Bean peptides have higher in silico binding affinities than ezetimibe for the N-terminal domain of cholesterol receptor Niemann-Pick C1 Like-1.

PubMed

Real Hernandez, Luis M; Gonzalez de Mejia, Elvira

2017-04-01

Niemann-Pick C1 like-1 (NPC1L1) mediates cholesterol absorption at the apical membrane of enterocytes through a yet unknown mechanism. Bean, pea, and lentil proteins are naturally hydrolyzed during digestion to produce peptides. The potential for pulse peptides to have high binding affinities for NPC1L1 has not been determined. In this study , in silico binding affinities and interactions were determined between the N-terminal domain of NPC1L1 and 14 pulse peptides (5≥ amino acids) derived through pepsin-pancreatin digestion. Peptides were docked in triplicate to the N-terminal domain using docking program AutoDock Vina, and results were compared to those of ezetimibe, a prescribed NPC1L1 inhibitor. Three black bean peptides (-7.2 to -7.0kcal/mol) and the cowpea bean dipeptide Lys-Asp (-7.0kcal/mol) had higher binding affinities than ezetimibe (-6.6kcal/mol) for the N-terminal domain of NPC1L1. Lentil and pea peptides studied did not have high binding affinities. The common bean peptide Tyr-Ala-Ala-Ala-Thr (-7.2kcal/mol), which can be produced from black or navy bean proteins, had the highest binding affinity. Ezetimibe and peptides with high binding affinities for the N-terminal domain are expected to interact at different locations of the N-terminal domain. All high affinity black bean peptides are expected to have van der Waals interactions with SER130, PHE136, and LEU236 and a conventional hydrogen bond with GLU238 of NPC1L1. Due to their high affinity for the N-terminal domain of NPC1L1, black and cowpea bean peptides produced in the digestive track have the potential to disrupt interactions between NPC1L1 and membrane proteins that lead to cholesterol absorption. Copyright © 2017 Elsevier Inc. All rights reserved.

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors.

PubMed

Ciordia, Myriam; Pérez-Benito, Laura; Delgado, Francisca; Trabanco, Andrés A; Tresadern, Gary

2016-09-26

Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of β-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting molecules showed pIC50 potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.

Cation-Cation pi-pi Stacking in Small Ionic Clusters of 1,2,4-Triazolium

DTIC Science & Technology

2008-01-01

ZPE ) obtained with MP2/aug-cc-pVDZ harmonic vibrational frequencies, the ionic tetramer is 1.2 kcal/mol lower in energy than that of the neutral one...respectively. Including ZPE , these three values become 5.7, 7.3, and 7.7 kcal/mol, respectively. Further corrections for the basis set effects from aug-cc-pVDZ

Cooperative unfolding of apolipoprotein A-1 induced by chemical denaturation.

PubMed

Eckhardt, D; Li-Blatter, X; Schönfeld, H-J; Heerklotz, H; Seelig, J

2018-05-25

Apolipoprotein A-1 (Apo A-1) plays an important role in lipid transfer and obesity. Chemical unfolding of α-helical Apo A-1 is induced with guanidineHCl and monitored with differential scanning calorimetry (DSC) and CD spectroscopy. The unfolding enthalpy and the midpoint temperature of unfolding decrease linearly with increasing guanidineHCl concentration, caused by the weak binding of denaturant. At room temperature, binding of 50-60 molecules guanidineHCl leads to a complete Apo A-1 unfolding. The entropy of unfolding decreases to a lesser extent than the unfolding enthalpy. Apo A-1 chemical unfolding is a dynamic multi-state equilibrium that is analysed with the Zimm-Bragg theory modified for chemical unfolding. The chemical Zimm-Bragg theory predicts the denaturant binding constant K D and the protein cooperativity σ. Chemical unfolding of Apo A-1 is two orders of magnitude less cooperative than thermal unfolding. The free energy of thermal unfolding is ~0.2 kcal/mol per amino acid residue and ~1.0 kcal/mol for chemical unfolding at room temperature. The Zimm-Bragg theory calculates conformational probabilities and the chemical Zimm-Bragg theory predicts stretches of α-helical segments in dynamic equilibrium, unfolding and refolding independently and fast. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Thermal dissociation and relaxation in vinyl fluoride, 1,1-difluoroethane and 1,3,5-triazine

NASA Astrophysics Data System (ADS)

Xu, Hui

This study reports measurements of the thermal dissociation of 1,1-difluoroethane in the shock tube. The experiments employ laser schlieren measurements of rate for the dominant HF elimination using 10% 1,1-difluoroethane in Kr over 1500--2000 K and 43 < P < 424 torr. The product vinyl then dissociates affecting the late density gradient. We include a laser schlieren study (1717--2332 K, 75 < P < 482 torr in 10% and 4% vinyl fluoride in Kr) of this dissociation. This latter work also includes a set of experiments using shock-tube time-of-flight mass-spectrometry (4% vinyl fluoride in neon, 1500--1980 K, 500 < P < 1300 torr), which confirm the theoretical expectation that the only reaction in vinyl fluoride is HF elimination. The relaxation experiments (1--20% C2H3F in Kr, 415--1975 K, 5 < P < 50 torr, and 2% and 5% C2H4F2 in Kr, 700--1350 K, 6 < P < 22 torr) exhibit very rapid relaxation, and incubation delays should be negligible in dissociation. A RRKM model of dissociation in 1,1-difluoroethane based on a G3B3 calculation of barrier and other properties fits the experiments but requires a very large down of 1600cm-1 . Dissociation of vinyl fluoride has two parallel HF eliminations both three-center and four-center with nearly equal barriers. An RRKM fit to the observed falloff again requires an unusually large down and the experiments actually support a slightly reduced barrier. Both 1,3,5-triazine and pyrazine relax extremely rapidly with energy transfer in a few collisions, any incubation delay can be confidently discounted in dissociation. 1,3,5-triazine dissociation experiments show fall-off with a clear pressure dependence. The three body product dissociation mechanism models this dissociation perfectly. Experimental data agree well with an RRKM calculation using a down of 1200cm-1 and a barrier E0 = 84.66 kcal/mol. Dyakov et al. suggested lower barrier of E0 = 81 kcal/mole. The new RRKM calculation using this barrier seems a better

Insights into the Lactonase Mechanism of Serum Paraoxonase 1 (PON1): Experimental and Quantum Mechanics/Molecular Mechanics (QM/MM) Studies.

PubMed

Le, Quang Anh Tuan; Kim, Seonghoon; Chang, Rakwoo; Kim, Yong Hwan

2015-07-30

Serum paraoxonase 1 (PON1) is a versatile enzyme for the hydrolysis of various substrates (e.g., lactones, phosphotriesters) and for the formation of a promising chemical platform γ-valerolactone. Elucidation of the PON1-catalyzed lactonase reaction mechanism is very important for understanding the enzyme function and for engineering this enzyme for specific applications. Kinetic study and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to investigate the PON1-catalyzed lactonase reaction of γ-butyrolactone (GBL) and (R)-γ-valerolactone (GVL). The activation energies obtained from the QM/MM calculations were in good agreement with the experiments. Interestingly, the QM/MM energy barriers at MP2/3-21G(d,p) level for the lactonase of GVL and GBL were respectively 14.3-16.2 and 11.5-13.1 kcal/mol, consistent with the experimental values (15.57 and 14.73 kcal/mol derived from respective kcat values of 36.62 and 147.21 s(-1)). The QM/MM energy barriers at MP2/6-31G(d) and MP2/6-31G(d,p) levels were also in relatively good agreements with the experiments. Importantly, the difference in the QM/MM energy barriers at MP2 level with all investigated basis sets for the lactonase of GVL and GBL were in excellent agreement with the experiments (0.9-3.1 and 0.8 kcal/mol, respectively). A detailed mechanism for the PON1-catalyzed lactonase reaction was also proposed in this study.

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

PubMed

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

2018-01-05

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

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

PubMed Central

2017-01-01

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

The ozone acetylene reaction: concerted or non-concerted reaction mechanism? A quantum chemical investigation

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Kraka, Elfi; Crehuet, Ramon; Anglada, Josep; Gräfenstein, Jürgen

2001-10-01

The ozone-acetylene reaction is found to proceed via an intermediate van der Waals complex (rather than a biradical), which is the precursor for a concerted symmetry-allowed [4+2] cycloaddition reaction leading to 1,2,3-trioxolene. CCSD(T)/6-311G+(2d, 2p) and CCSD(T)/CBS (complete basis set) calculations predict the ozone-acetylene van der Waals complex to be stable by 2.2 kcal mol -1, the calculated activation enthalpy for the cycloaddition reaction is 9.6 kcal mol -1 and the reaction enthalpy -55.5 kcal mol -1. Calculated kinetic data for the overall reaction ( k=0.8 l mol -1 s-1, A=1.71×10 6 l mol -1 s-1, E a=8.6 kcal mol -1) suggest that there is a need for refined kinetic measurements.

Gas-phase Raman spectra and the potential energy function for the internal rotation of 1,3-butadiene and its isotopologues.

PubMed

Boopalachandran, Praveenkumar; Craig, Norman; Groner, Peter; Laane, Jaan

2011-08-18

The gas-phase Raman spectra of 1,3-butadiene and its 2,3-d(2), 1,1,4,4-d(4), and -d(6) isotopologues have been recorded with high sensitivity in the region below 350 cm(-1) in order to investigate the internal rotation (torsional) vibration. Based on more accurate structural information, the internal rotor constants F(n) were calculated as a function of rotation angle (ϕ). The data for all the isotopologues were then fit using a one-dimensional potential energy function of the form V = (1)/(2)∑V(n)(1 - cos ϕ). Initial V(n) values were based on those generated from theoretical calculations. The agreement between observed and calculated frequencies is very good, although bands not taken into account were present in the spectra. The energy difference between the trans and gauche forms was determined to be about 1030 cm(-1) (2.94 kcal/mol), and the barrier between the two equivalent gauche forms was determined to be about 180 cm(-1) (0.51 kcal/mol), which agrees well with high-level ab initio calculations. An alternative set of assignments also fits the data quite well for all of the isotopologues. For this model, the energy difference between the trans and gauche forms is about 1080 cm(-1) (3.09 kcal/mol), and the barrier between gauche forms is about 405 cm(-1) (1.16 kcal/mol). © 2011 American Chemical Society

Development of a standard reference material containing 22 chlorinated hydrocarbon gases at 1 μmol/mol in nitrogen.

PubMed

Li, Ning; Du, Jian; Yang, Jing; Fan, Qiang; Tian, Wen

2017-11-01

A gas standard mixture containing 22 chlorinated hydrocarbons in high purity nitrogen was prepared using a two-step weighing method and a gasifying apparatus developed in-house. The concentration of each component was determined using a gas chromatograph with flame ionization detection (GC/FID). Linear regression analysis of every component was performed using the gas standard mixture with concentrations ranging from 1 to 10 μmol/mol, showing the complete gasification of volatile organic compound (VOCs) species in a selected cylinder. Repeatability was also examined to ensure the reliability of the preparation method. In addition, no significant difference was observed between domestic treated and imported treated cylinders, which were conducive to reduction of the cost of raw materials. Moreover, the results of stability testing at different pressures and long-term stability tests indicated that the gas standard at 1 μmol/mol level with relative expanded uncertainties of 5% was stable above 2 MPa for a minimum of 12 months. Finally, a quantity comparison was conducted between the gas standard and a commercial gas standard from Scott Specialty Gases (now Air Liquide America Specialty Gases). The excellent agreement of every species suggested the favorable accuracy of our gas standard. Therefore, this reference material can be applied to routine observation of VOCs and for other purposes.

Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase.

PubMed

Goldman, Lawrence M; Amyes, Tina L; Goryanova, Bogdana; Gerlt, John A; Richard, John P

2014-07-16

The mechanism for activation of orotidine 5'-monophosphate decarboxylase (OMPDC) by interactions of side chains from Gln215 and Try217 at a gripper loop and R235, adjacent to this loop, with the phosphodianion of OMP was probed by determining the kinetic parameters k(cat) and K(m) for all combinations of single, double, and triple Q215A, Y217F, and R235A mutations. The 12 kcal/mol intrinsic binding energy of the phosphodianion is shown to be equal to the sum of the binding energies of the side chains of R235 (6 kcal/mol), Q215 (2 kcal/mol), Y217 (2 kcal/mol), and hydrogen bonds to the G234 and R235 backbone amides (2 kcal/mol). Analysis of a triple mutant cube shows small (ca. 1 kcal/mol) interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC. These mutations result in the same change in the activation barrier to the OMPDC-catalyzed reactions of the whole substrate OMP and the substrate pieces (1-β-D-erythrofuranosyl)orotic acid (EO) and phosphite dianion. This shows that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The 12 kcal/mol intrinsic phosphodianion binding energy of OMP is divided between the 8 kcal/mol of binding energy, which is utilized to drive a thermodynamically unfavorable conformational change of the free enzyme, resulting in an increase in (k(cat))(obs) for OMPDC-catalyzed decarboxylation of OMP, and the 4 kcal/mol of binding energy, which is utilized to stabilize the Michaelis complex, resulting in a decrease in (K(m))(obs).

Thermochemistry, Tautomerism, and Thermal Decomposition of 1,5-Diaminotetrazole: A High-Level ab Initio Study.

PubMed

Shakhova, Margarita V; Muravyev, Nikita V; Gritsan, Nina P; Kiselev, Vitaly G

2018-04-19

Thermochemistry, kinetics, and mechanism of thermal decomposition of 1,5-diaminotetrazole (DAT), a widely used "building block" of nitrogen-rich energetic compounds, were studied theoretically at a high and reliable level of theory (viz., using the explicitly correlated CCSD(T)-F12/aug-cc-pVTZ procedure). Quantum chemical calculations provided detailed insight into the thermolysis mechanism of DAT missing in the existing literature. Moreover, several contradictory assumptions on the mechanism and key intermediates of thermolysis were resolved. The unimolecular primary decomposition reactions of the seven isomers of DAT were studied in the gas phase and in the melt using a simplified model of the latter. The two-step reaction of N 2 elimination from the diamino tautomer was found to be the primary decomposition process of DAT in the gas phase and melt. The effective Arrhenius parameters of this process were calculated to be E a = 43.4 kcal mol -1 and log( A/s -1 ) = 15.2 in a good agreement with the experimental values. Contrary to the existing literature data, all other decomposition channels of DAT isomers turned out to be kinetically unimportant. Apart from this, a new primary decomposition channel yielding N 2 , cyanamide, and 1,1-diazene was found for some H-bonded dimers of DAT. We also determined a reliable and mutually consistent set of thermochemical values for DAT (Δ f H solid 0 = 74.5 ± 1.5 kcal·mol -1 ) by combining theoretically calculated (W1 multilevel procedure along with an isodesmic reaction) gas phase enthalpy of formation (Δ f H gas 0 = 100.7 ± 1.0 kcal·mol -1 ) and experimentally measured sublimation enthalpy (Δ sub H 0 = 26.2 ± 0.5 kcal·mol -1 ).

Thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli.

PubMed

Fukada, H; Sturtevant, J M; Quiocho, F A

1983-11-10

The thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli have been studied by isothermal and scanning calorimetry. The binding reaction with arabinose is characterized by an enthalpy change of -15.3 +/- 0.5 kcal mol-1 at 25 degrees C, and a large decrease in apparent heat capacity, amounting to -0.44 +/- 0.05 kcal K-1 mol-1, which is constant over the temperature range 8 to 30 degrees C. Very similar results were obtained with D-galactose. These calorimetric results have been combined with binding constants determined by equilibrium dialysis (Clark, A. F., Gerken, T. A., and Hogg, R. W. (1982) Biochemistry 21, 2227-2233) to obtain free energy and entropy changes over the range 5 to 30 degrees C, and by extrapolation to 60 degrees C. The protein undergoes reversible unfolding on being heated with an increase in enthalpy at 53.5 degrees C of 151.8 +/- 1.1 kcal mol-1 (169.2 +/- 1.2 kcal mol-1 at 59.0 degrees C) and in apparent heat capacity of 3.16 +/- 0.07 kcal K-1 mol-1. In the presence of arabinose, the unfolding enthalpy is increased to 200.7 +/- 1.8 kcal mol-1 at 59.0 degrees C, the increase being due to the enthalpy of dissociation of the ligand which amounts to 31 kcal mol-1 at the unfolding temperature. The unfolding temperature is increased by the presence of excess arabinose or galactose, an effect which is due solely to displacement by the added ligand of the unfolding-dissociation equilibrium. The thermodynamic data are discussed in connection with the detailed structural information available for this system from x-ray crystallography (Newcomer, M. E., Gilliland, G. L. and Quiocho, F. A. (1981) J. Biol. Chem. 256, 13213-13217, and references cited therein).

The ethane + oxygen(,2) reaction mechanism: High-level ab initio characterizations

NASA Astrophysics Data System (ADS)

Rienstra-Kiracofe, Jonathan C.

The C2H˙5+O2 reaction, central to ethane oxidation and thus of fundamental importance to hydrocarbon combustion chemistry, has been examined in detail via highly sophisticated electronic structure methods. The geometries, energies, and harmonic vibrational frequencies of the reactants, transition states, intermediates, and products for the reaction of the ethyl radical (X~ 2A ') with O2 (X S-g3 , a 1Δg) have been investigated using the CCSD and CCSD(T) ab initio methods with basis sets ranging in quality from double-zeta plus polarization (DZP) to triple-zeta plus double polarization with f functions (TZ2Pf). Five mechanisms (M1-M5) involving the ground-state from the ethyl radical by O2 to give ethylene + HO˙2 with an overall 0 K activation energy, Ea(0 K) = +15.1 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P. (M2) Ethylperoxy β- hydrogen transfer with O-O bond rupture to yield oxirane + .OH Ea(0 K) = +5.3 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P. (M3) Ethylperoxy α- hydrogen transfer with O-O bond rupture to yield acetaldehyde + .OH Ea(0 K) = +11.5 kcal mol-1 with CCSD(T)/TZ2P//CCSD(T)/DZP. (M4) Ethylperoxy β- hydrogen transfer with C-O bond rupture to yield ethylene + HO˙2 ; Ea(0 K) = +5.3 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P, the C-O bond rupture barrier lying 1.2 kcal mol-1 above the O-O bond rupture barrier of M2 at the CCSD(T)/TZ2P//CCSD(T)/DZP level. (M5) Concerted elimination of HO˙2 from the ethylperoxy radical to give ethylene + HO˙2 ; Ea(0 K) = -0.9 kcal mol -1 with CCSD(T)/TZPf//CCSD(T)/TZ2P. We show that M5 is energetically preferred and is also the only mechanism consistent with experimental observations of a negative temperature coefficient. The reverse reaction (C2H 4 + HO˙2 --> .C2H4OOH) has a zero-point corrected barrier of 14.4 kcal mol-1 with CCSD(T)/TZ2P//CCSD(T)/DZP.

Ab initio study on the 1:2 reaction of CO 2 with dimethylamine

NASA Astrophysics Data System (ADS)

Jamróz, MichałH.; Dobrowolski, Jan Cz.; Borowiak, Marek A.

1997-02-01

The reaction between CO 2 and the dimethylamine molecule in the presence of a second dimethylamine molecule is modeled by the ab initio RHF/3-21G method. Starting from the most stable 1:2 complex, the most effective reaction pathway turned out to be proton transfer between amine molecules followed by immediate proton transfer from one of the amine molecules to the CO 2 moiety. The activation barrier for this pathway (9.54 kcal mol -1 with respect to the 1:2 complex) is within the range of activation energy values found in kinetic studies for similar reactions with different hydroxylamines (from 9.2 to 13.0 kcal mol -1). The reaction product is the cyclic hydrogen bonded complex of dimethylcarbamic acid with dimethylamine.

Trapping-mediated dissociative chemisorption of C3H8 and C3D8 on Ir(110)

NASA Astrophysics Data System (ADS)

Kelly, D.; Weinberg, W. H.

1996-07-01

We have employed molecular beam techniques to investigate the molecular trapping and trapping-mediated dissociative chemisorption of C3H8 and C3D8 on Ir(110) at low beam translational energies, Ei≤5 kcal/mol, and surface temperatures, Ts, from 85 to 1200 K. For Ts=85 K, C3H8 is molecularly adsorbed on Ir(110) with a trapping probability, ξ, equal to 0.94 at Ei=1.6 kcal/mol and ξ=0.86 at Ei=5 kcal/mol. At Ei=1.9 kcal/mol and Ts=85 K, ξ of C3D8 is equal to 0.93. From 150 K to approximately 700 K, the initial probabilities of dissociative chemisorption of propane decrease with increasing Ts. For Ts from 700 to 1200 K, however, the initial probability of dissociative chemisorption maintains the essentially constant value of 0.16. These observations are explained within the context of a kinetic model which includes both C-H (C-D) and C-C bond cleavage. Below 450 K propane chemisorption on Ir(110) arises essentially solely from C-H (C-D) bond cleavage, an unactivated mechanism (with respect to a gas-phase energy zero) for this system, which accounts for the decrease in initial probabilities of chemisorption with increasing Ts. With increasing Ts, however, C-C bond cleavage, the activation energy of which is greater than the desorption energy of physically adsorbed propane, increasingly contributes to the measured probability of dissociative chemisorption. The activation energies, referenced to the bottom of the physically adsorbed molecular well, for C-H and C-C bond cleavage for C3H8 on Ir(110) are found to be Er,CH=5.3±0.3 kcal/mol and Er,CC=9.9±0.6 kcal/mol, respectively. The activation energies for C-D and C-C bond cleavage for C3D8 on Ir(110) are 6.3±0.3 kcal/mol and 10.5±0.6 kcal/mol, respectively. The desorption activation energy of propane from Ir(110) is approximately 9.5 kcal/mol. These activation energies are compared to activation energies determined recently for ethane and propane adsorption on Ir(111), Ru(001), and Pt(110)-(1×2), and ethane

High level QM/MM modeling of the formation of the tetrahedral intermediate in the acylation of wild type and K73A mutant TEM-1 class A beta-lactamase.

PubMed

Hermann, Johannes C; Pradon, Juliette; Harvey, Jeremy N; Mulholland, Adrian J

2009-10-29

The breakdown of beta-lactam antibiotics by beta-lactamases is the most important resistance mechanism of gram negative bacteria against these drugs. The reaction mechanism of class A beta-lactamases, the most widespread family of these enzymes, consists of two main steps: acylation of an active site serine by the antibiotic, followed by deacylation and release of the cleaved compound. We have investigated the first step in acylation (the formation of the tetrahedral intermediate) for the reaction of benzylpenicillin in the TEM-1 enzyme using high level combined quantum mechanics/molecular mechanics (QM/MM) methods. Structures were optimized at the B3LYP/6-31+G(d)/CHARMM27 level, with energies for key points calculated up to the ab initio SCS-MP2/aug-cc-pVTZ/CHARMM27 level. The results support a mechanism in which Glu166 removes a proton (via an intervening water molecule) from Ser70, which in turn attacks the beta-lactam of the antibiotic. Depending on the method used, the calculated barriers range from 3 to 12 kcal mol(-1) for this step, consistent with experimental data. We have also modeled this reaction step in a model of the K73A mutant enzyme. The barrier to reaction in this mutant model is found to be slightly higher: the results indicate that Lys73 stabilizes the transition state, in particular deprotonated Ser70, lowering the barrier by about 1.7 kcal mol(-1). This finding may help to explain the conservation of Lys73, in addition to the role we have previously found for it in the later stages of the reaction (Hermann et al. Org. Biomol. Chem. 2006, 4, 206-210).

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A β-Lactamase

NASA Astrophysics Data System (ADS)

Hermann, Johannes C.; Pradon, Juliette; Harvey, Jeremy N.; Mulholland, Adrian J.

2009-09-01

The breakdown of β-lactam antibiotics by β-lactamases is the most important resistance mechanism of Gram negative bacteria against these drugs. The reaction mechanism of class A β-lactamases, the most widespread family of these enzymes, consists of two main steps: acylation of an active site serine by the antibiotic, followed by deacylation and release of the cleaved compound. We have investigated the first step in acylation (the formation of the tetrahedral intermediate) for the reaction of benzylpenicillin in the TEM-1 enzyme using high level combined quantum mechanics/molecular mechanics (QM/MM) methods. Structures were optimized at the B3LYP/6-31+G(d)/CHARMM27 level, with energies for key points calculated up to the ab initio SCS-MP2/aug-cc-pVTZ/CHARMM27 level. The results support a mechanism in which Glu166 removes a proton (via an intervening water molecule) from Ser70, which in turn attacks the β-lactam of the antibiotic. Depending on the method used, the calculated barriers range from 3 to 12 kcal mol-1 for this step, consistent with experimental data. We have also modeled this reaction step in a model of the K73A mutant enzyme. The barrier to reaction in this mutant model is found to be slightly higher: the results indicate that Lys73 stabilizes the transition state, in particular deprotonated Ser70, lowering the barrier by about 1.7 kcal mol-1. This finding may help to explain the conservation of Lys73, in addition to the role we have previously found for it in the later stages of the reaction ( Hermann et al. Org. Biomol. Chem. 2006, 4, 206 - 210 ).

Mechanism of atomic layer deposition of SiO2 on the silicon (100)-2×1 surface using SiCl4 and H2O as precursors

NASA Astrophysics Data System (ADS)

Kang, Jeung Ku; Musgrave, Charles B.

2002-03-01

We use density functional theory to investigate atomic layer deposition (ALD) mechanism of silicon dioxide on the Si(100)-2×1 surface from the precursors SiCl4 and H2O. First, we explore the reaction mechanism of water with the bare Si(100)-2×1 surface to produce surface hydroxyl groups. We find that this reaction proceeds through a two-step pathway with an overall barrier of 33.3 kcal/mol. Next, we investigate the ALD mechanism for the binary reaction sequence: the SiCl4 half reaction and the H2O half reaction. For the SiCl4 half reaction, SiCl4 first forms a σ-bond with the oxygen of the surface OH group and then releases an HCl molecule. The predicted barrier for this process is 15.8 kcal/mol. Next, adsorbed SiCl3 reacts with a neighboring OH group to form bridged SiCl2 with a barrier of 22.6 kcal/mol. The H2O half reaction also proceeds through two sequential steps with an overall barrier of 19.1 kcal/mol for the reaction of H2O with bridged SiCl2 to form bridged Si(OH)2. The predicted barrier of 22.6 kcal/mol for the rate-limiting step of the ALD binary reaction mechanism is consistent with the experimental value of 22.0 kcal/mol. In addition, we find that the calculated frequencies are in good agreement with the experimentally measured IR spectra.

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.

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

PubMed

Kóna, Juraj

2008-01-21

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

Incomplete APOBEC3G/F Neutralization by HIV-1 Vif Mutants Facilitates the Genetic Evolution from CCR5 to CXCR4 Usage.

PubMed

Alteri, Claudia; Surdo, Matteo; Bellocchi, Maria Concetta; Saccomandi, Patrizia; Continenza, Fabio; Armenia, Daniele; Parrotta, Lucia; Carioti, Luca; Costa, Giosuè; Fourati, Slim; Di Santo, Fabiola; Scutari, Rossana; Barbaliscia, Silvia; Fedele, Valentina; Carta, Stefania; Balestra, Emanuela; Alcaro, Stefano; Marcelin, Anne Genevieve; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Artese, Anna; Perno, Carlo Federico; Svicher, Valentina

2015-08-01

Incomplete APOBEC3G/F neutralization by a defective HIV-1Vif protein can promote genetic diversification by inducing G-to-A mutations in the HIV-1 genome. The HIV-1 Env V3 loop, critical for coreceptor usage, contains several putative APOBEC3G/F target sites. Here, we determined if APOBEC3G/F, in the presence of Vif-defective HIV-1 virus, can induce G-to-A mutations at V3 positions critical to modulation of CXCR4 usage. Peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM) from 2 HIV-1-negative donors were infected with CCR5-using 81.A-VifWT virus (i.e., with wild-type [WT] Vif protein), 81.A-VifE45G, or 81.A-VifK22E (known to incompletely/partially neutralize APOBEC3G/F). The rate of G-toA mutations was zero or extremely low in 81.A-VifWT- and 81.A-VifE45G-infected PBMC from both donors. Conversely, G-to-A enrichment was detected in 81.A-VifK22E-infected PBMC (prevalence ranging from 2.18% at 7 days postinfection [dpi] to 3.07% at 21 dpi in donor 1 and from 10.49% at 7 dpi to 8.69% at 21 dpi in donor 2). A similar scenario was found in MDM. G-to-A mutations occurred at 8 V3 positions, resulting in nonsynonymous amino acid substitutions. Of them, G24E and E25K strongly correlated with phenotypically/genotypically defined CXCR4-using viruses (P = 0.04 and 5.5e-7, respectively) and increased the CXCR4 N-terminal binding affinity for V3 (WT, -40.1 kcal/mol; G24E, -510 kcal/mol; E25K, -522 kcal/mol). The analysis of paired V3 and Vif DNA sequences from 84 HIV-1-infected patients showed that the presence of a Vif-defective virus correlated with CXCR4 usage in proviral DNA (P = 0.04). In conclusion, incomplete APOBEC3G/F neutralization by a single Vif amino acid substitution seeds a CXCR4-using proviral reservoir. This can have implications for the success of CCR5 antagonist-based therapy, as well as for the risk of disease progression. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Incomplete APOBEC3G/F Neutralization by HIV-1 Vif Mutants Facilitates the Genetic Evolution from CCR5 to CXCR4 Usage

PubMed Central

Alteri, Claudia; Surdo, Matteo; Bellocchi, Maria Concetta; Saccomandi, Patrizia; Continenza, Fabio; Armenia, Daniele; Parrotta, Lucia; Carioti, Luca; Costa, Giosuè; Fourati, Slim; Di Santo, Fabiola; Scutari, Rossana; Barbaliscia, Silvia; Fedele, Valentina; Carta, Stefania; Balestra, Emanuela; Alcaro, Stefano; Marcelin, Anne Genevieve; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Artese, Anna

2015-01-01

Incomplete APOBEC3G/F neutralization by a defective HIV-1Vif protein can promote genetic diversification by inducing G-to-A mutations in the HIV-1 genome. The HIV-1 Env V3 loop, critical for coreceptor usage, contains several putative APOBEC3G/F target sites. Here, we determined if APOBEC3G/F, in the presence of Vif-defective HIV-1 virus, can induce G-to-A mutations at V3 positions critical to modulation of CXCR4 usage. Peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM) from 2 HIV-1-negative donors were infected with CCR5-using 81.A-VifWT virus (i.e., with wild-type [WT] Vif protein), 81.A-VifE45G, or 81.A-VifK22E (known to incompletely/partially neutralize APOBEC3G/F). The rate of G-toA mutations was zero or extremely low in 81.A-VifWT- and 81.A-VifE45G-infected PBMC from both donors. Conversely, G-to-A enrichment was detected in 81.A-VifK22E-infected PBMC (prevalence ranging from 2.18% at 7 days postinfection [dpi] to 3.07% at 21 dpi in donor 1 and from 10.49% at 7 dpi to 8.69% at 21 dpi in donor 2). A similar scenario was found in MDM. G-to-A mutations occurred at 8 V3 positions, resulting in nonsynonymous amino acid substitutions. Of them, G24E and E25K strongly correlated with phenotypically/genotypically defined CXCR4-using viruses (P = 0.04 and 5.5e−7, respectively) and increased the CXCR4 N-terminal binding affinity for V3 (WT, −40.1 kcal/mol; G24E, −510 kcal/mol; E25K, −522 kcal/mol). The analysis of paired V3 and Vif DNA sequences from 84 HIV-1-infected patients showed that the presence of a Vif-defective virus correlated with CXCR4 usage in proviral DNA (P = 0.04). In conclusion, incomplete APOBEC3G/F neutralization by a single Vif amino acid substitution seeds a CXCR4-using proviral reservoir. This can have implications for the success of CCR5 antagonist-based therapy, as well as for the risk of disease progression. PMID:26055363

Synthesis, EPR and luminescent properties of YAlO3:Fe3+ (0.1-0.9mol%) nanopowders.

PubMed

Premkumar, H B; Nagabhushana, H; Sharma, S C; Daruka Prasad, B; Nagabhushana, B M; Rao, J L; Chakradhar, R P S

2014-05-21

A simple and inexpensive combustion method was used to prepare Fe(3+) doped YAlO3 perovskite within few minutes at low temperature (400±10°C). This might be useful in lowering the cost of the material. The final products were well characterized by various spectroscopic techniques such as PXRD, SEM, TEM, FTIR and UV-Visible. The average crystallite size was estimated from the broadening of the PXRD peaks and found to be in the range 45-90nm, the results were in good agreement with the W-H plots and TEM. The crystallites show dumbbell shape, agglomerated particles with different size. The TL glow curves of 1-5kGy γ-irradiated YAlO3:Fe(3+) (0.1mol%) nanopowder warmed at a heating rate of 3°Cs(-1) records a single glow peak at ∼260°C. The kinetic parameters namely activation energy (E), order of kinetics (b) and frequency factor (s) were determined at different gamma doses using the Chens glow peak shape method and the results were discussed in detail. The photoluminescence spectra for Fe(3+) (0.1-0.9mol%) doped YAlO3 records the lower energy band at 720nm ((4)T1 (4G)→(6)A1 (6S)) and the intermediate band located at 620nm ((4)T2 ((4)G)→(6)A1 (6S)) with the excitation of 378nm. The higher energy band located at 514nm was associated to (4)E+(4)A1 ((4)G)→(6)A1 (6S) transition. The resonance signals at g values 7.6, 4.97, 4.10, 2.94, 2.33 and 1.98 were observed in EPR spectra of Fe(3+) (0.1-0.9mol%) doped YAlO3 recorded at room temperature. The g values indicate that the iron ions were in trivalent state and distorted octahedral site symmetry was observed. Copyright © 2014 Elsevier B.V. All rights reserved.

The influence of excess K2O on the electrical properties of (K,Na)1/2Bi1/2TiO3 ceramics

NASA Astrophysics Data System (ADS)

Li, Linhao; Li, Ming; Sinclair, Derek C.

2018-04-01

The solid solution (KxNa0.50-x)Bi0.50TiO3 (KNBT) between Na1/2Bi1/2TiO3 and K1/2Bi1/2TiO3 (KBT) has been extensively researched as a candidate lead-free piezoelectric material because of its relatively high Curie temperature and good piezoelectric properties, especially near the morphotropic phase boundary (MPB) at x ˜ 0.10 (20 mol. % KBT). Here, we show that low levels of excess K2O in the starting compositions, i.e., (Ky+0.03Na0.50-y)Bi0.50TiO3.015 (y-series), can significantly change the conduction mechanism and electrical properties compared to a nominally stoichiometric KNBT series (KxNa0.50-x)Bi0.50TiO3 (x-series). Impedance spectroscopy measurements reveal significantly higher bulk conductivity (σb) values for y ≥ 0.10 samples [activation energy (Ea) ≤ 0.95 eV] compared to the corresponding x-series samples which possess bandgap type electronic conduction (Ea ˜ 1.26-1.85 eV). The largest difference in electrical properties occurs close to the MPB composition (20 mol. % KBT) where y = 0.10 ceramics possess σb (at 300 °C) that is 4 orders of magnitude higher than that of x = 0.10 and the oxide-ion transport number in the former is ˜0.70-0.75 compared to <0.05 in the latter (between 600 and 800 °C). The effect of excess K2O can be rationalised on the basis of the (K + Na):Bi ratio in the starting composition prior to ceramic processing. This demonstrates the electrical properties of KNBT to be sensitive to low levels of A-site nonstoichiometry and indicates that excess K2O in KNBT starting compositions to compensate for volatilisation can lead to undesirable high dielectric loss and leakage currents at elevated temperatures.

Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer.

PubMed

Reyes, Archie C; Amyes, Tina L; Richard, John P

2016-11-23

The stabilization of the transition state for hlGPDH-catalyzed reduction of DHAP due to the action of the phosphodianion of DHAP and the cationic side chain of R269 is between 12.4 and 17 kcal/mol. The R269A mutation of glycerol-3-phosphate dehydrogenase (hlGPDH) results in a 9.1 kcal/mol destabilization of the transition state for enzyme-catalyzed reduction of dihydroxyacetone phosphate (DHAP) by NADH, and there is a 6.7 kcal/mol stabilization of this transition state by 1.0 M guanidine cation (Gua + ) [J. Am. Chem. Soc. 2015, 137, 5312-5315]. The R269A mutant shows no detectable activity toward reduction of glycolaldehyde (GA), or activation of this reaction by 30 mM HPO 3 2- . We report the unprecedented self-assembly of R269A hlGPDH, dianions (X 2- = FPO 3 2- , HPO 3 2- , or SO 4 2- ), Gua + and GA into a functioning catalyst of the reduction of GA, and fourth-order reaction rate constants k cat /K GA K X K Gua . The linear logarithmic correlation (slope = 1.0) between values of k cat /K GA K X for dianion activation of wildtype hlGPDH-catalyzed reduction of GA and k cat /K GA K X K Gua shows that the electrostatic interaction between exogenous dianions and the side chain of R269 is not significantly perturbed by cutting hlGPDH into R269A and Gua + pieces. The advantage for connection of hlGPDH (R269A mutant + Gua + ) and substrate pieces (GA + HP i ) pieces, (ΔG S ‡ ) HPi+E+Gua = 5.6 kcal/mol, is nearly equal to the sum of the advantage to connection of the substrate pieces, (ΔG S ‡ ) GA+HPi = 3.3 kcal/mol, for wildtype hlGPDH-catalyzed reaction of GA + HP i , and for connection of the enzyme pieces, (ΔG S ‡ ) E+Gua = 2.4 kcal/mol, for Gua + activation of the R269A hlGPDH-catalyzed reaction of DHAP.

Mechanism of growth of the Ge wetting layer upon exposure of Si(100)-2 x 1 to GeH4.

PubMed

Liu, Chie-Sheng; Chou, Li-Wei; Hong, Lu-Sheng; Jiang, Jyh-Chiang

2008-04-23

This paper describes the initial reaction kinetics of Ge deposition after exposure of Si(100)-2 x 1 to GeH4 in a UHV-CVD system. The rate of Ge growth, especially at the wetting layer stage, was investigated using in situ X-ray photoelectron spectroscopy to measure the Ge signal at the onset of deposition. A kinetic analysis of the initial growth of the Ge wetting layer at temperatures ranging from 698 to 823 K revealed an activation energy of 30.7 kcal/mol. Density functional theory calculations suggested that opening of the Si dimer--with a closely matching energy barrier of 29.7 kcal/mol, following hydrogen atom migration--was the rate controlling step for the incorporation of a GeH2 unit into the lattice to complete the growth of the Ge wetting layer after dissociative adsorption of GeH4.

Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair.

PubMed

Reyes, Archie C; Koudelka, Astrid P; Amyes, Tina L; Richard, John P

2015-04-29

The side chain cation of R269 lies at the surface of l-glycerol 3-phosphate dehydrogenase (GPDH) and forms an ion pair to the phosphodianion of substrate dihydroxyacetone phosphate (DHAP), which is buried at the nonpolar protein interior. The R269A mutation of GPDH results in a 110-fold increase in K(m) (2.8 kcal/mol effect) and a 41,000-fold decrease in k(cat) (6.3 kcal/mol effect), which corresponds to a 9.1 kcal/mol destabilization of the transition state for GPDH-catalyzed reduction of DHAP by NADH. There is a 6.7 kcal/mol stabilization of the transition state for the R269A mutant GPDH-catalyzed reaction by 1.0 M guanidinium ion, and the transition state for the reaction of the substrate pieces is stabilized by an additional 2.4 kcal/mol by their covalent attachment at wildtype GPDH. These results provide strong support for the proposal that GPDH invests the 11 kcal/mol intrinsic phosphodianion binding energy of DHAP in trapping the substrate at a nonpolar active site, where strong electrostatic interactions are favored, and obtains a 9 kcal/mol return from stabilizing interactions between the side chain cation and transition state trianion. We propose a wide propagation for the catalytic motif examined in this work, which enables strong transition state stabilization from enzyme-phosphodianion pairs.

Molecular structure and conformational preferences of 1-bromo-1-silacyclohexane, CH2(CH2CH2)2SiH-Br, as studies by gas-phase electron diffraction and quantum chemistry

NASA Astrophysics Data System (ADS)

Belyakov, A. V.; Baskakov, A. A.; Naraev, V. N.; Rykov, A. N.; Oberhammer, H.; Arnason, I.; Wallevik, S. O.

2012-10-01

The molecular structure of axial and equatorial conformer of the 1-bromo-1-silacyclohexane molecule, CH2(CH2CH2)2SiH-Br, as well as thermodynamic equilibrium between these species are investigated by means of gas-phase electron diffraction and quantum chemistry on the MP2(full)/SDB-AUG-cc-PVTZ level of theory. It is revealed that according to electron diffraction data, the compound exists in the gasphase as a mixture of conformers possessing the chair conformation of the six-membered ring and C s symmetry and differing in the axial and equatorial position of the Si-Br bond (ax. = 80(5) mol %, eq. = 20(7) mol %) at 352 K, that corresponds to the value of A = ( G {ax/○} - G {eq/○}) = -0.82(32) kcal/mol. It is found that observed data agree well with theoretical ones. Using Natural Bond Orbital (NBO) analysis it is revealed that axial conformer of 1-bromo-1-silacyclohexane molecule is an example of the stabilization of the form that is unfavorable from the point of view of steric effects and effects of conjugations. It is concluded that stabilization is achieved due to electrostatic interactions.

The construction of space-like surfaces with k1k2 - m(k1 + k2) = 1 in Minkowski three-space

NASA Astrophysics Data System (ADS)

Cao, Xi-Fang

2002-07-01

From solutions of the sinh-Laplace equation, we construct a family of space-like surfaces with k1k2 - m(k1 + k2) = 1 in Minkowski three-space, where k1 and k2 are principal curvatures and m is an arbitrary constant.

The Unimolecular Reactions of CF3CHF2 Studied by Chemical Activation: Assignment of Rate Constants and Threshold Energies to the 1,2-H Atom Transfer, 1,1-HF and 1,2-HF Elimination Reactions, and the Dependence of Threshold Energies on the Number of F-Atom Substituents in the Fluoroethane Molecules.

PubMed

Smith, Caleb A; Gillespie, Blanton R; Heard, George L; Setser, D W; Holmes, Bert E

2017-11-22

The recombination of CF 3 and CHF 2 radicals in a room-temperature bath gas was used to prepare vibrationally excited CF 3 CHF 2 * molecules with 101 kcal mol -1 of vibrational energy. The subsequent 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions were observed as a function of bath gas pressure by following the CHF 3 , CF 3 (F)C: and C 2 F 4 product concentrations by gas chromatography using a mass spectrometer as the detector. The singlet CF 3 (F)C: concentration was measured by trapping the carbene with trans-2-butene. The experimental rate constants are 3.6 × 10 4 , 4.7 × 10 4 , and 1.1 × 10 4 s -1 for the 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions, respectively. These experimental rate constants were matched to statistical RRKM calculated rate constants to assign threshold energies (E 0 ) of 88 ± 2, 88 ± 2, and 87 ± 2 kcal mol -1 to the three reactions. Pentafluoroethane is the only fluoroethane that has a competitive H atom transfer decomposition reaction, and it is the only example with 1,1-HF elimination being more important than 1,2-HF elimination. The trend of increasing threshold energies for both 1,1-HF and 1,2-HF processes with the number of F atoms in the fluoroethane molecule is summarized and investigated with electronic-structure calculations. Examination of the intrinsic reaction coordinate associated with the 1,1-HF elimination reaction found an adduct between CF 3 (F)C: and HF in the exit channel with a dissociation energy of ∼5 kcal mol -1 . Hydrogen-bonded complexes between HF and the H atom migration transition state of CH 3 (F)C: and the F atom migration transition state of CF 3 (F)C: also were found by the calculations. The role that these carbene-HF complexes could play in 1,1-HF elimination reactions is discussed.

Berry Phenolic Compounds Increase Expression of Hepatocyte Nuclear Factor-1α (HNF-1α) in Caco-2 and Normal Colon Cells Due to High Affinities with Transcription and Dimerization Domains of HNF-1α

PubMed Central

Real Hernandez, Luis M.; Fan, Junfeng; Johnson, Michelle H.; Gonzalez de Mejia, Elvira

2015-01-01

Hepatocyte nuclear factor-1α (HNF-1α) is found in the kidneys, spleen, thymus, testis, skin, and throughout the digestive organs. It has been found to promote the transcription of various proteins involved in the management of type II diabetes, including dipeptidyl peptidase-IV (DPP-IV). Phenolic compounds from berries and citrus fruits are known to inhibit DPP-IV, but have not been tested for their interactions with wild-type HNF-1α. By studying the interactions of compounds from berries and citrus fruits have with HNF-1α, pre-transcriptional mechanisms that inhibit the expression of proteins such as DPP-IV may be elucidated. In this study, the interactions of berry phenolic compounds and citrus flavonoids with the dimerization and transcriptional domains of HNF-1α were characterized using the molecular docking program AutoDock Vina. The anthocyanin delphinidin-3-O-arabinoside had the highest binding affinity for the dimerization domain as a homodimer (-7.2 kcal/mol) and transcription domain (-8.3 kcal/mol) of HNF-1α. Anthocyanins and anthocyanidins had relatively higher affinities than resveratrol and citrus flavonoids for both, the transcription domain and the dimerization domain as a homodimer. The flavonoid flavone had the highest affinity for a single unit of the dimerization domain (-6.5 kcal/mol). Nuclear expression of HNF-1α was measured in Caco-2 and human normal colon cells treated with blueberry and blackberry anthocyanin extracts. All extracts tested increased significantly (P < 0.05) the nuclear expression of HNF-1α in Caco-2 cells by 85.2 to 260% compared to a control. The extracts tested increased significantly (P < 0.02) the nuclear expression of HNF-1α in normal colon cells by 48.6 to 243%. It was confirmed that delphinidin-3-O-glucoside increased by 3-fold nuclear HNF-1α expression in Caco-2 cells (P < 0.05). Anthocyanins significantly increased nuclear HNF-1α expression, suggesting that these compounds might regulate the genes HNF-1�

Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes.

PubMed

Reyes, Archie C; Amyes, Tina L; Richard, John P

2017-11-15

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the decarboxylation of 5-fluoroorotate (FO) with k cat /K m = 1.4 × 10 -7 M -1 s -1 . Combining this and related kinetic parameters shows that the 31 kcal/mol stabilization of the transition state for decarboxylation of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol stabilization by the substrate phosphodianion and the ribosyl ring, respectively, and an 8.6 kcal/mol stabilization from the orotate ring. The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively, by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization of binding interactions of the substrate fragments to drive an enzyme conformational change, which locks the orotate ring of the whole substrate, or the substrate pieces in a caged complex. We propose that enzyme-activation is a possible, and perhaps probable, consequence of any substrate-induced enzyme conformational change.

Revised values for the Gibbs free energy of formation of [Al(OH)4 aq-], diaspore, boehmite and bayerite at 298.15 K and 1 bar, the thermodynamic properties of kaolinite to 800 K and 1 bar, and the heats of solution of several gibbsite samples

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Kittrick, J.A.

1978-01-01

Solution calorimetric measurements compared with solubility determinations from the literature for the same samples of gibbsite have provided a direct thermochemical cycle through which the Gibbs free energy of formation of [Al(OH)4 aq-] can be determined. The Gibbs free energy of formation of [Al(OH)4 aq-] at 298.15 K is -1305 ?? 1 kJ/mol. These heat-of-solution results show no significant difference in the thermodynamic properties of gibbsite particles in the range from 50 to 0.05 ??m. The Gibbs free energies of formation at 298.15 K and 1 bar pressure of diaspore, boehmite and bayerite are -9210 ?? 5.0, -918.4 ?? 2.1 and -1153 ?? 2 kJ/mol based upon the Gibbs free energy of [A1(OH)4 aq-] calculated in this paper and the acceptance of -1582.2 ?? 1.3 and -1154.9 ?? 1.2 kJ/mol for the Gibbs free energy of formation of corundum and gibbsite, respectively. Values for the Gibbs free energy formation of [Al(OH)2 aq+] and [AlO2 aq-] were also calculated as -914.2 ?? 2.1 and -830.9 ?? 2.1 kJ/mol, respectively. The use of [AlC2 aq-] as a chemical species is discouraged. A revised Gibbs free energy of formation for [H4SiO4aq0] was recalculated from calorimetric data yielding a value of -1307.5 ?? 1.7 kJ/mol which is in good agreement with the results obtained from several solubility studies. Smoothed values for the thermodynamic functions CP0, ( HT0 - H2980) T, ( GT0 - H2980) T, ST0 - S00, ??Hf{hook},2980 kaolinite are listed at integral temperatures between 298.15 and 800 K. The heat capacity of kaolinite at temperatures between 250 and 800 K may be calculated from the following equation: CP0 = 1430.26 - 0.78850 T + 3.0340 ?? 10-4 T2 -1.85158 ?? 10-4 T2 1 2 + 8.3341 ?? 106 T-2. The thermodynamic properties of most of the geologically important Al-bearing phases have been referenced to the same reference state for Al, namely gibbsite. ?? 1978.

The reversible two-state unfolding of a monocot mannose-binding lectin from garlic bulbs reveals the dominant role of the dimeric interface in its stabilization.

PubMed

Bachhawat, K; Kapoor, M; Dam, T K; Surolia, A

2001-06-19

Allium sativum agglutinin (ASAI) is a heterodimeric mannose-specific bulb lectin possessing two polypeptide chains of molecular mass 11.5 and 12.5 kDa. The thermal unfolding of ASAI, characterized by differential scanning calorimetry and circular dichroism, shows it to be highly reversible and can be defined as a two-state process in which the folded dimer is converted directly to the unfolded monomers (A2 if 2U). Its conformational stability has been determined as a function of temperature, GdnCl concentration, and pH using a combination of thermal and isothermal GdnCl-induced unfolding monitored by DSC, far-UV CD, and fluorescence, respectively. Analyses of these data yielded the heat capacity change upon unfolding (DeltaC(p) and also the temperature dependence of the thermodynamic parameters, namely, DeltaG, DeltaH, and DeltaS. The fit of the stability curve to the modified Gibbs-Helmholtz equation provides an estimate of the thermodynamic parameters DeltaH(g), DeltaS(g), and DeltaC(p) as 174.1 kcal x mol(-1), 0.512 kcal x mol(-1) x K(-1), and 3.41 kcal x mol(-1) x K(-1), respectively, at T(g) = 339.4 K. Also, the free energy of unfolding, DeltaG(s), at its temperature of maximum stability (T(s) = 293 K) is 13.13 kcal x mol(-1). Unlike most oligomeric proteins studied so far, the lectin shows excellent agreement between the experimentally determined DeltaC(p) (3.2 +/- 0.28 kcal x mol(-1) x K(-1)) and those evaluated from a calculation of its accessible surface area. This in turn suggests that the protein attains a completely unfolded state irrespective of the method of denaturation. The absence of any folding intermediates suggests the quaternary interactions to be the major contributor to the conformational stability of the protein, which correlates well with its X-ray structure. The small DeltaC(p) for the unfolding of ASAI reflects a relatively small, buried hydrophobic core in the folded dimeric protein.

CH4 dehydrogenation on Cu(1 1 1), Cu@Cu(1 1 1), Rh@Cu(1 1 1) and RhCu(1 1 1) surfaces: A comparison studies of catalytic activity

NASA Astrophysics Data System (ADS)

Zhang, Riguang; Duan, Tian; Ling, Lixia; Wang, Baojun

2015-06-01

In the CVD growth of graphene, the reaction barriers of the dehydrogenation for hydrocarbon molecules directly decide the graphene CVD growth temperature. In this study, density functional theory method has been employed to comparatively probe into CH4 dehydrogenation on four types of Cu(1 1 1) surface, including the flat Cu(1 1 1) surface (labeled as Cu(1 1 1)) and the Cu(1 1 1) surface with one surface Cu atom substituted by one Rh atom (labeled as RhCu(1 1 1)), as well as the Cu(1 1 1) surface with one Cu or Rh adatom (labeled as Cu@Cu(1 1 1) and Rh@Cu(1 1 1), respectively). Our results show that the highest barrier of the whole CH4 dehydrogenation process is remarkably reduced from 448.7 and 418.4 kJ mol-1 on the flat Cu(1 1 1) and Cu@Cu(1 1 1) surfaces to 258.9 kJ mol-1 on RhCu(1 1 1) surface, and to 180.0 kJ mol-1 on Rh@Cu(1 1 1) surface, indicating that the adsorbed or substituted Rh atom on Cu catalyst can exhibit better catalytic activity for CH4 complete dehydrogenation; meanwhile, since the differences for the highest barrier between Cu@Cu(1 1 1) and Cu(1 1 1) surfaces are smaller, the catalytic behaviors of Cu@Cu(1 1 1) surface are very close to the flat Cu(1 1 1) surface, suggesting that the morphology of Cu substrate does not obviously affect the dehydrogenation of CH4, which accords with the reported experimental observations. As a result, the adsorbed or substituted Rh atom on Cu catalyst exhibit a better catalytic activity for CH4 dehydrogenation compared to the pure Cu catalyst, especially on Rh-adsorbed Cu catalyst, we can conclude that the potential of synthesizing high-quality graphene with the help of Rh on Cu foils may be carried out at relatively low temperatures. Meanwhile, the adsorbed Rh atom is the reaction active center, namely, the CVD growth can be controlled by manipulating the graphene nucleation position.

Bimetallo-radical carbon-hydrogen bond activation of methanol and methane.

PubMed

Cui, Weihong; Zhang, X Peter; Wayland, Bradford B

2003-04-30

Carbon-hydrogen bond cleavage reactions of CH3OH and CH4 by a dirhodium(II) diporphyrin complex with a m-xylyl tether (.Rh(m-xylyl)Rh.(1)) are reported. Kinetic-mechanistic studies show that the substrate reactions are bimolecular and occur through the use of two Rh(II) centers in the molecular unit of 1. Second-order rate constants (T = 296 K) for the reactions of 1 with methanol (k(CH3OH) = 1.45 x 10-2 M-1 s-1) and methane (k(CH4) = 0.105 M-1 s-1) show a clear kinetic preference for the methane activation process. The methanol and methane reactions with 1 have large kinetic isotope effects (k(CH3OH)/k(CD3OD) = 9.7 +/- 0.8, k(CH4)/k(CD4) = 10.8 +/- 1.0, T = 296 K), consistent with a rate-limiting step of C-H bond homolysis through a linear transition state. Activation parameters for reaction of 1 with methanol (DeltaH = 15.6 +/- 1.0 kcal mol-1; DeltaS = -14 +/- 5 cal K-1 mol-1) and methane (DeltaH = 9.8 +/- 0.5 kcal mol-1; DeltaS = -30 +/- 3 cal K-1 mol-1) are reported.

Propane in nitrogen, 1000 μmol/mol

NASA Astrophysics Data System (ADS)

Konopelko, L. A.; Kustikov, Y. A.; Kolobova, A. V.; Pankratov, V. V.; Pankov, A. A.; Efremova, O. V.; Rozhnov, M. S.; Melnyk, D. M.; Petryshyn, P. V.; Levbarg, O. S.; Kisel, S. P.; Shpilnyi, S. A.; Yakubov, S. Ye; Bakovec, N. V.; Mironchik, A. M.; Aleksandrov, V. V.

2017-01-01

This article presents the report on the COOMET key comparison COOMET.QM-K111, which is linking to the appropriate CCQM comparison—CCQM-K111 'Propane in nitrogen 1000 μmol/mol'. CCQM-K111 was carried out in 2014-2016 and it was one of a series of key comparisons in the gas analysis area assessing core competences. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

CH(X2∏, a4∑-) ... OH2 and CH2(X˜3B1, ã1A1) ... OH2 interactions. A first principles investigation

NASA Astrophysics Data System (ADS)

Tzeli, Demeter; Mavridis, Aristides

We have investigated the interaction of the methylidene, CH(X2∏, a4∑-) and methylene, CH2(X˜3B1, ã1A1) with H2O, employing the (P)MPn (n = 2, 4) techniques in conjunction with the sequence of correlation consistent basis sets aug-cc-pVxZ, x = 2, 3, and 4. For the CH ... OH2 system, we have located four minima (m) and three transition states (ts) and for the CH2 ... OH2, five minima and four transition states. All our results have been corrected for zero-point energy (ZPE) and basis set superposition errors (BSSE), while for the most important m_ structures, we report complete basis set (CBS) interaction limits. We also report fully optimized geometries, harmonic frequencies, dipole moments, Mulliken charges, and potential energy curves. The highest CH(X2∏) ... OH2 (m1_2∏) and CH2(ã1A1) ... OH2 (m1_1A1) interactions are the result of electron transfer from the oxygen atom to the empty pπ orbitals of CH(X2∏) and CH2(ã1A1), respectively (ylide-like structures). At the (P)MP4/AQZ//MP2/ATZ level, including ZPE, BSSE, and CBS extrapolation, we obtain ΔE0(BSSE)+CBS = -9.36 kcal/mol at rC ... O = 1.752 Å, and -9.73 kcal/mol at rC ... O = 1.741 Å for the m1_2∏ and m1_1A1, respectively.

An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs.

PubMed

Ghosh, Mrinmoy; Sodhi, Simrinder Singh; Sharma, Neelesh; Mongre, Raj Kumar; Kim, Nameun; Singh, Amit Kumar; Lee, Sung Jin; Kim, Dae Cheol; Kim, Sung Woo; Lee, Hak Kyo; Song, Ki-Duk; Jeong, Dong Kee

2016-02-04

This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association. The NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (-466.5 Kcal mol(-1)), van der Walls energy (-87.3 Kcal mol(-1)), and interaction energy (-835.7 Kcal mol(-1)) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2-0.55 nm) and lower root-mean-square fluctuation (approximately 0.08-0.3 nm) as compared to the mutant complexes. The results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for

Thermal decomposition of 1,3,3-trinitroazetidine (TNAZ): A density functional theory and ab initio study

NASA Astrophysics Data System (ADS)

Veals, Jeffrey D.; Thompson, Donald L.

2014-04-01

Density functional theory and ab initio methods are employed to investigate decomposition pathways of 1,3,3-trinitroazetidine initiated by unimolecular loss of NO2 or HONO. Geometry optimizations are performed using M06/cc-pVTZ and coupled-cluster (CC) theory with single, double, and perturbative triple excitations, CCSD(T), is used to calculate accurate single-point energies for those geometries. The CCSD(T)/cc-pVTZ energies for NO2 elimination by N-N and C-N bond fission are, including zero-point energy (ZPE) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can occur by a concerted H-atom and nitramine NO2 group elimination or by a concerted H-atom and nitroalkyl NO2 group elimination via barriers (at the CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of these four decomposition steps from energetically most favored to least favored is: NO2 elimination by N-N bond fission, HONO elimination involving the nitramine NO2 group, HONO elimination involving a nitroalkyl NO2 group, and finally NO2 elimination by C-N bond fission.

Desorption Kinetics of H2O from Cab-O-Sil-M-7D and Hi-Sil-233 Silica Particles

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

Dinh, L.; Balooch, M.; LeMay, J.D.

2000-01-26

Temperature programmed desorption (TPD) was performed at temperatures up to 850K on Cab-O-Sil-M-7D and Hi-Sil-233 silica particles. Physisorbed water molecules on both types of silica had activation energies in the range of 9-14.5 kcal/mol. However, the activation energies of desorption for chemisorbed water varied from {approx} 19 kcal/mol to > 59 kcal/mol for Cab-O-Sil-M-7D, and {approx} 23-37 kcal/mol for Hi-Sil-233. Our results suggest that physisorbed water can be effectively pumped away at room temperature (or preferably at 320 K) in a matter of hours. Chemisorbed water with high activation energies of desorption (>30 kcal/mol) will not escape the silica surfacesmore » in 100 years even at 320 K, while a significant amount of the chemisorbed water with medium activation energies (19-26 kcal/mol) will leave the silica surfaces in that time span. Most of the chemisorbed water with activation energies < 30 kcal/mol can be pumped away in a matter of days in a good vacuum environment at 500 K. We had previously measured about 0.1-0.4 wt. % of water in M9787 polysiloxane formulations containing {approx} 21% Cab-O-Sil-M-7D and {approx} 4% Hi-Sil-233. Comparing present results with these formulations, we conclude that absorbed H{sub 2}O and Si-OH bonds on the silica surfaces are the major contributors to water outgassing from M97 series silicones.« less

Mechanism of epoxide hydrolysis in microsolvated nucleotide bases adenine, guanine and cytosine: a DFT study.

PubMed

Vijayalakshmi, Kunduchi P; Mohan, Neetha; Ajitha, Manjaly J; Suresh, Cherumuttathu H

2011-07-21

Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that

Epoxidation of cottonseed oil by aqueous hydrogen peroxide catalysed by liquid inorganic acids.

PubMed

Dinda, Srikanta; Patwardhan, Anand V; Goud, Vaibhav V; Pradhan, Narayan C

2008-06-01

The kinetics of epoxidation of cottonseed oil by peroxyacetic acid generated in situ from hydrogen peroxide and glacial acetic acid in the presence of liquid inorganic acid catalysts were studied. It was possible to obtain up to 78% relative conversion to oxirane with very less oxirane cleavage by in situ technique. The rate constants for sulphuric acid catalysed epoxidation of cottonseed oil were in the range 0.39-5.4 x 10(-6)L mol(-1)s(-1) and the activation energy was found to be 11.7 kcal mol(-1). Some thermodynamic parameters such as enthalpy, entropy, and free energy of activation were determined to be of 11.0 kcal mol(-1), -51.4 cal mol(-1)K(-1) and 28.1 kcal mol(-1), respectively. The order of effectiveness of catalysts was found to be sulphuric acid>phosphoric acid>nitric acid>hydrochloric acid. Acetic acid was found to be superior to formic acid for the in situ cottonseed oil epoxidation.

Temperature-Dependent Kinetics Studies of the Reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction CH3SCH2 + HBr. Heat of Formation of the CH3SCH2 Radical

NASA Technical Reports Server (NTRS)

Jefferson, A.; Nicovich, J. M.; Wine, P. H.

1997-01-01

Time-resolved resonance fluorescence detection of Br((sup 2)P(sub 3/2)) atom disappearance or appearance 266 nm laser flash photolysis of CF2Br2/CH3SCH3/H2/N2 and Cl2CO/CH2SCH3/HBr/H2/N2 mixtures has been employed to study the kinetics of the reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction HBr + CH3SCH2 (1,-1) as a function of temperature over the range 386-604 K. Arrhenius expressions in units of cu cm/molecule which describe the results are k3= (9.0 +/- 2.9) x 10 (exp -11) exp[(-2386 +/- 151)/T]; errors are 2 sigma and represent precision only. To our knowledge, these are the first kinetic data reported for each of the two reactions studied. Second and third law analyses of the equilibrium data for reactions 1 and -1 have been employed to obtain the following enthalpies of reaction in units of kcal/mol: Delta-H(298) = 6.11 +/- 1.37 and Delta-H(0) = 5.37 +/- 1.38. Combining the above enthalpies of reaction with the well-known heats of formation of Br, HBr, CH3SCH3 gives the following heats of formation of the CH3SCH2 radical in units of kcal/mol: Delta-H(sub(f,298)) = 32.7 +/- 1.4 and Delta-H(sub (f,0)) = 35.3 +/- 1.4; errors are 2 sigma and represent estimates of absolute accuracy. The C-H bond dissociation energy in CH3SCH3 obtained from our data, 93.7 +/- 1.4 kcal/mol at 298 K and 92.0 +/- 1.4 kcal at 0 k, agrees well with a recent molecular beam photofragmentaion study but is 3 kcal/mol lower than the value obtained from an iodination kinetics study.

Molecular and Dissociative Adsorption of Water on (TiO 2 ) n Clusters, n = 1–4

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

Chen, Mingyang; Straatsma, Tjerk P.; Dixon, David A.

In the low energy structures of the (TiO 2) n(H 2O) m (n ≤ 4, m ≤ 2n) and (TiO 2) 8(H 2O) m (m = 3, 7, 8) clusters were predicted using a global geometry optimization approach, with a number of new lowest energy isomers being found. Water can molecularly or dissociatively adsorb on pure and hydrated TiO 2 clusters. Dissociative adsorption is the dominant reaction for the first two H 2O adsorption reactions for n = 1, 2, and 4, for the first three H 2O adsorption reactions for n = 3, and for the first four Hmore » 2O adsorption reactions for n = 8. As more H 2O’s are added to the hydrated (TiO 2)n cluster, dissociative adsorption becomes less exothermic as all the Ti centers become 4-coordinate. Furthermore two types of bonds can be formed between the molecularly adsorbed water and TiO 2 clusters: a Lewis acid–base Ti–O(H 2) bond or an O···H hydrogen bond. The coupled cluster CCSD(T) results show that at 0 K the H 2O adsorption energy at a 4-coordinate Ti center is ~15 kcal/mol for the Lewis acid–base molecular adsorption and ~7 kcal/mol for the H-bond molecular adsorption, in comparison to that of 8–10 kcal/mol for the dissociative adsorption. The cluster size and geometry independent dehydration reaction energy, ED, for the general reaction 2(-TiOH) → -TiOTi– + H 2O at 4-coordinate Ti centers was estimated from the aggregation reaction of nTi(OH) 4 to form the monocyclic ring cluster (TiO 3H 2) n + nH 2O. E D is estimated to be -8 kcal/mol, showing that intramolecular and intermolecular dehydration reactions are intrinsically thermodynamically allowed for the hydrated (TiO 2) n clusters with all of the Ti centers 4-coordinate, which can be hindered by cluster geometry changes caused by such processes. Finally by bending force constants for the TiOTi and OTiO bonds are determined to be 7.4 and 56.0 kcal/(mol·rad 2). Infrared vibrational spectra were calculated using density functional theory, and the new bands appearing upon water adsorption

Molecular and Dissociative Adsorption of Water on (TiO 2 ) n Clusters, n = 1–4

DOE PAGES

Chen, Mingyang; Straatsma, Tjerk P.; Dixon, David A.

2015-10-20

In the low energy structures of the (TiO 2) n(H 2O) m (n ≤ 4, m ≤ 2n) and (TiO 2) 8(H 2O) m (m = 3, 7, 8) clusters were predicted using a global geometry optimization approach, with a number of new lowest energy isomers being found. Water can molecularly or dissociatively adsorb on pure and hydrated TiO 2 clusters. Dissociative adsorption is the dominant reaction for the first two H 2O adsorption reactions for n = 1, 2, and 4, for the first three H 2O adsorption reactions for n = 3, and for the first four Hmore » 2O adsorption reactions for n = 8. As more H 2O’s are added to the hydrated (TiO 2)n cluster, dissociative adsorption becomes less exothermic as all the Ti centers become 4-coordinate. Furthermore two types of bonds can be formed between the molecularly adsorbed water and TiO 2 clusters: a Lewis acid–base Ti–O(H 2) bond or an O···H hydrogen bond. The coupled cluster CCSD(T) results show that at 0 K the H 2O adsorption energy at a 4-coordinate Ti center is ~15 kcal/mol for the Lewis acid–base molecular adsorption and ~7 kcal/mol for the H-bond molecular adsorption, in comparison to that of 8–10 kcal/mol for the dissociative adsorption. The cluster size and geometry independent dehydration reaction energy, ED, for the general reaction 2(-TiOH) → -TiOTi– + H 2O at 4-coordinate Ti centers was estimated from the aggregation reaction of nTi(OH) 4 to form the monocyclic ring cluster (TiO 3H 2) n + nH 2O. E D is estimated to be -8 kcal/mol, showing that intramolecular and intermolecular dehydration reactions are intrinsically thermodynamically allowed for the hydrated (TiO 2) n clusters with all of the Ti centers 4-coordinate, which can be hindered by cluster geometry changes caused by such processes. Finally by bending force constants for the TiOTi and OTiO bonds are determined to be 7.4 and 56.0 kcal/(mol·rad 2). Infrared vibrational spectra were calculated using density functional theory, and the new bands appearing upon water adsorption

Kinetics and Thermochemistry of the Cl((sup 2)P(sub J)) + C2Cl4 Association Reaction

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Wang, S.; Mckee, M. L.; Wine, P. H.

1997-01-01

A laser flash photolysis-resonance fluorescence technique has been employed to study the kinetics of the Cl(sup 2)P(sub j) + C2Cl4 association reaction as a function of temperature (231-390 K) and pressure (3-700 Torr) in nitrogen buffer gas. The reaction is found to be in the falloff regime between third and second order over the range of conditions investigated, although the second-order limit is approached at the highest pressures and lowest temperatures. At temperatures below 300 K, the association reaction is found to be irreversible on the experimental time scale of approximately 20 m-s. The kinetic data at T is less than 300 K have been employed to obtain falloff parameters in a convenient format for atmospheric modeling. At temperatures above 330 K, reversible addition is observed, thus allowing equilibrium constants for C2Cl5 formation and dissociation to be determined. Second- and third-law analyses of the equilibrium data lead to the following thermochemical parameters for the association reaction: Delta-H(298) = -18.1 +/- 1.3 kcal/mol, Delta-H(0) = -17.6 +/- 1.3 kcal/mol, and Delta-S(298) = -27.7 +/- 3.0 cal/mol.K. In conjunction with the well-known heats of formation of Cl((sup 2)P(sub j)) and C2Cl4 the above Delta-H values lead to the following heats of formation for C2Cl5, at 298 and 0 K: Delta-H(f,298) = 8.0 +/- 1.3 kcal/mol and Delta-H(f,0) = 8.1 +/- 1.5 kcal/mol. The kinetic and thermochemical parameters reported above are compared with other reported values, and the significance of reported association rate coefficients for understanding tropospheric chlorine chemistry is discussed.

Infrared Spectroscopy of 1-CHOLOROMETHYLALLYL and 1-METHYLALLYL Radicals Produced in a Solid Para-Hydrogen Matrix.

NASA Astrophysics Data System (ADS)

Bahou, Mohammed; Wu, Jen-Yu; Tanaka, Keiichi; Lee, Yuan-Pern

2012-06-01

The reaction of chlorine atoms with trans-1,3-butadiene in solid para-hydrogen (p-H_2) matrix has been studied using Fourier transform infrared spectroscopy. When a mixture of Cl_2, trans-1,3-butadiene and p-H_2 was deposited onto a cold target at 3 K and irradiated by UV light at 365 nm, new intense lines at 809.0, 962.1, 1240.6 cm-1 and several weaker ones appeared. The carrier of this spectrum was assigned to the 1-chloromethylallyl radical, - (CH_2CHCH)CH_2Cl, based on the anharmonic vibrational frequencies calculated with the DFT method, indicating that the addition of the Cl atom to trans-1,3-butadiene occurs primarily at the terminal carbon atom. This is in sharp contrast to the reaction of chlorine atoms with propene in a solid p-H_2 matrix in which the addition of Cl to the central carbon atom to produce selectively the 2-chloropropyl is favored due to the steric effects. The energy diagram calculated with B3PW91 method supports this selective reaction process because 1) the channel from trans-1,3-butadiene to 1-chloro-methylallyl is almost barrierless (0.4 kcal/mol), and 2) isomereization from 1-chloromethylally to the 2-chloro-3-buten-1-yl radical, CH_2CHCHClCH_2 - by migration of Cl atom from the terminal to the central C atom, hardly occur in the p-H_2 matrix because of the isomerization barrier height (18.8 kcal/mol). We also observed a second set of lines with intense ones at 781.6, 957.93, 1433.6 cm-1 and several weaker ones when the UV-irradiated Cl_2/trans-1,3-butadiene/p-H_2 matrix was further irradiated with infrared light from a globar source. These lines are assigned to the 1-methylallyl radical, - (CH_2CHCH)CH_3, produced from reaction of 1,3-butadiene with an H atom that was produced from the reaction of Cl atoms with IR-irradiated p-H_2, Cl + H_2^* → H + HCl. The energy diagram calculated at the G3//B3LYP level similarly supports the reaction process to form selectively 1-methylallyl in the p-H_2 matrix. J. C. Amicangelo and Y. P. Lee, J

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Solution structure, mutagenesis, and NH exchange studies of the MutT enzyme-Mg 2+-8-oxo-dGMP complex

NASA Astrophysics Data System (ADS)

Massiah, M. A.; Saraswat, V.; Azurmendi, H. F.; Mildvan, A. S.

2004-08-01

The MutT pyrophosphohydrolase from E. coli (129 residues) catalyzes the hydrolysis of nucleoside triphosphates (NTP), including 8-oxo-dGTP, by substitution at Pβ, to yield NMP and pyrophosphate. The product, 8-oxo-dGMP is an unusually tight binding, slowly exchanging inhibitor with a KD=52 nM, (Δ G°=-9.8 kcal/mol) which is 6.1 kcal/mol tighter than the binding of dGMP (Δ G°=-3.7 kcal/mol). The higher affinity for 8-oxo-dGMP results from a more favorable Δ Hbinding (-32 kcal/mol) despite an unfavorable - TΔ S° binding (+22 kcal/mol). The solution structure of the MutT-Mg 2+-8-oxo-dGMP complex shows a narrowed, hydrophobic nucleotide-binding cleft with Asn-119 and Arg-78 among the few polar residues. The N119A, N119D, R78K and R78A single mutations, and the R78K+N119A double mutant all showed largely intact active sites, on the basis of small changes in the kinetic parameters of dGTP hydrolysis and in 1H- 15N HSQC spectra. However, the N119A mutation profoundly weakened the active site binding of 8-oxo-dGMP by 4.3 kcal/mol (1650-fold). The N119D mutation also weakened 8-oxo-dGMP binding but only by 2.1 kcal/mol (37-fold), suggesting that Asn-119 functioned both as a hydrogen bond donor to C8O, and a hydrogen bond acceptor from N7H of 8-oxo-dGMP, while aspartate at position -119 functioned as an acceptor of a single hydrogen bond. Much smaller weakening effects (0.3-0.4 kcal/mol) on the binding of dGMP and dAMP were found, indicating specific hydrogen bonding of Asn-119 to 8-oxo-dGMP. While formation of the wild type MutT-Mg 2+-8-oxo-dGMP complex slowed the backbone NH exchange rates of 45 residues distributed throughout the protein, the same complex of the N119A mutant slowed the exchange rates of only 11 residues at or near the active site, indicating an increase in conformational flexibility of the N119A mutant. The R78K and R78A mutations weakened the binding of 8-oxo-dGMP by 1.7 and 1.1 kcal/mol, respectively, indicating a lesser role of Arg-78 than of

Single Molecule Measurements of Interaction Free Energies Between the Proteins Within Binary and Ternary SNARE Complexes

PubMed Central

Liu, W.; Montana, Vedrana; Parpura, Vladimir; Mohideen, U.

2010-01-01

We use an Atomic Force Microscope based single molecule measurements to evaluate the activation free energy in the interaction of SNARE proteins syntaxin 1A, SNAP25B and synaptobrevin 2 which regulate intracellular fusion of vesicles with target membranes. The dissociation rate of the binary syntaxin-synaptobrevin and the ternary syntaxin-SNAP25B-synaptobrevin complex was measured from the rupture force distribution as a function of the rate of applied force. The temperature dependence of the spontaneous dissociation rate was used to obtain the activation energy to the transition state of 19.8 ± 3.5 kcal/mol = 33 ± 6 kBT and 25.7 ± 3.0 kcal/mol = 43 ± 5 kBT for the binary and ternary complex, respectively. They are consistent with those measured previously for the ternary complex in lipid membranes and are of order expected for bilayer fusion and pore formation. The ΔG was 12.4–16.6 kcal/mol = 21–28 kBT and 13.8–18.0 kcal/mol = 23–30 kBT for the binary and ternary complex, respectively. The ternary complex was more stable by 1.4 kcal/mol = 2.3 kBT, consistent with the spontaneous dissociation rates. The higher adhesion energies and smaller molecular extensions measured with SNAP25B point to its possible unique and important physiological role in tethering/docking the vesicle in closer proximity to the plasma membrane and increasing the probability for fusion completion. PMID:20107522

Influence of OH⋯N and NH⋯O inter- and intramolecular hydrogen bonds in the conformational equilibrium of some 1,3-disubstituted cyclohexanes through NMR spectroscopy and theoretical calculations

NASA Astrophysics Data System (ADS)

de Oliveira, Paulo R.; Viesser, Renan V.; Guerrero, Palimécio G., Jr.; Rittner, Roberto

2011-05-01

The analysis of concentration effects in the 1H NMR data of cis-3-aminocyclohexanol ( ACOL) showed that its diequatorial conformer changes from 60% at 0.01 mol L -1 to 70% at 0.40 mol L -1 in acetone-d 6. A similar increase was also observed for the diequatorial conformer of cis-3-N-methylaminocyclohexanol ( MCOL), from 32% (CDCl 3 0.01 mol L -1) to 55% (CDCl 3 0.40 mol L -1). The increase in solvent basicity leads to a large stabilization effect for the diequatorial conformer of both compounds too. For ACOL, it changes from 47% (Δ Geqeq- axax = 0.06 kcal mol -1) in CCl 4 to 93% (Δ Geqeq- axax = -1.53 kcal mol -1) in DMSO, while for MCOL it goes from 7% (Δ Geqeq- axax = 1.54 kcal mol -1) in CCl 4 to 82% (Δ Geqeq- axax = -0.88 kcal mol -1) in pyridine-d 6. These results indicate that the intr amolecular hydrogen bonds (IAHB) OH⋯N and NH⋯O stabilize the diaxial conformers of these compounds in a non-polar solvent. For cis-3-amino-1-methoxycyclohexane ( ACNE) and cis-3-N-methylamino-1-methoxy-cyclohexane ( MCNE) no changes were observed in equilibrium with the variation of solvent polarity. These results indicate for the first time that the IAHB NH⋯O is not strong enough to stabilize the diaxial conformer of these compounds and that the conformation equilibria of the cis isomers of compounds ACOL and MCOL are influenced only by the IAHB OH⋯N. Moreover, the presence of a secondary amino group (93% of diaxial conformer in CCl 4) leads to an IAHB OH⋯N stronger than in primary and tertiary amino-derivatives (53 and 54% of diaxial conformer, respectively) for 1,3-disubstituted cyclohexanes. Values obtained from the theoretical data through the B3LYP functional are in agreement with the experimental results and indicate that the IAHB strength that influences the conformational equilibrium of these compounds is the IAHB OH⋯N. Thus, the IAHB NH⋯O do not stabilize the diaxial conformer of the cis isomer of compounds ACNE and MCNE

Thermal Decomposition of Methyl Acetate (CH_3COOCH_3) in a Flash-Pyrolysis Micro-Reactor

NASA Astrophysics Data System (ADS)

Porterfield, Jessica P.; Bross, David H.; Ruscic, Branko; Thorpe, James H.; Nguyen, Thanh Lam; Baraban, Joshua H.; Stanton, John F.; Daily, John W.; Ellison, Barney

2017-06-01

The thermal decomposition of methyl acetate (CH_3COOCH_3) has been studied in a set of flash pyrolysis micro-reactors. Samples were diluted to (0.06 - 0.13%) in carrier gases (He, Ar) and subjected to temperatures of 300 - 1600 K at roughly 20 Torr. After residence times of approximately 25 - 150 μseconds, the unimolecular pyrolysis products were detected by vacuum ultraviolet photoionization mass spectrometry at 10.487 eV (118.2 nm). Complementary product identification was provided by matrix isolation infrared spectroscopy. Decomposition began at 1000 K with the observation of (CH_2=C=O, CH_3OH), products of a four centered rearrangement with a Δ_{rxn}H_{298} = 39.1 ± 0.2 kcal mol^{-1}. As the micro-reactor was heated to 1300 K, a mixture of (CH_2=C=O, CH_3OH, CH_3, CH_2=O, H, CO, CO_2) appeared. A new novel pathway is calculated in which both methyl groups leave behind CO_2 simultaneously, Δ_{rxn}H_{298} = 74.5 ± 0.4 kcal mol^{-1}. This pathway is in contrast to step-wise loss of methyl radical, which can go in two ways: Δ_{rxn}H_{298} (CH_3COOCH_3 → CH_3 + COOCH_3) = 95.4 ± 0.4 kcal mol^{-1}, Δ_{rxn}H_{298} (CH_3COOCH_3 → CH_3COO + CH_3) = 88.0 ± 0.3 kcal mol^{-1}.

Nonempirical electron-correlation calculations on ALi/sub k/ and Ali/sub k+1//sup +/ clusters formed with elements from the second and third periods

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

Mebel', A.M.; Klimenko, N.M.; Charkin, O.P.

Several basic sets have been used (from 3-21 G/sub A//asterisk/ to DZHD + P/sub A/) with electron correlation in the Meller-Plesset MP3 approximation in nonempirical calculations on ALi/sub k+1//sup +/ and ALi/sub K+1//sup +/ lithium clusters (CLi/sub 2/, CLi/sub 3//sup +/, NLi/sub 3/, NLi/sub 4//sup +/, OLi/sub 2/, OLi/sub 3//sup +/, etc.) formed with elements from the second and third periods in the lowest singlet states. A study has been made on the effects of the approximation on the results. Several reference systems are used to show that the SCF/3-21G/sub A//asterisk/ approximation describes the lithide geometry satisfactorily, while MP3/DZHD +more » P/sub A/ gives a satisfactory description of the affinity of Ali/sub k/ for Li/sup +/. These approximations have been taken as optimal for calculations on the other compounds. The Li/sup +/ affinities are highest for NLi/sub 3/ and PLi/sub 3/ (90 and 84 kcal correspondingly) and decrease as A varies along the subgroups from the second to the third and the lower sp periods, as well as when A varies in each period from the middle to the start or end. The affinities of the analogous compounds for Na/sup +/ are less by 5-10 kcal than those for Li/sup +/. The values are compared with the proton affinities for the related hydrides AK/sub k/.« less

Vapor-liquid equilibria for 1,1-difluoroethane + acetylene and 1,1-difluoroethane + 1,1-dichloroethane at 303.2 K and 323.2 K

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

Lim, J.S.; Lee, Y.W.; Kim, J.D.

1996-09-01

Isothermal vapor-liquid equilibria for 1,1-difluoroethane (HFC-152a) + acetylene and 1,1-difluoroethane + 1,1-dichloroethane (HCC-150a) were measured in a circulation type apparatus at 303.2 K and 323.2 K. The experimental data were correlated with the Peng-Robinson equation of state using the Wong and Sandler mixing rule, and the relevant parameters are presented.

Nucleoli in human early erythroblasts (K2, K1, K1/2 cells).

PubMed

Smetana, K; Jirásková, I; Klamová, H

2005-01-01

Human early erythroid precursors classified according to the nuclear size were studied to provide information on nucleoli in these cells using simple cytochemical procedures for demonstration of RNA and proteins of silver-stained nucleolar organizers. K2 cells with nuclear diameter larger than 13 microm and K1 cells with nuclear diameter larger than 9 microm corresponding to proerythroblasts and macroblasts (large basophilic erythroblasts) mostly possessed large irregularly shaped nucleoli with multiple fibrillar centres representing "active nucleoli". K1/2 cells with nuclear diameter smaller than 9 microm corresponding to small basophilic erythroblasts were usually characterized by the presence of micronucleoli representing "inactive nucleolar types". On the other hand, a few K1/2 cells contained large nucleoli with multiple fibrillar centres similar to those present in K2 cells and thus appeared as "microproerythroblasts". The nucleolar asynchrony expressed by the presence of large irregularly shaped nucleoli with multiple nucleoli (active nucleoli) and ring-shaped nucleoli (resting nucleoli) in one and the same nucleus of K2 or K1 cells was not exceptional and might reflect a larger resistance of these cells to negative factors influencing the erythropoiesis. The intranucleolar translocation of silver-stained nucleolus organized regions was noted in K2 cells and might indicate the premature aging of these cells without further differentiation. More studies, however, are required in this direction.

Vitamin K1 (phylloquinone) and K2 (menaquinone-4) supplementation improves bone formation in a high-fat diet-induced obese mice.

PubMed

Kim, Misung; Na, Woori; Sohn, Cheongmin

2013-09-01

Several reports suggest that obesity is a risk factor for osteoporosis. Vitamin K plays an important role in improving bone metabolism. This study examined the effects of vitamin K1 and vitamin K2 supplementation on the biochemical markers of bone turnover and morphological microstructure of the bones by using an obese mouse model. Four-week-old C57BL/6J male mice were fed a 10% fat normal diet group or a 45% kcal high-fat diet group, with or without 200 mg/1000 g vitamin K1 (Normal diet + K1, high-fat diet + K1) and 200 mg/1000 g vitamin K2 (Normal diet + K2, high-fat diet + K2) for 12 weeks. Serum levels of osteocalcin were higher in the high-fat diet + K2 group than in the high-fat diet group. Serum OPG level of the high-fat diet group, high-fat diet + K1 group, and high-fat diet + K2 group was 2.31 ± 0.31 ng/ml, 2.35 ± 0.12 ng/ml, and 2.90 ± 0.11 ng/ml, respectively. Serum level of RANKL in the high-fat diet group was significantly higher than that in the high-fat diet + K1 group and high-fat diet + K2 group (p<0.05). Vitamin K supplementation seems to tend to prevent bone loss in high-fat diet induced obese state. These findings suggest that vitamin K supplementation reversed the high fat diet induced bone deterioration by modulating osteoblast and osteoclast activities and prevent bone loss in a high-fat diet-induced obese mice.

Rotational Mode Specificity in the F(-) + CH3Y [Y = F and Cl] SN2 Reactions.

PubMed

Szabó, István; Czakó, Gábor

2015-12-17

More than 12 million quasiclassical trajectories are computed for the F(-) + CH3Y(v = 0, JK) [Y = F and Cl] SN2 reactions using full-dimensional ab initio analytical potential energy surfaces. The initial (J, K = 0) and (J, K = J) [J = 0, 2, 4, 6, 8] rotational state specific cross sections are obtained at different collision energies (Ecoll) in the 1-20 kcal mol(-1) range, and the scattering angle and initial attack angle distributions as well as the mechanism-specific opacity functions are reported at Ecoll = 10 kcal mol(-1). The tumbling rotation (K = 0) inhibits the F(-) + CH3F reaction by a factor of 3 for J = 8 at Ecoll = 10 kcal mol(-1). This tumbling rotational effect becomes smaller at low and high Ecoll, and the tumbling motion affects the cross sections of F(-) + CH3Cl by only a few percent. The spinning rotation (K = J) hinders both reactions by factors in the 1.3-1.7 range for J = 8 at low Ecoll, whereas slight promotion is found as the Ecoll increases. The tumbling rotation may counteract the attractive ion-dipole forces, and the spinning motion hinders the complex formation, thereby decreasing the reactivity.

Mechanism and kinetics for ammonium dinitramide (ADN) sublimation: a first-principles study.

PubMed

Zhu, R S; Chen, Hui-Lung; Lin, M C

2012-11-08

The mechanism for sublimation of NH(4)N(NO(2))(2) (ADN) has been investigated quantum-mechanically with generalized gradient approximation plane-wave density functional theory calculations; the solid surface is represented by a slab model and the periodic boundary conditions are applied. The calculated lattice constants for the bulk ADN, which were found to consist of NH(4)(+)[ON(O)NNO(2)](-) units, instead of NH(4)(+)[N(NO(2))(2)](-), agree quite well with experimental values. Results show that three steps are involved in the sublimation/decomposition of ADN. The first step is the relaxation of the surface layer with 1.6 kcal/mol energy per NH(4)ON(O)NNO(2) unit; the second step is the sublimation of the surface layer to form a molecular [NH(3)]-[HON(O)NNO(2)] complex with a 29.4 kcal/mol sublimation energy, consistent with the experimental observation of Korobeinichev et al. (10) The last step is the dissociation of the [H(3)N]-[HON(O)NNO(2)] complex to give NH(3) and HON(O)NNO(2) with the dissociation energy of 13.9 kcal/mol. Direct formation of NO(2) (g) from solid ADN costs a much higher energy, 58.3 kcal/mol. Our calculated total sublimation enthalpy for ADN(s) → NH(3)(g) + HON(O)NNO(2)) (g), 44.9 kcal/mol via three steps, is in good agreement with the value, 42.1 kcal/mol predicted for the one-step sublimation process in this work and the value 44.0 kcal/mol computed by Politzer et al. (11) using experimental thermochemical data. The sublimation rate constant for the rate-controlling step 2 can be represented as k(sub) = 2.18 × 10(12) exp (-30.5 kcal/mol/RT) s(-1), which agrees well with available experimental data within the temperature range studied. The high pressure limit decomposition rate constant for the molecular complex H(3)N···HON(O)NNO(2) can be expressed by k(dec) = 3.18 × 10(13) exp (-15.09 kcal/mol/RT) s(-1). In addition, water molecules were found to increase the sublimation enthalpy of ADN, contrary to that found in the ammonium

Photoinitiated polymerization of 1-vinylimidazole

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

Joshi, M.G.; Rodriguez, F.

1984-04-01

The photoinitiated polymerization of 1-vinylimidazole (VI) does not follow the classical kinetic scheme for free radical polymerization. Kinetic results for VI suggest a degradative addition reaction between the macroradical and the monomer to produce a relatively stable, unreactive radical, which does not reinitiate polymerization, is low, 1.5 kcal/mol. Among the 3 photoinitiators used, the highest quantum efficiency was demonstrated by 2,2'-diethoxyacetophenone followed by bezoin methyl ether and benzoin isopropyl ether. Under the experimental conditions used, the polymerization of VI does not proceed to complete conversion, and the phenomenon of dead-end polymerization is observed.

Gas-Phase and Solution-Phase Homolytic Bond Dissociation Energies of H-N(+) Bonds in the Conjugate Acids of Nitrogen Bases.

PubMed

Liu, Wei-Zhong; Bordwell, Frederick G.

1996-07-12

The oxidation potentials of 19 nitrogen bases (abbreviated as B: six primary amines, five secondary amines, two tertiary amines, three anilines, pyridine, quinuclidine, and 1,4-diazabicyclo[2,2,2]octane), i.e., E(ox)(B) values in dimethyl sulfoxide (DMSO) and/or acetonitrile (AN), have been measured. Combination of these E(ox)(B) values with the acidity values of the corresponding acids (pK(HB)(+)) in DMSO and/or AN using the equation: BDE(HB)(+) = 1.37pK(HB)(+) + 23.1 E(ox)(B) + C (C equals 59.5 kcal/mol in AN and 73.3 kcal/mol in DMSO) gave estimates of solution phase homolytic bond dissociation energies of H-B(+) bonds. Gas-phase BDE values of H-B(+) bonds were estimated from updated proton affinities (PA) and adiabatic ionization potentials (aIP) using the equation, BDE(HB(+))(g) = PA + aIP - 314 kcal/mol. The BDE(HB)(+) values estimated in AN were found to be 5-11 kcal/mol higher than the corresponding gas phase BDE(HB(+))(g) values. These bond-strengthening effects in solution are interpreted as being due to the greater solvation energy of the HB(+) cation than that of the B(+*) radical cation.

Introduction of a unique tryptophan residue into various positions of Bacillus licheniformis DnaK.

PubMed

Chen, Bo-En; Lin, Min-Guan; Lo, Huei-Fen; Wang, Tzu-Fan; Chi, Meng-Chun; Lin, Long-Liu

2013-01-01

Site-directed mutagenesis together with biochemical and biophysical techniques were used to probe effects of single-tryptophan-incorporated mutations on a bacterial molecular chaperone, Bacillus licheniformis DnaK (BlDnaK). Specifically, five phenylalanine residues (Phe(120), Phe(174), Phe(186), Phe(378) and Phe(396)) of BlDnaK were individually replaced by single tryptophans, thus creating site-specific probes for the fluorescence analysis of the protein. The steady-state ATPase activity for BlDnaK, F120W, F174W, F186W, F378W, and F396W was determined to be 76.01, 52.82, 25.32, 53.31, 58.84, and 47.53 nmol Pi/min/mg, respectively. Complementation test revealed that the single mutation at codons 120, 186, and 378 of the dnaK gene still allowed an Escherichia coli dnaK756-Ts strain to grow at a stringent temperature of 44°C. Simultaneous addition of co-chaperones and NR-peptide did not synergistically stimulate the ATPase activity of F174W and F396W, and these two proteins were unable to assist the refolding of GdnHCl-denatured luciferase. The heat-induced denaturation of all variants could be fitted adequately to a three-state model, in agreement with the observation for the wild-type protein. By CD spectral analysis, GdnHCl-induced unfolding transition for BlDnaK was 1.51 M corresponding to ΔG(N-U) of 1.69 kcal/mol; however, the transitions for mutant proteins were 1.07-1.55 M equivalent to ΔG(N-U) of 0.94-2.93 kcal/mol. The emission maximum of single-tryptophan-incorporated variants was in the range of 333.2-335.8 nm. Acrylamide quenching analysis showed that the mutant proteins had a dynamic quenching constant of 3.0-4.2 M(-1). Taken together, these results suggest that the molecular properties of BlDnaK have been significantly changed upon the individual replacement of selected phenylalanine residues by tryptophan. Copyright © 2012 Elsevier B.V. All rights reserved.

Theoretical investigations on the mechanism of benzoin condensation catalyzed by pyrido[1,2-a]-2-ethyl[1,2,4]triazol-3-ylidene.

PubMed

He, Yunqing; Xue, Ying

2011-03-03

A new annulated N-heterocyclic carbene (NHC), pyrido[1,2-a]-2-ethyl[1,2,4]triazol-3-ylidene, has been synthesized and its good catalytic activity for benzoin condensation has been experimentally determined by You and co-workers recently [ Ma , Y. J. , Wei , S. P. , Lan , J. B. , Wang , J. Z. , Xie , R. G. , and You , J. S. J. Org. Chem. 2008 , 73 , 8256 ]. In this work, the mechanism of the title reaction has been intensively studied computationally by employing the density functional theory (B3LYP) method in conjunction with 6-31+G(d) and 6-311+G(2d,p) basis sets. Our results indicate that path A (in which a sequence of intermolecular proton transfers between two carbene/benzaldehyde coupling intermediates affords enamine) and path B (in which a t-BuOH assisted hydrogen transfer generates enamine) proposed on the basis of the Breslow mechanism are competitive for their similar barriers. In path A, the first intermolecular proton transfer between two N-heterocyclic carbene/benzaldehyde coupled intermediates to form tertiary alcohol and enolate anion is theoretically the rate-determining step with corresponding barrier (30.93 kcal/mol), while the t-BuOH assisted hydrogen transfer generating Breslow enamine is the rate-determining step with corresponding barrier (28.84 kcal/mol) in path B. The coupling of carbene and benzaldehyde, and the coupling of enamine and another benzaldehyde to form a C-C bond are partially rate-determining for their relatively significant barriers (24.06 and 26.95 kcal/mol, respectively), being the same in both paths A and B. Our results are in nice agreement with the experimental result in a kinetic investigation of thiazolium ion-catalyzed benzoin condensation performed by White and Leeper in 2001.

Isobaric heat capacity for liquid 1-chloro-1,1-difluoroethane and 1,1-difluoroethane

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

Nakagawa, Shinsuke; Hori, Tatsuhi; Sato, Haruki

1993-01-01

The isobaric heat capacities (C[sub P]) for liquid 1-chloro-1,1-difluoroethane (HCFC-142b) and 1,1-difluoroethane (HFC-152a) have been measured by means of flow calorimetry. For HCFC-142b, 31 C[sub P] values have been measured at temperatures from 276 to 350 K and pressures from 1.0 to 3.0 MPa. For HFC-152a, 36 C[sub P] have been measured at temperature from 276 to 360 K and pressures from 1.0 to 3.2 MPa. The uncertainties are estimated as [plus minus] 13 mK in temperature, [plus minus]3 kPa in pressure, and [plus minus] kPa in pressure, and [plus minus]0.4% for most of the C[sub P] measurements. The puritymore » of samples used for both HCFC-142b and HFC-152a measurements was 99.95 mol%. Correlations of liquid C[sub P] as a function of temperature and pressure have been developed for both refrigerants on the basis of the measurements.« less

Gas-Phase Anionic σ-Adduct (Trans)formations in Heteroaromatic Systems1

NASA Astrophysics Data System (ADS)

Zimnicka, Magdalena; Danikiewicz, Witold

2015-07-01

Anions of nitroderivatives of thiophene and furan were subjected to the reactions with selected C-H acids in the gas phase. Various structures and reaction pathways were proposed for the observed ionic products. In general, the reactions of heteroaromatic anions with C-H acids may be divided into three groups, depending on the proton affinity difference between C-H acid's conjugate base and heteroaromatic anion (ΔPA). The proton transfer from C-H acid to heteroaromatic anion is a dominant process in the reactions for which ΔPA < 0 kcal mol-1, whereas the reactions with high ΔPA (ΔPA > 16 kcal mol-1) do not lead to any ionic products. The formation of σ-adducts and products of their further transformations according to the VNS, SNAr, cine, and tele substitution mechanisms have been proposed for reactions with moderate ΔPA. The other possible mechanisms as SN2 reaction, nucleophilic addition to the cyano group, ring-opening pathway, and halogenophilic reaction have also been discussed to contribute in the reactions between heteroaromatic anions and C-H acids.

Novel Interactions Identified between μ-Conotoxin and the Na+ Channel Domain I P-loop: Implications for Toxin-Pore Binding Geometry

PubMed Central

Xue, Tian; Ennis, Irene L.; Sato, Kazuki; French, Robert J.; Li, Ronald A.

2003-01-01

μ-Conotoxins (μ-CTX) are peptides that inhibit Na+ flux by blocking the Na+ channel pore. Toxin residue arginine 13 is critical for both high affinity binding and for complete block of the single channel current, prompting the simple conventional view that residue 13 (R13) leads toxin docking by entering the channel along the pore axis. To date, the strongest interactions identified are between μ-CTX and domain II (DII) or DIII pore residues of the rat skeletal muscle (Nav1.4) Na+ channels, but little data is available for the role of the DI P-loop in μ-CTX binding due to the lack of critical determinants identified in this domain. Despite being an essential determinant of isoform-specific tetrodotoxin sensitivity, the DI-Y401C variant had little effect on μ-CTX block. Here we report that the charge-changing substitution Y401K dramatically reduced the μ-CTX affinity (∼300-fold). Using mutant cycle analysis, we demonstrate that K401 couples strongly to R13 (ΔΔG > 3.0 kcal/mol) but not R1, K11, or R14 (≪1 kcal/mol). Unlike K401, however, a significant coupling was detected between toxin residue 14 and DI-E403K (ΔΔG = 1.4 kcal/mol for the E403K-Q14D pair). This appears to underlie the ability of DI-E403K channels to discriminate between the GIIIA and GIIIB isoforms of μ-CTX (p < 0.05), whereas Y401K, DII-E758Q, and DIII-D1241K do not. We also identify five additional, novel toxin-channel interactions (>0.75 kcal/mol) in DII (E758-K16, D762-R13, D762-K16, E765-R13, E765-K16). Considered together, these new interactions suggest that the R13 side chain and the bulk of the bound toxin μ-CTX molecule may be significantly tilted with respect to pore axis. PMID:14507694

Structural Transition and Electrical Properties of (1 - x)(Na0.4K0.1Bi0.5)TiO3- xSrTiO3 Lead-Free Piezoceramics

NASA Astrophysics Data System (ADS)

Liu, Xing; Zhai, Jiwei; Shen, Bo; Li, Feng; Li, Peng

2017-10-01

(1 - x)(Na0.4K0.1Bi0.5)TiO3- xSrTiO3 (NKBT- xST) ceramics with x = 0 mol.%, 3 mol.%, and 5 mol.% (0ST, 3ST, and 5ST) have been prepared by a conventional solid-state reaction method and their ferroelectric, electrostrictive, and pyroelectric properties investigated. Addition of ST considerably disrupted the long-range ferroelectric order of NKBT- xST ceramics, and the 5ST ceramic exhibited ergodic relaxor phase structure. T FR shifted to near or below room temperature for 5ST ceramic, accompanied by a significant decline of ferroelectricity and enhanced strain. As the temperature approached T FR, the NKBT- xST ceramics exhibited predominantly electrostrictive effect, and the 5ST ceramic presented relatively high electrostrictive coefficient Q 33 of 0.0193 m4/C2. High pyroelectric response was observed for 0ST, 3ST, and 5ST ceramics in the vicinity of T FR due to the large polarization release during the ferroelectric-relaxor structural transition. The 5ST ceramic exhibited high and frequency-insensitive (100 Hz to 10 kHz) room-temperature pyroelectric properties with pyroelectric coefficient p of 656 μC m-2 K-1 and figures of merit F i, F v, and F d reaching 233 pm/V, 0.013 m2/C, and 7.61 μPa-1/2, respectively, indicating that 5ST ceramic is a promising candidate to replace PZT-based ceramics.

The 1,5-H-shift in 1-butoxy: A case study in the rigorous implementation of transition state theory for a multirotamer system

NASA Astrophysics Data System (ADS)

Vereecken, Luc; Peeters, Jozef

2003-09-01

The rigorous implementation of transition state theory (TST) for a reaction system with multiple reactant rotamers and multiple transition state conformers is discussed by way of a statistical rate analysis of the 1,5-H-shift in 1-butoxy radicals, a prototype reaction for the important class of H-shift reactions in atmospheric chemistry. Several approaches for deriving a multirotamer TST expression are treated: oscillator versus (hindered) internal rotor models; distinguishable versus indistinguishable atoms; and direct count methods versus degeneracy factors calculated by (simplified) direct count methods or from symmetry numbers and number of enantiomers, where applicable. It is shown that the various treatments are fully consistent, even if the TST expressions themselves appear different. The 1-butoxy H-shift reaction is characterized quantum chemically using B3LYP-DFT; the performance of this level of theory is compared to other methods. Rigorous application of the multirotamer TST methodology in an harmonic oscillator approximation based on this data yields a rate coefficient of k(298 K,1 atm)=1.4×105 s-1, and an Arrhenius expression k(T,1 atm)=1.43×1011 exp(-8.17 kcal mol-1/RT) s-1, which both closely match the experimental recommendations in the literature. The T-dependence is substantially influenced by the multirotamer treatment, as well as by the tunneling and fall-off corrections. The present results are compared to those of simplified TST calculations based solely on the properties of the lowest energy 1-butoxy rotamer.

Reactivity of organic micropollutants with ozone: A kinetic study

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

Brambilla, A.; Bolzacchini, E.; Meinardi, S.

1995-12-01

Studies about the chemical reactivity of compounds widely used in the environment are needed. The chemical reactivity of triazines (simazine, atrazine, terbutylazine) and phenylureas (linuron and diuron) was studied. The kinetics of the oxidation of the triazines and phenylureas with ozone at pH 3 and the kinetics of the saturation of the solution with ozone were evaluated. These data may be useful for the prediction of the persistency of these compuonds in the environment and for the treatment of wastewaters contaminated with these compounds. The solution was presaturated with ozone before the addition of the substrate, and the reaction constantsmore » for the pseudo first order kinetics -d[substrate]/dt = k{sub app} [substrate] at 298{degree}K were obtained, assuming a steady state concentration of ozone of 1.91 10{sup -4} mol L{sup -1} for the phenylureas and of 3.03 10{sup -4} and L{sup -1} for the triazines. The data obtained were: atrazine k = 6.86 (L mol{sup -1}s{sup -1}); simazine: 9.26; t-butylazine 7.26; linuron 11.00; diuron 43.90. The activation parameters for the reaction of simazine were {Delta}H{sup =} = 9.35 kcal mol{sup -1} and {Delta}S{sup =} = -22.3 cal mol{sup -1} {degree}K{sup -1} and for the reaction of diuron were {Delta}H{sup =} = 16.83 Kcal mol{sup -1}, {Delta}S{sup =} = 5.696 cal mol{sup -1} {degree}K{sup -1}.« less

26 CFR 1.501(k)-1 - Communist-controlled organizations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 7 2014-04-01 2013-04-01 true Communist-controlled organizations. 1.501(k)-1 Section 1.501(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(k)-1 Communist-controlled...

26 CFR 1.501(k)-1 - Communist-controlled organizations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 7 2010-04-01 2010-04-01 true Communist-controlled organizations. 1.501(k)-1 Section 1.501(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(k)-1 Communist-controlled...

26 CFR 1.501(k)-1 - Communist-controlled organizations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 7 2013-04-01 2013-04-01 false Communist-controlled organizations. 1.501(k)-1 Section 1.501(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(k)-1 Communist-controlled...

26 CFR 1.501(k)-1 - Communist-controlled organizations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 7 2012-04-01 2012-04-01 false Communist-controlled organizations. 1.501(k)-1 Section 1.501(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(k)-1 Communist-controlled...

26 CFR 1.501(k)-1 - Communist-controlled organizations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 7 2011-04-01 2009-04-01 true Communist-controlled organizations. 1.501(k)-1 Section 1.501(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(k)-1 Communist-controlled...

The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation.

PubMed

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

2018-03-01

We have re-evaluated the X40×10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)-MP2 "high-level corrections" (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies and turns out to be more important for noncovalent interactions than is generally realized; (n-1)sp subvalence correlation is much less important. The (n-1)d subvalence term is dominated by core-valence correlation; with the smaller cc-pVDZ-F12-PP and cc-pVTZ-F12-PP basis sets, basis set convergence for the core-core contribution becomes sufficiently erratic that it may compromise results overall. The two factors conspire to generate discrepancies of up to 0.9 kcal/mol (0.16 kcal/mol RMS) between the original X40×10 data and the present revision.

Structural, conformational and vibrational properties of 1,1,1-Trifluoro-N-(1,1,2,2,2-pentafluoroethyl) methanesulfinimidoyl chloride, CF₃CF₂-N=S(Cl)CF₃.

PubMed

Robles, Norma L; Chemes, Doly M; Oberhammer, Heinz; Cutin, Edgardo H

2015-06-15

The structural, conformational, and configurational properties of 1,1,1-Trifluoro-N-(1,1,2,2,2-pentafluoroethyl) methanesulfinimidoyl chloride, CF3CF2NS(Cl)CF3 have been studied by vibrational spectroscopy [IR (vapor) and Raman (liquid)] and quantum chemical calculations [B3LYP, MP2 and B3PW91 levels of theory using the 6-311+G(d), 6-311+G(df) and 6-311+G(2df) basis sets]. According to these theoretical approximations, CF₃CF₂-N=S(Cl)CF₃ exists in the gas phase as a mixture of a favored anticlinal form (CN bond anticlinal with respect to the CSCl bisector) with C1 symmetry and a less abundant syn conformer showing C1 symmetry as well (ΔG° ≈ 1.20 kcal mol(-1)). Due to the small contribution only a few corresponding vibrational modes of the syn conformer could be assigned confidently in the experimental spectra. Compared to CF₃CF₂-N=S(F)CF₃, the replacement of F by Cl produces a clear change in NS bond length and the corresponding stretching frequency, without affecting the conformational properties. Copyright © 2015 Elsevier B.V. All rights reserved.

Conformational stability, barriers to internal rotation, normal coordinate analyses, and vibrational assignments of bromoacetyl halides

NASA Astrophysics Data System (ADS)

Durig, J. R.; Phan, H. V.; Little, T. S.

1989-09-01

The Raman (3200-10 cm -1) and IR (3200-30 cm -1) spectra of bromoacetyl fluoride, bromoacetyl chloride and bromoacetyl bromide in the gaseous and annealed solid phases have been recorded. Additionally, the Raman spectra and the qualitative depolarization measurements for each molecule in the liquid phase have been obtained. All of these data indicate that these bromoacetyl halides exist in mixtures of two conformers, with the trans rotamer (halogen atoms oriented trans to one another) being the thermodynamically preferred, and the gauche conformation being the high energy form. From the studies of Raman spectra at different temperatures, the enthalpy differences have been determined for the gaseous and liquid phases, respectively, to be 185 ± 23 cm -1 (0.53 ± 0.06 kcal mol -1) and 249 ± 27 cm -1 (0.71 ± 0.08 kcal mol -1) for bromoacetyl fluoride, 391 ± 130 cm -1 (1.12 ± 0.37 kcal mol -1) and 317 ± 27 cm -1 (0.91 ± 0.08 kcal mol -1) for bromoacetyl chloride, and 341 ± 48 cm -1 (0.98 ± 0.14 kcal mol -1) and 286 ± 26 cm -1 (0.82 ± 0.07 kcal mol -1) for bromoacetyl bromide. Potential functions have been calculated for the fluoride and chloride from the observed asymmetric torsional frequencies and values of 580 ± 11 cm -1 (1.66 ± 0.03 kcal mol -1), 359 ± 8 cm -1 (1.03 ± 0.02 kcal mol -1), and 387 ± 16 cm -1 (1.11 ± 0.04 kcal mol -1) for the trans to gauche, gauche to gauche to gauche and gauche to trans barrier, respectively, were determined for bromoacetyl fluoride. The corresponding quantities were 967 ± 30 cm -1 (2.76 ± 0.08 kcal mol -1), 696 ± 67 cm -1 (1.99 ± 0.19 kcal mol -1), and 663 ± 30 cm -1 (1.61 ± 0.08 kcal mol -1) for bromoacetyl chloride. These potential functions are consistent with the dihedral angle of the gauche conformation being 120° and 117° for the fluoride and chloride, respectively. Complete vibrational assignments have been carried out based on the observed IR band contours, the depolarization ratios, and group

Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

PubMed Central

Ieong, Pek; Amaro, Rommie E.; Li, Wilfred W.

2015-01-01

The antibody immunoglobulin (Ig) 2D1 is effective against the 1918 hemagglutinin (HA) and also known to cross-neutralize the 2009 pandemic H1N1 influenza HA through a similar epitope. However, the detailed mechanism of neutralization remains unclear. We conducted molecular dynamics (MD) simulations to study the interactions between Ig-2D1 and the HAs from the 1918 pandemic flu (A/South Carolina/1/1918, 18HA), the 2009 pandemic flu (A/California/04/2009, 09HA), a 2009 pandemic flu mutant (A/California/04/2009, 09HA_mut), and the 2006 seasonal flu (A/Solomon Islands/3/2006, 06HA). MM-PBSA analyses suggest the approximate free energy of binding (ΔG) between Ig-2D1 and 18HA is −74.4 kcal/mol. In comparison with 18HA, 09HA and 06HA bind Ig-2D1 ∼6 kcal/mol (ΔΔG) weaker, and the 09HA_mut bind Ig-2D1 only half as strong. We also analyzed the contributions of individual epitope residues using the free-energy decomposition method. Two important salt bridges are found between the HAs and Ig-2D1. In 09HA, a serine-to-asparagine mutation coincided with a salt bridge destabilization, hydrogen bond losses, and a water pocket formation between 09HA and Ig-2D1. In 09HA_mut, a lysine-to-glutamic-acid mutation leads to the loss of both salt bridges and destabilizes interactions with Ig-2D1. Even though 06HA has a similar ΔG to 09HA, it is not recognized by Ig-2D1 in vivo. Because 06HA contains two potential glycosylation sites that could mask the epitope, our results suggest that Ig-2D1 may be active against 06HA only in the absence of glycosylation. Overall, our simulation results are in good agreement with observations from biological experiments and offer novel mechanistic insights, to our knowledge, into the immune escape of the influenza virus. PMID:26039171

The lowest-lying electronic singlet and triplet potential energy surfaces for the HNO-NOH system: energetics, unimolecular rate constants, tunneling and kinetic isotope effects for the isomerization and dissociation reactions.

PubMed

Bozkaya, Uğur; Turney, Justin M; Yamaguchi, Yukio; Schaefer, Henry F

2012-04-28

The lowest-lying electronic singlet and triplet potential energy surfaces (PES) for the HNO-NOH system have been investigated employing high level ab initio quantum chemical methods. The reaction energies and barriers have been predicted for two isomerization and four dissociation reactions. Total energies are extrapolated to the complete basis set limit applying focal point analyses. Anharmonic zero-point vibrational energies, diagonal Born-Oppenheimer corrections, relativistic effects, and core correlation corrections are also taken into account. On the singlet PES, the (1)HNO → (1)NOH endothermicity including all corrections is predicted to be 42.23 ± 0.2 kcal mol(-1). For the barrierless decomposition of (1)HNO to H + NO, the dissociation energy is estimated to be 47.48 ± 0.2 kcal mol(-1). For (1)NOH → H + NO, the reaction endothermicity and barrier are 5.25 ± 0.2 and 7.88 ± 0.2 kcal mol(-1). On the triplet PES the reaction energy and barrier including all corrections are predicted to be 7.73 ± 0.2 and 39.31 ± 0.2 kcal mol(-1) for the isomerization reaction (3)HNO → (3)NOH. For the triplet dissociation reaction (to H + NO) the corresponding results are 29.03 ± 0.2 and 32.41 ± 0.2 kcal mol(-1). Analogous results are 21.30 ± 0.2 and 33.67 ± 0.2 kcal mol(-1) for the dissociation reaction of (3)NOH (to H + NO). Unimolecular rate constants for the isomerization and dissociation reactions were obtained utilizing kinetic modeling methods. The tunneling and kinetic isotope effects are also investigated for these reactions. The adiabatic singlet-triplet energy splittings are predicted to be 18.45 ± 0.2 and 16.05 ± 0.2 kcal mol(-1) for HNO and NOH, respectively. Kinetic analyses based on solution of simultaneous first-order ordinary-differential rate equations demonstrate that the singlet NOH molecule will be difficult to prepare at room temperature, while the triplet NOH molecule is viable with respect to isomerization and dissociation reactions up to

Heat capacity and entropy at the temperatures 5 K to 720 K and thermal expansion from the temperatures 298 K to 573 K of synthetic enargite (Cu3AsS4)

USGS Publications Warehouse

Seal, R.R.; Robie, R.A.; Hemingway, B.S.; Evans, H.T.

1996-01-01

The heat capacity of synthetic Cu3AsS4 (enargite) was measured by quasi-adiabatic calorimetry from the temperatures 5 K to 355 K and by differential scanning calorimetry from T = 339 K to T = 720 K. Heat-capacity anomalies were observed at T = (58.5 ?? 0.5) K (??trsHom = 1.4??R??K; ??trsSom = 0.02??R) and at T = (66.5 ?? 0.5) K (??trsHom = 4.6??R??K; ??trsSom = 0.08??R), where R = 8.31451 J??K-1??mol-1. The causes of the anomalies are unknown. At T = 298.15 K, Cop,m and Som(T) are (190.4 ?? 0.2) J??K-1??mol-1 and (257.6 ?? 0.6) J??K-1??mol-1, respectively. The superambient heat capacities are described from T = 298.15 K to T = 944 K by the least-squares regression equation: Cop,m/(J??K-1??mol-1) = (196.7 ?? 1.2) + (0.0499 ?? 0.0016)??(T/K) -(1918 000 ?? 84 000)??(T/K)-2. The thermal expansion of synthetic enargite was measured from T = 298.15 K to T = 573 K by powder X-ray diffraction. The thermal expansion of the unit-cell volume (Z = 2) is described from T = 298.15 K to T = 573 K by the least-squares equation: V/pm3 = 106??(288.2 ?? 0.2) + 104??(1.49 ?? 0.04)??(T/K). ?? 1996 Academic Press Limited.

Catalytic and Thermal 1,2-Rearrangement of (α-Mercaptobenzyl)trimethylsilane

NASA Astrophysics Data System (ADS)

Zhang, Jie; Cui, Mengzhong; Feng, Shengyu; Sun, Xiaomin; Feng, Dacheng

2009-09-01

The mechanisms of catalytic and thermal 1,2-rearrangement of (α-mercaptobenzyl)trimethylsilane were studied by using density functional theory (DFT) at the MP2/6-31+G(d,p)//B3LYP/6-31G(d) levels. The results show that (α-mercaptobenzyl)trimethylsilane rearranges to (benzylthio)trimethylsilane through a trimethylsilyl group migration from C to S atom via a transition state of pentacoordinate Si atom with or without radical initiators. The low reaction activation energy (15.1 kcal/mol) is responsible for the fast rearrangement in the presence of radical initiators. Both radical and nonradical thermal rearrangement mechanisms were suggested, and the radical mechanism dominates through its self-catalyzing. These results are consistent with the experiment results. The activation energy (ΔHact = 15.1 kcal/mol) for the rate-determining step within the self-catalytic cycle is low enough to make (trimethylsilylbenzyl)thiyl radical be a reasonable catalyst for the thermal rearrangement. The catalytic and thermal 1,2-rearrangement mechanisms of (α-mercaptobenzyl)trimethylsilane, especially the self-catalytic radical mechanism, were revealed for the first time. The comparison of the rearrangement mechanisms between (α-mercaptobenzyl)trimethylsilane and silylmethanethiol discloses the factors in determining the reaction mechanism of such kinds of mercaptoalkyl-functionalized organosilanes. The phenyl group is found to be favorable for the radical rearrangement, thus making (α-mercaptobenzyl)trimethylsilane instable.

Derivatives of 1,5-diamino-1H-tetrazole: a new family of energetic heterocyclic-based salts.

PubMed

Gálvez-Ruiz, Juan Carlos; Holl, Gerhard; Karaghiosoff, Konstantin; Klapötke, Thomas M; Löhnwitz, Karolin; Mayer, Peter; Nöth, Heinrich; Polborn, Kurt; Rohbogner, Christoph J; Suter, Max; Weigand, Jan J

2005-06-13

1,5-Diamino-1H-tetrazole (2, DAT) can easily be protonated by reaction with strong mineral acids, yielding the poorly investigated 1,5-diaminotetrazolium nitrate (2a) and perchlorate (2b). A new synthesis for 2 is introduced that avoids lead azide as a hazardous byproduct. The reaction of 1,5-diamino-1H-tetrazole with iodomethane (7a) followed by the metathesis of the iodide (7a) with silver nitrate (7b), silver dinitramide (7c), or silver azide (7d) leads to a new family of heterocyclic-based salts. In all cases, stable salts were obtained and fully characterized by vibrational (IR, Raman) spectroscopy, multinuclear NMR spectroscopy, mass spectrometry, elemental analysis, X-ray structure determination, and initial safety testing (impact and friction sensitivity). Most of the salts exhibit good thermal stabilities, and both the perchlorate (2b) and the dinitramide (7c) have melting points well below 100 degrees C, yet high decomposition onsets, defining them as new (7c), highly energetic ionic liquids. Preliminary sensitivity testing of the crystalline compounds indicates rather low impact sensitivities for all compounds, the highest being that of the perchlorate (2b) and the dinitramide (7c) with a value of 7 J. In contrast, the friction sensitivities of the perchlorate (2b, 60 N) and the dinitramide (7c, 24 N) are relatively high. The enthalpies of combustion (Delta(c)H degrees ) of 7b-d were determined experimentally using oxygen bomb calorimetry: Delta(c)H degrees (7b) = -2456 cal g(-)(1), Delta(c)H degrees (7c) = -2135 cal g(-)(1), and Delta(c)H degrees (7d) = -3594 cal g(-)(1). The standard enthalpies of formation (Delta(f)H degrees ) of 7b-d were obtained on the basis of quantum chemical computations using the G2 (G3) method: Delta(f)H degrees (7b) = 41.7 (41.2) kcal mol(-)(1), Delta(f)H degrees (7c) = 92.1 (91.1) kcal mol(-)(1), and Delta(f)H degrees (7d) = 161.6 (161.5) kcal mol(-)(1). The detonation velocities (D) and detonation pressures (P) of 2b and 7b

Hydride affinities of cumulated, isolated, and conjugated dienes in acetonitrile.

PubMed

Zhu, Xiao-Qing; Liang, Hao; Zhu, Yan; Cheng, Jin-Pei

2008-11-07

The hydride affinities (defined as the enthalpy changes in this work) of 15 polarized dienes [five phenyl sulfone substituted allenes (1a), the corresponding five isolated dienes (1b), and the corresponding five conjugated dienes (1c)] in acetonitrile solution were determined by titration calorimetry for the first time. The results display that the hydride affinity scales of the 15 dienes in acetonitrile range from -71.6 to -73.9 kcal/mol for 1a, from -46.2 to -49.7 kcal/mol for 1b, and from -45.0 to -46.5 kcal/mol for 1c, which indicates that the hydride-obtaining abilities of the cumulated dienes (1a) are not only much larger than those of the corresponding conjugated dienes (1c) but also much larger than those of the corresponding isolated dienes (1b). The hydrogen affinities of the 15 dienes as well as the hydrogen affinities and the proton affinities of the radical anions of the dienes (1(-*)) in acetonitrile were also evaluated by using relative thermodynamic cycles according to Hess's law. The results show that (i) the hydrogen affinities of the neutral dienes 1 cover a range from -44.5 to -45.6 kcal/mol for 1a, from -20.4 to -21.4 kcal/mol for 1b, and from -17.3 to -18.5 kcal/mol for 1c; (ii) the hydrogen affinities of the radical anions of the dienes (1(-*)) in acetonitrile cover a range from -40.6 to -47.2 kcal/mol for 1a(-*), from -21.6 to -29.6 kcal/mol for 1b(-*), and from -10.0 to -15.4 kcal/mol for 1c(-*); (iii) the proton affinities of the 15 1a(-*) in acetonitrile cover a range from -97.0 to -100.6 kcal/mol for 1a(-*), from -77.8 to -83.4 kcal/mol for 1b(-*), and from -66.2 to -68.9 kcal/mol for 1c(-*). The main reasons for the great difference between the cumulated dienes and the corresponding isolated and conjugated dienes in the hydride affinity, hydrogen affinity, and proton affinity have been examined. It is evident that these experimental results should be quite valuable to facilitate the elucidation of the origins of the especially high

Solubility of lovastatin in a family of six alcohols: Ethanol, 1-propanol, 1-butanol, 1-pentanol, 1-hexanol, and 1-octanol.

PubMed

Nti-Gyabaah, J; Chmielowski, R; Chan, V; Chiew, Y C

2008-07-09

Accurate experimental determination of solubility of active pharmaceutical ingredients (APIs) in solvents and its correlation, for solubility prediction, is essential for rapid design and optimization of isolation, purification, and formulation processes in the pharmaceutical industry. An efficient material-conserving analytical method, with in-line reversed HPLC separation protocol, has been developed to measure equilibrium solubility of lovastatin in ethanol, 1-propanol, 1-butanol, 1-pentanol, 1-hexanol, and 1-octanol between 279 and 313K. Fusion enthalpy DeltaH(fus), melting point temperature, Tm, and the differential molar heat capacity, DeltaC(P), were determined by differential scanning calorimetry (DSC) to be 43,136J/mol, 445.5K, and 255J/(molK), respectively. In order to use the regular solution equation, simplified assumptions have been made concerning DeltaC(P), specifically, DeltaC(P)=0, or DeltaC(P)=DeltaS. In this study, we examined the extent to which these assumptions influence the magnitude of the ideal solubility of lovastatin, and determined that both assumptions underestimate the ideal solubility of lovastatin. The solubility data was used with the calculated ideal solubility to obtain activity coefficients, which were then fitted to the van't Hoff-like regular solution equation. Examination of the plots indicated that both assumptions give erroneous excess enthalpy of solution, H(infinity), and hence thermodynamically inconsistent activity coefficients. The order of increasing ideality, or solubility of lovastatin was butanol>1-propanol>1-pentanol>1-hexanol>1-octanol.

Antimalarial activity of HIV-1 protease inhibitor in chromone series.

PubMed

Lerdsirisuk, Pradith; Maicheen, Chirattikan; Ungwitayatorn, Jiraporn

2014-12-01

Increasing parasite resistance to nearly all available antimalarial drugs becomes a serious problem to human health and necessitates the need to continue the search for new effective drugs. Recent studies have shown that clinically utilized HIV-1 protease (HIV-1 PR) inhibitors can inhibit the in vitro and in vivo growth of Plasmodium falciparum. In this study, a series of chromone derivatives possessing HIV-1 PR inhibitory activity has been tested for antimalarial activity against P. falciparum (K1 multi-drug resistant strain). Chromone 15, the potent HIV-1 PR inhibitor (IC50=0.65μM), was found to be the most potent antimalarial compound with IC50=0.95μM while primaquine and tafenoquine showed IC50=2.41 and 1.95μM, respectively. Molecular docking study of chromone compounds against plasmepsin II, an aspartic protease enzyme important in hemoglobin degradation, revealed that chromone 15 exhibited the higher binding affinity (binding energy=-13.24kcal/mol) than the known PM II inhibitors. Thus, HIV-1 PR inhibitor in chromone series has the potential to be a new class of antimalarial agent. Copyright © 2014 Elsevier Inc. All rights reserved.

Temperature dependence of the low- and high-frequency Raman scattering from liquid water

NASA Astrophysics Data System (ADS)

Walrafen, G. E.; Fisher, M. R.; Hokmabadi, M. S.; Yang, W.-H.

1986-12-01

Low frequency Δν¯=0-350 cm-1, Raman intensity data were obtained from liquid water between 3.5 and 89.3 °C using holographic grating double and triple monochromators. The spectra were Bose-Einstein (BE) corrected, I/(1+n), and the total integrated (absolute) contour intensities were treated by an elaboration of the Young-Westerdahl (YW) thermodynamic method, assuming conservation of hydrogen-bonded (HB) and nonhydrogen-bonded (NHB=bent and/or stretched, O-H O) nearest-neighbor O-O pairs. A ΔH°1 value of 2.6±0.1 kcal/mol O-H ṡṡṡ O or 5.2±0.2 kcal/mol H2O (11 kJ/mol O-H ṡṡṡ O, or 22 kJ/mol H2O) resulted for the HB→NHB process. This intermolecular value agrees quantitatively with Raman and infrared ΔH° values from the one- and two-phonon OH-stretching regions, and from molecular dynamics, depolarized light scattering, neutron scattering, and ultrasonic absorption, thus indicating a common process. A population involving partial covalency of, i.e., charge transfer into, the H ṡṡṡ O units of linear and/or weakly bent hydrogen bonds, O-H ṡṡṡ O; is transformed into a second high energy population involving bent, e.g., 150° or less, and/or stretched, e.g., 3.2 Å, but otherwise strongly cohesive O-H O interactions. All difference spectra from the fundamental OH-stretching contours cross at the X(Z,X+Z)Y isobestic frequency of 3425 cm-1. Also, total integrated Raman intensity decreases occurring below 3425 cm-1 with temperature rise were found to be proportional to the total integrated intensity increases above 3425 cm-1, indicating conservation among the HB and NHB OH-stretching classes. From the enthalpy of vaporization of water at 0 °C, and the ΔH°1 of 2.6 kcal/mol O-H ṡṡṡ O, the additional enthalpy, ΔH°2, needed for the complete separation of the NHB O-O nearest neighbors is ˜3.2 kcal/mol O-H ṡṡṡ O or ˜6.4 kcal/mol H2O (13 kJ/mol O-H ṡṡṡ O or 27 kJ/mol H2O). The NHB O-O nearest neighbors are held by forces

Molecular dynamics simulation of nitric oxide in myoglobin

USGS Publications Warehouse

Lee, Myung Won; Meuwly, Markus

2012-01-01

The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm–1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm–1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is ΔGB→C = 1.7–2.0 kcal/mol. The reverse barrier is ΔGB←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical

NASA Astrophysics Data System (ADS)

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-01

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 1011 s-1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical.

PubMed

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-28

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 10 11 s -1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Accurate coupled cluster reaction enthalpies and activation energies for X+H2 --> XH+H (X=F, OH, NH2, and CH3)

NASA Astrophysics Data System (ADS)

Kraka, Elfi; Gauss, Jürgen; Cremer, Dieter

1993-10-01

Coupled cluster calculations at the CCSD(T)/[5s4p3d/4s3p] and CCSD(T)/[5s4p3d2 f1g/4s3p2d] level of theory are reported for reactions X+H2→XH+H [X=F (1a), OH (1b), NH2 (1c), and CH3 (1d)] utilizing analytical energy gradients for geometry, frequency, charge distribution, and dipole moment calculations of reactants, transition states, and products. A careful analysis of vibrational corrections leads to reaction enthalpies at 300 K, which are within 0.04, 0.15, 0.62, and 0.89 kcal/mol of experimental values. For reaction (1a) a bent transition state and for reactions (1b) and (1c) transition states with a cis arrangement of the reactants are calculated. The cis forms of transition states (1b) and (1c) are energetically favored because of electrostatic interactions, in particular dipole-dipole attraction as is revealed by calculated charge distributions. For reactions (1a)-(1d), the CCSD(T)/[5s4p3d2 f1g/4s3p2d] activation energies at 300 K are 1.1, 5.4, 10.8, and 12.7 kcal/mol which differ by just 0.1, 1.4, 2.3, and 1.8 kcal/mol, respectively, from the corresponding experimental values of 1±0.1, 4±0.5, 8.5±0.5, and 10.9±0.5 kcal/mol. For reactions (1), this is the best agreement between experiment and theory that has been obtained from ab initio calculations not including any empirically based corrections. Agreement is achieved after considering basis set effects, basis set superposition errors, spin contamination, tunneling effect and, in particular, zero-point energies as well as temperature corrections. Net corrections for the four activation energies are -1.05, -0.2, 1.25, and 0.89 kcal/mol, which shows that for high accuracy calculations a direct comparison of classical barriers and activation energies is misleading.

Kinetics and Thermochemistry of ClCO Formation from the Cl + CO Association Reaction

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Kreutter, K. D.; Wine, P. H.

1997-01-01

Laser flash photolysis of Cl2/CO/M mixtures (M = N2, CO, Ar, CO2) has been employed in conjunction with Cl((sup 2)P(sub J)) detection by time-resolved resonance fluorescence spectroscopy to investigate equilibration kinetics in the reactions Cl((sup 2)P(sub J)) + CO ClCO as a function of temperature (185-260 K) and pressure (14-200 Torr). The association and dissociation reactions are found to be in the low-pressure limit over the range of experimental conditions investigated. In N2 and/or CO buffer gases, the temperature dependences of the ClCO formation and dissociation reaction rate constants are described by the Arrhenius expressions k(sub 1) = (1.05 +/- 0.36) x 10(exp -34) exp[(810 +/- 70)/T] cm(exp 6)/molecules(exp 2).s and k(sub -1) = (4.1 +/- 3.1) x 10(exp -10) exp[(-2960 +/- 60)/T]cu cm/(molecule.s) (errors are 2 sigma). Second- and third-law analyses of the temperature dependence of the equilbrium constant (k/k-1) lead to the following thermodynamic parameters for the association reaction: Delta-H(sub 298) = -7.7 +/- 0.6 kcal/mol, Delta-H(sub 0) = -6.9 +/- 0.7 kcal/mol, Delta-S(sub 298) = -23.8 +/- 2.0 cal/mole.K, Delta-H(sub f,298)(ClCO) = 5.2 +/- 0.6 kcal/mol (errors are 2 sigma). The results repported in this study significantly reduce the uncertainties in all reported kinetic and thermodynamic parameters.

Triplet and ground state potential energy surfaces of 1,4-diphenyl-1,3-butadiene: theory and experiment.

PubMed

Saltiel, J; Dmitrenko, O; Pillai, Z S; Klima, R; Wang, S; Wharton, T; Huang, Z-N; van de Burgt, L J; Arranz, J

2008-05-01

Relative energies of the ground state isomers of 1,4-diphenyl-1,3-butadiene (DPB) are determined from the temperature dependence of equilibrium isomer compositions obtained with the use of diphenyl diselenide as catalyst. Temperature and concentration effects on photostationary states and isomerization quantum yields with biacetyl or fluorenone as triplet sensitizers with or without the presence of O(2), lead to significant modification of the proposed DPB triplet potential energy surface. Quantum yields for ct-DPB formation from tt-DPB increase with [tt-DPB] revealing a quantum chain process in the tt --> ct direction, as had been observed for the ct --> tt direction, and suggesting an energy minimum at the (3)ct* geometry. They confirm the presence of planar and twisted isomeric triplets in equilibrium (K), with energy transfer from planar or quasi-planar geometries (quantum chain events from tt and ct triplets) and unimolecular decay (k(d)) from twisted geometries. Starting from cc-DPB, varphi(cc-->tt) increases with increasing [cc-DPB] whereas varphi(cc-->ct) is relatively insensitive to concentration changes. The concentration and temperature dependencies of the decay rate constants of DPB triplets in cyclohexane are consistent with the mechanism deduced from the photoisomerization quantum yields. The experimental DeltaH between (3)tt-DPB* and (3)tp-DPB*, 2.7 kcal mol(-1), is compared with the calculated energy difference [DFT with B3LYP/6-31+G(d,p) basis set]. Use of the calculated DeltaS = 4.04 eu between the two triplets gives k(d) = (2.4-6.4) x 10(7) s(-1), close to 1.70 x 10(7) s(-1), the value for twisted stilbene triplet decay. Experimental and calculated relative energies of DPB isomers on the ground and triplet state surfaces agree and theory is relied upon to deduce structural characteristics of the equilibrated conformers in the DPB triplet state.

Development of a 1K x 1K GaAs QWIP Far IR Imaging Array

NASA Technical Reports Server (NTRS)

Jhabvala, M.; Choi, K.; Goldberg, A.; La, A.; Gunapala, S.

2003-01-01

In the on-going evolution of GaAs Quantum Well Infrared Photodetectors (QWIPs) we have developed a 1,024 x 1,024 (1K x1K), 8.4-9 microns infrared focal plane array (FPA). This 1 megapixel detector array is a hybrid using the Rockwell TCM 8050 silicon readout integrated circuit (ROIC) bump bonded to a GaAs QWIP array fabricated jointly by engineers at the Goddard Space Flight Center (GSFC) and the Army Research Laboratory (ARL). The finished hybrid is thinned at the Jet Propulsion Lab. Prior to this development the largest format array was a 512 x 640 FPA. We have integrated the 1K x 1K array into an imaging camera system and performed tests over the 40K-90K temperature range achieving BLIP performance at an operating temperature of 76K (f/2 camera system). The GaAs array is relatively easy to fabricate once the superlattice structure of the quantum wells has been defined and grown. The overall arrays costs are currently dominated by the costs associated with the silicon readout since the GaAs array fabrication is based on high yield, well-established GaAs processing capabilities. In this paper we will present the first results of our 1K x 1K QWIP array development including fabrication methodology, test data and our imaging results.

Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds.

PubMed

Liu, Min Hsien; Chen, Cheng; Hong, Yaw Shun

2005-02-08

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.

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

26 CFR 1.1031(k)-1 - Treatment of deferred exchanges.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 11 2012-04-01 2012-04-01 false Treatment of deferred exchanges. 1.1031(k)-1 Section 1.1031(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Common Nontaxable Exchanges § 1.1031(k)-1 Treatment of...

26 CFR 1.1031(k)-1 - Treatment of deferred exchanges.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 11 2011-04-01 2011-04-01 false Treatment of deferred exchanges. 1.1031(k)-1 Section 1.1031(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Common Nontaxable Exchanges § 1.1031(k)-1 Treatment of...

26 CFR 1.1031(k)-1 - Treatment of deferred exchanges.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 11 2013-04-01 2013-04-01 false Treatment of deferred exchanges. 1.1031(k)-1 Section 1.1031(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Common Nontaxable Exchanges § 1.1031(k)-1 Treatment of...

26 CFR 1.1031(k)-1 - Treatment of deferred exchanges.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 11 2010-04-01 2010-04-01 true Treatment of deferred exchanges. 1.1031(k)-1 Section 1.1031(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Common Nontaxable Exchanges § 1.1031(k)-1 Treatment of deferred...

26 CFR 1.1031(k)-1 - Treatment of deferred exchanges.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 11 2014-04-01 2014-04-01 false Treatment of deferred exchanges. 1.1031(k)-1 Section 1.1031(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Common Nontaxable Exchanges § 1.1031(k)-1 Treatment of...

The Heats of Formation of SiCl+n, for n=1-4

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Arnold, James O. (Technical Monitor)

1997-01-01

The heats of formation of SiCl(sub n) and SiCl+(sub n), for n=1-4, have been determined using the G2(B3LYP/MP2/CC) approach. The results for the neutral systems are in very good agreement with previous work. High level calibration calculations show that ion results have about the same accuracy as the neutrals, and allow us to refine the G2(B3LYP/MP2/CC) values. The calculations show that the adiabatic IP of SiCl4 is about 7 kcal/mol smaller than the accepted value. Using a rigid rotor/harmonic oscillator approximation, the temperature dependence of the heat of formation, heat capacity, and entropy are computed for 300 to 4000 K and fit to a polynomial.

The synthesis of 1,2-bis(1,5,9-triazacyclododecyl)ethane: a showcase for the importance of the linker length within bis(alkylating) reagents.

PubMed

Medina-Molner, Alfredo; Blacque, Olivier; Spingler, Bernhard

2007-11-08

The synthesis of 1,2-bis(1,5,9-triazacyclododecyl)ethane (1) showcases how different bis(alkylating) reagents change the reaction from an intra- to an intermolecular pathway. The isolation of the intermediate hexahydro-3a,6a-ethano-1H,4H,7H,9bH-9a-aza-3a,6a-diazoniaphenalene-3a,6a-diium (2) explained why initially the synthesis of 1 was not possible. Both isomers of 2 were found in solution. DFT calculations revealed that isomer 2a is 4.6 kcal/mol lower in energy than 2b. Synthesis of 1 was finally achieved by using oxalyl chloride.

Oxidation of 1,3,7-trimethylxanthine by hypochlorite ion

NASA Astrophysics Data System (ADS)

Kheidorov, V. P.; Ershov, Yu. A.; Chalyi, G. Yu.; Titorovich, O. V.

2011-08-01

The kinetics of the oxidative conversion of 1,3,7-trimethylxanthine upon treatment with hypochlorite ions (OCl-) in aqueous medium at 283-298 K and pH 8.2 was studied. The reaction order with respect to each component was determined and proved to be 1. It was established that the temperature dependence of the reaction rate follows the Arrhenius equation. The activation parameters of the reaction were measured: E a = 33.58 kJ/mol, Δ H ≠ = 31.12 kJ/mol, Δ S ≠ = -170.02 J/(K mol), Δ G ≠ = 81.45 kJ/mol. The stoichiometry of the reaction was studied, and the chemistry of the oxidative conversion of caffeine treated with OCl- is discussed.

Computational study of bindings of HK20 Fab and D5 Fab to HIV-1 gp41.

PubMed

Hartono, Yossa Dwi; Lazim, Raudah; Yip, Yew Mun; Zhang, Dawei

2012-02-15

Antibodies HK20 and D5 have been shown to target HIV-1 gp41, thereby inhibiting membrane fusion that facilitates viral entry. The binding picture is static, based on the X-ray crystal structures of the Fab regions and gp41 mimetic five-helix bundle. In this study, we carried out molecular dynamics simulation to provide the dynamic binding picture. Calculated binding free energies are within reasonable range of and follow the trend of the experimental values: -15.28 kcal/mol for HK20 Fab (expt. -11.60 kcal/mol) and -17.90 kcal/mol for D5 Fab (expt. -11.70 kcal/mol). Alanine scanning at protein-protein interface reveals that the highest contributors to binding for HK20 Fab are F54 and I56, both of V(H) region, as well as R30' of V(L) region; whereas for D5 Fab, F54 of V(H) region, as well as W32' and Y94' of V(L) region. HK20 F54 and I56, as well as D5 I52, F54, and T56, bind to the gp41 hydrophobic binding pocket, an important region targeted by many other fusion inhibitors. Hydrogen bonding analysis also identifies high-occupancy hydrogen bonds at the periphery of gp41 hydrophobic pocket. Considering that almost all interface residues are turn residues, further work may be directed to turn mimics. Pre-orientation by the hydrogen bonds to poise this particular turn towards the binding pocket may also be a point worth pursuing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Integral Representation of the Pictorial Proof of Sum of [superscript n][subscript k=1]k[superscript 2] = 1/6n(n+1)(2n+1)

ERIC Educational Resources Information Center

Kobayashi, Yukio

2011-01-01

The pictorial proof of the sum of [superscript n][subscript k=1] k[superscript 2] = 1/6n(n+1)(2n+1) is represented in the form of an integral. The integral representations are also applicable to the sum of [superscript n][subscript k-1] k[superscript m] (m greater than or equal to 3). These representations reveal that the sum of [superscript…

Reproducibility of the Helium-3 Constant-Volume Gas Thermometry and New Data Down to 1.9 K at NMIJ/AIST

NASA Astrophysics Data System (ADS)

Nakano, Tohru; Shimazaki, Takeshi; Tamura, Osamu

2017-07-01

This study confirms reproducibility of the International Temperature Scale of 1990 (ITS-90) realized by interpolation using the constant-volume gas thermometer (CVGT) of National Metrology Institute of Japan (NMIJ)/AIST with 3He as the working gas from 3 K to 24.5561 K by comparing the newly obtained results and those of earlier reports, indicating that the CVGT has retained its capability after renovation undertaken since strong earthquakes struck Japan. The thermodynamic temperature T is also obtained using the single-isotherm fit to four working gas densities (127 mol\\cdot m^{-3}, 145 mol\\cdot m^{-3}, 171 mol\\cdot m^{-3} and 278 mol\\cdot m^{-3}) down to 1.9 K, using the triple point temperature of Ne as a reference temperature. In this study, only the second virial coefficient is taken into account for the single-isotherm fit. Differences between T and the ITS-90 temperature, T-T_{90}, reported in earlier works down to 3 K were confirmed in this study. At the temperatures below 3 K down to 2.5 K, T-T_{90} is much smaller than the standard combined uncertainty of thermodynamic temperature measurement. However, T- T_{90} seems to increase with decreasing temperature below 2.5 K down to 1.9 K, although still within the standard combined uncertainty of thermodynamic temperature measurement. In this study, T is obtained also from the CVGT with a single gas density of 278 mol\\cdot m^{-3} using the triple-point temperature of Ne as a reference temperature by making correction for the deviation from the ideal gas using theoretical values of the second and third virial coefficients down to 2.6 K, which is the lowest temperature of the theoretical values of the third virial coefficient. T values obtained using this method agree well with those obtained from the single-isotherm fit. We also found that the second virial coefficient obtained by the single-isotherm fit to experimental results agrees well with that obtained by the single-isotherm fit to the theoretically

26 CFR 1.168(k)-1 - Additional first year depreciation deduction.

Code of Federal Regulations, 2011 CFR

2011-04-01

....168(k)-1 Section 1.168(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY... Corporations § 1.168(k)-1 Additional first year depreciation deduction. (a) Scope and definitions—(1) Scope... deduction allowable under section 168(k)(1) for qualified property and the 50-percent additional first year...

Sodium doping effect on physicochemical properties of K{sub 1−x}Na{sub x}CaPb{sub 3}(PO{sub 4}){sub 3} (0 ≤ x ≤ 1) for the determination of mercury(II): Application in seawater samples

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

Lahrich, Sara; University Hassan 1, Laboratoire Sciences des Matériaux, des Milieux et de la Modélisation, 25000 Khouribga; Manoun, Bouchaib

Highlights: • The apatite, K{sub 1−x}Na{sub x}CaPb{sub 3}(PO{sub 4}){sub 3} (0 ≤ x ≤ 1), was synthesized using reaction solid. • The obtained apatite was used to determine mercury in seawater samples from Morocco. • The effect of doping sodium into apatite on physic-chemical parameters was studied. • The influence of the electrochemical variables was investigated to determine mercury. - Abstract: A new chemically modified electrode was synthesized for the determination of mercury(II) using differential pulse anodic stripping voltammetry (DPASV). The electrode was modified by lacunar apatite K{sub 1−x}Na{sub x}CaPb{sub 3}(PO{sub 4}){sub 3} (0 ≤ x ≤ 1) synthesized usingmore » solid reaction. These powders were crystallized in the hexagonal system, space group P6{sub 3}/m. The effect of sodium content on structural, thermodynamic and electrochemical properties of prepared apatite has been studied. Therefore, the best results was obtained using NaCaPb{sub 3}(PO{sub 4}){sub 3} (x = 1) as modifier of carbon paste electrode for the electrochemical detection of mercury(II). The later ions were preconcentrated on the surface of the modified electrode and oxidized at 0.06 V vs. Ag/AgCl. The electroanalytical procedure comprises of two steps: the chemical accumulation of the analyte under open-circuit conditions followed by the electrochemical detection of the preconcentrated species using differential pulse voltammetry. The different parameters that govern the two steps were optimized. A linear response was obtained in the concentration range from 1.0 mol L{sup −1} × 10{sup −4} mol L{sup −1} to 2.0 mol L{sup −1} × 10{sup −7} mol L{sup −1} Hg(II) after activation of the electrode surface under the optimized conditions. The standard deviation was evaluated in a high and low concentration of mercury(II). The values ​​obtained for seven consecutive measurements were 1.24% and 5.07% of 1.0 mol L{sup −1} × 10{sup −4} mol L{sup −1} and

Stabilization of very rare tautomers of 1-methylcytosine by an excess electron.

PubMed

Harańczyk, Maciej; Rak, Janusz; Gutowski, Maciej

2005-12-22

We characterized valence anionic states of 1-methylcytosine using various electronic structure methods. We found that the most stable valence anion is related to neither the canonical amino-oxo nor a rare imino-oxo tautomer, in which a proton is transferred from the N4 to N3 atom. Instead, it is related to an imino-oxo tautomer, in which the C5 atom is protonated. This anion is characterized by an electron vertical detachment energy (VDE) of 2.12 eV and it is more stable than the anion based on the canonical tautomer by 1.0 kcal/mol. The latter is characterized by a VDE of 0.31 eV. Another unusual low-lying imino-oxo tautomer with a VDE of 3.60 eV has the C6 atom protonated and is 3.6 kcal/mol less stable than the anion of the canonical tautomer. All these anionic states are adiabatically unbound with respect to the canonical amino-oxo neutral, with the instability of 5.8 kcal/mol for the most stable valence anion. The mechanism of formation of anionic tautomers with carbon atoms protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to the C5 or C6 atom. The six-member ring structure of anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Indeed the neutral systems collapse without a barrier to a linear or a bicyclo structure, which might be viewed as lesions to DNA or RNA. Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated.

Docking of oxalyl aryl amino benzoic acid derivatives into PTP1B

PubMed Central

Verma, Neelam; Mittal, Minakshi; Verma, Raman kumar

2008-01-01

Protein Tyrosine Phosphatases (PTPs) that function as negative regulators of the insulin signaling cascade have been identified as novel targets for the therapeutic enhancement of insulin action in insulin resistant disease states. Reducing Protein Tyrosine Phosphatase1B (PTP1B) abundance not only enhances insulin sensitivity and improves glucose metabolism but also protects against obesity induced by high fat feeding. PTP1B inhibitors such as Formylchromone derivatives, 1, 2-Naphthoquinone derivatives and Oxalyl aryl amino benzoic derivatives may eventually find an important clinical role as insulin sensitizers in the management of Type-II Diabetes and metabolic syndrome. We have carried out docking of modified oxalyl aryl amino benzoic acid derivatives into three dimensional structure of PTP1B using BioMed CAChe 6.1. These compounds exhibit good selectivity for PTP1B over most of phosphatases in selectivity panel such as SHP-2, LAR, CD45 and TCPTP found in literature. This series of compounds identified the amino acid residues such as Gly220 and Arg221 are important for achieving specificity via H-bonding interactions. Lipophilic side chain of methionine in modified oxalyl aryl amino benzoic acid derivative [1b (a2, b2, c1, d)] lies in closer vicinity of hydrophobic region of protein consisted of Meth258 and Phe52 in comparison to active ligand. Docking Score in [1b (a2, b2, c1, d)] is -131.740Kcal/mol much better than active ligand score -98.584Kcal/mol. This information can be exploited to design PTP1B specific inhibitors. PMID:19238234

Investigating the ground-state rotamers of n-propylperoxy radical.

PubMed

Hoobler, Preston R; Turney, Justin M; Schaefer, Henry F

2016-11-07

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T) (coupled-cluster theory, incorporating single, double, and perturbative triple)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born-Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamer followed by the gauche-trans (0.12 kcal mol -1 above GG), trans-gauche (0.44 kcal mol -1 ), gauche'-gauche (0.47 kcal mol -1 ), and trans-trans (0.57 kcal mol -1 ). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory. This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm -1 for the GG structure) also has a significant IR intensity, 19.6 km mol -1 . The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged r g,0K bond lengths, accounting for zero-point vibrations present within the molecule.

Investigating the Ground-State Rotamers of n-Propylperoxy Radical

DOE PAGES

Hoobler, Preston Reece; Turney, Justin Matthew; Schaefer III, Henry

2016-11-01

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born--Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamermore » followed by the gauche-trans (0.12 kcal mol^-1 above GG), trans-gauche (0.44 kcal mol^-1), gauche'-gauche (0.47 kcal mol^-1), and trans-trans (0.57 kcal mol^-1). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory (VPT2). This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm^-1 for the GG structure) also has a significant IR intensity, 19.6 km mol^-1. The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged r_g,0 K bond lengths, accounting for zero-point vibrations present within the molecule.« less

Investigating the ground-state rotamers of n-propylperoxy radical

NASA Astrophysics Data System (ADS)

Hoobler, Preston R.; Turney, Justin M.; Schaefer, Henry F.

2016-11-01

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T) (coupled-cluster theory, incorporating single, double, and perturbative triple)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born-Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamer followed by the gauche-trans (0.12 kcal mol-1 above GG), trans-gauche (0.44 kcal mol-1), gauche'-gauche (0.47 kcal mol-1), and trans-trans (0.57 kcal mol-1). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory. This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm-1 for the GG structure) also has a significant IR intensity, 19.6 km mol-1. The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged rg,0K bond lengths, accounting for zero-point vibrations present within the molecule.

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

Hoobler, Preston Reece; Turney, Justin Matthew; Schaefer III, Henry

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born--Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamermore » followed by the gauche-trans (0.12 kcal mol^-1 above GG), trans-gauche (0.44 kcal mol^-1), gauche'-gauche (0.47 kcal mol^-1), and trans-trans (0.57 kcal mol^-1). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory (VPT2). This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm^-1 for the GG structure) also has a significant IR intensity, 19.6 km mol^-1. The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged r_g,0 K bond lengths, accounting for zero-point vibrations present within the molecule.« less

Enhanced biodegradation of mixed PAHs by mutated naphthalene 1,2-dioxygenase encoded by Pseudomonas putida strain KD6 isolated from petroleum refinery waste.

PubMed

Dutta, Kunal; Shityakov, Sergey; Das, Prangya P; Ghosh, Chandradipa

2017-12-01

Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental pollutant that are given top priority to maintain water and soil quality to the most amenable standard. Biodegradation of PAHs by bacteria is the convenient option for decontamination on site or off site. The aim of the present study was to isolate and identify naturally occurring bacteria having mixed PAHs biodegradation ability. The newly isolated Pseudomonas putida strain KD6 was found to efficiently degrade 97.729% of 1500 mg L -1 mixed PAHs within 12 days in carbon-deficient minimal medium (CSM). The half-life ( t 1/2 ) and degradation rate constant ( k ) were estimated to be 3.2 and 0.2165 days, respectively. The first-order kinetic parameters in soil by strain KD6 had shown efficient biodegradation potency with the higher concentration of total PAHs (1500 mg kg -1 soil), t 1/2  = 10.44 days -1 . However, the biodegradation by un-inoculated control soil was found slower ( t 1/2  = 140 days -1 ) than the soil inoculated with P. putida strain KD6. The enzyme kinetic constants are also in agreement with chemical data obtained from the HPLC analysis. In addition, the sequence analysis and molecular docking studies showed that the strain KD6 encodes a mutant version of naphthalene 1,2-dioxygenase which have better Benzpyrene binding energy (-9.90 kcal mol -1 ) than wild type (-8.18 kcal mol -1 ) enzyme (chain A, 1NDO), respectively, with 0.00 and 0.08 RMSD values. The mutated naphthalene 1,2-dioxygenase nah Ac has six altered amino acid residues near to the ligand binding site. The strain KD6 could be a good bioresource for in situ or ex situ biodegradation of polycyclic aromatic hydrocarbon.

Thermogravimetric analysis, kinetic study, and pyrolysis-GC/MS analysis of 1,1'-azobis-1,2,3-triazole and 4,4'-azobis-1,2,4-triazole.

PubMed

Jia, Chenhui; Li, Yuchuan; Zhang, Shujuan; Fei, Teng; Pang, Siping

2018-03-01

In general, the greater the number of directly linked nitrogen atoms in a molecule, the better its energetic performance, while the stability will be accordingly lower. But 1,1'-azobis-1,2,3-triazole (1) and 4,4'-azobis-1,2,4-triazole (2) show remarkable properties, such as high enthalpies of formation, high melting points, and relatively high stabilities. In order to rationalize this unexpected behavior of the two compounds, it is necessary to study their thermal decompositions and pyrolyses. Although a great deal of research has been focused on the synthesis and characterization of energetic materials with 1 and 2 as the backbone, a complete report on their fundamental thermodynamic parameters and thermal decomposition properties has not been published. Thermogravimetric-differential scanning calorimetry were used to obtain the thermal decomposition data of the title compounds. Kissinger and Ozawa-Doyle methods, the two selected non-isothermal methods, are presented for analysis of the solid-state kinetic data. Pyrolysis-gas chromatography/mass spectrometry was used to study the pyrolysis process of the title compounds. The DSC curves show that the thermal decompositions of 1 and 2 are at different heating rates involved a single exothermic process. The TG curves provide insight into the total weight losses from the compounds associated with this process. At different pyrolysis temperatures, the compositions and types of the pyrolysis products differ greatly and the pyrolysis reaction at 500 °C is more thorough than 400 °C. Apparent activation energies (E) and pre-exponential factors (lnA/s -1 ) are 291.4 kJ mol -1 and 75.53 for 1; 396.2 kJ mol -1 and 80.98 for 2 (Kissinger). The values of E are 284.5 kJ mol -1 for 1 and 386.1 kJ mol -1 for 2 (Ozawa-Doyle). The critical temperature of thermal explosion (T b ) is evaluated as 187.01 °C for 1 and 282.78 °C for 2. The title compounds were broken into small fragment ions under the pyrolysis conditions

Calorimetric studies of the heats of protonation of the dangling phosphorus in [eta][sup 1]-Ph[sub 2]PCH[sub 2]PPh[sub 2] complexes of chromium, molybdenum, and tungsten

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

Rottink, M.K.; Angelici, R.J.

1993-05-26

Titration calorimetry has been used to determine the heats of protonation ([Delta]H[sub HP]) of M(CO)[sub 5]([eta][sup 1]-dppm) (M = Cr, Mo, W) and fac-M(CO)[sub 3](N-N)([eta][sup 1]-dppm) (M = Mo, N-N = bipy, phen; M = w, N-N = bipy) complexes with CF[sub 3]SO[sub 3]H in 1,2-dichloroethane solvent at 25.0 [degrees]C. Spectroscopic studies show that protonation occurs at the uncoordinated phosphorus atom of the [eta][sup 1]-coordinated dppm (Ph[sub 2]PCH[sub 2]PPh[sub 2]) ligand. For dppm, its monoprotonated form (dppmH[sup +]), and these complexes, the basicity ([Delta]H[sub HP]) of the dangling phosphorus increases from -14.9 kcal/mol to -23.1 kcal/mol in the order: dppmH[supmore » +]« less

The 1,2-hydrogen shift reaction for monohalogenophosphanes PH2X and HPX (X = F, Cl)

NASA Astrophysics Data System (ADS)

Viana, Rommel B.; Varela, Jaldyr J. G., Jr.; Tello, Ana C. M.; Savedra, Ranylson M. L.; da Silva, Albérico B. F.

2016-10-01

The aim of the present study was to perform a quantum chemical investigation in the 1,2-hydrogen shift reaction for the PH2X and HPX molecules (X = F,Cl). Several phosphorus-halogen-bearing molecules were studied, including PH2F, PH2Cl, HPF, HPCl, HPFH, HPClH, PFH and PClH. The energies of stationary and saddle points on the ground electronic potential energy surface were investigated with post-Hartree-Fock methods [CCSD(T), MP2, QCISD] and different DFT functionals. The PH2F 1,2-hydrogen shift energy barrier was 75 kcal mol-1 at the CCSD(T) level and only a small increase in this value was observed for the HPF isomerisation. In contrast, the HPCl 1,2-hydrogen shift barrier is higher than the PH2Cl one, which presented a barrier height of 69 kcal mol-1 among CCSD(T) and composite methods. The rate constants of these unimolecular rearrangements varied from 10-44 to 10-38 s-1, and these isomerisation channels exhibited large half-lives. In addition, the heat of formation of each monohalogenophosphane was also calculated. The Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analysis were also employed to characterise the differences between the phosphorous-halogen bonds.

Preparation, crystal structure and thermal decomposition kinetics of 1-(2,4-dinitrophenyl)azo-1-nitrocyclohexane

NASA Astrophysics Data System (ADS)

Yang, Desuo; Ma, Haixia; Hu, Rongzu; Song, Jirong; Zhao, Fengqi

2005-11-01

A new three-nitro-group compound of 1-(2,4-dinitrophenyl)azo-1-nitrocyclohexane was prepared by the reaction of cyclohexanone-2,4-dinitrophenylhydrazine with nitric oxide at ambient temperature. The single crystal structure has been determined by a four-circle X-ray diffractometer. The compound is monoclinic with space group P2(1)/ c and unit-cell parameters a=11.300(2) Å, b=12.993(2) Å, c=10.155(1) Å, β=98.33(1) o, F(000)=672, the unit-cell volume V=1475.2(5) Å 3, the molecule number in one unit-cell Z=4, the absorption coefficient μ=1.19 cm -1, the calculated density Dc=1.456 g cm -3. The exothermic decomposition reaction kinetics of the compound has been studied by DSC. The kinetic model function in differential form, apparent activation energy and pre-exponential constant of this reaction are (3/4)(1-α)[-ln(1-α)] 1/4, 123.88 kJ mol -1 and 10 11.49 s -1, respectively. The critical temperature of thermal explosion of the title compound is 161.15 oC and the entropy of activation (ΔS), enthalpy of activation (ΔH), and free energy of activation (ΔG) are -34.16 J mol -1 K -1, 115.7, and 130.48 kJ mol -1, respectively.

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous p K a, and cyclohexane-water log D

NASA Astrophysics Data System (ADS)

Tielker, Nicolas; Tomazic, Daniel; Heil, Jochen; Kloss, Thomas; Ehrhart, Sebastian; Güssregen, Stefan; Schmidt, K. Friedemann; Kast, Stefan M.

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (p K a) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the "Minnesota Solvation Database" (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol-1 for water and 0.8-0.9 kcal mol-1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical p K a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the p K a) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.

PubMed

Tielker, Nicolas; Tomazic, Daniel; Heil, Jochen; Kloss, Thomas; Ehrhart, Sebastian; Güssregen, Stefan; Schmidt, K Friedemann; Kast, Stefan M

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4 ) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the "embedded cluster reference interaction site model" (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pK a ) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the "Minnesota Solvation Database" (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol -1 for water and 0.8-0.9 kcal mol -1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pK a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the pK a ) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

ExoMol line lists - XXIX. The rotation-vibration spectrum of methyl chloride up to 1200 K

NASA Astrophysics Data System (ADS)

Owens, A.; Yachmenev, A.; Thiel, W.; Fateev, A.; Tennyson, J.; Yurchenko, S. N.

2018-06-01

Comprehensive rotation-vibration line lists are presented for the two main isotopologues of methyl chloride, 12CH335Cl and 12CH337Cl. The line lists, OYT-35 and OYT-37, are suitable for temperatures up to T = 1200 K and consider transitions with rotational excitation up to J = 85 in the wavenumber range 0-6400 cm-1 (wavelengths λ > 1.56 μm). Over 166 billion transitions between 10.2 million energy levels have been calculated variationally for each line list using a new empirically refined potential energy surface, determined by refining to 739 experimentally derived energy levels up to J = 5, and an established ab initio dipole moment surface. The OYT line lists show excellent agreement with newly measured high-temperature infrared absorption cross-sections, reproducing both strong and weak intensity features across the spectrum. The line lists are available from the ExoMol database and the CDS database.

ExoMol line lists - XXII. The rotation-vibration spectrum of silane up to 1200 K

NASA Astrophysics Data System (ADS)

Owens, A.; Yachmenev, A.; Thiel, W.; Tennyson, J.; Yurchenko, S. N.

2017-11-01

A variationally computed 28SiH4 rotation-vibration line list applicable for temperatures up to T = 1200 K is presented. The line list, called OY2T, considers transitions with rotational excitation up to J = 42 in the wavenumber range 0-5000 cm-1 (wavelengths λ > 2 μm). Just under 62.7 billion transitions have been calculated between 6.1 million energy levels. Rovibrational calculations have utilized a new `spectroscopic' potential energy surface determined by empirical refinement to 1452 experimentally derived energy levels up to J = 6, and a previously reported ab initio dipole moment surface. The temperature-dependent partition function of silane, the OY2T line list format, and the temperature dependence of the OY2T line list are discussed. Comparisons with the PNNL spectral library and other experimental sources indicate that the OY2T line list is robust and able to accurately reproduce weaker intensity features. The full line list is available from the ExoMol data base and the CDS data base.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Thermochemical properties for isooctane and carbon radicals: computational study.

PubMed

Snitsiriwat, Suarwee; Bozzelli, Joseph W

2013-01-17

Thermochemical properties for isooctane, its internal rotation conformers, and radicals with corresponding bond energies are determined by use of computational chemistry. Enthalpies of formation are determined using isodesmic reactions with B3LYP density function theory and composite CBS-QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the isooctane parent and for the primary, secondary, and tertiary radicals in order to identify isomer energies. Intramolecular interactions are shown to have a significant effect on the enthalpy of formation of the isooctane parent and its radicals. The computed standard enthalpy of formation for the lowest energy conformers of isooctane from this study is -54.40 ± 1.60 kcal mol(-1), which is 0.8 kcal mol(-1) lower than the evaluated experimental value -53.54 ± 0.36 kcal mol(-1). The standard enthalpy of formation for the primary radical for a methyl on the quaternary carbon is -5.00 ± 1.69 kcal mol(-1), for the primary radical on the tertiary carbon is -5.18 ± 1.69 kcal mol(-1), for the secondary isooctane radical is -9.03 ± 1.84 kcal mol(-1), and for the tertiary isooctane radical is -12.30 ± 2.02 kcal mol(-1). Bond energy values for the isooctane radicals are 100.64 ± 1.73, 100.46 ± 1.73, 96.41 ± 1.88 and 93.14 ± 2.05 kcal mol(-1) for C3•CCCC2, C3CCCC2•, C3CC•CC2, and C3CCC•C2, respectively. Entropy and heat capacity values are reported for the lowest energy homologues.

Improved Kinetic Models for High-Speed Combustion Simulation

DTIC Science & Technology

2008-06-01

142 Appendix F1: USC_Skeletal_Ethylene_chem.inp ....................................................................... 143 ...to form a strong carbonyl double bond ( keto -Q) gaining 80 kcal mol-1, which is sufficient to immediately cleave the weak RO—OH bond (45 kcal mol-1...in the hydroperoxide. Relative to the stabilized adduct this reaction to ( keto -Q+OH), product set is 65.9 kcal mol-1 below the entrance channel

Spectroscopy and heats of formation of CXI (X = Br, Cl, F) iodocarbenes: quantum chemical characterisation of the ?, ? and ? states

NASA Astrophysics Data System (ADS)

Bacskay, George B.

2015-07-01

The equilibrium energies of the iodocarbenes CXI (X = Br, Cl, F) in their ?, ? and ? states and their atomisation and dissociation energies in the complete basis limit were determined by extrapolating valence correlated (R/U)CCSD(T) and Davidson corrected multi-reference configuration interaction (MRCI) energies calculated with the aug-cc-pVxZ (x = T,Q,5) basis sets and the ECP28MDF pseudopotential of iodine plus corrections for core and core-valence correlation, scalar relativity, spin-orbit coupling and zero-point energies. Spin-orbit energies were computed in a large basis of configurations chosen so as to accurately describe dissociation to the 3P and 2P states of C and of the halogens X and I, respectively. The computed singlet-triplet splittings are 13.6, 14.4 and 27.3 kcal mol-1 for X = Br, Cl and F, respectively. The enthalpies of formation at 0 K are predicted to be 97.4, 82.6 and 38.1 kcal mol-1 with estimated errors of ±1.0 kcal mol-1. The ? excitation energies (T00) in CBrI and CClI are calculated to be 41.1 and 41.7 kcal mol-1, respectively. The Renner-Teller intersections in both molecules are predicted to be substantially higher than the dissociation barriers on the ? surfaces. By contrast, in CFI the ? state is found to be unbound with respect to dissociation.

1,2-Fluorine Radical Rearrangements: Isomerization Events in Perfluorinated Radicals.

PubMed

Van Hoomissen, Daniel J; Vyas, Shubham

2017-11-16

Devising effective degradation technologies for perfluoroalkyl substances (PFASs) is an active area of research, where the molecular mechanisms involving both oxidative and reductive pathways are still elusive. One commonly neglected pathway in PFAS degradation is fluorine atom migration in perfluoroalkyl radicals, which was largely assumed to be implausible because of the high C-F bond strength. Using density functional theory calculations, it was demonstrated that 1,2-F atom migrations are thermodynamically favored when the fluorine atom migrated from a less branched carbon center to a more branched carbon center. Activation barriers for these rearrangements were within 19-29 kcal/mol, which are possible to easily overcome at elevated temperatures or in photochemically activated species in the gas or aqueous phase. It was also found that the activation barriers for the 1,2-F atom migration are lowered as much as by 10 kcal/mol when common oxidative degradation products such as HF assisted the rearrangements or if the resulting radical center was stabilized by vicinal π-bonds. Natural bond orbital analyses showed that fluorine moves as a radical in a noncharge-separated state. These findings add an important reaction to the existing knowledge of mechanisms for PFAS degradation and highlights the fact that 1,2-F atom shifts may be a small channel for isomerization of these compounds, but upon availability of mineralization products, this isomerization process could become more prominent.

The catalytic mechanism of mouse renin studied with QM/MM calculations.

PubMed

Brás, Natércia F; Ramos, Maria J; Fernandes, Pedro A

2012-09-28

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.

1,7-Cyclization of 1-diazo-2,4-pentadiene and its heteroanalogues: DFT study

NASA Astrophysics Data System (ADS)

Subbotina, Julia O.; Bakulev, V. A.; Herges, R.; Fabian, W. M. F.

1,7-Dipolar cyclizations of 1-diazo-2,4-pentadiene 1a and its heteroanalogues 1b,c and 4c were studied using density functional theory (DFT). Although the heteroanalogue 1c has an appropriate electronic structure to allow for pseudopericyclic cyclization, natural bond order (NBO) analysis has provided evidence for the electrocyclic ring closure. Magnetic criteria (anisotropy of the induced current density [ACID], nucleus-independent chemical shifts [NICS]) confirmed the pericyclic character of the located transition states 2a,c and 5c. The activation barriers for the cyclization of 1-diazo-2,4-pentadiene 1a and its aza analogues 1c, 4c are 3.3, 8.2, and 12.3 kcal/mol at the B3LYP/6-31G(d) level, respectively. The higher barrier of the 1c?3c and 4c?3c reactions compared with 1a?3a is in line with the Hammond postulate. The out-of-plane distorted geometry of the cyclic product is an additional factor arguing against a pseudopericyclic mechanism.

Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases.

PubMed

Sadiq, S Kashif; Wright, David W; Kenway, Owain A; Coveney, Peter V

2010-05-24

Accurate calculation of important thermodynamic properties, such as macromolecular binding free energies, is one of the principal goals of molecular dynamics simulations. However, single long simulation frequently produces incorrectly converged quantitative results due to inadequate sampling of conformational space in a feasible wall-clock time. Multiple short (ensemble) simulations have been shown to explore conformational space more effectively than single long simulations, but the two methods have not yet been thermodynamically compared. Here we show that, for end-state binding free energy determination methods, ensemble simulations exhibit significantly enhanced thermodynamic sampling over single long simulations and result in accurate and converged relative binding free energies that are reproducible to within 0.5 kcal/mol. Completely correct ranking is obtained for six HIV-1 protease variants bound to lopinavir with a correlation coefficient of 0.89 and a mean relative deviation from experiment of 0.9 kcal/mol. Multidrug resistance to lopinavir is enthalpically driven and increases through a decrease in the protein-ligand van der Waals interaction, principally due to the V82A/I84V mutation, and an increase in net electrostatic repulsion due to water-mediated disruption of protein-ligand interactions in the catalytic region. Furthermore, we correctly rank, to within 1 kcal/mol of experiment, the substantially increased chemical potency of lopinavir binding to the wild-type protease compared to saquinavir and show that lopinavir takes advantage of a decreased net electrostatic repulsion to confer enhanced binding. Our approach is dependent on the combined use of petascale computing resources and on an automated simulation workflow to attain the required level of sampling and turn around time to obtain the results, which can be as little as three days. This level of performance promotes integration of such methodology with clinical decision support systems for

Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent.

PubMed

Tsang, Wing-Yin; Wood, B McKay; Wong, Freeman M; Wu, Weiming; Gerlt, John A; Amyes, Tina L; Richard, John P

2012-09-05

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the

Binding Pattern Elucidation of NNK and NNAL Cigarette Smoke Carcinogens with NER Pathway Enzymes: an Onco- Informatics Study.

PubMed

Jamal, Qazi Mohammad Sajid; Dhasmana, Anupam; Lohani, Mohtashim; Firdaus, Sumbul; Ansari, Md Yousuf; Sahoo, Ganesh Chandra; Haque, Shafiul

2015-01-01

Cigarette smoke derivatives like NNK (4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone) and NNAL (4-(methylnitrosamino)-1-(3-pyridyl)-1-butan-1-ol) are well-known carcinogens. We analyzed the interaction of enzymes involved in the NER (nucleotide excision repair) pathway with ligands (NNK and NNAL). Binding was characterized for the enzymes sharing equivalent or better interaction as compared to +Ve control. The highest obtained docking energy between NNK and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.13 kcal/mol, -7.27 kcal/mol, -8.05 kcal/mol and -7.58 kcal/mol respectively. Similarly the highest obtained docking energy between NNAL and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.46 kcal/mol, -7.94 kcal/mol, -7.83 kcal/mol and -7.67 kcal/mol respectively. In order to find out the effect of NNK and NNAL on enzymes involved in the NER pathway applying protein-protein interaction and protein-complex (i.e. enzymes docked with NNK/NNAL) interaction analysis. It was found that carcinogens are well capable to reduce the normal functioning of genes like RAD23A (HR23A), CCNH, CDK7 and CETN2. In silico analysis indicated loss of functions of these genes and their corresponding enzymes, which possibly might be a cause for alteration of DNA repair pathways leading to damage buildup and finally contributing to cancer formation.

A multilayered-representation quantum mechanical/molecular mechanics study of the SN2 reaction of CH3Br + OH- in aqueous solution

NASA Astrophysics Data System (ADS)

Xu, Yulong; Wang, Tingting; Wang, Dunyou

2012-11-01

The bimolecular nucleophilic substitution (SN2) reaction of CH3Br and OH- in aqueous solution was investigated using a multilayered-representation quantum mechanical and molecular mechanics methodology. Reactant complex, transition state, and product complex are identified and characterized in aqueous solution. The potentials of mean force are computed under both the density function theory and coupled-cluster single double (triple) (CCSD(T)) levels of theory for the reaction region. The results show that the aqueous environment has a significant impact on the reaction process. The solvation effect and the polarization effect combined raise the activation barrier height by ˜16.2 kcal/mol and the solvation effect is the dominant contribution to the potential of mean force. The CCSD(T)/MM representation presents a free energy activation barrier height of 22.8 kcal/mol and the rate constant at 298 K of 3.7 × 10-25 cm3 molecule-1 s-1 which agree very well with the experiment values at 23.0 kcal/mol and 2.6 × 10-25 cm3 molecule-1 s-1, respectively.

26 CFR 1.162(k)-1 - Disallowance of deduction for reacquisition payments.

Code of Federal Regulations, 2010 CFR

2010-04-01

... payments. 1.162(k)-1 Section 1.162(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... and Corporations § 1.162(k)-1 Disallowance of deduction for reacquisition payments. (a) In general... corporation to reacquire its stock from an ESOP that are used in a manner described in section 404(k)(2)(A...

26 CFR 1.162(k)-1 - Disallowance of deduction for reacquisition payments.

Code of Federal Regulations, 2011 CFR

2011-04-01

... payments. 1.162(k)-1 Section 1.162(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... and Corporations § 1.162(k)-1 Disallowance of deduction for reacquisition payments. (a) In general... corporation to reacquire its stock from an ESOP that are used in a manner described in section 404(k)(2)(A...

26 CFR 1.162(k)-1 - Disallowance of deduction for reacquisition payments.

Code of Federal Regulations, 2014 CFR

2014-04-01

... payments. 1.162(k)-1 Section 1.162(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... and Corporations § 1.162(k)-1 Disallowance of deduction for reacquisition payments. (a) In general... corporation to reacquire its stock from an ESOP that are used in a manner described in section 404(k)(2)(A...

26 CFR 1.162(k)-1 - Disallowance of deduction for reacquisition payments.

Code of Federal Regulations, 2012 CFR

2012-04-01

... payments. 1.162(k)-1 Section 1.162(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... and Corporations § 1.162(k)-1 Disallowance of deduction for reacquisition payments. (a) In general... corporation to reacquire its stock from an ESOP that are used in a manner described in section 404(k)(2)(A...

26 CFR 1.162(k)-1 - Disallowance of deduction for reacquisition payments.

Code of Federal Regulations, 2013 CFR

2013-04-01

... payments. 1.162(k)-1 Section 1.162(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE... and Corporations § 1.162(k)-1 Disallowance of deduction for reacquisition payments. (a) In general... corporation to reacquire its stock from an ESOP that are used in a manner described in section 404(k)(2)(A...

Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

Exhaustive rotamer search of the 4C1 conformation of α- and β-d-galactopyranose.

PubMed

Del Vigo, Enrique A; Marino, Carla; Stortz, Carlos A

2017-08-07

An exhaustive search approach was used to establish all possible rotamers of α- and β-d-galactopyranose using DFT at the B3LYP/6-311+G** and M06-2X/6-311+G** levels, both in vacuum calculations, and including two variants of continuum solvent models as PCM and SMD to simulate water solutions. Free energies were also calculated. MM3 was used as the starting point for calculations, using a dielectric constant of 1.5 for vacuum modeling, and 80 for water solution modeling. For the vacuum calculations, out of the theoretically possible 729 rotamers, only about a hundred rendered stable minima, highly stabilized by hydrogen bonding and scattered in a ca. 14 kcal/mol span. The rotamer with a clockwise arrangement of hydrogen bonds was the most stable for the α-anomer, whereas that with a counterclockwise arrangement was the most stable for the β-anomer. Free energy calculations, and especially solvent modeling, tend to flatten the potential energy surface. With PCM, the total range of energies was reduced to 9-10 kcal/mol (α-anomer) or 7-8 kcal/mol (β-anomer). These figures fall to 4.5-6 kcal/mol using SMD. At the same time, the total number of possible rotamers increases dramatically to about 300 with PCM, and to 400 with SMD. Both models show a divergent behavior: PCM tends to underestimate the effect of solvent, thus rendering as the most stable many common rotamers with vacuum calculations, and giving underestimations of populations of β-anomers and gt rotamers in the equilibrium. On the other hand, SMD gives a better estimation of the solvent effect, yielding correct populations of gt rotamers, but more β-anomers than expected by the experimental values. The best agreement is observed when the functional M06-2X is combined with SMD. Both DFT models show minimal geometrical differences between the optimized conformers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Peralkynylated buta-1,2,3-trienes: exceptionally low rotational barriers of cumulenic C=C bonds in the range of those of peptide C--N bonds.

PubMed

Auffrant, Audrey; Jaun, Bernhard; Jarowski, Peter D; Houk, Kendall N; Diederich, François

2004-06-21

A variety of 1,1,4,4-tetraal kynylbutatrienes and 1,4-dialkynylbutatrienes was synthezized by dimerization of the corresponding gem-dibromoolefins. Both (1)H and (13)C NMR spectroscopy indicated that the di- and tetraalkynylated butatrienes are formed as a mixture of cis and trans isomers. Variable temperature NMR studies evidenced a facile cis-trans isomerization, thus preventing the separation of these isomers by gravity or high-performance liquid chromatography (HPLC). For 1,1,4,4-tetraalkynylbutatrienes, the activation barrier deltaG( not equal ) was measured by magnetization transfer to be around 20 kcal mol(-1), in the range of the barrier for internal rotation about a peptide bond. Unlike the tetraalkynylated [3]cumulenes, 1,4-dialkynylbutatrienes are more difficult to isomerize and could, in one case, be obtained isomerically pure. Based on experimental data, the rotational barrier DeltaG( not equal ) for 1,4-dialkynylbutatrienes is estimated to be around 25 kcal mol(-1). The hypothesis of a stabilizing effect of the four alkynyl substituents on the proposed but-2-yne-1,4-diyl singlet diradical transition state of this cis-trans isomerization is further supported by a computational study.

Development of a 100 nmol mol(-1) propane-in-air SRM for automobile-exhaust testing for new low-emission requirements.

PubMed

Rhoderick, George C

2007-04-01

New US federal low-level automobile emission requirements, for example zero-level-emission vehicle (ZLEV), for hydrocarbons and other species, have resulted in the need by manufacturers for new certified reference materials. The new emission requirement for hydrocarbons requires the use, by automobile manufacturing testing facilities, of a 100 nmol mol(-1) propane in air gas standard. Emission-measurement instruments are required, by federal law, to be calibrated with National Institute of Standards and Technology (NIST) traceable reference materials. Because a NIST standard reference material (SRM) containing 100 nmol mol(-1) propane was not available, the US Environmental Protection Agency (EPA) and the Automobile Industry/Government Emissions Research Consortium (AIGER) requested that NIST develop such an SRM. A cylinder lot of 30 gas mixtures containing 100 nmol mol(-1) propane in air was prepared in 6-L aluminium gas cylinders by a specialty gas company and delivered to the Gas Metrology Group at NIST. Another mixture, contained in a 30-L aluminium cylinder and included in the lot, was used as a lot standard (LS). Using gas chromatography with flame-ionization detection all 30 samples were compared to the LS to obtain the average of six peak-area ratios to the LS for each sample with standard deviations of <0.31%. The average sample-to-LS ratio determinations resulted in a range of 0.9828 to 0.9888, a spread of 0.0060, which corresponds to a relative standard deviation of 0.15% of the average for all 30 samples. NIST developed its first set of five propane in air primary gravimetric standards covering a concentration range 91 to 103 nmol mol(-1) with relative uncertainties of 0.15%. This new suite of propane gravimetric standards was used to analyze and assign a concentration value to the SRM LS. On the basis of these data each SRM sample was individually certified, furnishing the desired relative expanded uncertainty of +/-0.5%. Because automobile companies

Benzene-1,4-diol–5-(1H-imidazol-1-yl)pyrimidine (1/1)

PubMed Central

Jiang, Yan-Ke; Hou, Gui-Ge

2011-01-01

The asymmetric unit of title compound, C7H6N4·C6H6O2, contains one 5-(1H-imidazol-1-yl)pyrimidine mol­ecule and two half benzene-1,4-diol mol­ecules; the benzene-1,4-diol mol­ecules are located on individual inversion centers. In the pyrimidine mol­ecule, the imidazole ring is twisted with respect to the pyrimidine ring at a dihedral angle of 25.73 (7)°. In the crystal, O—H⋯N hydrogen bonds link the mol­ecules to form supra­molecular chains. π–π stacking is also observed in the crystal, the centroid–centroid distance between parallel imdazole rings being 3.5543 (16) Å. PMID:22220081

Haloacetonitriles are low K1 inhibitors of bacterial dichloromethane dehalogenases.

PubMed

Logan, M S; Blocki, F A; Stimpfl, K J; Wackett, L P

1993-12-15

Distinct dichloromethane dehalogenases from Methylobacterium sp. strain DM4 and Methylophilus DM11 were inhibited by low concentrations of haloacetonitriles. Chloroacetonitrile (ClCH2CN) showed maximal inhibition at a stoichiometry of 1 mol inhibitor:1 mol holoenzyme for both enzymes. This stoichiometry is suggestive of one active site per holoenzyme or extreme negative cooperativity amongst the subunits. Radiolabelled ClCH2CN dissociated completely or partially from the two dehalogenases, respectively, during chromatography. This suggested ClCH2CN was bound non-covalently.

Contributions of the Na+/K+-ATPase, NKCC1, and Kir4.1 to hippocampal K+ clearance and volume responses

PubMed Central

Larsen, Brian Roland; Assentoft, Mette; Cotrina, Maria L.; Hua, Susan Z.; Nedergaard, Maiken; Kaila, Kai; Voipio, Juha; MacAulay, Nanna

2015-01-01

Bursts of network activity in the brain are associated with a transient increase in extracellular K+ concentration. The excess K+ is removed from the extracellular space by mechanisms proposed to involve Kir4.1-mediated spatial buffering, the Na+/K+/2Cl− cotransporter (NKCC1), and/or Na+/K+-ATPase activity. Their individual contribution to [K+]o management has been of extended controversy. The present study aimed, by several complementary approaches, to delineate the transport characteristics of Kir4.1, NKCC1, and Na+/K+-ATPase and to resolve their involvement in clearance of extracellular K+ transients. Primary cultures of rat astrocytes displayed robust NKCC1 activity with [K+]o increases above basal levels. Increased [K+]o produced NKCC1-mediated swelling of cultured astrocytes and NKCC1 could thereby potentially act as a mechanism of K+ clearance while concomitantly mediate the associated shrinkage of the extracellular space. In rat hippocampal slices, inhibition of NKCC1 failed to affect the rate of K+ removal from the extracellular space while Kir4.1 enacted its spatial buffering only during a local [K+]o increase. In contrast, inhibition of the different isoforms of Na+/K+-ATPase reduced post-stimulusclearance of K+ transients. The glia-specific α2/β2 subunit composition of Na+/K+-ATPase, when expressed in Xenopus oocytes, displayed a K+ affinity and voltage-sensitivity that would render this astrocyte-specific subunit composition specifically geared for controlling [K+]o during neuronal activity. In rat hippocampal slices, simultaneous measurements of the extracellular space volume revealed that neither Kir4.1, NKCC1, nor Na+/K+-ATPase accounted for the stimulus-induced shrinkage of the extracellular space. Thus, NKCC1 plays no role in activity-induced extracellular K+ recovery in native hippocampal tissue while Kir4.1 and Na+/K+-ATPase serve temporally distinct roles. PMID:24482245

Final report of APMP.QM-K46 ammonia in nitrogen at 30 μmol/mol level

NASA Astrophysics Data System (ADS)

Uehara, Shinji; Qiao, Han; Shimosaka, Takuya

2017-01-01

This report describes the results for a bilateral comparison of ammonia in nitrogen gas mixture. The nominal amount-of-substance fraction was 30 μmol/mol. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

H Abstraction Channels in the Crossed-Beam Reaction of F + 1-Propanol, 1-Butene and 1-Hexene by DC Slice Imaging.

PubMed

Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G

2016-11-17

We report a crossed molecular beam study of the reaction dynamics of fluorine atom with 1-propanol, 1-butene, and 1-hexene. The product alkoxy and alkenyl radicals were detected via dc slice imaging by 157 nm single photon ionization at collision energies around 10 kcal mol -1 . The analyzed data is interpreted with the aid of theoretical investigation of the relevant potential energy surfaces. The translational energy distribution and center-of-mass angular distribution of F + 1-propanol is quite similar to our previous results for F + n-butane, albeit with an increased fraction of the available energy in translation. In F atom reaction with alkenes, we also detected the HF formation channel. The low translational energy release and presence of significant backward scattering suggests the importance of an addition/elimination mechanism. Our selective single photon ionization probe allows us to examine the dynamics in minor channels in these systems. Although the probe is not sensitive to reaction at vinylic H sites, theoretical calculations consistently suggest a lower barrier from the addition complex to HF elimination involving vinylic H atoms.

Loss of plastoglobule kinases ABC1K1 and ABC1K3 causes conditional degreening, modified prenyl-lipids, and recruitment of the jasmonic acid pathway

USDA-ARS?s Scientific Manuscript database

Plastoglobules (PGs) are plastid lipid-protein particles. This study examines the function of PG-localized kinases ABC1K1 and ABC1K3 in Arabidopsis thaliana. Several lines of evidence suggested that ABC1K1 and ABC1K3 form a protein complex. Null mutants for both genes (abc1k1 and abc1k3) and the dou...

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.

Effects of prescribing 1,000 versus 1,500 kilocalories per day in the behavioral treatment of obesity: a randomized trial.

PubMed

Nackers, Lisa M; Middleton, Kathryn R; Dubyak, Pamela J; Daniels, Michael J; Anton, Stephen D; Perri, Michael G

2013-12-01

Controversy exists regarding the optimal energy prescription to promote successful long-term behavioral management of obesity. Prescribing intake of 1,000 (vs. 1,500) kcal/day may produce larger initial weight reduction, but long-term advantage remains unclear. The effects of prescribing 1,000 versus 1,500 kcal/day on 6- and 12-month weight changes within behavioral treatment of obesity were examined. Participants were 125 obese women (mean ± SD; BMI = 37.84 ± 3.94 kg/m(2) ) randomly assigned goals of 1,000 or 1,500 kcal/day. From months 0 to 6, participants prescribed 1,000 kcal/day lost more weight than those prescribed 1,500 kcal/day (mean ± SE = -10.03 ± 0.92g vs. -6.23 ± 0.94 kg, P = 0.045); however, from months 7 through 12, only the 1,000 kcal/day condition experienced a significant weight regain (1.51 ± 0.77 kg, P = 0.025). Baseline caloric consumption moderated the effect of treatment on regain; participants with baseline intakes ≧2,000 kcal/day who were assigned 1,000 kcal/day were significantly more susceptible to weight regain than those assigned 1,500 kcal/day (P = 0.049). At month 12, a significantly greater percentage of 1,000 kcal/day participants achieved weight reductions of 5% or more than those prescribed 1,500 kcal/day. Encouraging obese individuals in behavioral treatment to adhere to a 1,000 kcal/day intake may increase their likelihood of achieving clinically meaningful weight losses. Copyright © 2013 The Obesity Society.

Quantification of Lewis acid induced Brønsted acidity of protogenic Lewis bases.

PubMed

Lathem, A Paige; Heiden, Zachariah M

2017-05-09

Proton transfer promoted by the coordination of protogenic Lewis bases to a Lewis acid is a critical step in catalytic transformations. Although the acidification of water upon coordination to a Lewis acid has been known for decades, no attempts have been made to correlate the Brønsted acidity of the coordinated water molecule with Lewis acid strength. To probe this effect, the pK a 's (estimated error of 1.3 pK a units) in acetonitrile of ten protogenic Lewis bases coordinated to seven Lewis acids containing Lewis acidities varying 70 kcal mol -1 , were computed. To quantify Lewis acid strength, the ability to transfer a hydride (hydride donor ability) from the respective main group hydride was used. Coordination of a Lewis acid to water increased the acidity of the bound water molecule between 20 and 50 pK a units. A linear correlation exhibiting a 2.6 pK a unit change of the Lewis acid-water adduct per ten kcal mol -1 change in hydride donor ability of the respective main group hydride was obtained. For the ten protogenic Lewis bases studied, the coordinated protogenic Lewis bases were acidified between 10 and 50 pK a units. On average, a ten kcal mol -1 change in hydride donor ability of the respective main group hydride resulted in about a 2.8 pK a unit change in the Brønsted acidity of the Lewis acid-Lewis base adducts. Since attempts to computationally investigate the pK a of main group dihydrogen complexes were unsuccessful, experimental determination of the first reported pK a of a main group dihydrogen complex is described. The pK a of H 2 -B(C 6 F 5 ) 3 was determined to be 5.8 ± 0.2 in acetonitrile.

Thermal decomposition mechanism of 1-ethyl-3-methylimidazolium bromide ionic liquid.

PubMed

Chambreau, Steven D; Boatz, Jerry A; Vaghjiani, Ghanshyam L; Koh, Christine; Kostko, Oleg; Golan, Amir; Leone, Stephen R

2012-06-21

In order to better understand the volatilization process for ionic liquids, the vapor evolved from heating the ionic liquid 1-ethyl-3-methylimidazolium bromide (EMIM(+)Br(-)) was analyzed via tunable vacuum ultraviolet photoionization time-of-flight mass spectrometry (VUV-PI-TOFMS) and thermogravimetric analysis mass spectrometry (TGA-MS). For this ionic liquid, the experimental results indicate that vaporization takes place via the evolution of alkyl bromides and alkylimidazoles, presumably through alkyl abstraction via an S(N)2 type mechanism, and that vaporization of intact ion pairs or the formation of carbenes is negligible. Activation enthalpies for the formation of the methyl and ethyl bromides were evaluated experimentally, ΔH(‡)(CH(3)Br) = 116.1 ± 6.6 kJ/mol and ΔH(‡)(CH(3)CH(2)Br) = 122.9 ± 7.2 kJ/mol, and the results are found to be in agreement with calculated values for the S(N)2 reactions. Comparisons of product photoionization efficiency (PIE) curves with literature data are in good agreement, and ab initio thermodynamics calculations are presented as further evidence for the proposed thermal decomposition mechanism. Estimates for the enthalpy of vaporization of EMIM(+)Br(-) and, by comparison, 1-butyl-3-methylimidazolium bromide (BMIM(+)Br(-)) from molecular dynamics calculations and their gas phase enthalpies of formation obtained by G4 calculations yield estimates for the ionic liquids' enthalpies of formation in the liquid phase: ΔH(vap)(298 K) (EMIM(+)Br(-)) = 168 ± 20 kJ/mol, ΔH(f, gas)(298 K) (EMIM(+)Br(-)) = 38.4 ± 10 kJ/mol, ΔH(f, liq)(298 K) (EMIM(+)Br(-)) = -130 ± 22 kJ/mol, ΔH(f, gas)(298 K) (BMIM(+)Br(-)) = -5.6 ± 10 kJ/mol, and ΔH(f, liq)(298 K) (BMIM(+)Br(-)) = -180 ± 20 kJ/mol.

Prevalence of genes encoding virulence factors among Escherichia coli with K1 antigen and non-K1 E. coli strains.

PubMed

Kaczmarek, Agnieszka; Budzynska, Anna; Gospodarek, Eugenia

2012-10-01

Multiplex PCR was used to detect genes encoding selected virulence determinants associated with strains of Escherichia coli with K1 antigen (K1(+)) and non-K1 E. coli (K1(-)). The prevalence of the fimA, fimH, sfa/foc, ibeA, iutA and hlyF genes was studied for 134 (67 K1(+) and 67 K1(-)) E. coli strains isolated from pregnant women and neonates. The fimA gene was present in 83.6 % of E. coli K1(+) and in 86.6 % of E. coli K1(-) strains. The fimH gene was present in all tested E. coli K1(+) strains and in 97.0 % of non-K1 strains. E. coli K1(+) strains were significantly more likely to possess the following genes than E. coli K1(-) strains: sfa/foc (37.3 vs 16.4 %, P = 0.006), ibeA (35.8 vs 4.5 %, P<0.001), iutA (82.1 vs 35.8 %, P<0.001) and hlyF (28.4 vs 6.0 %, P<0.001). In conclusion, E. coli K1(+) seems to be more virulent than E. coli K1(-) strains in developing severe infections, thereby increasing possible sepsis or neonatal bacterial meningitis.

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

CB1 Receptor Antagonist SR141716A Inhibits Ca2+-Induced Relaxation in CB1 Receptor–Deficient Mice

PubMed Central

Bukoski, Richard D.; Bátkai, Sándor; Járai, Zoltán; Wang, Yanlin; Offertaler, Laszlo; Jackson, William F.; Kunos, George

2006-01-01

Mesenteric branch arteries isolated from cannabinoid type 1 receptor knockout (CB1−/−) mice, their wild-type littermates (CB1+/+ mice), and C57BL/J wild-type mice were studied to test the hypothesis that murine arteries undergo high sensitivity Ca2+-induced relaxation that is CB1 receptor dependent. Confocal microscope analysis of mesenteric branch arteries from wild-type mice showed the presence of Ca2+ receptor–positive periadventitial nerves. Arterial segments of C57 control mice mounted on wire myographs contracted in response to 5 μmol/L norepinephrine and responded to the cumulative addition of extracellular Ca2+ with a concentration-dependent relaxation that reached a maximum of 72.0±6.3% of the prerelaxation tone and had an EC50 for Ca2+ of 2.90±0.54 mmol/L. The relaxation was antagonized by precontraction in buffer containing 100 mmol/L K+ and by pretreatment with 10 mmol/L tetraethylammonium. Arteries from CB1−/− and CB1+/+ mice also relaxed in response to extracellular Ca2+ with no differences being detected between the knockout and their littermate controls. SR141716A, a selective CB1 antagonist, caused concentration-dependent inhibition of Ca2+-induced relaxation in both the knockout and wild-type strains (60% inhibition at 1 μmol/L). O-1918, a cannabidiol analog, had a similar blocking effect in arteries of both wild-type and CB1−/− mice at 10 μmol/L. In contrast, 1 μmol/L SR144538, a cannabinoid type 2 receptor antagonist, or 50 μmol/L 18α-glycyrrhetinic acid, a gap junction blocker, were without effect. SR141716A (1 to 30 μmol/L) was also assessed for nonspecific actions on whole-cell K+ currents in isolated vascular smooth muscle cells. SR141716A inhibited macroscopic K+ currents at concentrations higher than those required to inhibit Ca2+-induced relaxation, and appeared to have little effect on currents through large conductance Ca2+-activated K+ channels. These data indicate that arteries of the mouse relax in response to

The Planck-Benzinger thermal work function in the condensation of water vapor

NASA Astrophysics Data System (ADS)

Chun, Paul W.

Based on the Planck-Benzinger thermal work function using Chun's method, the innate temperature-invariant enthalpy at 0 K, ?H0(T0), for the condensation of water vapor as well as the dimer, trimer, tetramer, and pentamer form in the vapor phase, was determined to be 0.447 kcal mol-1 for vapor, 1.127 for the dimer, 0.555 for the trimer, 0.236 for the tetramer, and 0.079 kcal mol-1 for the pentamer using ?G(T) data reported by Kell et al. in 1968 and Kell and McLaurin in 1969. These results suggest that the predominant dimeric form is the most stable of these n-mers. Using Nemethy and Scheraga's 1962 data for the Helmholtz free energy of liquid water, the value of ?H0(T0) was determined to be 1.21 kcal mol-1. This is very close to the value for the energy of the hydrogen bond EH of 1.32 kcal mol-1 reported by Nemethy and Scheraga, using statistical thermodynamics. It seems clear that very little energy is required for interconversion between the hypothetical supercooled water vapor and glassy water at 0 K. A hypothetical supercooled water vapor at 0 K is apparently almost as highly associated as glassy water at that temperature, suggesting a dynamic equilibrium between vapor and liquid. This water vapor condensation is highly similar in its thermodynamic behavior to that of sequence-specific pairwise (dipeptide) hydrophobic interaction, except that the negative Gibbs free energy change minimum at ?Ts?, the thermal setpoint for vapor condensation, where T?S = 0, occurs at a considerably lower temperature, 270 K (below 0°C) compared with ?350 K. The temperature of condensation ?Tcond? at which ?G(T) = 0, where water vapor begins to condense, was found to be 383 K. In the case of a sequence-specific pairwise hydrophobic interaction, the melting temperature, ?Tm?, where ?G(Tm) = 0 was found to be 460 K. Only between two temperature limits, ?Th? = 99 K and ?Tcond? = 383 K, where ?G(Tcond) = 0, is the net chemical driving force favorable for polymorphism of glassy water

Oxidation of CO by N/sub 2/O between 1076 and 1228 K: determination of the rate constant of the exchange reaction

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

Loirat, H.; Caralp, F.; Destriau, M.

New measurements of the rate constant of the direct reaction of CO with N/sub 2/O are reported with the principal purpose of removing some of the remaining discrepancies on its value. Experiments were performed at lower temperatures (1076-1228 K) and lower pressure (approx. 15 Torr) than those prevailing in most of previous works, by using a static reactor. It is shown that, under these experimental conditions, the reaction proceeds essentially according to the direct reaction CO + N/sub 2/O ..-->.. CO/sub 2/ + N/sub 2/ (1). The previously proposed wet mechanism is not significant under our experimental conditions. It hasmore » to be taken into account, however, to describe the observed production and consumption of molecular oxygen. The Arrhenius expression derived from these experiments is k/sub 1/ = 10/sup 14.4 +/- 0.3 exp(-(46 +- 2) kcal mol/sup -1/RT) cm/sup 3/ mol/sup -1/ s/sup -1/. A detailed analysis of the results shows that the uncertainties in side reactions do not greatly influence the value of k/sub 1/. A critical discussion of the data reported in the literature is presented. In spite of remaining uncertainties in the reaction mechanism, the present results, obtained in a low-temperature range, show that the low activation energy values of reaction 1, reported in several works performed at higher temperatures, are highly unlikely« less

Catalytic dehydrofluorination of 1,1,1,3,3-pentafluoropropane to 1,3,3,3-tetrafluoropropene over fluorinated NiO/Cr2O3 catalysts

NASA Astrophysics Data System (ADS)

Luo, Jian-Wei; Song, Jian-Dong; Jia, Wen-Zhi; Pu, Zhi-Ying; Lu, Ji-Qing; Luo, Meng-Fei

2018-03-01

Catalytic dehydrofluorination of 1,1,1,3,3-pentafluoropropane to 1,3,3,3-tetrafluoropropene was performed on a series of fluorinated NiO/Cr2O3 catalysts. The NiO/Cr2O3 catalysts were more active than the Cr2O3 because the new acid sites provided by NiF2 had higher turnover frequencies (9.43 × 10-3 - 12.08 × 10-3 s-1) than those on the Cr2O3 (4.55 × 10-3 s-1). Also, the NiO/Cr2O3 was more stable than the Cr2O3 due to its lower density of surface acid sites, which alleviated the coke deposition on the catalyst as evidenced by the Raman spectroscopic results. The kinetic results revealed that the15NiO/Cr2O3 had much lower activation energy (63.6 ± 4.5 kJ mol-1) than the Cr2O3 (127.6 ± 3.8 kJ mol-1). Accordingly, different reaction pathways on the two catalysts were proposed, which involved the cleavage of the Csbnd F and Csbnd H bonds on the surface acid and base sites, respectively.

Thermal properties of cubic KTa1-xNbxO3 crystals

NASA Astrophysics Data System (ADS)

Wang, X. P.; Wang, J. Y.; Zhang, H. J.; Yu, Y. G.; Wu, J.; Gao, W. L.; Boughton, R. I.

2008-02-01

Cubic potassium tantalite niobate [KTa1-xNbxO3 (KTN)] crystals of large size, good quality, and varying Nb concentration have been grown by the Czochralski method and their thermal properties have been systematically studied. The melting point, molar enthalpy of fusion, and molar entropy of fusion of the crystals were determined to be: 1536.9 K, 12 068.521 J mol-1, and 7.85 J K-1 mol-1 for KTa0.67Nb0.33O3; and 1520.61 K, 15 352.511 J mol-1, and 10.098 J K-1 mol-1 for KTa0.67Nb0.33O3, respectively. Based on the data, the Jackson factor was calculated to be 0.994f and 1.214f for KTa0.67Nb0.33O3 and KTa0.63Nb0.37O3, respectively. The thermal expansion coefficients over the temperature range of 298.15-773.15 K are: α =4.0268×10-6/K, 6.4428×10-6/K, 6.5853×10-6/K for KTaO3, KTa0.67Nb0.33O3, and KTa0.63Nb0.37O3, respectively. The density follows an almost linear decrease when the temperature increases=from 298.15 to 773.15 K. The measured specific heats at 303.15 K are: 0.375 J g-1 K-1 for KTaO3; 0.421 J g-1 K-1 for KTa0.67Nb0.33O3, and 0.430 J g-1 K-1 for KTa0.63Nb0.37O3 The thermal diffusion coefficients of the crystals were measured over the temperature range from 303.15-563.15 K. The calculated thermal conductivity values of KTaO3, KTa0.67Nb0.33O3, and KTa0.63Nb0.37O3 at 303.15 K are 8.551, 5.592, and 4.489 W m-1 K-1, respectively. The variation of these thermal properties versus Nb concentration is qualitatively analyzed. These results show that crystalline KTN is a promising material for optical applications.

Results and evaluation of key comparison CCM.P-K12.1 for very low helium flow rates (leak rates)

NASA Astrophysics Data System (ADS)

Šetina, Janez; Vičar, Martin; Pražák, Dominik

2015-01-01

The Czech Metrology Institute (CMI) took part and failed to prove equivalence in the Key Comparison CCM.P-K12 of helium leak artefacts (leak rates) into vacuum. After identifying and eliminating the cause of the failure, the Institute of Metals and Technology (IMT) of Slovenia, a successful participant in CCM.P-K12, volunteered to serve as pilot and link in a following bilateral comparison of IMT and CMI that obtained designation CCM.P-K12.1 in June 2012. It was decided to perform the comparison with a glass permeation helium leak artefact at nominally 3.10-11 mol/s (7.4.10-7 mbar.L.s-1) at 23 °C. Both the laboratory standards took part in CCM.P-K12 and were considered as primary. The comparison measurements were performed in October 2012. CMI proved equivalence both with IMT and with the reference value of the key comparison CCM.P-K12. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Coupling of electronic and magnetic properties in Fe1+y(Te1-xSex)

NASA Astrophysics Data System (ADS)

Hu, J.; Liu, T. J.; Qian, B.; Mao, Z. Q.

2013-09-01

We have studied the coupling of electronic and magnetic properties in Fe1+y(Te1-xSex) via systematic specific heat, magnetoresistivity (MR), and Hall coefficient measurements on two groups of samples with y=0.02 and 0.1. In the y=0.02 series, we find that the 0.09mol K2), positive Hall coefficient RH, and negative MR at low temperature, in sharp contrast with the x = 0.4-0.5 region, where γ drops to ˜26 mJ/mol K2 and RH and MR become negative and positive, respectively, at low temperature. Dramatic changes of γ, as well as sign reversal in low-temperature RH and MR, are also observed across the x˜0.1 boundary, where the long-range antiferromagnetic order is suppressed. However, for the system with rich interstitial excess Fe (y=0.1), where bulk superconductivity is suppressed even for x = 0.4-0.5, the variations of γ, RH, and MR with x are distinct from those seen in y=0.02 system: γ is ˜40 mJ/mol K2 for 0.1mol K2 for x = 0.4-0.5; RH and MR do not show any sign reversal as x is increased above 0.3. We will show that all these results can be understood in light of the evolution of the incoherent magnetic scattering by (π,0) magnetic fluctuations with Se concentration. In addition, with the suppression of magnetic scattering by the magnetic field, we observed the surprising effect of a remarkable increase in the superconducting volume fraction under moderate magnetic fields for x = 0.3-0.4 samples in the y=0.02 system.

Hurdles in low k1 mass production

NASA Astrophysics Data System (ADS)

Yim, Donggyu; Yang, Hyunjo; Park, Chanha; Hong, Jongkyun; Choi, Jaeseung

2005-05-01

As the optical lithography pushes toward its theoretical resolution limit 0.25k1, the application of aggressive Resolution Enhancement Techniques (RETs) are required in order to ensure necessary resolution, sufficient process window, and reasonable MEEF in critical layers. When chip makers are adopting RETs in low k1 device, there are a lot of crucial factors to take into account in the development and mass production. Those hurdles are not only difficult to overcome but also highly risky to the company, which adopts low k1 mass production strategy. But, low k1 production strategy is very attractive to all chip makers, owing to improving production capacity and cost of ownership. So, low k1 technology has been investigated by many lithography engineers. Lots of materials have been introduced. Most of them are just in RnD level. In this study, low k1 mass production issues shall be introduced, mainly. The definition of low k1 in mass production shall be suggested. And, a lot of low_k1 issues shall be introduced, also. Most of them were investigated/experienced in RnD development stage and final mass production line. Low k1 mass production, is some what different from only RnD development.

Computational Prediction of Kinetic Rate Constants

DTIC Science & Technology

2006-06-09

24 Reactant: P(CH3)F2O (Difluor) Energetics: RHF DZP Frozen Core CCSD: -655.069925 Hartree CCSD(T): -655.090871 Hartree ZPE : 30.59 kcal...655.069925 Hartree CCSD(T): -655.090871 Hartree ZPE : 30.59 kcal/mol Geometry: RHF CCSD(T) Geom. Opt. PC Bond (Å): 1.79575 OP Bond (Å): 1.47117 FP Bond (Å... ZPE : 18.67 kcal/mol Intensity (km/mol)Frequency (cm -1)Symmetry 11.03833324.0968A1 11.03833324.0968A1 0.00003133.6602A1 2.38681429.9058A1

Different metabolic profiles of K1 serotype and non-serotype K1 and K2 Klebsiella pneumoniae isolates in oral infection mice model.

PubMed

Chen, Nan; Wang, Lin-Lin; Xue, Juan; Ma, Xiang-Bo; Zhao, Sheng; Rong, Rui-Xue; Li, Hong-Quan; Ding, Liang; Zheng, Ming-Zhi; Chen, Ying-Ying; Duan, Fei; Shen, Yue-Liang

2014-10-01

K1 or K2 serotype Klebsiella pneumoniae isolate caused clinical pyogenic liver abscess (KLA) infection is prevalent in many areas. It has been identified that K1 or K2 serotype K. pneumoniae isolates caused KLA infection in mice by oral inoculation. In our study, K1 serotype K. pneumoniae isolate Kp1002 with hypermucoviscosity (HV)-positive phenotype caused KLA infection in C57BL/6 mice by oral inoculation. Simultaneously, non-serotype K1 and K2 isolate Kp1014 with HV-negative phenotype failed to cause KLA infection in the same manner. It seems that gastrointestinal tract translocation is the pathway by which K1 or K2 serotype K. pneumoniae caused KLA infection. Liquid chromatography-tandem mass spectrometry was used to further analyze metabolic profile changes in mice with KLA infection. Data showed that after Kp1002 or Kp1014 oral inoculation, serum Phosphatidylcholine (PC) and Lysophosphatidylcholine (LPC) levels significantly changed in mice. Some PC and LPC molecules showed changes both in the Kp1002 KLA group and the Kp1014 no-KLA group compared with the control group. The level of 18:1/18:2-PC significantly changed in the Kp1002 KLA group compared with the control group, but showed no change between the Kp1014 no-KLA group and the control group. The level of 18:1/18:2-PC might have been particularly affected by KLA infection caused by K1 serotype K. pneumoniae Kp1002. It may be a potential biomarker for KLA infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R.

PubMed

de Lint, Klaas; Poell, Jos B; Soueidan, Hayssam; Jastrzebski, Katarzyna; Vidal Rodriguez, Jordi; Lieftink, Cor; Wessels, Lodewyk F A; Beijersbergen, Roderick L

2016-07-01

Targeted therapies have proven invaluable in the treatment of breast cancer, as exemplified by tamoxifen treatment for hormone receptor-positive tumors and trastuzumab treatment for HER2-positive tumors. In contrast, a subset of breast cancer negative for these markers, triple-negative breast cancer (TNBC), has met limited success with pathway-targeted therapies. A large fraction of TNBCs depend on the PI3K pathway for proliferation and survival, but inhibition of PI3K alone generally has limited clinical benefit. We performed an RNAi-based genetic screen in a human TNBC cell line to identify kinases whose knockdown synergizes with the PI3K inhibitor GDC-0941 (pictilisib). We discovered that knockdown of insulin-like growth factor-1 receptor (IGF1R) expression potently increased sensitivity of these cells to GDC-0941. Pharmacologic inhibition of IGF1R using OSI-906 (linsitinib) showed a strong synergy with PI3K inhibition. Furthermore, we found that the combination of GDC-0941 and OSI-906 is synergistic in 8 lines from a panel of 18 TNBC cell lines. In these cell lines, inhibition of IGF1R further decreases the activity of downstream PI3K pathway components when PI3K is inhibited. Expression analysis of the panel of TNBC cell lines indicates that the expression levels of IGF2BP3 can be used as a potential predictor for sensitivity to the PI3K/IGF1R inhibitor combination. Our data show that combination therapy consisting of PI3K and IGF1R inhibitors could be beneficial in a subset of TNBCs. Mol Cancer Ther; 15(7); 1545-56. ©2016 AACR. ©2016 American Association for Cancer Research.

Effect of Caloric Intake 25 or 30 kcal/kg/day on the Glycemic Control in Obese Patients With Type 2 Diabetes

PubMed Central

Masuda, Kiyomi; Aoki, Kazutaka; Kawaguchi, Junko; Yamakawa, Tadashi; Matsuba, Ikuro; Terauchi, Yasuo

2013-01-01

Background The recommended total dietary energy intake prescribed medical nutrition therapy for obese or overweight patients with type 2 diabetes in Japan is often set at 25 kcal/kg ideal body weight (IBW)/day. This study was conducted to determine the impact of the total dietary energy intake (25 or 30 kcal/kg IBW/day) on the glycemic control, lipid profile, and satisfaction level in overweight patients with type 2 diabetes. Methods We performed interview and a designed prospective, randomized, controlled, multicenter study trial. Recruitment for interview for doctors and hospitalization of the obese or overweight patients with type 2 diabetes began from September 2008 and continued until June 2010. The subjects were randomly assigned to 25 kcal/kg IBW/day group (25 kcal group) or 30 kcal/kg IBW/day group (30 kcal group). The primary endpoint was the body weight of the subjects at the time of hospitalization, at the time of discharge from the hospital, and at 3, 6 and 12 months after discharge from the hospital. Results The glycemic control, lipid control and body weight were similar between the 25 and 30 kcal groups during the 12-month follow-up, and the degree of satisfaction in respect of the medical treatment was significantly higher in the 30 kcal group than in the 25 kcal group at 1 year after discharge. Conclusions It is considered to be preferable for the caloric intake to be set at 30kcal/kg IBW/day rather than at 25 kcal/kg IBW/day for obese or overweight patients with type 2 diabetes. PMID:23976909

Comment on Chem. Phys. Lett. 371 (2003) 568: Barrier height for dissociation of acetaldehyde, CH 3CHO → CH 3 + HCO, in the triplet state T 1

NASA Astrophysics Data System (ADS)

Robert Huber, J.

2003-08-01

Based on recently reported experimental results from various groups, the barrier height (or transition state energy) for the T 1 dissociation of acetaldehyde, CH 3CHO → CH 3 + HCO, is determined to lie between 12.3 and 12.9 kcal mol -1. This result is compared with predictions from recent ab initio calculations.

26 CFR 1.401(k)-4 - SIMPLE 401(k) plan requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 5 2010-04-01 2010-04-01 false SIMPLE 401(k) plan requirements. 1.401(k)-4 Section 1.401(k)-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-4 SIMPLE...

A high level computational study of the CH4/CF4 dimer: how does it compare with the CH4/CH4 and CF4/CF4 dimers?

NASA Astrophysics Data System (ADS)

Biller, Matthew J.; Mecozzi, Sandro

2012-04-01

The interaction within the methane-methane (CH4/CH4), perfluoromethane-perfluoromethane (CF4/CF4) methane-perfluoromethane dimers (CH4/CF4) was calculated using the Hartree-Fock (HF) method, multiple orders of Møller-Plesset perturbation theory [MP2, MP3, MP4(DQ), MP4(SDQ), MP4(SDTQ)], and coupled cluster theory [CCSD, CCSD(T)], as well as the PW91, B97D, and M06-2X density functional theory (DFT) functionals. The basis sets of Dunning and coworkers (aug-cc-pVxZ, x = D, T, Q), Krishnan and coworkers [6-311++G(d,p), 6-311++G(2d,2p)], and Tsuzuki and coworkers [aug(df, pd)-6-311G(d,p)] were used. Basis set superposition error (BSSE) was corrected via the counterpoise method in all cases. Interaction energies obtained with the MP2 method do not fit with the experimental finding that the methane-perfluoromethane system phase separates at 94.5 K. It was not until the CCSD(T) method was considered that the interaction energy of the methane-perfluoromethane dimer (-0.69 kcal mol-1) was found to be intermediate between the methane (-0.51 kcal mol-1) and perfluoromethane (-0.78 kcal mol-1) dimers. This suggests that a perfluoromethane molecule interacts preferentially with another perfluoromethane (by about 0.09 kcal mol-1) than with a methane molecule. At temperatures much lower than the CH4/CF4 critical solution temperature of 94.5 K, this energy difference becomes significant and leads perfluoromethane molecules to associate with themselves, forming a phase separation. The DFT functionals yielded erratic results for the three dimers. Further development of DFT is needed in order to model dispersion interactions in hydrocarbon/perfluorocarbon systems.

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

Halpern, A.M.; Ruggles, C.J.; Zhang, X.K.

Fluorescence spectra and decay curves of dilute solutions (<3 x 10/sup -4/ M) of triethylamine (TEA), tri-n-propylamine (TPA), and 1,4-diazabicyclo(2.2.2)octane (DABCO) in H/sub 2/O- and D/sub 2/O-saturated n-hexane reveal the presence of a complex formed between the electronically excited amine and water. The decay curves, measured between 273 and 323 K (and at 280 and 360 nm; 300 and 400 nm for DABCO), conform to the standard monomer-excimer photokinetic scheme and are analyzed accordingly. These results indicate that the binding energy of the excited TEA-H/sub 2/O complex (B*) is ca. 7.8 kcal/mol, which is larger than that of the ground-statemore » TEA hydrate. B* for the TPA and DABCO-H/sub 2/O complexes is estimated to be ca. 10 and 8.8 kcal/mol, respectively. Stationary-state measurements are consistent with these assignments. The activation energy for the diffusion of water in n-hexane (assumed to be monomeric) appears to be very small (<1 kcal/mol). The decay constants of the three complexes studied are ca. 3.4 x 10/sup 7/ s/sup -1/ for amine-H/sub 2/O and 2.9 x 10/sup 7/ s/sup -1/ for the amine-D/sub 2/O systems. Intrinsic fluorescence quantum efficiencies of the amine-H/sub 2/O complexes are 0.17, 0.23, and 0.28 for TEA, TPA, and DABCO, respectively, at 303 K. A Foerster cycle analysis of the dry and H/sub 2/O-saturated fluorescence spectra of TEA, when taking the ground-state hydrate into account indicates that the repulsion energy of the post-fluorescence (TEA-H/sub 2/O) complex is ca. 10 kcal/mol.« less

Kinetics and mechanisms of the unimolecular elimination of 2,2-diethoxypropane and 1,1-diethoxycyclohexane in the gas phase: experimental and theoretical study.

PubMed

Rosas, Felix; Maldonado, Alexis; Lezama, Jesus; Domínguez, Rosa M; Mora, José R; Cordova, Tania; Chuchani, Gabriel

2012-01-19

The gas-phase thermal elimination of 2,2-diethoxypropane was found to give ethanol, acetone, and ethylene, while 1,1-diethoxycyclohexane yielded 1-ethoxycyclohexene and ethanol. The kinetics determinations were carried out, with the reaction vessels deactivated with allyl bromide, and the presence of the free radical suppressor cyclohexene and toluene. Temperature and pressure ranges were 240.1-358.3 °C and 38-102 Torr. The elimination reactions are homogeneous, unimolecular, and follow a first-order rate law. The rate coefficients are given by the following Arrhenius equations: for 2,2-diethoxypropane, log k(1) (s(-1)) = (13.04 ± 0.07) - (186.6 ± 0.8) kJ mol(-1) (2.303RT)(-1); for the intermediate 2-ethoxypropene, log k(1) (s(-1)) = (13.36 ± 0.33) - (188.8 ± 3.4) kJ mol(-1) (2.303RT)(-1); and for 1,1-diethoxycyclohexane, log k = (14.02 ± 0.11) - (176.6 ± 1.1) kJ mol(-1) (2.303RT)(-1). Theoretical calculations of these reactions using DFT methods B3LYP, MPW1PW91, and PBEPBE, with 6-31G(d,p) and 6-31++G(d,p) basis set, demonstrated that the elimination of 2,2-diethoxypropane and 1,1-diethoxycyclohexane proceeds through a concerted nonsynchronous four-membered cyclic transition state type of mechanism. The rate-determining factor in these reactions is the elongation of the C-O bond. The intermediate product of 2,2-diethoxypropane elimination, that is, 2-ethoxypropene, further decomposes through a concerted cyclic six-membered cyclic transition state mechanism.

Nitrosation of amides involves a pseudopericyclic 1,3-sigmatropic rearrangement.

PubMed

Birney, David M

2004-03-04

Two possible pathways for the nitrosation of formamide and N-methyl formamide by nitrosonium ion (NO(+)) have been investigated at the B3LYP/6-31G(d,p) level. The key steps are pseudopericyclic 1,3-sigmatropic rearrangements to give the observed N-nitrosamides. The transition structures (8a and 8b) are close to planar on the amide moiety and have remarkably low barriers of only 6.6 and 4.8 kcal/mol from the lowest energy conformations of 6a and 6b, respectively. [reaction: see text

26 CFR 1.401(k)-6 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 5 2011-04-01 2011-04-01 false Definitions. 1.401(k)-6 Section 1.401(k)-6...) INCOME TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-6 Definitions. Unless otherwise provided, the definitions of this section govern for purposes of section 401(k) and the...

26 CFR 1.401(k)-6 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 5 2012-04-01 2011-04-01 true Definitions. 1.401(k)-6 Section 1.401(k)-6...) INCOME TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-6 Definitions. Unless otherwise provided, the definitions of this section govern for purposes of section 401(k) and the...

26 CFR 1.401(k)-6 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 5 2010-04-01 2010-04-01 false Definitions. 1.401(k)-6 Section 1.401(k)-6...) INCOME TAXES Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-6 Definitions. Unless otherwise provided, the definitions of this section govern for purposes of section 401(k) and the regulations...

26 CFR 1.401(k)-6 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 5 2014-04-01 2014-04-01 false Definitions. 1.401(k)-6 Section 1.401(k)-6...) INCOME TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-6 Definitions. Unless otherwise provided, the definitions of this section govern for purposes of section 401(k) and the...

26 CFR 1.401(k)-6 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 5 2013-04-01 2013-04-01 false Definitions. 1.401(k)-6 Section 1.401(k)-6...) INCOME TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-6 Definitions. Unless otherwise provided, the definitions of this section govern for purposes of section 401(k) and the...

Protection against Escherichia coli K1 infection in newborn rats by antibody to K1 capsular polysaccharide antigen.

PubMed

Bortolussi, R; Ferrier, P

1980-04-01

The protective value of antibody to the K1 capsular polysaccharide antigen of Escherichia coli was investigated in a newborn rat model of E. coli K1 infection. Pregnant rats were immunized intravenously with E. coli, and the agglutinating titer to meningococcal group B polysaccharide, which is identical to K1 polysaccharide, was measured in the serum of rats and their offspring. Convalescent serum from rat mothers showed an increased antibody titer in animals injected twice but not once with E. coli K1. Although no agglutinating antibody was detected in the serum of rat pups, animals suckled by mothers having a meningococcal group B agglutinating titer of 1:8 or greater had reduced infection and mortality rates after intraperitoneal injection with E. coli K1 compared with animals suckled by mothers having a low titer of agglutinating antibody (P less than 0.05). In addition, greater protection could be conferred on rat sucklings by oral supplementation with a horse serum rich in antibody to meningococcal group B polysaccharide, suggesting that antibody was abosorbed from the gastrointestinal tract and by itself could be protective. These studies demonstrated that antibody to the capsular polysaccharide of E. coli K1 altered the severity of E. coli K1 infection. Final clearance of bacteria from the blood appeared to await the maturation of other host defense systems in the newborn rat.

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.

Adequate representation of charge polarization effects leads to a successful treatment of the CF4 + SiCl4 → CCl4 + SiF4 reaction by density functional theory.

PubMed

Li, Ruifang; Zhao, Yan; Truhlar, Donald G

2011-02-28

Adequate polarization functions reduce the error of density functional theory (DFT) for the heat of reaction for CF(4) + SiCl(4) from ∼9-12 kcal mol(-1) to ∼2-4 kcal mol(-1), and using an improved density functional further reduces it to ∼1 kcal mol(-1). This reaction was previously identified as a stumbling block for DFT, but we show that the problem with the previous calculations was not DFT but rather inadequate basis sets to account for intramolecular charge polarization.

Spectroscopic investigations and molecular docking study of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one, a potential precursor to bioactive agents

NASA Astrophysics Data System (ADS)

Al-Alshaikh, Monirah A.; Mary Y, Sheena; Panicker, C. Yohannan; Attia, Mohamed I.; El-Emam, Ali A.; Alsenoy, C. Van

2016-04-01

The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one have been investigated theoretically and experimentally. The calculated geometrical parameters of the title compound are in agreement with the reported XRD data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and from the MEP plot, it is evident that the negative charge covers the carbonyl group and the nitrogen atom N3 of the imidazole ring and the positive region is over the remaining portions of the molecule. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compound is 16.99 times that of standard NLO material urea and the title compound and its derivatives are good object for further studies in nonlinear optics. The docked ligand title compound forms a stable complex with plasmodium falciparum and gives a binding affinity value of -5.5 kcal/mol and the preliminary results suggest that the compound might exhibit antimalarial activity against plasmodium falciparum.

Kinetics of Ni3S2 sulfide dissolution in solutions of sulfuric and hydrochloric acids

NASA Astrophysics Data System (ADS)

Palant, A. A.; Bryukvin, V. A.; Vinetskaya, T. N.; Makarenkova, T. A.

2008-02-01

The kinetics of Ni3S2 sulfide (heazlewoodite) dissolution in solutions of hydrochloric and sulfuric acids is studied. The process under study in the temperature range of 30 90°C is found to occur in a kinetic regime and is controlled by the corresponding chemical reactions of the Ni3S2 decomposition by solutions of inorganic acids ( E a = 67 92 kJ/mol, or 16 22 kcal/mol). The only exception is the Ni3S2-HCl system at elevated temperatures (60 90°C). In this case, the apparent activation energy decreases sharply to 8.8 kJ/mol (2.1 kcal/mol), which is explained by the catalytic effect of gaseous chlorine formed under these conditions. The studies performed are related to the physicochemical substantiation of the hydrometallurgical processing of the copper-nickel converter mattes produced in the industrial cycle of the Norilsk Mining Company.

Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning.

PubMed

Fletcher, Timothy L; Popelier, Paul L A

2016-06-14

A machine learning method called kriging is applied to the set of all 20 naturally occurring amino acids. Kriging models are built that predict electrostatic multipole moments for all topological atoms in any amino acid based on molecular geometry only. These models then predict molecular electrostatic interaction energies. On the basis of 200 unseen test geometries for each amino acid, no amino acid shows a mean prediction error above 5.3 kJ mol(-1), while the lowest error observed is 2.8 kJ mol(-1). The mean error across the entire set is only 4.2 kJ mol(-1) (or 1 kcal mol(-1)). Charged systems are created by protonating or deprotonating selected amino acids, and these show no significant deviation in prediction error over their neutral counterparts. Similarly, the proposed methodology can also handle amino acids with aromatic side chains, without the need for modification. Thus, we present a generic method capable of accurately capturing multipolar polarizable electrostatics in amino acids.

Extreme Entropy-Enthalpy Compensation in a Drug Resistant Variant of HIV-1 Protease

PubMed Central

King, Nancy M.; Prabu-Jeyabalan, Moses; Bandaranayake, Rajintha M.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.; Özen, Ayşegül; Haliloglu, Türkan; Yılmaz, Neşe Kurt; Schiffer, Celia A.

2012-01-01

The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5–15 kcal/mol, while losing only 1–3 kcal/mol in total binding free energy for any of six FDA approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wildtype protease and another drug resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design. PMID:22712830

Calorimetric determination of the enthalpy of 1-butyl-3-methylimidazolium bromide synthesis: a key quantity in thermodynamics of ionic liquids.

PubMed

Paulechka, Yauheni U; Kabo, Andrey G; Blokhin, Andrey V

2009-11-05

The enthalpy of the 1-butyl-3-methylimidazolium bromide [C(4)mim]Br ionic liquid synthesis reaction 1-methylimidazole (liq) + 1-bromobutane (liq) --> [C(4)mim]Br (liq) was determined in a homemade small-volume isoperibol calorimeter to be Delta(r)H degrees (298) = -87.7 +/- 1.6 kJ x mol(-1). The activation energy for this reaction in a homogeneous system E(A) = 73 +/- 4 kJ x mol(-1) was found from the results of calorimetric measurements. The formation enthalpies for the crystalline and liquid [C(4)mim]Br were determined from the calorimetric data: Delta(f)H degrees (298)(cr) = -178 +/- 5 kJ x mol(-1) and Delta(f)H degrees (298)(liq) = -158 +/- 5 kJ x mol(-1). The ideal-gas formation enthalpy of this compound Delta(f)H degrees (298)(g) = 16 +/- 7 kJ x mol(-1) was calculated using the methods of quantum chemistry and statistical thermodynamics. The vaporization enthalpy of [C(4)mim]Br, Delta(vap)H degrees (298) = 174 +/- 9 kJ x mol(-1), was estimated from the experimental and calculated formation enthalpies. It was demonstrated that vapor pressure of this ionic liquid cannot be experimentally determined.

2-Pyridinethiol/2-pyridinethione tautomeric equilibrium. A comparative experimental and computational study.

PubMed

Moran, Damian; Sukcharoenphon, Kengkaj; Puchta, Ralph; Schaefer, Henry F; Schleyer, Paul V R; Hoff, Carl D

2002-12-13

The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable

π to σ Radical Tautomerization in One-Electron Oxidized 1-Methylcytosine and its Analogs

PubMed Central

Adhikary, Amitava; Kumar, Anil; Bishop, Casandra T.; Wiegand, Tyler J.; Hindi, Ragda M.; Adhikary, Ananya; Sevilla, Michael D.

2015-01-01

In this work iminyl σ-radical formation in several one-electron oxidized cytosine analogs including 1-MeC, cidofovir, 2′-deoxycytidine (dCyd), and 2′-deoxycytidine 5′-monophosphate (5′-dCMP) were investigated in homogeneous aqueous (D2O or H2O) glassy solutions at low temperatures employing electron spin resonance (ESR) spectroscopy. Employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones thus confirming its assignment. ESR and DFT studies show that the cytosine-iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical (cytosine π-aminyl radical, C(N4-H)•). Employing 1-MeC samples at various pHs ranging ca. 8 to ca. 11, ESR studies show that the tautomeric equilibrium between C(N4-H)• and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that in the iminyl-σ radical, the unpaired spin is localized to the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG= −32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA-radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in dsDNA by a radiation-induced ionization–deprotonation process that is only 10 kcal/mol above the lowest energy path. PMID:26237072

26 CFR 1.401(k)-4 - SIMPLE 401(k) plan requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 5 2012-04-01 2011-04-01 true SIMPLE 401(k) plan requirements. 1.401(k)-4 Section 1.401(k)-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED...(k)-4 SIMPLE 401(k) plan requirements. (a) General rule. A cash or deferred arrangement satisfies the...

26 CFR 1.401(k)-4 - SIMPLE 401(k) plan requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 5 2014-04-01 2014-04-01 false SIMPLE 401(k) plan requirements. 1.401(k)-4 Section 1.401(k)-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED...(k)-4 SIMPLE 401(k) plan requirements. (a) General rule. A cash or deferred arrangement satisfies the...

26 CFR 1.401(k)-4 - SIMPLE 401(k) plan requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 5 2011-04-01 2011-04-01 false SIMPLE 401(k) plan requirements. 1.401(k)-4 Section 1.401(k)-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED...(k)-4 SIMPLE 401(k) plan requirements. (a) General rule. A cash or deferred arrangement satisfies the...

26 CFR 1.401(k)-4 - SIMPLE 401(k) plan requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 5 2013-04-01 2013-04-01 false SIMPLE 401(k) plan requirements. 1.401(k)-4 Section 1.401(k)-4 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED...(k)-4 SIMPLE 401(k) plan requirements. (a) General rule. A cash or deferred arrangement satisfies the...

Prevalence of O1/K1- and O2/K3-Reactive Actinobacillus suis in Healthy and Diseased Swine

PubMed Central

Slavić, ĐurĐa; Toffner, Tania L.; Monteiro, Mario A.; Perry, Malcolm B.; MacInnes, Janet I.

2000-01-01

A cell surface antigen-typing system was devised for the swine pathogen Actinobacillus suis and used to examine the prevalence of different lipopolysaccharide (O) types in healthy and diseased pigs. The strains examined in this study were isolated from a variety of locations in Canada and from Kansas. Lipopolysaccharide preparations of 151 isolates of A. suis were characterized by immunoblotting using polyclonal antisera generated to strains SO4 (O1/K1), H89-1173 (O2/K3), and VSB 3714, a rough strain. Approximately 54% (62 of 114) of A. suis isolates from diseased pigs, all (11 of 11) isolates from healthy pigs, and all (4 of 4) reference strains reacted with O1/K1 antiserum. More than 80% (18 of 22) of A. suis strains used for bacterin production and approximately 41% (47 of 114) of isolates from diseased pigs bound O2/K3 antiserum. One isolate appeared to be rough, and five were untypeable. O1/K1- and O2/K3-reactive strains were equally prevalent in Kansas, whereas O2/K3-reactive strains were more common in Québec and western Canada and O1/K1 strains were most common in Ontario. The fact that virtually all of the strains submitted for bacterin production were O2/K3-reactive strains is consistent with the notion that these strains may be more virulent than O1/K1 strains; alternatively, this may reflect geographic or other biases. In addition, we observed cross-reactivity between A. suis cell surface antigens and swine antisera to several other important pathogens. This finding may explain why previous attempts to develop a simple serodiagnostic test for A. suis have been unsuccessful. PMID:11015398

Crystal structures of three co-crystals of 1,2-bis-(pyridin-4-yl)ethane with 4-alk-oxy-benzoic acids: 4-eth-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), 4-n-propoxybenzoic acid-1,2-bis(pyridin-4-yl)ethane (2/1) and 4-n-but-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1).

PubMed

Tabuchi, Yohei; Gotoh, Kazuma; Ishida, Hiroyuki

2015-11-01

The crystal structures of three hydrogen-bonded co-crystals of 4-alk-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), namely, 2C9H10O3·C12H12N2, (I), 2C10H12O3·C12H12N2, (II), and 2C11H14O3·C12H12N2, (III), have been determined at 93, 290 and 93 K, respectively. In (I), the asymmetric unit consists of one 4-eth-oxy-benzoic acid mol-ecule and one half-mol-ecule of 1,2-bis-(pyridin-4-yl)ethane, which lies on an inversion centre. In (II) and (III), the asymmetric units each comprise two crystallographically independent 4-alk-oxy-benzoic acid mol-ecules and one 1,2-bis-(pyridin-4-yl)ethane mol-ecule. In each crystal, the two components are linked by O-H⋯N hydrogen bonds, forming a linear hydrogen-bonded 2:1unit of the acid and the base. Similar to the structure of 2:1 unit of (I), the units of (II) and (III) adopt nearly pseudo-inversion symmetry. The 2:1 units of (I), (II) and (III) are linked via C-H⋯O hydrogen bonds, forming tape structures.

Transition state characterization for the reversible binding of dihydrogen to bis(2,2'-bipyridine)rhodium(I) from temperature- and pressure-dependent experimental and theoretical studies.

PubMed

Fujita, Etsuko; Brunschwig, Bruce S; Creutz, Carol; Muckerman, James T; Sutin, Norman; Szalda, David; van Eldik, Rudi

2006-02-20

Thermodynamic and kinetic parameters for the oxidative addition of H2 to [Rh(I)(bpy)2]+ (bpy = 2,2'-bipyridine) to form [Rh(III)(H)2(bpy)2]+ were determined from either the UV-vis spectrum of equilibrium mixtures of [Rh(I)(bpy)2]+ and [Rh(III)(H)2(bpy)2]+ or from the observed rates of dihydride formation following visible-light irradiation of solutions containing [Rh(III)(H)2(bpy)2]+ as a function of H2 concentration, temperature, and pressure in acetone and methanol. The activation enthalpy and entropy in methanol are 10.0 kcal mol(-1) and -18 cal mol(-1) K(-1), respectively. The reaction enthalpy and entropy are -10.3 kcal mol(-1) and -19 cal mol(-1) K(-1), respectively. Similar values were obtained in acetone. Surprisingly, the volumes of activation for dihydride formation (-15 and -16 cm(3) mol(-1) in methanol and acetone, respectively) are very close to the overall reaction volumes (-15 cm(3) mol(-1) in both solvents). Thus, the volumes of activation for the reverse reaction, elimination of dihydrogen from the dihydrido complex, are approximately zero. B3LYP hybrid DFT calculations of the transition-state complex in methanol and similar MP2 calculations in the gas phase suggest that the dihydrogen has a short H-H bond (0.823 and 0.810 Angstroms, respectively) and forms only a weak Rh-H bond (1.866 and 1.915 Angstroms, respectively). Equal partial molar volumes of the dihydrogenrhodium(I) transition state and dihydridorhodium(III) can account for the experimental volume profile found for the overall process.

A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Scuseria, Gustavo E.

1992-01-01

The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

Bidirectional transepithelial water transport: measurement and governing mechanisms.

PubMed

Phillips, J E; Wong, L B; Yeates, D B

1999-02-01

In the search for the mechanisms whereby water is transported across biological membranes, we hypothesized that in the airways, the hydration of the periciliary fluid layer is regulated by luminal-to-basolateral water transport coupled to active transepithelial sodium transport. The luminal-to-basolateral (JWL-->B) and the basolateral-to-luminal (JWB-->L) transepithelial water fluxes across ovine tracheal epithelia were measured simultaneously. The JWL-->B (6.1 microliter/min/cm2) was larger than JWB-->L (4.5 microliter/min/cm2, p < 0.05, n = 30). The corresponding water diffusional permeabilities were PdL-->B = 1.0 x 10(-4) cm/s and PdB-->L = 7.5 x 10(-5) cm/s. The activation energy (Ea) of JWL-->B (11.6 kcal/mol) was larger than the Ea of JWB-->L (6.5 kcal/mol, p < 0.05, n = 5). Acetylstrophanthidin (100 microM basolateral) reduced JWL-->B from 6.1 to 4.4 microliter/min/cm2 (p < 0. 05, n = 5) and abolished the PD. Amiloride (10 microM luminal) reduced JWL-->B from 5.7 to 3.7 microliter/min/cm2 (p < 0.05, n = 5) and reduced PD by 44%. Neither of these agents significantly changed JWB-->L. These data indicate that in tracheal epithelia under homeostatic conditions, JWB-->L was dominated by diffusion (Ea = 4.6 kcal/mol), whereas approximately 30% of JWL-->B was coupled to the active Na+,K+-ATPase pump (Ea = 27 kcal/mol).

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

Mautner, M.M.N.

The ionization energy of ferrocene (Cp{sub 2}Fe) was measured by charge-transfer equilibria as 6.81 {plus minus} 0.07 eV (157.1 {plus minus} 1.6 kcal/mol). The proton affinity was obtained from equilibrium temperature studies as 207 {plus minus} 1 kcal/mol. The protonation of Cp{sub 2}Fe also involves a significant entropy change of +6.3 cal/mol{center dot}K. Deuteration experiments show that, in the protonation of Cp{sub 2}Fe, the incoming proton goes to a sterically unique position and does not exchange with the ring protons. This is consistent with protonation on iron, but ring protonation exclusively in an exo position or an agostic ring-to-iron bridgedmore » structure are also possible. The results suggest that the proton affinity at Fe is greater by at least 5 kcal/mol than for ring protonation. The solvation energies of Cp{sub 2}Fe{sup +} and Cp{sub 2}FeH{sup +} by a CH{sub 3}CN molecule, 11.4 and 12.9 kcal/mol, respectively, are weaker than those of most gas-phase cations, and the attachment energies of dimethyl ether and benzene, <9 kcal/mol, are even weaker. These results support that the weak solution basicity of Cp{sub 2}Fe is due to inefficient ion solvation. The kinetics of proton transfer between Cp{sub 2}Fe and some cyclic compounds is unusually slow, with reaction efficiencies of 0.1-0.01, without significant temperature dependence. These are the first proton-transfer reactions to show such behavior, which may be due to a combination of an energy barrier and steric hindrance. Proton transfer is also observed from (RCN){sub 2}H{sup +} dimer ions to Cp{sub 2}Fe. These reactions may be direct or involve ligand switching, and in several cases either mechanism is endothermic and entropy-driven.« less

The [C{sub 6}H{sub 10}]{sup {sm{underscore}bullet}+} hypersurface: The parent radical cation Diels-Alder reaction

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

Hoffmann, M.; Schaefer, H.F. III

1999-07-21

Various possible reaction pathways between ethene and butadiene radical cation (cis- and trans-), have been investigated at different levels of theory up to UCCSD(T)/DZP/UMP2(fc)/DZP and with density functional theory at B3LYP/DZP. A stepwise addition involving open chain intermediates and leading to the Diels-Alder product, the cyclohexene radical cation, was found to have a total activation barrier {Delta}G{sup 298{ne}} = 6.3 kcal mol{sup {minus}1} and a change in free Gibbs energy, {Delta}G{sup 298}, of {minus}33.5 kcal mol{sup {minus}1}. On the E{degree} potential energy surface, all transition states are lower in energy than separated ethene and butadiene, the exothermicity {Delta}E = -45.6more » kcal mol{sup {minus}1}. A more direct path could be characterized as stepwise with one intermediate only at the SCF level but not at electron-correlated levels and hence might actually be a concerted strongly asynchronous addition with a very small or no activation barrier (UCCSD(T)/DZP/UHF/6-31G* gives a {Delta}G{sup 298{ne}} of 0.8 kcal mol{sup {minus}1}). The critical step for another alternative, the cyclobutanation-vinylcyclobutane/cyclohexene rearrangement, is a 1,3-alkyl shift which involves a barrier ({Delta}G{sup 298{ne}}) only 1.7 kcal mol{sup {minus}1} higher than that of stop use addition for both cis-, and trans-butadiene radical cation. However, from the (ethene and trans-butadiene) reactions, ring expansion of the vinylcyclobutane radical cation intermediate, to a methylene cyclopentane radical cation, requires an activation only 1.3 kcal mol{sup {minus}1} larger than for (trans-butadiene radical). While cis/trans isomerization of free butadiene radical cation requires a high activation (24.9 kcal mol{sup {minus}1}), a reaction sequence involving addition of ethene (to stepwise give an open chain intermediate and vinyl cyclobutane radical cation) has a barrier of only 3.5 kcal mol{sup {minus}1} ({Delta}G{sup 298{ne}}). This sequence also makes ethene

Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

PubMed

Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

2016-02-11

The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.

PubMed

Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D

2002-03-01

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.

Computational assessment of the electronic structures of cyclohexa-1,2,4-triene, 1-oxacyclohexa-2,3,5-triene (3delta(2)-pyran), their benzo derivatives, and cyclohexa-1,2-diene. An experimental approach to 3delta(2)-pyran.

PubMed

Engels, Bernd; Schöneboom, Jan C; Münster, Arno F; Groetsch, Stefan; Christl, Manfred

2002-01-16

The six-membered cyclic allenes given in the title have been studied theoretically by means of an MR-CI approach. For all compounds, the allene structures were found to be the ground states in the gas phase. In the cases of cyclohexa-1,2-diene (1), the isobenzene 2, and the isonaphthalene 7, the most stable structures having a planar allene moiety are the diradicals 1b, 2b, and 7b, representing the transition states for the racemization of 1a, 2a, and 7a and being less stable than the latter by 14.1, 8.9, and 11.2 kcal/mol, respectively. At variance with this order, the 3delta(2)-pyran 4 and the chromene 5 have the zwitterions 4c and 5c as the most stable planar structures, which lie only 1.0 and 5.4 kcal/mol above 4a and 5a, respectively. According to the simulation of the solvent effect, 4c even becomes the ground state of 4 in THF solution. The frontier orbitals of the respective states of 2 and 4 suggest different rates and sites for the reaction with nucleophiles. For the first time, the pyran 4 has been generated and trapped. As a precursor for 4, 3-bromo-4H-pyran (9) was chosen, the synthesis of which was achieved on two routes from 4H-pyran. The treatment of 9 with potassium tert-butoxide (KOt-Bu)/18-crown-6 gave 4-tert-butoxy-4H-pyran as the only discernible product, whether styrene or furan was present, indicating the interception of 4 by KOt-Bu. Finally, the disagreement between the experiment and the theory concerning the heat of formation and the electronic nature of the isobenzene 2 is resolved by demonstrating that the experimental data can provide only an upper limit of the DeltaH(f) degrees value.

Lattice potential energy and standard molar enthalpy in the formation of 1—dodecylamine hydrobromide (1-C12H25NH3·Br)(s)

NASA Astrophysics Data System (ADS)

Liu, Yu-Pu; Di, You-Ying; Dan, Wen-Yan; He, Dong-Hua; Kong, Yu-Xia; Yang, Wei-Wei

2011-02-01

This paper reports that 1-dodecylamine hydrobromide (1-C12H25NH3·Br)(s) has been synthesized using the liquid phase reaction method. The lattice potential energy of the compound 1-C12H25NH3·Br and the ionic volume and radius of the 1-C12H25NH3+ cation are obtained from the crystallographic data and other auxiliary thermodynamic data. The constant-volume energy of combustion of 1-C12H25NH3·Br(s) is measured to be ΔcUmo(1-C12H25NH3·Br, s) = -(7369.03±3.28) kJ·mol-1 by means of an RBC-II precision rotating-bomb combustion calorimeter at T = (298.15±0.001) K. The standard molar enthalpy of combustion of the compound is derived to be ΔcHmo(1-C12H25NH3·Br, s) = -(7384.52±3.28) kJ·mol-1 from the constant-volume energy of combustion. The standard molar enthalpy of formation of the compound is calculated to be ΔfHmo(1-C12H25NH3·Br, s)=-(1317.86±3.67) kJ·mol-1 from the standard molar enthalpy of combustion of the title compound and other auxiliary thermodynamic quantities through a thermochemical cycle.

An insight into the structure, vibrations, electronic and reactivity properties of the tautomers 1-(diaminomethylene)thiourea and 2-imino-4-thiobiuret

NASA Astrophysics Data System (ADS)

Arjunan, V.; Anitha, R.; Durgadevi, G.; Marchewka, M. K.; Mohan, S.

2017-04-01

The conformational analysis of 1-(diaminomethylene)thiourea (MTU) has been done to find out the more stable conformer. The more stable geometry of MTU and 2-imino-4-thiobiuret (ITB) are optimised with B3LYP method using 6-311++G** and cc-pVTZ basis sets. The molecules are not planar. The complete molecular structural parameters and thermodynamic properties of the optimised geometry have been determined. The molecule of MTU is not a planar but twisted. The MEP of MTU lies in the region from +1.175e × 10-2 to -1.175e × 10-2 while the total electron density spread between +6.371e × 10-2 and -6.371e × 10-2. The MEP of ITB distributed between +1.179e × 10-2 and -1.179e × 10-2 while the total electron density of ITB lies in the region +7.729e × 10-2 and -7.729e × 10-2. The energies of important MOs of the compound were also evaluated from DFT method. The LUMO shows that the nitrogen and sulphur atoms are the most nucleophilic attacking sites whereas the HOMO reveals that nitrogen, sulphur and carbon atoms are for the electrophilic substitutions. The vibrational frequencies of the fundamental modes of the compounds have been precisely assigned, analysed and the theoretical results were compared with the experimental wavenumbers. 1H and 13C NMR isotropic chemical shifts were determined and the assignments are compared with the experimental values. In MTU molecule, the n → π* transitions such as n(N5) → π*C4-S6 and n(N1) → π*C2-N3 interactions are strongly stabilised by 66.60 and 41.24 kcal mol-1, respectively. In the case of ITB compound, the stabilisation energy of lone pair donor orbital, n(N5) → σ*C4-S6 is 46.03 kcal mol-1. The dual descriptors Δfk, Δsk and Δωk values clearly indicate that the order of nucleophilic attack in MTU is S6 > N11 > N1 > N5 > N3 while in ITB the order follows as N1 > N11 > N5>S6 > N3.

26 CFR 1.401(k)-0 - Table of contents.

Code of Federal Regulations, 2014 CFR

2014-04-01

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26 CFR 1.401(k)-0 - Table of contents.

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2012-04-01

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26 CFR 1.401(k)-0 - Table of contents.

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2013-04-01

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2010-04-01

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26 CFR 1.401(k)-0 - Table of contents.

Code of Federal Regulations, 2011 CFR

2011-04-01

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Structures, internal rotor potentials, and thermochemical properties for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals.

PubMed

Snitsiriwat, Suarwee; Asatryan, Rubik; Bozzelli, Joseph W

2011-12-01

Structures, enthalpy (Δ(f)H°(298)), entropy (S°(T)), and heat capacity (C(p)(T)) are determined for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals using the density functional B3LYP and composite CBS-QB3 calculations. Enthalpies of formation (Δ(f)H°(298)) are determined at the B3LYP/6-31G(d,p), B3LYP/6-31+G(2d,2p), and composite CBS-QB3 levels using several work reactions for each species. Entropy (S) and heat capacity (C(p)(T)) values from vibration, translational, and external rotational contributions are calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional studies. Contribution to Δ(f)H(T), S, and C(p)(T) from the analysis on the internal rotors is included. Recommended values for enthalpies of formation of the most stable conformers of nitroacetone cc(═o)cno2, acetonitrite cc(═o)ono, nitroacetate cc(═o)no2, and acetyl nitrite cc(═o)ono are -51.6 kcal mol(-1), -51.3 kcal mol(-1), -45.4 kcal mol(-1), and -58.2 kcal mol(-1), respectively. The calculated Δ(f)H°(298) for nitroethylene c═cno2 is 7.6 kcal mol(-1) and for vinyl nitrite c═cono is 7.2 kcal mol(-1). We also found an unusual phenomena: an intramolecular transfer reaction (isomerization) with a low barrier (3.6 kcal mol(-1)) in the acetyl nitrite. The NO of the nitrite (R-ONO) in CH(3)C(═O')ONO moves to the C═O' oxygen in a motion of a stretching frequency and then a shift to the carbonyl oxygen (marked as O' for illustration purposes). © 2011 American Chemical Society

Opposing influences by subsite -1 and subsite +1 residues on relative xylopyranosidase/arabinofuranosidase activities of bifunctional beta-D-xylosidase/alpha-L-arabinofuranosidase

USDA-ARS?s Scientific Manuscript database

Conformational inversion occurs 7-8 kcal/mol more readily in furanoses than pyranoses. This difference is exploited here to disclose active-site residues involved in distorting substrate towards reactivity. Spontaneous glycoside hydrolysis rates are ordered 4-nitrophenyl-alpha-L-arabinofuranoside (4...

Direct evaluation of the hyperconjugative interactions in 1,1,1-trihaloethane (CH3CX3, X = F, Cl, and Br).

PubMed

Chen, Zhenhua; Corminboeuf, Clémence; Mo, Yirong

2014-08-07

Following the computational strategy proposed by Mulliken in 1939 ( J. Chem. Phys. 1939, 7 (5), 339-352), when the concept of hyperconjugation was coined, we evaluated the hyperconjugative stabilization energy in 1,1,1-trihaloethane using the block-localized wave function (BLW) method. The BLW method is the simplest and most efficient variant of ab initio valence bond (VB) theory and can derive the strictly electron-localized state wave function self-consistently. The latter serves as a reference for the quantification of the electron delocalization effect in terms of the resonance theory. Computations show that the overall hyperconjugative interactions in 1,1,1-trihaloethane, dominated by σ(CH) → σ'(CX) with minor contribution from σ(CX) → σ'(CH), ranges from 9.59 to 7.25 kcal/mol in the staggered structures and decreases in the order Br > Cl > F. This is in accord with the (1)H NMR spectra of CH3CX3. Notably, the hyperconjugation effect accounts for 35-40% of the rotation barriers in these molecules, which are dominated by the conventional steric repulsion. This is consistent with the recent findings with 1,2-difluoroethane (Freitas, Bühl, and O'Hagan. Chem. Comm. 2012, 48, 2433-2435) that the variation of (1)J(CF) with the FCCF torsional angle cannot be well explained by the hyperconjugation model

A theoretical study of the cyclization processes of energized CCCSi and CCCP.

PubMed

Maclean, Micheal J; Eichinger, Peter C H; Wang, Tianfang; Fitzgerald, Mark; Bowie, John H

2008-12-11

Calculations at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31+G(d) level of theory have shown that cyclization of both the ground state triplet and the corresponding singlet state of CCCSi may rearrange to give cyclic isomers which upon ring opening may reform linear C(3)Si isomers in which the carbon atoms are scrambled. The cyclization processes are energetically favorable with barriers to the transition states from 13 to 16 kcal mol(-1). This should be contrasted with the analogous process of triplet CCCC to triplet rhombic C(4), which requires an excess energy of 25.8 kcal mol(-1). A similar cyclization of doublet CCCP requires 50.4 kcal mol(-1) of excess energy; this should be contrasted with the same process for CCCN, which requires 54.7 kcal mol(-1) to effect cyclization.

Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan.

PubMed

Harada, Sohei; Ishii, Yoshikazu; Saga, Tomoo; Aoki, Kotaro; Tateda, Kazuhiro

2018-03-20

Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological study of K. pneumoniae K1 and K2 isolates in Japan. Of the 259K. pneumoniae isolates collected, 14 and 16 isolates were identified as capsular genotypes K1 and K2, respectively. All K1 isolates were ST23 or its closely related clones and showed high genetic similarity by pulsed-field gel electrophoresis (PFGE) and the DiversiLab system (DL). K2 isolates, belonging to ST14, ST25, ST65, ST86, and ST110, were more genetically diverse than K1 isolates. Isolates belonging to a specific ST showed identical virulence gene profiles with a few exceptions. PFGE and DL results using K1 and K2 isolates were generally in agreement. Copyright © 2018. Published by Elsevier Inc.

An additional role for the Brønsted acid-base catalysts of mandelate racemase in transition state stabilization.

PubMed

Nagar, Mitesh; Bearne, Stephen L

2015-11-10

Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reaction direction, their roles are reversed. Using isothermal titration calorimetry (ITC), MR is shown to bind the intermediate/transition state (TS) analogue inhibitor benzohydroxamate (BzH) in an entropy-driven process with a value of ΔCp equal to -358 ± 3 cal mol(-1) K(-1), consistent with an increased number of hydrophobic interactions. However, MR binds BzH with an affinity that is ∼2 orders of magnitude greater than that predicted solely on the basis of hydrophobic interactions [St. Maurice, M., and Bearne, S. L. (2004) Biochemistry 43, 2524], suggesting that additional specific interactions contribute to binding. To test the hypothesis that cation-π/NH-π interactions between the side chains of Lys 166 and His 297 and the aromatic ring and/or the hydroxamate/hydroximate moiety of BzH contribute to the binding of BzH, site-directed mutagenesis was used to generate the MR variants K166M, K166C, H297N, and K166M/H297N and their binding affinity for various ligands determined using ITC. Comparison of the binding affinities of these MR variants with the intermediate/TS analogues BzH and cyclohexanecarbohydroxamate revealed that cation-π/NH-π interactions between His 297 and the hydroxamate/hydroximate moiety and the phenyl ring of BzH contribute approximately 0.26 and 0.91 kcal/mol to binding, respectively, while interactions with Lys 166 contribute approximately 1.74 and 1.74 kcal/mol, respectively. Similarly, comparison of the binding affinities of these mutants with substrate analogues revealed that Lys 166 contributes >2.93 kcal/mol to the binding of (R

Quercetin ameliorates pulmonary fibrosis by inhibiting SphK1/S1P signaling.

PubMed

Zhang, Xingcai; Cai, Yuli; Zhang, Wei; Chen, Xianhai

2018-06-25

Idiopathic pulmonary fibrosis (IPF) is an agnogenic chronic disorder with high morbidity and low survival rate. Quercetin is a flavonoid found in a variety of herbs with anti-fibrosis function. In this study, bleomycin was employed to induce a pulmonary fibrosis mouse model. The quercetin administration ameliorated bleomycin-induced pulmonary fibrosis, evidenced by the expression level changes of hydroxyproline, fibronectin, α-smooth muscle actin, Collagen I and Collagen III. The similar results were observed in transforming growth factor (TGF)-β-treated human embryonic lung fibroblast (HELF). The bleomycin or TGF-β administration caused the increase of sphingosine-1-phosphate (S1P) level in pulmonary tissue and HELF cells, as well as its activation-required kinase, sphingosine kinase 1 (SphK1), and its degradation enzyme, sphinogosine-1-phosphate lyase (S1PL). However, the increase of S1P, SphK1 and S1PL was attenuated by application of quercetin. In addition, the effect of quercetin on fibrosis was abolished by the ectopic expression of SphK1. The colocalization of SphK1/S1PL and fibroblast specific protein 1 (FSP1) suggested the roles of fibroblasts in pulmonary fibrosis. In summary, we demonstrated that quercetin ameliorated pulmonary fibrosis in vivo and in vitro by inhibiting SphK1/S1P signaling.

Structural and catalytic roles of amino acid residues located at substrate-binding pocket in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase.

PubMed

Chen, Je-Hsin; Tsai, Li-Chu; Huang, Hsiao-Chuan; Shyur, Lie-Fen

2010-10-01

We created 12 mutant enzymes (E11L, F40I, Y42L, N44L, N44Q, E47I, L62G, K64A, K64M, R137M, R137Q, and N139A) from the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (TF-glucanase). The enzymes were used to investigate the structural and catalytic roles of specific amino acid residues located at the catalytic pocket and having direct interactions with glucose subsites of the product beta-1,3-1,4-cellotriose (CLTR). Fluorescence spectrometry showed no discernible changes in secondary structures among purified TF-glucanase and the mutants. Kinetic analyses showed E11L, F40I, Y42L, R137M, and R137Q with a >10-fold decrease of specific activity (11.2- to 67.4-fold), and E11L, N44Q, E47I, K64M, R137M, R137Q, and N139A with a 2.17- to 4.3-fold increase of K(m) value when compared with TF-glucanase. Notably, E11L, R137Q, R137M, F40I, and N139A showed the most significant decrease in catalytic efficiency relative to TF-glucanase, by 2155-, 84.9-, 48.5-, 41.1-, and 19.1-fold, respectively; the five mutants showed the greatest changes in comparative energy DeltaDeltaG(b), with values of 1.94 to 4.92 kcal/mol. Combined with results from kinetic and structure modeling analyses of all mutant enzymes and X-ray crystallography of F40I, we elucidate that Glu11, Phe40, Arg137, and Asn139 play a crucial role in the catalysis of TF-glucanase owing to their local and direct interaction through hydrogen bonds or van der Waals stacking interaction by aromatic rings onto the glucose subsites -3, -2, and -1 of CLTR/substrate. The overall globular structures in the wild-type and mutant F40I enzymes do not differ. 2010 Wiley-Liss, Inc.

Ultracold-neutron production and up-scattering in superfluid helium between 1.1 K and 2.4 K

NASA Astrophysics Data System (ADS)

Leung, K. K. H.; Ivanov, S.; Piegsa, F. M.; Simson, M.; Zimmer, O.

2016-02-01

Ultracold neutrons (UCNs) were produced in superfluid helium using the PF1B cold-neutron beam facility at the Institut Laue-Langevin. A 4-liter beryllium-coated converter volume with a mechanical valve and windowless stainless-steel extraction system were used to accumulate and guide UCNs to a detector at room temperature. At a converter temperature of 1.08 K the total storage time constant in the vessel was (20.3 ±1.2 )s and the number of UCNs counted after accumulated was 91 700 ±300 . From this, we derive a volumetric UCN production rate of (6.9 ±1.7 ) cm-3s-1 , which includes a correction for losses in the converter during UCN extraction caused by the short storage time, but not accounting for UCN transport and detection efficiencies. The up-scattering rate of UCNs caused by excitations in the superfluid was studied by scanning the temperature between 1.2 K and 2.4 K . Using the temperature-dependent UCN production rate calculated from inelastic neutron scattering data, the only UCN up-scattering process found to occur was from two-phonon scattering. Our analysis for T <1.95 K rules out the contributions from roton-phonon scattering to <29 % (95% C.I.) and from one-phonon absorption to <47 % (95% C.I.) of their predicted levels.

Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise.

PubMed

Zhang, Xiaodong; Bruice, Thomas C

2006-10-31

We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetate methyltransferase catalyzed reaction, which shows that proton transfer from guanidinoacetate (GAA) to Asp-134 and methyl transfer from S-adenosyl-L-methionine (AdoMet) to GAA are concerted. By self-consistent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted mechanism's transition state are 1.26 A for both the OD1 (Asp-134)-H(E) (GAA) and H(E) (GAA)-N(E) (GAA) bonds, and 2.47 and 2.03 A for the S8 (AdoMet)-C9 (AdoMet) and C9 (AdoMet)-N(E) (GAA) bonds, respectively. The potential-energy barrier (DeltaE++) determined by single-point B3LYP/6-31+G*//MM is 18.9 kcal/mol. The contributions of the entropy (-TDeltaS++) and zero-point energy corrections Delta(ZPE)++ by normal mode analysis are 2.3 kcal/mol and -1.7 kcal/mol, respectively. Thus, the activation enthalpy of this concerted mechanism is predicted to be DeltaH++ = DeltaE++ plus Delta(ZPE)++ = 17.2 kcal/mol. The calculated free-energy barrier for the concerted mechanism is DeltaG++ = 19.5 kcal/mol, which is in excellent agreement with the value of 19.0 kcal/mol calculated from the experimental rate constant (3.8 +/- 0.2.min(-1)).

Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise

PubMed Central

Zhang, Xiaodong; Bruice, Thomas C.

2006-01-01

We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetate methyltransferase catalyzed reaction, which shows that proton transfer from guanidinoacetate (GAA) to Asp-134 and methyl transfer from S-adenosyl-l-methionine (AdoMet) to GAA are concerted. By self-consistent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted mechanism's transition state are 1.26 Å for both the OD1 (Asp-134)–HE (GAA) and HE (GAA)–NE (GAA) bonds, and 2.47 and 2.03 Å for the S8 (AdoMet)–C9 (AdoMet) and C9 (AdoMet)–NE (GAA) bonds, respectively. The potential-energy barrier (ΔE‡) determined by single-point B3LYP/6–31+G*//MM is 18.9 kcal/mol. The contributions of the entropy (−TΔS‡) and zero-point energy corrections Δ(ZPE)‡ by normal mode analysis are 2.3 kcal/mol and −1.7 kcal/mol, respectively. Thus, the activation enthalpy of this concerted mechanism is predicted to be ΔH‡ = ΔE‡ + Δ(ZPE)‡ = 17.2 kcal/mol. The calculated free-energy barrier for the concerted mechanism is ΔG‡ = 19.5 kcal/mol, which is in excellent agreement with the value of 19.0 kcal/mol calculated from the experimental rate constant (3.8 ± 0.2·min−1). PMID:17053070

The reactions of SO3 with HO2 radical and H2O...HO2 radical complex. Theoretical study on the atmospheric formation of HSO5 and H2SO4.

PubMed

Gonzalez, Javier; Torrent-Sucarrat, Miquel; Anglada, Josep M

2010-03-07

The influence of a single water molecule on the gas-phase reactivity of the HO(2) radical has been investigated by studying the reactions of SO(3) with the HO(2) radical and with the H(2)O...HO(2) radical complex. The naked reaction leads to the formation of the HSO(5) radical, with a computed binding energy of 13.81 kcal mol(-1). The reaction with the H(2)O...HO(2) radical complex can give two different products, namely (a) HSO(5) + H(2)O, which has a binding energy that is computed to be 4.76 kcal mol(-1) more stable than the SO(3) + H(2)O...HO(2) reactants (Delta(E + ZPE) at 0K) and an estimated branching ratio of about 34% at 298K and (b) sulfuric acid and the hydroperoxyl radical, which is computed to be 10.51 kcal mol(-1) below the energy of the reactants (Delta(E + ZPE) at 0K), with an estimated branching ratio of about 66% at 298K. The fact that one of the products is H(2)SO(4) may have relevance in the chemistry of the atmosphere. Interestingly, the water molecule acts as a catalyst, [as it occurs in (a)] or as a reactant [as it occurs in (b)]. For a sake of completeness we have also calculated the anharmonic vibrational frequencies for HO(2), HSO(5), the HSO(5)...H(2)O hydrogen bonded complex, H(2)SO(4), and two H(2)SO(4)...H(2)O complexes, in order to help with the possible experimental identification of some of these species.

26 CFR 1.168(k)-0 - Table of contents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 2 2010-04-01 2010-04-01 false Table of contents. 1.168(k)-0 Section 1.168(k)-0...) INCOME TAXES (CONTINUED) Itemized Deductions for Individuals and Corporations § 1.168(k)-0 Table of contents. This section lists the headings that appear in § 1.168(k)-1. § 1.168(k)-1Additional first year...

26 CFR 1.168(k)-0 - Table of contents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 2 2014-04-01 2014-04-01 false Table of contents. 1.168(k)-0 Section 1.168(k)-0...) INCOME TAXES (CONTINUED) Itemized Deductions for Individuals and Corporations § 1.168(k)-0 Table of contents. This section lists the headings that appear in § 1.168(k)-1. § 1.168(k)-1Additional first year...

26 CFR 1.168(k)-0 - Table of contents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 2 2011-04-01 2011-04-01 false Table of contents. 1.168(k)-0 Section 1.168(k)-0...) INCOME TAXES (CONTINUED) Itemized Deductions for Individuals and Corporations § 1.168(k)-0 Table of contents. This section lists the headings that appear in § 1.168(k)-1. § 1.168(k)-1Additional first year...

26 CFR 1.168(k)-0 - Table of contents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 2 2013-04-01 2013-04-01 false Table of contents. 1.168(k)-0 Section 1.168(k)-0...) INCOME TAXES (CONTINUED) Itemized Deductions for Individuals and Corporations § 1.168(k)-0 Table of contents. This section lists the headings that appear in § 1.168(k)-1. § 1.168(k)-1Additional first year...

26 CFR 1.168(k)-0 - Table of contents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 2 2012-04-01 2012-04-01 false Table of contents. 1.168(k)-0 Section 1.168(k)-0...) INCOME TAXES (CONTINUED) Itemized Deductions for Individuals and Corporations § 1.168(k)-0 Table of contents. This section lists the headings that appear in § 1.168(k)-1. § 1.168(k)-1Additional first year...

Correlation consistent basis sets for lanthanides: The atoms La–Lu

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

Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

Interactions of vitamin K3 with herring-sperm DNA using spectroscopy and electrochemistry.

PubMed

Huang, Jianhang; Wang, Xingming; Fei, Dan; Ding, Lisheng

2010-10-01

By means of ultraviolet-visible (UV-Vis) and fluorescence spectra, the binding ratio between vitamin K(3) and herring-sperm DNA in a physiological pH environment (pH = 7.40) was determined as n(K3):n(DNA) = 2:1, and the binding constants of vitamin K(3) binding to DNA at different temperatures were determined as K(θ)(298K) = 1.28 × 10(5) L·mol(-1) and K(θ)(310K) = 7.19 × 10(4) L·mol(-1), which were confirmed using the double reciprocal method are Δ(r)H(m)(θ) = -3.57 × 10(4) J·mol(-1), Δ(r)G(m)(θ) = -2.92 × 10(4) J·mol(-1), and Δ(r)S(m)(θ) = 217.67 J·mol(-1)K(-1). The driving power of this process was enthalpy. An intercalation binding of the vitamin K(3) with DNA was supported by a competitive experiment using acridine orange (AO) as a spectral probe. By combination analysis of the Scatchard method and cyclic voltammetry, we suggested that the interaction mode between vitamin K(3) and herring-sperm DNA would be a mixed mode. The quinonoid, duality fused-ring of vitamin K(3) can intercalate into the base pairs of DNA, and there is an electrostatic binding along with intercalation binding.

Surface and bulk effects of K in Cu 1-xK xIn 1-yGa ySe 2 solar cells

DOE PAGES

Muzzillo, Christopher P.; Anderson, Timothy J.

2017-12-29

Two strategies for enhancing photovoltaic (PV) performance in chalcopyrite solar cells were investigated: Cu 1-xK xIn 1-yGa ySe 2 absorbers with low K content (K/(K+Cu), or x ~ 0.07) distributed throughout the bulk, and CuIn 1-yGa ySe 2 absorbers with KIn 1-yGa ySe 2 grown on their surfaces. Distributing K throughout the bulk absorbers improved power conversion efficiency, open-circuit voltage (VOC) and fill factor (FF) for Ga/(Ga+In) of 0, 0.3 and 0.5. Surface KIn 1-yGa ySe 2 and bulk x ~ 0.07 Cu 1-xK xIn 1-yGa ySe 2 films with Ga/(Ga+In), or y of 0.3 and 0.5 also had improvedmore » efficiency, VOC, and FF, relative to CuIn 1-yGa ySe 2 baselines. On the other hand, y ~ 1 absorbers did not benefit from K introduction. Similar to Cu 1-xK xInSe 2, the formation of Cu 1-xK xGaSe 2 alloys was favored at low temperatures and high Na supply by the substrate, relative to the formation of mixed-phase CuGaSe 2 + KGaSe 2. KIn 1-yGa ySe 2 alloys were grown for the first time, as evidenced by X-ray diffraction and ultraviolet/visible spectroscopy. For all Ga/(Ga+In) compositions, the surface KIn 1-yGa ySe 2 absorbers had superior PV performance in buffered and buffer-free devices. However, the bulk x ~ 0.07 absorbers only outperformed the baselines in buffered devices. The data demonstrate that KIn 1-yGa ySe 2 passivates the surface of CuIn 1-yGa ySe 2 to increase efficiency, VOC, and FF, while bulk Cu 1-xK xIn 1-yGa ySe 2 absorbers with x ~ 0.07 enhance efficiency, VOC, and FF by some other mechanism.« less

Surface and bulk effects of K in Cu 1-xK xIn 1-yGa ySe 2 solar cells

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

Muzzillo, Christopher P.; Anderson, Timothy J.

Two strategies for enhancing photovoltaic (PV) performance in chalcopyrite solar cells were investigated: Cu 1-xK xIn 1-yGa ySe 2 absorbers with low K content (K/(K+Cu), or x ~ 0.07) distributed throughout the bulk, and CuIn 1-yGa ySe 2 absorbers with KIn 1-yGa ySe 2 grown on their surfaces. Distributing K throughout the bulk absorbers improved power conversion efficiency, open-circuit voltage (VOC) and fill factor (FF) for Ga/(Ga+In) of 0, 0.3 and 0.5. Surface KIn 1-yGa ySe 2 and bulk x ~ 0.07 Cu 1-xK xIn 1-yGa ySe 2 films with Ga/(Ga+In), or y of 0.3 and 0.5 also had improvedmore » efficiency, VOC, and FF, relative to CuIn 1-yGa ySe 2 baselines. On the other hand, y ~ 1 absorbers did not benefit from K introduction. Similar to Cu 1-xK xInSe 2, the formation of Cu 1-xK xGaSe 2 alloys was favored at low temperatures and high Na supply by the substrate, relative to the formation of mixed-phase CuGaSe 2 + KGaSe 2. KIn 1-yGa ySe 2 alloys were grown for the first time, as evidenced by X-ray diffraction and ultraviolet/visible spectroscopy. For all Ga/(Ga+In) compositions, the surface KIn 1-yGa ySe 2 absorbers had superior PV performance in buffered and buffer-free devices. However, the bulk x ~ 0.07 absorbers only outperformed the baselines in buffered devices. The data demonstrate that KIn 1-yGa ySe 2 passivates the surface of CuIn 1-yGa ySe 2 to increase efficiency, VOC, and FF, while bulk Cu 1-xK xIn 1-yGa ySe 2 absorbers with x ~ 0.07 enhance efficiency, VOC, and FF by some other mechanism.« less

Studies on interaction of insect repellent compounds with odorant binding receptor proteins by in silico molecular docking approach.

PubMed

Gopal, J Vinay; Kannabiran, K

2013-12-01

The aim of the study was to identify the interactions between insect repellent compounds and target olfactory proteins. Four compounds, camphor (C10H16O), carvacrol (C10H14O), oleic acid (C18H34O2) and firmotox (C22H28O5) were chosen as ligands. Seven olfactory proteins of insects with PDB IDs: 3K1E, 1QWV, 1TUJ, 1OOF, 2ERB, 3R1O and OBP1 were chosen for docking analysis. Patch dock was used and pymol for visualizing the structures. The interactions of these ligands with few odorant binding proteins showed binding energies. The ligand camphor had showed a binding energy of -136 kcal/mol with OBP1 protein. The ligand carvacrol interacted with 1QWV and 1TUJ proteins with a least binding energy of -117.45 kcal/mol and -21.78 kcal/mol respectively. The ligand oleic acid interacted with 1OOF, 2ERB, 3R1O and OBP1 with least binding energies. Ligand firmotox interacted with OBP1 and showed least binding energies. Three ligands (camphor, oleic acid and firmotox) had one, two, three interactions with a single protein OBP1 of Nilaparvatha lugens (Rice pest). From this in silico study we identified the interaction patterns for insect repellent compounds with the target insect odarant proteins. The results of our study revealed that the chosen ligands showed hydrogen bond interactions with the target olfactory receptor proteins.

Kinetic modeling and thermodynamic study to remove Pb(II), Cd(II), Ni(II) and Zn(II) from aqueous solution using dead and living Azolla filiculoides.

PubMed

Rakhshaee, Roohan; Khosravi, Morteza; Ganji, Masoud Taghi

2006-06-30

Dead Azolla filiculoides can remove Pb(2+),Cd(2+), Ni(2+) and Zn(2+) corresponding to second-order kinetic model. The maximum adsorption capacity (Q(max)) to remove these metal ions by the alkali and CaCl(2)/MgCl(2)/NaCl (2:1:1, molar ratio) activated Azolla from 283 to 313K was 1.431-1.272, 1.173-0.990, 1.365-1.198 and 1.291-0.981mmol/g dry biomass, respectively. Q(max) to remove these heavy metals by the non-activated Azolla at the mentioned temperature range was obtained 1.131-0.977, 1.092-0.921, 1.212-0.931 and 1.103-0.923mmol/g dry biomass, respectively. In order to remove these metal ions by the activated Azolla, the enthalpy change (DeltaH) was -4.403, -4.495, -4.557 and -4.365kcal/mol and the entropy change (DeltaS) was 2.290, 1.268, 1.745 and 1.006cal/molK, respectively. While, to remove these metal ions by the non-activated Azolla, DeltaH was -3.685, -3.766, -3.967 and -3.731kcal/mol and DeltaS was 2.440, 1.265, 1.036 and 0.933cal/molK, respectively. On the other hand, the living Azolla removed these heavy metals corresponding to first-order kinetic model. It was also shown that pH, temperature and photoperiod were effective both on the rate of Azolla growth and the rate of heavy metals uptake during 10 days. It was appeared the use of Ca(NO(3))(2) increased both Azolla growth rate and the rate of heavy metals uptake while the using KNO(3) although increased Azolla growth rate but decreased the rate of heavy metals uptake.

QM/MM nonadiabatic dynamics simulations on photoinduced Wolff rearrangements of 1,2,3-thiadiazole

NASA Astrophysics Data System (ADS)

Liu, Xiang-Yang; Fang, Ye-Guang; Xie, Bin-Bin; Fang, Wei-Hai; Cui, Ganglong

2017-06-01

The photoinduced rearrangement reaction mechanism of 1,2,3-thiadiazole remains experimentally elusive. Two possible mechanisms have been proposed to date. The first is a stepwise mechanism via a thiocarbene intermediate; the second is an excited-state concerted rearrangement mechanism. Herein we have adopted both the electronic structure calculations and nonadiabatic dynamics simulations to study the photoinduced rearrangement reactions of 1,2,3-thiadiazole in the S2, S1, and S0 states in solution. On the basis of QM(CASPT2)/MM [quantum mechanics(complete active space self-consistent field second-order perturbation theory)/molecular mechanics] calculations, we have found that (1) the thiocarbene intermediate is not stable; thus, the stepwise mechanism should be unfavorable; (2) the excited-state decay from the S2 via S1 to S0 state is ultrafast and completed within ca. 200 fs; therefore, both the S2 and S1 states should not have a long enough time for the excited-state rearrangements. Instead, we have computationally proposed a modified photoinduced rearrangement mechanism. Upon irradiation, the S2 state is first populated (114.0 kcal/mol), followed by an ultrafast S2 → S1 → S0 excited-state decay along the S-N bond fission, which eventually leads to a very "hot" intermediate with the S-N bond broken (18.3 kcal/mol). Then, thermal rearrangements to thioketene, thiirene, and ethynethiol occur in a concerted asynchronous way. This mechanistic scenario has been verified by full-dimensional trajectory-based nonadiabatic dynamics simulations at the QM(CASPT2)/MM level. Finally, our present computational work provides experimentally interesting mechanistic insights into the photoinduced rearrangement reactions of cyclic and acyclic diazo compounds.

A molecular dynamics study of the relaxation of an excited molecule in crystalline nitromethane

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Siavosh-Haghighi, Ali; Sewell, Thomas D.; Thompson, Donald L.

2014-07-01

Classical molecular dynamics simulations were used to study the relaxation of an excited nitromethane molecule in perfect crystalline nitromethane at 250 K and 1 atm pressure. The molecule was instantaneously excited by statistically distributing energy E∗ between 25.0 kcal/mol and 125.0 kcal/mol among the 21 degrees of freedom of the molecule. The relaxation occurs exponentially with time constants between 11.58 ps and 13.57 ps. Energy transfer from the excited molecule to surrounding quasi-spherical shells of molecules occurs concurrently to both the nearest and next-nearest neighbor shells, but with more energy per molecule transferred more rapidly to the first shell.

The protonation of N2O reexamined - A case study on the reliability of various electron correlation methods for minima and transition states

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1993-01-01

The protonation of N2O and the intramolecular proton transfer in N2OH(+) are studied using various basis sets and a variety of methods, including second-order many-body perturbation theory (MP2), singles and doubles coupled cluster (CCSD), the augmented coupled cluster (CCSD/T/), and complete active space self-consistent field (CASSCF) methods. For geometries, MP2 leads to serious errors even for HNNO(+); for the transition state, only CCSD/T/ produces a reliable geometry due to serious nondynamical correlation effects. The proton affinity at 298.15 K is estimated at 137.6 kcal/mol, in close agreement with recent experimental determinations of 137.3 +/- 1 kcal/mol.

A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.

PubMed

Stewart, James J P

2016-11-01

A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol -1 to ±0.1 kcal mol -1 . This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated-an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.

Synthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo[1,2-a]pyrimidines.

PubMed

Gómez-García, Omar; Andrade-Pavón, Dulce; Campos-Aldrete, Elena; Ballinas-Indilí, Ricardo; Méndez-Tenorio, Alfonso; Villa-Tanaca, Lourdes; Álvarez-Toledano, Cecilio

2018-03-07

A series of 3-benzoyl imidazo[1,2- a ]pyrimidines, obtained from N -heteroarylformamidines in good yields, was tested in silico and in vitro for binding and inhibition of seven Candida species ( Candida albicans (ATCC 10231), Candida dubliniensis (CD36), Candida glabrata (CBS138), Candida guilliermondii (ATCC 6260), Candida kefyr , Candida krusei (ATCC 6358) and Candida tropicalis (MYA-3404)). To predict binding mode and energy, each compound was docked in the active site of the lanosterol 14α-demethylase enzyme (CYP51), essential for fungal growth of Candida species. Antimycotic activity was evaluated as the 50% minimum inhibitory concentration (MIC50) for the test compounds and two reference drugs, ketoconazole and fluconazole. All test compounds had a better binding energy (range: -6.11 to -9.43 kcal/mol) than that found for the reference drugs (range: 48.93 to -6.16 kcal/mol). In general, the test compounds showed greater inhibitory activity of yeast growth than the reference drugs. Compounds 4j and 4f were the most active, indicating an important role in biological activity for the benzene ring with electron-withdrawing substituents. These compounds show the best MIC50 against C. guilliermondii and C. glabrata, respectively. The current findings suggest that the 3-benzoyl imidazo[1,2- a ]pyrimidine derivatives, herein synthesized by an accessible methodology, are potential antifungal drugs.

G4CEP: A G4 theory modification by including pseudopotential for molecules containing first-, second- and third-row representative elements.

PubMed

Silva, Cleuton de Souza; Pereira, Douglas Henrique; Custodio, Rogério

2016-05-28

The G4CEP composite method was developed from the respective G4 all-electron version by considering the implementation of compact effective pseudopotential (CEP). The G3/05 test set was used as reference to benchmark the adaptation by treating in this work atoms and compounds from the first and second periods of the periodic table, as well as representative elements of the third period, comprising 440 thermochemical data. G4CEP has not reached a so high level of accuracy as the G4 all-electron theory. G4CEP presented a mean absolute error around 1.09 kcal mol(-1), while the original method presents a deviation corresponding to 0.83 kcal mol(-1). The similarity of the optimized molecular geometries between G4 and G4CEP indicates that the core-electron effects and basis set adjustments may be pointed out as a significant factor responsible for the large discrepancies between the pseudopotential results and the experimental data, or even that the all-electron calculations are more efficient either in its formulation or in the cancellation of errors. When the G4CEP mean absolute error (1.09 kcal mol(-1)) is compared to 1.29 kcal mol(-1) from G3CEP, it does not seem so efficient. However, while the G3CEP uncertainty is ±4.06 kcal mol(-1), the G4CEP deviation is ±2.72 kcal mol(-1). Therefore, the G4CEP theory is considerably more reliable than any previous combination of composite theory and pseudopotential, particularly for enthalpies of formation and electron affinities.

A novel ALDH5A1 mutation is associated with succinic semialdehyde dehydrogenase deficiency and severe intellectual disability in an Iranian family.

PubMed

Püttmann, Lucia; Stehr, Henning; Garshasbi, Masoud; Hu, Hao; Kahrizi, Kimia; Lipkowitz, Bettina; Jamali, Payman; Tzschach, Andreas; Najmabadi, Hossein; Ropers, Hans-Hilger; Musante, Luciana; Kuss, Andreas W

2013-08-01

Succinic semialdehyde dehydrogenase (SSADH) deficiency is a disorder of the catabolism of the neurotransmitter gamma-aminobutyric acid (GABA) with a very variable clinical phenotype ranging from mild intellectual disability to severe neurological defects. We report here on a large Iranian family with four affected patients presenting with severe intellectual disability, developmental delay and generalized tonic-clonic seizures. Molecular genetic analysis revealed a missense mutation c.901A>G (p.K301E, RefSeq number NM_001080) in ALDH5A1 co-segregating with the disease in the family. The missense mutation affects an amino acid residue that is highly conserved across the animal kingdom. Protein modeling showed that p.K301E most likely leads to a loss of NAD(+) binding and a predicted decrease in the free energy by 6.67 kcal/mol furthermore suggests a severe destabilization of the protein. In line with these in silico observations, no SSADH enzyme activity could be detected in patient lymphoblasts. Copyright © 2013 Wiley Periodicals, Inc.

26 CFR 1.401(k)-2 - ADP test.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 5 2012-04-01 2011-04-01 true ADP test. 1.401(k)-2 Section 1.401(k)-2 Internal... TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-2 ADP test. (a) Actual...(k)(3)(F), the ADP test is performed under the plan (determined without regard to disaggregation...

26 CFR 1.401(k)-2 - ADP test.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 5 2011-04-01 2011-04-01 false ADP test. 1.401(k)-2 Section 1.401(k)-2 Internal... TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-2 ADP test. (a) Actual...(k)(3)(F), the ADP test is performed under the plan (determined without regard to disaggregation...

The K-1 Active Dispenser for Orbit Transfer

NASA Astrophysics Data System (ADS)

Lai, G.; Cochran, D.; Curtis, R.

2002-01-01

Kistler Aerospace Corporation is building the K-1, the world's first fully reusable launch vehicle. The two-stage K- 1 is designed primarily to service the market for low-earth orbit (LEO) missions, due to Kistler's need to recover both stages. For customers requiring payload delivery to high-energy orbits, Kistler can outfit the payload with a K- 1 Active Dispenser (an expendable third stage). The K-1 second stage will deploy the Active Dispenser mated with its payload into a 200 km circular LEO parking orbit. From this orbit, the Active Dispenser would use its own propulsion to place its payload into the final desired drop-off orbit or earth-escape trajectory. This approach allows Kistler to combine the low-cost launch services offered by the reusable two-stage K-1 with the versatility of a restartable, expendable upper stage. Enhanced with an Active Dispenser, the K-1 will be capable of delivering 1,500 kg to a geosynchronous transfer orbit or up to approximately 1,000 kg into a Mars rendezvous trajectory. The list price of a K-1 Active Dispenser launch is 25 million (plus the price of mission unique integration services) significantly less than the price of any launch vehicle service in the world with comparable capability.

Computational prediction of the spectroscopic parameters of methanediol, an elusive molecule for interstellar detection

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

Barrientos, Carmen; Redondo, Pilar; Largo, Antonio

2014-04-01

The molecular structure of methanediol has been investigated by means of quantum chemical calculations. Two conformers, corresponding to C{sub 2} and C {sub s} symmetries, respectively, were considered. The C{sub 2} conformer is found to lie about 1.7 (at 298 K) or 2.3 (at 0 K) kcal mol{sup –1} below the C {sub s} conformer. Predictions for their rotational constants, vibrational frequencies, IR intensities, and dipole moments have been provided. The lowest-lying isomer has a very low dipole moment, around 0.03 D, whereas the C {sub s} conformer has a relatively high dipole moment, namely, 2.7 D. The barrier formore » the C {sub s} →C{sub 2} process is predicted to be around 0.7-1 kcal mol{sup –1}. Based on the energetic results the proportion of the C{sub s} conformer is likely to be negligible under low temperature conditions, such as in the interstellar medium. Therefore, it is predicted that detection by radioastronomy of methanediol would be rather unlikely.« less

A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

NASA Astrophysics Data System (ADS)

Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

2017-04-01

A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

Acetylcholine receptor gating at extracellular transmembrane domain interface: the "pre-M1" linker.

PubMed

Purohit, Prasad; Auerbach, Anthony

2007-12-01

Charged residues in the beta10-M1 linker region ("pre-M1") are important in the expression and function of neuromuscular acetylcholine receptors (AChRs). The perturbation of a salt bridge between pre-M1 residue R209 and loop 2 residue E45 has been proposed as being a principle event in the AChR gating conformational "wave." We examined the effects of mutations to all five residues in pre-M1 (positions M207-P211) plus E45 in loop 2 in the mouse alpha(1)-subunit. M207, Q208, and P211 mutants caused small (approximately threefold) changes in the gating equilibrium constant (K(eq)), but the changes for R209, L210, and E45 were larger. Of 19 different side chain substitutions at R209 on the wild-type background, only Q, K, and H generated functional channels, with the largest change in K(eq) (67-fold) from R209Q. Various R209 mutants were functional on different E45 backgrounds: H, Q, and K (E45A), H, A, N, and Q (E45R), and K, A, and N (E45L). Phi values for R209 (on the E45A background), L210, and E45 were 0.74, 0.35, and 0.80, respectively. Phi values for R209 on the wt and three other backgrounds could not be estimated because of scatter. The average coupling energy between 209/45 side chains (six different pairs) was only -0.33 kcal/mol (for both alpha subunits, combined). Pre-M1 residues are important for expression of functional channels and participate in gating, but the relatively modest changes in closed- vs. open-state energy caused mutations, the weak coupling energy between these residues and the functional activity of several unmatched-charge pairs are not consistent with the perturbation of a salt bridge between R209 and E45 playing the principle role in gating.

26 CFR 1.401(k)-2 - ADP test.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 5 2013-04-01 2013-04-01 false ADP test. 1.401(k)-2 Section 1.401(k)-2 Internal... TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-2 ADP test. (a) Actual deferral percentage (ADP) test—(1) In general—(i) ADP test formula. A cash or deferred arrangement...

26 CFR 1.401(k)-2 - ADP test.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 5 2010-04-01 2010-04-01 false ADP test. 1.401(k)-2 Section 1.401(k)-2 Internal... TAXES Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-2 ADP test. (a) Actual deferral percentage (ADP) test—(1) In general—(i) ADP test formula. A cash or deferred arrangement satisfies the ADP...

26 CFR 1.401(k)-2 - ADP test.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 5 2014-04-01 2014-04-01 false ADP test. 1.401(k)-2 Section 1.401(k)-2 Internal... TAXES (CONTINUED) Pension, Profit-Sharing, Stock Bonus Plans, Etc. § 1.401(k)-2 ADP test. (a) Actual deferral percentage (ADP) test—(1) In general—(i) ADP test formula. A cash or deferred arrangement...

Influence of a high carbohydrate diet on the functional activity of 5-HT1B/1D receptors on human peripheral blood lymphocytes during intense military training.

PubMed

Chennaoui, Mounir; Drogou, Catherine; Guezennec, Charles-Yannick; Gomez-Merino, Danielle

2006-03-01

The present study was undertaken to examine the effect of a high carbohydrate diet on the functional activity of 5-HT1B/1D receptors in human peripheral blood lymphocytes, and on serum cortisol and plasma cytokine responses during intense military training. Thirty two male soldiers (mean age: 21 +/- 2 years) were randomly assigned to two groups and received either 3200 kcal/24 h [13440 kJ; habitual diet group (HD)] or 4200 kcal/24 h [17640 kJ, high carbohydrate diet group (HCD)] by adding 1000 kcal (4200 kJ) of fruit jelly to the HD. They took part in a three-week training program followed by a five-day combat course. Blood samples were collected from each group before entry into the commando training and after the five-day combat course. The results of [35S] GTPgammaS binding assays showed that h5-HT1B/1D receptors were desensitized after the training program in the HD group, whereas no change was observed between the beginning and the end of the military training in the HCD group [(HD : IC50 = 100 +/- 14 nM to 544 +/- 178 nM; n = 16) and (HCD: IC50 = 68 +/- 14 nM to 101 +/- 22 nM; n = 16)]. Serum cortisol was only significantly increased after the commando training in the HD group (from 532.2 +/- 30 to 642 +/- 45 nmol.L(-1), p < 0.05), whereas values were not significantly changed in the HCD group (441 +/- 31 to 502 +/- 40 nmol.L(-1)). No changes were observed in IL-10, TNF-alpha and IFN-gamma levels after the training program in either group. Carbohydrate ingestion or additional dietary energy during repeated bouts of high-intensity exercise could attenuate the alterations in immune function via 5-HT1B/1D receptors and the action of 5-HT moduline, an endogenous tetrapeptide (Leu-Ser-Ala-Leu) that specifically modulates the sensitivity of 5-HT1B/1D receptors.

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

PubMed

Veljković, Dušan Ž

2018-03-01

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

First evidence for the production of OH radicals by carbonyl oxides in solution phase A DFT investigation

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Kraka, Elfi; Sosa, Carlos

2001-03-01

Dimesitylketone O-oxide ( 1) rearranges in solution to yield the alcohol 2-methylhydroxy-pentamethylbenzophenone ( 5) and dimesitylketone ( 6). DFT-B3LYP/cc-pVTZ calculations reveal that H migration from an o-methyl group to the terminal O atom of the COO unit of 1 rather than the isomerization of 1 is energetically the most favorable process. Calculated activation enthalpies (gas phase: 12.8 kcal/mol; CH 3CN solution: 12.4 kcal/mol) are in excellent agreement with measured activation enthalpies (CFCl 3 solution: 13.2±0.2 kcal/mol; CH 3CN solution: 12.5±0.3 kcal/mol). The hydroperoxide formed by H migration decomposes to a OH and a benzyl radical. Recombination in the solvent cage leads to alcohol 5 while diffusion of OH out of the solvent cage yields 6.

COOMET.QM-K93 (COOMET 615/RU/13): key comparison in the field of measuring of the ethanol amount fraction in nitrogen (120 μmol/mol)

NASA Astrophysics Data System (ADS)

Konopelko, L. A.; Efremova, O. V.; Fatina, O. V.; Orshanskaia, A. A.; Rozhnov, M. S.; Melnyk, D. M.; Petryshyn, P. V.

2016-01-01

The relevance of the COOMET.QM-K93 comparison is founded on paying particular attention to reliability of measurements which are performed during the medical examination of drivers of vehicles in order to assess the degree of alcoholic intoxication. Standard gas mixtures of ethanol in nitrogen in cylinders under pressure play a key role in providing metrological assurance of breath-alcohol analyzers. Participating laboratories: VNIIM and Ukrmetrteststandart. This comparison was carried out in 2014-2015. This supplementary comparison supports CMC claims for: ethanol in the range 50-500 μmol/mol in a matrix of either nitrogen or synthetic air. Results: The results are consistent with the reference values. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Conformations of 1,3,3,5,7,7-Hexamethyl-1,5-diazacyclooctane and Its Bis-BH(3) Adduct. Mono- and Bis-BH(3) Adducts of Di-Tertiary Amines.

PubMed

Livant, P.; Majors, A. W.; Webb, T. R.

1996-05-03

A variable-temperature (1)H- and (13)C-NMR study revealed a conformational equilibrium for 1,3,3,5,7,7-hexamethyl-1,5-diazacyclooctane (4) having DeltaG() = 8.8 +/- 0.6 kcal/mol at 184 K. This activation barrier connects a major and a minor form of 4. Molecular mechanics calculations on 4 led to the conclusion that the major form is a set of twist-chair-chairs interconverting rapidly via the chair-chair and that the minor form is most likely a set of twist-boat-boats interconverting rapidly via the boat-boat. The proximity of the two nitrogen lone pairs in the major form of 4 made plausible the expectation that 4, as well as a related diamine with apposed nitrogens, 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonane (3), might bind a Lewis acid, namely BH(3), using both lone pairs simultaneously and equally. This proved not to be the case: for 3 only the bis-BH(3) adduct was found and for 4 the mono-BH(3) adduct utilized only one nitrogen lone pair. The structure of the bis-BH(3) adduct of 4 (12) was determined by X-ray crystallography to be a twist-boat-boat with BH(3)s cis. Molecular mechanics calculations on 12 were consistent with the solid state conformation found.

The PR-Set7 binding domain of Riz1 is required for the H4K20me1-H3K9me1 trans-tail 'histone code' and Riz1 tumor suppressor function.

PubMed

Congdon, Lauren M; Sims, Jennifer K; Tuzon, Creighton T; Rice, Judd C

2014-04-01

PR-Set7/Set8/KMT5a is the sole histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail 'histone code'. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail 'histone code'. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.

Acylation of Superoxide Dismutase 1 (SOD1) at K122 Governs SOD1-Mediated Inhibition of Mitochondrial Respiration

PubMed Central

Banks, Courtney J.; Rodriguez, Nathan W.; Gashler, Kyle R.; Pandya, Rushika R.; Mortenson, Jeffrey B.; Whited, Matthew D.; Soderblom, Erik J.; Thompson, J. Will; Moseley, M. Arthur; Reddi, Amit R.; Tessem, Jeffery S.; Torres, Matthew P.; Bikman, Benjamin T.

2017-01-01

ABSTRACT In this study, we employed proteomics to identify mechanisms of posttranslational regulation on cell survival signaling proteins. We focused on Cu-Zn superoxide dismutase (SOD1), which protects cells from oxidative stress. We found that acylation of K122 on SOD1, while not impacting SOD1 catalytic activity, suppressed the ability of SOD1 to inhibit mitochondrial metabolism at respiratory complex I. We found that deacylase depletion increased K122 acylation on SOD1, which blocked the suppression of respiration in a K122-dependent manner. In addition, we found that acyl-mimicking mutations at K122 decreased SOD1 accumulation in mitochondria, initially hinting that SOD1 may inhibit respiration directly within the intermembrane space (IMS). However, surprisingly, we found that forcing the K122 acyl mutants into the mitochondria with an IMS-targeting tag did not recover their ability to suppress respiration. Moreover, we found that suppressing or boosting respiration levels toggled SOD1 in or out of the mitochondria, respectively. These findings place SOD1-mediated inhibition of respiration upstream of its mitochondrial localization. Lastly, deletion-rescue experiments show that a respiration-defective mutant of SOD1 is also impaired in its ability to rescue cells from toxicity caused by SOD1 deletion. Together, these data suggest a previously unknown interplay between SOD1 acylation, metabolic regulation, and SOD1-mediated cell survival. PMID:28739857

26 CFR 31.3306(k)-1 - Agricultural labor.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 15 2013-04-01 2013-04-01 false Agricultural labor. 31.3306(k)-1 Section 31.3306(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) EMPLOYMENT... Federal Unemployment Tax Act (Chapter 23, Internal Revenue Code of 1954) § 31.3306(k)-1 Agricultural labor...

26 CFR 31.3306(k)-1 - Agricultural labor.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 15 2014-04-01 2014-04-01 false Agricultural labor. 31.3306(k)-1 Section 31.3306(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) EMPLOYMENT... Federal Unemployment Tax Act (Chapter 23, Internal Revenue Code of 1954) § 31.3306(k)-1 Agricultural labor...

26 CFR 31.3306(k)-1 - Agricultural labor.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 15 2012-04-01 2012-04-01 false Agricultural labor. 31.3306(k)-1 Section 31.3306(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) EMPLOYMENT... Federal Unemployment Tax Act (Chapter 23, Internal Revenue Code of 1954) § 31.3306(k)-1 Agricultural labor...

26 CFR 31.3306(k)-1 - Agricultural labor.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 15 2011-04-01 2011-04-01 false Agricultural labor. 31.3306(k)-1 Section 31.3306(k)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) EMPLOYMENT... Federal Unemployment Tax Act (Chapter 23, Internal Revenue Code of 1954) § 31.3306(k)-1 Agricultural labor...

A compact cryogen-free platform operating at 1 K or 50 mK

NASA Astrophysics Data System (ADS)

Matthews, A. J.; Patton, M.; Marsh, T.; van der Vliet, H.

2018-03-01

We report the design and performance characteristics of a compact cryogen-free platform. The system is based around a continuous 1 K pot which operates using a small (10 m3 h‑1) room temperature circulation pump. The pot cools an experimental plate to ≈ 1.2 K, and has a cooling capacity of 100 mW at a temperature ≈ 1.9 K. Cooling the pot from room temperature to < 2 K takes around 12 hours. The temperature range of the platform can be lowered to < 50 mK with the addition of a small dilution refrigerator, using the 1 K pot as a pre-cooling stage for the circulating 3He. The dilution stage has a typical (continuous) cooling capacity of 30 µW at 100 mK (300 µW at 250 mK) and is designed to operate with just 3 litres of (NTP) 3He.

Mechanical Coupling via the Membrane Fusion SNARE Protein Syntaxin 1A: A Molecular Dynamics Study

PubMed Central

Knecht, Volker; Grubmüller, Helmut

2003-01-01

SNARE trans complexes between membranes likely promote membrane fusion. For the t-SNARE syntaxin 1A involved in synaptic transmission, the secondary structure and bending stiffness of the five-residue juxtamembrane linker is assumed to determine the required mechanical energy transfer from the cytosolic core complex to the membrane. These properties have here been studied by molecular dynamics and annealing simulations for the wild-type and a C-terminal-prolongated mutant within a neutral and an acidic bilayer, suggesting linker stiffnesses above 1.7 but below 50 × 10−3 kcal mol−1 deg−2. The transmembrane helix was found to be tilted by 15° and tightly anchored within the membrane with a stiffness of 4–5 kcal mol−1 Å−2. The linker turned out to be marginally helical and strongly influenced by its lipid environment. Charged lipids increased the helicity and H3 helix tilt stiffness. For the wild type, the linker was seen embedded deeply within the polar region of the bilayer, whereas the prolongation shifted the linker outward. This reduced its helicity and increased its average tilt, thereby presumably reducing fusion efficiency. Our results suggest that partially unstructured linkers provide considerable mechanical coupling; the energy transduced cooperatively by the linkers in a native fusion event is thus estimated to be 3–8 kcal/mol, implying a two-to-five orders of magnitude fusion rate increase. PMID:12609859

Reaction of benzene with atomic carbon: pathways to fulvenallene and the fulvenallenyl radical in extraterrestrial atmospheres and the interstellar medium.

PubMed

da Silva, Gabriel

2014-06-05

The reaction of benzene with ground-state atomic carbon, C((3)P), has been investigated using the G3X-K composite quantum chemical method. A suite of novel energetically favorable pathways that lead to previously unconsidered products are identified. Reaction is initiated by barrierless C atom cycloaddition to benzene on the triplet surface, producing a vibrationally excited [C7H6]* adduct that can dissociate to the cycloheptatrienyl radical (+ H) via a relatively loose transition state 4.4 kcal mol(-1) below the reactant energies. This study also identifies that this reaction adduct can isomerize to generate five-membered ring intermediates that can further dissociate to the global C7H5 minima, the fulvenallenyl radical (+ H), or to c-C5H4 and acetylene, with limiting barriers around 20 and 10 kcal mol(-1) below the reactants, respectively. If intersystem crossing to the singlet surface occurs, isomerization pathways that are lower-yet in energy are available leading to the C7H6 minima fulvenallene, with all barriers over 40 kcal mol(-1) below the reactants. From here further barrierless fragmentation to fulvenallenyl + H can proceed at ca. 25 kcal mol(-1) below the reactants. In the reducing atmospheres of planets like Jupiter and satellites like Titan, where benzene and C((3)P) are both expected, it is proposed that fulvenallene and the fulvenallenyl radical would be the dominant products of the C6H6 + C((3)P) reaction. Fulvenallenyl may also be a significant reaction product under collision-free conditions representative of the interstellar medium, although further work is required here to confirm the identity of the C7H5 radical product.

Final report, ongoing key comparison BIPM.QM-K1, ozone at ambient level, comparison with ISCIII (December 2014)

NASA Astrophysics Data System (ADS)

Viallon, Joële; Moussay, Philippe; Idrees, Faraz; Wielgosz, Robert; Sanchez, Carmen; Morillo Gomez, Pilar

2015-01-01

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the Instituto de Salud Carlos III (ISCIII) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range of 0 nmol/mol to 500 nmol/mol. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Composite thermochemistry of gas phase U(VI)-containing molecules

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

Bross, David H.; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Reaction energies have been calculated for a series of reactions involving UF{sub 6}, UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2} using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with themore » accurately known heat of formation of UF{sub 6} to determine the enthalpies of formation of UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2}. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO{sub 2}F{sub 2} was in excellent agreement with experiment, while the two results obtained for UO{sub 3} were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO{sub 2}(OH){sub 2} is predicted from this work to be −288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of −292.7 ± 6 kcal/mol.« less

4-[(1-Benzyl-1H-1,2,3-triazol-4-yl)meth-oxy]benzene-1,2-dicarbo-nitrile: crystal structure, Hirshfeld surface analysis and energy-minimization calculations.

PubMed

Shamsudin, Norzianah; Tan, Ai Ling; Young, David J; Jotani, Mukesh M; Otero-de-la-Roza, A; Tiekink, Edward R T

2016-04-01

In the solid state, the title compound, C18H13N5O, adopts a conformation whereby the phenyl ring and meth-oxy-benzene-1,2-dicarbo-nitrile residue (r.m.s. deviation of the 12 non-H atoms = 0.041 Å) lie to opposite sides of the central triazolyl ring, forming dihedral angles of 79.30 (13) and 64.59 (10)°, respectively; the dihedral angle between the outer rings is 14.88 (9)°. This conformation is nearly 7 kcal mol(-1) higher in energy than the energy-minimized structure which has a syn disposition of the outer rings, enabling intra-molecular π-π inter-actions. In the crystal, methyl-ene-C-H⋯N(triazol-yl) and carbo-nitrile-N⋯π(benzene) inter-actions lead to supra-molecular chains along the a axis. Supra-molecular layers in the ab plane arise as the chains are connected by benzene-C-H⋯N(carbo-nitrile) inter-actions; layers stack with no directional inter-actions between them. The specified inter-molecular contacts along with other, weaker contributions to the supra-molecular stabilization are analysed in a Hirshfeld surface analysis.

An Ab Initio Study of CuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

Modified coupled-pair functional (MCPF) calculations and coupled cluster singles and doubles calculations, which include a perturbational estimate of the connected triples [CCSD(T)], yield a bent structure for CuCO, thus, supporting the prediction of a nonlinear structure based on density functional (DF) calculations. Our best estimate for the binding energy is 4.9 +/- 1.4 kcal/mol; this is in better agreement with experiment (6.0 +/- 1.2 kcal/mol) than the DF approach which yields a value (19.6 kcal/mol) significantly larger than experiment.

Critical Test of Some Computational Chemistry Methods for Prediction of Gas-Phase Acidities and Basicities.

PubMed

Toomsalu, Eve; Koppel, Ilmar A; Burk, Peeter

2013-09-10

Gas-phase acidities and basicities were calculated for 64 neutral bases (covering the scale from 139.9 kcal/mol to 251.9 kcal/mol) and 53 neutral acids (covering the scale from 299.5 kcal/mol to 411.7 kcal/mol). The following methods were used: AM1, PM3, PM6, PDDG, G2, G2MP2, G3, G3MP2, G4, G4MP2, CBS-QB3, B1B95, B2PLYP, B2PLYPD, B3LYP, B3PW91, B97D, B98, BLYP, BMK, BP86, CAM-B3LYP, HSEh1PBE, M06, M062X, M06HF, M06L, mPW2PLYP, mPW2PLYPD, O3LYP, OLYP, PBE1PBE, PBEPBE, tHCTHhyb, TPSSh, VSXC, X3LYP. The addition of the Grimmes empirical dispersion correction (D) to B2PLYP and mPW2PLYP was evaluated, and it was found that adding this correction gave more-accurate results when considering acidities. Calculations with B3LYP, B97D, BLYP, B2PLYPD, and PBE1PBE methods were carried out with five basis sets (6-311G**, 6-311+G**, TZVP, cc-pVTZ, and aug-cc-pVTZ) to evaluate the effect of basis sets on the accuracy of calculations. It was found that the best basis sets when considering accuracy of results and needed time were 6-311+G** and TZVP. Among semiempirical methods AM1 had the best ability to reproduce experimental acidities and basicities (the mean absolute error (mae) was 7.3 kcal/mol). Among DFT methods the best method considering accuracy, robustness, and computation time was PBE1PBE/6-311+G** (mae = 2.7 kcal/mol). Four Gaussian-type methods (G2, G2MP2, G4, and G4MP2) gave similar results to each other (mae = 2.3 kcal/mol). Gaussian-type methods are quite accurate, but their downside is the relatively long computational time.

A Novel Association and Therapeutic Targeting of Neuropilin-1 and MUC1 in Pancreatic Cancer

DTIC Science & Technology

2013-10-01

1999, 3(4):353-359. 2. Norrby K: In vivo models of angiogenesis. J Cell Mol Med 2006, 10(3):588-612. 3. Besmer DM, Curry JM, Roy LD, Tinder TL...6):669-676. 5. Roy LD, Sahraei M, Subramani DB, Besmer D, Nath S, Tinder TL, Bajaj E, Shanmugam K, Lee YY, Hwang SI et al: MUC1 enhances

G4CEP: A G4 theory modification by including pseudopotential for molecules containing first-, second- and third-row representative elements

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

Silva, Cleuton de Souza; Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Campus de Itacoatiara, 69100-021 Itacoatiara, Amazonas; Pereira, Douglas Henrique

2016-05-28

The G4CEP composite method was developed from the respective G4 all-electron version by considering the implementation of compact effective pseudopotential (CEP). The G3/05 test set was used as reference to benchmark the adaptation by treating in this work atoms and compounds from the first and second periods of the periodic table, as well as representative elements of the third period, comprising 440 thermochemical data. G4CEP has not reached a so high level of accuracy as the G4 all-electron theory. G4CEP presented a mean absolute error around 1.09 kcal mol{sup −1}, while the original method presents a deviation corresponding to 0.83more » kcal mol{sup −1}. The similarity of the optimized molecular geometries between G4 and G4CEP indicates that the core-electron effects and basis set adjustments may be pointed out as a significant factor responsible for the large discrepancies between the pseudopotential results and the experimental data, or even that the all-electron calculations are more efficient either in its formulation or in the cancellation of errors. When the G4CEP mean absolute error (1.09 kcal mol{sup −1}) is compared to 1.29 kcal mol{sup −1} from G3CEP, it does not seem so efficient. However, while the G3CEP uncertainty is ±4.06 kcal mol{sup −1}, the G4CEP deviation is ±2.72 kcal mol{sup −1}. Therefore, the G4CEP theory is considerably more reliable than any previous combination of composite theory and pseudopotential, particularly for enthalpies of formation and electron affinities.« less

Involvement of PI3K/Akt pathway in the inhibition of hepatocarcinoma cell invasion and metastasis induced by SASH1 through downregulating Shh-Gli1 signaling.

PubMed

Sun, Changyu; Zhang, Zhihao; He, Ping; Zhou, Yan; Xie, Xuhua

2017-08-01

The SASH1 gene is discovered as a tumor suppressor recently. However, the molecular mechanisms of SASH1 in hepatocarcinoma (HCC) remain unclear. In present studies, we investigated the molecular mechanisms of SASH1 on cell invasion and metastasis of hepatocarcinoma in vivo and in vitro. In this study, SASH1 overexpression HCC cell lines were treated with purmorphamine (0, 0.5, 1, 2μmol/l). Western blot and qRT-PCR were used to examine the related gene expression of EMT markers and the Shh-Gli1 and PI3K/Akt-dependent pathway. Cell migration and invasion were assessed by Transwell assay. In addition, a mice SASH1 overexpression HCC orthotopic xenograft model was established and treated with purmorphamine or 740Y-P or PDGF. Tumor volume was assessed, and H&E staining was applied to histopathologic analysis. The results showed that purmorphamine exposure significantly increased the mRNA and protein expression levels of Shh and Gli1 in a dose-dependent manner in the SASH1 overexpression HepG2 and HCCLM3 cells. Besides, purmorphamine promoted the migration and invasion of SASH1 overexpression HCC cells, as well as the EMT progress. Moreover, purmorphamine significantly increased the synthesis of PI3K and pAkt in a dose-dependent manner. Furthermore, the invasion and migration abilities were also improved by treatment with 740Y-P or PDGF in the SASH1 overexpression HCC cells. Additionally, the agonists promoted tumor growth and intrahepatic and pulmonary metastasis of the orthotopic transplantation tumors grown from SASH1 overexpression HCC cells in vivo. In conclusion, SASH1 may inhibit hepatocarcinoma cell invasion and metastasis through down-regulating the Shh-Gli1 and PI3K-AKT pathways in vivo and in vitro. Copyright © 2017. Published by Elsevier Ltd.

The protective effect of the EP2 receptor on TGF-β1 induced podocyte injury via the PI3K / Akt signaling pathway

PubMed Central

Zhu, Xue-ling; Chen, Xu; Wu, Jian-hua; Guo, Nai-feng

2018-01-01

Transforming growth factor β1 (TGF-β1) plays a central role in chronic kidney diseases. TGF-β1 induction causes podocyte injury, which results in proteinuria and renal failure. However, the effect of the prostaglandin E2 /E-prostanoid receptor (EP2) on TGF-β1-induced podocyte injury remains unknown. Previous studies have shown that phosphoinositide 3-OH kinase (PI3K)/Akt is widespread in cells, and is vital for the regulation of cell proliferation, differentiation, apoptosis and metabolism. In this study, we cultured immortalized mouse podocytes in vitro in different groups: control group; TGF-β1 (5ng/ml) group; EP2 agonist Butaprost treatment (10−7, 10−6, or 10-5mol/L) +TGF-β1 group; EP2 antagonist AH6809 treatment (10−7, 10−6, or 10-5mol / L) + TGF-β1 group. We found that compared with the control group, proliferation of podocytes in the TGF-β1 group significantly decreased and apoptosis increased. Expression of cAMP decreased, whereas PGE2 increased. Meanwhile, expressions of nephrin, podocin and CD2AP mRNA and protein were dramatically downregulated, activated caspase-3 was increased, and activated PI3K/Akt activity were depressed. Butaprost intervention promoted podocyte proliferation with reduced apoptosis. Conversely, AH6809 intervention led to opposite results (P<0.05). Our findings suggested that EP2 agonist protects podocytes by increasing expression of cAMP, which creates feedback of inhibiting PGE2 expression. This causes the interaction of nephrin, podocin and CD2AP resulting the inhibition of apoptosis induced by activation of the PI3K / Akt signaling pathway. PMID:29746568

Divalent cation and ionic strength effects on Vinca alkaloid-induced tubulin self-association.

PubMed

Lobert, S; Boyd, C A; Correia, J J

1997-01-01

We present here a systematic study of ionic strength and divalent cation effects on Vinca alkaloid-induced tubulin spiral formation. We used sedimentation velocity experiments and quantitative fitting of weight-average sedimentation coefficients versus free drug concentrations to obtain thermodynamic parameters under various solution conditions. The addition of 50-150 mM NaCl to our standard buffer (10 mM piperazine-N,N'-bis(2-ethanesulfonic acid), 1 mM Mg, 50 microM GDP or GTP, pH 6.9) enhances overall vinblastine- or vincristine-induced tubulin self-association. As demonstrated in previous studies, GDP enhances overall self-association more than GTP, although in the presence of salt, GDP enhancement is reduced. For example, in 150 mM NaCl, GDP enhancement is 0.24 kcal/mol for vinblastine and 0.36 kcal/mol for vincristine versus an average enhancement of 0.87 (+/- 0.34) kcal/mol for the same drugs in the absence of salt. Wyman linkage analysis of experiments with vinblastine or vincristine over a range of NaCl concentrations showed a twofold increase in the change in NaCl bound to drug-induced spirals in the presence of GTP compared to GDP. These data indicate that GDP enhancement of Vinca alkaloid-induced tubulin self-association is due in part to electrostatic inhibition in the GTP state. In the absence of NaCl, we found that vinblastine and 1 mM Mn2+ or Ca2+ causes immediate condensation of tubulin. The predominant aggregates observed by electron microscopy are large sheets. This effect was not found with 1 mM Mg2+. At 100 microM cation concentrations (Mn2+, Mg2+, or Ca2+), GDP enhances vinblastine-induced spiral formation by 0.55 (+/- 0.26) kcal/mol. This effect is found only in K2, the association of liganded heterodimers at the ends of growing spirals. There is no GDP enhancement of K1, the binding of drug to heterodimer, although K1 is dependent upon the divalent cation concentration. NaCl diminishes tubulin condensation, probably by inhibiting lateral

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.

Recirculating 1-K-Pot for Pulse-Tube Cryostats

NASA Technical Reports Server (NTRS)

Paine, Christopher T.; Naylor, Bret J.; Prouve, Thomas

2013-01-01

A paper describes a 1-K-pot that works with a commercial pulse tube cooler for astrophysics instrumentation testbeds that require temperatures <1.7 K. Pumped liquid helium-4 cryostats were commonly used to achieve this temperature. However, liquid helium-4 cryostats are being replaced with cryostats using pulse tube coolers. The closed-cycle 1K-pot system for the pulse tube cooler requires a heat exchanger on the pulse tube, a flow restriction, pump-out line, and pump system that recirculates helium-4. The heat exchanger precools and liquefies helium- 4 gas at the 2.5 to 3.5 K pulse tube cold head. This closed-cycle 1-K-pot system was designed to work with commercially available laboratory pulse tube coolers. It was built using common laboratory equipment such as stainless steel tubing and a mechanical pump. The system is self-contained and requires only common wall power to operate. The lift of 15 mW at 1.1 K and base temperature of 0.97 K are provided continuously. The system can be scaled to higher heat lifts of .30 to 50 mW if desired. Ground-based telescopes could use this innovation to improve the efficiency of existing cryo

Octahydriodo diborane (B2H8) and its protonated cations containing five-, six-, and seven-coordinate boron atoms

PubMed Central

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

2012-01-01

Structures of octahydriodo diborane (B2H8) 1 and its protonated 3, diprotonated 5, triprotonated 6, and tetraprotonated 7 ions were found to be calculationally viable minima at the MP2/cc-pVTZ level of theory. Each structure contains two-electron three-center (2e-3c) bonds. The protonation of 1 to form 3 was found to be strongly exothermic by 176.0 kcal/mol. Subsequent protonation of 3 to form 5 was also found to be exothermic by 28.4 kcal/mol. Further protonation of 5 to form 6 was, however, computed to be endothermic by 122.0 kcal/mol whereas protonation of 6 to form 7 was again highly endothermic by 238.8 kcal/mol. Deprotonation barriers of the ions were also computed. PMID:22511715

A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

PubMed

Lv, Jing; Zhang, Jingxue; Wang, Dunyou

2016-02-17

We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices.

PubMed

Lundell, Jan; Olbert-Majkut, Adriana

2015-02-05

The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be+8.0 kJ mol(-1) higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex structures were identified, with the most stable complex structure (T2A) also being the most abundant in the matrices. The difference between experiment and computational energetic order of the two complex structures of the same GA conformer is explained by contributions of deformation energy upon complexation and the effect of the environment. The computed BSSE-corrected interaction energies are for the two most stable complexes of the two GA conformers for T1A and T2A -42.11 and -45.03 kJ mol(-1), respectively, at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory. Copyright © 2013 Elsevier B.V. All rights reserved.

Solvent effects and potential of mean force study of the SN2 reaction of CH3+CN‑ in water

NASA Astrophysics Data System (ADS)

Li, Chen; Liu, Peng; Li, Yongfang; Wang, Dunyou

2018-03-01

We used a combined quantum mechanics and molecular mechanics (QM/MM) method to investigate the solvent effects and potential of mean force of the CH3F+CN‑ reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects’ contributions to the reaction: 1.7 kcal/mol to the activation barrier and ‑26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at ‑43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at ‑39.7 kcal/mol. Project supported by the National Natural Science Foundation of China (Grant No. 11774206) and Taishan Scholarship Fund from Shandong Province, China.

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.

Coupled cluster investigation on the thermochemistry of dimethyl sulphide, dimethyl disulphide and their dissociation products: the problem of the enthalpy of formation of atomic sulphur

NASA Astrophysics Data System (ADS)

Denis, Pablo A.

2014-04-01

By means of coupled cluster theory and correlation consistent basis sets we investigated the thermochemistry of dimethyl sulphide (DMS), dimethyl disulphide (DMDS) and four closely related sulphur-containing molecules: CH3SS, CH3S, CH3SH and CH3CH2SH. For the four closed-shell molecules studied, their enthalpies of formation (EOFs) were derived using bomb calorimetry. We found that the deviation of the EOF with respect to experiment was 0.96, 0.65, 1.24 and 1.29 kcal/mol, for CH3SH, CH3CH2SH, DMS and DMDS, respectively, when ΔHf,0 = 65.6 kcal/mol was utilised (JANAF value). However, if the recently proposed ΔHf,0 = 66.2 kcal/mol was used to estimate EOF, the errors dropped to 0.36, 0.05, 0.64 and 0.09 kcal/mol, respectively. In contrast, for the CH3SS radical, a better agreement with experiment was obtained if the 65.6 kcal/mol value was used. To compare with experiment avoiding the problem of the ΔHf,0 (S), we determined the CH3-S and CH3-SS bond dissociation energies (BDEs) in CH3S and CH3SS. At the coupled cluster with singles doubles and perturbative triples correction level of theory, these values are 48.0 and 71.4 kcal/mol, respectively. The latter BDEs are 1.5 and 1.2 kcal/mol larger than the experimental values. The agreement can be considered to be acceptable if we take into consideration that these two radicals present important challenges when determining their EOFs. It is our hope that this work stimulates new studies which help elucidate the problem of the EOF of atomic sulphur.

The substitution reaction of (CNC)Fe-2N₂ with CO.

PubMed

Liu, Hongyan; Liu, Shuangshuang; Zhang, Xiang

2013-06-01

The substitution mechanism of two N₂ ligands in (CNC)Fe-2N₂ replaced by CO was studied theoretically at the B3LYP/LACVP* level. Both SN1 and SN₂ mechanisms were considered. The calculated results for the gas phase suggested that: 1) in SN1 mechanism, N₂ elimination, which involves S₀-T₁ PESs crossing, is the rate control step for both substitution stages. The barrier heights are 9.7 kcal mol(-1) and 13.05 kcal mol(-1), respectively. 2) In SN2 mechanism, the calculated barrier heights on LS PES are respectively 13.7 and 19.83 kcal mol(-1) for the two substitution steps, but S₀-T₁ PESs crossing lowers the two barriers to 10.7 and 15.7 kcal mol(-1), respectively. 3) Inclusion of solvation effect of THF by PCM model, the relative energies of all the key species (including minima, transition states and S₀-T₁ crossing points) do not have great difference from their gas phase relative energies. Considering that for each substitution step, SN1 barrier heights is slightly smaller than SN2 barrier, SN1 mechanism seems to be slightly preferable to SN2 mechanism.

[Changes of biological behavioral of E. coli K1 after ppk1 gene deletion].

PubMed

Peng, Liang; Pan, Jiayun; Luo, Su; Yang, Zhenghui; Huang, Mufang; Cao, Hong

2014-06-01

To study the changes in biological behaviors of meningitis E. coli K1 strain E44 after deletion of polyphosphate kinase 1 (ppk1) gene and explore the role of ppk1 in the pathogenesis of E. coli K1-induced meningitis. The wild-type strain E. coli K1 and ppk1 deletion mutant were exposed to heat at 56 degrees celsius; for 6 min, and their survival rates were determined. The adhesion and invasion of the bacteria to human brain microvascular endothelial cells (HBMECs) were observed using electron microscopy and quantitative tests. HBMECs were co-incubated with wild-type strain or ppk1 deletion mutant, and the cytoskeleton rearrangement was observed under laser scanning confocal microscope. The survival rate of the ppk1 deletion mutant was significantly lower than that of the wild-type strain after heat exposure. The ppk1 deletion mutant also showed lowered cell adhesion and invasion abilities and weakened ability to induce cytoskeleton rearrangement in HBMECs. ppk1 gene is important for E.coli K1 for heat resistance, cell adhesion and invasion, and for inducing cytoskeletal rearrangement in HBMECs.

The role of KCNQ1/KCNE1 K(+) channels in intestine and pancreas: lessons from the KCNE1 knockout mouse.

PubMed

Warth, R; Garcia Alzamora, M; Kim, J K; Zdebik, A; Nitschke, R; Bleich, M; Gerlach, U; Barhanin, J; Kim, S J

2002-03-01

KCNE1 (IsK, minK) co-assembles with KCNQ1 (KvLQT1) to form voltage-dependent K(+) channels. Both KCNQ1 and KCNE1 are expressed in epithelial cells of gut and exocrine pancreas. We examined the role of KCNQ1/KCNE1 in Cl(-) secretion in small and large intestine and exocrine pancreas using the KCNE1 knockout mouse. Immunofluorescence revealed a similar basolateral localization of KCNQ1 in jejunum and colon of KCNE1 wild-type and knockout mice. Electrogenic Cl(-) secretion in the colon was not affected by gene disruption of KCNE1; in jejunum forskolin-induced short-circuit current was some 40% smaller but without being significantly different. Inhibition of KCNQ1 channels by 293B (IC(50) 1 micromol l(-1)) and by IKS224 (IC(50) 14 nmol l(-1)) strongly diminished intestinal Cl(-) secretion. In exocrine pancreas of wild-type mice, KCNQ1 was predominantly located at the basolateral membrane. In KCNE1 knockout mice, however, the basolateral staining was less pronounced and the distribution of secretory granules was irregular. A slowly activating and 293B-sensitive K(+) current was activated via cholinergic stimulation in pancreatic acinar cells of wild-type mice. In KCNE1 knockout mice this K(+) current was strongly reduced. In conclusion intestinal Cl(-) secretion is independent from KCNE1 but requires KCNQ1. In mouse pancreatic acini KCNQ1 probably co-assembled with KCNE1 leads to a voltage-dependent K(+) current that might be of importance for electrolyte and enzyme secretion.

Interaction Mode between Inclusion Complex of Vitamin K3 with γ- Cyclodextrin and Herring-Sperm DNA.

PubMed

Tang, Yan; Cai, Li; Xue, Kang; Wang, Chunling; Xiong, Xiaoli

2016-05-03

Methods including spectroscopy, electronic chemistry and thermodynamics were used to study the inclusion effect between γ-cyclodextrin (CD) and vitamin K3(K3), as well as the interaction mode between herring-sperm DNA (hsDNA) and γ-CD-K3 inclusion complex. The results from ultraviolet spectroscopic method indicated that VK3 and γ-CD formed 1:1 inclusion complex, with the inclusion constant Kf = 1.02 × 10(4) L/mol, which is based on Benesi-Hildebrand's viewpoint. The outcomes from the probe method and Scatchard methods suggested that the interaction mode between γ-CD-K3 and DNA was a mixture mode, which included intercalation and electrostatic binding effects. The binding constants were K (θ)25°C = 2.16 × 10(4) L/mol, and K(θ)37°C = 1.06 × 10(4) L/mol. The thermodynamic functions of the interaction between γ-CD-K3 and DNA were ΔrHm(θ) = -2.74 × 10(4) J/mol, ΔrSm(θ) = 174.74 J·mol(-1)K(-1), therefore, both ΔrHm(θ) (enthalpy) and ΔrSm(θ) (entropy) worked as driven forces in this action.

Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.

PubMed

Liang, Huiyun; Bourdon, Allen K; Chen, Liao Y; Phelix, Clyde F; Perry, George

2018-06-11

Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K M and high V MAX , specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free energy for β-d-glucose to be -4.6 kcal/mol in agreement with the experimental value of -4.4 kcal/mol ( K M = 1.4 mM). We also compute the hydration energy of β-d-glucose, -18.0 kcal/mol vs the experimental data, -17.8 kcal/mol. In this, we establish a dynamics-based connection from GLUT3's crystal structure to its cellular thermodynamics with quantitative accuracy. We predict equal Arrhenius barriers for glucose uptake and efflux through GLUT3 to be tested in future experiments.

Therapeutic Application of Phage Capsule Depolymerases against K1, K5, and K30 Capsulated E. coli in Mice.

PubMed

Lin, Han; Paff, Matthew L; Molineux, Ian J; Bull, James J

2017-01-01

Capsule depolymerase enzymes offer a promising class of new antibiotics. In vivo studies are encouraging but it is unclear how well this type of phage product will generalize in therapeutics, or whether different depolymerases against the same capsule function similarly. Here, in vivo efficacy was tested using cloned bacteriophage depolymerases against Escherichia coli strains with three different capsule types: K1, K5, and K30. When treating infections with the cognate capsule type in a mouse thigh model, the previously studied K1E depolymerase rescued poorly, whereas K1F, K1H, K5, and K30 depolymerases rescued well. K30 gp41 was identified as the catalytically active protein. In contrast to the in vivo studies, K1E enzyme actively degraded K1 capsule polysaccharide in vitro and sensitized K1 bacteria to serum killing. The only in vitro correlate of poor K1E performance in vivo was that the purified enzyme did not form the expected trimer. K1E appeared as an 18-mer which might limit its in vivo distribution. Overall, depolymerases were easily identified, cloned from phage genomes, and as purified proteins they proved generally effective.

The K1 internal tide simulated by a 1/10° OGCM

NASA Astrophysics Data System (ADS)

Li, Zhuhua; von Storch, Jin-Song; Müller, Malte

2017-05-01

This paper quantifies the K1 internal tide simulated by the 1/10° STORMTIDE model, which simultaneously resolves the eddying general circulation and tides. An evident feature of the K1 internal tide is the critical latitude φc at 30°, which in the STORMTIDE model is characterized by variations from a high energy level equatorward of 30° to a low energy level poleward of 30°. This critical latitude separates the internal tide dynamics into bottom-trapped (at latitudes |φ| > |φc|) and freely propagating (at |φ| < |φc|) motions, respectively. Both types of motions are examined. The bottom-trapping process reveals a gradual vertical decrease of wave energy away from the bottom. The vertical scale, over which the wave energy decrease occurs, is smaller in shallow than in deep water regions. For the freely propagating K1 internal tides, the STORMTIDE model is able to simulate the first three low modes, with the wavelengths ranging from 200-400 km, 100-200 km, to 60-120 km. These wavelength distributions reveal not only a zonal asymmetry but also a poleward increase up to φc, in particular in the Pacific. Such distributions indicate the impact of stratification N and the Coriolis frequency f on the wavelengths. The large wavelength gradient near φc is caused by the wavelength increase from finite values at subcritical latitudes to infinity at φc. Compared to the M2 internal tide, the lower K1 tidal frequency leads to a stronger role of f, hence a weaker effect of N, for the K1 internal tide.

Hydrogen bonding Part 53. Correlation of differential scanning calorimetric data with IR and dissociation vapor pressure studies of transitions of hexamethonium chloride and bromide dihydrates and hexamethonium bromide monohydrate

NASA Astrophysics Data System (ADS)

Snider, Barbara L.; Harmon, Kenneth M.

1994-03-01

Differential scanning calorimetry of hexamethonium chloride dihydrate shows an endothermic transition of 2.70 kcal mol -1 at 36.81°C. This correlates well with the temperatures observed by IR spectra (36°C) and equilibrium dissociation vapor pressure studies (37°C) for the transition between Type I planar cluster and Type II extended linear HOH⋯Cl - hydrogen bonding, and with the value of 2.77 kcal mol -1 for this transition derived by Hess' law treatment of dissociation vapor pressure data. Differential scanning calorimetry of hexamethonium bromide shows a rapid endothermic transition of 2.38 kcal mol -1 at 35.15°C and a very slow endothermic transition of about 12-13 kcal mol -1 centered near 50°C. This latter endotherm corresponds to the transition between Type I and Type II HOH⋯Br - hydrogen bonding observed by IR and vapor pressure studies at 49°C. The nature of the 35.15°C endotherm is not known. Hexamethonium bromide also shows a third endotherm at 142.91°C, which presumably results from melting of hydrate in the sealed DSC cell. Combined analysis of differential scanning calorimetry and dissociation vapor pressure data predicts a value of about -13 kcal mol -1 for an exothermic disproportionation at 52°C of two hexamethonium bromide monohydrate to Type II dihydrate and anhydrous bromide.

Spectral and quantum chemical studies on 1,3-bis(N(1)-4-amino-6-methoxypyrimidinebenzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane and its erbium complex.

PubMed

Al-Mogren, Muneerah M; Alaghaz, Abdel-Nasser M A; El-Gogary, Tarek M

2014-01-24

Novel 1,3-bis(N(1)-4-amino-6-methoxypyrimidine-benzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane (L), was prepared and their coordinating behavior towards the lanthanide ion Er(III) was studied. The structures of the isolated products are proposed based on elemental analyses, IR, UV-VIS., (1)H NMR, (13)C NMR, (31)P NMR, SEM, XRD, mass spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of L and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 17.7 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which compared by the measured electronic spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with ISCIII, March 2017

NASA Astrophysics Data System (ADS)

Viallon, Joële; Moussay, Philippe; Wielgosz, Robert; Sanchez, Carmen; Morillo Gomez, Pilar

2017-01-01

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the Instituto de Salud Carlos III (ISCIII) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range of 0 nmol/mol to 500 nmol/mol. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NPL, April 2017

NASA Astrophysics Data System (ADS)

Viallon, Joële; Idrees, Faraz; Moussay, Philippe; Wielgosz, Robert; Sweeney, Bryan; Quincey, Paul

2018-01-01