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.

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 ...

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

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.

Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

NASA Astrophysics Data System (ADS)

Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

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.

Accurate energetics of small molecules containing third-row atoms Ga-Kr: A comparison of advanced ab initio and density functional theory

NASA Astrophysics Data System (ADS)

Yockel, Scott; Mintz, Benjamin; Wilson, Angela K.

2004-07-01

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

Ab initio Potential Energy Surface for H-H2

NASA Technical Reports Server (NTRS)

Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

1993-01-01

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

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.

On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

NASA Astrophysics Data System (ADS)

Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

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.

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.

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.

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

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1988-01-01

Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials

NASA Technical Reports Server (NTRS)

Bagayoko, D.; Zhao, G. L.; Hasan, S.

2001-01-01

We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.

A full-dimensional ab initio potential energy surface and rovibrational energies of the Ar–HF complex

NASA Astrophysics Data System (ADS)

Huang, Jing; Zhou, Yanzi; Xie, Daiqian

2018-04-01

We report a new full-dimensional ab initio potential energy surface for the Ar-HF van der Waals complex at the level of coupled-cluster singles and doubles with noniterative inclusion of connected triples levels [CCSD(T)] using augmented correlation-consistent quintuple-zeta basis set (aV5Z) plus bond functions. Full counterpoise correction was employed to correct the basis-set superposition error. The hypersurface was fitted using artificial neural network method with a root mean square error of 0.1085 cm-1 for more than 8000 ab initio points. The complex was found to prefer a linear Ar-H-F equilibrium structure. The three-dimensional discrete variable representation method and the Lanczos propagation algorithm were then employed to calculate the rovibrational states without separating inter- and intra- molecular nuclear motions. The calculated vibrational energies of Ar-HF differ from the experiment values within about 1 cm-1 on the first four HF vibrational states, and the predicted pure rotational energies on (0000) and (1000) vibrational states are deviated from the observed value by about 1%, which shows the accuracy of our new PES.

Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule.

PubMed

Kumar Deb, Debojit; Sarkar, Biplab

2017-01-18

The torsional potential of OH and SH rotations in 2-hydroxy thiophenol is systematically studied using the MP2 ab initio method. The outcome of state-of-the-art calculations is used in the investigation of the structures and conformational preferences of 2-hydroxy thiophenol and aims at further interaction studies with a gas phase water molecule. SCS-MP2 and CCSD(T) complete basis set (CBS) limit interaction energies for these complexes are presented. The SCS-MP2/CBS limit is achieved using various two-point extrapolation methods with aug-cc-pVDZ and aug-cc-pVTZ basis sets. The CCSD(T) correction term is determined as the difference between CCSD(T) and SCS-MP2 interaction energies calculated using a smaller basis set. The effect of counterpoise correction on the extrapolation to the CBS limit is discussed. The performance of DFT based wB97XD, M06-2X and B3LYP-D3 functionals is tested against the benchmark energy from ab initio calculations. Hydrogen bond interactions are characterized by carrying out QTAIM, NCIPLOT, NBO and SAPT analyses.

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.

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.

2017-10-01

We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.

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.

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

PubMed

Varandas, A J C

2011-05-28

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data. This journal is © the Owner Societies 2011

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

High order discretization techniques for real-space ab initio simulations

NASA Astrophysics Data System (ADS)

Anderson, Christopher R.

2018-03-01

In this paper, we present discretization techniques to address numerical problems that arise when constructing ab initio approximations that use real-space computational grids. We present techniques to accommodate the singular nature of idealized nuclear and idealized electronic potentials, and we demonstrate the utility of using high order accurate grid based approximations to Poisson's equation in unbounded domains. To demonstrate the accuracy of these techniques, we present results for a Full Configuration Interaction computation of the dissociation of H2 using a computed, configuration dependent, orbital basis set.

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

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

Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr

2013-11-07

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality.more » By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.« less

Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

PubMed

Li, Y Q; Varandas, A J C

2010-09-16

An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

High-level ab initio enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan.

PubMed

Feller, David; Simmie, John M

2012-11-29

A high-level ab initio thermochemical technique, known as the Feller-Petersen-Dixon method, is used to calculate the total atomization energies and hence the enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan itself as a means of rationalizing significant discrepancies in the literature. In order to avoid extremely large standard coupled cluster theory calculations, the explicitly correlated CCSD(T)-F12b variation was used with basis sets up to cc-pVQZ-F12. After extrapolating to the complete basis set limit and applying corrections for core/valence, scalar relativistic, and higher order effects, the final Δ(f)H° (298.15 K) values, with the available experimental values in parentheses are furan -34.8 ± 3 (-34.7 ± 0.8), 2-methylfuran -80.3 ± 5 (-76.4 ± 1.2), and 2,5-dimethylfuran -124.6 ± 6 (-128.1 ± 1.1) kJ mol(-1). The theoretical results exhibit a compelling internal consistency.

Projected Hybrid Orbitals: A General QM/MM Method

PubMed Central

2015-01-01

A projected hybrid orbital (PHO) method was described to model the covalent boundary in a hybrid quantum mechanical and molecular mechanical (QM/MM) system. The PHO approach can be used in ab initio wave function theory and in density functional theory with any basis set without introducing system-dependent parameters. In this method, a secondary basis set on the boundary atom is introduced to formulate a set of hybrid atomic orbtials. The primary basis set on the boundary atom used for the QM subsystem is projected onto the secondary basis to yield a representation that provides a good approximation to the electron-withdrawing power of the primary basis set to balance electronic interactions between QM and MM subsystems. The PHO method has been tested on a range of molecules and properties. Comparison with results obtained from QM calculations on the entire system shows that the present PHO method is a robust and balanced QM/MM scheme that preserves the structural and electronic properties of the QM region. PMID:25317748

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

Applicability of effective fragment potential version 2 - Molecular dynamics (EFP2-MD) simulations for predicting excess properties of mixed solvents

NASA Astrophysics Data System (ADS)

Kuroki, Nahoko; Mori, Hirotoshi

2018-02-01

Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

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

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less

HeI photoelectron spectroscopic studies on the electronic structure of alkyl nitrosamines

NASA Astrophysics Data System (ADS)

Jiang, Peng; Qian, Ximei; Li, Chunhui; Qiao, Chunhua; Wang, Dianxun

1997-10-01

HeI photoelectron spectroscopic (PES) studies on the electronic structure of alkyl nitrosamines R 2N 2O (R = CH 3-, CH 3CH 2-, and CH 3CH 2CH 2-) are reported. The assignment of the PES bands for this series of compounds has been made with the aid of the band shapes, the band intensity and ab initio SCF MO calculations based on the 631 ∗ G basis sets. Both PES experiment and the ab initio SCF MO calculations show that the detoxification ability of nitrosamine with longer alkyl chain is stronger.

An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

1995-01-01

A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

Use of Biodescriptors and Chemodescriptors in Predictive Toxicology: A Mathematical/Computational Approach

DTIC Science & Technology

2005-01-01

proteomic gel analyses. The research group has explored the use of chemodescriptors calculated using high-level ab initio quantum chemical basis sets...descriptors that characterize the entire proteomics map, local descriptors that characterize a subset of the proteins present in the gel, and spectrum...techniques for analyzing the full set of proteins present in a proteomics map. 14. SUBJECT TERMS 1S. NUMBER OF PAGES Topological indices

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.

Benchmark of Ab Initio Bethe-Salpeter Equation Approach with Numeric Atom-Centered Orbitals

NASA Astrophysics Data System (ADS)

Liu, Chi; Kloppenburg, Jan; Kanai, Yosuke; Blum, Volker

The Bethe-Salpeter equation (BSE) approach based on the GW approximation has been shown to be successful for optical spectra prediction of solids and recently also for small molecules. We here present an all-electron implementation of the BSE using numeric atom-centered orbital (NAO) basis sets. In this work, we present benchmark of BSE implemented in FHI-aims for low-lying excitation energies for a set of small organic molecules, the well-known Thiel's set. The difference between our implementation (using an analytic continuation of the GW self-energy on the real axis) and the results generated by a fully frequency dependent GW treatment on the real axis is on the order of 0.07 eV for the benchmark molecular set. We study the convergence behavior to the complete basis set limit for excitation spectra, using a group of valence correlation consistent NAO basis sets (NAO-VCC-nZ), as well as for standard NAO basis sets for ground state DFT with extended augmentation functions (NAO+aug). The BSE results and convergence behavior are compared to linear-response time-dependent DFT, where excellent numerical convergence is shown for NAO+aug basis sets.

CCSD(T) potential energy and induced dipole surfaces for N2–H2(D2): retrieval of the collision-induced absorption integrated intensities in the regions of the fundamental and first overtone vibrational transitions.

PubMed

Buryak, Ilya; Lokshtanov, Sergei; Vigasin, Andrey

2012-09-21

The present work aims at ab initio characterization of the integrated intensity temperature variation of collision-induced absorption (CIA) in N(2)-H(2)(D(2)). Global fits of potential energy surface (PES) and induced dipole moment surface (IDS) were made on the basis of CCSD(T) (coupled cluster with single and double and perturbative triple excitations) calculations with aug-cc-pV(T,Q)Z basis sets. Basis set superposition error correction and extrapolation to complete basis set (CBS) limit techniques were applied to both energy and dipole moment. Classical second cross virial coefficient calculations accounting for the first quantum correction were employed to prove the quality of the obtained PES. The CIA temperature dependence was found in satisfactory agreement with available experimental data.

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Technical Reports Server (NTRS)

Rogers, J. D.; Hillman, J. J.

1982-01-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Astrophysics Data System (ADS)

Rogers, J. D.; Hillman, J. J.

1982-04-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

On the ab initio evaluation of Hubbard parameters. II. The κ-(BEDT-TTF)2Cu[N(CN)2]Br crystal

NASA Astrophysics Data System (ADS)

Fortunelli, Alessandro; Painelli, Anna

1997-05-01

A previously proposed approach for the ab initio evaluation of Hubbard parameters is applied to BEDT-TTF dimers. The dimers are positioned according to four geometries taken as the first neighbors from the experimental data on the κ-(BEDT-TTF)2Cu[N(CN)2]Br crystal. RHF-SCF, CAS-SCF and frozen-orbital calculations using the 6-31G** basis set are performed with different values of the total charge, allowing us to derive all the relevant parameters. It is found that the electronic structure of the BEDT-TTF planes is adequately described by the standard Extended Hubbard Model, with the off-diagonal electron-electron interaction terms (X and W) of negligible size. The derived parameters are in good agreement with available experimental data. Comparison with previous theoretical estimates shows that the t values compare well with those obtained from Extended Hückel Theory (whereas the minimal basis set estimates are completely unreliable). On the other hand, the Uaeff values exhibit an appreciable dependence on the chemical environment.

Ab Initio Potential Energy Surface for H-H2

NASA Technical Reports Server (NTRS)

Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

1993-01-01

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

Ab initio intermolecular potential energy surface for the CO2—N2 system and related thermophysical properties

NASA Astrophysics Data System (ADS)

Crusius, Johann-Philipp; Hellmann, Robert; Castro-Palacio, Juan Carlos; Vesovic, Velisa

2018-06-01

A four-dimensional potential energy surface (PES) for the interaction between a rigid carbon dioxide molecule and a rigid nitrogen molecule was constructed based on quantum-chemical ab initio calculations up to the coupled-cluster level with single, double, and perturbative triple excitations. Interaction energies for a total of 1893 points on the PES were calculated using the counterpoise-corrected supermolecular approach and basis sets of up to quintuple-zeta quality with bond functions. The interaction energies were extrapolated to the complete basis set limit, and an analytical site-site potential function with seven sites for carbon dioxide and five sites for nitrogen was fitted to the interaction energies. The CO2—N2 cross second virial coefficient as well as the dilute gas shear viscosity, thermal conductivity, and binary diffusion coefficient of CO2—N2 mixtures were calculated for temperatures up to 2000 K to validate the PES and to provide reliable reference values for these important properties. The calculated values are in very good agreement with the best experimental data.

A DFT and ab initio benchmarking study of metal-alkane interactions and the activation of carbon-hydrogen bonds.

PubMed

Flener-Lovitt, Charity; Woon, David E; Dunning, Thom H; Girolami, Gregory S

2010-02-04

Density functional theory and ab initio methods have been used to calculate the structures and energies of minima and transition states for the reactions of methane coordinated to a transition metal. The reactions studied are reversible C-H bond activation of the coordinated methane ligand to form a transition metal methyl hydride complex and dissociation of the coordinated methane ligand. The reaction sequence can be summarized as L(x)M(CH(3))H <==> L(x)M(CH(4)) <==> L(x)M + CH(4), where L(x)M is the osmium-containing fragment (C(5)H(5))Os(R(2)PCH(2)PR(2))(+) and R is H or CH(3). Three-center metal-carbon-hydrogen interactions play an important role in this system. Both basis sets and functionals have been benchmarked in this work, including new correlation consistent basis sets for a third transition series element, osmium. Double zeta quality correlation consistent basis sets yield energies close to those from calculations with quadruple-zeta basis sets, with variations that are smaller than the differences between functionals. The energies of important species on the potential energy surface, calculated by using 10 DFT functionals, are compared both to experimental values and to CCSD(T) single point calculations. Kohn-Sham natural bond orbital descriptions are used to understand the differences between functionals. Older functionals favor electrostatic interactions over weak donor-acceptor interactions and, therefore, are not particularly well suited for describing systems--such as sigma-complexes--in which the latter are dominant. Newer kinetic and dispersion-corrected functionals such as MPW1K and M05-2X provide significantly better descriptions of the bonding interactions, as judged by their ability to predict energies closer to CCSD(T) values. Kohn-Sham and natural bond orbitals are used to differentiate between bonding descriptions. Our evaluations of these basis sets and DFT functionals lead us to recommend the use of dispersion corrected functionals in conjunction with double-zeta or larger basis sets with polarization functions for calculations involving weak interactions, such as those found in sigma-complexes with transition metals.

The molecular structure and conformation of tetrabromoformaldazine: ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-06-01

Ab initio and density functional theory methods are applied to investigate the molecular structure and conformational nature of tetrabromoformaldazine. The calculations including the effects of the electron correlation at the B3LYP and MP2 levels with the basis set 6-311+G(d) can reproduce the experimental geometrical parameters at the skew conformation. The N-N bond torsional angle φ calculated at the MP2/6-311+G(d) level is found to be closest to the observed angle. The scanning of the potential energy surface suggests that the anti-conformation is at a saddle point corresponding to the transition state.

Ab initio approaches for the determination of heavy element energetics: Ionization energies of trivalent lanthanides (Ln = La-Eu)

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

Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K., E-mail: wilson@chemistry.msu.edu

2015-11-21

An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.

Interaction potentials and transport properties of Ba, Ba+, and Ba2+ in rare gases from He to Xe

NASA Astrophysics Data System (ADS)

Buchachenko, Alexei A.; Viehland, Larry A.

2018-04-01

A highly accurate, consistent set of ab initio interaction potentials is obtained for the title systems at the coupled cluster with singles, doubles, and non-iterative triples level of theory with extrapolation to the complete basis set limit. These potentials are shown to be more reliable than the previous potentials based on their long-range behavior, equilibrium properties, collision cross sections, and transport properties.

Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

NASA Astrophysics Data System (ADS)

Langhoff, P. W.; Winstead, C. L.

Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

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.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

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].

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

NASA Technical Reports Server (NTRS)

Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

1992-01-01

An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

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 study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry

NASA Astrophysics Data System (ADS)

Varandas, António J. C.

2018-04-01

Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Because they are frequently based on the gold-standard coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)], correlated calculations are often affordable only with the smallest basis sets, and hence single-level extrapolations from one raw energy could attain maximum usefulness. This possibility is examined. Whenever possible, this review uses raw data from second-order Møller-Plesset perturbation theory, as well as CCSD, CCSD(T), and multireference configuration interaction methods. Inescapably, the emphasis is on work done by the author's research group. Certain issues in need of further research or review are pinpointed.

High-level ab initio studies of the complex formed between CO and O2

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2017-05-01

The explicitly correlated CCSD(T)-F12 method with VXZ-F12 basis sets was used to find the most stable structures of the van der Waals CO-O2 complexes. With geometry optimizations performed up to the quadruple-zeta level and basis set extrapolation, the calculated interaction energies for the triplet complexes are 123 cm-1 for the H complex in Cs symmetry (slipped near-parallel structure), 118 cm-1 for the X complex, also in Cs symmetry (perpendicular alignment) and 116 cm-1 for the CO-O2 T complex in C2v symmetry. The corresponding CCSD(T)-F12 results using the aug-cc-pVXZ basis sets are nearly the same. Similar calculations were performed for the CO-O2 singlet complexes, which are shown to have much higher stabilization energies, the highest being 206 cm-1 for the X complex.

The molecular structures and conformation of o-selenobenzyl fluoride derivatives, ArSeX (Ar=C 6H 4CH 2F; X=CN, Cl, Me): ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-10-01

Ab initio and density functional theory methods are applied to investigate the molecular structures, intramolecular orbital interactions, and 19F and 77Se NMR chemical shifts of o-selenobenzyl fluoride derivatives, ArSeX ( Ar= C6H4CH2F; X= CN, Cl, Me) , at both RHF and B3LYP levels with the basis sets 6-311G ∗∗ and 6-311+G ∗∗. There are two stable rotational conformers for ArSeX. The energy differences between both conformers for each compound are small (within 2 kcal/mol) at various levels.

Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

PubMed

Koukounas, Constantine; Mavridis, Aristides

2008-11-06

The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

The dissociation energy of N2

NASA Technical Reports Server (NTRS)

Almloef, Jan; Deleeuw, Bradley J.; Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Siegbahn, Per

1989-01-01

The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory.

PubMed

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-24

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3). Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-01

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G* basis set. The -311++G** basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of Csbnd H bond length and the elongation of Nsbnd H bond length suggest the existence of weak Csbnd H⋯O and Nsbnd H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P21 space group, with lattice parameters Z = 4, a = 14.9989 Å, b = 4.0367 Å, c = 12.9913 Å, ρ = 0.998 g cm-3.

A correlated ab initio study of linear carbon-chain radicals CnH (n = 2-7)

NASA Technical Reports Server (NTRS)

Woon, D. E.; Loew, G. H. (Principal Investigator)

1995-01-01

Linear carbon-chain radicals CnH for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2 sigma+ to 2 pi as the chain is extended. For C4H, the 2 sigma+ state was found to lie only 72 cm-1 below the 2 pi state in the estimated complete basis set limit for valence correlation. The C2H- and C3H- anions have also been characterized.

A correlated ab initio study of the A2 pi <-- X2 sigma+ transition in MgCCH

NASA Technical Reports Server (NTRS)

Woon, D. E.

1997-01-01

The A2 pi <-- X2 sigma+ transition in MgCCH was studied with correlation consistent basis sets and single- and multireference correlation methods. The A2 pi excited state was characterized in detail; the x2 sigma+ ground state has been described elsewhere recently. The estimated complete basis set (CBS) limits for valence correlation, including zero-point energy corrections, are 22668, 23191, and 22795 for the RCCSD(T), MRCI, and MRCI + Q methods, respectively. A core-valence correction of +162 cm-1 shifts the RCCSD(T) value to 22830 cm-1, in good agreement with the experimental result of 22807 cm-1.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

Electronic and spectroscopic characterizations of SNP isomers

NASA Astrophysics Data System (ADS)

Trabelsi, Tarek; Al Mogren, Muneerah Mogren; Hochlaf, Majdi; Francisco, Joseph S.

2018-02-01

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ˜2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

Vibrational spectroscopic study of fluticasone propionate

NASA Astrophysics Data System (ADS)

Ali, H. R. H.; Edwards, H. G. M.; Kendrick, J.; Scowen, I. J.

2009-03-01

Fluticasone propionate is a synthetic glucocorticoid with potent anti-inflammatory activity that has been used effectively in the treatment of chronic asthma. The present work reports a vibrational spectroscopic study of fluticasone propionate and gives proposed molecular assignments on the basis of ab initio calculations using BLYP density functional theory with a 6-31G* basis set and vibrational frequencies predicted within the quasi-harmonic approximation. Several spectral features and band intensities are explained. This study generated a library of information that can be employed to aid the process monitoring of fluticasone propionate.

Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

NASA Astrophysics Data System (ADS)

Frisch, Michael J.; Binkley, J. Stephen; Schaefer, Henry F., III

1984-08-01

The relative energies of the stationary points on the FH2 and H2CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Møller-Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H2→FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol-1 of the experimental value using the largest basis set considered. The qualitative features of the H2CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended.

Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

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

Sylvetsky, Nitai, E-mail: gershom@weizmann.ac.il; Martin, Jan M. L., E-mail: gershom@weizmann.ac.il; Peterson, Kirk A., E-mail: kipeters@wsu.edu

2016-06-07

In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H–He, B–Ne, and Al–Ar, is shown to be very close to the basis setmore » limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl{sub 4}) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than “valence limit + CV correction” approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12 calculations, but the (T) component from conventional CCSD(T)/aug’-cc-pV{Q,5}Z + d calculations using Schwenke’s extrapolation; post-CCSD(T), core-valence, and relativistic corrections are to be obtained as in the original W4 theory. W4-F12 is found to agree slightly better than W4 with ATcT (active thermochemical tables) data, at a substantial saving in computation time and especially I/O overhead. A W4-F12 calculation on benzene is presented as a proof of concept.« less

Electronic Structure and Absorption Spectra of Sodium 2-Hydroxy-5-({2-Methoxy-4[(4-Sulfophenyl)Diazenyl]Phenyl}Diazenyl)Benzoate

NASA Astrophysics Data System (ADS)

Almodarresiyeh, H. A.; Shahab, S. N.; Zelenkovsky, V. M.; Agabekov, V. E.

2014-03-01

The electronic structure and geometry of the synthesized azodye sodium 2-hydroxy-5-({2-methoxy-4[(4-sulfophenyl) diazenyl]phenyl}diazenyl)benzoate (M12) were calculated theoretically by an ab initio Hartree-Fock method in basis set 6-31G. The nature of absorption bands in the visible and near-UV spectral regions was interpreted.

Static electric polarizabilities and first hyperpolarizabilities of molecular ions RgH + (Rg = He, Ne, Ar, Kr, Xe): ab initio study

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Antušek, Andrej; Holka, Filip; Sadlej, Joanna

2009-06-01

Extensive ab initio calculations of static electric properties of molecular ions of general formula RgH + (Rg = He, Ne, Ar, Kr, Xe) involving the finite field method and coupled cluster CCSD(T) approach have been done. The relativistic effects were taken into account by Douglas-Kroll-Hess approximation. The numerical stability and reliability of calculated values have been tested using the systematic sequence of Dunning's cc-pVXZ-DK and ANO-RCC-VQZP basis sets. The influence of ZPE and pure vibrational contribution has been discussed. The component αzz has increasing trend in RgH + while the relativistic effect on αzz leads to a small increase of this molecular parameter.

Collisional excitation of interstellar PO(X2Π) by He: new ab initio potential energy surfaces and scattering calculations

NASA Astrophysics Data System (ADS)

Lique, François; Jiménez-Serra, Izaskun; Viti, Serena; Marinakis, Sarantos

2018-01-01

We present the first ab initio potential energy surfaces (PESs) for the PO(X2Π)-He van der Waals system. The PESs were obtained using the open-shell partially spin-restricted coupled cluster approach with single, double and perturbative triple excitations [UCCSD(T)]. The augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) basis set was employed supplemented by mid-bond functions. Integral and differential cross sections for the rotational excitation in PO-He collisions were calculated using the new PES and compared with results in similar systems. Finally, our work presents the first hyperfine-resolved cross sections for this system that are needed for accurate modelling in astrophysical environments.

Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

2017-02-14

Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16 O 3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν 3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm -1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

A Correlated Ab Initio Study of Linear Carbon-Chain Radicals C(sub n)H (n=2-7)

NASA Technical Reports Server (NTRS)

Woon, David E.

1995-01-01

Linear carbon-chain radicals C(sub n) H for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2Sigma(+) to 2Pi as the chain is extended. For C4H, the 2Sigma(+) state was found to lie only 72 cm(exp -1) below the 2Pi state in the estimated complete basis set limit for valence correlation. The C2H(-) and C3H(-) anions have also been characterized.

On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

NASA Astrophysics Data System (ADS)

Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

Locally dense basis sets (

Non-expanded dispersion energies and damping functions for Ar 2 and Li 2

NASA Astrophysics Data System (ADS)

Knowles, Peter J.; Meath, William J.

1986-02-01

The non-expanded second-order dispersion energies and damping functions associated with the long-range dispersion energies varying as R-6, R-8and R-10 have been calculated for Ar 2 and Li 2 with the time-dependent Hartree-Fock method, using extended Gaussian basis sets. These results are used to discuss the difficulties associated with ab initio computations of these quantities.

Accurate ab initio binding energies of the benzene dimer.

PubMed

Park, Young Choon; Lee, Jae Shin

2006-04-20

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.

Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

A metallic isolated band in the middle of the band gap of several III-V semiconductors has been predicted as photovoltaic materials with the possibility of providing substantially enhanced efficiencies. We have investigated the electronic band structures and lattice constants of GanAsmM and GanPmM with M=Sc, Ti, V, and Cr, to identify whether this isolated band is likely to exist by means of accurate calculations. For this task, we use the SIESTA program, an ab initio periodic density-functional method, fully self consistent in the local-density approximation. Norm-conserving, nonlocal pseudopotentials and confined linear combination of atomic orbitals have been used. We have carried out a case study of GanAsmTi and GanPmTi energy-band structure including analyses of the effect of the basis set, fine k-point mesh to ensure numerical convergence, structural parameters, and generalized gradient approximation for exchange and correlation corrections. We find the isolated intermediate band when one Ti atom replaces the position of one As (or P) atom in the crystal structure. For this kind of compound we show that the intermediate band relative position inside the band gap and width are sensitive to the dynamic relaxation of the crystal and the size of the basis set.

Vibrational spectroscopic study of terbutaline hemisulphate

NASA Astrophysics Data System (ADS)

Ali, H. R. H.; Edwards, H. G. M.; Kendrick, J.; Scowen, I. J.

2009-05-01

The Raman spectrum of terbutaline hemisulphate is reported for the first time, and molecular assignments are proposed on the basis of ab initio BLYP DFT calculations with a 6-31G* basis set and vibrational frequencies predicted within the quasi-harmonic approximation; these predictions compare favourably with the observed vibrational spectra. Comparison with previously published infrared data explains several spectral features. The results from this study provide data that can be used for the preparative process monitoring of terbutaline hemisulphate, an important β 2 agonist drug in various dosage forms and its interaction with excipients and other components.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

NASA Astrophysics Data System (ADS)

Lee, Hee-Seung; Tuckerman, Mark E.

2007-04-01

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit.

PubMed

Lee, Hee-Seung; Tuckerman, Mark E

2007-04-28

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

An ab initio global potential-energy surface for NH2(A(2)A') and vibrational spectrum of the Renner-Teller A(2)A'-X(2)A" system.

PubMed

Zhou, Shulan; Li, Zheng; Xie, Daiqian; Lin, Shi Ying; Guo, Hua

2009-05-14

A global potential-energy surface for the first excited electronic state of NH(2)(A(2)A(')) has been constructed by three-dimensional cubic spline interpolation of more than 20,000 ab initio points, which were calculated at the multireference configuration-interaction level with the Davidson correction using the augmented correlation-consistent polarized valence quadruple-zeta basis set. The (J=0) vibrational energy levels for the ground (X(2)A(")) and excited (A(2)A(')) electronic states of NH(2) were calculated on our potential-energy surfaces with the diagonal Renner-Teller terms. The results show a good agreement with the experimental vibrational frequencies of NH(2) and its isotopomers.

Ab initio/DFT/GIAO-CCSD(T) calculational study of the t-butyl cation: comparison of experimental data with structures, energetics, IR vibrational frequencies, and 13C NMR chemical shifts indicating preferred C(s) conformation.

PubMed

Rasul, Golam; Chen, Jonathan L; Prakash, G K Surya; Olah, George A

2009-06-18

The C(s) conformation of the tert-butyl cation 3 was established to be the preferred global energy minimum using a combination of ab initio, DFT, and CCSD(T) methodology with correlation-consistent basis sets. The potential energy surface of methyl rotation involving the C(3v), C(s), and C(3h) forms, however, in accord with previous studies, is quite flat. The computed IR absorptions of 3 indicate that it has the greatest degree of electron donation from C-H bonds into the C(+)-C bonds. The experimental (13)C NMR chemical shifts also agree very well with the experimental data.

FTIR, FT-Raman spectra and ab initio, DFT vibrational analysis of 2,4-dinitrophenylhydrazine.

PubMed

Sundaraganesan, N; Ayyappan, S; Umamaheswari, H; Joshua, B Dominic

2007-01-01

The FTIR and FT-Raman spectra of 2,4-dinitrophenylhydrazine (2,4-DNPH) has been recorded in the region 4000-400 and 3500-50cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,4-DNPH were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

FTIR, FT-Raman spectra and ab initio, DFT vibrational analysis of 2,4-dinitrophenylhydrazine

NASA Astrophysics Data System (ADS)

Sundaraganesan, N.; Ayyappan, S.; Umamaheswari, H.; Dominic Joshua, B.

2007-01-01

The FTIR and FT-Raman spectra of 2,4-dinitrophenylhydrazine (2,4-DNPH) has been recorded in the region 4000-400 and 3500-50 cm -1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,4-DNPH were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Ab initio calculation of one-nucleon halo states

NASA Astrophysics Data System (ADS)

Rodkin, D. M.; Tchuvil'sky, Yu M.

2018-02-01

We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accurate wavelengths for X-ray spectroscopy and the NIST hydrogen-like ion database

NASA Astrophysics Data System (ADS)

Kotochigova, S. A.; Kirby, K. P.; Brickhouse, N. S.; Mohr, P. J.; Tupitsyn, I. I.

2005-06-01

We have developed an ab initio multi-configuration Dirac-Fock-Sturm method for the precise calculation of X-ray emission spectra, including energies, transition wavelengths and transition probabilities. The calculations are based on non-orthogonal basis sets, generated by solving the Dirac-Fock and Dirac-Fock-Sturm equations. Inclusion of Sturm functions into the basis set provides an efficient description of correlation effects in highly charged ions and fast convergence of the configuration interaction procedure. A second part of our study is devoted to developing a theoretical procedure and creating an interactive database to generate energies and transition frequencies for hydrogen-like ions. This procedure is highly accurate and based on current knowledge of the relevant theory, which includes relativistic, quantum electrodynamic, recoil, and nuclear size effects.

Cotton-Mouton effect and shielding polarizabilities of ethylene: An MCSCF study

NASA Astrophysics Data System (ADS)

Coriani, Sonia; Rizzo, Antonio; Ruud, Kenneth; Helgaker, Trygve

1997-03-01

The static hypermagnetizabilities and nuclear shielding polarizabilities of the carbon and hydrogen atoms of ethylene have been computed using multiconfigurational linear-response theory and a finite-field method, in a mixed analytical-numerical approach. Extended sets of magnetic-field-dependent basis functions have been employed in large MCSCF calculations, involving active spaces giving rise to a few million configurations in the finite-field perturbed symmetry. The convergence of the observables with respect to the extension of the basis set as well as the effect of electron correlation have been investigated. Whereas for the shielding polarizabilities we can compare with other published SCF results, the ab initio estimates for the static hypermagnetizabilities and the observable to which they are related - the Cotton-Mouton constant, - are presented for the first time.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

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.

A converged calculation of the energy barrier to internal rotation in the ethylene-sulfur dioxide dimer

NASA Astrophysics Data System (ADS)

Resende, Stella M.; De Almeida, Wagner B.; van Duijneveldt-van de Rijdt, Jeanne G. C. M.; van Duijneveldt, Frans B.

2001-08-01

Geometrical parameters for the equilibrium (MIN) and lowest saddle-point (TS) geometries of the C2H4⋯SO2 dimer, and the corresponding binding energies, were calculated using the Hartree-Fock and correlated levels of ab initio theory, in basis sets ranging from the D95(d,p) double-zeta basis set to the aug-cc-pVQZ correlation consistent basis set. An assessment of the effect of the basis set superposition error (BSSE) on these results was made. The dissociation energy from the lowest vibrational state was estimated to be 705±100 cm-1 at the basis set limit, which is well within the range expected from experiment. The barrier to internal rotation was found to be 53±5 cm-1, slightly higher than the (revised) experimental result of 43 cm-1, probably due to zero-point vibrational effects. Our results clearly show that, in direct contrast with recent ideas, the BSSE correction affects differentially the MIN and TS binding energies and so has to be included in the calculation of small energy barriers such as that in the C2H4⋯SO2 dimer. Previous reports of positive MP2 frozen-core binding energies for this complex in basis D95(d,p) are confirmed. The anomalies are shown to be an artifact arising from an incorrect removal of virtual orbitals by the default frozen-core option in the GAUSSIAN program.

A new ab initio potential energy surface for the Ne-H 2 interaction

NASA Astrophysics Data System (ADS)

Lique, François

2009-03-01

A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

An Extended Ab Initio and Theoretical Thermodynamics Studies of the Bergman Reaction and the Energy Splitting of the Singlet Ortho-, Meta-, and Para-Benzynes

NASA Technical Reports Server (NTRS)

Lindh, Roland; Lee, Timothy J.; Bernhardsson, Anders; Persson, B. Joakim; Karlstroem, Gunnar; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The autoaromatization of (Z)-hex-3-ene-1,5-diyne to the singlet biradical para-benzyne has been reinvestigated by state of the art ab initio methods. Previous CCSD(T)/6-31G(d,p) and CASPT2[0]/ANO[C(5s4p2d1f)/H(3s2p)] calculations estimated the the reaction heat at 298 K to be 8-10 and 4.9 plus or minus 3.2 kcal/mol, respectively. Recent NO- and oxygen-dependent trapping experiments and collision-induced dissociation threshold energy experiments estimate the heat of reaction to be 8.5 plus or minus 1.0 at 470 K (recomputed to 9.5 plus or minus 1.0 at 298 K) and 8.4 plus or minus 3.0 kcal/mol at 298 K, respectively. New theoretical estimates at 298 K predict the values at the basis set limit for the CCSD(T) and CASPT2(g1) methods to be 12.7 plus or minus 2.0 and 5.4 plus or minus 2.0 kcal/mol, respectively. The experimentally predicted electronic contribution to the heat of activation is 28.6 kcal/mol. This can be compared with 25.5 and 29.8 kcal/mol from the CASPT2[g1] and the CCSD(T) methods, respectively. The new study has in particular improved on the one-particle basis set for the CCSD(T) method as compared to earlier studies. For the CASPT2 investigation the better suited CASPT2[g1] approximation is utilized. The original CASPT2 method, CASPT2[0], systematically favors open shell systems relative to closed shell systems. This was previously corrected empirically. The study shows that the energy difference between CCSD(T) and CASPT2[g1] at the basis set limit is estimated to be 7 plus or minus 2 kcal/mol. The study also demonstrates that the estimated heat of reaction is very sensitive to the quality of the basis set.

Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging

DOE PAGES

Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.; ...

2014-12-11

In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less

Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging

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

Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.

In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less

A potential energy surface for the process H2 + H2O yielding H + H + H2O - Ab initio calculations and analytical representation

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

1991-01-01

Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.

An ab initio study of HCuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

HCuCO is studied using a large Gaussian basis set at the coupled cluster singles and doubles level of theory, including a perturbational estimate of the connected triples (CCSD(T)). In contrast with CuCO, HCuCO is linear. The Cu-CO bond in HCuCO is significantly stronger than in CuCO. These differences between HCuCO and CuCO are discussed in terms of theCu-H bond polarizing the Cu 4s electron away from the CO.

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.

Quantum-mechanical ab initio simulation of the Raman and IR spectra of Mn3Al2Si3O12 spessartine

NASA Astrophysics Data System (ADS)

Valenzano, Loredana; Meyer, Alessio; Demichelis, Raffaella; Civalleri, Bartolomeo; Dovesi, Roberto

2009-07-01

The IR and Raman spectra of spessartine garnet Mn3Al2Si3O12, are simulated with the periodic ab initio CRYSTAL code by adopting an all-electron Gaussian-type basis set and the B3LYP Hamiltonian. The frequencies of the 25 Raman active modes (3 of A 1 g , 8 of E g and 14 of F 2 g symmetry) and of the two sets of 17 F 1 u transverse-optical and longitudinal-optical frequencies are generated, as well as the IR oscillator strength. The agreement between calculated and experimental data is excellent: for the IR and Raman sets, the mean absolute difference overline{|Updelta|} is 4.0 and 6.8 cm-1, respectively. Isotopic substitution permits to highlight the Mn, Al and Si participation to the various zones of the spectrum. Graphical animation, available on the authors’ web-site ( http://www.crystal.unito.it/vibs/garnets/spessartine/ ), provides a very readable description of the movement of atoms and groups in each vibrational mode.

Novel silicon-carbon fullerene-like nanostructures: an Ab initio study on the stability of Si54C6 and Si60C6 clusters.

PubMed

Srinivasan, Aravind; Ray, Asok K

2006-01-01

Silicon fullerene like nanostructures with six carbon atoms on the surface of Si60 cages by substitution, as well as inside the cage at various symmetry orientations have been studied within the generalized gradient approximation to density functional theory. Full geometry optimizations have been performed without any symmetry constraints using the Gaussian 03 suite of programs and the LANL2DZ basis set. Thus, for the silicon atom, the Hay-Wadt pseudopotential with the associated basis set are used for the core electrons and the valence electrons, respectively. For the carbon atom, the Dunning/Huzinaga double zeta basis set is employed. Electronic and geometric properties of the nanostructures are presented and discussed in detail. It was found that optimized silicon-carbon fullerene like nanostructures have increased stability compared to bare Si60 cage and the stability depends on the orientation of carbon atoms, as well as on the nature of bonding between silicon and carbon atoms and also on the carbon-carbon bonding.

Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.

PubMed

Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J

2013-09-01

The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Uncertainties in scaling factors for ab initio vibrational zero-point energies

NASA Astrophysics Data System (ADS)

Irikura, Karl K.; Johnson, Russell D.; Kacker, Raghu N.; Kessel, Rüdiger

2009-03-01

Vibrational zero-point energies (ZPEs) determined from ab initio calculations are often scaled by empirical factors. An empirical scaling factor partially compensates for the effects arising from vibrational anharmonicity and incomplete treatment of electron correlation. These effects are not random but are systematic. We report scaling factors for 32 combinations of theory and basis set, intended for predicting ZPEs from computed harmonic frequencies. An empirical scaling factor carries uncertainty. We quantify and report, for the first time, the uncertainties associated with scaling factors for ZPE. The uncertainties are larger than generally acknowledged; the scaling factors have only two significant digits. For example, the scaling factor for B3LYP/6-31G(d) is 0.9757±0.0224 (standard uncertainty). The uncertainties in the scaling factors lead to corresponding uncertainties in predicted ZPEs. The proposed method for quantifying the uncertainties associated with scaling factors is based upon the Guide to the Expression of Uncertainty in Measurement, published by the International Organization for Standardization. We also present a new reference set of 60 diatomic and 15 polyatomic "experimental" ZPEs that includes estimated uncertainties.

Theoretical studies of potential energy surface and rotational spectra of Xe -H2O van der Waals complex

NASA Astrophysics Data System (ADS)

Wang, Lin; Yang, Minghui

2008-11-01

In this work we report an ab initio intermolecular potential energy surface and theoretical spectroscopic studies for Xe -H2O complex. The ab initio energies are calculated with CCSD(T) method and large basis sets (aug-cc-pVQZ for H and O and aug-cc-pVQZ-PP for Xe) augmented by a {3s3p2d2f1g} set of bond functions. This potential energy surface has a global minimum corresponding to a planar and nearly linear hydrogen bonded configuration with a well depth of 192.5cm-1 at intermolecular distance of 4.0Å, which is consistent with the previous determined potential by Wen and Jäger [J. Phys. Chem. A 110, 7560 (2006)]. The bound state calculations have been performed for the complex by approximating the water molecule as a rigid rotor. The theoretical rotational transition frequencies, isotopic shifts, nuclear quadrupole coupling constants, and structure parameters are in good agreement with the experimental observed values. The wavefunctions are analyzed to understand the dynamics of the ground and the first excited states.

Electron affinities of the alkali dimers - Na2, K2, and Rb2

NASA Technical Reports Server (NTRS)

Partridge, H.; Dixon, D. A.; Walch, S. P.; Bauschlicher, C. W., Jr.; Gole, J. L.

1983-01-01

Ab initio calculations on the ground states of the alkali dimers, Na2, K2, and Rb2, and their anions are reported. The calculations employ large Gaussian basis sets and account for nearly all of the valence correlation energy. The calculated atomic electron affinities are within 0.02 eV of experiment and the calculated adiabatic electron affinities for Na2, K2, and Rb2 are, respectively, 0.470, 0.512, and 0.513 eV.

Relativity and the lead-acid battery.

PubMed

Ahuja, Rajeev; Blomqvist, Andreas; Larsson, Peter; Pyykkö, Pekka; Zaleski-Ejgierd, Patryk

2011-01-07

The energies of the solid reactants in the lead-acid battery are calculated ab initio using two different basis sets at nonrelativistic, scalar-relativistic, and fully relativistic levels, and using several exchange-correlation potentials. The average calculated standard voltage is 2.13 V, compared with the experimental value of 2.11 V. All calculations agree in that 1.7-1.8 V of this standard voltage arise from relativistic effects, mainly from PbO2 but also from PbSO4.

A potential-energy surface study of the 2A1 and low-lying dissociative states of the methoxy radical

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Accurate, ab initio quantum chemical techniques are applied in the present study of low lying bound and dissociative states of the methoxy radical at C3nu conformations, using a double zeta quality basis set that is augmented with polarization and diffuse functions. Excitation energy estimates are obtained for vertical excitation, vertical deexcitation, and system origin. The rate of methoxy photolysis is estimated to be too small to warrant its inclusion in atmospheric models.

Ab initio molecular orbital calculations on the associated complexes of lithium cyanide with ammonia

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

Mohandas, P.; Shivaglal, M.C.; Chandrasekhar, J.

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets are carried out on a series of complexes of NH{sub 3} with Li{sup +}, C{triple_bond}N{sup -}, LiCN, and its isomer LiNC. The BSSE-corrected interaction energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies are evaluated for 15 species. Complexes with trifurcated (C{sub 3v}) structures are calculated to be saddle points on the potential energy surfaces and have one imaginary frequency each. Calculated energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies of the various species considered are discussed in terms of the nature of associationmore » of LiCN with ammonia. The vibrational frequencies of the relevant complexed species are compared with the experimental frequencies reported earlier for solutions of lithium cyanide in liquid ammonia. 40 refs., 1 fig., 4 tabs.« less

An ab initio variationally computed room-temperature line list for (32)S(16)O3.

PubMed

Underwood, Daniel S; Tennyson, Jonathan; Yurchenko, Sergei N

2013-07-07

Ab initio potential energy and dipole moment surfaces are computed for sulfur trioxide (SO3) at the CCSD(T)-F12b level of theory with appropriate triple-zeta basis sets. The analytical representations of these surfaces are used, with a slight correction, to compute pure rotational and rotation-vibration spectra of (32)S(16)O3 using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0-4000 cm(-1) with rotational states up to J = 85. The resulting line list of 174,674,257 transitions is appropriate for modelling room temperature (32)S(16)O3 spectra. Good agreement is found with the observed infrared absorption spectra and the calculations are used to place the measured relative intensities on an absolute scale. A list of 10,878 experimental transitions is provided in a form suitable for inclusion in standard atmospheric and planetary spectroscopic databases.

The large amplitude motions of methylamine from the perspective of the highly correlated ab initio methods

NASA Astrophysics Data System (ADS)

Senent, M. L.

2018-01-01

CCSD(T)-F12 theory in connection with extended basis sets is employed to determine the electronic ground state spectroscopic parameters of methylamine at low temperatures. The geometry, the rotational constants, all the fundamental frequencies, the dipole moment and its components, and the centrifugal distortion constants, are provided. The ground vibrational state rotational constants were found to be A0 = 103067.15 MHz, B0 = 22588.29 MHz, and C0 = 21710.50 MHz and the dipole moment to be 1.4071D. Fermi displacements of the vibrational bands are predicted. The low vibrational energy levels corresponding to the large amplitude motions are determine variationally using a flexible three-dimensional model depending on three variables: the HNH bending, the NH2 wagging and the CH3 torsional coordinates. The computed levels are compared with previous experimental and calculated energies. Methylamine parameters are very sensitive to the level of ab initio calculations.

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

PubMed

Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

2018-05-09

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

NASA Astrophysics Data System (ADS)

Ramasami, Ponnadurai; Ford, Thomas A.

2018-07-01

The properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller-Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.

Lattice dynamics of Cs2NaYbF6 and Cs2NaYF6 elpasolites: Ab initio calculation

NASA Astrophysics Data System (ADS)

Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.

2015-06-01

The ab initio calculations of the crystal structure and the phonon spectrum of Cs2NaYbF6 and Cs2NaYF6 crystals with the elpasolite structure have been performed. The frequencies and types of fundamental vibrations have been determined. The calculations have been performed in the framework of the density functional theory using the molecular orbital method with hybrid functionals in the CRYSTAL09 program developed for the simulation of periodic structures. The outer 5 s and 5 p shells of the rare-earth ion have been described in Gaussian-type basis sets. The influence of inner shells, including 4 f electron shells, on the outer shells has been described using the pseudopotential. It has been shown that this approach allows the description of the phonon spectrum with the inclusion of the splitting of the longitudinal and transverse optical modes.

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

Makarewicz, Jan, E-mail: jama@amu.edu.pl; Shirkov, Leonid

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center ofmore » mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy D{sub e} of 392 cm{sup −1} is close to that of 387 cm{sup −1} calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, D{sub e} for PAr becomes slightly lower than D{sub e} for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.« less

Near infrared overtone (vOH = 2 ← 0) spectroscopy of Ne-H2O clusters

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Wojcik, Michael; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-03-01

Vibrationally state selective overtone spectroscopy and dynamics of weakly bound Ne-H2O complexes (D0(para) = 31.67 cm-1, D0(ortho) = 34.66 cm-1) are reported for the first time, based on near infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-⟩←|00+⟩ and |02+⟩ ←|00+⟩ ) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level ab initio potential energy surface (CCSD(T)/VnZ-f12 (n = 3,4), corrected for basis set superposition error and extrapolated to the complete basis set limit) are employed for assignment of Σ ←Σ ,Π ←Σ , and Σ ←Π infrared bands in the overtone spectra, where Σ ( K = 0) and Π (K = 1) represent approximate projections (K) of the body angular momentum along the Ne-H2O internuclear axis. End-over-end tumbling of the ortho Ne-H2O cluster is evident via rotational band contours observed, with band origins and rotational progressions in excellent agreement with ab initio frequency and intensity predictions. A clear Q branch in the corresponding |02+⟩fΠ (111) ←eΣ (000) para Ne-H2O spectrum provides evidence for a novel e/f parity-dependent metastability in these weakly bound clusters, in agreement with ab initio bound state calculations and attributable to the symmetry blocking of an energetically allowed channel for internal rotor predissociation. Finally, Boltzmann analysis of the rotational spectra reveals anomalously low jet temperatures (Trot ≈ 4(1) K), which are attributed to "evaporative cooling" of weakly bound Ne-H2O clusters and provide support for similar cooling dynamics in rare gas-tagging studies.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

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).

Use of Molecular Modeling to Determine the Interaction and Competition of Gases within Coal for Carbon Dioxide Sequestration

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

Jeffrey D. Evanseck; Jeffry D. Madura

A 3-dimensional coal structural model for the Argonne Premium Coal Pocahontas No. 3 has been generated. The model was constructed based on the wealth of structural information available in the literature with the enhancement that the structural diversity within the structure was represented implicitly (for the first time) based on image analysis of HRTEM in combination with LDMS data. The complex and large structural model (>10,000 carbon atoms) will serve as a basis for examining the interaction of gases within this low volatile bituminous coal. Simulations are of interest to permit reasonable simulations of the host-guest interactions with regard tomore » carbon dioxide sequestration within coal and methane displacement from coal. The molecular structure will also prove useful in examining other coal related behavior such as solvent swelling, liquefaction and other properties. Molecular models of CO{sub 2} have been evaluated with water to analyze which classical molecular force-field parameters are the most reasonable to predict the interactions of CO{sub 2} with water. The comparison of the molecular force field models was for a single CO{sub 2}-H{sub 2}O complex and was compared against first principles quantum mechanical calculations. The interaction energies and the electrostatic interaction distances were used as criteria in the comparison. The ab initio calculations included Hartree-Fock, B3LYP, and Moeller-Plesset 2nd, 3rd, and 4th order perturbation theories with basis sets up to the aug-cc-pvtz basis set. The Steele model was the best literature model, when compared to the ab initio data, however, our new CO{sub 2} model reproduces the QM data significantly better than the Steele force-field model.« less

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.

1988-01-01

The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.

The Anharmonic Force Field of Ethylene, C2H4, by Means of Accurate Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Martin, Jan M. L.; Lee, Timothy J.; Taylor, Peter R.; Francois, Jean-Pierre; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The quartic force field of ethylene, C2H4, has been calculated ab initio using augmented coupled cluster, CCSD(T), methods and correlation consistent basis sets of spdf quality. For the C-12 isotopomers C2H4, C2H3D, H2CCD2, cis-C2H2D2, trans-C2H2D2, C2HD3, and C2D4, all fundamentals could be reproduced to better than 10 per centimeter, except for three cases of severe Fermi type 1 resonance. The problem with these three bands is identified as a systematic overestimate of the Kiij Fermi resonance constants by a factor of two or more; if this is corrected for, the predicted fundamentals come into excellent agreement with experiment. No such systematic overestimate is seen for Fermi type 2 resonances. Our computed harmonic frequencies suggest a thorough revision of the accepted experimentally derived values. Our computed and empirically corrected re geometry differs substantially from experimentally derived values: both the predicted rz geometry and the ground-state rotational constants are, however, in excellent agreement with experiment, suggesting revision of the older values. Anharmonicity constants agree well with experiment for stretches, but differ substantially for stretch-bend interaction constants, due to equality constraints in the experimental analysis that do not hold. Improved criteria for detecting Fermi and Coriolis resonances are proposed and found to work well, contrary to the established method based on harmonic frequency differences that fails to detect several important resonances for C2H4 and its isotopomers. Surprisingly good results are obtained with a small spd basis at the CCSD(T) level. The well-documented strong basis set effect on the v8 out-of-plane motion is present to a much lesser extent when correlation-optimized polarization functions are used. Complete sets of anharmonic, rovibrational coupling, and centrifugal distortion constants for the isotopomers are available as supplementary material to the paper.

Theoretical dissociation energies for ionic molecules

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

1986-01-01

Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.

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.

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 1. Accurate thermochemistry and barrier heights.

PubMed

Alecu, I M; Truhlar, Donald G

2011-04-07

The reactions of CH(3)OH with the HO(2) and CH(3) radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)(Q)), core-valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol(-1) agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

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).

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

Absolute configuration of (-)-myrtenal by vibrational circular dichroism.

PubMed

Burgueño-Tapia, Eleuterio; Zepeda, L Gerardo; Joseph-Nathan, Pedro

2010-07-01

The VCD spectrum of the monoterpene (-)-myrtenal (1) was compared with theoretical spectra using ab initio density functional theory (DFT) calculations at the B3LYP/6-31G(d,p), B3LYP/6-31G+(d,p), B3LYP/6-311G+(d,p), B3LYP/DGDZVP, and B3PW91/DGTZVP levels of theory. Conformational analysis of 1 indicated that the lowest energy conformer was s-trans-C2-C10, which contributes more than 98.5% to the total conformational population regardless of the employed level of theory. The use of a recently developed confidence level algorithm demonstrated that VCD spectra calculated for the main conformer, using the indicated hybrid functionals and basis set, gave no significant changes, from where it follows that B3LYP/DGDZVP calculations provide a superior balance between computer cost and VCD spectral accuracy. The DGDZVP basis set demanded around a quarter the time than the 6-311G+(d,p) basis set while providing similar results. The spectral comparison also provided evidence that the levorotatory enantiomer of myrtenal has the 1R absolute configuration. 2010 Elsevier Ltd. All rights reserved.

Heavier alkali-metal monosulfides (KS, RbS, CsS, and FrS) and their cations.

PubMed

Lee, Edmond P F; Wright, Timothy G

2005-10-08

The heavier alkali-metal monosulfides (KS, RbS, CsS, and FrS) have been studied by high-level ab initio calculations. The RCCSD(T) method has been employed, combined with large flexible valence basis sets. All-electron basis sets are used for potassium and sulfur, with effective core potentials being used for the other metals, describing the core electrons. Potential-energy curves are calculated for the lowest two neutral and cationic states: all neutral monosulfide species have a (2)Pi ground state, in contrast with the alkali-metal monoxide species, which undergo a change in the electronic ground state from (2)Pi to (2)Sigma(+) as the group is descended. In the cases of KS, RbS, and CsS, spin-orbit curves are also calculated. We also calculate potential-energy curves for the lowest (3)Sigma(-) and (3)Pi states of the cations. From the potential-energy curves, spectroscopic constants are derived, and for KS the spectroscopic results are compared to experimental spectroscopic values. Ionization energies, dissociation energies, and heats of formation are also calculated; for KS, we explore the effects of relativity and basis set extrapolation on these values.

Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

PubMed

Taşal, Erol; Kumalar, Mustafa

2012-09-01

In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Conformational stability, r(0) structural parameters, vibrational assignments and ab initio calculations of ethyldichlorophosphine.

PubMed

Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R

2015-02-05

Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9 cm(-1) (1.04±0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

PubMed Central

2017-01-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

NASA Astrophysics Data System (ADS)

Jäger, Benjamin; Bich, Eckard

2017-06-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

Ab initio study on the ground and low-lying states of BAlk (Alk = Li, Na, K) molecules.

PubMed

Xiao, Ke-La; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang

2014-10-02

The potential energy curves (PECs) and dipole moment functions of (1)Π, (3)Π, (1)Σ(+), and (3)Σ(+) states of BAlk (Alk = Li, Na, K) are calculated using multireference configuration interaction method and large all-electron basis sets. The effects of inner-shell correlation electron for BAlk are considered. The ro-vibrational energy levels are obtained by solving the Schrödinger equation of nuclear motion based on the ab initio PECs. The spectroscopic parameters are determined from the ro-vibrational levels with Dunham expansion. The PECs are fitted into analytical potential energy functions using the Morse long-range potential function. The dipole moment functions for the states of BAlk are presented. The transition dipole moments for (1)Σ(+) → (1)Π and (3)Σ(+) → (3)Π states of BAlk are obtained. The interactions between the outermost electron of Alk and B 2p electrons for (1)Π, (3)Π, (1)Σ(+), and (3)Σ(+) states are also analyzed, 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.

Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

NASA Technical Reports Server (NTRS)

Stallcop, James R.; Partridge, Harry; Levin, Eugene

1996-01-01

Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

Preface: Introductory Remarks: Linear Scaling Methods

NASA Astrophysics Data System (ADS)

Bowler, D. R.; Fattebert, J.-L.; Gillan, M. J.; Haynes, P. D.; Skylaris, C.-K.

2008-07-01

It has been just over twenty years since the publication of the seminal paper on molecular dynamics with ab initio methods by Car and Parrinello [1], and the contribution of density functional theory (DFT) and the related techniques to physics, chemistry, materials science, earth science and biochemistry has been huge. Nevertheless, significant improvements are still being made to the performance of these standard techniques; recent work suggests that speed improvements of one or even two orders of magnitude are possible [2]. One of the areas where major progress has long been expected is in O(N), or linear scaling, DFT, in which the computer effort is proportional to the number of atoms. Linear scaling DFT methods have been in development for over ten years [3] but we are now in an exciting period where more and more research groups are working on these methods. Naturally there is a strong and continuing effort to improve the efficiency of the methods and to make them more robust. But there is also a growing ambition to apply them to challenging real-life problems. This special issue contains papers submitted following the CECAM Workshop 'Linear-scaling ab initio calculations: applications and future directions', held in Lyon from 3-6 September 2007. A noteworthy feature of the workshop is that it included a significant number of presentations involving real applications of O(N) methods, as well as work to extend O(N) methods into areas of greater accuracy (correlated wavefunction methods, quantum Monte Carlo, TDDFT) and large scale computer architectures. As well as explicitly linear scaling methods, the conference included presentations on techniques designed to accelerate and improve the efficiency of standard (that is non-linear-scaling) methods; this highlights the important question of crossover—that is, at what size of system does it become more efficient to use a linear-scaling method? As well as fundamental algorithmic questions, this brings up implementation questions relating to parallelization (particularly with multi-core processors starting to dominate the market) and inherent scaling and basis sets (in both normal and linear scaling codes). For now, the answer seems to lie between 100-1,000 atoms, though this depends on the type of simulation used among other factors. Basis sets are still a problematic question in the area of electronic structure calculations. The linear scaling community has largely split into two camps: those using relatively small basis sets based on local atomic-like functions (where systematic convergence to the full basis set limit is hard to achieve); and those that use necessarily larger basis sets which allow convergence systematically and therefore are the localised equivalent of plane waves. Related to basis sets is the study of Wannier functions, on which some linear scaling methods are based and which give a good point of contact with traditional techniques; they are particularly interesting for modelling unoccupied states with linear scaling methods. There are, of course, as many approaches to linear scaling solution for the density matrix as there are groups in the area, though there are various broad areas: McWeeny-based methods, fragment-based methods, recursion methods, and combinations of these. While many ideas have been in development for several years, there are still improvements emerging, as shown by the rich variety of the talks below. Applications using O(N) DFT methods are now starting to emerge, though they are still clearly not trivial. Once systems to be simulated cross the 10,000 atom barrier, only linear scaling methods can be applied, even with the most efficient standard techniques. One of the most challenging problems remaining, now that ab initio methods can be applied to large systems, is the long timescale problem. Although much of the work presented was concerned with improving the performance of the codes, and applying them to scientificallyimportant problems, there was another important theme: extending functionality. The search for greater accuracy has given an implementation of density functional designed to model van der Waals interactions accurately as well as local correlation, TDDFT and QMC and GW methods which, while not explicitly O(N), take advantage of localisation. All speakers at the workshop were invited to contribute to this issue, but not all were able to do this. Hence it is useful to give a complete list of the talks presented, with the names of the sessions; however, many talks fell within more than one area. This is an exciting time for linear scaling methods, which are already starting to contribute significantly to important scientific problems. Applications to nanostructures and biomolecules A DFT study on the structural stability of Ge 3D nanostructures on Si(001) using CONQUEST Tsuyoshi Miyazaki, D R Bowler, M J Gillan, T Otsuka and T Ohno Large scale electronic structure calculation theory and several applications Takeo Fujiwara and Takeo Hoshi ONETEP:Linear-scaling DFT with plane waves Chris-Kriton Skylaris, Peter D Haynes, Arash A Mostofi, Mike C Payne Maximally-localised Wannier functions as building blocks for large-scale electronic structure calculations Arash A Mostofi and Nicola Marzari A linear scaling three dimensional fragment method for ab initio calculations Lin-Wang Wang, Zhengji Zhao, Juan Meza Peta-scalable reactive Molecular dynamics simulation of mechanochemical processes Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, Fuyuki Shimojo and Priya Vashishta Recent developments and applications of the real-space multigrid (RMG) method Jerzy Bernholc, M Hodak, W Lu, and F Ribeiro Energy minimisation functionals and algorithms CONQUEST: A linear scaling DFT Code David R Bowler, Tsuyoshi Miyazaki, Antonio Torralba, Veronika Brazdova, Milica Todorovic, Takao Otsuka and Mike Gillan Kernel optimisation and the physical significance of optimised local orbitals in the ONETEP code Peter Haynes, Chris-Kriton Skylaris, Arash Mostofi and Mike Payne A miscellaneous overview of SIESTA algorithms Jose M Soler Wavelets as a basis set for electronic structure calculations and electrostatic problems Stefan Goedecker Wavelets as a basis set for linear scaling electronic structure calculationsMark Rayson O(N) Krylov subspace method for large-scale ab initio electronic structure calculations Taisuke Ozaki Linear scaling calculations with the divide-and-conquer approach and with non-orthogonal localized orbitals Weitao Yang Toward efficient wavefunction based linear scaling energy minimization Valery Weber Accurate O(N) first-principles DFT calculations using finite differences and confined orbitals Jean-Luc Fattebert Linear-scaling methods in dynamics simulations or beyond DFT and ground state properties An O(N) time-domain algorithm for TDDFT Guan Hua Chen Local correlation theory and electronic delocalization Joseph Subotnik Ab initio molecular dynamics with linear scaling: foundations and applications Eiji Tsuchida Towards a linear scaling Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics Thomas Kühne, Michele Ceriotti, Matthias Krack and Michele Parrinello Partial linear scaling for quantum Monte Carlo calculations on condensed matter Mike Gillan Exact embedding of local defects in crystals using maximally localized Wannier functions Eric Cancès Faster GW calculations in larger model structures using ultralocalized nonorthogonal Wannier functions Paolo Umari Other approaches for linear-scaling, including methods formetals Partition-of-unity finite element method for large, accurate electronic-structure calculations of metals John E Pask and Natarajan Sukumar Semiclassical approach to density functional theory Kieron Burke Ab initio transport calculations in defected carbon nanotubes using O(N) techniques Blanca Biel, F J Garcia-Vidal, A Rubio and F Flores Large-scale calculations with the tight-binding (screened) KKR method Rudolf Zeller Acknowledgments We gratefully acknowledge funding for the workshop from the UK CCP9 network, CECAM and the ESF through the PsiK network. DRB, PDH and CKS are funded by the Royal Society. References [1] Car R and Parrinello M 1985 Phys. Rev. Lett. 55 2471 [2] Kühne T D, Krack M, Mohamed F R and Parrinello M 2007 Phys. Rev. Lett. 98 066401 [3] Goedecker S 1999 Rev. Mod. Phys. 71 1085

Accurate ab initio quartic force fields for the ions HCO(+) and HOC(+)

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Taylor, Peter R.; Lee, Timothy J.

1993-01-01

The quartic force fields of HCO(+) and HOC(+) have been computed using augmented coupled cluster methods and basis sets of spdf and spdfg quality. Calculations on HCN, CO, and N2 have been performed to assist in calibrating the computed results. Going from an spdf to an spdfg basis shortens triple bonds by about 0.004 A, and increases the corresponding harmonic frequency by 10-20/cm, leaving bond distances about 0.003 A too long and triple bond stretching frequencies about 5/cm too low. Accurate estimates for the bond distances, fundamental frequencies, and thermochemical quantities are given. HOC(+) lies 37.8 +/- 0.5 kcal/mol (0 K) above HCO(+); the classical barrier height for proton exchange is 76.7 +/- 1.0 kcal/mol.

In search of the X{sub 2}BO and X{sub 2}BS (X = H, F) free radicals: Ab initio studies of their spectroscopic signatures

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

Clouthier, Dennis J., E-mail: dclaser@uky.edu

2014-12-28

The F{sub 2}BO free radical is a known, although little studied, species but similar X{sub 2}BY (X = H, D, F; Y = O, S) molecules are largely unknown. High level ab initio methods have been used to predict the molecular structures, vibrational frequencies (in cm{sup −1}), and relative energies of the ground and first two excited electronic states of these free radicals, as an aid to their eventual spectroscopic identification. The chosen theoretical methods and basis sets were tested on F{sub 2}BO and found to give good agreement with the known experimental quantities. In particular, complete basis set extrapolationsmore » of coupled-cluster single and doubles with perturbative triple excitations/aug-cc-pVXZ (X = 3, 4, 5) energies gave excellent electronic term values, due to small changes in geometry between states and the lack of significant multireference character in the wavefunctions. The radicals are found to have planar C{sub 2v} geometries in the X{sup ~2}B{sub 2} ground state, the low-lying A{sup ~2}B{sub 1} first excited state, and the higher B{sup ~2}A{sub 1} state. Some of these radicals have very small ground state dipole moments hindering microwave measurements. Infrared studies in matrices or in the gas phase may be possible although the fundamentals of H{sub 2}BO and H{sub 2}BS are quite weak. The most promising method of identifying these species in the gas phase appears to be absorption or laser-induced fluorescence spectroscopy through the allowed B{sup ~}-X{sup ~} transitions which occur in the visible-near UV region of the electromagnetic spectrum. The ab initio results have been used to calculate the Franck-Condon profiles of the absorption and emission spectra, and the rotational structure of the B{sup ~}-X{sup ~}0{sub 0}{sup 0} bands has been simulated. The calculated single vibronic level emission spectra provide a unique, readily recognizable fingerprint of each particular radical, facilitating the experimental identification of new X{sub 2}BY species in the gas phase.« less

Accurate double many-body expansion potential energy surface of HS2A2A‧) by scaling the external correlation

NASA Astrophysics Data System (ADS)

Lu-Lu, Zhang; Yu-Zhi, Song; Shou-Bao, Gao; Yuan, Zhang; Qing-Tian, Meng

2016-05-01

A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method, such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal·mol-1. The topographical features of the HS2(A2A‧) global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS2(A2A‧) can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system. Project supported by the National Natural Science Foundation of China (Grant No. 11304185), the Taishan Scholar Project of Shandong Province, China, the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014AM022), the Shandong Province Higher Educational Science and Technology Program, China (Grant No. J15LJ03), the China Postdoctoral Science Foundation (Grant No. 2014M561957), and the Post-doctoral Innovation Project of Shandong Province, China (Grant No. 201402013).

Computational Study of the Reactions of Methanol with the Hydroperoxyl and Methyl Radicals. Part I: Accurate Thermochemistry and Barrier Heights

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

Alecu, I. M.; Truhlar, D. G.

2011-04-07

The reactions of CH 3OH with the HO 2 and CH 3 radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2) Q), core–valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGAmore » density functionals can achieve sub-kcal mol -1 agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.« less

Accurate double many-body expansion potential energy surface for the 2(1)A' state of N2O.

PubMed

Li, Jing; Varandas, António J C

2014-08-28

An accurate double many-body expansion potential energy surface is reported for the 2(1)A' state of N2O. The new double many-body expansion (DMBE) form has been fitted to a wealth of ab initio points that have been calculated at the multi-reference configuration interaction level using the full-valence-complete-active-space wave function as reference and the cc-pVQZ basis set, and subsequently corrected semiempirically via double many-body expansion-scaled external correlation method to extrapolate the calculated energies to the limit of a complete basis set and, most importantly, the limit of an infinite configuration interaction expansion. The topographical features of the novel potential energy surface are then examined in detail and compared with corresponding attributes of other potential functions available in the literature. Exploratory trajectories have also been run on this DMBE form with the quasiclassical trajectory method, with the thermal rate constant so determined at room temperature significantly enhancing agreement with experimental data.

A new potential energy surface of the OH2+ system and state-to-state quantum dynamics studies of the O+ + H2 reaction.

PubMed

Li, Wentao; Yuan, Jiuchuang; Yuan, Meiling; Zhang, Yong; Yao, Minghai; Sun, Zhigang

2018-01-03

A new global potential energy surface (PES) of the O + + H 2 system was constructed with the permutation invariant polynomial neural network method, using about 63 000 ab initio points, which were calculated by employing the multi-reference configuration interaction method with aug-cc-pVTZ and aug-cc-pVQZ basis sets. For improving the accuracy of the PES, the basis set was extrapolated to the complete basis set limit by the two-point extrapolation method. The root mean square error of fitting was only 5.28 × 10 -3 eV. The spectroscopic constants of the diatomic molecules were calculated and compared with previous theoretical and experimental results, which suggests that the present results agree well with the experiment. On the newly constructed PES, reaction dynamics studies were performed using the time-dependent wave packet method. The calculated integral cross sections (ICSs) were compared with the available theoretical and experimental results, where a good agreement with the experimental data was seen. Significant forward and backward scatterings were observed in the whole collision energy region studied. At the same time, the differential cross sections biased the forward scattering, especially at higher collision energies.

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

Moore, Keith; McLaughlin, Brendan M.; Lane, Ian C., E-mail: i.lane@qub.ac.uk

BaH (and its isotopomers) is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of a highly accurate ab initio {sup 2}Σ{sup +} potential for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction is tested and taken to the Complete Basis Set (CBS) limit. It is shown that the calculated molecular constants using a 46more » electron effective core-potential and even-tempered augmented polarized core-valence basis sets (aug-pCVnZ-PP, n = 4 and 5) but only including three active electrons in the MRCI calculation are in excellent agreement with the available experimental values. The predicted dissociation energy D{sub e} for the X{sup 2}Σ{sup +} state (extrapolated to the CBS limit) is 16 895.12 cm{sup −1} (2.094 eV), which agrees within 0.1% of a revised experimental value of <16 910.6 cm{sup −1}, while the calculated r{sub e} is within 0.03 pm of the experimental result.« less

Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

2013-09-01

Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

Ab initio relativistic effective potentials with spin--orbit operators. III. Rb through Xe

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

LaJohn, L.A.; Christiansen, P.A.; Ross, R.B.

A refined version of the ''shape consistent'' effective potential procedure of Christiansen, Lee, and Pitzer was used to compute averaged relativistic effective potentials (AREP) and spin--orbit operators for the elements Rb through Xe. Particular attention was given to the partitioning of the core and valence space and, where appropriate, more than one set of potentials is provided. These are tabulated in analytic form. Gaussian basis sets with contraction coefficients for the lowest energy state of each atom are given. The reliability of the transition metal AREPs was examined by comparing computed atomic excitation energies with accurate all-electron relativistic values. Themore » spin--orbit operators were tested in calculations on selected atoms.« less

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.

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.

Theoretical dissociation energies for the alkali and alkaline-earth monofluorides and monochlorides

NASA Technical Reports Server (NTRS)

Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

1986-01-01

Spectroscopic parameters are accurately determined for the alkali and alkaline-earth monofluorides and monochlorides by means of ab initio self-consistent field and correlated wave function calculations. Numerical Hartree-Fock calculations are performed on selected systems to ensure that the extended Slater basis sets employed are near the Hartree-Fock limit. Since the bonding is predominantly electrostatic in origin, a strong correlation exists between the dissociation energy (to ions) and the spectroscopic parameter r(e). By dissociating to the ionic limits, most of the differential correlation effects can be embedded in the accurate experimental electron affinities and ionization potentials.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

The C4H7+ cation. A theoretical investigation

NASA Technical Reports Server (NTRS)

Koch, W.; Liu, B.; DeFrees, D. J.

1988-01-01

The potential energy surface of the C4H7+ cation has been investigated with ab initio quantum chemical theory. Extended basis set calculations, including electronic correlation, show that cyclobutyl and cyclopropylcarbinyl cation are equally stable isomers. The saddle point connecting these isomers lies 0.6 kcal/mol above the minima. The global C4H7+ minimum corresponds to the 1-methylallyl cation, which is 9.0 kcal/mol more stable than the cyclobutyl and the cyclopropylcarbinyl cation and 9.5 kcal/mol below the 2-methylallyl cation. These results are in excellent agreement with experimental data.

Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

PubMed

Galvão, B R L; Rodrigues, S P J; Varandas, A J C

2008-07-28

A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

Electronic absorption, vibrational spectra, nonlinear optical properties, NBO analysis and thermodynamic properties of N-(4-nitro-2-phenoxyphenyl) methanesulfonamide molecule by ab initio HF and density functional methods.

PubMed

Rajamani, T; Muthu, S; Karabacak, M

2013-05-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-100 cm(-1) and 4000-400 cm(-1), respectively, for N-(4-nitro-2-phenoxyphenyl) methanesulfonamide molecule. Theoretical calculations were performed by ab initio RHF and density functional theory (DFT) method using 6-31G(d,p) and 6-311G(d,p) basis sets. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The frontier orbital energy gap and dipole moment illustrates the high reactivity of the title molecule. The first order hyperpolarizability (β0) and related properties (μ, α and Δα) of the molecule were also calculated. Stability of the molecule arising from hyperconjugative interactions and charge delocalization were analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) anti-bonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. UV-vis spectrum of the compound was recorded in the region 200-500 nm in ethanol and electronic properties such as excitation energies, oscillator strength and wavelength were calculated by TD-DFT/B3LYP, CIS and TD-HF methods using 6-31G(d,p) basis set. Molecular electrostatic potential (MEP) and HOMO-LUMO energy levels are also constructed. The thermodynamic properties of the title compound were calculated at different temperatures and the results reveals the heat capacity (C), and entropy (S) increases with rise in temperature. Copyright © 2013 Elsevier B.V. All rights reserved.

Light focusing through a multiple scattering medium: ab initio computer simulation

NASA Astrophysics Data System (ADS)

Danko, Oleksandr; Danko, Volodymyr; Kovalenko, Andrey

2018-01-01

The present study considers ab initio computer simulation of the light focusing through a complex scattering medium. The focusing is performed by shaping the incident light beam in order to obtain a small focused spot on the opposite side of the scattering layer. MSTM software (Auburn University) is used to simulate the propagation of an arbitrary monochromatic Gaussian beam and obtain 2D distribution of the optical field in the selected plane of the investigated volume. Based on the set of incident and scattered fields, the pair of right and left eigen bases and corresponding singular values were calculated. The pair of right and left eigen modes together with the corresponding singular value constitute the transmittance eigen channel of the disordered media. Thus, the scattering process is described in three steps: 1) initial field decomposition in the right eigen basis; 2) scaling of decomposition coefficients for the corresponding singular values; 3) assembling of the scattered field as the composition of the weighted left eigen modes. Basis fields are represented as a linear combination of the original Gaussian beams and scattered fields. It was demonstrated that 60 independent control channels provide focusing the light into a spot with the minimal radius of approximately 0.4 μm at half maximum. The intensity enhancement in the focal plane was equal to 68 that coincided with theoretical prediction.

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.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Ab initio anharmonic vibrational frequency predictions for linear proton-bound complexes OC-H(+)-CO and N(2)-H(+)-N(2).

PubMed

Terrill, Kasia; Nesbitt, David J

2010-08-01

Ab initio anharmonic transition frequencies are calculated for strongly coupled (i) asymmetric and (ii) symmetric proton stretching modes in the X-H(+)-X linear ionic hydrogen bonded complexes for OCHCO(+) and N(2)HN(2)(+). The optimized potential surface is calculated in these two coordinates for each molecular ion at CCSD(T)/aug-cc-pVnZ (n = 2-4) levels and extrapolated to the complete-basis-set limit (CBS). Slices through both 2D surfaces reveal a relatively soft potential in the asymmetric proton stretching coordinate at near equilibrium geometries, which rapidly becomes a double minimum potential with increasing symmetric proton acceptor center of mass separation. Eigenvalues are obtained by solution of the 2D Schrödinger equation with potential/kinetic energy coupling explicity taken into account, converged in a distributed Gaussian basis set as a function of grid density. The asymmetric proton stretch fundamental frequency for N(2)HN(2)(+) is predicted at 848 cm(-1), with strong negative anharmonicity in the progression characteristic of a shallow "particle in a box" potential. The corresponding proton stretch fundamental for OCHCO(+) is anomalously low at 386 cm(-1), but with a strong alternation in the vibrational spacing due to the presence of a shallow D(infinityh) transition state barrier (Delta = 398 cm(-1)) between the two equivalent minimum geometries. Calculation of a 2D dipole moment surface and transition matrix elements reveals surprisingly strong combination and difference bands with appreciable intensity throughout the 300-1500 cm(-1) region. Corrected for zero point (DeltaZPE) and thermal vibrational excitation (DeltaE(vib)) at 300 K, the single and double dissociation energies in these complexes are in excellent agreement with thermochemical gas phase ion data.

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.

Monomeric and dimeric structures, electronic properties and vibrational spectra of azelaic acid by HF and B3LYP methods

NASA Astrophysics Data System (ADS)

Kumar, Amarendra; Narayan, Vijay; Prasad, Onkar; Sinha, Leena

2012-08-01

Quantum chemical calculations of energies, dipole moment, polarizability, hyperpolarizability and vibrational wavenumbers of Azelaic acid (AZA) were carried out by using ab initio HF and B3LYP methods with 6-311++G(d,p) basis set. Hydrogen-bonded dimer of AZA, optimized by counterpoise correction, has also been studied by HF and B3LYP at the 6-311++G(d,p) level and the effects of molecular association through Osbnd H⋯O hydrogen bonding have been discussed. A complete vibrational analysis of AZA has been performed and assignments are made on the basis of potential energy distribution. The comparisons and assignments of the vibrational frequencies indicate that the experimental spectra also correspond acceptably with those of theoretically simulated spectra except the hydrogen-bonded coupled infrared vibrations.

Potential energy curves of the Na2+ molecular ion from all-electron ab initio relativistic calculations

NASA Astrophysics Data System (ADS)

Bewicz, Anna; Musiał, Monika; Kucharski, Stanisław A.

2017-11-01

The equation-of-motion coupled-cluster method for electron affinity calculations has been used to study potential energy curves (PECs) for the Na+2 molecular ion. Although the studied molecule represents the open shell system the applied approach employs the closed shell Na+ 22 ion as the reference. In addition the Na+ 22 system dissociates into the closed shell fragments; hence, the restricted Hartree-Fock scheme can be used within the whole range of interatomic distances, from 2 to 45 Å. We used large basis set engaging 268 basis functions with all 21 electrons correlated. The relativistic effects are included via second-order Douglas-Kroll method. The computed PECs, spectroscopic molecular constants and vibrational energy levels agree well with experimental values if the latter are available or with other theoretical data.

Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

NASA Astrophysics Data System (ADS)

Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

2017-01-01

The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

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.

Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.

PubMed

Arjunan, V; Rani, T; Mythili, C V; Mohan, S

2011-08-01

A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Vibrational spectrum and assignments of 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole by ab initio Hartree-Fock and density functional methods

NASA Astrophysics Data System (ADS)

Arslan, Hakan; Algül, Öztekin

2008-06-01

The room temperature attenuated total reflection Fourier transform infrared spectrum of the 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole has been recorded with diamond/ZnSe prism. The conformational behaviour, structural stability of optimized geometry, frequency and intensity of the vibrational bands of the title compound were investigated by utilizing ab initio calculations with 6-311G** basis set at HF, B3LYP, BLYP, B3PW91 and mPW1PW91 levels. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions using VEDA 4 program. Furthermore, the optimal uniform scaling factors calculated for the title compound are 0.9120, 0.9596, 0.9660, 0.9699, and 0.9993 for HF, mPW1PW91, B3PW91, B3LYP and BLYP methods, respectively.

Ab initio calculation of harmonic force fields and vibrational spectra for the arsine oxides and sulfides R sub 3 AsY (R = H, F; Y = O, S) and related compounds

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

Schneider, W.; Thiel, W.; Komornicki, A.

1990-04-05

Ab initio self-consistent-field calculations using effective core potentials and polarized double-zeta basis sets are reported for the arsenic compounds H{sub 3}As, H{sub 3}AsO, H{sub 3}AsS, F{sub 3}As, F{sub 3}AsO, F{sub 3}AsS, cis- and trans-H{sub 2}AsOH, and HAsO. The calculated geometries, rotational constants, vibrational frequencies, Coriolis coupling constants, centrifugal distortion constants, infrared band intensities, and force fields are compared with the available experimental data. Good agreement is found in the case of the known molecules, especially H{sub 3}As and F{sub 3}As, so that the predictions for the unknown molecules are expected to be realistic. The theoretical results confirm a recent spectroscopicmore » identification of H{sub 3}AsO, H{sub 2}AsOH, and HAsO and suggest reassignment of several observed frequencies.« less

An ab initio study of Fe(CO)n, n = 1,5, and Cr(CO)6

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Rosi, Marzio; Bauschlicher, Charles W., Jr.

1991-01-01

Ab initio calculations have been performed for Cr(CO)6 and Fe(CO)n, n = 1,5. Basis sets of better than double zeta quality are used, and correlation is included using the modified coupler-pair functional method. The computed geometries and force constants are in reasonable agreement with experiment. The sequential bond dissociation energies of CO from Fe(CO)5 are estimated to be: 39, 31, 25, 22, and greater than 5 kcal/mol. It is noted that the first bond dissociation energy is relative to the singlet ground state of Fe(CO)5 and the lowest singlet state of Fe(CO)4, whereas the second is relative to the ground triplet states of Fe(CO)4 and Fe(CO)3. In addition, the binding energy for Fe-CO would be modified to 18 kcal/mol if dissociation occurred to the Fe(5F) excited state asymptote. The CO binding energies for Fe and Cr are found to be in poorer agreement with experiment than those found in a previous study on Ni(CO)4. The origins of this difference are discussed.

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.

Vibrational spectral investigation, NBO, first hyperpolarizability and UV-Vis spectral analysis of 3,5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods.

PubMed

Senthil kumar, J; Jeyavijayan, S; Arivazhagan, M

2015-02-05

The FT-IR and FT-Raman spectra of 3,5-dichlorobenzonitrile and m-bromobenzonitrile have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The optimized geometry, wave numbers and intensity of vibrational bonds of title molecules are obtained by ab initio and DFT level of theory with complete relaxation in the potential energy surface using 6-311++G(d, p) basis set. A complete vibrational assignments aided by the theoretical harmonic frequency, analysis have been proposed. The harmonic vibrational frequencies calculated have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The UV-Vis spectral analysis of the molecules has also been done which confirms the charge transfer of the molecules. Furthermore, the first hyperpolarizability and total dipole moment of the molecules have been calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab initio electronic transport and thermoelectric properties of solids from full and range-separated hybrid functionals

NASA Astrophysics Data System (ADS)

Sansone, Giuseppe; Ferretti, Andrea; Maschio, Lorenzo

2017-09-01

Within the semiclassical Boltzmann transport theory in the constant relaxation-time approximation, we perform an ab initio study of the transport properties of selected systems, including crystalline solids and nanostructures. A local (Gaussian) basis set is adopted and exploited to analytically evaluate band velocities as well as to access full and range-separated hybrid functionals (such as B3LYP, PBE0, or HSE06) at a moderate computational cost. As a consequence of the analytical derivative, our approach is computationally efficient and does not suffer from problems related to band crossings. We investigate and compare the performance of a variety of hybrid functionals in evaluating Boltzmann conductivity. Demonstrative examples include silicon and aluminum bulk crystals as well as two thermoelectric materials (CoSb3, Bi2Te3). We observe that hybrid functionals other than providing more realistic bandgaps—as expected—lead to larger bandwidths and hence allow for a better estimate of transport properties, also in metallic systems. As a nanostructure prototype, we also investigate conductivity in boron-nitride (BN) substituted graphene, in which nanoribbons (nanoroads) alternate with BN ones.

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.

Electronic Structure and Bonding in Transition Metal Inorganic and Organometallic Complexes: New Basis Sets, Linear Semibridging Carbonyls and Thiocarbonyls, and Oxidative Addition of Molecular Hydrogen to Square - Iridium Complexes.

NASA Astrophysics Data System (ADS)

Sargent, Andrew Landman

Approximate molecular orbital and ab initio quantum chemical techniques are used to investigate the electronic structure, bonding and reactivity of several transition metal inorganic and organometallic complexes. Modest-sized basis sets are developed for the second-row transition metal atoms and are designed for use in geometry optimizations of inorganic and organometallic complexes incorporating these atoms. The basis sets produce optimized equilibrium geometries which are slightly better than those produced with standard 3-21G basis sets, and which are significantly better than those produced with effective core potential basis sets. Linear semibridging carbonyl ligands in heterobimetallic complexes which contain a coordinatively unsaturated late transition metal center are found to accept electron density from, rather than donate electron density to, these centers. Only when the secondary metal center is a coordinatively unsaturated early transition metal center does the semibridging ligand donate electron density to this center. Large holes in the d shell around the metal center are more prominent and prevalent in early than in late transition metal centers, and the importance of filling in these holes outweighs the importance of mitigating the charge imbalance due to the dative metal-metal interaction. Semibridging thiocarbonyl ligands are more effective donors of electron density than the carbonyl ligands since the occupied donor orbitals of pi symmetry are higher in energy. The stereoselectivity of H_2 addition to d^8 square-planar transition metal complexes is controlled by the interactions between the ligands in the plane of addition and the concentrations of electronic charge around the metal center as the complex evolves from a four-coordinate to a six-coordinate species. Electron -withdrawing ligands help stabilize the five-coordinate species while strong electron donor ligands contribute only to the destabilizing repulsive interactions. The relative thermodynamic stabilities of the final complexes can be predicted based on the relative orientations of the strongest sigma-donor ligands.

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.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

High-level ab initio studies of NO(X2Π)-O2(X3Σg -) van der Waals complexes in quartet states

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2018-05-01

Geometry optimisations were performed on nine different structures of NO(X2Π)-O2(X3Σg-) van der Waals complexes in their quartet states, using the explicitly correlated RCCSD(T)-F12b method with basis sets up to the cc-pVQZ-F12 level. For the most stable configurations, counterpoise-corrected optimisations as well as extrapolations to the complete basis set (CBS) were performed. The X structure in the 4A‧ state was found to be most stable, with a CBS binding energy of -157 cm-1. The slipped tilted structures with N closer to O2 (Slipt-N), as well as the slipped parallel structure with O of NO closer to O2 (Slipp-O) in 4A″ states have binding energies of about -130 cm-1. C2v and linear complexes are less stable. According to calculated harmonic frequencies, the X isomer is bound. Isotropic hyperfine coupling constants of the complex are compared with those of the monomers.

Ab initio investigation of sulfur monofluoride and its singly charged cation and anion in their ground electronic state

NASA Astrophysics Data System (ADS)

Song, Li; Shan-Jun, Chen; Yan, Chen; Peng, Chen

2016-03-01

The SF radical and its singly charged cation and anion, SF+ and SF-, have been investigated on the MRCI/aug-cc-pVXZ (X = Q, 5, 6) levels of theory with Davidson correction. Both the core-valence correlation and the relativistic effect are considered. The extrapolating to the complete basis set (CBS) limit is adopted to remove the basis set truncation error. Geometrical parameters, potential energy curves (PECs), vibrational energy levels, spectroscopic constants, ionization potentials, and electron affinities of the ground electronic state for all these species are obtained. The information with respect to molecular characteristics of the SFn (n = -1, 0, +1) systems derived in this work will help to extend our knowledge and to guide further experimental or theoretical researches. Project supported by the National Natural Science Foundation of China (Grant Nos. 11304023 and 11447172), the Young and Middle-Aged Talent of Education Burea of Hubei Province, China (Grant No. Q20151307), and the Yangtze Youth Talents Fund of Yangtze University, China (Grant No. 2015cqr21).

An ab initio study of the C3(+) cation using multireference methods

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Martin, J. M. L.; Francois, J. P.; Gijbels, R.

1991-01-01

The energy difference between the linear 2 sigma(sup +, sub u) and cyclic 2B(sub 2) structures of C3(+) has been investigated using large (5s3p2d1f) basis sets and multireference electron correlation treatments, including complete active space self consistent fields (CASSCF), multireference configuration interaction (MRCI), and averaged coupled-pair functional (ACPF) methods, as well as the single-reference quadratic configuration interaction (QCISD(T)) method. Our best estimate, including a correction for basis set incompleteness, is that the linear form lies above the cyclic from by 5.2(+1.5 to -1.0) kcal/mol. The 2 sigma(sup +, sub u) state is probably not a transition state, but a local minimum. Reliable computation of the cyclic/linear energy difference in C3(+) is extremely demanding of the electron correlation treatment used: of the single-reference methods previously considered, CCSD(T) and QCISD(T) perform best. The MRCI + Q(0.01)/(4s2p1d) energy separation of 1.68 kcal/mol should provide a comparison standard for other electron correlation methods applied to this system.

Interaction of monovalent cations with acetonitrile

NASA Astrophysics Data System (ADS)

Černušák, Ivan; Aranyosiová, Monika; Vollárová, Ol'ga; Velič, Dušan; Kirdajová, Ol'ga; Benko, Ján

Solvation of monovalent cations (Me+) of alkali metals=Na+, K+, Rb+, and Cs+, coinage metals=Cu+, Ag+, Au+, and p-block elements Ga+, In+, and Tl+ with acetonitrile was studied by means of ab initio calculations and time-of-flight secondary ion mass spectrometry (TOF-SIMS). The intermolecular interactions in the complexes Me+···CH3CN were investigated using the coupled clusters theory including single, double, and noniterative triple substitutions (CCSD(T)) in conjunction with the Pol and Pol-dk basis sets. The binding energies of these donor-acceptor complexes were estimated; taking into account the basis set superposition error, zero-point vibrations, correlation contribution, and scalar relativistic corrections. The theoretical ΔG0298 K values based on CCSD(T)/Pol and/or CCSD(T)/Pol-dk binding energies correlated well with experimental transfer Gibbs energies (from water to acetonitrile) for the series of cations. In the case of Au monocation, relativistic correction turned out to be extremely important. Composition of the complex of Ag+ and Na+ with acetonitrile was determined by using SIMS supporting both theoretical and experimental transfer Gibbs energies.

Monte Carlo explicitly correlated second-order many-body perturbation theory

NASA Astrophysics Data System (ADS)

Johnson, Cole M.; Doran, Alexander E.; Zhang, Jinmei; Valeev, Edward F.; Hirata, So

2016-10-01

A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method. Applications of this method to 17 molecular correlation energies and 12 gas-phase reaction energies reveal that both the nonvariational and variational formulas for the correction give reliable correlation energies (98% or higher) and reaction energies (within 2 kJ mol-1 with a smaller statistical uncertainty) near the complete-basis-set limits by using just the aug-cc-pVDZ basis set. The nonvariational formula is found to be 2-10 times less expensive to evaluate than the variational one, though the latter yields energies that are bounded from below and is, therefore, slightly but systematically more accurate for energy differences. Being capable of using virtually any geminal form, the method confirms the best overall performance of the Slater-type geminal among 6 forms satisfying the same cusp conditions. Not having to precompute lower-dimensional integrals analytically, to store them on disk, or to transform them in a nonscalable dense-matrix-multiplication algorithm, the method scales favorably with both system size and computer size; the cost increases only as O(n4) with the number of orbitals (n), and its parallel efficiency reaches 99.9% of the ideal case on going from 16 to 4096 computer processors.

Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

1981-09-01

Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

NASA Astrophysics Data System (ADS)

Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

2017-08-01

The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.

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.

Optically induced circular and axial birefringences in achiral fluids: an ab initio study of the optical Faraday effect

NASA Astrophysics Data System (ADS)

Baranowska, Angelika; Rizzo, Antonio; Coriani, Sonia

2006-07-01

A computational analysis of the effects (intensity-dependent change in the refractive index and the optical Faraday effect, OFE) induced in an achiral fluid by circularly polarized, linearly polarized or unpolarized light is presented. The connection between the molecular parameters appearing in the expression of the observable, as derived by Woźniak in the 1990s, and the appropriate linear and cubic frequency dependent response functions is made for the general case of both chiral and non-chiral fluid. The parameters which are non-vanishing in the case of achiral systems are then computed employing a coupled cluster singles and doubles wave function model and a wide choice of correlation consistent basis sets, for a set of reference systems, including a rare gas (neon), a non-dipolar (N2) and a dipolar (CO) molecule. Contributions due to magnetic and quadrupolar interactions between the fields and the gases are neglected, since they are in principle of much less importance than the purely electric dipolar interactions. Nevertheless a rough estimate of their size is given. The aim of the study is to assess the detectability of OFE. To this end, the ab initio results are compared with those obtained in this work for the closely related optical Kerr effect (OKE) and with those yielded by the classical Faraday effect.

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1989-01-01

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

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)).

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

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

The study of molecular spectroscopy by ab initio methods

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1991-01-01

This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

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.

Ab Initio Calculations of Spin-Orbit Coupling for Heavy-Metal Containing Radicals

NASA Astrophysics Data System (ADS)

Cheng, Lan

2016-06-01

The perturbative treatment of spin-orbit coupling (SOC) on top of scalar-relativistic calculations is a cost-effective alternative to rigorous fully relativistic calculations. In this work the applicability of the perturbative scheme in the framework of spin-free exact two-component theory is demonstrated with calculations of SO splittings and SOC contributions to molecular properties in small heavy-metal containing radicals, including AuO, AuS, and ThO^+. The equation of motion coupled cluster techniques have been used to accurately account for the electron-correlation effects in these radicals, and basis-set effects are carefully analyzed. The computed results are compared with experimental measurements for SO splittings and dipole moments when available.

Microwave spectrum and structure of bicyclo /1.1.1/ pentanone and comparison with several theoretical structures

NASA Technical Reports Server (NTRS)

Mcrae, Glenn A.; Cohen, Edward A.; Sponsler, Michael B.; Dougherty, Dennis A.

1986-01-01

The microwave spectra of five isotopic species of bicyclo (1.1.1) pentanone have been investigated. The rotational constants along with various centrifugal distortion constants for each species have been determined. From the rotational constants, a complete r(s) structure has been determined for the heavy atoms. Analysis of Stark effect measurements has shown the dipole moment to be along the a principal inertial axis with a magnitude of 3.164 (5) D. These results are compared with those obtained by four current theoretical methods: molecular mechanics (MM2), MNDO, and Hartree-Fock ab initio theory with STO-3G and 3-21G basis sets.

The 3d Rydberg (3A2) electronic state observed by Herzberg and Shoosmith for methylene

NASA Astrophysics Data System (ADS)

Yamaguchi, Yukio; Schaefer, Henry F., III

1997-06-01

In 1959 and 1961 Herzberg and Shoosmith reported the vacuum ultraviolet spectrum of the triplet state of CH2. The present study focuses on a characterization of the upper state, the 3d Rydberg (3A2) state, observed at 1415 Å. The theoretical interpretation of these experiments is greatly complicated by the presence of a lower-lying 3A2 valence state with a very small equilibrium bond angle. Ab initio electronic structure methods involving self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), complete active space (CAS) SCF, state-averaged (SA) CASSCF, coupled cluster with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CASSCF second-order (SO) CI, and SACASSCF-SOCI have been employed with six distinct basis sets. With the largest basis set, triple zeta plus triple polarization with two sets of higher angular momentum functions and three sets of diffuse functions TZ3P(2 f,2d)+3diff, the CISD level of theory predicts the equilibrium geometry of the 3d Rydberg (3A2) state to be re=1.093 Å and θe=141.3 deg. With the same basis set the energy (Te value) of the 3d Rydberg state relative to the ground (X˜ 3B1) state has been determined to be 201.6 kcal mol-1 (70 500 cm-1) at the CCSD (T) level, 200.92kcal mol-1 (70 270 cm-1) at the CASSCF-SOCI level, and 200.89kcal mol-1 (70 260 cm-1) at the SACASSCF-SOCI level of theory. These predictions are in excellent agreement with the experimental T0 value of 201.95 kcalmol-1 (70 634 cm-1) reported by Herzberg.

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.

Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

PubMed

Kutateladze, Andrei G; Mukhina, Olga A

2014-09-05

Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

Photoinduced dynamics to photoluminescence in Ln3+ (Ln = Ce, Pr) doped β-NaYF4 nanocrystals computed in basis of non-collinear spin DFT with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Han, Yulun; Vogel, Dayton J.; Inerbaev, Talgat M.; May, P. Stanley; Berry, Mary T.; Kilin, Dmitri S.

2018-03-01

In this work, non-collinear spin DFT + U approaches with spin-orbit coupling (SOC) are applied to Ln3+ doped β-NaYF4 (Ln = Ce, Pr) nanocrystals in Vienna ab initio Simulation Package taking into account unpaired spin configurations using the Perdew-Burke-Ernzerhof functional in a plane wave basis set. The calculated absorption spectra from non-collinear spin DFT + U approaches are compared with that from spin-polarised DFT + U approaches. The spectral difference indicates the importance of spin-flip transitions of Ln3+ ions. Suite of codes for nonadiabatic dynamics has been developed for 2-component spinor orbitals. On-the-fly nonadiabatic coupling calculations provide transition probabilities facilitated by nuclear motion. Relaxation rates of electrons and holes are calculated using Redfield theory in the reduced density matrix formalism cast in the basis of non-collinear spin DFT + U with SOC. The emission spectra are calculated using the time-integrated method along the excited state trajectories based on nonadiabatic couplings.

Ab-initio Computation of the Electronic, transport, and Bulk Properties of Calcium Oxide.

NASA Astrophysics Data System (ADS)

Mbolle, Augustine; Banjara, Dipendra; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We report results from ab-initio, self-consistent, local Density approximation (LDA) calculations of electronic and related properties of calcium oxide (CaO) in the rock salt structure. We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. Our calculations are non-relativistic. We implemented the LCAO formalism following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method involves a methodical search for the optimal basis set that yields the absolute minima of the occupied energies, as required by density functional theory (DFT). Our calculated, indirect band gap of 6.91eV, from towards the L point, is in excellent agreement with experimental value of 6.93-7.7eV, at room temperature (RT). We have also calculated the total (DOS) and partial (pDOS) densities of states as well as the bulk modulus. Our calculated bulk modulus is in excellent agreement with experiment. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

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

Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study

DOE PAGES

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; ...

2015-07-29

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

An ab initio study of the electronic structure and relative stability of the halogenated thiophosphorus compounds SPX (X = Cl, F, Br) and their isomers

NASA Astrophysics Data System (ADS)

Nowek, Andrzej; Richardson, Rhonda; Babinec, Peter; Leszczyński, Jerzy

1997-12-01

The electronic structure and relative stability of the halogenated thiophosphorus compounds SPCl, SPF, and SPBr and their isomers ClSP, FSP, and BrSP were investigated using ab initio post-Hartree-Fock methods. Molecular geometries of all these structures together with the transition states between isomers, have been optimized at the SCF, MP2, and CCSD levels. Single-point CCSD(T) and MP4 calculations have been performed at the optimal CCSD and MP2 geometries. All calculations have been done using the standard 6-311G(2d) basis set. Harmonic vibrational frequencies and IR intensities for all species were calculated at the correlated levels, and they are in good agreement with the available data from matrix-isolated IR spectroscopy. Because the isomers ClSP, FSP, and BrSP have not yet been experimentally observed, we extended our study by calculating of equilibrium constants of isomerization using Eyring transition state theory, and we have found that at sufficiently high temperatures (≈ 1000 K) the equilibrium constants are large enough for the possible detection of these isomers.

Ab initio computational study of reaction mechanism of peptide bond formation on HF/6-31G(d,p) level

NASA Astrophysics Data System (ADS)

Siahaan, P.; Lalita, M. N. T.; Cahyono, B.; Laksitorini, M. D.; Hildayani, S. Z.

2017-02-01

Peptide plays an important role in modulation of various cell functions. Therefore, formation reaction of the peptide is important for chemical reactions. One way to probe the reaction of peptide synthesis is a computational method. The purpose of this research is to determine the reaction mechanism for peptide bond formation on Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine by ab initio computational approach. The calculations were carried out by theory and basis set HF/6-31G(d,p) for four mechanisms (path 1 to 4) that proposed in this research. The results show that the highest of the rate determining step between reactant and transition state (TS) for path 1, 2, 3, and 4 are 163.06 kJ.mol-1, 1868 kJ.mol-1, 5685 kJ.mol-1, and 1837 kJ.mol-1. The calculation shows that the most preferred reaction of Ac-PV-NH2 and Ac-VP-NH2 synthesis from amino acid proline and valine are on the path 1 (initiated with the termination of H+ in proline amino acid) that produce Ac-PV-NH2.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Conformational and Structural Studies of Isopropylamine from Temperature Dependent Raman Spectra of Xenon Solutions and {AB INITIO} Calculations

NASA Astrophysics Data System (ADS)

Klaassen, Joshua J.; Darkhalil, Ikhlas D.; Durig, James R.

2012-06-01

The Raman and infrared spectra (4000 to 50 cm-1) of the gas, liquid or solution, and solid have been recorded of isopropylamine, (CH3)2CHNH2. Variable temperature (-50 to -100oC) studies of the Raman spectra (3500 to 100 cm-1) dissolved in liquid xenon have been carried out. From these data, both the {trans} and {gauche} conformers have been identified and their relative stability obtained. The enthalpy difference has been determined from 20 band pairs at 6 temperatures to be 113 +/- 11 cm-1 (1.35 +/- 0.13 kJ mol-1) with the {trans} conformer the more stable form. The percentage of the {gauche} conformer is estimated to be 54 +/- 1 percent at ambient temperature. The conformational stabilities have been predicted from {ab initio} calculations utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. By utilizing previously reported microwave rotational constants along with {ab initio} MP2(full)/6-311+G(d,p) predicted structural values, adjusted r0 parameters have been obtained for the {trans} conformer. The determined heavy atom and NH2 distances in angstroms are C-C = 1.530(3), C-N = 1.465(3), N-H = 1.019(3) and angles in degrees NCC = 108.9(5), CCC = 111.0(5), HNC = 110.3(5). The structural parameters for the {gauche} conformer were estimated by using the same adjustment differences to the {gauche} form as those obtained for the corresponding {trans} parameters. Vibrational assignments have been provided for the observed bands for both conformers which are supported by MP2(full)/6-31G(d) {ab initio} calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are discussed and compared to the corresponding properties of some related molecules.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO reversible reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HNO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X double bond H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate (Delta)H(sub f, sup o) value for HNO using state-of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +/- 0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO rev. reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X=H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate(DELTA)H(sup o)(sub f) value for HNO using state of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

NASA Technical Reports Server (NTRS)

Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

2012-01-01

Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

DOE PAGES

Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; ...

2015-12-09

In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D 4h-symmetric, 1,2,3,4-cyclobutanetetraone (C 4O 4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π( 1A 1g) state, the singlet 10π( 1A 1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π( 1A 1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π( 1B 2u) and 9π( 3B 2u), respectively, originating from single occupancy of the HOMO and LUMO.more » Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneracies in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π( 3B 2u) < 8π( 1A 1g) < 9π( 1B 2u) < 10π( 1A 1g) and that the 8π( 1A 1g) - 9π( 3B 2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.« less

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-02-01

In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

PubMed

Bandyopadhyay, D; Bhattacharyya, D

2006-10-15

It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.

High level theoretical study of benzene-halide adducts: the importance of C-H-anion hydrogen bonding.

PubMed

Coletti, Cecilia; Re, Nazzareno

2009-02-26

High level ab initio calculations were performed on the interaction of halide anions (F(-), Cl(-), Br(-), and I(-)) to benzene. For these systems recent experimental and theoretical data are rather scarce, in spite of their growingly acknowledged importance for binding in complex biological systems. We have thus explored the complete basis set limit and the effect of counterpoise basis set superposition error corrections on the minimum geometries and energies of benzene-halide adducts in their possible interaction modes. The binding energy and enthalpy values (ranging from -15.3 kcal/mol for fluoride to -6.1 kcal/mol for iodide) show that the hydrogen bonding occurring in these complexes cannot be described as a weak interaction. We have furthermore investigated the topology of the minima and of other selected sections of the potential energy surface, so to gain further insight on the nature of the halide-benzene interaction. In particular, the geometry corresponding to the C(6v) symmetry, although being overall repulsive, has displayed the unprecedented presence of a small flex (a minimum in C(6v) symmetry) with interaction energy close to zero or slightly attractive.

A new ab initio potential energy surface for the NH-He complex

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Kłos, J.; Lique, F.

2018-02-01

We present a new three-dimensional potential energy surface (PES) for the NH(X3Σ-)-He van der Waals system, which explicitly takes into account the NH vibrational motion. The NH-He PES was obtained using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = Q, 5, 6) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. Using this new PES, we have studied the spectroscopy of the NH-He complex and we have determined a new rotational constant that agrees well with the available experimental data. Collisional excitation of NH(X3Σ-) by He was also studied at the close-coupling level. Calculations of the collisional excitation cross sections of the fine-structure levels of NH by He were performed for energies up to 3500 cm-1, which yield, after thermal average, rate coefficients up to 350 K. The calculated rate coefficients are compared with available experimental measurements at room temperature, and a reasonably good agreement is found between experimental and theoretical data.

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

Bazante, Alexandre P., E-mail: abazante@chem.ufl.edu; Bartlett, Rodney J.; Davidson, E. R.

The benzene radical anion is studied with ab initio coupled-cluster theory in large basis sets. Unlike the usual assumption, we find that, at the level of theory investigated, the minimum energy geometry is non-planar with tetrahedral distortion at two opposite carbon atoms. The anion is well known for its instability to auto-ionization which poses computational challenges to determine its properties. Despite the importance of the benzene radical anion, the considerable attention it has received in the literature so far has failed to address the details of its structure and shape-resonance character at a high level of theory. Here, we examinemore » the dynamic Jahn-Teller effect and its impact on the anion potential energy surface. We find that a minimum energy geometry of C{sub 2} symmetry is located below one D{sub 2h} stationary point on a C{sub 2h} pseudo-rotation surface. The applicability of standard wave function methods to an unbound anion is assessed with the stabilization method. The isotropic hyperfine splitting constants (A{sub iso}) are computed and compared to data obtained from experimental electron spin resonance experiments. Satisfactory agreement with experiment is obtained with coupled-cluster theory and large basis sets such as cc-pCVQZ.« less

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).

Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

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).

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Ab Initio Simulation of Charge Transfer at the Semiconductor Quantum Dot/TiO 2 Interface in Quantum Dot-Sensitized Solar Cells

DOE PAGES

Xin, Xukai; Li, Bo; Jung, Jaehan; ...

2014-07-24

Quantum dot-sensitized solar cells (QDSSCs) have emerged as a promising solar architecture for next-generation solar cells. The QDSSCs exhibit a remarkably fast electron transfer from the quantum dot (QD) donor to the TiO 2 acceptor with size quantization properties of QDs that allows for the modulation of band energies to control photoresponse and photoconversion efficiency of solar cells. In order to understand the mechanisms that underpin this rapid charge transfer, the electronic properties of CdSe and PbSe QDs with different sizes on the TiO 2 substrate are simulated using a rigorous ab initio density functional method. Our method capitalizes onmore » localized orbital basis set, which is computationally less intensive. Quite intriguingly, a remarkable set of electron bridging states between QDs and TiO 2 occurring via the strong bonding between the conduction bands of QDs and TiO 2 is revealed. Such bridging states account for the fast adiabatic charge transfer from the QD donor to the TiO 2 acceptor, and may be a general feature for strongly coupled donor/acceptor systems. All the QDs/TiO 2 systems exhibit type II band alignments, with conduction band offsets that increase with the decrease in QD size. This facilitates the charge transfer from QDs donors to TiO 2 acceptors and explains the dependence of the increased charge transfer rate with the decreased QD size.« less

Basis set and electron correlation effects on the polarizability and second hyperpolarizability of model open-shell π-conjugated systems

NASA Astrophysics Data System (ADS)

Champagne, Benoı̂t; Botek, Edith; Nakano, Masayoshi; Nitta, Tomoshige; Yamaguchi, Kizashi

2005-03-01

The basis set and electron correlation effects on the static polarizability (α) and second hyperpolarizability (γ) are investigated ab initio for two model open-shell π-conjugated systems, the C5H7 radical and the C6H8 radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C6H8 whereas diffuse functions are compulsory for C5H7, in particular, p diffuse functions. In addition to the 6-31G*+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for α and γ of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order Møller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree-Fock results. Moreover, the differences between the restricted open-shell Hartree-Fock and restricted open-shell second-order Møller-Plesset methods are small. In what concerns the second hyperpolarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset values remain of similar quality while using spin-projected schemes fails for the charged system but performs nicely for the neutral one. The restricted open-shell schemes, and especially the restricted open-shell second-order Møller-Plesset method, provide for both compounds γ values close to the results obtained at the unrestricted coupled cluster level including singles and doubles with a perturbative inclusion of the triples. Thus, to obtain well-converged α and γ values at low-order electron correlation levels, the removal of spin contamination is a necessary but not a sufficient condition. Density-functional theory calculations of α and γ have also been carried out using several exchange-correlation functionals. Those employing hybrid exchange-correlation functionals have been shown to reproduce fairly well the reference coupled cluster polarizability and second hyperpolarizability values. In addition, inclusion of Hartree-Fock exchange is of major importance for determining accurate polarizability whereas for the second hyperpolarizability the gradient corrections are large.

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.

Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease

NASA Astrophysics Data System (ADS)

Martínez-González, José Ángel; Rodríguez, Alex; Puyuelo, María Pilar; González, Miguel; Martínez, Rodrigo

2015-01-01

The main reactions of the hepatitis C virus NS3/NS4A serine protease are studied using the second-order Møller-Plesset ab initio method and rather large basis sets to correct the previously reported AM1/CHARMM22 potential energy surfaces. The reaction efficiencies measured for the different substrates are explained in terms of the tetrahedral intermediate formation step (the rate-limiting process). The energies of the barrier and the corresponding intermediate are so close that the possibility of a concerted mechanism is open (especially for the NS5A/5B substrate). This is in contrast to the suggested general reaction mechanism of serine proteases, where a two-step mechanism is postulated.

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

A quantum chemistry study of Qinghaosu

NASA Astrophysics Data System (ADS)

Gu, Jian-De; Chen, Kai-Xian; Jiang, Hua-Liang; Zhu, Wei-Liang; Chen, Jian-Zhong; Ji, Ru-Yun

1997-10-01

The powerful anti-malarial drug, Qinghaosu (Artemisinin), has been studied using ab initio methods. The DFT B3LYP method with the 6-31G ∗ basis set gives an excellent geometry compared to experiments, especially for the OO bond length and the 1,2,4-Trioxane ring subsystem. The R(OO) bond length predicted at this level is 1.460 Å, only 0.018 Å shorter than the experimental measurement. The vibrational analysis shows that the OO stretching mode is combined with the OC vibration mode, having the character of an OOC entity. The OO vibrational band at 722 cm -1 suggested in the experimental studies has been assigned as 1,2,4-trioxane ring breathing.

A refined quartic potential energy surface and large scale vibrational calculations for S0 thiophosgene.

PubMed

Rashev, Svetoslav; Moule, David C

2015-04-05

In this work we present a full 6D quartic potential energy surface (PES) for S0 thiophosgene in curvilinear symmetrized bond-angle coordinates. The PES was refined starting from an ab initio field derived from acc-pVTZ basis set with CCSD(T) corrections for electron correlation. In the present calculations we used our variational method that was recently tested on formaldehyde and some of its isotopomers, along with additional improvements. The lower experimentally known vibrational levels for 35Cl2CS were reproduced quite well in the calculations, which can be regarded as a test for the feasibility of the obtained quartic PES. Copyright © 2015 Elsevier B.V. All rights reserved.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Kinetic and equilibrium lithium acidities of arenes: theory and experiment.

PubMed

Streitwieser, Andrew; Shah, Kamesh; Reyes, Julius R; Zhang, Xingyue; Davis, Nicole R; Wu, Eric C

2010-08-26

Kinetic acidities of arenes, ArH, measured some time ago by hydrogen isotope exchange kinetics with lithium cyclohexylamide (LiCHA) in cyclohexylamine (CHA) show a wide range of reactivities that involve several electronic mechanisms. These experimental reactivities give an excellent Brønsted correlation with equilibrium lithium ion pair acidities (pK(Li)) derived as shown recently from computations of ArLi.2E (E = dimethyl ether). The various electronic mechanisms are well modeled by ab initio HF calculations with modest basis sets. Additional calculations using NH(3) as a model for CHA further characterize the TS of the exchange reactions. The slopes of Brønsted correlations of ion pair systems can vary depending on the nature of the ion pairs.

Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. II. Validation and comparison with experiments

NASA Astrophysics Data System (ADS)

Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

2013-10-01

In this work, we validate a new, fully analytical method for calculating Raman intensities of periodic systems, developed and presented in Paper I [L. Maschio, B. Kirtman, M. Rérat, R. Orlando, and R. Dovesi, J. Chem. Phys. 139, 164101 (2013)]. Our validation of this method and its implementation in the CRYSTAL code is done through several internal checks as well as comparison with experiment. The internal checks include consistency of results when increasing the number of periodic directions (from 0D to 1D, 2D, 3D), comparison with numerical differentiation, and a test of the sum rule for derivatives of the polarizability tensor. The choice of basis set as well as the Hamiltonian is also studied. Simulated Raman spectra of α-quartz and of the UiO-66 Metal-Organic Framework are compared with the experimental data.

{ITALIC AB INITIO} Large-Basis no-Core Shell Model and its Application to Light Nuclei

NASA Astrophysics Data System (ADS)

Barrett, Bruce R.; Navratil, Petr; Ormand, W. E.; Vary, James P.

2002-01-01

We discuss the {ITALIC ab initio} No-Core Shell Model (NCSM). In this method the effective Hamiltonians are derived microscopically from realistic nucleon-nucleon (NN) potentials, such as the CD-Bonn and the Argonne AV18 NN potentials, as a function of the finite Harmonic Oscillator (HO) basis space. We present converged results, i.e. , up to 50 Ω and 18 Ω HO excitations, respectively, for the A=3 and 4 nucleon systems. Our results for these light systems are in agreement with results obtained by other exact methods. We also calculate properties of 6Li and 6He in model spaces up to 10 Ω and of 12C up to 6 Ω. Binding energies, rms radii, excitation spectra and electromagnetic properties are discussed. The favorable comparison with available data is a consequence of the underlying NN interaction rather than a phenomenological fit.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

PubMed

Greenberg, Ido; Shkolnisky, Yoel

2017-11-01

We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE PAGES

Dytrych, T.; Maris, P.; Launey, K. D.; ...

2016-06-22

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell’s strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states withmore » a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

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

Dytrych, T.; Maris, Pieter; Launey, K. D.

2016-06-09

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations ofmore » states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Accurate virial coefficients of gaseous krypton from state-of-the-art ab initio potential and polarizability of the krypton dimer

NASA Astrophysics Data System (ADS)

Song, Bo; Waldrop, Jonathan M.; Wang, Xiaopo; Patkowski, Konrad

2018-01-01

We have developed a new krypton-krypton interaction-induced isotropic dipole polarizability curve based on high-level ab initio methods. The determination was carried out using the coupled-cluster singles and doubles plus perturbative triples method with very large basis sets up to augmented correlation-consistent sextuple zeta as well as the corrections for core-core and core-valence correlation and relativistic effects. The analytical function of polarizability and our recently constructed reference interatomic potential [J. M. Waldrop et al., J. Chem. Phys. 142, 204307 (2015)] were used to predict the thermophysical and electromagnetic properties of krypton gas. The second pressure, acoustic, and dielectric virial coefficients were computed for the temperature range of 116 K-5000 K using classical statistical mechanics supplemented with high-order quantum corrections. The virial coefficients calculated were compared with the generally less precise available experimental data as well as with values computed from other potentials in the literature {in particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]}. The detailed examination in this work suggests that the present theoretical prediction can be applied as reference values in disciplines involving thermophysical and electromagnetic properties of krypton gas.

A Simple ab initio Model for the Hydrated Electron that Matches Experiment

PubMed Central

Kumar, Anil; Walker, Jonathan A.; Bartels, David M.; Sevilla, Michael D.

2015-01-01

Since its discovery over 50 years ago, the “structure” and properties of the hydrated electron has been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy zero “Kelvin” structure found for any 4-water (or larger) anion cluster, at any post-Hartree-Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (UMJ: Uhlig, Marsalek, and Jungwirth, Journal of Physical Chemistry Letters 2012, 3, 3071-5), with four OH bonds oriented toward the maximum charge density in a small central “void”. The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

A new ab initio potential energy surface for the collisional excitation of HCN by para- and ortho-H2

NASA Astrophysics Data System (ADS)

Denis-Alpizar, Otoniel; Kalugina, Yulia; Stoecklin, Thierry; Vera, Mario Hernández; Lique, François

2013-12-01

We present a new four-dimensional potential energy surface for the collisional excitation of HCN by H2. Ab initio calculations of the HCN-H2 van der Waals complex, considering both molecules as rigid rotors, were carried out at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12a] level of theory using an augmented correlation-consistent triple zeta (aVTZ) basis set. The equilibrium structure is linear HCN-H2 with the nitrogen pointing towards H2 at an intermolecular separation of 7.20 a0. The corresponding well depth is -195.20 cm-1. A secondary minimum of -183.59 cm-1 was found for a T-shape configuration with the H of HCN pointing to the center of mass of H2. We also determine the rovibrational energy levels of the HCN-para-H2 and HCN-ortho-H2 complexes. The calculated dissociation energies for the para and ortho complexes are 37.79 cm-1 and 60.26 cm-1, respectively. The calculated ro-vibrational transitions in the HCN-H2 complex are found to agree by more than 0.5% with the available experimental data, confirming the accuracy of the potential energy surface.

Ab initio study of the neutral and anionic alkali and alkaline earth hydroxides: Electronic structure and prospects for sympathetic cooling of OH−

PubMed Central

2017-01-01

We have performed a systematic ab initio study on alkali and alkaline earth hydroxide neutral (MOH) and anionic (MOH−) species where M = Li, Na, K, Rb, Cs or Be, Mg, Ca, Sr, Ba. The CCSD(T) method with extended basis sets and Dirac-Fock relativistic effective core potentials for the heavier atoms has been used to study their equilibrium geometries, interaction energies, electron affinities, electric dipole moment, and potential energy surfaces. All neutral and anionic species exhibit a linear shape with the exception of BeOH, BeOH−, and MgOH−, for which the equilibrium structure is found to be bent. Our analysis shows that the alkaline earth hydroxide anions are valence-bound whereas the alkali hydroxide anions are dipole bound. In the context of sympathetic cooling of OH− by collision with ultracold alkali and alkaline earth atoms, we investigate the 2D MOH− potential energy surfaces and the associative detachment reaction M + OH→− MOH + e−, which is the only energetically allowed reactive channel in the cold regime. We discuss the implication for the sympathetic cooling of OH− and conclude that Li and K are the best candidates for an ultracold buffer gas. PMID:28527437

Rotational Quenching Study in Isovalent H+ + CO and H+ + CS Systems

NASA Astrophysics Data System (ADS)

Kaur, Rajwant; Dhilip Kumar, T. J.

2016-06-01

Cooling and trapping of polar molecules has attracted attention at cold and ultracold temperatures. Extended study of molecular inelastic collision processes of polar interstellar species with proton finds an important astrophysical application to model interstellar medium. Present study includes computation of rate coefficient for molecular rotational quenching process in proton collision with isovalent CO and CS molecules using quantum dynamical close-coupling calculations. Full dimensional ab initio potential energy surfaces have been computed for the ground state for both the systems using internally contracted multireference configuration interaction method and basis sets. Quantum scattering calculations for rotational quenching of isovalent species are studied in the rigid-rotor approximation with CX (X=O, S) bond length fixed at an experimental equilibrium value of 2.138 and 2.900 a.u., respectively. Asymptotic potentials are computed using the dipole and quadrupole moments, and the dipole polarizability components. The resulting long-range potentials with the short-range ab initio interaction potentials have been fitted to study the anisotropy of the rigid-rotor surface using the multipolar expansion coefficients. Rotational quenching cross-section and corresponding rates from j=4 level of CX to lower j' levels have been obtained and found to obey Wigner's threshold law at ultra cold temperatures.

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

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

2008-06-01

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

PubMed

Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

2008-06-14

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

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.

Theoretical study of the changes in the vibrational characteristics arising from the hydrogen bonding between Vitamin C ( L-ascorbic acid) and H 2O

NASA Astrophysics Data System (ADS)

Dimitrova, Yordanka

2006-02-01

The vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) for the hydrogen-bonded system of Vitamin C ( L-ascorbic acid) with five water molecules have been predicted using ab initio SCF/6-31G(d, p) calculations and DFT (BLYP) calculations with 6-31G(d, p) and 6-31++G(d, p) basis sets. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between Vitamin C and five water molecules leads to large red shifts of the stretching vibrations for the monomer bonds involved in the hydrogen bonding and very strong increase in their IR intensity. The predicted frequency shifts for the stretching vibrations from Vitamin C taking part in the hydrogen bonding are up to -508 cm -1. The magnitude of the wavenumber shifts is indicative of relatively strong OH···H hydrogen-bonded interactions. In the same time the IR intensity and Raman activity of these vibrations increase upon complexation. The IR intensity increases dramatically (up to 12 times) and Raman activity increases up to three times. The ab initio and BLYP calculations show, that the symmetric OH vibrations of water molecules are more sensitive to the complexation. The hydrogen bonding leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The asymmetric OH stretching vibrations of water, free from hydrogen bonding are less sensitive to the complexation than the hydrogen-bonded symmetric O sbnd H stretching vibrations. The increases of the IR intensities for these vibrations are lower and red shifts are negligible.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

PubMed Central

Li, Jun; Riehle, Michelle M; Zhang, Yan; Xu, Jiannong; Oduol, Frederick; Gomez, Shawn M; Eiglmeier, Karin; Ueberheide, Beatrix M; Shabanowitz, Jeffrey; Hunt, Donald F; Ribeiro, José MC; Vernick, Kenneth D

2006-01-01

Background Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. Results We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. Conclusion Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. PMID:16569258

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.

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.

Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2018-02-01

We compute numerically exact rovibrational levels of water dimer, with 12 vibrational coordinates, on the accurate CCpol-8sf ab initio flexible monomer potential energy surface [C. Leforestier et al., J. Chem. Phys. 137, 014305 (2012)]. It does not have a sum-of-products or multimode form and therefore quadrature in some form must be used. To do the calculation, it is necessary to use an efficient basis set and to develop computational tools, for evaluating the matrix-vector products required to calculate the spectrum, that obviate the need to store the potential on a 12D quadrature grid. The basis functions we use are products of monomer vibrational wavefunctions and standard rigid-monomer basis functions (which involve products of three Wigner functions). Potential matrix-vector products are evaluated using the F matrix idea previously used to compute rovibrational levels of 5-atom and 6-atom molecules. When the coupling between inter- and intra-monomer coordinates is weak, this crude adiabatic type basis is efficient (only a few monomer vibrational wavefunctions are necessary), although the calculation of matrix elements is straightforward. It is much easier to use than an adiabatic basis. The product structure of the basis is compatible with the product structure of the kinetic energy operator and this facilitates computation of matrix-vector products. Compared with the results obtained using a [6 + 6]D adiabatic approach, we find good agreement for the inter-molecular levels and larger differences for the intra-molecular water bend levels.

Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2018-02-21

We compute numerically exact rovibrational levels of water dimer, with 12 vibrational coordinates, on the accurate CCpol-8sf ab initio flexible monomer potential energy surface [C. Leforestier et al., J. Chem. Phys. 137, 014305 (2012)]. It does not have a sum-of-products or multimode form and therefore quadrature in some form must be used. To do the calculation, it is necessary to use an efficient basis set and to develop computational tools, for evaluating the matrix-vector products required to calculate the spectrum, that obviate the need to store the potential on a 12D quadrature grid. The basis functions we use are products of monomer vibrational wavefunctions and standard rigid-monomer basis functions (which involve products of three Wigner functions). Potential matrix-vector products are evaluated using the F matrix idea previously used to compute rovibrational levels of 5-atom and 6-atom molecules. When the coupling between inter- and intra-monomer coordinates is weak, this crude adiabatic type basis is efficient (only a few monomer vibrational wavefunctions are necessary), although the calculation of matrix elements is straightforward. It is much easier to use than an adiabatic basis. The product structure of the basis is compatible with the product structure of the kinetic energy operator and this facilitates computation of matrix-vector products. Compared with the results obtained using a [6 + 6]D adiabatic approach, we find good agreement for the inter-molecular levels and larger differences for the intra-molecular water bend levels.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Discovery of the Electronic Spectra of Hps and Dps

NASA Astrophysics Data System (ADS)

Grimminger, Robert A.; Wei, Jie; Ellis, Blaine; Clouthier, Dennis J.; Wang, Zhong; Sears, Trevor

2009-06-01

The hitherto unknown electronic spectrum of the closed shell transient molecule HPS has been observed in the 685 - 846 nm region by laser-induced fluorescence and single vibronic level emission techniques. HPS (and DPS) were produced in a pulsed electric discharge jet using a precursor mixture of 3% PH_3 and 1% H_2S (or PD_3 and D_2S) in high pressure argon. The weak set of observed bands are assigned to the à ^1A^''-X˜ ^1A^' electronic transition on the basis of chemical evidence, isotope shifts and the correspondence of the vibrational frequencies, excitation energy, and band contours with predictions based on our own high level ab initio calculations. Theory predicts that the HPS bond angle decreases on electronic excitation, contrary to expectations based on Walsh diagrams.

New DMFT capabilities in CASTEP

NASA Astrophysics Data System (ADS)

Plekhanov, Evgeny; Sacksteder, Vincent; Hasnip, Phil; Probert, Matt; Clark, Stewart; Weber, Cedric; Refson, Keith

We present the first implementation of Dynamical Mean-Field Theory in UK's major ab-initio code CASTEP. This implementation: i) is modular; ii) allows great flexibility in choosing local basis set for downfolding/upfolding of self-energy; iii) permits wide choice of impurity solvers (including external solver libraries); and iv) gives the user a possibility to use several self-consistency schemes and calculate total energy and forces. We explain in details the theoretical framework used. We benchmark our implementation on several strongly-correlated insulating systems with d- and f-shells: γ-Ce and Ce2O3 by using Hubbard I and CTHYB-QMC solvers. Our results appear to be in excellent agreement with the reference data published previously in the literature. EPSRC-funded project ''Strong Correlation meets Materials Modelling: DMFT and GW in CASTEP''.

Vibrational spectroscopic investigation of p-, m- and o-nitrobenzonitrile by using Hartree-Fock and density functional theory

NASA Astrophysics Data System (ADS)

Sert, Y.; Ucun, F.

2013-08-01

In the present work, the theoretical vibrational spectra of p-, m- and o-nitrobenzonitrile molecules have been analyzed. The harmonic vibrational frequencies and geometric parameters (bond lengths and bond angles) of these molecules have been calculated using ab initio Hartree-Fock and density functional theory methods with 6-311++G(d,p) basis set by Gaussian 03 W, for the first time. Assignments of the vibrational frequencies have been performed by potential energy distribution by using VEDA 4 program. The optimized geometric parameters and harmonic vibrational frequencies have been compared with the corresponding experimental data and seen to be in a good agreement with each other. Also, the highest occupied molecular orbital and lowest unoccupied molecular orbital energies have been obtained.

A note on the electric quadrupole and higher electric moments of ozone (O3)

NASA Astrophysics Data System (ADS)

Maroulis, George

2012-02-01

We have obtained accurate ab initio and density functional theory values for the quadrupole, octopole and hexadecapole electric moments of the cyclic and open forms of ozone. Our best values have been calculated at the coupled cluster level of theory with molecule-specific basis sets. For the quadrupole moment (Θαβ/ea02) they are Θyy = -1.366 (cyclic), Θxx = -1.202, Θyy = 1.426 and Θxx = -0.223 (open). For the octopole (Ωαβγ/ea03) and hexadecapole (Φαβγδ/ea04) moments our best results are Ωzzz = 2.25, Φyyyy = 19.53 (cyclic), Ωxxz = 3.28, Ωzzz = -2.97, Φxxxx = -6.00, Φyyyy = -3.90 and Φzzzz = -3.54 (open).

An ab initio study on MgX 3- and CaX 3- superhalogen anions (X=F, Cl, Br)

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Sobczyk, Monika; Dąbkowska, Iwona; Skurski, Piotr

2003-06-01

The vertical electron detachment energies (VDEs) of twenty MX 3- (M=Mg, Ca; X=F, Cl, Br) anions were calculated at the OVGF level with the 6-311++G(3df) basis sets. The largest vertical electron binding energy was found for MgF 3- system (8.793 eV). All negatively charged species possess the VDEs that are larger than 5.9 eV and thus may be termed superhalogen anions. The strong dependence of the VDE of the MX 3- species on the ligand-central atom (M-X) distance and on the partial atomic charge localized on Mg or Ca was observed and discussed, as well as the other factors that may influence the electronic stability of such anions.

Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Liu, Xiang-Ru; Zhang, Xian-Zhou

2011-01-01

The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

Improved Potential Energy Surface of Ozone Constructed Using the Fitting by Permutationally Invariant Polynomial Function

DOE PAGES

Ayouz, Mehdi; Babikov, Dmitri

2012-01-01

New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are added tomore » the vicinity of the minimum energy path in order to improve accuracy of the fit, particularly in the region where the surface of ozone exhibits a shallow van der Waals well. New surface can be used to study formation of ozone at thermal energies and its spectroscopy near the dissociation threshold.« less

New potential energy surface for the HCS{sup +}–He system and inelastic rate coefficients

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

Dubernet, Marie-Lise; Quintas-Sánchez, Ernesto; Tuckey, Philip

2015-07-28

A new high quality potential energy surface is calculated at a coupled-cluster single double triple level with an aug-cc-pV5Z basis set for the HCS{sup +}–He system. This potential energy surface is used in low energy quantum scattering calculations to provide a set of (de)-excitation cross sections and rate coefficients among the first 20 rotational levels of HCS{sup +} by He in the range of temperature from 5 K to 100 K. The paper discusses the impact of the new ab initio potential energy surface on the cross sections at low energy and provides a comparison with the HCO{sup +}–He system.more » The HCS{sup +}–He rate coefficients for the strongest transitions differ by factors of up to 2.5 from previous rate coefficients; thus, analysis of astrophysical spectra should be reconsidered with the new rate coefficients.« less

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

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Combined electron beam imaging and ab initio modeling of T1 precipitates in Al-Li-Cu alloys

NASA Astrophysics Data System (ADS)

Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.

2011-05-01

Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T1 precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T1 structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.

Ab initio study on electronically excited states of lithium isocyanide, LiNC

NASA Astrophysics Data System (ADS)

Yasumatsu, Hisato; Jeung, Gwang-Hi

2014-01-01

The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Ab initio study of excited state electronic circular dichroism. Two prototype cases: methyl oxirane and R-(+)-1,1'-bi(2-naphthol).

PubMed

Rizzo, Antonio; Vahtras, Olav

2011-06-28

A computational approach to the calculation of excited state electronic circular dichroism (ESECD) spectra of chiral molecules is discussed. Frequency dependent quadratic response theory is employed to compute the rotatory strength for transitions between excited electronic states, by employing both a magnetic gauge dependent and a (velocity-based) magnetic gauge independent approach. Application is made to the lowest excited states of two prototypical chiral molecules, propylene oxide, also known as 1,2-epoxypropane or methyl oxirane, and R-(+)-1,1'-bi(2-naphthol), or BINOL. The dependence of the rotatory strength for transitions between the lowest three excited states of methyl oxirane upon the quality and extension of the basis set is analyzed, by employing a hierarchy of correlation consistent basis sets. Once established that basis sets of at least triple zeta quality, and at least doubly augmented, are sufficient to ensure sufficiently converged results, at least at the Hartree-Fock self-consistent field (HF-SCF) level, the rotatory strengths for all transitions between the lowest excited electronic states of methyl oxirane are computed and analyzed, employing HF-SCF, and density functional theory (DFT) electronic structure models. For DFT, both the popular B3LYP and its recently highly successful CAM-B3LYP extension are exploited. The strong dependence of the spectra upon electron correlation is highlighted. A HF-SCF and DFT study is carried out also for BINOL, a system where excited states show the typical pairing structure arising from the interaction of the two monomeric moieties, and whose conformational changes following photoexcitation were studied recently with via time-resolved CD.

Ab initio studies of the Rg–NO{sup +}(X{sup 1}Σ{sup +}) van der Waals complexes (Rg = He, Ne, Ar, Kr, and Xe)

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

Orek, Cahit; Bulut, Niyazi, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com; Kłos, Jacek, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com

2016-05-28

We used the explicitly correlated variant of the coupled clusters method with single, double, and noniterative triple excitations [CCSD(T)-F12] to compute two-dimensional potential energy surfaces of van der Waals complexes formed by rare gas atoms (Rg) and NO{sup +}(X{sup 1}Σ{sup +}) cations. We used the correlation-consistent, triple-zeta (cc-pVTZ-F12) atomic basis sets, and for Kr and Xe rare gases, we employed corresponding pseudopotential cc-pVTZ-PP-F12 atomic basis sets. These basis sets were additionally augmented with mid-bond functions. The complexes are all of skewed T-shape type with Rg atom being closer to the N-side. Using analytical representation of the potentials, we have estimatedmore » zero-point energy corrected dissociation energies from anharmonic calculations with BOUND program and also from the harmonic approximation. The binding energies increase with the polarization of the Rg atom in series from He to Xe and are 196 cm{sup −1}, 360 cm{sup −1}, 1024 cm{sup −1}, 1434 cm{sup −1}, and 2141 cm{sup −1}, respectively. Their corresponding dissociation energies are 132 cm{sup −1}, 300 cm{sup −1}, 927 cm{sup −1}, 1320 cm{sup −1}, and 1994 cm{sup −1} for the complexes with He to Xe, respectively. We find good agreement with previous theoretical and experimental results. The harmonic vibrational frequencies were calculated for the bending and stretching modes of the Rg–NO{sup +} complexes.« less

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

PubMed

Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

2008-06-01

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

The PSEUDODOJO: Training and grading a 85 element optimized norm-conserving pseudopotential table

NASA Astrophysics Data System (ADS)

van Setten, M. J.; Giantomassi, M.; Bousquet, E.; Verstraete, M. J.; Hamann, D. R.; Gonze, X.; Rignanese, G.-M.

2018-05-01

First-principles calculations in crystalline structures are often performed with a planewave basis set. To make the number of basis functions tractable two approximations are usually introduced: core electrons are frozen and the diverging Coulomb potential near the nucleus is replaced by a smoother expression. The norm-conserving pseudopotential was the first successful method to apply these approximations in a fully ab initio way. Later on, more efficient and more exact approaches were developed based on the ultrasoft and the projector augmented wave formalisms. These formalisms are however more complex and developing new features in these frameworks is usually more difficult than in the norm-conserving framework. Most of the existing tables of norm-conserving pseudopotentials, generated long ago, do not include the latest developments, are not systematically tested or are not designed primarily for high precision. In this paper, we present our PSEUDODOJO framework for developing and testing full tables of pseudopotentials, and demonstrate it with a new table generated with the ONCVPSP approach. The PSEUDODOJO is an open source project, building on the ABIPY package, for developing and systematically testing pseudopotentials. At present it contains 7 different batteries of tests executed with ABINIT, which are performed as a function of the energy cutoff. The results of these tests are then used to provide hints for the energy cutoff for actual production calculations. Our final set contains 141 pseudopotentials split into a standard and a stringent accuracy table. In total around 70,000 calculations were performed to test the pseudopotentials. The process of developing the final table led to new insights into the effects of both the core-valence partitioning and the non-linear core corrections on the stability, convergence, and transferability of norm-conserving pseudopotentials. The PSEUDODOJO hence provides a set of pseudopotentials and general purpose tools for further testing and development, focusing on highly accurate calculations and their use in the development of ab initio packages. The pseudopotential files are available on the PSEUDODOJO web-interface pseudo-dojo.org under the name NC (ONCVPSP) v0.4 in the psp8, UPF2, and PSML 1.1 formats. The webinterface also provides the inputs, which are compatible with the 3.3.1 and higher versions of ONCVPSP. All tests have been performed with ABINIT 8.4.

Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal?

PubMed

Hu, Lianrui; Chen, Kejuan; Chen, Hui

2017-10-10

Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE ‡ ) and reaction energy (ΔE R ) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE ‡ quite accurately, which is not true for the ΔE R calculations. Using highest-level CCSD(T) results of ΔE ‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.

B-spline algebraic diagrammatic construction: Application to photoionization cross-sections and high-order harmonic generation

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

Ruberti, M.; Averbukh, V.; Decleva, P.

2014-10-28

We present the first implementation of the ab initio many-body Green's function method, algebraic diagrammatic construction (ADC), in the B-spline single-electron basis. B-spline versions of the first order [ADC(1)] and second order [ADC(2)] schemes for the polarization propagator are developed and applied to the ab initio calculation of static (photoionization cross-sections) and dynamic (high-order harmonic generation spectra) quantities. We show that the cross-section features that pose a challenge for the Gaussian basis calculations, such as Cooper minima and high-energy tails, are found to be reproduced by the B-spline ADC in a very good agreement with the experiment. We also presentmore » the first dynamic B-spline ADC results, showing that the effect of the Cooper minimum on the high-order harmonic generation spectrum of Ar is correctly predicted by the time-dependent ADC calculation in the B-spline basis. The present development paves the way for the application of the B-spline ADC to both energy- and time-resolved theoretical studies of many-electron phenomena in atoms, molecules, and clusters.« less

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

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

Trevisanutto, Paolo E.; Vignale, Giovanni, E-mail: vignaleg@missouri.edu

Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basicmore » tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.« 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.

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.

Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

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

Orimoto, Yuuichi; Xie, Peng; Liu, Kai

2015-03-14

An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligiblymore » small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.« less

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.

Nuclear spin/parity dependent spectroscopy and predissociation dynamics in vOH = 2 ← 0 overtone excited Ne-H2O clusters: Theory and experiment

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-12-01

Vibrationally state selective overtone spectroscopy and state- and nuclear spin-dependent predissociation dynamics of weakly bound ortho- and para-Ne-H2O complexes (D0(ortho) = 34.66 cm-1 and D0(para) = 31.67 cm-1) are reported, based on near-infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-〉 and |02+〉) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level potential energy surface [CCSD(T)/VnZf12 (n = 3, 4)], corrected for basis set superposition error and extrapolated to the complete basis set (CBS) limit, are employed to successfully predict and assign Π-Σ, Σ-Σ, and Σ-Π infrared bands in the spectra, where Σ or Π represent approximate projections of the body-fixed H2O angular momentum along the Ne-H2O internuclear axis. IR-UV pump-probe experimental capabilities permit real-time measurements of the vibrational predissociation dynamics, which indicate facile intramolecular vibrational energy transfer from the H2O vOH = 2 overtone vibrations into the VdWs (van der Waals) dissociation coordinate on the τprediss = 15-25 ns time scale. Whereas all predicted strong transitions in the ortho-Ne-H2O complexes are readily detected and assigned, vibrationally mediated photolysis spectra for the corresponding para-Ne-H2O bands are surprisingly absent despite ab initio predictions of Q-branch intensities with S/N > 20-40. Such behavior signals the presence of highly selective nuclear spin ortho-para predissociation dynamics in the upper state, for which we offer a simple mechanism based on Ne-atom mediated intramolecular vibrational relaxation in the H2O subunit (i.e., |02±〉 → {|01±〉; v2 = 2}), which is confirmed by the ab initio energy level predictions and the nascent OH rotational (N), spin orbit (Π1/2,3/2), and lambda doublet product distributions.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Correlated ab initio calculations of spectroscopic parameters of SnO within the framework of the higher-order generalized Douglas-Kroll transformation.

PubMed

Wolf, Alexander; Reiher, Markus; Hess, Bernd Artur

2004-05-08

The first molecular calculations with the generalized Douglas-Kroll method up to fifth order in the external potential (DKH5) are presented. We study the spectroscopic parameters and electron affinity of the tin oxide molecule SnO and its anion SnO(-) applying nonrelativistic as well as relativistic calculations with higher orders of the DK approximation. In order to guarantee highly accurate results close to the basis set limit, an all-electron basis for Sn of at least quintuple-zeta quality has been constructed and optimized. All-electron CCSD(T) calculations of the potential energy curves of both SnO and SnO(-) reproduce the experimental values very well. Relative energies and valence properties are already well described with the established standard second-order approximation DKH2 and the higher-order corrections DKH3-DKH5 hardly affect these quantities. However, an accurate description of total energies and inner-shell properties requires superior relativistic schemes up to DKH5. (c) 2004 American Institute of Physics.

Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

NASA Astrophysics Data System (ADS)

Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

2015-04-01

A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.

PubMed

Jirousková, Zuzana; Vareková, Radka Svobodová; Vanek, Jakub; Koca, Jaroslav

2009-05-01

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges. 2008 Wiley Periodicals, Inc.

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.

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

NASA Technical Reports Server (NTRS)

Manchester, John I.; Shibata, Masayuki; Setlik, Robert F.; Ornstein, Rick L.; Rein, Robert

1993-01-01

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

``Phantom'' Modes in Ab Initio Tunneling Calculations: Implications for Theoretical Materials Optimization, Tunneling, and Transport

NASA Astrophysics Data System (ADS)

Barabash, Sergey V.; Pramanik, Dipankar

2015-03-01

Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

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

Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it; Tosoni, Sergio

2013-11-28

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, andmore » phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.« less

Ab initio chemical kinetic study on Cl + ClO and related reverse processes.

PubMed

Xu, Z F; Lin, M C

2010-11-04

The reaction of ClO with Cl and its related reverse processes have been studied theoretically by ab initio quantum chemical and statistical mechanical calculations. The geometric parameters of the reactants, products, and transition states are optimized by both UMPW1PW91 and unrestricted coupled-cluster single and double excitation (UCCSD) methods with the 6-311+G(3df) basis set. The potential energy surface has been further refined (with triple excitations, T) at the UCCSD(T)/6-311+G(3df) level of theory. The results show that Cl(2) and O ((3)P) can be produced by chlorine atom abstraction via a tight transition state, while ClOCl ((1)A(1)) and ClClO ((1)A') can be formed by barrierless association processes with exothermicities of 31.8 and 16.0 kcal/mol, respectively. In principle the O ((1)D) atom can be generated with a large endothermicity of 56.9 kcal/mol; on the other hand, its barrierless reaction with Cl(2) can readily form ClClO ((1)A'), which fragments rapidly to give ClO + Cl. The rate constants of both forward and reverse processes have been predicted at 150-2000 K by the microcanonical variational transition state theory (VTST)/Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The predicted rate constants are in good agreement with available experimental data within reported errors.

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.

A new analytical potential energy surface for the singlet state of He{sub 2}H{sup +}

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

Liang Jingjuan; Zhang Qinggang; Yang Chuanlu

2012-03-07

The analytic potential energy surface (APES) for the exchange reaction of HeH{sup +} (X{sup 1}{Sigma}{sup +}) + He at the lowest singlet state 1{sup 1}A{sup /} has been built. The APES is expressed as Aguado-Paniagua function based on the many-body expansion. Using the adaptive non-linear least-squares algorithm, the APES is fitted from 15 682 ab initio energy points calculated with the multireference configuration interaction calculation with a large d-aug-cc-pV5Z basis set. To testify the new APES, we calculate the integral cross sections for He + H{sup +}He (v= 0, 1, 2, j= 0) {yields} HeH{sup +}+ He by means ofmore » quasi-classical trajectory and compare them with the previous result in literature.« less

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.

Structural elucidation of antihemorrhage drug molecule Diethylammonium 2,5-dihydroxybenzene sulfonate - an insilico approach

NASA Astrophysics Data System (ADS)

Kumar, S. Anil; Bhaskar, BL

2018-02-01

Ab-initio computational study of antihemorrhage drug molecule diethylammonium 2,5-dihydroxybenzene sulfonate, popularly known as ethamsylate, has been attempted using Gaussian 09. The optimized molecular geometry has been envisaged using density functional theory method at B3LYP/6-311 basis set. Different geometrical parameters like bond lengths and bond angles were computed and compared against the experimental results available in literature. Fourier transform infrared scanning of the title molecule was performed and vibrational frequencies were also computed using Gaussian software. The presence of O-H---O hydrogen bonds between C6H5O5S- anions and N-H---O hydrogen bonds between anion and cation is evident in the computational studies also. In general, satisfactory agreement of concordance has been observed between computational and experimental results.

Ab initio multireference study of the BN molecule

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Scuseria, Gustavo E.; Taylor, Peter R.

1992-01-01

The lowest 1Sigma(+) and 3Pi states of the BN molecule are studied using multireference configuration interaction (MRCI) and averaged coupled-pair functional (ACPF) methods and large atomic natural orbital (ANO) basis sets, as well as several coupled cluster methods. Our calculations strongly support a 3Pi ground state, but the a1Sigma(+) state lies only 381 +/- 100/cm higher. The a1Sigma(+) state wave function exhibits strong multireference character and, consequently, the predictions of the perturbationally-based single-reference CCSD(T) coupled cluster method are not as reliable in this case as the multireference results. The theoretical predictions for the spectroscopic constants of BN are in good agreement with experiment for the Chi3Pi state, but strongly suggest a misassignment of the fundamental vibrational frequency for the a1Sigma(+) state.

An accurate ab initio quartic force field for ammonia

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Taylor, Peter R.

1992-01-01

The quartic force field of ammonia is computed using basis sets of spdf/spd and spdfg/spdf quality and an augmented coupled cluster method. After correcting for Fermi resonance, the computed fundamentals and nu 4 overtones agree on average to better than 3/cm with the experimental ones except for nu 2. The discrepancy for nu 2 is principally due to higher-order anharmonicity effects. The computed omega 1, omega 3, and omega 4 confirm the recent experimental determination by Lehmann and Coy (1988) but are associated with smaller error bars. The discrepancy between the computed and experimental omega 2 is far outside the expected error range, which is also attributed to higher-order anharmonicity effects not accounted for in the experimental determination. Spectroscopic constants are predicted for a number of symmetric and asymmetric top isotopomers of NH3.

First-principles studies of electronic, transport and bulk properties of pyrite FeS2

NASA Astrophysics Data System (ADS)

Banjara, Dipendra; Mbolle, Augustine; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results of ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of pyrite FeS2. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) formalism, following the Bagayoko, Zhao and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method requires successive, self consistent calculations with increasing basis sets to reach the ground state of the system under study. We report the band structure, the band gap, total and partial densities of states, effective masses, and the bulk modulus. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

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

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen

2016-03-01

On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

Ab Initio Computations and Active Thermochemical Tables Hand in Hand: Heats of Formation of Core Combustion Species.

PubMed

Klippenstein, Stephen J; Harding, Lawrence B; Ruscic, Branko

2017-09-07

The fidelity of combustion simulations is strongly dependent on the accuracy of the underlying thermochemical properties for the core combustion species that arise as intermediates and products in the chemical conversion of most fuels. High level theoretical evaluations are coupled with a wide-ranging implementation of the Active Thermochemical Tables (ATcT) approach to obtain well-validated high fidelity predictions for the 0 K heat of formation for a large set of core combustion species. In particular, high level ab initio electronic structure based predictions are obtained for a set of 348 C, N, O, and H containing species, which corresponds to essentially all core combustion species with 34 or fewer electrons. The theoretical analyses incorporate various high level corrections to base CCSD(T)/cc-pVnZ analyses (n = T or Q) using H 2 , CH 4 , H 2 O, and NH 3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zero-point energy, core-valence, relativistic, and diagonal Born-Oppenheimer effects are ordered in decreasing importance. Independent ATcT values are presented for a subset of 150 species. The accuracy of the theoretical predictions is explored through (i) examination of the magnitude of the various corrections, (ii) comparisons with other high level calculations, and (iii) through comparison with the ATcT values. The estimated 2σ uncertainties of the three methods devised here, ANL0, ANL0-F12, and ANL1, are in the range of ±1.0-1.5 kJ/mol for single-reference and moderately multireference species, for which the calculated higher order excitations are 5 kJ/mol or less. In addition to providing valuable references for combustion simulations, the subsequent inclusion of the current theoretical results into the ATcT thermochemical network is expected to significantly improve the thermochemical knowledge base for less-well studied species.

Ab Initio Computations and Active Thermochemical Tables Hand in Hand: Heats of Formation of Core Combustion Species

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

Klippenstein, Stephen J.; Harding, Lawrence B.; Ruscic, Branko

Here, the fidelity of combustion simulations is strongly dependent on the accuracy of the underlying thermochemical properties for the core combustion species that arise as intermediates and products in the chemical conversion of most fuels. High level theoretical evaluations are coupled with a wide-ranging implementation of the Active Thermochemical Tables (ATcT) approach to obtain well-validated high fidelity predictions for the 0 K heat of formation for a large set of core combustion species. In particular, high level ab initio electronic structure based predictions are obtained for a set of 348 C, N, O, and H containing species, which corresponds tomore » essentially all core combustion species with 34 or fewer electrons. The theoretical analyses incorporate various high level corrections to base CCSD(T)/cc-pVnZ analyses (n = T or Q) using H 2, CH 4, H 2O, and NH 3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zeropoint energy, core–valence, relativistic, and diagonal Born–Oppenheimer effects are ordered in decreasing importance. Independent ATcT values are presented for a subset of 150 species. The accuracy of the theoretical predictions is explored through (i) examination of the magnitude of the various corrections, (ii) comparisons with other high level calculations, and (iii) through comparison with the ATcT values. The estimated 2σ uncertainties of the three methods devised here, ANL0, ANL0-F12, and ANL1, are in the range of ±1.0–1.5 kJ/mol for single-reference and moderately multireference species, for which the calculated higher order excitations are 5 kJ/mol or less. In addition to providing valuable references for combustion simulations, the subsequent inclusion of the current theoretical results into the ATcT thermochemical network is expected to significantly improve the thermochemical knowledge base for less-well studied species.« less

Ab Initio Computations and Active Thermochemical Tables Hand in Hand: Heats of Formation of Core Combustion Species

DOE PAGES

Klippenstein, Stephen J.; Harding, Lawrence B.; Ruscic, Branko

2017-07-31

Here, the fidelity of combustion simulations is strongly dependent on the accuracy of the underlying thermochemical properties for the core combustion species that arise as intermediates and products in the chemical conversion of most fuels. High level theoretical evaluations are coupled with a wide-ranging implementation of the Active Thermochemical Tables (ATcT) approach to obtain well-validated high fidelity predictions for the 0 K heat of formation for a large set of core combustion species. In particular, high level ab initio electronic structure based predictions are obtained for a set of 348 C, N, O, and H containing species, which corresponds tomore » essentially all core combustion species with 34 or fewer electrons. The theoretical analyses incorporate various high level corrections to base CCSD(T)/cc-pVnZ analyses (n = T or Q) using H 2, CH 4, H 2O, and NH 3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zeropoint energy, core–valence, relativistic, and diagonal Born–Oppenheimer effects are ordered in decreasing importance. Independent ATcT values are presented for a subset of 150 species. The accuracy of the theoretical predictions is explored through (i) examination of the magnitude of the various corrections, (ii) comparisons with other high level calculations, and (iii) through comparison with the ATcT values. The estimated 2σ uncertainties of the three methods devised here, ANL0, ANL0-F12, and ANL1, are in the range of ±1.0–1.5 kJ/mol for single-reference and moderately multireference species, for which the calculated higher order excitations are 5 kJ/mol or less. In addition to providing valuable references for combustion simulations, the subsequent inclusion of the current theoretical results into the ATcT thermochemical network is expected to significantly improve the thermochemical knowledge base for less-well studied species.« less

Ab initio Eliashberg Theory: Making Genuine Predictions of Superconducting Features

NASA Astrophysics Data System (ADS)

Sanna, Antonio; Flores-Livas, José A.; Davydov, Arkadiy; Profeta, Gianni; Dewhurst, Kay; Sharma, Sangeeta; Gross, E. K. U.

2018-04-01

We present an application of Eliashberg theory of superconductivity to study a set of novel superconducting systems with a wide range of structural and chemical properties. The set includes three intercalated group-IV honeycomb layered structures, SH3 at 200 GPa (the superconductor with the highest measured critical temperature), the similar system SeH3 at 150 GPa, and a lithium doped mono-layer of black phosphorus. The theoretical approach we adopt is a recently developed, fully ab initio Eliashberg approach that takes into account the Coulomb interaction in a full energy-resolved fashion avoiding any free parameters like μ*. This method provides reasonable estimations of superconducting properties, including TC and the excitation spectra of superconductors.

Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

An ab initio study of the low-lying doublet states of AgO and AgS

NASA Astrophysics Data System (ADS)

Bauschlicher, Charles W.; Partridge, Harry; Langhoff, Stephen R.

1990-11-01

Spectroscopic constants ( Do, re, μ e, Te) are determined for the doublet states of AgO and AgS below ≈ 30000 cm -1. valence basis sets are employed in conjunction with relativistic effective core potentials (RECPs). Electron correlation is included using the modified coupled-pair functional (MCPF) and multireferenceconfiguration interaction (MRCI) methods. The A 2Σ +-X 2Π band system is found to occur in the near infrared ( ≈ 9000 cm -1) and to be relatively weak with a radiative lifetime of 900 μs for A 2Σ + (ν = 0). The weakly bound C 2Π state (our notation), the upper state of the blue system, is found to require high levels of theoretical treatment to determine a quantitatively accurate potential. The red system is assigned as a transition from the C 2Π state to the previously unobserved A 2Σ + state. Several additional transitions are identified that should be detectable experiment A more limited study is performed for the vertical excitation spectrum of AgS. In addition, a detailed all-electron study of the X 2Π and A 2Σ + states of AgO is carried out using large atomic natural orbital (ANO) basis sets. Our best calculated Do value for AgO is significantly less than the experimental value, which suggests that there may be some systematic error in the experimental determination.

Synthesis and structural study on (1E,2E,1'E,2'E)-3,3'-bis[(4-bromophenyl)-3,3'-(4-methy-1,2-phenylene diimine)] acetaldehyde dioxime: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Topal, T.; Kart, H. H.; Tunay Taşlı, P.; Karapınar, E.

2015-06-01

Tetradentate (1E,2E,1'E,2'E)-3,3'-bis[(4-bromophenyl)-3,3'-(4-methy-1,2-phenylene diimine)] acetaldehyde dioxime which possess N4 donor sets derived from the condensation of isonitroso- p-bromoacetophenone and 3,4-diaminotoluene are synthesized and characterized. The characterization of tetradentate Schiff base ligand has been deduced from LC-MS, FTIR, 13C and 1H NMR spectra and elemental analysis. Furthermore, the molecular geometry, infrared and NMR spectra of the title molecule in the ground state have been calculated by using the quantum chemical computational methods such as density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the 6-31G(d) and 6-311G(d) basis sets. The computed bond lengths and bond angles by using the both methods show the good agreement with each other. Moreover, the vibrational frequencies have been calculated and the scaled values have been compared with the experimental FTIR spectroscopic data. Assignments of the vibrational modes are made on the basis of potential energy distribution (PED) calculated from by using VEDA program. The correlations between the observed and calculated frequencies are in good agreement with each other as well as the correlation of the NMR data.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics

NASA Astrophysics Data System (ADS)

Ünal, Aslı; Bozkaya, Uǧur

2018-03-01

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

PubMed

Ünal, Aslı; Bozkaya, Uğur

2018-03-28

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol -1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol -1 . Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol -1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

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.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Molecular Symmetry in Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Madhavan, P. V.; Written, J. L.

1987-05-01

A scheme is presented for the construction of the Fock matrix in LCAO-SCF calculations and for the transformation of basis integrals to LCAO-MO integrals that can utilize several symmetry unique lists of integrals corresponding to different symmetry groups. The algorithm is fully compatible with vector processing machines and is especially suited for parallel processing machines.

Calculations of total electron-impact ionization cross sections for Fluoroketone C5F10O and Fluoronitrile C4F7N using modified Deutsch-Märk formula

NASA Astrophysics Data System (ADS)

Xiong, Jiayu; Li, Xingwen; Wu, Jian; Guo, Xiaoxue; Zhao, Hu

2017-11-01

Both fluoroketone C5F10O and fluoronitrile C4F7N are promising substitute gases for SF6. The electron-impact ionization cross sections for these two gases are calculated using the Deutsch-Märk (DM) formula and its modified method. The necessary molecular geometry optimization and electron population were determined by ab initio calculation, which was performed with quantum chemistry code. The level of calculation, including the theoretical method and basis-set, are carefully determined. To eliminate the drawbacks of the DM formula, a modified DM formula is set in this paper. The modified DM formula, of which the weighting factors are changed, has a better agreement with the experimental data on both the peak and shape of the cross-section curves. The results calculated by DM formula and modified DM formula are given as references to fill in gaps in further research into C5F10O and C4F7N.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

An efficient method for quantum transport simulations in the time domain

NASA Astrophysics Data System (ADS)

Wang, Y.; Yam, C.-Y.; Frauenheim, Th.; Chen, G. H.; Niehaus, T. A.

2011-11-01

An approximate method based on adiabatic time dependent density functional theory (TDDFT) is presented, that allows for the description of the electron dynamics in nanoscale junctions under arbitrary time dependent external potentials. The density matrix of the device region is propagated according to the Liouville-von Neumann equation. The semi-infinite leads give rise to dissipative terms in the equation of motion which are calculated from first principles in the wide band limit. In contrast to earlier ab initio implementations of this formalism, the Hamiltonian is here approximated in the spirit of the density functional based tight-binding (DFTB) method. Results are presented for two prototypical molecular devices and compared to full TDDFT calculations. The temporal profile of the current traces is qualitatively well captured by the DFTB scheme. Steady state currents show considerable variations, both in comparison of approximate and full TDDFT, but also among TDDFT calculations with different basis sets.

An adiabatic spectroscopic investigation of the CsRb system in ground and numerous excited states

NASA Astrophysics Data System (ADS)

Souissi, Hanen; Jellali, Soulef; Maha, Chaieb; Habli, Héla; Oujia, Brahim; Gadéa, Florent Xavier

2017-10-01

Via ab-initio approximations, we investigate the electronic and structural features of the CsRb molecule. Adiabatic potential energy curves of 261,3Σ+, 181,3Π and 61,3Δ electronic states with their derived spectroscopic constants as well as vibrational levels spacing have been carried out and well explained. Our approach is founded on an Effective Core Potential (ECP) describing the valence electrons of the system. Using a large Gaussian basis set, the full valence Configuration Interaction can be applied easily on the two-effective valence electrons of the CsRb system. Furthermore, a detailed analysis of the electric dipolar properties has been made through the investigation of both permanent and transition dipole moments (PDM and TDM). It is significant that the ionic character connected with electron transfer that is linked to Cs+ Rb- state has been clearly illustrated in the adiabatic permanent dipole moment.

Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Çırak, Çağrı; Ucun, Fatih

2013-04-01

In the present study, the experimental and theoretical harmonic and anharmonic vibrational frequencies of 4-chloro-3-nitrobenzonitrile were investigated. The experimental FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF), density functional B3LYP and M06-2X methods with 6-311++G(d,p) basis set by Gaussian 09 W program, for the first time. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.

Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method

NASA Astrophysics Data System (ADS)

Diwaker

2014-07-01

The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the 1H and 13C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods.

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.

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

NASA Technical Reports Server (NTRS)

Lindh, Roland; Rice, Julia E.; Lee, Timothy J.

1991-01-01

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

Excitonic structure of the optical conductivity in MoS2 monolayers

NASA Astrophysics Data System (ADS)

Ridolfi, Emilia; Lewenkopf, Caio H.; Pereira, Vitor M.

2018-05-01

We investigate the excitonic spectrum of MoS2 monolayers and calculate its optical absorption properties over a wide range of energies. Our approach takes into account the anomalous screening in two dimensions and the presence of a substrate, both cast by a suitable effective Keldysh potential. We solve the Bethe-Salpeter equation using as a basis a Slater-Koster tight-binding model parameterized to fit the ab initio MoS2 band structure calculations. The resulting optical conductivity is in good quantitative agreement with existing measurements up to ultraviolet energies. We establish that the electronic contributions to the C excitons arise not from states at the Γ point, but from a set of k points over extended portions of the Brillouin zone. Our results reinforce the advantages of approaches based on effective models to expeditiously explore the properties and tunability of excitons in TMD systems.

Ab initio characterization of ClOOH - Implications for atmospheric chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rendell, Alistair P.

1993-01-01

The equilibrium structure, dipole moment, harmonic vibrational frequencies, and infrared intensities of ClOOH are determined using the CCSD(T) (singles and doubles coupled-cluster theory plus a perturbational estimate of the effects of connected triple excitations) electronic structure method in conjunction with a TZ2P (triple xi plus double polarization) basis set. The heat of formation of CIOOH is determined (using two different isodesmic reactions) to be +1.5 +/- 1 kcal/mol at 0 K or +0.2 +/- 1 kcal/mol at 298.15 K. Using the computed heat of formation, we examined the stability of ClOOH with respect to the ClO + OH, ClOO + H, and HOO + Cl dissociation limits. Since ClOOH is found to be quite stable, it is argued that the chemistry of ClOOH should be included in any accurate modeling of the stratosphere.

An ab initio study on BeX 3- superhalogen anions (X = F, Cl, Br)

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Skurski, Piotr

2002-06-01

The vertical electron detachment energies (VDE) of 10 BeX 3- (X = F, Cl, Br) anions were calculated at the outer valence Green function (OVGF) level with the 6-311++G(3df) basis sets. The largest vertical electron binding energy was found for BeF 3- system (7.63 eV). All negatively charged species possess the vertical electron detachment energies that are larger than 5.5 eV and thus may be termed superhalogen anions. The strong dependence of the VDE of the BeX 3- species on the ligand-central atom (Be-X) distance and on the partial atomic charge localized on Be was observed and discussed, as well as the other factors that may influence the electronic stability of such anions. In addition, the usefulness of the various theoretical treatments for estimating the VDEs of superhalogen anions was tested and analyzed.

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

Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

NASA Astrophysics Data System (ADS)

Tan, Yaohua P.; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

2015-08-01

Empirical tight-binding (ETB) methods are widely used in atomistic device simulations. Traditional ways of generating the ETB parameters rely on direct fitting to bulk experiments or theoretical electronic bands. However, ETB calculations based on existing parameters lead to unphysical results in ultrasmall structures like the As-terminated GaAs ultrathin bodies (UTBs). In this work, it is shown that more transferable ETB parameters with a short interaction range can be obtained by a process of mapping ab initio bands and wave functions to ETB models. This process enables the calibration of not only the ETB energy bands but also the ETB wave functions with corresponding ab initio calculations. Based on the mapping process, ETB models of Si and GaAs are parameterized with respect to hybrid functional calculations. Highly localized ETB basis functions are obtained. Both the ETB energy bands and wave functions with subatomic resolution of UTBs show good agreement with the corresponding hybrid functional calculations. The ETB methods can then be used to explain realistically extended devices in nonequilibrium that cannot be tackled with ab initio methods.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

NASA Technical Reports Server (NTRS)

Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

2000-01-01

The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations.

PubMed

Suhasini, M; Sailatha, E; Gunasekaran, S; Ramkumaar, G R

2015-04-15

A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the (13)C and (1)H NMR chemical shifts of Carbamazepine. Copyright © 2015 Elsevier B.V. All rights reserved.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

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

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

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.

The spectroscopic (FTIR, FT-IR gas phase and FT-Raman), first order hyperpolarizabilities, NMR analysis of 2,4-dichloroaniline by ab initio HF and density functional methods.

PubMed

Sundaraganesan, N; Karpagam, J; Sebastian, S; Cornard, J P

2009-07-01

In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 2,4-dichloroaniline (2,4-DCA) were studied. The Fourier transform infrared (gas phase) and Fourier transform Raman spectra of 2,4-DCA were recorded. The molecular geometry and vibrational frequencies of 2,4-DCA in the ground state were calculated by using the Hartree-Fock (HF) and density functional (DF) methods (BLYP, B3LYP and SVWN) with 6-31G(d,p) as basis set. Comparison of the observed fundamental vibrational frequencies of 2,4-DCA with calculated results by HF and density functional methods indicates that BLYP is superior to other methods for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The electric dipole moment (micro) and the first hyperpolarizability (beta) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4-DCA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Natural atomic charges of 2,4-DCA and 4-chloroaniline was calculated and compared. The isotropic chemical shift computed by (13)C NMR analyses also shows good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.

A new ab initio potential energy surface for the collisional excitation of HCN by para- and ortho-H{sub 2}

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

Denis-Alpizar, Otoniel, E-mail: otonieldenisalpizar@gmail.com; Departamento de Física, Universidad de Matanzas, Matanzas 40100; Kalugina, Yulia

We present a new four-dimensional potential energy surface for the collisional excitation of HCN by H{sub 2}. Ab initio calculations of the HCN–H{sub 2} van der Waals complex, considering both molecules as rigid rotors, were carried out at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12a] level of theory using an augmented correlation-consistent triple zeta (aVTZ) basis set. The equilibrium structure is linear HCN–H{sub 2} with the nitrogen pointing towards H{sub 2} at an intermolecular separation of 7.20 a{sub 0}. The corresponding well depth is −195.20 cm{sup −1}. A secondary minimum of −183.59 cm{sup −1}more » was found for a T-shape configuration with the H of HCN pointing to the center of mass of H{sub 2}. We also determine the rovibrational energy levels of the HCN–para-H{sub 2} and HCN–ortho-H{sub 2} complexes. The calculated dissociation energies for the para and ortho complexes are 37.79 cm{sup −1} and 60.26 cm{sup −1}, respectively. The calculated ro-vibrational transitions in the HCN–H{sub 2} complex are found to agree by more than 0.5% with the available experimental data, confirming the accuracy of the potential energy surface.« less

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

PubMed

Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

2010-03-01

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

The 129Xe nuclear shielding surfaces for Xe interacting with linear molecules CO2, N2, and CO

NASA Astrophysics Data System (ADS)

de Dios, Angel C.; Jameson, Cynthia J.

1997-09-01

We have calculated the intermolecular nuclear magnetic shielding surfaces for 129Xe in the systems Xe-CO2, Xe-N2, and Xe-CO using a gauge-invariant ab initio method at the coupled Hartree-Fock level with gauge-including atomic orbitals (GIAO). Implementation of a large basis set (240 basis functions) on the Xe gives very small counterpoise corrections which indicates that the basis set superposition errors in the calculated shielding values are negligible. These are the first intermolecular shielding surfaces for Xe-molecule systems. The surfaces are highly anisotropic and can be described adequately by a sum of inverse even powers of the distance with explicit angle dependence in the coefficients expressed by Legendre polynomials P2n(cos θ), n=0-3, for Xe-CO2 and Xe-N2. The Xe-CO shielding surface is well described by a similar functional form, except that Pn(cos θ), n=0-4 were used. When averaged over the anisotropic potential function these shielding surfaces provide the second virial coefficient of the nuclear magnetic resonance (NMR) chemical shift observed in gas mixtures. The energies from the self-consistent field (SCF) calculations were used to construct potential surfaces, using a damped dispersion form. These potential functions are compared with existing potentials in their predictions of the second virial coefficients of NMR shielding, the pressure virial coefficients, the density coefficient of the mean-square torque from infrared absorption, and the rotational constants and other average properties of the van der Waals complexes. Average properties of the van der Waals complexes were obtained by quantum diffusion Monte Carlo solutions of the vibrational motion using the various potentials and compared with experiment.

Accurate ab initio calculations which demonstrate a 3 Pi u ground state for Al2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.; Taylor, Peter R.; Walch, Stephen P.

1986-01-01

The spectroscopic parameters and separations between the three low-lying X 3 Pi u, A 3 Sigma g -, and a 1 Sigma g + states of Al2 are studied as a function of both the one-particle and n-particle basis set. Approximate correlation treatments are calibrated against full Cl calculations correlating the six valence electrons in a double-zeta plus two d-function basis set. Since the CASSCF/MRCI 3 Pi u to 3 Sigma g - separation is in excellent agreement wtih the FCI value, the MRCI calculations were carried out in an extended (20s13p6d4f)/(6s5p3d2f) gaussian basis. Including a small correction for relativistic effects, the best estimate is that 3 Sigma g - state lies 174/cm above the 3 Pi u ground state. The 1 Sigma g + state lies at least 2000/cm higher in energy. At the CPF level, inclusion of 2s and 2p correlation has little effect on D sub e, reduces T sub e by only 26/cm, and shortens the bond lengths by about 0.02 a sub o. Further strong support for a 3 Pi u ground state comes from the experimental absorption spectra, since both observed transitions can be convincingly assigned as 3 Pi u yields 3 Pi g. The (2) 3 Pi g state is observed to be sensitive to the level of correlation treatment, and to have its minimum shifted to shorter rho values, such that the strongest experimental absorption peak probably corresponds to the 0 yields 2 transition.

Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

PubMed

France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

2016-03-14

In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

A Classical Trajectory Study of the Dissociation and Isomerization of C2H5

DTIC Science & Technology

2013-01-01

modifications are possible but would be sensible only in the context of systematic ab initio calculations to provide the basis for such changes. As the... Ciudad , T.; Ramírez, R.; Schulte, J.; Böhm, M. C. Anharmonic Effects on the Structural and Vibrational Properties of the Ethyl Radical: A Path Integral

Complexes and saddle point structures, vibrational frequencies and relative energies of intermediates for CH2Br + HBr «-» CH3Br + Br

NASA Astrophysics Data System (ADS)

Espinosa-Garcia, J.

Ab initio molecular orbital theory was used to study parts of the reaction between the CH2Br radical and the HBr molecule, and two possibilities were analysed: attack on the hydrogen and attack on the bromine of the HBr molecule. Optimized geometries and harmonic vibrational frequencies were calculated at the second-order Moller-Plesset perturbation theory levels, and comparison with available experimental data was favourable. Then single-point calculations were performed at several higher levels of calculation. In the attack on the hydrogen of HBr, two stationary points were located on the direct hydrogen abstraction reaction path: a very weak hydrogen bonded complex of reactants, C···HBr, close to the reactants, followed by the saddle point (SP). The effects of level of calculation (method + basis set), spin projection, zeropoint energy, thermal corrections (298K), spin-orbit coupling and basis set superposition error (BSSE) on the energy changes were analysed. Taking the reaction enthalpy (298K) as reference, agreement with experiment was obtained only when high correlation energy and large basis sets were used. It was concluded that at room temperature (i.e., with zero-point energy and thermal corrections), when the BSSE was included, the complex disappears and the activation enthalpy (298K) ranges from 0.8kcal mol-1 to 1.4kcal mol-1 above the reactants, depending on the level of calculation. It was concluded also that this result is the balance of a complicated interplay of many factors, which are affected by uncertainties in the theoretical calculations. Finally, another possible complex (X complex), which involves the alkyl radical being attracted to the halogen end of HBr (C···BrH), was explored also. It was concluded that this X complex does not exist at room temperature.

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.

The V + I defects in diamond: An ab initio investigation of the electronic structure, of the Raman and IR spectra, and of their possible recombination.

PubMed

Salustro, S; Nöel, Y; Zicovich-Wilson, C M; Olivero, P; Dovesi, R

2016-11-14

The double defect in diamond, vacancy (V) plus 〈100〉 self-split-interstitial (V+I), is investigated at the ab initio quantum mechanical level, by considering the vicinal case VI 1 (V is one of the first neighbors of one of the two C atoms constituting the I defect) and the two possible "second neighbors" cases, VI 2 D , VI 2 S , in which a carbon atom is a first neighbor of both V and I. The case in which the two defects are at a larger distance is simulated by considering the two isolated defects separately (VI ∞ ). A 6-21G local Gaussian-type basis set and the B3LYP hybrid functional are used for most of the calculations; richer basis sets and other functionals (a global hybrid as PBE0, a range-separated hybrid as HSE06, LDA, PBE, and Hartree-Fock) have also been used for comparison. With this computational approach we evaluate the energy difference between the various spin states, the location of the corresponding bands in the energy gap of pristine diamond, as well as the defect formation energy of the four defects. The path for the recombination of V and I is explored for the vicinal case, by using the distinguished reaction coordinate strategy. A barrier as high as 0.75 eV is found with B3LYP between VI 1 and the perfect diamond recombined structure; when other hybrids are used, as PBE0 or HSE06, the barrier increases up to 1.01 eV (pure density functional theory produces lower barriers: 0.62 and 0.67 for PBE and LDA, respectively). Such a barrier is lower than the one estimated in a very indirect way through experimental data, ranging from 1.3 to 1.7 eV. It confirms however the evidence of the extremely low recombination rate also at high temperature. The Raman (and IR) spectra of the various defects are generated, which permit one to unambiguously attribute to these defects (thanks also to the graphical animation of the modes) many of the peaks observed in damaged diamond above the dominant peak of perfect bulk. For the residual non-attributed peaks, more complicated aggregations of defects should be explored.

Computational study on hydroxybenzotriazoles as reagents for ester hydrolysis.

PubMed

Kumar, V Praveen; Ganguly, Bishwajit; Bhattacharya, Santanu

2004-12-10

1-Hydroxybenzotriazole (1) and several of its derivatives (2-5) demonstrate potent esterolytic activity toward activated esters such as p-nitrophenyl diphenyl phosphate (PNPDPP) and p-nitrophenyl hexanoate (PNPH) in cationic micelles at pH 8.2 and 25 degrees C. The deprotonated anionic forms of such reagents act as reactive species in the hydrolysis of ester. To rationalize the origin of their nucleophilic character, a detailed ab initio/DFT computational study has been performed on 1-5 along with additional hydroxybenzotriazole derivatives (6-13). The geometries of 1-hydroxybenzotriazoles (1-13) and their corresponding bases are discussed in detail. All calculations were carried out using different methods, i.e., restricted Hartree-Fock (RHF) and hybrid ab initio/DFT (B3LYP) using 6-31G and 6-31+G basis sets. Free energy of protonation ("fep") of the 1-hydroxybenzotriazoles (1-13), free energy of solvation DeltaG(aq), and the corresponding pK(a) values have been calculated. Solvation-free energies were calculated using density functional theory and the polarizable continuum model. In addition, to examine the reliability of calculated fep, benzaldehyde oxime (14) and 2-methyl propionaldehyde oxime (15) have been computed as reference systems using different methods and basis sets, the experimental feps of which are known. Our experimental finding shows that the compound 4 is the most effective catalyst for the hydrolytic cleavages of PNPDPP and PNPH. This has been predicted from our calculated fep, pK(a), and natural charge analysis results as well. In general, the introduction of electron-withdrawing substituents on 1-hydroxybenzotriazoles facilitates the lowering of pK(a) and fep. As the pK(a) values are lowered, a greater percentage of such hydroxybenzotriazoles remain in their deprotonated, anionic forms at pH 8.2. Since the anionic forms are nucleophilic, pK(a) lowering should enhance their ester cleaving capacity. However, such substitution also decreases the charge density on the catalytically active oxido atom (O(7)). Taking these two factors together, the derivatives are only modestly better nucleophiles in comparison to the parent 1-hydroxybenzotriazole. Interestingly, the introduction of electron-donating groups does not significantly enhance the charge accumulation on the oxido atom (O(7)) of 1-hydroxybenzotriazoles.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Ab initio and density functional computations of the vibrational spectrum, molecular geometry and some molecular properties of the antidepressant drug sertraline (Zoloft) hydrochloride

NASA Astrophysics Data System (ADS)

Sagdinc, Seda; Kandemirli, Fatma; Bayari, Sevgi Haman

2007-02-01

Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.

Raman scattering tensors in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Tsuboi, Masamichi; Kumakura, Akiko; Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ushizawa, Koichi; Ueda, Toyotoshi

1997-03-01

Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.

An ab-initio study of the relative stability of the ggg and the gtg conformer in hexane

NASA Astrophysics Data System (ADS)

Koglin, Eckhard; Meier, Robert J.

1999-10-01

Earlier ab-initio work suggested, on the basis of MP2 level calculations, that the hexane ggg conformer is more stable than the gtg conformer. Because this is unexpected and if true might have a significant impact on force field parametrisations, we have applied Hartree-Fock and post-HF methods to evaluate the relative stability of these conformers. We find that at levels higher than MP2 the gtg conformer is more stable than the ggg conformer, in agreement with the conventional idea that each additional gauche bond causes a further decrease in stability of the conformer. DFT methods were also applied, but although DFT methods including gradient corrections show correct qualitative behaviour, quantitatively the relative energies are far off compared to the post-HF results.

Theoretical calculations of homogeneous catalysis in the gas phase: elimination kinetics of 2,2-dimethoxypropane in the presence of HCl, F3CCOOH and CH3COOH

NASA Astrophysics Data System (ADS)

Guerra, Raul J.; Lezama, Jesus; Cordova-Sintjago, Tania; Chuchani, Gabriel

2018-05-01

The mechanisms of gas-phase elimination kinetics of 2,2-dimethoxypropane in the presence of hydrogen chloride, trifluoroacetic acid and acetic acid were studied using Moller Plesset, ab initio combined method Complete Basis Set (CBS)-QB3 and various density functional theory methods with 6-311G(d,p) and 6-311++G(d,p) basis sets. The M06-2X/6-311++G(d,p) method provided reasonable agreement with the experimental enthalpy and energy of activation. Formation of 2-methoxypropene and methanol products occurs through six-membered cyclic ring transition state (TS) structure. The TS was characterised by single imaginary frequency, and confirmed through intrinsic reaction coordinate (IRC) calculations. The IRC calculations suggest the development of a van der Waal complex between the 2, 2-dimethoxy propane and the acid catalyst, leading to the TS formation. The process of decomposition in the absence of the acid catalyst requires much higher temperature with an energy of activation above 200 kJ/mol. This fact appears to be a consequence of a four-membered cyclic TS-type of mechanism in the non-catalysed reaction. Structural parameters, analyses of natural bond orbital charges and bond orders of the acid-catalysed elimination reactions in this study suggest that the polarisation of the C-O bond, in the direction Cδ+-Oδ-, is rate-determining in the TS. These reactions are non-synchronous concerted polar in nature.

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

Nonadiabatic dynamics on the two coupled electronic PESs: the H+ + O2 system.

PubMed

Xavier, F George D

2010-09-30

Multistate adiabatic and diabatic PESs were computed for the H+ + O2 collision system in Jacobi coordinates, (R,r,γ) using the cc-pVTZ basis set and the ic-MRCI level of theory. In addition, all possible interaction potentials and nonadiabatic coupling matrix elements among those different electronic states were also computed. Comparisons with earlier computed interaction potentials were made wherever possible, and the differences between them is attributed to the multistate diabatization and the chosen level of theory and basis set. Focusing our attention on the ground-state (GS) and the first excited-state (ES) PES, quantum dynamics were performed using the 2 × 2 diabatic potential submatrix obtained from the multistate (four) diabatic potential matrix within the VCC-RIOSA scheme at two experimentally reported collision energies, E(cm) = 9.5 and 23 eV. The scattering quantities were computed for two experimentally observed collision processes, namely, the inelastic vibrational excitation (IVE), H+ + O2 (X3Σg(−),v = 0) → H+ + O2 (X3Σg(−),v′), and the vibrational charge transfer (VCT), H+ + O2 (X3Σg(−),v = 0) → H (2S) + O (X2Πg,v′′). Comparisons were made with experimental results and found an overall improvement relative to the earlier computed results, and the discrepancies, if any, could be brought down to minimum by further modification in employed ab initio PESs and the interaction potential.

Spectroscopic studies (FTIR, FT-Raman and UV-Visible), normal coordinate analysis, NBO analysis, first order hyper polarizability, HOMO and LUMO analysis of (1R)-N-(Prop-2-yn-1-yl)-2,3-dihydro-1H-inden-1-amine molecule by ab initio HF and density functional methods.

PubMed

Muthu, S; Ramachandran, G

2014-01-01

The Fourier transform infrared (FT-IR) and FT-Raman of (1R)-N-(Prop-2-yn-1-yl)-2,3-dihydro-1H-inden-1-amine (1RNPDA) were recorded in the regions 4000-400 cm(-1) and 4000-100 cm(-1) respectively. A complete assignment and analysis of the fundamental vibrational modes of the molecule were carried out. The observed fundamental modes have been compared with the harmonic vibrational frequencies computed using HF method by employing 6-31G(d,p) basis set and DFT(B3LYP) method by employing 6-31G(d,p) basis set. The vibrational studies were interpreted in terms of Potential Energy Distribution (PED). The complete vibrational frequency assignments were made by Normal Co-ordinate Analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The first order hyper polarizability (β0) of this molecular system and related properties (α, μ, and Δα) are calculated using B3LYP/6-31G(d,p) method based on the finite-field approach. The thermodynamic functions of the title compound were also performed at the above methods and basis set. A detailed interpretation of the infrared and Raman spectra of 1RNPDA is reported. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated using the GIAO method confirms with the experimental values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using Natural Bond Orbital (NBO) analysis. UV-vis spectrum of the compound was recorded and electronic properties such as excitation energies, oscillator strength and wavelength were performed by TD-DFT/B3LYP using 6-31G(d,p) basis set. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The observed and calculated wave numbers are formed to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

Ab initio calculations of optical properties of silver clusters: cross-over from molecular to nanoscale behavior

NASA Astrophysics Data System (ADS)

Titantah, John T.; Karttunen, Mikko

2016-05-01

Electronic and optical properties of silver clusters were calculated using two different ab initio approaches: (1) based on all-electron full-potential linearized-augmented plane-wave method and (2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter ~1.7 nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag147, gives way to a dominant plasmon peak localized at wavelengths 350 nm ≤ λ ≤ 600 nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters.

A Model for Predicting Thermoelectric Properties of Bi2Te3

NASA Technical Reports Server (NTRS)

Lee, Seungwon; VonAllmen, Paul

2009-01-01

A parameterized orthogonal tight-binding mathematical model of the quantum electronic structure of the bismuth telluride molecule has been devised for use in conjunction with a semiclassical transport model in predicting the thermoelectric properties of doped bismuth telluride. This model is expected to be useful in designing and analyzing Bi2Te3 thermoelectric devices, including ones that contain such nano - structures as quantum wells and wires. In addition, the understanding gained in the use of this model can be expected to lead to the development of better models that could be useful for developing other thermoelectric materials and devices having enhanced thermoelectric properties. Bi2Te3 is one of the best bulk thermoelectric materials and is widely used in commercial thermoelectric devices. Most prior theoretical studies of the thermoelectric properties of Bi2Te3 have involved either continuum models or ab-initio models. Continuum models are computationally very efficient, but do not account for atomic-level effects. Ab-initio models are atomistic by definition, but do not scale well in that computation times increase excessively with increasing numbers of atoms. The present tight-binding model bridges the gap between the well-scalable but non-atomistic continuum models and the atomistic but poorly scalable ab-initio models: The present tight-binding model is atomistic, yet also computationally efficient because of the reduced (relative to an ab-initio model) number of basis orbitals and flexible parameterization of the Hamiltonian.

Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding.

PubMed

Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha

2004-09-22

Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.

Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution.

PubMed

Alkorta, Ibon; Popelier, Paul L A

2015-02-02

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

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

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

DOE PAGES

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.; ...

2017-10-17

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Investigation of the highest bound ro-vibrational states of H+ 3, DH+ 2, HD+ 2, D+ 3, and T+ 3: use of a non-direct product basis to compute the highest allowed J > 0 states

NASA Astrophysics Data System (ADS)

Jaquet, Ralph

2013-09-01

A Lanczos algorithm with a non-direct product basis was used to compute energy levels of H+ 3, H2D+, D2H+, D+ 3, and T+ 3 with J values as large as 46, 53, 66, 66, and 81. The energy levels are based on a modified potential surface of M. Pavanello et al. that is better adapted to the ab initio energies near the dissociation limit.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Linear electro-optic effect in semiconductors: Ab initio description of the electronic contribution

NASA Astrophysics Data System (ADS)

Prussel, Lucie; Véniard, Valérie

2018-05-01

We propose an ab initio framework to derive the electronic part of the second-order susceptibility tensor for the electro-optic effect in bulk semiconductors. We find a general expression for χ(2 ) evaluated within time-dependent density-functional theory, including explicitly the band-gap corrections at the level of the scissors approximation. Excitonic effects are accounted for, on the basis of a simple scalar approximation. We apply our formalism to the computation of the electro-optic susceptibilities for several semiconductors, such as GaAs, GaN, and SiC. Taking into account the ionic contribution according to the Faust-Henry coefficient, we obtain a good agreement with experimental results. Finally, using different types of strain to break centrosymmetry, we show that high electro-optic coefficients can be obtained in bulk silicon for a large range of frequencies.

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

Unified theory of quantized electrons, phonons, and photons out of equilibrium: A simplified ab initio approach based on the generalized Baym-Kadanoff ansatz

NASA Astrophysics Data System (ADS)

de Melo, Pedro Miguel M. C.; Marini, Andrea

2016-04-01

We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.

Ab initio computational study of –N-C and –O-C bonding formation : functional group modification reaction based chitosan

NASA Astrophysics Data System (ADS)

Siahaan, P.; Salimah, S. N. M.; Sipangkar, M. J.; Hudiyanti, D.; Djunaidi, M. C.; Laksitorini, M. D.

2018-04-01

Chitosan application in pharmaceutics and cosmeceutics industries is limited by its solubility issue. Modification of -NH2 and -OH fuctional groups of chitosan by adding carboxyl group has been shown to improve its solubility and application. Attempt to synthesize carboxymethyl chitosan (CMC) from monocloroacetic acid (MCAA) has been done prior this report. However no information is available wether –OH (-O-C bonding formation) or -NH2 (-N-C bonding formation) is the preference for - CH2COOH to attach. In the current study, the reaction mechanism between chitosan and MCAA reactants into carboxymethyl chitosan (CMC) was examined by computational approach. Dimer from of chitosan used as a molecular model in calculation All the molecular structure involved in the reaction mechanism was optimized by ab initio computational on the theory and basis set HF/6-31G(d,p). The results showed that the - N-C bonding formation via SN2 than the -O-C bonding formation via SN2 which have activation energy 469.437 kJ/mol and 533.219 kJ/mol respectively. However, the -O-C bonding formation more spontaneous than the -N-C bonding formation because ΔG the formation of O-CMC-2 reaction is more negative than ΔG of formation N-CMC-2 reaction is -4.353 kJ/mol and -1.095 kJ/mol respectively. The synthesis of N,O-CMC first forms -O-CH2COOH, then continues to form -NH-CH2COOH. This information is valuable to further optimize the reaction codition for CMC synthesis.

Ab initio calculation of Ti NMR shieldings for titanium oxides and halides

NASA Astrophysics Data System (ADS)

Tossell, J. A.

Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.

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.

Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches

NASA Astrophysics Data System (ADS)

Ramírez-Solís, A.; Poteau, R.; Vela, A.; Daudey, J. P.

2005-04-01

The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case.

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.

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.

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.

Spectroscopic and quantum chemical analysis of a natural product - Hayatin hydrochloride

NASA Astrophysics Data System (ADS)

Mishra, Rashmi; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

2015-08-01

Majority of drugs in use today are natural products, natural product mimics or semi synthetic derivatives. Therefore in recent times, focus on plant research has increased all over the world and large body of evidence has been collected to show immense potential of medicinal plants used in various traditional systems. Therefore, in the present communication to aid that research, structural and spectroscopic analysis of a natural product, an alkaloid Hayatin hydrochloride was performed. Both ab initio Hartree-Fock and density functional theory employing B3LYP with complete relaxation in the potential energy surface using 6-311G (d,p) basis set were used for the calculations. The vibrational frequencies were calculated and scaled values were compared with experimental FT-IR and micro-Raman spectra. The complete assignments were performed on the basis of potential energy distribution. The structure-activity relationship has also been interpreted by mapping electrostatic potential surface, which are valuable information for the quality control of medicines and drug-receptor interactions. Electronic properties have been analysed employing TD-DFT for both gaseous and solvent phase. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

miREE: miRNA recognition elements ensemble

PubMed Central

2011-01-01

Background Computational methods for microRNA target prediction are a fundamental step to understand the miRNA role in gene regulation, a key process in molecular biology. In this paper we present miREE, a novel microRNA target prediction tool. miREE is an ensemble of two parts entailing complementary but integrated roles in the prediction. The Ab-Initio module leverages upon a genetic algorithmic approach to generate a set of candidate sites on the basis of their microRNA-mRNA duplex stability properties. Then, a Support Vector Machine (SVM) learning module evaluates the impact of microRNA recognition elements on the target gene. As a result the prediction takes into account information regarding both miRNA-target structural stability and accessibility. Results The proposed method significantly improves the state-of-the-art prediction tools in terms of accuracy with a better balance between specificity and sensitivity, as demonstrated by the experiments conducted on several large datasets across different species. miREE achieves this result by tackling two of the main challenges of current prediction tools: (1) The reduced number of false positives for the Ab-Initio part thanks to the integration of a machine learning module (2) the specificity of the machine learning part, obtained through an innovative technique for rich and representative negative records generation. The validation was conducted on experimental datasets where the miRNA:mRNA interactions had been obtained through (1) direct validation where even the binding site is provided, or through (2) indirect validation, based on gene expression variations obtained from high-throughput experiments where the specific interaction is not validated in detail and consequently the specific binding site is not provided. Conclusions The coupling of two parts: a sensitive Ab-Initio module and a selective machine learning part capable of recognizing the false positives, leads to an improved balance between sensitivity and specificity. miREE obtains a reasonable trade-off between filtering false positives and identifying targets. miREE tool is available online at http://didattica-online.polito.it/eda/miREE/ PMID:22115078

Advanced ab initio relativistic calculations of transition probabilities for some O I and O III emission lines

NASA Astrophysics Data System (ADS)

Nguyen, T. V. B.; Chantler, C. T.; Lowe, J. A.; Grant, I. P.

2014-06-01

This work presents new ab initio relativistic calculations using the multiconfiguration Dirac-Hartree-Fock method of some O I and O III transition lines detected in B-type and Wolf-Rayet stars. Our results are the first able to be presented in both the length and velocity gauges, with excellent gauge convergence. Compared to previous experimental and theoretical uncertainties of up to 50 per cent, our accuracies appear to be in the range of 0.33-5.60 per cent, with gauge convergence up to 0.6 per cent. Similar impressive convergence of the calculated energies is also shown. Two sets of theoretical computations are compared with earlier tabulated measurements. Excellent agreement is obtained with one set of transitions but an interesting and consistent discrepancy exists between the current work and the prior literature, deserving of future experimental studies.

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

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.

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.

Photodissociation of CS from Excited Rovibrational Levels

NASA Astrophysics Data System (ADS)

Pattillo, R. J.; Cieszewski, R.; Stancil, P. C.; Forrey, R. C.; Babb, J. F.; McCann, J. F.; McLaughlin, B. M.

2018-05-01

Accurate photodissociation cross sections have been computed for transitions from the X 1Σ+ ground electronic state of CS to six low-lying excited electronic states. New ab initio potential curves and transition dipole moment functions have been obtained for these computations using the multi-reference configuration interaction approach with the Davidson correction (MRCI+Q) and aug-cc-pV6Z basis sets. State-resolved cross sections have been computed for transitions from nearly the full range of rovibrational levels of the X 1Σ+ state and for photon wavelengths ranging from 500 Å to threshold. Destruction of CS via predissociation in highly excited electronic states originating from the rovibrational ground state is found to be unimportant. Photodissociation cross sections are presented for temperatures in the range between 1000 and 10,000 K, where a Boltzmann distribution of initial rovibrational levels is assumed. Applications of the current computations to various astrophysical environments are briefly discussed focusing on photodissociation rates due to the standard interstellar and blackbody radiation fields.

A full-dimensional potential energy surface and quantum dynamics of inelastic collision process for H2-HF

NASA Astrophysics Data System (ADS)

Yang, Dongzheng; Huang, Jing; Zuo, Junxiang; Hu, Xixi; Xie, Daiqian

2018-05-01

A full-dimensional ab initio potential energy surface for the H2-HF van der Waals complex was constructed by employing the coupled-cluster singles and doubles with noniterative inclusion of connected triples with augmented correlation-consistent polarised valence quadruple-zeta basis set plus bond functions. Using the improved coupled-states approximation including the nearest neighbor Coriolis couplings, we calculated the state-to-state scattering dynamics for pure rotational and ro-vibrational energy transfer processes. For pure rotational energy transfer, our results showed a different dynamical behavior for para-H2 and ortho-H2 in collision with hydrogen fluoride (HF), which is consistent with the previous study. Interestingly, some strong resonant peaks were presented in the cross sections for ro-vibrational energy transfer. In addition, the calculated vibrational-resolved rate constant is in agreement with the experimental results reported by Bott et al. These dynamics data can be further applied to the numerical simulation of HF chemical lasers.

Ab initio calculation of hyperfine splitting constants of molecules

NASA Astrophysics Data System (ADS)

Ohta, K.; Nakatsuji, H.; Hirao, K.; Yonezawa, T.

1980-08-01

Hyperfine splitting (hfs) constants of molecules, methyl, ethyl, vinyl, allyl, cyclopropyl, formyl, O3-, NH2, NO2, and NF2 radicals have been calculated by the pseudo-orbital (PO) theory, the unrestricted HF (UHF), projected UHF (PUHF) and single excitation (SE) CI theories. The pseudo-orbital (PO) theory is based on the symmetry-adapted-cluster (SAC) expansion proposed previously. Several contractions of the Gaussian basis sets of double-zeta accuracy have been examined. The UHF results were consistently too large to compare with experiments and the PUHF results were too small. For molecules studied here, the PO theory and SECI theory gave relatively close results. They were in fair agreement with experiments. The first-order spin-polarization self-consistency effect, which was shown to be important for atoms, is relatively small for the molecules. The present result also shows an importance of eliminating orbital-transformation dependence from conventional first-order perturbation calculations. The present calculations have explained well several important variations in the experimental hfs constants.

A variation-perturbation method for atomic and molecular interactions. I - Theory. II - The interaction potential and van der Waals molecule for Ne-HF

NASA Astrophysics Data System (ADS)

Gallup, G. A.; Gerratt, J.

1985-09-01

The van der Waals energy between the two parts of a system is a very small fraction of the total electronic energy. In such cases, calculations have been based on perturbation theory. However, such an approach involves certain difficulties. For this reason, van der Waals energies have also been directly calculated from total energies. But such a method has definite limitations as to the size of systems which can be treated, and recently ab initio calculations have been combined with damped semiempirical long-range dispersion potentials to treat larger systems. In this procedure, large basis set superposition errors occur, which must be removed by the counterpoise method. The present investigation is concerned with an approach which is intermediate between the previously considered procedures. The first step in the new approach involves a variational calculation based upon valence bond functions. The procedure includes also the optimization of excited orbitals, and an approximation of atomic integrals and Hamiltonian matrix elements.

Experimental and computational study on molecular structure and vibrational analysis of an antihyperglycemic biomolecule: Gliclazide

NASA Astrophysics Data System (ADS)

Karakaya, Mustafa; Kürekçi, Mehmet; Eskiyurt, Buse; Sert, Yusuf; Çırak, Çağrı

2015-01-01

In present study, the experimental and theoretical harmonic vibrational frequencies of gliclazide molecule have been investigated. The experimental FT-IR (400-4000 cm-1) and Laser-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) have been calculated using ab initio Hartree Fock (HF), density functional theory (B3LYP hybrid function) methods with 6-311++G(d,p) and 6-31G(d,p) basis sets by Gaussian 09W program. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. Theoretical optimized geometric parameters and vibrational frequencies have been compared with the corresponding experimental data, and they have been shown to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been found.

Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method.

PubMed

Diwaker

2014-07-15

The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the (1)H and (13)C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 3-(6-benzoyl-2-oxobenzo[ d]oxazol-3(2 H)-yl)propanoic acid

NASA Astrophysics Data System (ADS)

Arslan, Hakan; Algül, Öztekin; Önkol, Tijen

2008-08-01

The molecular structure, vibrational frequencies and infrared intensities of the 3-(6-benzoyl-2-oxobenzo[ d]oxazol-3(2 H)-yl)propanoic acid were calculated by the HF and DFT methods using 6-31G(d) basis set. The FT-infrared spectra have been measured for the title compound in the solid state. We obtained 11 stable conformers for the title compound, however the Conformer 1 is approximately 3.88 kcal/mol more stable than the Conformer 11. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of the Conformer 1. The harmonic vibrations computed of this compound by the B3LYP/6-31G(d) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using VEDA 4 program.

Experimental and computational study on molecular structure and vibrational analysis of a modified biomolecule: 5-Bromo-2'-deoxyuridine

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

In the present study, the experimental and theoretical vibrational spectra of 5-bromo-2'-deoxyuridine were investigated. The experimental FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF) and density functional B3LYP method with 6-31G(d), 6-31G(d,p), 6-311++G(d) and 6-311++G(d,p) basis sets by Gaussian program, for the first time. The assignments of vibrational frequencies were performed by potential energy distribution by using VEDA 4 program. The optimized geometric parameters and theoretical vibrational frequencies are compared with the corresponding experimental data and they were seen to be in a good agreement with the each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.

Experimental and theoretical study on the structure and vibrational spectra of β-2-aminopyridinium dihydrogenphosphate

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Demir, Selçuk; Ucun, Fatih; Çubuk, Osman

2011-08-01

Experimental and theoretical vibrational spectra of β-2-aminopyridinium dihydrogenphosphate (β-2APDP) have been investigated. The FT-IR spectrum of β-2APDP was recorded in the region 4000-400 cm -1. The optimized molecular structure and theoretical vibrational frequencies of β-2APDP have been investigated using ab initio Hartree-Fock (HF) and density functional B3LYP method with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths and bond angles) and theoretical frequencies have been compared with the corresponding experimental data and it is found that they agree well with each other. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Furthermore, the used scale factors were obtained from the ratio of the frequency values of the strongest peaks in the experimental and theoretical IR spectra. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies.

Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations.

PubMed

Sert, Yusuf; Çırak, Çağrı; Ucun, Fatih

2013-04-15

In the present study, the experimental and theoretical harmonic and anharmonic vibrational frequencies of 4-chloro-3-nitrobenzonitrile were investigated. The experimental FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF), density functional B3LYP and M06-2X methods with 6-311++G(d,p) basis set by Gaussian 09 W program, for the first time. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found. Copyright © 2013 Elsevier B.V. All rights reserved.

Experimental and computational study on molecular structure and vibrational analysis of an antihyperglycemic biomolecule: gliclazide.

PubMed

Karakaya, Mustafa; Kürekçi, Mehmet; Eskiyurt, Buse; Sert, Yusuf; Çırak, Çağrı

2015-01-25

In present study, the experimental and theoretical harmonic vibrational frequencies of gliclazide molecule have been investigated. The experimental FT-IR (400-4000 cm(-1)) and Laser-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) have been calculated using ab initio Hartree Fock (HF), density functional theory (B3LYP hybrid function) methods with 6-311++G(d,p) and 6-31G(d,p) basis sets by Gaussian 09W program. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. Theoretical optimized geometric parameters and vibrational frequencies have been compared with the corresponding experimental data, and they have been shown to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been found. Copyright © 2014 Elsevier B.V. All rights reserved.

Noncovalent Interactions of DNA Bases with Naphthalene and Graphene.

PubMed

Cho, Yeonchoo; Min, Seung Kyu; Yun, Jeonghun; Kim, Woo Youn; Tkatchenko, Alexandre; Kim, Kwang S

2013-04-09

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base-naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31, 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered.

Phosphine polymerization by nitric oxide: experimental characterization and theoretical predictions of mechanism.

PubMed

Zhao, Yi-Lei; Flora, Jason W; Thweatt, William David; Garrison, Stephen L; Gonzalez, Carlos; Houk, K N; Marquez, Manuel

2009-02-02

A yellow solid material [P(x)H(y)] has been obtained in the reaction of phosphine (PH(3)) and nitric oxide (NO) at room temperature and characterized by thermogravimetric analysis mass spectrometry (TGA-MS) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. In this work using complete basis set (CBS-QB3) methods a plausible mechanism has been investigated for phosphine polymerization in the presence of nitric oxide (NO). Theoretical explorations with the ab initio method suggest (a) instead of the monomer the nitric oxide dimer acts as an initial oxidant, (b) the resulting phosphine oxides (H(3)P=O <--> H(3)P(+)O(-)) in the gas phase draw each other via strong dipolar interactions between the P-O groups, and (c) consequently an autocatalyzed polymerization occurs among the phosphine oxides, forming P-P chemical bonds and losing water. The possible structures of polyhydride phosphorus polymer were discussed. In the calculations a series of cluster models was computed to simulate polymerization.

New insights into thermal decomposition of polycyclic aromatic hydrocarbon oxyradicals.

PubMed

Liu, Peng; Lin, He; Yang, Yang; Shao, Can; Gu, Chen; Huang, Zhen

2014-12-04

Thermal decompositions of polycyclic aromatic hydrocarbon (PAH) oxyradicals on various surface sites including five-membered ring, free-edge, zigzag, and armchair have been systematically investigated by using ab initio density functional theory B3LYP/6-311+G(d,p) basis set. The calculation based on Hückel theory indicates that PAHs (3H-cydopenta[a]anthracene oxyradical) with oxyradicals on a five-membered ring site have high chemical reactivity. The rate coefficients of PAH oxyradical decomposition were evaluated by using Rice-Ramsperger-Kassel-Marcus theory and solving the master equations in the temperature range of 1500-2500 K and the pressure range of 0.1-10 atm. The kinetic calculations revealed that the rate coefficients of PAH oxyradical decomposition are temperature-, pressure-, and surface site-dependent, and the oxyradical on a five-membered ring is easier to decompose than that on a six-membered ring. Four-membered rings were found in decomposition of the five-membered ring, and a new reaction channel of PAH evolution involving four-membered rings is recommended.

Stability of Hydrocarbons of the Polyhedrane Family: Convergence of ab Initio Calculations and Corresponding Assessment of DFT Main Approximations.

PubMed

Sancho-García, J C

2011-09-13

Highly accurate coupled-cluster (CC) calculations with large basis sets have been performed to study the binding energy of the (CH)12, (CH)16, (CH)20, and (CH)24 polyhedral hydrocarbons in two, cage-like and planar, forms. We also considered the effect of other minor contributions: core-correlation, relativistic corrections, and extrapolations to the limit of the full CC expansion. Thus, chemically accurate values could be obtained for these complicated systems. These nearly exact results are used to evaluate next the performance of main approximations (i.e., pure, hybrid, and double-hybrid methods) within density functional theory (DFT) in a systematic fashion. Some commonly used functionals, including the B3LYP model, are affected by large errors, and only those having reduced self-interaction error (SIE), which includes the last family of conjectured expressions (double hybrids), are able to achieve reasonable low deviations of 1-2 kcal/mol especially when an estimate for dispersion interactions is also added.

A Systematic Theoretical Study of UC6: Structure, Bonding Nature, and Spectroscopy.

PubMed

Du, Jiguang; Jiang, Gang

2017-11-20

The study of uranium carbides has received renewed attention in recent years due to the potential use of these compounds as fuels in new generations of nuclear reactors. The isomers of the UC 6 cluster were determined by DFT and ab initio methods. The structures obtained using SC-RECP for U were generally consistent with those obtained using an all-electron basis set (ZORA-SARC). The CCSD(T) calculations indicated that two isomers had similar energies and may coexist in laser evaporation experiments. The nature of the U-C bonds in the different isomers was examined via a topological analysis of the electron density, and the results indicated that the U-C bonds are predominantly closed-shell (ionic) interactions with a certain degree of covalent character in all cases, particularly in the linear species. The IR and UV-vis spectra of the isomers were theoretically simulated to provide information that can be used to identify the isomers of UC 6 in future experiments.

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.

Density functional theory and Ab initio studies of vibrational spectroscopic (FT-IR, FT-Raman and UV) first order hyperpolarizabilities, NBO, HOMO-LUMO and TD-DFT analysis of the 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one

NASA Astrophysics Data System (ADS)

Ramachandran, G.; Muthu, S.; Uma Maheswari, J.

2013-02-01

Fourier transform Raman and Fourier transform infrared spectra of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one were recorded in the regions 3500-100 cm-1 and 4000-400 cm-1 respectively in the solid phase. 1,2-Dihydropyrazolo (4, 3-E) Pyrimidin-4-one is used to treat hyperuricemia and its complication including chronic gout. The equilibrium geometry harmonic vibrational frequencies, infrared intensities and Raman intensities were calculated by Hartee Fock and density functional B3LYP methods with 6-31G (d, p) basis set, using Gaussian 03W program package on a Pentium IV/1.6 GHz personal computer. The thermodynamic functions of the title compound were also performed at the above methods and basis set. A detailed interpretation of the infrared and Raman spectra of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one is reported. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis of the compound was recorded. The calculated HOMO and LUMO energies show that chemical activity of the molecule. The first order hyperpolarizability (β) of this novel molecular system and related properties of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one are calculated using HF/6-31G (d, p) method on the finite field approach. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra.

Infrared, Raman and NMR spectra, conformational stability, normal coordinate analysis and B3LYP calculations of 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde

NASA Astrophysics Data System (ADS)

Bahgat, Khaled; EL-Emary, Talaat

2013-02-01

FT Raman and IR spectra of the crystallized biologically active molecule, 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (5-APHC, C11H11N3O) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of 5-APHC have been investigated with the help of B3LYP density functional theory (DFT) method with 6-31G(d) and 6-311+G(d,p) as basis set. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field (SQM) technique. The optimized geometry shows the co-planarity of the aldehyde group with pyrazole ring. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G(d,p) basis set. The red shifting of NH2 stretching wavenumber indicates the formation of N-H⋯O hydrogen bonding. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-Vis spectrum of the compound was recorded in the region 200-400 nm and the electronic properties HOMO and LUMO energies were calculated by time-dependent TD-DFT approach. Mulliken charges of the 5-APHC molecule was also calculated and interpreted.

An Ab Initio Study of the Low-Lying Doublet States of AgO and AgS

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

1990-01-01

Spectroscopic constants (D(sub o), r(sub e), mu(sub e), T(sub e)) are determined for the doublet states of AgO and AgS below approx. = 30000/cm. Large valence basis sets are employed in conjunction with relativistic effective core potentials (RECPs). Electron correlation is included using the modified coupled-pair functional (MCPF) and multireference configuration interaction (MRCI) methods. The A(sup 2)Sigma(sup +) - X(sup 2)Pi band system is found to occur in the near infrared (approx. = 9000/cm) and to be relatively weak with a radiative lifetime of 900 microns for A(sup 2)Sigma(sup +) (upsilon = 0). The weakly bound C(sup 2)Pi state (our notation), the upper state of the blue system, is found to require high levels of theoretical treatment to determine a quantitatively accurate potential. The red system is assigned as a transition from the C(sup 2)Pi state to the previously unobserved A(sup 2)Sigma(sup +) state. Several additional transitions are identified that should be detectable experimentally. A more limited study is performed for the vertical excitation spectrum of AgS. In addition, a detailed all-electron study of the X(sup 2)Pi and A(sup 2)Sigma(sup +) states of AgO is carried out using large atomic natural orbital (ANO) basis sets. Our best calculated D(sub o) value for AgO is significantly less than the experimental value, which suggests that there may be some systematic error in the experimental determination.

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.

Excited states of 4He

NASA Astrophysics Data System (ADS)

Aoyama, Shigeyoshi

2013-04-01

The study of the 4He nucleus is important because it is the most basic sub-unit (cluster) in nuclei. We have investigated the structures and the reaction mechanisms in 4He by using the correlated Gaussian basis function with the global vector representation. In order to treat the boundary condition for the ab-initio calculation of the four nucleons, we employ the Microscopic R-matrix Method (MRM) and the Complex Scaling Method (CSM) . Elastic-scattering phase shifts for four-nucleon systems are studied in an ab-initio type cluster model with MRM in order to clarify the role of the tensor force and to investigate cluster distortions in low energy d+d and t+p scattering. For 1S0, the calculated phase shifts show that the t+p and h+n channels are strongly coupled to the d+d channel for the case of the realistic interaction.

Ab Initio Study of Polarizabilities of Oligothiophene, Oligocyclopentadiene and Oligofulvene and their Cyano Substituted Oligomers

NASA Astrophysics Data System (ADS)

Lagowski, Jolanta; Ferdous, Sultana

2005-03-01

Ab Initio polarizabilities of thiophene, fulvene and cyclopentadiene based conducting oligomers and polymers and their cyano derivatives have been calculated using the Hartree-Fock (HF), configuration interaction (singles) (CIS ) and density functional (DF) theories with 3-21G* basis using Gaussian software. The main motivation of this investigation is to determine the correlation between the excitation energies and polarizabilities for the conjugated systems studied. It has been found that HF and DF approaches give similar magnitudes for polarizabilities whereas CIS theory provides results that are considerably different. All three methods predict similar trends in polarizabilities as a function of oligomer length and bond alternation along the backbone of the oligomers. It has also been observed that the end groups and the number of `double' bonds have a significant effect on the magnitude of polarizability per C-C bond. Comparison with experimental results will be made where possible.

A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

PubMed

Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

2009-07-28

Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

Ab initio calculation of a global potential, vibrational energies, and wave functions for HCN/HNC, and a simulation of the (A-tilde)-(X-tilde) emission spectrum

NASA Technical Reports Server (NTRS)

Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.

1993-01-01

A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Photodissociation of phenol via nonadiabatic tunneling: Comparison of two ab initio based potential energy surfaces

NASA Astrophysics Data System (ADS)

Xie, Changjian; Guo, Hua

2017-09-01

The nonadiabatic tunneling-facilitated photodissociation of phenol is investigated using a reduced-dimensional quantum model on two ab initio-based coupled potential energy surfaces (PESs). Although dynamics occurs largely on the lower adiabat, the proximity to a conical intersection between the S1 and S2 states requires the inclusion of both the geometric phase (GP) and diagonal Born-Oppenheimer correction (DBOC). The lifetime of the lowest-lying vibronic state is computed using the diabatic and various adiabatic models. The GP and DBOC terms are found to be essential on one set of PESs, but have a small impact on the other.

Defect Genome of Cubic Perovskites for Fuel Cell Applications

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

Balachandran, Janakiraman; Lin, Lianshan; Anchell, Jonathan S.

Heterogeneities such as point defects, inherent to material systems, can profoundly influence material functionalities critical for numerous energy applications. This influence in principle can be identified and quantified through development of large defect data sets which we call the defect genome, employing high-throughput ab initio calculations. However, high-throughput screening of material models with point defects dramatically increases the computational complexity and chemical search space, creating major impediments toward developing a defect genome. In this paper, we overcome these impediments by employing computationally tractable ab initio models driven by highly scalable workflows, to study formation and interaction of various point defectsmore » (e.g., O vacancies, H interstitials, and Y substitutional dopant), in over 80 cubic perovskites, for potential proton-conducting ceramic fuel cell (PCFC) applications. The resulting defect data sets identify several promising perovskite compounds that can exhibit high proton conductivity. Furthermore, the data sets also enable us to identify and explain, insightful and novel correlations among defect energies, material identities, and defect-induced local structural distortions. Finally, such defect data sets and resultant correlations are necessary to build statistical machine learning models, which are required to accelerate discovery of new materials.« less

Defect Genome of Cubic Perovskites for Fuel Cell Applications

DOE PAGES

Balachandran, Janakiraman; Lin, Lianshan; Anchell, Jonathan S.; ...

2017-10-10

Heterogeneities such as point defects, inherent to material systems, can profoundly influence material functionalities critical for numerous energy applications. This influence in principle can be identified and quantified through development of large defect data sets which we call the defect genome, employing high-throughput ab initio calculations. However, high-throughput screening of material models with point defects dramatically increases the computational complexity and chemical search space, creating major impediments toward developing a defect genome. In this paper, we overcome these impediments by employing computationally tractable ab initio models driven by highly scalable workflows, to study formation and interaction of various point defectsmore » (e.g., O vacancies, H interstitials, and Y substitutional dopant), in over 80 cubic perovskites, for potential proton-conducting ceramic fuel cell (PCFC) applications. The resulting defect data sets identify several promising perovskite compounds that can exhibit high proton conductivity. Furthermore, the data sets also enable us to identify and explain, insightful and novel correlations among defect energies, material identities, and defect-induced local structural distortions. Finally, such defect data sets and resultant correlations are necessary to build statistical machine learning models, which are required to accelerate discovery of new materials.« less

Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

PubMed

Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

2016-08-25

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin-Wigner or Rayleigh-Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of "on-the-fly" interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.

Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

NASA Astrophysics Data System (ADS)

Vanicek, Jiri

2014-03-01

Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

Ab initio study of Pd carbonyls and CO/Pd(110)

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

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

A new single-particle basis for nuclear many-body calculations

NASA Astrophysics Data System (ADS)

Puddu, G.

2017-10-01

Predominantly, harmonic oscillator single-particle wave functions are the preferred choice for a basis in ab initio nuclear many-body calculations. These wave-functions, although very convenient in order to evaluate the matrix elements of the interaction in the laboratory frame, have too fast a fall-off at large distances. In the past, as an alternative to the harmonic oscillator, other single-particle wave functions have been proposed. In this work, we propose a new single-particle basis, directly linked to nucleon-nucleon interaction. This new basis is orthonormal and complete, has the proper asymptotic behavior at large distances and does not contain the continuum which would pose severe convergence problems in nuclear many body calculations. We consider the newly proposed NNLO-opt nucleon-nucleon interaction, without any renormalization. We show that, unlike other bases, this single-particle representation has a computational cost similar to the harmonic oscillator basis with the same space truncation and it gives lower energies for 6He and 6Li.

High sensitivity CRDS of CO2 in the 1.74 μm transparency window. A validation test for the spectroscopic databases

NASA Astrophysics Data System (ADS)

Čermák, P.; Karlovets, E. V.; Mondelain, D.; Kassi, S.; Perevalov, V. I.; Campargue, A.

2018-03-01

The very weak absorption spectrum of natural CO2 near 1.74 μm (5702-5879 cm-1) is studied at high sensitivity. The investigated region corresponds to a transparency window of very weak opacity which is of particular interest for Venus. Very weak lines with intensity value as low as 10-30 cm/molecule at 296 K are detected by Cavity Ring Down Spectroscopy. On the basis of the predictions of effective Hamiltonian models, 1135 lines of six carbon dioxide isotopologues - 12C16O2, 13C16O2, 16O12C18O, 16O12C17O, 16O13C18O and 16O13C17O - were rovibrationnally assigned to 26 bands. The accurate spectroscopic parameters of 16 bands are determined from standard band-by-band analysis (typical rms deviations of the line positions are 8 × 10-4 cm-1). These newly observed bands include perturbed bands, weak hot bands and bands of minor isotopologues (in particular 16O12C18O in natural abundance) and provide critical validation tests for the most recent spectroscopic databases. The comparison to the Carbon Dioxide Spectroscopic Databank (CDSD), HITRAN2016 database and recent ab initio line lists is presented. Deficiencies are evidenced for some weak perpendicular bands of the HITRAN2016 list and identified as due to inaccurate CDSD intensities which were preferred to ab initio intensities. While Ames and UCL ab initio intensities are believed to be accurate within a few % for the strong unperturbed bands, the reported measurements allow testing important (>50%) differences between ab initio values of some weak perturbed bands.

Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

NASA Technical Reports Server (NTRS)

Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

1994-01-01

We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

Potential energy function for CH3+CH3 ⇆ C2H6: Attributes of the minimum energy path

NASA Astrophysics Data System (ADS)

Robertson, S. H.; Wardlaw, D. M.; Hirst, D. M.

1993-11-01

The region of the potential energy surface for the title reaction in the vicinity of its minimum energy path has been predicted from the analysis of ab initio electronic energy calculations. The ab initio procedure employs a 6-31G** basis set and a configuration interaction calculation which uses the orbitals obtained in a generalized valence bond calculation. Calculated equilibrium properties of ethane and of isolated methyl radical are compared to existing theoretical and experimental results. The reaction coordinate is represented by the carbon-carbon interatomic distance. The following attributes are reported as a function of this distance and fit to functional forms which smoothly interpolate between reactant and product values of each attribute: the minimum energy path potential, the minimum energy path geometry, normal mode frequencies for vibrational motion orthogonal to the reaction coordinate, a torsional potential, and a fundamental anharmonic frequency for local mode, out-of-plane CH3 bending (umbrella motion). The best representation is provided by a three-parameter modified Morse function for the minimum energy path potential and a two-parameter hyperbolic tangent switching function for all other attributes. A poorer but simpler representation, which may be satisfactory for selected applications, is provided by a standard Morse function and a one-parameter exponential switching function. Previous applications of the exponential switching function to estimate the reaction coordinate dependence of the frequencies and geometry of this system have assumed the same value of the range parameter α for each property and have taken α to be less than or equal to the ``standard'' value of 1.0 Å-1. Based on the present analysis this is incorrect: The α values depend on the property and range from ˜1.2 to ˜1.8 Å-1.

Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

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

Roemelt, Michael, E-mail: michael.roemelt@theochem.rub.de

Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctionsmore » are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.« less

Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

PubMed

Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

2015-08-05

Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer.

PubMed

Li, Jinshan; Zhao, Feng; Jing, Fuqian

2003-02-01

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345-352, 2003

DFT and AIM study of the protonation of nitrous acid and the pKa of nitrous acidium ion.

PubMed

Crugeiras, Juan; Ríos, Ana; Maskill, Howard

2011-11-10

The gas phase and aqueous thermochemistry, NMR chemical shifts, and the topology of chemical bonding of nitrous acid (HONO) and nitrous acidium ion (H(2)ONO(+)) have been investigated by ab initio methods using density functional theory. By the same methods, the dissociation of H(2)ONO(+) to give the nitrosonium ion (NO(+)) and water has also been investigated. We have used Becke's hybrid functional (B3LYP), and geometry optimizations were performed with the 6-311++G(d,p) basis set. In addition, highly accurate ab initio composite methods (G3 and CBS-Q) were used. Solvation energies were calculated using the conductor-like polarizable continuum model, CPCM, at the B3LYP/6-311++G(d,p) level of theory, with the UAKS cavity model. The pK(a) value of H(2)ONO(+) was calculated using two different schemes: the direct method and the proton exchange method. The calculated pK(a) values at different levels of theory range from -9.4 to -15.6, showing that H(2)ONO(+) is a strong acid (i.e., HONO is only a weak base). The equilibrium constant, K(R), for protonation of nitrous acid followed by dissociation to give NO(+) and H(2)O has also been calculated using the same methodologies. The pK(R) value calculated by the G3 and CBS-QB3 methods is in best (and satisfactory) agreement with experimental results, which allows us to narrow down the likely value of the pK(a) of H(2)ONO(+) to about -10, a value appreciably more acidic than literature values.

Model Order Reduction Algorithm for Estimating the Absorption Spectrum

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

Van Beeumen, Roel; Williams-Young, David B.; Kasper, Joseph M.

The ab initio description of the spectral interior of the absorption spectrum poses both a theoretical and computational challenge for modern electronic structure theory. Due to the often spectrally dense character of this domain in the quantum propagator’s eigenspectrum for medium-to-large sized systems, traditional approaches based on the partial diagonalization of the propagator often encounter oscillatory and stagnating convergence. Electronic structure methods which solve the molecular response problem through the solution of spectrally shifted linear systems, such as the complex polarization propagator, offer an alternative approach which is agnostic to the underlying spectral density or domain location. This generality comesmore » at a seemingly high computational cost associated with solving a large linear system for each spectral shift in some discretization of the spectral domain of interest. In this work, we present a novel, adaptive solution to this high computational overhead based on model order reduction techniques via interpolation. Model order reduction reduces the computational complexity of mathematical models and is ubiquitous in the simulation of dynamical systems and control theory. The efficiency and effectiveness of the proposed algorithm in the ab initio prediction of X-ray absorption spectra is demonstrated using a test set of challenging water clusters which are spectrally dense in the neighborhood of the oxygen K-edge. On the basis of a single, user defined tolerance we automatically determine the order of the reduced models and approximate the absorption spectrum up to the given tolerance. We also illustrate that, for the systems studied, the automatically determined model order increases logarithmically with the problem dimension, compared to a linear increase of the number of eigenvalues within the energy window. Furthermore, we observed that the computational cost of the proposed algorithm only scales quadratically with respect to the problem dimension.« less

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

The vibrational spectrum of H2O3: An ab initio investigation

NASA Technical Reports Server (NTRS)

Jackels, Charles F.

1991-01-01

Theoretically determined frequencies and absorption intensities are reported for the vibrational spectrum of the covalent HOOOH and hydrogen bonded HO---HOO intermediates that may form in the reaction of the hydroxyl and hydroperoxyl radicals. Basis sets of DZP quality, augmented by diffuse and second sets of polarization functions have been used with CASSCF wave functions. The calculated harmonic vibrational frequencies of HOOOH have been corrected with empirical factors and presented in the form of a 'stick' spectrum. The oxygen backbone vibrations, predicted to occur at 519, 760, and 870 cm(exp -1), are well separated from most interferences, and may be the most useful for the species' identification. In the case of the hydrogen bonded isomer, emphasis has been placed upon prediction of the shifts in the intramolecular vibrational frequencies that take place upon formation of the complex. In particular, the HO stretch and HOO bend of HO2 are predicted to have shifts of -59 and 53 cm(exp -1), respectively, which should facilitate their identification. It is also noted that the antisymmetric stretching frequency of the oxygen backbone in HOOOH exhibits a strong sensitivity to the degree of electron correlation, such as has been previously observed for the same mode in ozone.

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

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

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Vibrational spectra and normal coordinate analysis of 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate

NASA Astrophysics Data System (ADS)

Muthu, S.; Renuga, S.

2014-11-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FTIR spectroscopy in the range 50-4000 cm-1 and 450-4000 cm-1 respectively, for 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate (2H3MPPLC) molecule. The molecular structure, fundamental vibrational frequencies and intensities of the vibrational bands were interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) and ab initio HF methods with 6-31G(d,p) basis set. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The scaled B3LYP/6-31G(d,p) results show the best agreement with the experimental values over the other method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results confirm the occurrence of intramolecular charge-transfer (ICT) within the molecule. The dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the investigated molecule has been computed using B3LYP/6-31G(d,p) method. Mulliken population analysis on atomic charges was also calculated. Besides, frontier molecular orbitals, molecular electrostatic potential (MEP) and thermodynamic properties were performed.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

10 μm High-resolution spectrum of trans -acrolein: Rotational analysis of the ν 11 , ν 16 , ν 14 and ν 16 + ν 18 - ν 18 bands

NASA Astrophysics Data System (ADS)

Xu, Li-Hong; Jiang, Xingjie; Shi, Hongyu; Lees, R. M.; McKellar, A. R. W.; Tokaryk, D. W.; Appadoo, D. R. T.

2011-07-01

High-resolution Fourier transform spectra of trans-acrolein, H 2C dbnd C(H) sbnd C(H) dbnd O, have been recorded in the 10 μm region at both room and cooled temperatures on the modified Bomem DA3.002 at the National Research Council of Canada and the Bruker IFS 125HR spectrometer at the far infrared beam line of the Canadian Light Source in Saskatoon. Vibrational fundamentals analyzed so far include the ν11, ν16 and ν14 bands centered at 911.3, 958.7 and 992.7 cm -1 corresponding respectively to the A' in-plane dbnd CH 2-rocking mode, the A″ out-of-plane dbnd CH 2-wagging mode, and the A″ wagging mode highly mixed between the ⩾C sbnd H vinyl and ⩾C sbnd H formyl groups [Vibrational mode descriptions are based on Y.N. Panchenko, P. Pulay, F. Török, J. Mol. Spectrosc. 34 (1976) 283-289.] As well, the ν16 + ν18 - ν18 hot band centred at 957.6 cm -1 has been analyzed, where ν18 is the low-frequency (157.9 cm -1) A″ ⩾C sbnd C ⪕ torsional mode. The ν11 band is a/ b type while the ν16, ν14 and ν16 + ν18 - ν18 bands are c-type. The assigned transitions of each band have been fitted to a Watson asymmetric rotor Hamiltonian, with ground state parameters fixed to values obtained from rotational analyses in the literature. As well, a combined 3-state fit for ν11, ν16 and ν14 was carried out including Coriolis and Z1 constants which account for J and Δ K interactions. Transition dipole moments have been calculated for each of the fundamentals using the ab initio B3LYP method and 6-311++G ∗∗ basis set. For the A' vibrational modes, we have also evaluated transition dipole a- and b-components in the principal axis system from vibrational displacements and dipole moment derivatives. Our ab initio results predict that the ν11 in-plane dbnd CH 2 rocking mode has an a-type transition strength about three times greater than the b-type, which is consistent with our observations. Our ab initio force field analysis gives vibrational mode descriptions consistent with previously published work for all 13 A' modes. However, for the five A″ vibrational modes, our ab initio results disagree with two of the descriptions of Panchenko et al. and three of the descriptions of Hamada et al. [Y. Hamada, Y. Nishimura, M. Tsuboi, Chem. Phys. 100 (1985) 365-375].

Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1995-01-01

The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBrO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee. Timothy J.

1995-01-01

The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBRO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE PAGES

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

2016-09-09

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

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

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

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

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.

An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

2008-12-01

A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm-1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J =0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J =0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J =0-2 is 0.023cm-1 and that for each band is always ⩽0.06cm-1. For J =3-5 the rms error is always ⩽0.15cm-1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

PubMed

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

2016-10-11

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Microscopic Mechanism of Doping-Induced Kinetically Constrained Crystallization in Phase-Change Materials.

PubMed

Lee, Tae Hoon; Loke, Desmond; Elliott, Stephen R

2015-10-07

A comprehensive microscopic mechanism of doping-induced kinetically constrained crystallization in phase-change materials is provided by investigating structural and dynamical dopant characteristics via ab initio molecular dynamics simulations. The information gained from this study may provide a basis for a fast screening of dopant species for electronic memory devices, or for understanding the general physics involved in the crystallization of doped glasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The CO 2 with dimethylamine reaction: ab initio predicted vibrational spectra

NASA Astrophysics Data System (ADS)

Jamróz, M. H.; Dobrowolski, J. Cz.; Borowiak, M. A.

1999-05-01

The IR spectra of CO 2, dimethylamine (DMA), (DMA) 2 dimers, DMA⋯CO 2 (2 : 1) complex, dimethylcarbamic acid (DMCA), DMCA⋯DMA (1 : 1) complex, DMCA -, and DMA(H) + were calculated at the B3PW91/6-31G** level. Potential energy distribution (PED) was calculated for predicted spectra to form basis for elucidation of experimental IR data. The stabilisation energy of the studied complexes was corrected by counterpoise method.

Prediction of folding preference of 10 kDa silk-like proteins using a Lego approach and ab initio calculations.

PubMed

Pohl, Gábor; Beke, Tamás; Borbély, János; Perczel, András

2006-11-15

Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.

Short-range stabilizing potential for computing energies and lifetimes of temporary anions with extrapolation methods.

PubMed

Sommerfeld, Thomas; Ehara, Masahiro

2015-01-21

The energy of a temporary anion can be computed by adding a stabilizing potential to the molecular Hamiltonian, increasing the stabilization until the temporary state is turned into a bound state, and then further increasing the stabilization until enough bound state energies have been collected so that these can be extrapolated back to vanishing stabilization. The lifetime can be obtained from the same data, but only if the extrapolation is done through analytic continuation of the momentum as a function of the square root of a shifted stabilizing parameter. This method is known as analytic continuation of the coupling constant, and it requires--at least in principle--that the bound-state input data are computed with a short-range stabilizing potential. In the context of molecules and ab initio packages, long-range Coulomb stabilizing potentials are, however, far more convenient and have been used in the past with some success, although the error introduced by the long-rang nature of the stabilizing potential remains unknown. Here, we introduce a soft-Voronoi box potential that can serve as a short-range stabilizing potential. The difference between a Coulomb and the new stabilization is analyzed in detail for a one-dimensional model system as well as for the (2)Πu resonance of CO2(-), and in both cases, the extrapolation results are compared to independently computed resonance parameters, from complex scaling for the model, and from complex absorbing potential calculations for CO2(-). It is important to emphasize that for both the model and for CO2(-), all three sets of results have, respectively, been obtained with the same electronic structure method and basis set so that the theoretical description of the continuum can be directly compared. The new soft-Voronoi-box-based extrapolation is then used to study the influence of the size of diffuse and the valence basis sets on the computed resonance parameters.

SETTING UP A LABORATORY AB INITIO IN A REMOTE LOCATION

EPA Science Inventory

For many years the USEPA's National Risk Management Research Laboratory in Cincinnati, OH has operated a pilot plant approximately 5 kilometers from its main research facility. Originally, this Tet and Evaluation (T&E) facility was sited to be adjacent to the City of Cincinnati's...

The AB Initio Mia Method: Theoretical Development and Practical Applications

NASA Astrophysics Data System (ADS)

Peeters, Anik

The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.

Electronic structure, thermodynamic properties and hydrogenation of LaPtIn and CePtIn compounds by ab-initio methods

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

Jezierski, Andrzej, E-mail: andrzej.jezierski@ifmpan.poznan.pl; Szytuła, Andrzej

2016-02-15

The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in amore » good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier–Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0« less

Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

PubMed

Karthikeyan, S; Singh, Jiten N; Park, Mina; Kumar, Rajesh; Kim, Kwang S

2008-06-28

Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

Ab initio quantum chemical calculations of the interaction between radioactive elements and imidazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Saravanan, A. V. Sai; Abishek, B.; Anantharaj, R.

2018-04-01

The fundamental natures of the molecular level interaction and charge transfer between specific radioactive elements and ionic liquids of 1-butyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide ([BMIM]+[NTf2]-), 1-Butyl-3-methylimidazolium ethylsulfate ([BMIM]+[ES]-) and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]+[BF4]-) were investigated utilising HF theory and B3LYP hybrid DFT. The ambiguity in reaction mechanism of the interacting species dictates to employ Effective Core Potential (ECP) basis sets such as UGBS, SDD, and SDDAll to account for the relativistic effects of deep core electrons in the system involving potential, heavy and hazardous radioactive elements present in nuclear waste. The SCF energy convergence of each system validates the characterisation of the molecular orbitals as a linear combination of atomic orbitals utilising fixed MO coefficients and the optimized geometry of each system is visualised based on which Mulliken partial charge analysis is carried out to account for the polarising behaviour of the radioactive element and charge transfer between the IL phase by comparison with the bare IL species.

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.

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

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

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

Potential energy surfaces related to the ion-molecule reaction C/sup +/ + H/sub 2/

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

Liskow, D.H.; Bender, C.F.; Schaefer, H.F. III

1974-10-01

The C/sup +/ + H/sub 2/ ion-molecule reaction has been studied by several experimental groups and appears likely to become the focal point of much experimental and theoretical activity. Ab initio self-consistent-field and configuration interaction calculations have accordingly been carried out for this system. A double zeta basis set of contracted Gaussian functions was employed and as many as 648 configurations included. For isosceles triangle configurations (C/sub 2V/ point group) the /sup 2/A/sub 1/, /sup 2/B/sub 1/, and /sup 2/B/sub 2/ potential surfaces were considered, while for linear geometries (C/sub infinity V) the /sup 2/..sigma../sup +/ and /sup 2/PI surfacesmore » were studied. For general (C/sub S/) geometry, the lowest /sup 2/A' potential surface was considered. Properties reported include minimum energy paths and energy profiles for the various processes considered. The intuitive correlation diagram of Mahan and Sloane is given qualitative reliability. Pathways to CH/sub 2//sup +/ complex formation are shown to depend crucially on the C/sub S/ potential surface.« less

Molecular geometry and vibrational studies of 3,5-diamino-1,2,4-triazole using quantum chemical calculations and FT-IR and FT-Raman spectroscopies

NASA Astrophysics Data System (ADS)

Guennoun, L.; El jastimi, J.; Guédira, F.; Marakchi, K.; Kabbaj, O. K.; El Hajji, A.; Zaydoun, S.

2011-01-01

The 3,5-diamino-1,2,4-triazole (guanazole) was investigated by vibrational spectroscopy and quantum methods. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm -1 and 3600-50 cm -1 respectively, and the band assignments were supported by deuteration effects. The results of energy calculations have shown that the most stable form is 1H-3,5-diamino-1,2,4-triazole under C 1 symmetry. For this form, the molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated by the ab initio/HF and DFT/B3LYP methods using 6-31G* basis set. The calculated geometrical parameters of the guanazole molecule using B3LYP methodology are in good agreement with the previously reported X-ray data, and the scaled vibrational wave number values are in good agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PEDs) using VEDA 4 program.

Structures, energetics, vibrational spectra of NH4+(H2O)n=4,6 clusters: Ab initio calculations and first principles molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Karthikeyan, S.; Singh, Jiten N.; Park, Mina; Kumar, Rajesh; Kim, Kwang S.

2008-06-01

Important structural isomers of NH4+(H2O)n=4,6 have been studied by using density functional theory, Møller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n=4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.

Ab initio molecular orbital studies of the vibrational spectra of the van der Waals complexes of boron trifluoride with the noble gases.

PubMed

Ford, Thomas A

2005-05-01

The molecular structures, interaction energies, charge transfer properties and vibrational spectra of the van der Waals complexes formed between boron trifluoride and the noble gases neon, argon, krypton and xenon have been computed using second and fourth order Møller-Plesset perturbation theory and the Los Alamos National Laboratory LANL2DZ basis set. The complexes are all symmetric tops, with the noble gas atom acting as a sigma electron donor along the C3 axis of the BF3 molecule. The interaction energies are all vanishingly small, and the amount of charge transferred in each case is of the order of 0.01e. The directions of the wavenumber shifts of the symmetric bending (nu2) and antisymmetric stretching (nu3) modes of the BF3 fragment confirm those determined experimentally, and the shifts are shown to correlate well with the polarizability of the noble gas atom and the inverse sixth power of the intermonomer separation. The nu2 mode is substantially more sensitive to complexation than the nu3 vibration.

Titan's Ionic Species: Theoretical Treatment of N2H+ and Related Ions

NASA Astrophysics Data System (ADS)

Brites, V.; Hochlaf, M.

2009-06-01

We use different ab initio methods to compute the three-dimensional potential energy surface (3D-PES) of the ground state of N2H+. This includes the standard coupled cluster, the complete active space self-consistent field, the internally contacted multi reference configuration interaction, and the newly developed CCSD(T)-F12 methods. For the description of H and N atoms, several basis sets are tested. Then, we incorporate the 3D-PES analytical representations into variational calculations of the rovibrational spectrum of N2H+(X˜1Σ+) up to 7200 cm-1 above the zero point vibrational energy. Our data show that the CCSD(T)-F12/aug-cc-pVTZ approach represents a compromise for good description of the PES and computation cost. This technique is recommended for full dimensional PES generation of atmospheric and astrophysical relevant polyatomic systems. We applied this method to derive the rovibrational spectra of N2H+(X˜1Σ+) and of N2H++(X˜2Σ+). Finally, we discuss the existence of the N2H++(X˜2Σ+) in Titan's atmosphere.

Increasing the applicability of density functional theory. IV. Consequences of ionization-potential improved exchange-correlation potentials.

PubMed

Verma, Prakash; Bartlett, Rodney J

2014-05-14

This paper's objective is to create a "consistent" mean-field based Kohn-Sham (KS) density functional theory (DFT) meaning the functional should not only provide good total energy properties, but also the corresponding KS eigenvalues should be accurate approximations to the vertical ionization potentials (VIPs) of the molecule, as the latter condition attests to the viability of the exchange-correlation potential (VXC). None of the prominently used DFT approaches show these properties: the optimized effective potential VXC based ab initio dft does. A local, range-separated hybrid potential cam-QTP-00 is introduced as the basis for a "consistent" KS DFT approach. The computed VIPs as the negative of KS eigenvalue have a mean absolute error of 0.8 eV for an extensive set of molecule's electron ionizations, including the core. Barrier heights, equilibrium geometries, and magnetic properties obtained from the potential are in good agreement with experiment. A similar accuracy with less computational efforts can be achieved by using a non-variational global hybrid variant of the QTP-00 approach.

Ab initio investigation of the ground and low-lying states of the diatomic fluorides TiF, VF, CrF, and MnF

NASA Astrophysics Data System (ADS)

Koukounas, Constantine; Kardahakis, Stavros; Mavridis, Aristides

2004-06-01

The electronic structure of the ground and low-lying states of the diatomic fluorides TiF, VF, CrF, and MnF was examined by multireference and coupled cluster methods in conjunction with extended basis sets. For a total of 34 states we report binding energies, spectroscopic constants, dipole moments, separation energies, and charge distributions. In addition, for all states we have constructed full potential curves. The suggested ground state binding energies of TiF(X 4Φ), VF(X 5Π), CrF(X 6Σ+), and MnF(X 7Σ+) are 135, 130, 110, and 108 kcal/mol, respectively, with first excited states A 4Σ-, A 5Δ, A 6Π, and a 5Σ+ about 2, 3, 23, and 19 kcal/mol higher. In essence all our numerical findings are in harmony with experimental results. For all molecules and states studied it is clear that the in situ metal atom (M) shows highly ionic character, therefore the binding is described realistically by M+F-.

Ab initio investigation of the ground and low-lying states of the diatomic fluorides TiF, VF, CrF, and MnF.

PubMed

Koukounas, Constantine; Kardahakis, Stavros; Mavridis, Aristides

2004-06-22

The electronic structure of the ground and low-lying states of the diatomic fluorides TiF, VF, CrF, and MnF was examined by multireference and coupled cluster methods in conjunction with extended basis sets. For a total of 34 states we report binding energies, spectroscopic constants, dipole moments, separation energies, and charge distributions. In addition, for all states we have constructed full potential curves. The suggested ground state binding energies of TiF(X (4)Phi), VF(X (5)Pi), CrF(X (6)Sigma(+)), and MnF(X (7)Sigma(+)) are 135, 130, 110, and 108 kcal/mol, respectively, with first excited states A (4)Sigma(-), A (5)Delta, A (6)Pi, and a (5)Sigma(+) about 2, 3, 23, and 19 kcal/mol higher. In essence all our numerical findings are in harmony with experimental results. For all molecules and states studied it is clear that the in situ metal atom (M) shows highly ionic character, therefore the binding is described realistically by M(+)F(-). (c) 2004 American Institute of Physics.

Theoretical studies of the electronic spectrum of tellurium monosulfide.

PubMed

Chattopadhyaya, Surya; Nath, Abhijit; Das, Kalyan Kumar

2013-08-01

Ab initio based multireference singles and doubles configuration interaction (MRDCI) study including spin-orbit coupling is carried out to explore the electronic structure and spectroscopic properties of tellurium monosulfide (TeS) molecule by employing relativistic effective core potentials (RECP) and suitable Gaussian basis sets of the constituent atoms. Potential energy curves correlating with the lowest and second dissociation limit are constructed and spectroscopic constants (T(e), r(e), and ω(e)) of several low-lying bound Λ-S electronic states up to 3.68 eV of energy are computed. The binding energies and electric dipole moments (μ(e)) of the ground and the low-lying excited Λ-S states are also computed. The effects of the spin-orbit coupling on the electronic spectrum of the species are studied in details and compared with the available data. The transition probabilities of some dipole-allowed and spin-forbidden transitions are computed and radiative lifetimes of some excited states at lowest vibrational level are estimated from the transition probability data. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

High-level theoretical rovibrational spectroscopy beyond fc-CCSD(T): The C3 molecule.

PubMed

Schröder, Benjamin; Sebald, Peter

2016-01-28

An accurate local (near-equilibrium) potential energy surface (PES) is reported for the C3 molecule in its electronic ground state (X̃(1)Σg (+)). Special care has been taken in the convergence of the potential relative to high-order correlation effects, core-valence correlation, basis set size, and scalar relativity. Based on the aforementioned PES, several rovibrational states of all (12)C and (13)C substituted isotopologues have been investigated, and spectroscopic parameters based on term energies up to J = 30 have been calculated. Available experimental vibrational term energies are reproduced to better than 1 cm(-1) and rotational constants show relative errors of not more than 0.01%. The equilibrium bond length has been determined in a mixed experimental/theoretical approach to be 1.294 07(10) Å in excellent agreement with the ab initio composite value of 1.293 97 Å. Theoretical band intensities based on a newly developed electric dipole moment function also suggest that the infrared active (1, 1(1), 0)←(0, 0(0), 0) combination band might be observable by high-resolution spectroscopy.

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

A theoretical study of the photoinduced desorption of I — from a CF3I dimer

NASA Astrophysics Data System (ADS)

Tossell, J. A.

1997-04-01

Ab initio SCF-MO calculations using effective core-potential basis sets are employed to evaluate ionization potentials and electron affinities for CF3I and the geometries and energies of the singlet and triplet states of the CF3I dimer. The calculated geometry of the single state of the dimer is in qualitative agreement with the experimental geometry for condensed phase CF3I. The calculated energy for vertical excitation from the singlet to the triplet state is 4.1 eV at the Hartree-Fock level and 4.5 eV after incorporation of correlation at the Moller-Plesset 2nd-order level, consistent with excitation by 193 nm (6.4 eV) light. The equilibrium geometry of the triplet consists essentially of a CF3I+, CF3I- ion pair, in which the Csbnd I bond distance in the anionic component has increased to 5.5Å, compared with 2.1Åin the neutral molecule. The calculated binding energy of the triplet ion pair is about 4 eV.

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.

Ethanol Dimer: Observation of Three New Conformers by Broadband Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Loru, Donatella; Peña, Isabel; Sanz, M. Eugenia

2017-06-01

The conformational behaviour of the hydrogen-bonded cluster ethanol dimer has been reinvestigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency region. Three new conformers ({tt}, {tg}+, and {g}-{g}+) have been identified together with the three ({g}+{g}+, {g}-{t}, and {g}+{t}) previously observed by Hearn et al. (J. Chem. Phys. 123, 134324, 2005) and their rotational and centrifugal distortion constants have been determined. By using different carrier gases in the supersonic expansion, the relative abundances of the observed conformers have been estimated. The monosubstituted ^{13}C species and some of the ^{18}O species of the most abundant conformers {g}+{g}+, {g}-{t}, and {tt} have been observed in their natural abundance, which led to the partial determination of their r_{s} structures, and the r_{0} structure for the {tt} conformer. The six observed conformers are stabilized by the delicate interplay of primary O-H...O and secondary C-H...O hydrogen bonds, and dispersion interactions between the methyl groups. Density functional and ab initio methods with different basis sets are benchmarked against the experimental data.

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

De La Pierre, Marco, E-mail: cedric.carteret@univ-lorraine.fr, E-mail: marco.delapierre@unito.it; Maschio, Lorenzo; Orlando, Roberto

Powder and single crystal Raman spectra of the two most common phases of calcium carbonate are calculated with ab initio techniques (using a “hybrid” functional and a Gaussian-type basis set) and measured both at 80 K and room temperature. Frequencies of the Raman modes are in very good agreement between calculations and experiments: the mean absolute deviation at 80 K is 4 and 8 cm{sup −1} for calcite and aragonite, respectively. As regards intensities, the agreement is in general good, although the computed values overestimate the measured ones in many cases. The combined analysis permits to identify almost all themore » fundamental experimental Raman peaks of the two compounds, with the exception of either modes with zero computed intensity or modes overlapping with more intense peaks. Additional peaks have been identified in both calcite and aragonite, which have been assigned to {sup 18}O satellite modes or overtones. The agreement between the computed and measured spectra is quite satisfactory; in particular, simulation permits to clearly distinguish between calcite and aragonite in the case of powder spectra, and among different polarization directions of each compound in the case of single crystal spectra.« less

Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

NASA Astrophysics Data System (ADS)

Patel, Kinjal D.; Patel, Urmila H.

2017-01-01

Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

PubMed

Karthikeyan, S; Lee, Han Myoung; Kim, Kwang S

2010-10-12

There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

First-principles study of point defects at a semicoherent interface

DOE PAGES

Metsanurk, E.; Tamm, A.; Caro, A.; ...

2014-12-19

Most of the atomistic modeling of semicoherent metal-metal interfaces has so far been based on the use of semiempirical interatomic potentials. Here, we show that key conclusions drawn from previous studies are in contradiction with more precise ab-initio calculations. In particular we find that single point defects do not delocalize, but remain compact near the interfacial plane in Cu-Nb multilayers. Lastly, we give a simple qualitative explanation for this difference on the basis of the well known limited transferability of empirical potentials.

Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry

NASA Astrophysics Data System (ADS)

Haworth, Naomi L.; Bacskay, George B.

2002-12-01

The heats of formation of a range of phosphorus containing molecules (P2, P4, PH, PH2, PH3, P2H2, P2H4, PO, PO2, PO3, P2O, P2O2, HPO, HPOH, H2POH, H3PO, HOPO, and HOPO2) have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the B3LYP/6-31G(2df,p) functional and basis set. Atomization energies were obtained by the application of ab initio coupled cluster theory with single and double excitations from (spin)-restricted Hartree-Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with cc-pVnZ basis sets (n=T, Q, 5) which include an extra d function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core-valence (CV) correlation and scalar relativistic effects, as well as for basis set superposition errors (BSSE) in the CV terms. This methodology is effectively the same as the one adopted by Bauschlicher in his study of PO, PO2, PO3, HPO, HOPO, and HOPO2. Consequently, for these molecules the results of this work closely match Bauschlicher's computed values. The theoretical heats of formation, whose accuracy is estimated as ranging from ±1.0 to ±2.5 kcal mol-1, are consistent with the available experimental data. The current set of theoretical data represent a convenient benchmark, against which the results of other computational procedures, such as G3, G3X, and G3X2, can be compared. Despite the fact that G3X2 [which is an approximation to the quadratic CI procedure QCISD(T,Full)/G3Xlarge] is a formally higher level theory than G3X, the heats of formation obtained by these two methods are found to be of comparable accuracy. Both reproduce the benchmark heats of formation on the average to within ±2 kcal mol-1 and, for these molecules at least, they are superior to the basic G3 method. The performance of G3X2 is further improved, however, by the incorporation of BSSE corrections in the CV component of the energies. All the G3n methods have difficulties, however, with molecules which have multiple or highly strained P-P bonds, such as P2 and P4.

The role of NH3 and hydrocarbon mixtures in GaN pseudo-halide CVD: a quantum chemical study.

PubMed

Gadzhiev, Oleg B; Sennikov, Peter G; Petrov, Alexander I; Kachel, Krzysztof; Golka, Sebastian; Gogova, Daniela; Siche, Dietmar

2014-11-01

The prospects of a control for a novel gallium nitride pseudo-halide vapor phase epitaxy (PHVPE) with HCN were thoroughly analyzed for hydrocarbons-NH3-Ga gas phase on the basis of quantum chemical investigation with DFT (B3LYP, B3LYP with D3 empirical correction on dispersion interaction) and ab-initio (CASSCF, coupled clusters, and multireference configuration interaction including MRCI+Q) methods. The computational screening of reactions for different hydrocarbons (CH4, C2H6, C3H8, C2H4, and C2H2) as readily available carbon precursors for HCN formation, potential chemical transport agents, and for controlled carbon doping of deposited GaN was carried out with the B3LYP method in conjunction with basis sets up to aug-cc-pVTZ. The gas phase intermediates for the reactions in the Ga-hydrocarbon systems were predicted at different theory levels. The located π-complexes Ga…C2H2 and Ga…C2H4 were studied to determine a probable catalytic activity in reactions with NH3. A limited influence of the carbon-containing atmosphere was exhibited for the carbon doping of GaN crystal in the conventional GaN chemical vapor deposition (CVD) process with hydrocarbons injected in the gas phase. Our results provide a basis for experimental studies of GaN crystal growth with C2H4 and C2H2 as auxiliary carbon reagents for the Ga-NH3 and Ga-C-NH3 CVD systems and prerequisites for reactor design to enhance and control the PHVPE process through the HCN synthesis.

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

The ab-initio density matrix renormalization group in practice.

PubMed

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-21

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

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

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

A new potential energy surface for vibration-vibration coupling in HF-HF collisions. Formulation and quantal scattering calculations

NASA Astrophysics Data System (ADS)

Schwenke, David W.; Truhlar, Donald G.

1988-04-01

We present new ab initio calculations of the HF-HF interaction potential for the case where both molecules are simultaneously displaced from their equilibrium internuclear distance. These and previous ab initio calculations are then fit to a new analytic representation which is designed to be efficient to evaluate and to provide an especially faithful account of the forces along the vibrational coordinates. We use the new potential for two sets of quantal scattering calculations for collisions in three dimensions with total angular momentum zero. First we test that the angular harmonic representation of the anisotropy is adequate by comparing quantal rigid rotator calculations to those carried out for potentials involving higher angular harmonics and for which the expansion in angular harmonics is systematically increased to convergence. Then we carry out large-scale quantal calculations of vibration-vibration energy transfer including the coupling of both sets of vibrational and rotational coordinates. These calculations indicate that significant rotational energy transfer accompanies the vibration-to-vibration energy transfer process.

Ab Initio Design of Potent Anti-MRSA Peptides based on Database Filtering Technology

PubMed Central

Mishra, Biswajit; Wang, Guangshun

2012-01-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed.1 This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g. amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database2 by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 minutes. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. A combination of our ab initio design with database screening3 led to yet another peptide with enhanced potency. Because of simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well. PMID:22803960

Ab initio design of potent anti-MRSA peptides based on database filtering technology.

PubMed

Mishra, Biswajit; Wang, Guangshun

2012-08-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.

Rate Constants for Fine-Structure Excitations in O - H Collisions with Error Bars Obtained by Machine Learning

NASA Astrophysics Data System (ADS)

Vieira, Daniel; Krems, Roman

2017-04-01

Fine-structure transitions in collisions of O(3Pj) with atomic hydrogen are an important cooling mechanism in the interstellar medium; knowledge of the rate coefficients for these transitions has a wide range of astrophysical applications. The accuracy of the theoretical calculation is limited by inaccuracy in the ab initio interaction potentials used in the coupled-channel quantum scattering calculations from which the rate coefficients can be obtained. In this work we use the latest ab initio results for the O(3Pj) + H interaction potentials to improve on previous calculations of the rate coefficients. We further present a machine-learning technique based on Gaussian Process regression to determine the sensitivity of the rate coefficients to variations of the underlying adiabatic interaction potentials. To account for the inaccuracy inherent in the ab initio calculations we compute error bars for the rate coefficients corresponding to 20% variation in each of the interaction potentials. We obtain these error bars by fitting a Gaussian Process model to a data set of potential curves and rate constants. We use the fitted model to do sensitivity analysis, determining the relative importance of individual adiabatic potential curves to a given fine-structure transition. NSERC.

Ab initio, density functional theory, and continuum solvation model prediction of the product ratio in the S(N)2 reaction of NO2(-) with CH3CH2Cl and CH3CH2Br in DMSO solution.

PubMed

Westphal, Eduard; Pliego, Josefredo R

2007-10-11

The reaction pathways for the interaction of the nitrite ion with ethyl chloride and ethyl bromide in DMSO solution were investigated at the ab initio level of theory, and the solvent effect was included through the polarizable continuum model. The performance of BLYP, GLYP, XLYP, OLYP, PBE0, B3PW91, B3LYP, and X3LYP density functionals has been tested. For the ethyl bromide case, our best ab initio calculations at the CCSD(T)/aug-cc-pVTZ level predicts product ratio of 73% and 27% for nitroethane and ethyl nitrite, respectively, which can be compared with the experimental values of 67% and 33%. This translates to an error in the relative DeltaG* of only 0.17 kcal mol(-1). No functional is accurate (deviation <0.5 kcal mol(-1)) for predicting relative DeltaG*. The hybrid X3LYP functional presents the best performance with deviation 0.82 kcal mol(-1). The present problem should be included in the test set used for the evaluation of new functionals.

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by hydrogen atoms.

PubMed

Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos G; Marin, Guy B

2014-10-09

Hydrogen-abstraction reactions play a significant role in thermal biomass conversion processes, as well as regular gasification, pyrolysis, or combustion. In this work, a group additivity model is constructed that allows prediction of reaction rates and Arrhenius parameters of hydrogen abstractions by hydrogen atoms from alcohols, ethers, esters, peroxides, ketones, aldehydes, acids, and diketones in a broad temperature range (300-2000 K). A training set of 60 reactions was developed with rate coefficients and Arrhenius parameters calculated by the CBS-QB3 method in the high-pressure limit with tunneling corrections using Eckart tunneling coefficients. From this set of reactions, 15 group additive values were derived for the forward and the reverse reaction, 4 referring to primary and 11 to secondary contributions. The accuracy of the model is validated upon an ab initio and an experimental validation set of 19 and 21 reaction rates, respectively, showing that reaction rates can be predicted with a mean factor of deviation of 2 for the ab initio and 3 for the experimental values. Hence, this work illustrates that the developed group additive model can be reliably applied for the accurate prediction of kinetics of α-hydrogen abstractions by hydrogen atoms from a broad range of oxygenates.

Potential surfaces for O atom-polymer reactions

NASA Technical Reports Server (NTRS)

Laskowski, B. C.; Jaffe, R. L.

1987-01-01

Ab initio quantum chemistry methods are used to study the energetics of interactions of O atoms with organic compounds. Polyethylene (CH2)n has been chosen as the model system to study the interactions of O(3P) and O(1D) atoms with polymers. In particular, H abstraction is investigated and polyethylene is represented by a C3 (propane) oligomeric model. The gradient method, as implemented in the GRADSCF package of programs, is used to determine the geometries and energies of products and reactants. The saddle point, barrier geometry is determined by minimizing the squares of the gradients of the potential with respect to the internal coordinates. To correctly describe the change in bonding during the reaction at least a two configuration MCSCF (multiconfiguration self consistent field) or GVB (generalized valence bond) wave function has to be used. Basis sets include standard Pople and Dunning sets, however, increased with polarization functions and diffuse p functions on both the C and O atoms. The latter is important due to the O(-) character of the wave function at the saddle point and products. Normal modes and vibrational energy levels are given for the reactants, saddle points and products. Finally, quantitative energetics are obtained by implementing a small CAS (complete active space) approach followed by limited configuration interaction (CI) calculations. Comparisons are made with available experimental data.