Molecular Dipole Moment Computed with Ab Initio MKS Charges

1 INTRODUCTION Dipole moment (DM) can be measured by a variety of experimental methods[1] or computed with atomic charge distribution directly derived from molecular orbital calculations[2~10]. The average errors in DM computed with AM1, PM3 and MNDO methods for 125 organic compounds are 0.35 D, 0.45 D and 0.45 D, respectively[2]. Feller et al. reported that the average errors in the computed DM at the HF level are 0.65 D, 0.49 D and 0.30 D with the basis set STO-3G, 3-21G and…     

On the keto-enol tautomerization of malonaldehyde: an effective fragment potential study

Recent studies have mapped the keto-enol tautomerization of malonaldehyde through a general transition structure that leads exclusively to the Z isomer of the enol. However, it will be shown that a competing general transition structure exists that leads to both the E and Z isomers of the enol at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels of theory. Both the RHF- and DFT-based effective fragment potential methods have been used to model solvation effects, and the results are compared with full ab initio calculations. It is found that two bridging water molecules with two discrete DFT-based effective fragment potential solvent waters at the MP2/6-31G(d,p) level of ab initio theory provides the most computationally effective model for solvent effects in this system. It is shown that the relative energies for this QM/MM model differ from the full MP2/6-31G(d,p) energies by an average absolute relative difference of 2.2 kcal mol-1 across the reaction path when the zero-point vibrational energy correction is included.     

Theoretical studies on electron delocalisation in selenourea

Ab initio and density functional calculations have been performed on the different possible structures of selenourea(su), urea(u) and thiourea(tu) to understand the extent of delocalisation in selenourea in comparison to urea and thiourea. Selenourea(su-1) withC ₂ symmetry has the minima on the potential energy surface at MP2(fu)/6-31+G* level. The C-N rotational barrier in selenourea is 8.69 kcal/mol, which is 0.29 and 0.11 kcal/mol more than that of urea and thiourea respectively at MP2(fu)/6-31+G* level. N-inversion barrier is 0.55 kcal/mol at MP2(fu)6-31+G* level. NBO analysis has been carried out to understand the nature of different interactions responsible for the electron delocalisation.     

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.     

The remarkably invariant interaction energies of lithium first-row compounds with water and with ammonia

Solvation energies of lithium first-row compounds LiX (X ? H, Li, BeH, BH₂, CH₃, NH₂, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6-31 + G^*//6-31G^* with zero-point vibrational energy corrections at 3-21G//3-21G). The solvation energies are found to be remarkably constant: ?18.0 ± 1.2 and ?21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (?14.3 and ?17.8 kcal/mol, respectively) are due to the polarizability of Li₂. At the same level, the lithium cation has interaction energies with H₂O and NH₃ of ?34.1 and ?39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.     

Theoretical studies on the conformations of selenamides

Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe-NH₂ to estimate the Se-N rotational barriers and N-inversion barriers. Two conformers have been found withsyn andanti arrangement of the NH₂ hydrogens with respect to Se-H bond. The N inversion barriers in selenamide are 1.65, 2.47, 1.93 kcal/mol and the Se-N rotational barriers are 6.58, 6.56 and 6.12 kcal/mol respectively at HF/6-31+G*, MP2/6-31+G* and B3LYP/6-31+G* levels respectively. The n_N →Σ *_Se-H negative hyperconjugation is found to be responsible for the higher rotational barriers.     

Methyl and trifluoromethyl vinyl sulfoxides. Steric and electronic structure

Potential functions of internal rotation about the $C_{sp^2 } $ -S bond in H₂C=CHSOCY₃ (Y = H or F) were determined and stationary points were identified by vibrational analysis at the MP2(full)/6-31+G(d), B3PW91/6-31+G(d), and B3PW91/6-311+G(3df,p) levels. Energetically favorable conformations were established, and rotation barriers and molecular geometry parameters were evaluated. Wave functions [MP2(full)/6-31+G(d)] were analyzed by the NBO method. Energies and dipole moments of bond and lone-pair orbitals, principal types of donor-acceptor interactions, bond orders, and atomic charges were determined.     

Determination of the ground- and excited-state dipole moments of 4’-(hexyloxy)-4-biphenylcarbonitrile and 4-isothiocyanatophenyl 4-pentylbicyclo [2,2,2] octane-1-carboxylate nematic liquid crystals and their mixtures

The dipole moments of the ground and excited states of 4′-(hexyloxy)-4-biphenylcarbonitrile and 4-isothiocyanatophenyl 4-pentylbicyclo [2.2.2] octane-1-carboxylate nematic liquid crystals and their mixtures prepared in chloroform and dichloromethane were studied at room temperature. The dipole moments of the ground states of the all samples were calculated according to the Guggenheim–Smith method. The dipole moments of their excited states were determined with the help of the Lippert equation by measuring the absorption and fluorescence spectra, solvent polarity and refractive index values. It was determined that dipole moments of the excited states were higher than those of the ground states. Moreover, the dipole moments of the ground and excited states of two nematic liquid crystals were also estimated by using molecular mechanic method (Gaussian09 program (DFT/B3LYP 6-31G(dp)). The results obtained are interpreted in detail.     

Thermolysis of alkyl sulfoxides and derivatives: a comparison of experiment and theory.

Gas-phase activation data were obtained for model sulfoxide elimination reactions. The activation enthalpy for methyl 3-phenylpropyl sulfoxide is 32.9 +/- 0.9 kcal/mol. Elimination by methyl vinyl sulfoxide to form acetylene has an enthalpic barrier of 41.6 +/- 0.8 kcal/mol and that of 3-phenylpropyl methanesulfinate to form hydrocinnamaldehyde is 34.6 +/- 0.6 kcal/mol. Calculations at the MP2/6-311+G(3df,2p)//MP2/6-31G(d,p) level for simplified models of these reactions provide barriers of 32.3, 40.3, and 32.7 kcal/mol, respectively. A series of other compounds are examined computationally, and it is shown that the substituent effects on the sulfoxide elimination reaction are much more straightforward to interpret if DeltaH data are available in addition to the usually determined DeltaH++. The activation enthalpy of the reverse addition reaction is also subject to structural variation and can usually be rationalized on the basis of nucleophilicity of the sulfur or polarity matching between the sulfenic acid and olefin derivative.     

Reactivity of alkyl versus silyl peroxides. The consequences of 1, 2-silicon bridging on the epoxidation of alkenes with silyl hydroperoxides and bis(trialkylsilyl)peroxides

The bond dissociation energies for a series of silyl peroxides have been calculated at the G2 and CBS-Q levels of theory. A comparison is made with the O-O BDE of the corresponding dialkyl peroxides, and the effect of the O-O bond strength on the activation barrier for oxygen atom transfer is discussed. The O-O bond dissociation enthalpies (DeltaH(298)) for bis (trimethylsilyl) peroxide (1) and trimethylsilyl hydroperoxide (2) are 54.8 and 53.1 kcal/mol, respectively at the G2 (MP2) and CBS-Q levels of theory. The O-O bond dissociation energies computed at G2 and G2(MP2) levels for bis(tert-butyl) peroxide and tert-butyl hydroperoxide are 45.2 and 48.3 kcal/mol, respectively. The barrier height for 1,2-methyl migration from silicon to oxygen in trimethylsilyl hydroperoxide is 47.9 kcal/mol (MP4//MP2/6-31G). The activation energy for the oxidation of trimethylamine to its N-oxide by bis(trimethylsilyl) peroxide is 28.2 kcal/mol (B3LYP/6-311+G(3df,2p)// B3LYP/6-31G(d)). 1,2-Silicon bridging in the transition state for oxygen atom transfer to a nucleophilic amine results in a significant reduction in the barrier height. The barrier for the epoxidation of E-2-butene with bis(dimethyl(trifluoromethyl))silyl peroxide is 25.8 kcal/mol; a reduction of 7.5 kcal/mol relative to epoxidation with 1. The activation energy calculated for the epoxidation of E-2-butene with F(3)SiOOSiF(3) is reduced to only 2.2 kcal/mol reflecting the inductive effect of the electronegative fluorine atoms.     

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.     

HNNH3的从头计算研究

Ab-Initio studies applying the 3-21G, 6-31G and 6-31G** basis sets and also including the MP2 correction were carried out on H2NNH2, HNNH3 and the transition state molecule of the reaction H2NNH2=HNNH3. First, the geometry of the three molecules was optimized using the theoretical methods mentioned in the Hartree-Fock(HF) scheme. The energies of the molecules corresponding to RHF/6-31 G** geometries were subsequently calculated including electron correlation effects at the level of the second-order Moller-Plesset(MP2) perturbation theory. The vibrational frequencies, net charges and dipole moments were obtained from the theoretical calculations. The results of our ab-initio calculations indicate unambiguously that H2NNH2 is thermodynamically more stable than HNNH3. On the other hand, an isolated HNNH3 molecule once created would be rather stable since barriers for its unimolecular isomerization and decomposition are relatively high. Nevertheless, HNNH3 can be considered as an intermediate in chemical processes involving N2H4. This assumption has been supported by further calculation at higher level of theory.     

Ab initio studies on the mechanism of the size-dependent hydrogen-loss reaction in Mg+(H2O)n

The mechanism of size-dependent intracluster hydrogen loss in the cluster ions Mg(+)(H(2)O)(n), which is switched on around n=6, and off around n=14, was studied by ab initio calculations at the MP2/6-31G* and MP2/6-31G** levels for n=1-6. The reaction proceeds by Mg(+)-assisted breaking of an H-O bond in one of the H(2)O molecules. The reaction barrier is dependent on both the cluster size and the solvation structure. As n increases from 1 to 6, there is a dramatic drop in the reaction barrier, from greater than 70 kcal mol(-1) for n=1 to less than 10 kcal mol(-1) for n=6. In the transition structures, the Mg atom is close to the oxidation state of +2, and H(2)O molecules in the first solvation shell are much more effective in stabilizing the transition structures and lowering the reaction barriers than H(2)O molecules in the other solvation shells. While the reaction barrier for trimer core structures with only three H(2)O molecules in the first shell is greater than 24 kcal mol(-1), even for Mg(+)(H(2)O)(6), it drops considerably for clusters with four-six H(2)O molecules in the first shell. The more highly coordinated complexes have comparable or slightly higher energy than the trimer core structures, and the presence of such high coordination number complexes is the underlying kinetic factor for the switching on of the hydrogen-loss reaction around n=6. For clusters with trimer core structures, the hydrogen loss reaction is much easier when it is preceded by an isomerization step that increases the coordination number around Mg(+). Delocalization of the electron on the singly occupied molecular orbital (SOMO) away from the Mg(+) ion is observed for the hexamer core structure, while at the same time this isomer is the most reactive for the hydrogen-loss reaction, with an energy barrier of only 2.7 kcal mol(-1) at the MP2/6-31G** level.     

Allylic hydrogen abstraction II. H-abstraction from 1,4 type polyalkenes as a model for free radical trapping by polyunsaturated fatty acids (PUFAs)

Unsaturated radicals, containing different number of delocalized electrons, are formed via H-atom abstractions with CH(3), iso-C(3)H(7), OOH and OH radicals from (Z,Z) and (E,E)-hepta-2,5-dienes. These reactions and the relative stability of the different allyl-type radicals formed, were studied within the BH&HLYP method, using a 6-311+G(3df,2p) basis set, as well as within the G3MP2 level of theory on BH&HLYP/6-31G(d) geometries. The biallyl type radicals (involving 5 electrons delocalized on 5 carbon atoms) are more stable, by about 47.6 +/- 0.4 kJ mol(-1), than monoallyl type radicals (which involve 3 electrons delocalized on 3 carbon atoms). Three types of the H-atom abstractions were distinguished: direct H-abstraction with CH(3), indirect abstraction with a higher barrier height with iso-C(3)H(7), OOH and a non-direct quasi-barrierless H-abstraction with OH radicals. These observations were also confirmed by the activation entropy versus activation enthalpy as well as the Evans-Polányi's plots. The OOH-hepta-2,5-diene complexes are found to be extremely stable (from -19.6 to 22.3 kJ mol(-1)). The room temperature rate constants were calculated with transition state theory. Formations of monoallyl and biallyl radicals through H-abstraction with OH are fast; the calculated rate constants range from 5.84 x 10(-11) to 1.92 x 10(-9) cm(3) molecule(-1) s(-1) at room temperature. These reactions may play a key role in the "very low temperature combustion" like biological oxidations.     

Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of diazomethane to ethene

The electronic mechanism for the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane (CH2N2) to ethene (C2H4) is described through spin-coupled (SC) calculations at a sequence of geometries along the intrinsic reaction coordinate obtained at the MP2/6-31G(d) level of theory. It is shown that the bonding rearrangements occurring during the course of this reaction follow a heterolytic pattern, characterized by the movement of three well-identifiable orbital pairs, which are initially responsible for the pi bond in ethene and the C-N pi bond and one of the N-N pi bonds in diazomethane and are retained throughout the entire reaction path from reactants to product. Taken together with our previous SC study of the electronic mechanism of the 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne (C2H2) (Theor. Chim. Acc. 1998, 100, 222), the results of the present work suggest strongly that most gas-phase concerted 1,3-dipolar cycloaddition reactions can be expected to follow a heterolytic mechanism of this type, which does not involve an aromatic transition state. The more conventional aspects of the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane to ethene, including optimized transition structure geometry, electronic activation energy, activation barrier corrected for zero-point energies, standard enthalpy, entropy and Gibbs free energy of activation, have been calculated at the HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p), QCISD/6-31G(d) and CCD/6-31G(d) levels of theory. We also report the CCD/6-311++G(2d, 2p)//CCD/6-31G(d), MP4(SDTQ)/6-311++G(2d,2p)//CCD/6-31G(d) and CCSD(T)/6-311++G(2d, 2p)//CCD/6-31G(d) electronic activation energies.     

Molecular structure of 6-(N,N-dimethylamino)fulvene from a joint gas-phase electron diffraction and quantum-chemical study

The molecular structure of 6-(N,N-dimethylamino)fulvene was studied by gas-phase electron diffraction and quantum-chemical methods (HF/6-31G(d), MP2/3Z, MP2/4Z, density functional theory with the B3LYP/6-31G(d) and PBE/3Z functionals). Pronounced flattening of the nitrogen atom and equalization of the intracyclic C—C bonds were found to be a consequence of the electron delocalization in the molecule.     

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases

The strongest gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass. Our calculations reveal that the stacking interactions of adducts for a given nucleobase are dependent on the methylation site (by up to 20 kJ mol(-1)), where the relative magnitudes of the interactions are determined by the dipole moments of the adducts and the proton affinities of nucleobase methylation sites. Nevertheless, the differences in the (gas-phase) stacking of methylated adducts are small compared with the differences between the stacking of the corresponding natural and methylated nucleobases. Indeed, methylation increases the stacking energy by up to 40 kJ mol(-1) (or 135%). Although immersing the dimers in different solvents decreases the gas-phase stacking energies with an increase in the polarity of the environment, base methylation still has a significant effect on the nucleobase stacking ability in solvents with large dipole moments, and, perhaps more importantly, environments that mimic enzyme active sites. Our results shed light on the workings of DNA repairs enzymes that selectively remove a wide variety of alkylated nucleobases over the natural bases.     

DFT Study of Solvent Effects for Some Organic Molecules Using a Polarizable Continuum Model

Forty ionic molecules are studied by DFT (B3LYP, B3P86), MP4 with different basis sets using the PCM/UAHF model within the self-consistent reaction-field method to assess solvent effects. For these molecules, the solvation free energies (ΔG _sol) in water and the dipole moments in vacuoas well as in water are obtained. By comparing the calculated values of ΔG _sol with experimental values and molecular simulation results, it is found that the ΔG _sol values generated by the DFT method are in better agreement with experimental values. Moreover, especially for the B3LYP/6-31+G_∗ level, the results of both ΔG _sol and dipole moments are more accurate considering the lower computational cost. It can be noted that the dipole moments of solutes in water show some increase relative to those in vacuo.     

双自由基CF2与O3的反应机理

主要用作致冷剂和发泡剂的氯氟烃（CFCs）是破坏臭氧层的主要物质之一．对氯氟烃类化合物及其降解产物（包括光解、光氧化、化学反应产物等）在大气中行为问题的研究是大气化学研究的重要内容．前人[1-3]从理论和实验两方面研究了自由基与臭氧的反应机制，但是氯氟烃光解过程中     

Ab Initio Quantum Mechanical Study on the Origin of the pK(a) Differences of the Proton Sponges 1,8-Bis(dimethylamino)naphthalene, 1,8-Bis(dimethylamino)-2,7-dimethoxynaphthalene, 1,6-Dimethyl-1,6-diazacyclodecane, and 1,6-Diazabicyclo[4.4.4]tetradecane

Ab initio quantum mechanical calculations were used in studying the origin of the exceptionally high basicities of four diamines (13-16) with pK(a1) values ranging from 12.1 to 25. The computational approach involved the calculation of the gas-phase proton affinities of the molecules studied at the MP2/6-31G//HF/6-31G level and the solvation energies with the polarizable continuum model at the HF/6-31G level. The calculated gas-phase and aqueous-phase proton affinities of a structurally diverse series of amines were compared with the corresponding experimental gas-phase proton affinities and pK(a1) values. The calculated values were found to be in reasonable agreement with the experimental ones. The high basicities of the studied diamines were found to originate from the nitrogen lone-pair repulsion, solvation effects, and strong intramolecular hydrogen bonds. Each of these factors were found to be able to increase the pK(a1) values of the high-basicity diamines by 2-6 pK(a) units. The relative contributions of the factors varied between the compounds. The nitrogen lone-pair repulsion was estimated to be the most important factor in increasing the pK(a1) values. In addition, barriers for proton transfers between the nitrogens of selected diamines were calculated, and comparison was made between the barrier heights and the geometries of the diamines.