polymorpha. The MpABI1 cDNA encoded a 568-amino acid protein consisting of the carboxy-terminal protein phosphatase 2C (PP2C) domain and a novel amino-terminal regulatory domain. The MpABI1 transcript was detected in the gametophyte, and its expression level was increased by exogenous ABA treatment in the gemma, whose growth was strongly inhibited by ABA. Experiments using green fluorescent protein fusion constructs indicated that MpABI1 was mainly localized in the nucleus and that its nuclear localization was directed by the amino-terminal domain. Transient overexpression of MpABI1 in M. polymorpha and Physcomitrella patens cells resulted in suppression of ABA-induced expression of the wheat Em promoter fused to the β -glucuronidase gene. Transgenic P. patens expressing MpABI1 and its mutant construct, MpABI1-d2, lacking the amino-terminal domain, had reduced freezing and osmotic stress tolerance, and associated with reduced accumulation of ABA-induced late embryogenesis abundant-like boiling-soluble proteins. Furthermore, ABA-induced morphological changes leading to brood cells were not prominent in these transgenic plants. These results suggest that MpABI1 is a negative regulator of ABA signaling, providing unequivocal molecular evidence of PP2C-mediated ABA response mechanisms functioning in liverworts. PMID:20097789

Evolutionarily conserved regulatory mechanisms of abscisic acid signaling in land plants: characterization of ABSCISIC ACID INSENSITIVE1-like type 2C protein phosphatase in the liverwort Marchantia polymorpha.

PubMed

Tougane, Ken; Komatsu, Kenji; Bhyan, Salma Begum; Sakata, Yoichi; Ishizaki, Kimitsune; Yamato, Katsuyuki T; Kohchi, Takayuki; Takezawa, Daisuke

2010-03-01

Abscisic acid (ABA) is postulated to be a ubiquitous hormone that plays a central role in seed development and responses to environmental stresses of vascular plants. However, in liverworts (Marchantiophyta), which represent the oldest extant lineage of land plants, the role of ABA has been least emphasized; thus, very little information is available on the molecular mechanisms underlying ABA responses. In this study, we isolated and characterized MpABI1, an ortholog of ABSCISIC ACID INSENSITIVE1 (ABI1), from the liverwort Marchantia polymorpha. The MpABI1 cDNA encoded a 568-amino acid protein consisting of the carboxy-terminal protein phosphatase 2C (PP2C) domain and a novel amino-terminal regulatory domain. The MpABI1 transcript was detected in the gametophyte, and its expression level was increased by exogenous ABA treatment in the gemma, whose growth was strongly inhibited by ABA. Experiments using green fluorescent protein fusion constructs indicated that MpABI1 was mainly localized in the nucleus and that its nuclear localization was directed by the amino-terminal domain. Transient overexpression of MpABI1 in M. polymorpha and Physcomitrella patens cells resulted in suppression of ABA-induced expression of the wheat Em promoter fused to the beta -glucuronidase gene. Transgenic P. patens expressing MpABI1 and its mutant construct, MpABI1-d2, lacking the amino-terminal domain, had reduced freezing and osmotic stress tolerance, and associated with reduced accumulation of ABA-induced late embryogenesis abundant-like boiling-soluble proteins. Furthermore, ABA-induced morphological changes leading to brood cells were not prominent in these transgenic plants. These results suggest that MpABI1 is a negative regulator of ABA signaling, providing unequivocal molecular evidence of PP2C-mediated ABA response mechanisms functioning in liverworts.

Hydrodynamic interactions in metachronal paddling: effects of varying stroke kinematics

NASA Astrophysics Data System (ADS)

Samaee, Milad; Kasoju, Vishwa; Lai, Hong Kuan; Santhanakrishnan, Arvind

2017-11-01

Crustaceans such as shrimp and krill use a drag-based technique for propulsion, in which multiple pairs of limbs are paddled rhythmically from the tail to the head. Each limb is phase-shifted in time relative to its neighbor. Most studies of this type of metachronal swimming have focused on the jet formed in the animal's wake. However, synergistic hydrodynamic interactions between adjacent limbs in metachrony have received minimal attention. We used a dynamically scaled robotic model to experimentally investigate how variations in stroke kinematics impact inter-paddle hydrodynamic interactions and thrust generation. Physical models of limbs were fitted to the robot and paddled with two different motion profiles (MPs)-1) MP1: metachronal power stroke (PS) and metachronal recovery stroke (RS); and 2) MP2: metachronal PS and synchronous RS. Stroke frequency and amplitude were maintained constant across both MPs. Our results show that MP2 produced faster jets in the thrust-generating direction as compared to MP1. The necessity for a pause in MP2 after completion of PS by the paddles leading the motion, prior to executing the synchronous RS, aided in further downstream flow propagation. The effect of using asymmetric stroke kinematics on thrust generated will be discussed.

A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cole, Callie A.; Wehres, Nadine; Yang Zhibo

2012-07-20

The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowingmore » afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.« less

Genomic Analysis of the Appearance of Ovarian Mast Cells in Neonatal MRL/MpJ Mice

PubMed Central

Nakamura, Teppei; Sakata, Yuko; Otsuka-Kanazawa, Saori; Ichii, Osamu; Chihara, Masataka; Nagasaki, Ken-ichi; Namiki, Yuka; Kon, Yasuhiro

2014-01-01

In MRL/MpJ mice, ovarian mast cells (OMCs) are more abundant than in other mouse strains, and tend to distribute beneath the ovarian surface epithelium at birth. This study investigated the factors regulating the appearance of neonatal OMCs in progeny of the cross between MRL/MpJ and C57BL/6N strains. F1 neonates had less than half the number of OMCs than MRL/MpJ. Interestingly, MRLB6F1 had more neonatal OMCs than B6MRLF1, although they were distributed over comparable areas. Furthermore, in MRL/MpJ fetuses for which parturition was delayed until embryonic day 21.5, the number of OMCs was significantly higher than in age-matched controls at postnatal day 2. These results suggest that the number of OMCs was influenced by the environmental factors during pregnancy. Quantitative trait locus analysis using N2 backcross progeny revealed two significant loci on chromosome 8: D8Mit343–D8Mit312 for the number of OMCs and D8Mit86–D8Mit89 for their distribution, designated as mast cell in the ovary of MRL/MpJ 1 (mcom1) and mcom2, respectively. Among MC migration-associated genes, ovarian expression of chemokine (C-C motif) ligand 17 at mcom1 locus was significantly higher in MRL/MpJ than in C57BL/6N, and positively correlated with the expression of OMC marker genes. These results indicate that the appearance of neonatal OMCs in MRL/MpJ is controlled by environmental factors and filial genetic factors, and that the abundance and distribution of OMCs are regulated by independent filial genetic elements. PMID:24956472

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 4 : I\\0x2010205 NB flow\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various flow-occupancy plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2;...

Using archived ITS data to measure the operational benefits of a system-wide adaptive ramp metering system : appendix online 3 : I\\0x2010205 NB speed\\0x2010occupancy plots.

DOT National Transportation Integrated Search

2008-12-01

The appendix includes various speed-occupancy plots, including: I-205 NB, Gladstone MP 11.05; I-205 NB, Gladstone Hway MP 12.94; I-205 NB, Lawnfield MP 13.58; I-205 NB, Sunnybrook MP 14.32; I-205 NB, Sunnyside MP 14.7; I-205 NB, Johnson Creek MP 16.2...

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

Improving students’ mathematical representational ability through RME-based progressive mathematization

NASA Astrophysics Data System (ADS)

Warsito; Darhim; Herman, T.

2018-01-01

This study aims to determine the differences in the improving of mathematical representation ability based on progressive mathematization with realistic mathematics education (PMR-MP) with conventional learning approach (PB). The method of research is quasi-experiments with non-equivalent control group designs. The study population is all students of class VIII SMPN 2 Tangerang consisting of 6 classes, while the sample was taken two classes with purposive sampling technique. The experimental class is treated with PMR-MP while the control class is treated with PB. The instruments used are test of mathematical representation ability. Data analysis was done by t-test, ANOVA test, post hoc test, and descriptive analysis. The result of analysis can be concluded that: 1) there are differences of mathematical representation ability improvement between students treated by PMR-MP and PB, 2) no interaction between learning approach (PMR-MP, PB) and prior mathematics knowledge (PAM) to improve students’ mathematical representation; 3) Students’ mathematical representation improvement in the level of higher PAM is better than medium, and low PAM students. Thus, based on the process of mathematization, it is very important when the learning direction of PMR-MP emphasizes on the process of building mathematics through a mathematical model.

Establishment of dsDNA/GNs/chit/GCE biosensor and electrochemical study on interaction between 6-mercaptopurine and DNA.

PubMed

Tang, Wenwei; Zhang, Min; Zeng, Xinping

2014-01-01

In this paper, the anti-cancer drug 6-mercaptopurine (6-MP) was taken as the detection object. The biosensor of dsDNA/GNs/chit/GCE was established using the grapheme (GNs) and chitosan (chit) as the compound modified material. The electrochemical behavior of 6-MP on the sensor was discussed, and the damage and its mechanism of 6-MP on DNA were studied. The experimental result showed that, after the modification of GNs-chit, the electrode activation area of GNs/chit/GCE increased remarkably, which was improved from 1.76cm2 to 8.64 cm2, and the responsive oxidation peak current of GNs/chit/GCE to K3[Fe(CN)6] also increased remarkably. At the meantime, it was demonstrated that DNA was effectively fixed on the GNs/chit/GCE electrode;6-MP caused obvious damage to dsDNA, and the damage degree on the adenine was bigger than that on the guanine; the interaction between 6-MP and dsDNA was preliminarily deduced as the intercalation, and its electrochemical oxidation process was an irreversible process controlled by the adsorption.

Preparation of porous magnesium oxide foam and study on its enrichment of uranium

NASA Astrophysics Data System (ADS)

Wang, Yunsheng; Chen, Yuantao; Liu, Chen; Yu, Fang

2018-06-01

Herein, we prepared porous magnesium oxide (MP-MgO) by in situ carbonization and using Mg(NO3)2 as precursor along with P123 as soft template. The BET surface area, and total pore volume of MP-MgO were found to be 14.76 m2 g, 0.15 cm3 g-1, respectively. The adsorption behavior of U (Ⅵ) by the porous MgO was studied by static adsorption experiments, and also the effects of adsorption time, pH of wastewater and U (Ⅵ) concentration were discussed. The results indicated that the optimum pH for MP-MgO was 3.0-4.5, the removal of uranium in this case was mainly due to surface complexation. Through the study, we found that the adsorption capacity of MP-MgO for uranium was more than 2500 mg g-1, the adsorption equilibrium time was about 150 min. Moreover, the kinetic study showed that the process followed the pseudo-first-order model, and the adsorption process was spontaneous and endothermic.

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Millán, Judith; Basterretxea, Francisco; Fernández, José A; Castaño, Fernando

2011-04-28

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).

Amperometric determination of 6-mercaptopurine on functionalized multi-wall carbon nanotubes modified electrode by liquid chromatography coupled with microdialysis and its application to pharmacokinetics in rabbit.

PubMed

Cao, Xu-Ni; Lin, Li; Zhou, Yu-Yan; Shi, Guo-Yue; Zhang, Wen; Yamamoto, Katsunobu; Jin, Li-Tong

2003-07-27

In this paper, multi-wall carbon nanotubes functionalized with carboxylic groups modified electrode (MWNT-COOH CME) was fabricated. This chemically modified electrode (CME) can be used as the working electrode in the liquid chromatography for the determination of 6-mercaptopurine (6-MP). The results indicate that the CME exhibits efficiently electrocatalytic oxidation for 6-MP with relatively high sensitivity, stability and long-life. The peak currents of 6-MP are linear to its concentrations ranging from 4.0 x 10(-7) to 1.0 x 10(-4) mol l(-1) with the calculated detection limit (S/N=3) of 2.0 x 10(-7) mol l(-1). Coupled with microdialysis, the method has been successfully applied to the pharmacokinetic study of 6-MP in rabbit blood. This method provides a fast, sensible and simple technique for the pharmacokinetic study of 6-MP in vivo.

Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods.

PubMed

Lindenmaier, Rodica; Williams, Stephen D; Sams, Robert L; Johnson, Timothy J

2017-02-16

Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm -1 range. Vibrational assignments of all fundamental modes are made for both molecules on the basis of far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-trans conformer, but a few appear to be uniquely associated with the s-cis conformer, notably ν 16 c at 730.90 cm -1 , which displays a substantial intensity increase with temperature (70% upon going from 5 to 50 o C). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, approximately doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.

Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindenmaier, Rodica; Williams, Stephen D.; Sams, Robert L.

Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm-1 range. Vibrational assignments of all fundamental modes are made for both molecules based on far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-transmore » conformer, but a few appear to be uniquely associated the s-cis conformer, notably ν16c at 730.90 cm-1, which displays a substantial intensity increase with temperature (62% upon going from 5 to 50 oC). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, ~doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.« less

Interaction of the Tobacco mosaic virus movement protein with microtubules during the cell cycle in tobacco BY-2 cells.

PubMed

Boutant, Emmanuel; Fitterer, Chantal; Ritzenthaler, Christophe; Heinlein, Manfred

2009-10-01

Cell-to-cell movement of Tobacco mosaic virus (TMV) involves the interaction of virus-encoded 30-kDa movement protein (MP) with microtubules. In cells behind the infection front that accumulate high levels of MP, this activity is reflected by the formation of stabilized MP/microtubule complexes. The ability of MP to bind along and stabilize microtubules is conserved upon expression in mammalian cells. In mammalian cells, the protein also leads to inhibition of mitosis and cell division through a microtubule-independent process correlated with the loss of centrosomal gamma-tubulin and of centrosomal microtubule-nucleation activity. Since MP has the capacity to interact with plant factors involved in microtubule nucleation and dynamics, we used inducible expression in BY-2 cells to test whether MP expression inhibits mitosis and cell division also in plants. We demonstrate that MP:GFP associates with all plant microtubule arrays and, unlike in mammalian cells, does not interfere with mitosis. Thus, MP function and the interaction of MP with factors of the cytoskeleton do not entail an inhibition of mitosis in plants. We also report that the protein targets primary plasmodesmata in BY-2 cells immediately upon or during cytokinesis and that the accumulation of MP in plasmodesmata occurs in the presence of inhibitors of the cytoskeleton and the secretory pathway.

The influence of prostate-specific antigen density on positive and negative predictive values of multiparametric magnetic resonance imaging to detect Gleason score 7-10 prostate cancer in a repeat biopsy setting.

PubMed

Hansen, Nienke L; Barrett, Tristan; Koo, Brendan; Doble, Andrew; Gnanapragasam, Vincent; Warren, Anne; Kastner, Christof; Bratt, Ola

2017-05-01

To evaluate the influence of prostate-specific antigen density (PSAD) on positive (PPV) and negative (NPV) predictive values of multiparametric magnetic resonance imaging (mpMRI) to detect Gleason score ≥7 cancer in a repeat biopsy setting. Retrospective study of 514 men with previous prostate biopsy showing no or Gleason score 6 cancer. All had mpMRI, graded 1-5 on a Likert scale for cancer suspicion, and subsequent targeted and 24-core systematic image-fusion guided transperineal biopsy in 2013-2015. The NPVs and PPVs of mpMRIs for detecting Gleason score ≥7 cancer were calculated (±95% confidence intervals) for PSAD ≤0.1, 0.1-0.2, ≤0.2 and >0.2 ng/mL/mL, and compared by chi-square test for linear trend. Gleason score ≥7 cancer was detected in 31% of the men. The NPV of Likert 1-2 mpMRI was 0.91 (±0.04) with a PSAD of ≤0.2 ng/mL/mL and 0.71 (±0.16) with a PSAD of >0.2 ng/mL/mL (P = 0.003). For Likert 3 mpMRI, PPV was 0.09 (±0.06) with a PSAD of ≤0.2 ng/mL/mL and 0.44 (±0.19) with a PSAD of >0.2 ng/mL/mL (P = 0.002). PSAD also significantly affected the PPV of Likert 4-5 mpMRI lesions: the PPV was 0.47 (±0.08) with a PSAD of ≤0.2 ng/mL/mL and 0.66 (±0.10) with a PSAD of >0.2 ng/mL/mL (P < 0.001). In a repeat biopsy setting, a PSAD of ≤0.2 ng/mL/mL is associated with low detection of Gleason score ≥7 prostate cancer, not only in men with negative mpMRI, but also in men with equivocal imaging. Surveillance, rather than repeat biopsy, may be appropriate for these men. Conversely, biopsies are indicated in men with a high PSAD, even if an mpMRI shows no suspicious lesion, and in men with an mpMRI suspicious for cancer, even if the PSAD is low. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Quantum-Chemical ab initio Calculations on the Three Isomers of Diborabenzene (C4H4B2)

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Wang, Yuekui; Raabe, Gerhard

2010-01-01

Quantum-chemical ab initio calculations up to the ZPE+CCSD(T)/aug-cc-pVTZ//MP2/6- 311++G** level were performed on three possible structural isomers of diborabenzene (C4H4B2). All three molecules were found to be local minima on the C4H4B2 energy surface and to have closed shell singlet ground states. While the ground states of the 1,3- and 1,4-isomer are planar and of C2v and D2h symmetry, respectively, 1,2-diborabenzene is non-planar with a C2 axis passing through the center of the BB bond and the middle of the opposite carbon-carbon bond as the only symmetry element. The energetically most favourable 1,3-diborabenzene was found to be about 19 and 36 kcal/mol lower in energy than the 1,2- and the 1,4-isomer. Planar 1,3- and 1,4-diborabenzene have three doubly occupied π orbitals while non-planar 1,2-diborabenzene has also three doubly occupied orbitals which can be derived from the π orbitals of its 3.7 kcal/mol energetically less favourable planar form ("π-like" orbitals). The lowest unoccupied orbitals of all three isomers have σ symmetry with large coefficients at the two boron atoms. These orbitals are lower in energy than the lowest unoccupied molecular orbitals (LUMOs) of e. g. benzene and pyridine and might cause pronounced acceptor properties which could be one of the reasons for the elusiveness of the title compounds. The results of bond separation reactions show that cyclic conjugation stabilizes all three diborabenzenes relative to their isolated fragments. The most effective stabilization energy of about 24 kcal/mol was found for the energetically lowest 1,3-isomer. This value amounts to approximately one third of the experimental value for the bond separation energy of pyridine. In all cases the energetically lowest triplet states are significantly (16 - 24 kcal/mol) higher in energy than the singlet ground states. Also among the triplets the 1,3-isomer is the energetically most fabourable species.

[Cervical vertebrae: Mandibular growth dynamism indicators?].

PubMed

Raberin, Monique; Cozor, Ilinca; Gobert-Jacquart, Stéphanie

2012-03-01

A study of mandibular growth maturation was performed on a population of 103 patients during orthodontic treatment (69 girls and 34 boys) from 11 to 16 years, having initially a Class II skeletal discrepancy. The relationship between wrist maturation indices and the cervical vertebrae maturation was studied by Lamparski classification. Significant correlations were found between Björk stages, MP3=, MP3 cap and MP3 U and respectively Lamparski stages as CVS 2, CVS 3-4 and CVS 5-6. This retrospective longitudinal study identified three mandibular variables at three different maturation stages according to Björk classification and to the six stages of Lamparski classification. The relationships between these different maturation stages and a quantitative mandibular response permit to estimate optimal time for our orthodontic therapy. The results indicate a significant increase in mandibular length between CVS 4 and CVS 5, suggesting the persistence of a condylar response to a stimulation therapy after CVS3 or CVS 4 stages (MP3 cap). Mandibular growth seems to continue after MP3 U stage or CVS 5 stage. © EDP Sciences, SFODF, 2012.

Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative.

PubMed

Rasheed, Tabish; Ahmad, Shabbir

2010-10-01

Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values. Copyright 2010 Elsevier B.V. All rights reserved.

Mycoplasma Pneumoniae among Children Hospitalized with Community-acquired Pneumonia.

PubMed

Kutty, Preeta K; Jain, Seema; Taylor, Thomas H; Bramley, Anna M; Diaz, Maureen H; Ampofo, Krow; Arnold, Sandra R; Williams, Derek J; Edwards, Kathryn M; McCullers, Jonathan A; Pavia, Andrew T; Winchell, Jonas M; Schrag, Stephanie J; Hicks, Lauri A

2018-05-17

The burden and epidemiology of Mycoplasma pneumoniae (Mp) among U.S. children (<18 years) hospitalized with community-acquired pneumonia (CAP) are poorly understood. In the Etiology of Pneumonia in the Community (EPIC) study, we prospectively enrolled 2254 children hospitalized with radiographically-confirmed pneumonia from January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp using real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp-PCR-positive and -negative children were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. In the EPIC study, 182(8%) children were Mp-PCR-positive (median age: 7 years); 12% required intensive care and 26% had pleural effusion. No in-hospital deaths occurred. Macrolide resistance was found in 6/169(4%) isolates. Of 178(98%) Mp-PCR-positive children tested for co-pathogens, 50(28%) had ≥1 co-pathogen detected. Variables significantly associated with higher odds of Mp detection included age {10-17 years [adjusted odds ratio (aOR): 7.9 (95% confidence interval (CI): 4.5-13.6)] and 5-9 years [aOR: 4.8 (CI: 2.9-7.8)] vs. 2-4 years}, outpatient antibiotics ≤5 days pre-admission [aOR: 2.3 (CI: 1.5-3.4)], and co-pathogen detection [aOR: 2.1 (CI: 1.3-3.1)]. Clinical characteristics often seen included hilar lymphadenopathy, rales, headache, sore throat, and decreased breath sounds. Usually considered as a mild respiratory infection, M. pneumoniae was the most commonly detected bacteria among children ≥5 years hospitalized with CAP; one-quarter of whom had co-detections. Although associated with clinically non-specific symptoms, there was a need for intensive care support in some cases. M. pneumoniae should be included in the differential diagnosis for school-aged children hospitalized with CAP.

Pulmonary emphysema induced by methylphenidate: experimental study.

PubMed

Rapello, Gabriel Victor Guimarães; Antoniolli, Andréia; Pereira, Daniel Martins; Facco, Gilberto; Pêgo-Fernandes, Paulo Manuel; Pazetti, Rogério

2015-01-01

Methylphenidate is the most widely used drug for treating attention deficit hyperactivity disorder. However, it has important side effects, such as abdominal pain, insomnia, anorexia and loss of appetite, and also some cases of early severe emphysema after drug abuse have been reported. Our aim was to investigate the development of pulmonary emphysema in rats that were subjected to different doses of methylphenidate. Experimental study carried out at the laboratory of a public university. Eighteen male Wistar rats were divided into three groups: control (0.9% saline solution); MP 0.8 (methylphenidate, 0.8 mg/kg); MP 1.2 (methylphenidate, 1.2 mg/kg). After 90 days of daily gavage, the animals were sacrificed and lung tissue samples were prepared for analysis on the mean alveolar diameter (Lm). The Lm was greater in MP 0.8 (47.91 ± 3.13; P < 0.01) and MP 1.2 (46.36 ± 4.39; P < 0.05) than in the control group (40.00 ± 3.48). Methylphenidate caused an increase in the alveolar diameter of rats, which was compatible with human pulmonary emphysema.

Effects of local application of methylprednisolone delivered by the C/GP-hydrogel on the recovery of facial nerves.

PubMed

Chao, Xiuhua; Fan, Zhaomin; Han, Yuechen; Wang, Yan; Li, Jianfeng; Chai, Renjie; Xu, Lei; Wang, Haibo

2015-01-01

Local administration of MP delivered by the C/GP-MP-hydrogel can improve the recovery of facial nerve following crush injury. The findings suggested that locally injected MP delivered by C/GP-hydrogel might be a promising treatment for facial nerve damage. In this study, the aim is to assess the effectiveness of locally administrating methylprednisolone(MP) loaded by chitosan-β-glycerophosphate hydrogel (C/GP-hydrogel) on the regeneration of facial nerve crush injury. After the crush of left facial nerves, Wistar rats were randomly divided into four different groups. Then, four different therapies were used to treat the damaged facial nerves. At the 1(st), 2(nd), 3(rd), and 4(th) week after injury, the functional recovery of facial nerves and the morphological changes of facial nerves were assessed. The expression of growth associated protein-43 (GAP-43) protein in the facial nucleus were also evaluated. Locally injected MP delivered by C/GP-hydrogel effectively accelerated the facial functional recovery. In addition, the regenerated facial nerves in the C/GP-MP group were more mature than those in the other groups. The expression of GAP-43 protein was also improved by the MP, especially in the C/GP-MP group.

Wearable cameras can reduce dietary under-reporting: doubly labelled water validation of a camera-assisted 24 h recall.

PubMed

Gemming, Luke; Rush, Elaine; Maddison, Ralph; Doherty, Aiden; Gant, Nicholas; Utter, Jennifer; Ni Mhurchu, Cliona

2015-01-28

Preliminary research has suggested that wearable cameras may reduce under-reporting of energy intake (EI) in self-reported dietary assessment. The aim of the present study was to test the validity of a wearable camera-assisted 24 h dietary recall against the doubly labelled water (DLW) technique. Total energy expenditure (TEE) was assessed over 15 d using the DLW protocol among forty adults (n 20 males, age 35 (sd 17) years, BMI 27 (sd 4) kg/m2 and n 20 females, age 28 (sd 7) years, BMI 22 (sd 2) kg/m2). EI was assessed using three multiple-pass 24 h dietary recalls (MP24) on days 2-4, 8-10 and 13-15. On the days before each nutrition assessment, participants wore an automated wearable camera (SenseCam (SC)) in free-living conditions. The wearable camera images were viewed by the participants following the completion of the dietary recall, and their changes in self-reported intakes were recorded (MP24+SC). TEE and EI assessed by the MP24 and MP24+SC methods were compared. Among men, the MP24 and MP24+SC measures underestimated TEE by 17 and 9%, respectively (P< 0.001 and P= 0.02). Among women, these measures underestimated TEE by 13 and 7%, respectively (P< 0.001 and P= 0.004). The assistance of the wearable camera (MP24+SC) reduced the magnitude of under-reporting by 8% for men and 6% for women compared with the MP24 alone (P< 0.001 and P< 0.001). The increase in EI was predominantly from the addition of 265 unreported foods (often snacks) as revealed by the participants during the image review. Wearable cameras enhance the accuracy of self-report by providing passive and objective information regarding dietary intake. High-definition image sensors and increased imaging frequency may improve the accuracy further.

Pharmacokinetic, bioavailability and tissue distribution study of MP3950, a new gastroprokinetic candidate compound, in rat using UPLC-MS/MS.

PubMed

Zhao, Yu; Zhao, Min; Jiang, Qi; Qin, Feng; Wang, Chengying; Xiong, Zhili; Wang, Shaojie; He, Zhonggui; Guo, Xingjie; Zhao, Longshan

2018-06-02

MP3950 is being developed as a gastroprokinetic candidate compound. To illustrate the pharmacokinetic profiles, absolute bioavailability after intravenous administration and oral administration with MP3950 as well as tissue distribution in vivo, an UPLC-MS/MS approach which was rapid and selective was developed to determine MP3950 in plasma and tissue of rat. Sample pre-treatment of plasma sample was one-step protein precipitation. 0.1% formic acid containing 5 mmol/L ammonium acetate-methanol(55/45,v/v) was used for isocratic elution on a Waters ACQUITY UPLC® BEH C18 (50 mm × 2.1 mm, 1.7 μm) to achieve the separation. The analysis was performed in MRM mode via positive ESI mode. LLOQ of the method was 10 ng/mL, and the linearity up to 10,000 ng/mL. The intra-day precision (relative standard deviation, RSD) was 4.0-9.0% and the inter-day precision was 4.2-10.6%. The accuracy (relative error, RE) was -1.2-2.4%. Tissue samples were collected from the brain, heart, liver, spleen, lung, kidney, stomach, duodenum, small intestine, large intestine, appendix and skeletal muscle. The same liquid chromatographic and mass spectrometric conditions were used, and it's proven that this method was feasible to analyze the MP3950 in tissues with good precision and accuracy over the range from 10 to 5000 ng·mL -1 . It was found that the concentration of MP3950 is higher in digestive system. The tissue distribution, pharmacokinetic and bioavailability of MP3950 in rats were carried out by the method for the first time, which can provide enough information for the further development and investigation of MP3950. Copyright © 2018. Published by Elsevier B.V.

Maternal folic acid supplementation to dams on marginal protein level alters brain fatty acid levels of their adult offspring.

PubMed

Rao, Shobha; Joshi, Sadhana; Kale, Anvita; Hegde, Mahabaleshwar; Mahadik, Sahebarao

2006-05-01

Studies on fetal programming of adult diseases have highlighted the importance of maternal nutrition during pregnancy. Folic acid and long-chain essential polyunsaturated fatty acids (LC-PUFAs) have independent effects on fetal growth. However, folic acid effects may also involve alteration of LC-PUFA metabolism. Because marginal deficiency of LC-PUFAs during critical periods of brain growth and development is associated with risks for adult diseases, it is highly relevant to investigate how maternal supplementation of such nutrients can alter brain fatty acid levels. We examined the impact of folic acid supplementation, conventionally used in maternal intervention, on brain essential fatty acid levels and plasma corticosterone concentrations in adult offspring at 11 months of age. Pregnant female rats from 4 groups (6 in each) were fed with casein diets either with 18 g protein/100 g diet (control diet) or treatment diets that were marginal in protein (MP), such as 12 g protein/100 g diet supplemented with 8 mg folic acid (FAS/MP), 12 g protein/100 g diet without folic acid (FAD/MP), or 12 g protein/100 g diet (MP) with 2 mg folic acid. Pups were weaned to a standard laboratory diet with 18 g protein/100 g diet. All male adult offspring in the FAS/MP group showed lower docosahexaenoic acid (P<.05) as compared with control adult offspring (6.04+/-2.28 vs 10.33+/-0.86 g/100 g fatty acids) and higher n-6/n-3 ratio (P<.05). Docosahexaenoic acid levels in FAS/MP adult offspring were also lower (P<.05) when compared with the MP group. Plasma corticosterone concentrations were higher (P<.05) in male adult offspring from the FAS/MP group compared with control as well as the MP adult offspring. Results suggest that maternal folic acid supplementation at MP intake decreased brain docosahexaenoic acid levels probably involving corticosterone increase.

Rift Valley fever MP-12 vaccine Phase 2 clinical trial: Safety, immunogenicity, and genetic characterization of virus isolates.

PubMed

Pittman, Phillip R; Norris, Sarah L; Brown, Elizabeth S; Ranadive, Manmohan V; Schibly, Barbara A; Bettinger, George E; Lokugamage, Nandadeva; Korman, Lawrence; Morrill, John C; Peters, Clarence J

2016-01-20

An outbreak or deliberate release of Rift Valley fever (RVF) virus could have serious public health and socioeconomic consequences. A safe RVF vaccine capable of eliciting long-lasting immunity after a single injection is urgently needed. The live attenuated RVF MP-12 vaccine candidate has shown promise in Phase 1 clinical trials; no evidence of reversion to virulence has been identified in numerous animal studies. The objective of this Phase 2 clinical trial was to (a) further examine the safety and immunogenicity of RVF MP-12 in RVF virus-naïve humans and (b) characterize isolates of RVF MP-12 virus recovered from the blood of vaccinated subjects to evaluate the genetic stability of MP-12 attenuation. We found that RVF MP-12 was well tolerated, causing mostly mild reactions that resolved without sequelae. Of 19 subjects, 18 (95%) and 19 (100%) achieved, respectively, 80% and 50% plaque reduction neutralization titers (PRNT80 and PRNT50)≥1:20 by postvaccination day 28. All 18 PRNT80 responders maintained PRNT80 and PRNT50≥1:40 until at least postvaccination month 12. Viremia was undetectable in the plasma of any subject by direct plaque assay techniques. However, 5 of 19 vaccinees were positive for MP-12 isolates in plasma by blind passage of plasma on Vero cells. Vaccine virus was also recovered from buffy coat material from one of those vaccinees and from one additional vaccinee. Through RNA sequencing of MP-12 isolates, we found no reversions of amino acids to those of the parent virulent virus (strain ZH548). Five years after a single dose of RVF MP-12 vaccine, 8 of 9 vaccinees (89%) maintained a PRNT80≥1:20. These findings support the continued development of RVF MP-12 as a countermeasure against RVF virus in humans. Published by Elsevier Ltd.

Cu2+ triggers reversible aggregation of a disordered His-rich dehydrin MpDhn12 from Musa paradisiaca.

PubMed

Mu, Peiqiang; Feng, Dongru; Su, Jianbin; Zhang, Yang; Dai, Jinran; Jin, Honglei; Liu, Bing; He, Yanming; Qi, Kangbiao; Wang, Hongbin; Wang, Jinfa

2011-11-01

Copper is an essential nutrient, but it is toxic in excess. Here, we cloned and characterized a His-rich low molecular weight dehydrin from Musa paradisiaca, MpDhn12. Analysis by circular dichroism (CD) spectra and a thermal stability assay showed that MpDhn12 is an intrinsically disordered protein, and immobilized-metal affinity chromatography (IMAC) analysis revealed that MpDhn12 can bind Cu(2+) both in vitro and in vivo. Interestingly, MpDhn12 aggregated under excess Cu(2+) conditions, and the aggregation was reversible and impaired by histidine modification with diethylpyrocarbonate (DEPC), while the disordered structure of another dehydrin ERD14 (as a control) was not changed. Furthermore, MpDhn12 could complement the copper-sensitive phenotype of yeast mutant Δsod1. These results together suggested that MpDhn12 may take part in buffering copper levels through chelation and formation of aggregates in excess Cu(2+) conditions. To the best of our knowledge, it is the first report that a dehydrin interchanged between disordered and aggregated state triggered by copper.

Mitochondrial stress and redox failure in steroid-associated osteonecrosis

PubMed Central

Tsuchiya, Masanobu; Ichiseki, Toru; Ueda, Shusuke; Ueda, Yoshimichi; Shimazaki, Miyako; Kaneuji, Ayumi; Kawahara, Norio

2018-01-01

The purpose of the role of antioxidant enzymes and mitochondria in the developmental mechanism of steroid-associated osteonecrosis in the femur. In the present study Japanese white rabbits (mean weight 3.5kg) were injected into the gluteus with methylprednisolone (MP) 20mg/kg, and killed after 3 days (MP3 group), 5 days (MP5 group), and 14 days (MP14 group) (n=3 each). As a Control group (C group) Japanese white rabbits not administered MP were used. In experiment 1, the expression of the antioxidant enzymes Superoxide dismutade (SOD) and catalase was compared in liver, kidney, heart, humerus, and femur in C group, and the presence/absence of mitochondria transcription factor A (TFAM) expression was determined by Western blotting (WB) and used to evaluate the number of mitochondria and their function. In experiment 2, the presence/absence of necrosis was determined by immunohistochemistry, while changes in the expression of SOD, catalase, and TFAM in the femur after steroid administration were determined by Western blotting (WB). In experiment 1, intense expression of all of SOD, catalase, and TFAM was found in the liver, kidney, and heart as compared to the humerus and femur. In experiment 2, the expression of all of SOD, catalase, and TFAM in MP3 and MP5 groups was decreased on WB as compared with C group, while in MP14 group a tendency to improvement was seen. Accordingly, steroid-associated mitochondrial injury and redox failure are concluded to be important elements implicated in the pathogenesis of osteonecrosis. PMID:29483810

Characterization of microparticles in patients with venous malformations of the head and neck.

PubMed

Zhu, J-Y; Ren, J-G; Zhang, W; Wang, F-Q; Cai, Y; Zhao, J-H; Chen, G; Zhao, Y-F

2017-01-01

To determine the basic biochemical features of microparticles (MP) in patients with venous malformation (VM) of the head and neck. Microparticles were isolated from peripheral venous blood of VM patients or healthy subjects and from lesional fluid of VM patients. Flow cytometry and real-time polymerase chain reaction were employed to determine the concentration, cellular origin, and RNA expression of obtained MP. A functional coagulation test was applied to measure the coagulant activity of MP. Circulating levels of total MP, platelet-derived MP, and endothelial MP were significantly elevated in VM patients and were consistently increased in VM patients with more extensive lesions. Lesional MP (MP from lesional fluid of VM) in VM patients were more abundant than circulating MP from VM patients or healthy subjects. Moreover, MP from VM patients displayed markedly distinct mRNA and microRNA expression compared with healthy subjects. Furthermore, MP from VM patients exhibited enhanced procoagulant activity, as evidenced by significantly shorter coagulation time. This study demonstrates for the first time that patients with VM have an altered MP profile and MP may be associated with VM-associated thrombogenesis. Further studies are required to explore the precise pathophysiological roles of MP in VM. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Raman spectrum, quantum mechanical calculations and vibrational assignments of (95% alpha-TeO2/5% Sm2O3) glass.

PubMed

Shaltout, I; Mohamed, Tarek A

2007-06-01

Chozen system of tellurite glasses doped with rare earth oxides (95% alpha-TeO(2)+5% Sm2O3) was prepared by melt quenching. Consequently, the Raman spectrum (150-1250 cm(-1)) of the modified tellurite have been recorded. As a continuation to our normal coordinate analysis, force constants and quantum mechanical (QM) calculations for tbp TeO4(4-) (triagonal bipyramid, C(2v)) and TeO(3+1); Te2O7(6-) (bridged tetrahedral), we have carried out ab initio frequency calculations for tpy TeO3(2-) (triagonal pyramidal, C(3v) and C(s)) and tp TeO3(2-) (triagonal planar, D(3h)) ions. The quantum mechanical calculations at the levels of RHF, B3LYP and MP2 allow confident vibrational assignments and structural identification in the binary oxide glass (95% alpha-TeO2 +5% Sm2O3). The dominant three-dimensional network structures in the modified glass are triagonal pyramidal TeO3 with minor features of short range distorted tbp TeO4 and bridged tetrahedral unit of TeO(3+1), leading to a structure of infinite chain. Therefore, alpha-TeO2/Sm2O3 (95/5%) glass experience structural changes from TeO4 (tbp); Te2O7 (TeO(3+1))-->TeO3 (tpy).

Kinetic mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae.

PubMed

Maenpuen, Somchart; Watthaisong, Pratchaya; Supon, Pacharee; Sucharitakul, Jeerus; Parsonage, Derek; Karplus, P Andrew; Claiborne, Al; Chaiyen, Pimchai

2015-08-01

L-α-glycerophosphate oxidase is an FAD-dependent enzyme that catalyzes the oxidation of L-α-glycerophosphate (Glp) by molecular oxygen to generate dihydroxyacetone phosphate (DHAP) and hydrogen peroxide (H2O2). The catalytic properties of recombinant His6-GlpO from Mycoplasma pneumoniae (His6-MpGlpO) were investigated through transient and steady-state kinetics and ligand binding studies. The results indicate that the reaction mechanism of His6-MpGlpO follows a ping-pong model. Double-mixing mode stopped-flow experiments show that, after flavin-mediated substrate oxidation, DHAP leaves rapidly prior to the oxygen reaction. The values determined for the individual rate constants and kcat (4.2 s(-1) at 4 °C), in addition to the finding that H2 O2 binds to the oxidized enzyme, suggest that H2O2 release is the rate-limiting step for the overall reaction. The results indicate that His6 -MpGlpO contains mixed populations of fast- and slow-reacting species. It is predominantly the fast-reacting species that participates in turnover. In contrast to other GlpO enzymes previously described, His6-MpGlpO is able to catalyze the reverse reaction of reduced enzyme and DHAP. This result may be explained by the standard reduction potential value of His6-MpGlpO (-167 ± 1 mV), which is lower than those of GlpO from other species. We found that D,L-glyceraldehyde 3-phosphate (GAP) may be used as a substrate in the His6-MpGlpO reaction, although it exhibited an approximately 100-fold lower kcat value in comparison with the reaction of Glp. These results also imply involvement of GlpO in glycolysis, as well as in lipid and glycerol metabolism. The kinetic models and distinctive properties of His6-MpGlpO reported here should be useful for future drug development against Mycoplasma pneumoniae infection. © 2015 FEBS.

A study of the effectiveness of MP3 players to support family carers of people living with dementia at home.

PubMed

Lewis, Virginia; Bauer, Michael; Winbolt, Margaret; Chenco, Carol; Hanley, Francine

2015-03-01

Music can be therapeutic to people with dementia; however, little is known about its effect on the family carers. This project aimed to (1) assess the effects of MP3 player use by a person with dementia on caregivers' mental health and wellbeing, including their self-care and health-promoting behavior and (2) determine whether MP3 player use increases caregivers' self-reported capacity to cope with their role. A pre-post quantitative and qualitative design was used. Carers completed a survey prior to commencing and four weeks after using the player. The survey included validated measures to assess the level of stress and coping among carers. Carers also kept a diary of the way they used the MP3 player. Half of the carers were interviewed about their experiences at the end of the study. Of 59 people who started using the MP3 player, 51 carers completed the four-week study period and surveys. Use of the MP3 player significantly decreased psychological distress, significantly improved the mental health and wellbeing of carers, significantly increased caregiver self-efficacy to manage symptoms of dementia, and was reported to provide valued respite from the high level of vigilance required for caring for a person with dementia. An MP3 player loaded with music can be a low cost and relatively simple and effective additional strategy to support families caring for people with dementia in the community.

The ten-year single-center experience with 6-mercaptopurine in the treatment of inflammatory bowel disease.

PubMed

Glazier, Kenneth D; Palance, Adam L; Griffel, Louis H; Das, Kiron M

2005-01-01

To report the 10-year experience of a single center in treating patients with refractory inflammatory bowel disease (IBD) with relatively lower dose of 6-mercaptopurine (6-MP). The charts of 285 patients with IBD (Crohn's disease 160 and ulcerative colitis 125) receiving 6-MP were reviewed. Clinical response, subsequent breakthrough while taking 6-MP, and relapse rates when 6-MP was discontinued and side effects were assessed. Ninety-three percent of the patients were taking 50 to 75 mg/day of 6-MP. Complete remission was achieved in 62%, partial remission in 14.5%, and failure to achieve remission in 23.5% of the patients. Of complete responders, 27.5% had breakthrough while continuing 6-MP. Nine percent of those that achieved a complete remission experienced a relapse after 6-MP was discontinued. Side effects included leukopenia (11.2%), abnormal liver function tests (3.8%), various infections, including pneumonia (3.1%), pancreatitis (2.5%), nausea (2.1%), headache (2.8%), fever (1.4%), hair loss (1%), and rash (0.7%). Two cancers occurred while taking 6-MP: melanoma on the finger and a fatal colonic lymphoma. Four patients continued 6-MP throughout pregnancies and had normal outcomes. In our experience 6-MP is relatively safe and appears to be as effective at a lower dosage (0.84 mg/kg per day) compared with the recommended higher dosage (1-1.5 mg/kg per day), when leukopenia was more frequent. Serious side effects, although rare, need to be monitored.

Ab initio and kinetic study of the reaction of ketones with OH for T = 500-2000 K. Part I: hydrogen-abstraction from H3CC(O)CH(3-x)(CH3)x, x = 0 ↦ 2.

PubMed

Zhou, Chong-Wen; Simmie, John M; Curran, Henry J

2011-06-21

A theoretical study is presented of the mechanism and kinetics of the reactions of the hydroxyl radical with three ketones: dimethyl (DMK), ethylmethyl (EMK) and iso-propylmethyl (iPMK) ketones. CCSD(T) values extrapolated to the basis set limit are used to benchmark the computationally less expensive methods G3 and G3MP2BH&H, for the DMK + OH reaction system. These latter methods are then used in computations involving the reactions of the larger ketones. All possible abstraction channels have been modeled. A stepwise mechanism involving the formation of a reactant complex in the entrance channel and a product complex in the exit channel has been recognized in part of the abstracting processes. High-pressure limit rate constants of the title reactions have been calculated in the temperature range of 500-2000 K using the Variflex code including Eckart tunneling corrections. Variable reaction coordinate transition state theory (VRC-TST) has been used for the rate constants of the barrier-less entrance channel. Calculated total rate constants (cm(3) mol(-1) s(-1)) are reported as follows: k(DMK) = 1.32 × 10(2)×T(3.30)exp(503/T), k(EMK) = 3.84 × 10(1)×T(3.51)exp(1515/T), k(iPMK) = 2.08 × 10(1)×T(3.58)exp(2161/T). Group rate constants (on a per H atom basis) for different carbon sites in title reactions have also been provided.

Influence of chemical and mechanical polishing on water sorption and solubility of denture base acrylic resins.

PubMed

Rahal, Juliana Saab; Mesquita, Marcelo Ferraz; Henriques, Guilherme Elias Pessanha; Nóbilo, Mauro Antonio Arruda

2004-01-01

Influence of polishing methods on water sorption and solubility of denture base acrylic resins was studied. Eighty samples were divided into groups: Classico (CL), and QC 20 (QC) - hot water bath cured; Acron MC (AC), and Onda Cryl (ON) - microwave cured; and submitted to mechanical polishing (MP) - pumice slurry, chalk powder, soft brush and felt cone in a bench vise; or chemical polishing (CP) - heated monomer fluid in a chemical polisher. The first desiccation process was followed by storage in distilled water at 37 +/- 1 degrees C for 1 h, 1 day, 1, 2, 3 and 4 weeks. Concluding each period, water sorption was measured. After the fourth week, a second desiccation process was done to calculate solubility. Data were submitted to analysis of variance, followed by Tukey test (p

Gossypol-Capped Mitoxantrone-Loaded Mesoporous SiO2 NPs for the Cooperative Controlled Release of Two Anti-Cancer Drugs.

PubMed

Heleg-Shabtai, Vered; Aizen, Ruth; Sharon, Etery; Sohn, Yang Sung; Trifonov, Alexander; Enkin, Natalie; Freage, Lina; Nechushtai, Rachel; Willner, Itamar

2016-06-15

Mesoporous SiO2 nanoparticles, MP-SiO2 NPs, are functionalized with the boronic acid ligand units. The pores of the MP-SiO2 NPs are loaded with the anticancer drug mitoxantrone, and the pores are capped with the anticancer drug gossypol. The resulting two-drug-functionalized MP-SiO2 NPs provide a potential stimuli-responsive anticancer drug carrier for cooperative chemotherapeutic treatment. In vitro experiments reveal that the MP-SiO2 NPs are unlocked under environmental conditions present in cancer cells, e.g., acidic pH and lactic acid overexpressed in cancer cells. The effective unlocking of the capping units under these conditions is attributed to the acidic hydrolysis of the boronate ester capping units and to the cooperative separation of the boronate ester bridges by the lactate ligand. The gossypol-capped mitoxantrone-loaded MP-SiO2 NPs reveals preferential cytotoxicity toward cancer cells and cooperative chemotherapeutic activities toward the cancer cells. The MCF-10A epithelial breast cells and the malignant MDA-MB-231 breast cancer cells treated with the gossypol-capped mitoxantrone-loaded MP-SiO2 NPs revealed after a time-interval of 5 days a cell death of ca. 8% and 60%, respectively. Also, the gossypol-capped mitoxantrone-loaded MP-SiO2 NPs revealed superior cancer-cell death (ca. 60%) as compared to control carriers consisting of β-cyclodextrin-capped mitoxantrone-loaded (ca. 40%) under similar loading of the mitoxantrone drug. The drugs-loaded MP-SiO2 NPs reveal impressive long-term stabilities.

Physical demands in elite team handball: comparisons between male and female players.

PubMed

Michalsik, L B; Aagaard, P

2015-09-01

The aim of the present study was to examine potential differences in the physical demands imposed on male vs. female adult elite team handball players during match-play. Male and female elite team handball players were monitored over a six and five season time span, respectively. Each player was evaluated during match-play by use of video recording and subsequent computerized locomotive and technical match analysis. Furthermore, physiological measurements during match-play, physical testing and anthropometric measurements were performed. Female players (FP, N.=82) covered a longer mean total distance per match (4693±333 m, group means±SD) compared to male players (MP, N.=83, 3945±538 m) when playing full time (P<0.01). FP exercised at a greater relative workload (79.4% of VO2-max) than MP (70.9% of VO2-max, P<0.05), but performed less high-intense running per match (2.5% of total distance covered) than MP (7.9%, P<0.01). FP also spent less time standing still (10.8% of total effective playing time) compared to MP (36.9%, P<0.001) and showed fewer activity changes (663.8±99.7) compared to MP (1482.4±312.6, P<0.001). MP received more tackles in total in offence (34.5±21.3) and performed more tackles in total in defence (29.9±12.3) compared to FP (14.6±9.2, 20.7±9.7, P<0.05). Furthermore, MP performed more high-intense technical playing actions per match (36.9±13.1) than FP (28.3±11.0, P<0.05). The mean body height and body mass differed between MP (189.6±5.8 cm, 91.7±7.5 kg) and FP (175.4±6.1 cm, 69.5±6.5 kg, P<0.001). Substantial gender-specific differences in the physical demands in elite team handball were observed, with MP performing more high-intense, strength-related playing actions and high-intensity running than FP. Conversely, FP covered a greater total distance and demonstrated a higher relative workload than MP. The physical training of male and female elite team handball players should be designed to reflect these contrasting needs.

Safety, Tolerability and Immunogenicity of Pentavalent Rotavirus Vaccine Manufactured by a Modified Process.

PubMed

Martinón-Torres, Federico; Greenberg, David; Varman, Meera; Killar, John A; Hille, Darcy; Strable, Erica L; Stek, Jon E; Kaplan, Susan S

2017-04-01

Rotavirus is the leading cause of severe diarrhea in infants and young children. The current formulation of pentavalent rotavirus vaccine (RV5) must be stored refrigerated at 2-8°C. A modified formulation of RV5 (RV5mp) has been developed with stability at 37°C for 7 days and an expiry extended to 36 months when stored at 2-8°C. This study (ClinicalTrials.gov identifier: NCT01600092; EudraCT number: 2012-001611-23) evaluated the safety, tolerability and immunogenicity of RV5mp versus the currently marketed RV5 in infants. To maintain blinding, both vaccine formulations were stored refrigerated at 2-8°C for the duration of the study. Immunogenicity endpoints were (1) serum neutralizing antibody titers to human rotavirus serotypes G1, G2, G3, G4 and P1A[8] and (2) proportion of subjects with a ≥3-fold rise from baseline for serum neutralizing antibody to human rotavirus serotypes G1, G2, G3, G4 and P1A[8] and serum antirotavirus immunoglobulin A. The RV5mp group (n = 505) and RV5 group (n = 509) had comparable safety profiles. There were no deaths and no vaccine-related serious adverse events in this study. With respect to immunogenicity, RV5mp was noninferior compared with RV5. Serum neutralizing antibody responses by country and breast-feeding status were generally consistent with the overall results. RV5mp enhances storage requirements while maintaining the immunogenicity and safety profile of the currently licensed RV5. A vaccine that is stable at room temperature may be more convenient for vaccinators, particularly in places where the cold chain is unreliable, and ultimately will permit more widespread use.

The Atomization Energy of Mg4

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

1999-01-01

The atomization energy of Mg4 is determined using the MP2 and CCSD(T) levels of theory. Basis set incompleteness, basis set extrapolation, and core-valence effects are discussed. Our best atomization energy, including the zero-point energy and scalar relativistic effects, is 24.6+/-1.6 kcal per mol. Our computed and extrapolated values are compared with previous results, where it is observed that our extrapolated MP2 value is good agreement with the MP2-R12 value. The CCSD(T) and MP2 core effects are found to have the opposite signs.

Distinct Subtypes of Microparticle-containing Immune Complexes Are Associated with Disease Activity, Damage, and Carotid Intima-media Thickness in Systemic Lupus Erythematosus.

PubMed

Fortin, Paul R; Cloutier, Nathalie; Bissonnette, Vincent; Aghdassi, Ellie; Eder, Lihi; Simonyan, David; Laflamme, Nathalie; Boilard, Eric

2016-11-01

Microparticles (MP) are small extracellular vesicles present in body fluids. MP originate from different cellular lineages, principally from platelets in blood, and may expose phosphatidylserine (PS). In systemic lupus erythematosus (SLE), MP harbor immunoglobulin G (IgG), thereby forming MP-containing immune complexes (mpIC). We aimed to verify an association between SLE disease activity, damage, and surrogate markers of atherosclerosis and MP harboring IgG, taking into account the platelet origin and PS exposure of MP. MP expressing surface IgG, platelet antigen (CD41+), and PS were quantified using flow cytometry in plasma of 191 women with SLE. Carotid ultrasounds (US) were available in 113 patients. Spearman correlation analysis was used to analyze whether levels of MP were associated with the following outcomes: SLE Disease Activity Index 2000 (SLEDAI-2K), Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI), and carotid US plaques and intima-media thickness (CIMT) as surrogates for vascular damage. We found CD41+ MP harboring IgG present in SLE. A positive correlation was found between SLEDAI-2K and levels of CD41+ MP harboring IgG and exposing (p = 0.027) and non-exposing PS (p = 0.001). Conversely, SDI (p = 0.024) and CIMT (p = 0.016) correlated with concentrations of CD41- MP harboring IgG and exposing PS. Associations were independent of low-density lipoprotein cholesterol level, body mass index, and antimalarial drug use. Different subtypes of mpIC are produced in SLE and are associated with distinct clinical characteristics such as disease activity and vascular damage. The assessment of MP subtypes might serve for the design of predictive markers of disease activity and vascular damage in patients.

Microporous Poly(L-Lactic Acid) Membranes Fabricated by Polyethylene Glycol Solvent-Cast/Particulate Leaching Technique

PubMed Central

Selvam, Shivaram; Chang, Wenji V.; Nakamura, Tamako; Samant, Deedar M.; Thomas, Padmaja B.; Trousdale, Melvin D.; Mircheff, Austin K.; Schechter, Joel E.

2009-01-01

With the eventual goal of developing a tissue-engineered tear secretory system, we found that primary lacrimal gland acinar cells grown on solid poly(L-lactic acid) (PLLA) supports expressed the best histiotypic morphology. However, to be able to perform vectorial transport functions, epithelia must be supported by a permeable substratum. In the present study, we describe the use of a solvent-cast/particulate leaching technique to fabricate microporous PLLA membranes (mpPLLAm) from PLLA/polyethylene glycol blends. Scanning electron microscopy revealed pores on both the air-cured (∼4 μm) and glass-cured sides (<2 μm) of the mpPLLAm. Diffusion studies were performed with mpPLLAm fabricated from 57.1% PLLA/42.9% polyethylene glycol blends to confirm the presence of channelized pores. The data reveal that glucose, L-tryptophan, and dextran (a high molecular weight glucose polymer) readily permeate mpPLLAm. Diffusion of the immunoglobulin G through the mpPLLAm decreased with time, suggesting the possible adsorption and occlusion of the pores. Cells cultured on the mpPLLAm (57.1/42.9 wt%) grew to subconfluent monolayers but retained histiotypic morphological and physiological characteristics of lacrimal acinar cells in vivo. Our results suggest that mpPLLAm fabricated using this technique may be useful as a scaffold for a bioartificial lacrimal gland device. PMID:19260769

6-Mercaptopurine transport by equilibrative nucleoside transporters in conditionally immortalized rat syncytiotrophoblast cell lines TR-TBTs.

PubMed

Lee, Na-young; Sai, Yoshimichi; Nakashima, Emi; Ohtsuki, Sumio; Kang, Young-sook

2011-09-01

Recently, more women were provided with 6-mercaptopurine (6-MP) during pregnancy. Therefore, we attempted to clarify the transport mechanisms of 6-MP through blood-placenta barrier using rat conditionally immortalized syncytiotrophoblast cell lines (TR-TBTs). The uptake of 6-MP was time- and ATP dependent, but sodium independent in TR-TBTs. 6-MP was eliminated over 50% from the cells within 30 min. The uptake of 6-MP was saturable with Michaelis-Menten constant values of 198 μM and 250 μM in TR-TBT 18d-1 and TR-TBT 18d-2, respectively. 6-Thioguanine, azathioprine, and hypoxantine, structural analogues of 6-MP, strongly inhibited [(14) C]6-MP uptake. Equilibrative nucleoside transporter (ENT) inhibitors, adenosine and uridine, significantly inhibited [(14) C]6-MP uptake. However, several organic anions and cations had no effect on [(14) C]6-MP uptake in TR-TBTs. These results suggest that sodium-independent transporters, ENTs, may be involved in 6-MP uptake at the placenta. In addition, multidrug resistance protein (MRP) inhibitors, methotrexate, probenecid, cefmetazole, and sulfinpyrazone, significantly increased the accumulation of [(14) C]6-MP in the cells. It is indicated that 6-MP may be eliminated across the blood-placental barrier via MRPs. TR-TBTs expressed mRNA of ENT1, ENT2, MRP4, and MRP5. These findings are important for the therapy of acute lymphoblastic leukemia and autoimmune diseases of pregnant women, and should be useful data in elucidating teratogenicity of 6-MP during pregnancy. Copyright © 2011 Wiley-Liss, Inc.

Dissociation reactions of potassiated glucose: deionization, potassium hydroxide loss, and cross-ring dissociation

NASA Astrophysics Data System (ADS)

Dyakov, Y. A.; Kazaryan, M. A.; Golubkov, M. G.; Gubanova, D. P.; Asratyan, A. A.

2018-04-01

Photochemical properties of carbohydrates, including mono- and polysaccharides, as well as various kinds of glycoproteins, proteoglycans, and glycolipids, take great attention last decades due to their significance for clarifying physical and chemical processes happening in biological molecules under irradiation. Understanding of excitation and ionization processes is important for interpretation of mass spectrometric (MS) experiments, which is the main instrument for quick and reliable analysis of biological samples. While polynucleotides and simple proteins can be easily studied by standard MS techniques (MALDI, ESI, and CID), carbohydrates and complicated biomolecules containing oligosaccharide residues are difficult to be ionized. Carbohydrates give a low signal yield. Their detection and analysis requires the special equipment and technology. Therefore, the development of new efficient methods for identification of carbohydrates in biological samples currently is the critical scientific and technical problem. In this work we study dissociation processes taking place in potassiated α- and β-glucose, which can be concerned as the modelling molecule for investigation of wide range of carbohydrates and carbohydrate fragments of biomolecules containing potassium ion as the ionization source. Here we compare deionization process with H2O and KOH elimination channels, as far as their competition with cross-ring dissociation processes. Potential energy surface were optimized by the density functional B3LYP/6-31G* method. Single point energy calculations in minima and transition state points were performed by G3(MP2,CCSD) ab initio method.

Efficient CO2 capture by functionalized graphene oxide nanosheets as fillers to fabricate multi-permselective mixed matrix membranes.

PubMed

Li, Xueqin; Cheng, Youdong; Zhang, Haiyang; Wang, Shaofei; Jiang, Zhongyi; Guo, Ruili; Wu, Hong

2015-03-11

A novel multi-permselective mixed matrix membrane (MP-MMM) is developed by incorporating versatile fillers functionalized with ethylene oxide (EO) groups and an amine carrier into a polymer matrix. The as-prepared MP-MMMs can separate CO2 efficiently because of the simultaneous enhancement of diffusivity selectivity, solubility selectivity, and reactivity selectivity. To be specific, MP-MMMs were fabricated by incorporating polyethylene glycol- and polyethylenimine-functionalized graphene oxide nanosheets (PEG-PEI-GO) into a commercial low-cost Pebax matrix. The PEG-PEI-GO plays multiple roles in enhancing membrane performance. First, the high-aspect ratio GO nanosheets in a polymer matrix increase the length of the tortuous path of gas diffusion and generate a rigidified interface between the polymer matrix and fillers, enhancing the diffusivity selectivity. Second, PEG consisting of EO groups has excellent affinity for CO2 to enhance the solubility selectivity. Third, PEI with abundant primary, secondary, and tertiary amine groups reacts reversibly with CO2 to enhance reactivity selectivity. Thus, the as-prepared MP-MMMs exhibit excellent CO2 permeability and CO2/gas selectivity. The MP-MMM doped with 10 wt % PEG-PEI-GO displays optimal gas separation performance with a CO2 permeability of 1330 Barrer, a CO2/CH4 selectivity of 45, and a CO2/N2 selectivity of 120, surpassing the upper bound lines of the Robeson study of 2008 (1 Barrer = 10(-10) cm(3) (STP) cm(-2) s(-1) cm(-1) Hg).

Microplastic in Aquatic Ecosystems.

PubMed

Ivleva, Natalia P; Wiesheu, Alexandra C; Niessner, Reinhard

2017-02-06

The contamination of marine and freshwater ecosystems with plastic, and especially with microplastic (MP), is a global ecological problem of increasing scientific concern. This has stimulated a great deal of research on the occurrence of MP, interaction of MP with chemical pollutants, the uptake of MP by aquatic organisms, and the resulting (negative) impact of MP. Herein, we review the major issues of MP in aquatic environments, with the principal aims 1) to characterize the methods applied for MP analysis (including sampling, processing, identification and quantification), indicate the most reliable techniques, and discuss the required further improvements; 2) to estimate the abundance of MP in marine/freshwater ecosystems and clarify the problems that hamper the comparability of such results; and 3) to summarize the existing literature on the uptake of MP by living organisms. Finally, we identify knowledge gaps, suggest possible strategies to assess environmental risks arising from MP, and discuss prospects to minimize MP abundance in aquatic ecosystems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tautomeric equilibria of 5-fluorouracil anionic species in water.

PubMed

Markova, Nadezhda; Enchev, Venelin; Ivanova, Galya

2010-12-23

It has long been postulated that rare tautomeric or ionized forms of nucleic acid bases may play a role in mispair formation. Therefore, ab initio quantum chemical investigations on the tautomeric equilibrium in 5-fluorouracil (5FU) and its anions (deprotonated from N1, AN1, and from N3, AN3) and their tautomeric forms in water were performed. The effect of the water as solvent was introduced using solute-solvent clusters (four water molecules). The influence of the water molecules on the tautomeric reactions between different forms was considered by multiple proton transfer mechanisms. We show that when a water dimer is located in the reaction site between the two pairs of N-H and C═O groups, the assistive effect of the water molecules is strengthened. All calculations of the solute-water complexes were carried out at an MP2 level of theory and supplemented with correction for higher order correlation terms at CCSD(T) level, using the 6-31+G(d,p) basis set. The ab initio calculated frequencies and Raman intensities of 5FU and its anions AN1, AN3, and dianion are in good agreement with the experimental Raman frequencies in aqueous solution at different pH. In order to establish the pH-induced structural transformation in the molecule of 5FU, further (1)H, (19)F, and (13)C NMR spectra in water solution for pH = 6.9-13.8 were acquired and the chemical shift alterations were determined as a function of pH. On the basis of NMR spectroscopic data obtained for 5FU in aqueous solution at alkaline pH, we suggest the existence of a mixture of the anionic tautomeric forms predicted by our theoretical calculations.

Resolution enhancement using a new multiple-pulse decoupling sequence for quadrupolar nuclei.

PubMed

Delevoye, L; Trébosc, J; Gan, Z; Montagne, L; Amoureux, J-P

2007-05-01

A new decoupling composite pulse sequence is proposed to remove the broadening on spin S=1/2 magic-angle spinning (MAS) spectra arising from the scalar coupling with a quadrupolar nucleus I. It is illustrated on the (31)P spectrum of an aluminophosphate, AlPO(4)-14, which is broadened by the presence of (27)Al/(31)P scalar couplings. The multiple-pulse (MP) sequence has the advantage over the continuous wave (CW) irradiation to efficiently annul the scalar dephasing without reintroducing the dipolar interaction. The MP decoupling sequence is first described in a rotor-synchronised version (RS-MP) where one parameter only needs to be adjusted. It clearly avoids the dipolar recoupling in order to achieve a better resolution than using the CW sequence. In a second improved version, the MP sequence is experimentally studied in the vicinity of the perfect rotor-synchronised conditions. The linewidth at half maximum (FWHM) of 65 Hz using (27)Al CW decoupling decreases to 48 Hz with RS-MP decoupling and to 30 Hz with rotor-asynchronised MP (RA-MP) decoupling. The main phenomena are explained using both experimental results and numerical simulations.

Towards Highly Scalable Ab Initio Molecular Dynamics (AIMD) Simulations on the Intel Knights Landing Manycore Processor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacquelin, Mathias; De Jong, Wibe A.; Bylaska, Eric J.

2017-07-03

The Ab Initio Molecular Dynamics (AIMD) method allows scientists to treat the dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. This extremely important method has tremendous computational requirements, because the electronic Schr¨odinger equation, approximated using Kohn-Sham Density Functional Theory (DFT), is solved at every time step. With the advent of manycore architectures, application developers have a significant amount of processing power within each compute node that can only be exploited through massive parallelism. A compute intensive application such as AIMD forms a good candidate to leverage this processing power. In this paper, wemore » focus on adding thread level parallelism to the plane wave DFT methodology implemented in NWChem. Through a careful optimization of tall-skinny matrix products, which are at the heart of the Lagrange multiplier and nonlocal pseudopotential kernels, as well as 3D FFTs, our OpenMP implementation delivers excellent strong scaling on the latest Intel Knights Landing (KNL) processor. We assess the efficiency of our Lagrange multiplier kernels by building a Roofline model of the platform, and verify that our implementation is close to the roofline for various problem sizes. Finally, we present strong scaling results on the complete AIMD simulation for a 64 water molecules test case, that scales up to all 68 cores of the Knights Landing processor.« less

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology.

PubMed

García-Prieto, Francisco F; Fdez Galván, Ignacio; Aguilar, Manuel A; Martín, M Elena

2011-11-21

The ASEP/MD method has been employed for studying the solvent effect on the conformational equilibrium of the alanine dipeptide in water solution. MP2 and density functional theory (DFT) levels of theory were used and results were compared. While in gas phase cyclic structures showing intramolecular hydrogen bonds were found to be the most stable, the stability order is reversed in water solution. Intermolecular interaction with the solvent causes the predominance of extended structures as the stabilizing contacts dipeptide-water are favoured. Free-energy differences in solution were calculated and PPII, α(R), and C5 conformers were identified as the most stable at MP2 level. Experimental data from Raman and IR techniques show discrepancies about the relative abundance of α(R) y C5, our results support the Raman data. The DFT level of theory agrees with MP2 in the location and stability of PPII and α(R) forms but fails in the location of C5. MP2 results suggest the possibility of finding traces of C7eq conformer in water solution, in agreement with recent experiments.

Clinical Value of Mercaptopurine After Failing Azathioprine Therapy in Patients With Inflammatory Bowel Disease.

PubMed

Meijer, Berrie; Seinen, Margien L; Leijte, Niek N W; Mulder, Chris J J; van Bodegraven, Adriaan A; de Boer, Nanne K H

2016-08-01

Thiopurines have been widely accepted as immunosuppressive therapy in inflammatory bowel disease. However, many patients have to discontinue thiopurines due to intolerance or ineffectiveness. A therapeutically beneficial effect of switching from azathioprine (AZA) to mercaptopurine (MP) after developing adverse events (AEs) has been reported. The authors assessed the clinical value of MP therapy after AZA discontinuation due to intolerance and, secondary, due to ineffectiveness. In this retrospective single-center study, the authors analyzed data from patients in whom AZA therapy had failed and who were subsequently treated with MP. Thirty-eight patients initiated MP therapy after intolerance to AZA. Intolerance reoccurred in 22 (58%) patients and the remaining 16 (42%) tolerated MP. In 18 out of 48 patients (38%), the AEs that led to discontinuation of MP were similar to those of AZA. A longer duration of prior AZA use was more common in patients who were subsequently tolerant for MP (5.3 versus 1.2 months; P = 0.04). Twenty-two patients discontinued AZA due to ineffectiveness. Eight (36%) patients had clinical benefit from a switch to MP. Six out of these 8 (75%) patients used allopurinol alongside MP, due to ineffectiveness based on a skewed thiopurine metabolism. Patients were more likely to have clinical benefit if the interval between both thiopurines was longer (4.4 versus 0.01 months; P < 0.05). The authors showed that a noteworthy number of patients benefitted therapeutically from a switch from AZA to MP when failing due to intolerance or ineffectiveness; however, the percentage was lower than previously reported in literature.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2016-05-01

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N2.6 for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity.

PubMed

Song, Chenchen; Martínez, Todd J

2016-05-07

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N(2.6) for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

Carcinogenicity of 4-methoxyphenol and 4-methylcatechol in F344 rats.

PubMed

Asakawa, E; Hirose, M; Hagiwara, A; Takahashi, S; Ito, N

1994-01-02

The carcinogenic potentials of 4-methoxyphenol (4-MP) and 4-methylcatechol (4-MC), phenolic compounds which are structurally similar to the known forestomach carcinogen BHA and the glandular stomach carcinogen catechol respectively, and cause considerably enhanced cell proliferation and cytotoxicities in rat forestomach and/or glandular stomach epithelium, were examined in male and female F344 rats. Groups of 30 male and female animals were administered diets containing 2% 4-MP or 2% 4-MC for 104 weeks. Histopathological findings in the 4-MP case included atypical hyperplasias (male, 67%, female, 37%), papillomas (50%, 23%) and squamous-cell carcinomas (77%, 20%) in the forestomach. 4-MC induced forestomach papillomas (70%, 93%) and squamous-cell carcinomas (53%, 37%), also glandular stomach submucosal hyperplasias (90%, 93%), adenomas (100%, 100%) and adenocarcinomas (57%, 47%), with ulceration or erosion. The degree of differentiation of the squamous-cell carcinomas induced by 4-MP was less than with 4-MC. The present study demonstrated unequivocal forestomach carcinogenicity for 4-MP and forestomach and glandular stomach carcinogenicity for 4-MC, with cytotoxicity and cell proliferation both appearing as important factors for these non-genotoxic carcinogens.

Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.

PubMed

Ye, Yuxin; Saburi, Wataru; Odaka, Rei; Kato, Koji; Sakurai, Naofumi; Komoda, Keisuke; Nishimoto, Mamoru; Kitaoka, Motomitsu; Mori, Haruhide; Yao, Min

2016-03-01

In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding. © 2016 Federation of European Biochemical Societies.

Nutritional manipulation of primate retinas, I: effects of lutein or zeaxanthin supplements on serum and macular pigment in xanthophyll-free rhesus monkeys.

PubMed

Neuringer, Martha; Sandstrom, Marita M; Johnson, Elizabeth J; Snodderly, D Max

2004-09-01

The xanthophylls lutein (L) and zeaxanthin (Z) are the primary components of macular pigment (MP) and may protect the macula from age-related degeneration (AMD). In this study, L or Z was fed to rhesus monkeys reared on xanthophyll-free diets to follow the accumulation of serum carotenoids and MP over time. Eighteen rhesus monkeys were fed xanthophyll-free semipurified diets from birth until 7 to 16 years. The diets of six were then supplemented with pure L and six with pure Z at 3.9 micromol/kg per day (2.2 mg/kg per day) for 24 to 56 weeks. At baseline and 4- to 12-week intervals during supplementation, serum carotenoids were measured by HPLC, and MP density was estimated by two-wavelength reflectometry. Serum carotenoids and MP were also measured in monkeys fed a stock diet. Monkeys fed xanthophyll-free diets had no L or Z in serum and no detectable MP. During supplementation, serum L or Z increased rapidly over the first 4 weeks and from 16 weeks onward maintained similar levels, both several times higher than in stock-diet-fed monkeys. The central peak of MP optical density increased to a relatively steady level by 24 to 32 weeks in both L- and Z-fed groups. Rhesus monkeys fed a stock diet had lower blood concentrations of L than those found in humans and other nonhuman primates. Rhesus monkeys respond to either dietary L or Z supplementation with increases in serum xanthophylls and MP, even after life-long xanthophyll deficiency. These animals provide a potential model to study mechanisms of protection from AMD. Copyright Association for Research in Vision and Ophthalmology

Role of serial multiparametric magnetic resonance imaging in prostate cancer active surveillance

PubMed Central

Vos, Larissa J; Janoski, Michele; Wachowicz, Keith; Yahya, Atiyah; Boychak, Oleksandr; Amanie, John; Pervez, Nadeem; Parliament, Matthew B; Pituskin, Edith; Fallone, B Gino; Usmani, Nawaid

2016-01-01

AIM: To examine whether addition of 3T multiparametric magnetic resonance imaging (mpMRI) to an active surveillance protocol could detect aggressive or progressive prostate cancer. METHODS: Twenty-three patients with low risk disease were enrolled on this active surveillance study, all of which had Gleason score 6 or less disease. All patients had clinical assessments, including digital rectal examination and prostate specific antigen (PSA) testing, every 6 mo with annual 3T mpMRI scans with gadolinium contrast and minimum sextant prostate biopsies. The MRI images were anonymized of patient identifiers and clinical information and each scan underwent radiological review without the other results known. Descriptive statistics for demographics and follow-up as well as the sensitivity and specificity of mpMRI to identify prostate cancer and progressive disease were calculated. RESULTS: During follow-up (median 24.8 mo) 11 of 23 patients with low-risk prostate cancer had disease progression and were taken off study to receive definitive treatment. Disease progression was identified through upstaging of Gleason score on subsequent biopsies for all 11 patients with only 2 patients also having a PSA doubling time of less than 2 years. All 23 patients had biopsy confirmed prostate cancer but only 10 had a positive index of suspicion on mpMRI scans at baseline (43.5% sensitivity). Aggressive disease prediction from baseline mpMRI scans had satisfactory specificity (81.8%) but low sensitivity (58.3%). Twenty-two patients had serial mpMRI scans and evidence of disease progression was seen for 3 patients all of whom had upstaging of Gleason score on biopsy (30% specificity and 100% sensitivity). CONCLUSION: Addition of mpMRI imaging in active surveillance decision making may help in identifying aggressive disease amongst men with indolent prostate cancer earlier than traditional methods. PMID:27158428

A quantum chemical calculation of the potential energy surface in the formation of HOSO 2 from OH + SO 2

NASA Astrophysics Data System (ADS)

Sitha, Sanyasi; Jewell, Linda L.; Piketh, Stuart J.; Fourie, Gerhard

2011-01-01

The formation of HOSO 2 from OH and SO 2 has been thoroughly investigated using several different methods (MP2=Full, MP2=FC, B3LYP, HF and composite G∗ methods) and basis sets (6-31G(d,p), 6-31++G(d,p), 6-31++G(2d,2p), 6-31++G(2df,2p) and aug-cc-pVnZ). We have found two different possible transition state structures, one of which is a true transition state since it has a higher energy than the reactants and products (MP2=Full, MP2=FC and HF), while the other is not a true transition state since it has an energy which lies between that of the reactants and products (B3LYP and B3LYP based methods). The transition state structure (from MP2) has a twist angle of the OH fragment relative to the SO bond of the SO 2 fragment of -50.0°, whereas this angle is 26.7° in the product molecule. Examination of the displacement vectors confirms that this is a true transition state structure. The MP2=Full method with a larger basis set (MP2=Full/6-31++G(2df,2p)) predicts the enthalpy of reaction to be -112.8 kJ mol -1 which is close to the experimental value of -113.3 ± 6 kJ mol -1, and predicts a rather high barrier of 20.0 kJ mol -1. When the TS structure obtained by the MP2 method is used as the input for calculating the energetics using the QCISD/6-31++G(2df,2p) method, a barrier of 4.1 kJ mol -1 is obtained (ZPE corrected). The rate constant calculated from this barrier is 1.3 × 10 -13 cm 3 molecule -1 s -1. We conclude that while the MP2 methods correctly predict the TS from a structural point of view, higher level energy corrections are needed for estimation of exact barrier height.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhong; Matus, Myrna H; Velazquez, Hector A

Gas-phase acidities (GA or ΔG acid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage’s importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBSmore » and B3LYP/aug-cc-pVDZ results are 3–4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH 2 groups and the CO 2 - group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pK a. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.« less

Scanning electron microscopy study of new bone formation following small and large defects preserved with xenografts supplemented with pamidronate-A pilot study in Fox-Hound dogs at 4 and 8 weeks.

PubMed

Lozano-Carrascal, Naroa; Satorres-Nieto, Marta; Delgado-Ruiz, Rafael; Maté-Sánchez de Val, José Eduardo; Gehrke, Sergio Alexandre; Gargallo-Albiol, Jorge; Calvo-Guirado, José Luis

2017-01-01

The aim of the present study was to evaluate the feasibility of SEM and EDX microanalysis on evaluating the effect of porcine xenografts (MP3 ® ) supplemented with pamidronate during socket healing. Mandibular second premolars (P2) and first molars (M1) were extracted from six Beagle dogs. P2 were categorized as small defects (SD) and M1 as large defects (LD). Four random groups were created: SC (small control defects with MP3 ® ), ST (small test defects MP3 ® +pamidronate), LC (large control defects with MP3 ® ), and LT (large test defects MP3 ® +pamidronate). At four and eight weeks of healing the samples were evaluated fisically through scanning electron microscopy (SEM), and chemical element mapping was carried out by Energy dispersive X-ray spectroscopy (EDX). After four weeks of healing, SEM and EDX analysis revealed more mineralized bone in ST and LT groups compared with control groups (p<0.05). After eight weeks, Ca/P ratios were slightly higher for small defects (groups SC and ST); in SEM description, in both control and test groups, trabecular bone density was similar to the adjacent mineralized cortical bone. Within the limitations of this experimental study, SEM description and EDX elemental microanalysis have demonstrated to be useful techniques to assess bone remodelling of small and large defects. Both techniques show increased bone formation in test groups (MP3 ® modified with pamidronate) after four and eight weeks of healing. Copyright © 2016 Elsevier GmbH. All rights reserved.

Effects of the hydroethanolic extract of Mucuna pruriens (L.) DC (Fabaceae) on haematological profile in normal and haloperidol treated rats.

PubMed

Akindele, Abidemi J; Busayo, Fadeyibi I

2011-01-01

Mucuna pruriens (L.) DC (Fabaceae) is a climbing plant claimed in traditional medicine to possess anti-anaemic effect. The study is to investigate the effects of the hydroethanolic extract of M. pruriens (MP) on haematological profile in normal and haloperidol treated rats. MP was administered p.o. at doses of 50, 100, 200, and 400 mg/kg to groups of rats daily for 28 days. Control animals received distilled water. Rats were sacrificed on the 28th day and blood samples collected for evaluation of haematological parameters and serum iron. Another set of animals received MP p.o. at same doses but along with haloperidol (0.2 mg/kg, i.p.) daily for 4 days. Three other groups of rats received distilled water, haloperidol, and MP at 400 mg/kg alone. Haematological parameters and serum iron were determined. Extract iron content, phytochemical analysis and acute toxicity studies were also carried out. MP administered to normal rats for 28 days significantly (p < 0.05) reduced the number of platelets and proportion of neutrophils. In haloperidol treated rats, MP significantly reversed the reduction in mean corpuscular haemoglobin (MCH) and mean corpuscular haemoglobin concentration (MCHC) values and increased the red blood cell (RBC) count and packed cell volume (PCV). MP also caused significant reduction in the number of platelets and proportion of neutrophils. Administered alone, MP caused a significant increase in the concentration of haemoglobin. The iron content of MP was found to be 61.20 mg/100 g and it was found to contain alkaloids, cardiac glycosides, saponins and tannins. Given up to 10 g/kg p.o., no deaths and visible signs of toxicity were observed while the LD50 for the i.p. route was estimated to be 1509.46 mg/kg. The findings in the study suggest that the hydroethanolic extract of Mucuna pruriens possibly possess beneficial effects in anaemic conditions especially associated with iron deficiency.

Effects of pH-Shift Processing and Microbial Transglutaminase on the Gel and Emulsion Characteristics of Porcine Myofibrillar System

PubMed Central

Hong, Geun-Pyo; Chun, Ji-Yeon; Jo, Yeon-Ji

2014-01-01

This study investigated the effects of microbial transglutaminase (MTGase) and pH-shift processing on the functional properties of porcine myofibrillar proteins (MP). The pH-shift processing was carried out by decreasing the pH of MP suspension to 3.0, followed by re-adjustment to pH 6.2. The native (CM) and pH-shifted MP (PM) was reacted with and without MTGase, and the gelling and emulsion characteristics were compared. To compare the pH-shifted MTGase-treated MP (PT), deamidation (DM) was conducted by reacting MTGase with MP at pH 3.0. Rigid thermal gel was produced by MTGase-treated native MP (CT) and PT. PM and DM showed the lowest storage modulus (G') at the end of thermal scanning. Both MTGase and pH-shifting produced harder MP gel, and the highest gel strength was obtained in PT. All treatments yielded lower than CM, and CT showed significantly higher yield than PM and DM treatments. For emulsion characteristics, pH-shifting improved the emulsifying ability of MP-stabilized emulsion, while the treatments had lower emulsion stability. PM-stabilized emulsion exhibited the lowest creaming stability among all treatments. The emulsion stability could be improved by the usage of MTGase. The results indicated that pH-shifting combined with MTGase had a potential application to modify or improve functional properties of MP in manufacturing of meat products. PMID:26760940

Lifespan metabolic potential of the unicellular organisms expressed by Boltzmann constant, absolute temperature and proton mass

NASA Astrophysics Data System (ADS)

Atanasov, Atanas Todorov

2016-12-01

The unicellular organisms and phages are the first appeared fundamental living organisms on the Earth. The total metabolic energy (Els, J) of these organisms can be expressed by their lifespan metabolic potential (Als, J/kg) and body mass (M, kg): Els =Als M. In this study we found a different expression - by Boltzmann's constant (k, J/K), nucleon mass (mp+, kg) of protons (and neutrons), body mass (M, kg) of organism or mass (Ms) of biomolecules (proteins, nucleotides, polysaccharides and lipids) building organism, and the absolute temperature (T, K). The found equations are: Els= (M/mp+)kT for phages and Els=(Ms/mp+)kT for the unicellular organisms. From these equations the lifespan metabolic potential can be expressed as: Als=Els/M= (k/mp+)T for phages and Als=Els/M= (k/3.3mp+)T for unicellular organisms. The temperature-normated lifespan metabolic potential (Als/T, J/K.kg) is equals to the ratio between Boltzmann's constant and nucleon mass: Als/T=k/mp+ for phages and Als/T=k/3.3mp+ for unicellular organisms. The numerical value of the k/mp+ ratio is equals to 8.254×103 J/K.kg, and the numerical value of k/3.3mp+ ratio is equal to 2.497×103 J/K.kg. These values of temperature-normated lifespan metabolic potential could be considered fundamental for the unicellular organisms.

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

Prognostic Value of Myocardial Perfusion Analysis in Patients with Coronary Artery Disease: A Meta-Analysis.

PubMed

Xiu, Jiancheng; Cui, Kai; Wang, Yuegang; Zheng, Hua; Chen, Gangbin; Feng, Qian; Bin, Jianping; Wu, Juefei; Porter, Thomas R

2017-03-01

Myocardial perfusion (MP) imaging during stress myocardial contrast echocardiography (MCE) improves the detection of coronary artery disease (CAD). However, its prognostic value to predict cardiac events in patients with known or suspected CAD is still undefined. A search was conducted for single- or multicenter prospective studies that evaluated the prognostic value of stress MCE in patients with known or suspected CAD. A database search was performed through June 2015. Effect sizes of relative risk ratios (RRs) with their corresponding 95% CIs were used to evaluate the association between the occurrence of total cardiac events (cardiac death, nonfatal myocardial infarction, coronary revascularization) and hard cardiac events (cardiac death and nonfatal myocardial infarction) in subjects with normal and abnormal MP measured by MCE. The Cochran Q statistic and the I 2 statistic were used to assess heterogeneity. A comprehensive literature search of the MEDLINE, Google Scholar, Cochrane, and Embase databases identified 11 studies enrolling a total of 4,045 patients. The overall analysis of RRs revealed that patients with abnormal MP were at higher risk for total cardiac events compared with patients with normal MP (RR, 5.58; 95% CI, 3.64-8.57; P < .001), with low heterogeneity among trials (I 2  = 48.15%, Q = 7.71, P = .103). Similarly, patients with abnormal MP were at higher risk for hard cardiac events compared with patients with normal MP (RR, 4.99; 95% CI, 1.75-14.32; P = .003), with significant heterogeneity among trials (I 2  = 81.48%, Q = 21.59, P < .001). The results of this meta-analysis suggest that MP assessment using stress MCE is an effective prognostic tool for predicting the occurrence of cardiac events in patients with known or suspected CAD. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Evaluation of measures to promote desert bighorn sheep highway permeability : U.S. Route 93.

DOT National Transportation Integrated Search

2014-01-01

This study evaluated desert bighorn sheephighway relationships from 2008 to 2010 along a 17mi stretch of U.S. Route 93 : (U.S. 93), in northwestern Arizona. Highway reconstruction between mileposts (MP) 2.3 and MP 17.0 was completed in October ...

SLCO1B1 Polymorphisms are Associated With Drug Intolerance in Childhood Leukemia Maintenance Therapy.

PubMed

Eldem, İrem; Yavuz, Duygu; Cumaoğullari, Özge; İleri, Talia; Ünal İnce, Elif; Ertem, Mehmet; Doğanay Erdoğan, Beyza; Bindak, Recep; Özdağ, Hilal; Şatiroğlu-Tufan, N Lale; Uysal, L Zümrüt

2018-04-20

Therapy discontinuations and toxicities occur because of significant interindividual variations in 6-mercaptopurine (6-MP) and methotrexate (MTX) response during maintenance therapy of childhood acute lymphoblastic leukemia (ALL). 6-MP/MTX intolerance in some of the patients cannot be explained by thiopurine S-methyl transferase (TPMT) gene variants. In this study, we aimed to investigate candidate pharmacogenetic determinants of 6-MP and MTX intolerance in Turkish ALL children. In total, 48 children with ALL who had completed or were receiving maintenance therapy according to Children's Oncology Group (COG) protocols were enrolled. Fifteen single-nucleotide polymorphisms in 8 candidate genes that were related to drug toxicity or had a role in the 6-MP/MTX metabolism (TPMT, ITPA, MTHFR, IMPDH2, PACSIN2, SLCO1B1, ABCC4, and PYGL) were genotyped by competitive allele-specific PCR (KASP). Drug doses during maintenance therapy were modified according to the protocol. The median drug dose intensity was 50% (28% to 92%) for 6-MP and 58% (27% to 99%) for MTX in the first year of maintenance therapy, which were lower than that scheduled in all patients. Among the analyzed polymorphisms, variant alleles in SLCO1B1 rs4149056 and rs11045879 were found to be associated with lower 6-MP/MTX tolerance. SLCO1B1 rs4149056 and rs11045879 polymorphisms may be important genetic markers to individualize 6-MP/MTX doses.

Theoretical studies of chemisorption and dimer model systems: Moller-Plesset and configuration interaction calculations on PdH, PdC, PdO, PdF, Pd sub 2 , and PdCO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwerdtfeger, P.; McFeaters, J.S.; Moore, J.J.

1991-01-01

Ab initio SCF studies have been performed to study the molecular properties of several single-bonded palladium compounds, PdH, PdC, PdO, PdF, Pd{sub 2}, and PdCO, which are important in surface and materials science. Electron correlation effects were evaluated by a second- and third-order Moller-Plesset (MP) perturbation theory and a size-consistency-corrected configuration interaction with single and double substitutions (CISC). Relativistic effects were investigated for PdH and PdF. The ground state of PdC has been calculated at the CISC level to be a {sup 3}{Pi} state which is only 0.26 eV below the {sup 3}{Sigma}{sup {minus}} state (previously assigned ground state) andmore » 0.51 eV below the {sup 1}{Sigma}{sup +} state. PdC is predicted to be stable in the gas phase, and the possibility of preparing this compound is investigated. The bonding in CO chemisorbed on palladium is studied by using the model Pd-CO system. The effect of d{sub {pi}}-{pi}{sup *} back-bonding, discussed at the Hartree-Fock and CI level, is compared with results from multiple-scattering {Chi}{alpha} calculations. The C-O stretching frequency shift for CO on palladium was analyzed at various levels of theory, and the results indicated that the decrease in the CO force constant associated with chemisorption is not solely the result of d{sub {pi}}-{pi}{sup *} back-bonding.« less

Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

NASA Astrophysics Data System (ADS)

Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

2011-04-01

We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).