Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

On the flexibility of beta-peptides

The full conformational space was explored for an achiral and two chiral beta-peptide models: namely For-beta-Ala-NH2, For-beta-Abu-NH2, and For-beta-Aib-NH2. Stability and conformational properties of all three model systems were computed at different levels of theory: RHF/3-21G, B3LYP/6-311++G(d,p)//RHF/3-21G, B3LYP/6-311++G(d,p), MP2//B3LYP/6-311++G(d,p), CCSD//B3LYP/6-311++G(d,p), and CCSD(T)//B3LYP/6-311++G(d,p). In addition, ab initio E = E(phi, micro, psi) potential energy hypersurfaces of all three models were determined, and their topologies were analyzed to determine the inherent flexibility properties of these beta-peptide models. Fewer points were found and assigned than expected on the basis of Multidimensional Conformational Analysis (MDCA). Furthermore, it has been demonstrated, that the four-dimensional surface, E = E(phi, mu, psi), can be reduced into a three-dimensional one: E = E[phi, f(phi), psi]. This reduction of dimensionality of freedom of motion suggests that beta-peptides are less flexible than one would have thought. This agrees with experimental data published on the conformational properties of peptides composed of beta-amino acid residues.     

甲醛与乙腈相互作用的理论研究

在HF/6-311G(d,p)、 MP2/6-311G(d,p)和B3LYP/6-311G(d,p)水平上,对H2CO和CH3CN以及设计的4种结构H2CO…CH3CN复合物等进行几何全优化和振动频率计算,排除振动频率为负值的非局域极小点结构,并对稳定的环状构型复合物结合能进行基组重叠误差校正和零点振动能校正.分子间相互作用的能量分解分析显示,静电能在H2CO...CH3CN相互作用能量中占主导地位,电荷转移能居第二位.     

Effect of dimerization and racemization processes on the electron density and the optical rotatory power of hydrogen peroxide derivatives

The variation of the electron density properties and optical rotatory power of the monomers and dimers of seven monosubstituted hydrogen peroxide derivatives, HOOX (X = CCH, CH(3), CF(3), t-Bu, CN, F, Cl), upon racemization has been studied using DFT (B3LYP/6-31+G) and MP2 (MP2/6-311+G) methods. The geometrical results have been rationalized on the basis of natural bond orbital (NBO) analysis. The atomic partition of the electron density properties within the atoms in molecules (AIM) methodology has allowed investigating the energy and charge redistribution in the different structures considered. The calculated optical rotatory power (ORP) of the dimers are, in general, twice of the values obtained for the monomers.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.     

Structure and energetics of water-silanol binding on the surface of silicalite-1: quantum chemical calculations

Quantum mechanical calculations have been carried out to investigate the structural properties and the interaction between water molecules and silanol groups on the surface of silicalite-1. The (010) surface, which is perpendicular to the straight channel, has been selected and represented by three fragments taken from different parts of the surface. Calculations have been performed using different levels of accuracy: HF/6-31G(d,p), B3LYP/6-31G(d,p), HF/6-31++G(d,p), and B3LYP/6-31++G(d,p). The basis set superposition error has been taken into account. The geometry of the silanol groups and that of the water molecules have been fully optimized. The results show that the most stable conformation takes place when a water molecule forms two hydrogen bonds with two silanols, with only one silanol lying on the opening of the pore of the straight channel. The corresponding binding energy is -48.82 kJ/mol. These areas are supposed to be the first binding sites which have to be covered when the water molecule approaches the surface. When the water loading increases, the next favorable silanols are those of the opening of the pore in which the four possible complex conformations yield a binding energy between -25.62 and -37.41 kJ/mol. It was also found that the calculated O-H bond length of the silanol in the free form was slightly shorter than that in the complex. In terms of the stretching frequency, the complexation leads to a red shift of the O-H stretching of the silanol group.     

Computational and experimental studies of the effect of substituents on the singlet-triplet energy gap in phenyl(carbomethoxy)carbene

The effect of aromatic substitution on the singlet-triplet energy gap in substituted phenyl(carbomethoxy)carbene (X-Ph-C-CO(2)CH(3), PCC) has been explored by time-resolved infrared (TRIR) spectroscopy and gas-phase computational methods. The ground state of para-substituted PCC is calculated to change from the triplet state in p-NO(2)-PCC (Delta G(ST) = 6.1 kcal/mol) to the singlet state in p-NH(2)-PCC (Delta G(ST) = -2.8 kcal/mol). The absence of solvent perturbation in the TRIR spectra of p-N(CH(3))(2)-PCC (which should have electronic properties similar to p-NH(2)-PCC) and parent PCC is consistent with their ground states lying > +/-2 kcal/mol from the next available electronic state, in line with the computational results. The observation of solvent perturbation in the TRIR spectra of p-OCH(3)-PCC and p-CH(3)-PCC implies that their ground states lie < +/-1 kcal/mol from their next available electronic state. This is in agreement with our computational results, which predict a gas-phase Delta G(ST) of -0.8 and 1.6 kcal/mol for p-OCH(3)-PCC and p-CH(3)-PCC as compared to Delta G(ST) values of -3.9 and -1.3 kcal/mol from polarizable continuum model (PCM) calculations with acetonitrile as a solvent. Gas-phase computational results for the meta- and ortho-substituted PCC species are also presented, along with selected linear free energy (LFE) relationships for the para and meta species.     

Gas-phase structures of acetyl peroxynitrate and trifluoroacetyl peroxynitrate

The molecular structures and conformational properties of acetyl peroxynitrate (PAN, CH3C(O)OONO2) and trifluoroacetyl peroxynitrate (FPAN, CF3C(O)OONO2) were investigated in the gas phase by electron diffraction (GED), microwave spectroscopy (MW), and quantum chemical methods (HF/3-21G, HF/6-31G*, MP2/6-31G*, B3PW91/6-31G*, and B3PW91/6-311+G*). All experimental and theoretical methods show the syn conformer (C=O bond of acetyl group syn to O-O bond) to be strongly predominant relative to the anti conformer. The O-NO2 bonds are extremely long, 1.492(7) A in PAN and 1.526(10) A in FPAN, which correlates with their low bond energy and the easy formation of CX3C(O)OO* and *NO2 radicals in the atmosphere. The O-O bonds (1.418(12) A in PAN and 1.408(8) A in FPAN) are shorter than that in hydrogen peroxide (1.464 A). In both compounds the C-O-O-N dihedral angle is close to 85 degrees.     

Aromaticity and antiaromaticity in fulvenes, ketocyclopolyenes, fulvenones, and diazocyclopolyenes

The structures, energies, natural charges, and magnetic properties of 3-, 5-, 7-, and 9-membered cyclic polyenes 1-4, respectively, with exocyclic methylene, keto, ketenyl, and diazo substituents (a-d, respectively) were computed at the B3LYP/6-311G+ **//B3LYP/6-311+G** level to elucidate their aromatic and antiaromatic properties. The corresponding conjugated cyclic cations le and 3e were also studied. The criteria used are isomerization energies (ISE), magnetic susceptibility exaltations (lambda), aromatic stabilization energies (ASE), nucleus independent chemical shifts (NICS), and bond length alternation (deltaR). Planar C2v structures were found to be the lowest energy minima with the exceptions of diazocyclopropene (1d), cycloheptafulvenone (3c), diazocycloheptatriene (3d), and all of the cyclononatetraene derivatives (4). The fulvenes (1a-4a) have modest aromatic or antiaromatic character, and are used as standards for comparison. By these criteria the ketenylidene and diazo cyclopropenes and cycloheptatrienes 1,3-c,d and oxo cyclopentadiene and cyclononatetraene 2,4b are antiaromatic, while the 5- and 9-ring ketenyl and diazo compounds and 3- and 7-ring ketones are aromatic. The degree of aromatic/antiaromatic character decreases with ring size. The consistent agreement with Hückel rule predictions for all the criteria shows their utility for the evaluation of the elusive properties of aromaticity and antiaromaticity.     

Analysis of interfacial and micellar behavior of sodium dioctyl sulphosuccinate salt (AOT) with zwitterionic surfactants in aqueous media

The interfacial and bulk properties of mixtures of the anionic surfactant (dioctyl sulphosuccinate sodium salt, AOT) with zwitterionic surfactants 3-(N,N-dimethyldodecylammonio) propane sulfonate (DPS), 3-(N,N-dimethyltetradecylammonio) propane sulfonate (TPS), 3-(N,N-dimethylhexadecylammonio) propane sulfonate (HPS) have been studied employing surface tension, fluorescence, and viscometric techniques in aqueous media at 25 °C. It is observed that these mixtures exhibit synergism and these synergistic interactions increase with the enhancement of the hydrocarbon chain of the zwitterionic surfactant. The various physicochemical properties such as critical micelle concentration (cmc), surface excess concentration (Г(max)), minimum area per molecule (A(min)), aggregation number (N(agg)), interaction parameters (β(σ), β(m)), and thermodynamic parameters such as standard Gibbs free energy of adsorption (ΔG(ads)(o)), excess free energy of micellization (ΔG(ex)), and standard Gibbs free energy of micellization (ΔG(m)(o)) have been evaluated. The negative values of ΔG(m)(o) and ΔG(ads)(o) show that the micelle formation and adsorption of surfactant at the air/solution interface is energetically favorable, while a negative value of ΔG(ex) ensures stability of the mixed micelles formed. The Regular Solution Approximation, Motomura and Rosen's approaches have been used to explain and compare the results. The packing parameter (p) ensures the formation of vesicles or bilayers for AOT+DPS/TPS mixtures, which can potentially be used as delivery agents for industrial applications.     

Ab initio and density functional theory studies of the structure,gas-phase acidity and aromaticity of tetraselenosquaric acid

Results of ab initio self-consistent-field (SCF) and density functional theory (DFT) calculations of the gas-phase structure,acidity (free energy of deprotonation,G0) and aro-maticity of tetraselenosquaric acid (3,4-diselenyl-3-cy-dobutene-1,2-diselenone,H2C4Se4) are reported.The global minimum found on the potential energy surface of tetraselenosquaric acid presents a planar conformation.The ZZ iso-mer was found to have the lowest energy among the three planar conformers and the ZZ and ZE isomers are very dose in energy.The optimized geometric parameters exhibit a bond length equalization relative to reference compounds,cyclobu-tanediselenone,and cydobutenediselenol.The computed aromatic stabilization energy (ASE) by homodesmotic reaction is -77.4 (MP2(fu)/6 - 311 G //RHF/6 - 311 G) and - 54.8 kJ/mol (B3LYP/6 - 311 G //B3LYP/6 -311 G).The aromaticity of tetraselenosquaric add is indicated by the calculated diamagnetic susceptibility exaltation (A) - 19.13 (CSGT(IGAEM) - RHF/6 - 311 G// RHF/6-     

Theoretical study of the reactions of CF3OCHF2 with the hydroxyl radical and the chlorine atom.

Theoretical investigations are carried out on the reaction mechanism of the reactions of CF3OCHF2 (HFOC-125) with the OH radials and Cl atoms, as well as the heats of formation of CF3OCHF2 and CF3OCF2. The electronic structure information on the potential energy surface for each reaction is obtained at the B3LYP/6-311G(d,p) level, and energetic information is further refined by G3(MP2) theory. The direct dynamics calculation of the hydrogen abstraction reactions are also performed at the G3(MP2)//B3LYP/ 6-311G(d,p) level. The classical energy profile is corrected by interpolated single-point energies (ISPE) approach, incorporating the small-curvature tunnelling effect (SCT) calculated by the variational transition-state theory (VTST). The rate constants are in good agreement with the experimental data and are found to be k1 = 4.95 x 10(-30)T(5.40)exp(-347/T) and k2 = 1.86 x 10(-23)T(3.43)exp(-1579/T) cm3 molecule(-1)s(-1) over the temperature range 200-2000 K. The rate constants at 298 K for these two reactions are 3.38 x 10(-16) and 2.80 x 10(-17) cm3 molecule(-1)s(-1), respectively. Using group-balanced isodesmic reactions as working chemical reactions, the standard enthalpies of formation for CF3OCHF2 and CF3OCF2 are -312.3 +/- 1.0 and -257.3 +/- 1.0 kcalmol(-1), respectively, evaluated by G3(MP2) theory based on the B3LYP/6-311G(d,p) geometries. The theoretical studies provide rate constants of the title reactions and the enthalpies of the species, which are important parameters in determining the atmospheric lifetime and the feasible pathways for the loss of HFOC-125.     

低硝酸盐离子N2O22-和亚硝酸HONO的异构体及其异构化反应的量化研究

采用Gaussian-98程序进行，在HF／6—31G(d)，B3LYP／6—31G(d)和MP2／6—31G(d)水平下优化分子结构并寻找过渡态，对于MP2／6—31G(d)结果在QCISD(T，E4T)，MP4／6—311 G(d，p)，MP4／6—311 G(2df，p)水平下重新计算能级．并用内禀反应坐标(IRC)法研究了N2O2^2-和亚硝酸HONO的异构化反应机理。     

On the structure and relative stability of C50 fullerenes

The complete set of 271 classical fullerene isomers of C50 has been studied by full geometry optimizations at the SAM1, PM3, AM1, and MNDO quantum-chemical levels, and their lower energy structures have also been partially computed at the ab initio levels of theory. A D(5h) species, with the least number of pentagon adjacency, is predicted by all semiempirical methods and the HF/4-31G calculations as the lowest energy structure, but the B3LYP/6-31G* geometry optimizations favor a D3 structure (with the largest HOMO-LUMO gap and the second least number of adjacent pentagons) energetically lower (-2 kcal/mol) than the D(5h) isomer. To clarify the relative stabilities at elevated temperatures, the entropy contributions are taken into account on the basis of the Gibbs energy at the HF/4-31G level for the first time. The computed relative-stability interchanges show that the D3 isomer behaves more thermodynamically stable than the D(5h) species within a wide temperature interval related to fullerene formation. According to a newly reported experimental observation, the structural/energetic properties and relative stabilities of both critical isomers (D(5h) and D3) are analyzed along with the experimentally identified decachlorofullerene C50Cl10 of D(5h) symmetry. Some features of higher symmetry C50 nanotube-type isomers are also discussed.     

1,3,5-三硝基苯在高岭石表面吸附的理论研究

构造了高岭石硅氧层和铝氧层的团簇模型(分别为Si₁₃O₃₇H₂₂和Al₆O₂₄H₃₀), 并分别在B3LYP/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d)和B3LYP/6-311++G(d,p)//B3LYP/6-31G(d)理论水平上对1,3,5-三硝基苯(TNB)在高岭石表面的吸附性质(如优化的几何构型、 结构参数、 吸附能、 振动频率、 静电势和分子轨道等)进行了研究. 结果表明, TNB和硅氧层表面间的相互作用以静电和范德华相互作用为主; TNB与铝氧层间的相互作用以氢键为主, 且TNB和铝氧层间相互作用的能量更低, 结构更稳定.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

Conformational studies in the cyclohexane series. 2. Phenylcyclohexane and 1-methyl-1-phenylcyclohexane

The structures and relative energies of the conformers of phenylcyclohexane, and 1-methyl-1-phenylcyclohexane have been calculated at theoretical levels including HF/6-31G, B3LYP/6-311G, MP2/6-311G, MP2/6-311(2df,p), QCISD/6-311G, and QCISD/6-311G(2df,p). The latter gives conformational enthalpy (DeltaH degrees ), entropy (DeltaS degrees ), and free energy (DeltaG degrees ) values for phenylcyclohexane that are in excellent agreement with the experimental data. The calculations for 1-methyl-1-phenylcyclohexane find a free energy difference of 1.0 kcal/mol at -100 degrees C, favoring the conformation having an axial phenyl group, that is in only modest agreement with the experimental value of 0.32 +/- 0.04 kcal/mol. The origin of the phenyl rotational profiles for the conformers of phenylcyclohexane and 1-methyl-1-phenylcyclohexane is discussed.