Quantum chemical study of solvent and substituent effects on the 1,5-hydride shift in 2,6-dimethyl-2-heptyl cations

The mechanism of the degenerate 1,5-hydride shift in 2,6-dimethyl-2-heptyl cations has been investigated using ab initio MP2 and density functional theory (DFT) hybrid (B3LYP) calculations. The potential-energy profile for the 1,5-hydride shift consists of three minima corresponding to two equivalent acyclic carbocations and one symmetrically mu-hydrido-bridged carbocation, while two equivalent unsymmetrically hydrido-bridged carbocations were located as transition-state structures. The calculated relative energy differences between acyclic carbocations and symmetrically mu-hydrido-bridged structure are significantly affected by introduction of alkyl and (CH2)n-substituents at the C4 position of the 2,6-dimethyl-2-heptyl cation structure. DFT self-consistent isodensity polarizable continuum method (SCI-PCM) and MP2 PCM continuum methods have been used to calculate the effect of solvation on geometries and relative energies of the species involved in the 1,5-hydride shift. It is found that relative energies of acyclic and mu-hydrido-bridged carbocation structures as well as the energy barriers for 1,5-hydride shifts are in accord with experimental data if solvation effects are taken into account.     

Theoretical studies of 31P NMR spectral properties of phosphanes and related compounds in solution

Selected theoretical methods, basis sets and solvation models have been tested in their ability to predict (31)P NMR chemical shifts of large phosphorous-containing molecular systems in solution. The most efficient strategy was found to involve NMR shift calculations at the GIAO-MPW1K/6-311++G(2d,2p)//MPW1K/6-31G(d) level in combination with a dual solvation model including the explicit consideration of single solvent molecules and a continuum (PCM) solvation model. For larger systems it has also been established that reliable (31)P shift predictions require Boltzmann averaging over all accessible conformations in solution.     

氟比洛芬构象异构体的理论计算

用Hypercbem软件中构象搜寻模块,对氟比洛芬进行构象搜索,寻找分子低能构象．用B3LYP／6-31G（d）法优化计算22个低能构象,PCM溶剂模型用于水相计算,获得低能构象的优化几何结构、分子总能量和标准吉布斯自由能．结果表明,在气相和水相时,Z-型构象异构体稳定性最高．     

Hydration-dependent structural deformation of guanine in the electronic singlet excited state

Theoretical study was performed to investigate how the degree of hydration affects the structures and properties of the canonical form (keto-N9H) of guanine in the ground and lowest singlet pipi* excited state. This work is the continuation of our earlier work where we have studied the hydration of guanine in the first solvation shell with one, three, five, and six water molecules. In the present investigation, we have considered 7-13 water molecules in hydrating guanine. Ground-state geometries were optimized at the Hartree-Fock level, whereas the configuration interaction-singles (CIS) method was used for the excited-state geometry optimization. The 6-311G(d,p) basis set was used in all calculations. The harmonic vibrational frequency analysis was used to determine the nature of the optimized ground- and excited-state potential energy surfaces; all geometries were found to be minima at the respective potential surfaces. It was found that the degree of hydration has a significant influence on the excited-state structural nonplanarity of guanine. It is expected that excited-state dynamics of guanine will depend on the degree of hydration. Ground- and excited-state geometries of selected hydrated species were also optimized in the bulk water solution using the polarizable continuum model (PCM). It was found that bulk water solution generally does not have significant influence on the structure of the hydrated species. Effects of hydration on different stretching vibrations in the ground and excited states are also discussed.     

Conformational analysis and stereoelectronic effects in trans-1,2-dihalocyclohexanes: 1H NMR and theoretical investigation

The conformational equilibrium of trans-1,2-difluoro- (1), trans-1,2-dichloro- (2) and trans-1,2-dibromo-cyclohexane (3) was studied through a combined method of NMR, theoretical calculations and solvation theory. The solvent dependence of the 3JH1,H2 NMR coupling constants together with theoretical calculations allow the direct determination of the conformational equilibria without recourse to model compounds. The coupling constants were obtained with the aid of spectrum simulation, since these symmetric molecules present complex coupling systems. The observed couplings, when analysed by solvation theory and utilising DFT geometries (B3LYP/6-311+G**), gave energy values of E(ee) -E(aa) of 0.10, 0.95 and 1.40 kcalmol(-1) in the vapour phase for 1, 2 and 3, respectively, decreasing to -0.63, 0.36 and 0.93 kcalmol(-1) in CCl4 and to -1.91, -0.80 and -0.05 kcalmol(-1) in DMSO solution. The diaxial preference for all compounds is explained by natural bond orbital (NBO) analysis, which shows important hyperconjugative effects in this conformation. The "gauche effect" for compounds with more electronegative substituents, which are in gauche arrangement in the ee conformation, also plays a relevant role in more polar solvents.     

计算机模拟原子簇的稳定构型和能量性质

用密度泛函(DFT)方法研究了铜原子簇Cu~n(n=2,3,4,6)的稳定几何构型和电子结构。通过拟合从头算势能面构造铜原子簇势能函数的双体、三体及四体项,并利用该函数和全局优化“Basin-Hopping”算法得到较大铜原子簇(n=13～56)能量极小的结构,计算结果与实验及其它计算结果相一致。     

Symmetry-dependent solvation of donor-substituted triarylboranes

Donor-substituted triarylboranes are investigated by femtosecond absorption spectroscopy to study the influence of molecular symmetry on solvation. In solvents of varying polarity and differently fast solvation response, the solvation dynamics of a highly symmetric triple carbazole-substituted triarylborane (TCB) is compared to a single carbazole-substituted triarylborane (CB). The decomposition of the transient absorption spectra allows us to measure the solvation time by means of the time-dependent solvatochromic shift of the excited-state absorption (ESA) and the stimulated emission (SE). For all polar solvents under study we find an accelerated solvation process for TCB compared to the less symmetric CB. The difference is particularly large for solvents with a slow response. In order to explain these findings we propose that the electronic excitation is mobile in the symmetric molecule and can change between the three carbazole chromophores probably by a hopping mechanism. The excited-state dipole moment of TCB can thereby respond to the solvent relaxation and changes its direction according to the local field of the solvation shell. Thus, in a symmetric solute the possibility of an intramolecular charge delocalization over equivalent sites accelerates the approach of the minimum-energy configuration.     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution

The absolute pKa values of 24 representative amine compounds, including cocaine, nicotine, 10 neurotransmitters, and 12 anilines, in aqueous solution were calculated by performing first-principles electronic structure calculations that account for the solvent effects using four different solvation models, i.e., the surface and volume polarization for electrostatic interaction (SVPE) model, the standard polarizable continuum model (PCM), the integral equation formalism for the polarizable continuum model (IEFPCM), and the conductor-like screening solvation model (COSMO). Within the examined computational methods, the calculations using the SVPE model lead to the absolute pKa values with the smallest root-mean-square-deviation (rmsd) value (1.18). When the SVPE model was replaced by the PCM, IEFPCM, and COSMO, the rmsd value of the calculated absolute pKa values became 3.21, 2.72, and 3.08, respectively. All types of calculated pKa values linearly correlate with the experimental pKa values very well. With the empirical corrections using the linear correlation relationships, the theoretical pKa values are much closer to the corresponding experimental data and the rmsd values become 0.51-0.83. The smallest rmsd value (0.51) is also associated with the SVPE model. All of the results suggest that the first-principles electronic structure calculations using the SVPE model are a reliable approach to the pKa prediction for the amine compounds.     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001     

Theoretical investigation of isotopic scrambling mechanisms in 2-chloroethyl methyl sulfide

Ab initio and semiempirical molecular orbital calculations have been applied to study the concerted and stepwise isotopic scrambling mechanisms of 2-chloroethyl methyl sulfide in the gas phase and in aqueous solution. The calculations reveal the structural details of the reactants, transition structures, and intermediates involved in this reaction and provide relative energy estimates. The concerted mechanism is found to be competitive with the stepwise mechanism in the gas phase, but the stepwise mechanism is favored in aqueous solution as no true transition structure for the concerted mechanism could be found using the solvation models. A combined approach of evaluating solvation energies with the generalized-Bom-plus-surface-tensions SM _x solvation models of Cramer and Truhlar at ab initio optimized geometries is found to deliver the best agreement with experimentally determined reaction barriers. Together with the recent experimental results of McManus and co-workers, the present study provides insights into the controlling factors involved in the elementary reaction steps of sulfur mustards and a solid foundation for investigations into more complex reactions of related compounds.     

Rearrangements involving the phenonium ion: a theoretical investigation.

Rearrangements involving the phenonium ion were investigated by means of a B3LYP/6-311G(d,p) study in which the effect of solvent has been incorporated by using a PCM solvation model. A rationalization of the whole set of experimental facts reported both in the gas phase and in solution was possible thanks to the characterization of protonated benzocyclobutene as a minimum energy structure and, particularly, to the important preferential stabilization in solution of the TS for the isomerization of the phenonium ion to the alpha-methylbenzyl ion, which reduces the Gibbs energy barrier of 26.6 kcal/mol for this process in the gas phase to a more accessible one of 18.7 kcal/mol in solution.     

Theoretical studies for structures and energetics of Rgn-N2O (Rg=He, Ne, Ar) clusters

Minimum-energy structures of the Rg(2)-N(2)O (Rg=He, Ne, Ar) clusters have been determined with ab initio MP2 optimization, whereas the minimum-energy structures of the Rg(n)-N(2)O clusters with n = 3-7 have been obtained with the pairwise additive potentials. Interaction energies and nonadditive three-body effects of the Rg(2)-N(2)O ternary complex have been calculated using supermolecule method at MP4 and CCSD(T) levels. It was found from the calculations that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The nonadditive three-body effects were found to be small for Rg(2)-N(2)O complexes. Our calculations also indicated that, for He(n)-N(2)O and Ne(n)-N(2)O clusters, the first six He and Ne atoms form the first solvation ring around the middle nitrogen of the N(2)O monomer, while for Ar(n)-N(2)O, the first five Ar atoms form the first solvation ring.     

A study on orientation and absorption spectrum of interfacial molecules by using continuum model

In this work, a numerical procedure based on the continuum model is developed and applied to the solvation energy for ground state and the spectral shift against the position and the orientation of the interfacial molecule. The interface is described as a sharp boundary separating two bulk media. The polarizable continuum model (PCM) allows us to account for both electrostatic and nonelectrostatic solute-solvent interactions when we calculate the solvation energy. In this work we extend PCM to the interfacial system and the information about the position and orientation of the interfacial molecule can be obtained. Based on the developed expression of the electrostatic free energy of a nonequilibrium state, the numerical procedure has been implemented and used to deal with a series of test molecules. The time-dependent density functional theory (TDDFT) associated with PCM is used for the electron structure and the spectroscopy calculations of the test molecules in homogeneous solvents. With the charge distribution of the ground and excited states, the position- and orientation-dependencies of the solvation energy and the spectrum have been investigated for the interfacial systems, taking the electrostatic interaction, the cavitation energy, and the dispersion-repulsion interaction into account. The cavitation energy is paid particular attention, since the interface portion cut off by the occupation of the interfacial molecule contributes an extra part to the stabilization for the interfacial system. The embedding depth, the favorable orientational angle, and the spectral shift for the interfacial molecule have been investigated in detail. From the solvation energy calculations, an explanation has been given on why the interfacial molecule, even if symmetrical in structure, tends to take a tilting manner, rather than perpendicular to the interface.     

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations. The calculations show that while the force field reproduces the experimental solvation free energies of nonpolar analogs with reasonable accuracy the solvation free energies of polar analogs in water are systematically overestimated (too positive). The dependence of the calculated free energies on the atomic partial charges was also studied.     

Thermochemistry of arylselanyl radicals and the pertinent ions in acetonitrile

Reduction and oxidation potentials of a series of parasubstituted phenylselanyl radicals, XC(6)H(4)Se(*), have been measured using photomodulated voltammetry in acetonitrile. The thermodynamic significance of these data was substantiated through a study of the oxidation process of the pertinent selenolates in linear sweep voltammetry. Both the reduction and the oxidation potentials correlate linearly with the Hammett substituent coefficients sigma and sigma(+) leading in the latter case to slopes, rho(+), of 2.5 and 3.8, respectively. Through comparison of these slopes with those published previously for the O- and S-centered analogues, it is revealed that the pi-interaction becomes progressively smaller as the size of the radical center increases in the order O, S, and Se. Solvation energies of the pertinent selenolates and selanylium ions have been extracted from thermochemical cycles incorporating the measured electrode potentials for XC(6)H(4)Se(*) as well as electron affinities and ionization potentials obtained from theoretical calculations at the B3LYP/6-31+G(d) level. The extracted data show the expected overall substituent dependency for both kinds of ions; that is, the absolute value of the solvation energy decreases as the charge becomes more delocalized. The data have also been compared with solvation energies computed using the polarizable continuum model (PCM). Interestingly, we find that, while the model seems to work well for selenolates, it underestimates the solvation of selanylium ions in acetonitrile by as much as 25 kcal mol(-)(1). These large deviations are ascribed to the fact that the PCM method does not take specific solvent effects into account as it treats the solvent as a continuum described solely by its dielectric constant. Gas-phase calculations show that the arylselanylium ions can coordinate covalently to one or two molecules of acetonitrile in strong Ritter-type adducts. When this strong interaction is included in the solvation energy calculations by means of a combined supermolecule and PCM approach, the experimental data are reproduced within a few kcal mol(-)(1). Although the energy difference of the singlet and triplet spin states of the arylselanylium ions is small for the gas-phase structures, the singlet cation is undoubtedly the dominating species in solution because the triplet cation lacks the ability to form covalent bonds.     

Theoretical study of helical structure caused by chirality of cysteine dimer

In this work we report a theoretical study of the helix structure and chiral discrimination on the interactions between the chiral cysteine–cysteine. Two reasonable geometries on the potential energy hypersurface of the cysteine–cysteine system are considered with the global minimum. Accurate geometric structures, relative stabilities, harmonic vibrational frequencies, and infrared (IR) intensities were investigated. To take into account the water solvation effect, the Onsager model within the self‐consistent reaction field (SCRF) method and the polarized continuum (PCM) method were used to evaluate the interaction energy, ΔG_solv at the same level employed in the gas phase. The results indicate that the polarity of the solvent plays an important role in the structures and relative stabilities of different isomers. Computational results indicate that the global minimum should be conformer I regardless of whether in the gas phase or in aqueous solution, which differs from previous theoretical reports. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Quantum chemical calculations of reduction potentials of AnO2(2+)/AnO2+ (An = U, Np, Pu, Am) and Fe3+/Fe2+ couples

The reduction potentials of the AnO(2)(H(2)O)(5)(2+)/AnO(2)(H(2)O)(5)(+) couple (An = U, Np, Pu, and Am) and Fe(H(2)O)(6)(3+) to Fe(H(2)O)(6)(2+) in aqueous solution were calculated at MP2, CASPT2, and CCSD(T) levels of theory. Spin-orbit effects for all species were estimated at the CASSCF level. Solvation of the hydrated metal cations was modeled both by polarizable conductor model (PCM) calculation and by solvating the solutes with over one thousand TIP3P water molecules in the QM/MM framework. The redox reaction energy calculated by QM/MM method agreed well with the PCM method after corrections using the classical Born formula for the contribution from the rest of the solvation sphere and correction for dynamic response of solvent polarization in the MM region. Calculated reduction potentials inclusive of spin-orbit effect, zero-point energy, thermal corrections, entropy effect, and PCM solvation energy were found to be comparable with experimental data. The difference between CASPT2 calculated and experimental reduction energies were less than 35 kJ/mol in all cases, which ensures that CASPT2 (and CCSD(T)) calculations provide reasonable estimates of the thermochemistry of these reactions.