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1.
Computational analysis of the molecular ordering of nematic p -phenylene-4-methoxy benzoyl 4-trifluoromethylbenzoate (FLUORO1) and smectic 4-propyloxyphenyl 4-(4-trifluoromethylbenzoyloxy) benzoate (FLUORO2) mesogens has been carried out with respect to translatory and orientational motions. The net atomic charge and atomic dipole components at each atomic centre of the molecule have been evaluated using the CNDO/2 method. Rayleigh-Schrodinger perturbation theory, along with the multicentred-multipole expansion method, has been employed to evaluate long range intermolecular interactions while a '6-exp' potential function has been assumed for short range interactions. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at the phase transition temperature using the Maxwell-Boltzmann formula. The flexibility of various configurations has been studied in terms of the variation of probability due to small departures from the most probable configuration. The results obtained enable the determination of the peculiarities of the molecular ordering, as well as the construction of models of the structures of FLUORO1 and FLUORO2 in different modes of interaction. The mesophase nature has been correlated with the parameters introduced in this paper. 相似文献
2.
We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into "core" and "reservoir" modes with the former to be treated quantum mechanically and the latter classically. The presented method only requires the calculation of the system's reduced density matrix averaged over the quantum core degrees of freedom which is then coupled to a classically evolved reservoir to treat the remaining modes. We demonstrate our approach by applying it to the spin-boson problem using the noninteracting blip approximation to treat the system and core, and Ehrenfest dynamics to treat the reservoir. The resulting hybrid methodology is accurate for both fast and slow baths, since it naturally reduces to its composite methods in their respective regimes of validity. In addition, our combined method is shown to yield good results in intermediate regimes where neither approximation alone is accurate and to perform equally well for both strong and weak system-bath coupling. Our approach therefore provides an accurate and efficient methodology for calculating quantum dynamics in complex systems. 相似文献
3.
Ramn F. Alvarez-Estrada 《Macromolecular theory and simulations》1995,4(2):367-395
This work studies large three-dimensional open molecular chains at thermal equilibrium in which bond lengths and angles are fixed (hard variables), based upon quantum statistics. A model for a chain formed by N particles interacting through harmonic-like vibrational potentials is treated in the high-frequency limit in which all bond lengths and angles become constrained, while other N angles (soft variables) remain unconstrained. The associated quantum partition function is bounded rigorously, using a variational inequality (related to the Born-Oppenheimer approximation), by another quantum partition function, Z. The total vibrational zero-point energy is shown to be independent of the soft variables thereby solving for this model a generic difficulty in the elimination of hard variables. Z depends only on soft variables and, under certain conditions, it can be approximated by a classical partition function Zc. The latter satisfies the equipartition principle and it differs from other classical partition functions for related molecular chains. The extension of the model when only part of the bond angles become fixed in the high-frequency limit is outlined. As another generalization, a systematic study of macromolecules, as composed of electrons and heavy particles with Coulomb interactions, is also presented. Its exact quantum partition function is bounded, supposing that the effective molecular potential also tends to constrain all bond lengths and angles, and under suitable assumptions, by another quantum partition function. The latter depends only on the remaining soft variables and it generalizes the one obtained for the first model. 相似文献
4.
Josiane Serre 《International journal of quantum chemistry》1984,26(5):593-605
In this survey paper the different possible theoretical ways of treating the SN2 reaction are explained. It is shown that, in the future, experience and theory will very likely complement each other. 相似文献
5.
The lowest-lying triplet and singlet potential energy surfaces for the O(3P) + C6H6 reaction were theoretically characterized using the "complete basis set" CBS-QB3 model chemistry. The primary product distributions for the multistate multiwell reactions on the individual surfaces were then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. It is newly found that electrophilic O-addition onto a carbon atom in benzene can occur in parallel on two triplet surfaces, 3A' and 3A' '; the results predict O-addition to be dominant up to combustion temperatures. Major expected end-products of the addition routes include phenoxy radical + H*, phenol and/or benzene oxide/oxepin, in agreement with the experimental evidence. While c-C6H5O* + H* are nearly exclusively formed via a spin-conservation mechanism on the lowest-lying triplet surface, phenol and/or benzene oxide/oxepin are mainly generated from the lowest-lying singlet surface after inter-system crossing from the initial triplet surface. CO + c-C5H6 are predicted to be minor products in flame conditions, with a yield < or = 5%. The O + C6H6 --> c-C5H5* + *CHO channel is found to be unimportant under all relevant combustion conditions, in contrast with previous theoretical conclusions (J. Phys. Chem. A 2001, 105, 4316). Efficient H-abstraction pathways are newly identified, occurring on two different electronic state surfaces, 3B1 and 3B2, resulting in hydroxyl plus phenyl radicals; they are predicted to play an important role at higher temperatures in hydrocarbon combustion, with estimated contributions of ca. 50% at 2000 K. The overall thermal rate coefficient k(O + C6H6) at 300-800 K was computed using multistate transition state theory: k(T) = 3.7 x 10-16 x T 1.66 x exp(-1830 K/T) cm(3) molecule(-1) s(-1), in good agreement with the experimental data available. 相似文献
6.
Koyama M Hayakawa J Onodera T Ito K Tsuboi H Endou A Kubo M Del Carpio CA Miyamoto A 《The journal of physical chemistry. B》2006,110(35):17507-17511
To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe surface. Phosphoric ester was shown to interact with the nascent Fe surface, forming both covalent and ionic bonds. Formation and dissociation dynamics of covalent bonds during tribochemical reaction was clearly observed during the simulation. The effect of friction condition on the tribochemical reaction dynamics was then studied, and it was indicated that friction would influence the formation and the dissociation of covalent bonds. By using a hybrid tight-binding quantum chemical molecular dynamics method, we obtained insights on initial tribochemical reaction processes for the formation of tribofilm from the phosphoric ester molecule on the nascent Fe surface. 相似文献
7.
A detailed QM/MM study on the reaction mechanism of Cytochrome P450 NO reductase is reported. Two reaction pathways connecting the two well-characterized intermediates as well as two putative intermediates that represent the unknown third intermediate are explored, with emphasis on the unusual direct reduction of the enzymatic active site by the cofactor NADH. Activation barriers and kinetic isotope effect are calculated and reveal that reduction of the NO-bound species occurs in form of a hydride ion transfer. Furthermore, the impact of different hydrogen bonds in the active site to binding and reactivity of NADH is explored. The calculated kinetic and thermodynamic properties for both modelled pathways are used for the kinetic simulation of the entire reaction course. It is thus shown that the unknown key intermediate is the singlet diradical Fe(III)-NHOH(?). It is also found that the mechanism of the N-N bond formation is spin-recoupling, which is only possible due to the diradical character of the key intermediate. 相似文献
8.
In recent years there has been a resurgence of interest in Bohmian mechanics as a numerical tool because of its local dynamics, which suggest the possibility of significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared-it has simply been swept under the rug into the quantum force. In this paper we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This leads to a single equation for complex S, and ultimately complex x and p but there is a reward for this complexification-a significantly higher degree of localization. The quantum force in the new approach vanishes for Gaussian wave packet dynamics, and its effect on barrier tunneling processes is orders of magnitude lower than that of the classical force. In fact, the current method is shown to be a rigorous extension of generalized Gaussian wave packet dynamics to give exact quantum mechanics. We demonstrate tunneling probabilities that are in virtually perfect agreement with the exact quantum mechanics down to 10(-7) calculated from strictly localized quantum trajectories that do not communicate with their neighbors. The new formulation may have significant implications for fundamental quantum mechanics, ranging from the interpretation of non-locality to measures of quantum complexity. 相似文献
9.
The accuracy of quantum chemical predictions of structures and thermodynamic data for metal complexes depends both on the quantum chemical methods and the chemical models used. A thermodynamic analogue of the Eigen-Wilkins mechanism for ligand substitution reactions (Model A) turns out to be sufficiently simple to catch the essential chemistry of complex formation reactions and allows quantum chemical calculations at the ab initio level of thermodynamic quantities both in gas phase and solution; the latter by using the conductor-like polarizable continuum (CPCM) model. Model A describes the complex formation as a two-step reaction: 1. [M(H2O)x](aq) + L(aq) <==>[M(H2O)x], L(aq); 2. [M(H2O)x], L(aq) <==>[M(H2O)(x-1)L],(H2O)(aq). The first step, the formation of an outer-sphere complex is described using the Fuoss equation and the second, the intramolecular exchange between an entering ligand from the second and water in the first coordination shell, using quantum chemical methods. The thermodynamic quantities for this model were compared to those for the reaction: [M(H2O)x](aq) + L(aq) <==>[M(H2O)(x-1)L](aq) + (H2O)(aq) (Model B), as calculated for each reactant and product separately. The models were tested using complex formation between Zn(2+) and ammonia, methylamine, and ethylenediamine, and complex formation and chelate ring closure reactions in binary and ternary UO(2)(2+)-oxalate systems. The results show that the Gibbs energy of reaction for Model A are not strongly dependent on the number of water ligands and the structure of the second coordination sphere; it provides a much more precise estimate of the thermodynamics of complex formation reactions in solution than that obtained from Model B. The agreement between the experimental and calculated data for the formation of Zn(NH(3))(2+)(aq) and Zn(NH(3))(2)(2+)(aq) is better than 8 kJ/mol for the former, as compared to 30 kJ/mol or larger, for the latter. The Gibbs energy of reaction obtained for the UO(2)(2+) oxalate systems using model B differs between 80 and 130 kJ/mol from the experimental results, whereas the agreement with Model A is better. The errors in the quantum chemical estimates of the entropy and enthalpy of reaction are somewhat larger than those for the Gibbs energy, but still in fair agreement with experiments; adding water molecules in the second coordination sphere improves the agreement significantly. Reasons for the different performance of the two models are discussed. The quantum chemical data were used to discuss the microscopic basis of experimental enthalpy and entropy data, to determine the enthalpy and entropy contributions in chelate ring closure reactions and to discuss the origin of the so-called "chelate effect". Contrary to many earlier suggestions, this is not even in the gas phase, a result of changes in translation entropy contributions. There is no simple explanation of the high stability of chelate complexes; it is a result of both enthalpy and entropy contributions that vary from one system to the other. 相似文献
10.
Amara P Volbeda A Fontecilla-Camps JC Field MJ 《Journal of the American Chemical Society》2005,127(8):2776-2784
Recent experimental and theoretical studies have focused on the mechanism of the A-cluster active site of acetyl-CoA synthase that produces acetyl-CoA from a methyl group, carbon monoxide, and CoA. Several proposals have been made concerning the redox states of the (Ni-Ni) bimetallic center and the iron-sulfur cluster connected to one of the metals. Using hybrid density functional theory, we have investigated putative intermediate states from the catalytic cycle. Among our conclusions are the following: (i) the zerovalent state proposed for the proximal metal is unlikely if the charge on the iron-sulfur cluster is +2; (ii) a mononuclear mechanism in which both CO and CH(3) bind the proximal nickel is favored over the binuclear mechanism in which CO and CH(3) bind the proximal and distal nickel ions, respectively; (iii) the formation of a disulfide bond in the active site could provide the two electrons necessary for the reaction but only if methylation occurs simultaneously; and (iv) the crystallographic closed form of the active site needs to open to accommodate ligands in the equatorial site. 相似文献
11.
The Pt-BO bonding nature and the formation reaction of the experimentally reported platinum(II) oxoboryl complex, simplified to PtBr(BO)(PMe(3))(2), were theoretically investigated with the density functional theory method. The BO(-) ligand was quantitatively demonstrated to have extremely strong σ-donation but very weak d(π)-electron-accepting abilities. Therefore, it exhibits a strong trans influence. The formation reaction occurs through a four-center transition state, in which the B(δ+)-Br(δ-) polarization and the Br → Si and O p(π) → B p(π) charge-transfer interactions play key roles. The Gibbs activation energy (ΔG°(++)) and Gibbs reaction energy (ΔG°) of the formation reaction are 32.2 and -6.1 kcal/mol, respectively. The electron-donating bulky phosphine ligand is found to be favorable for lowering both ΔG°(++) and ΔG°. In addition, the metal effect is examined with the nickel and palladium analogues and MBrCl[BBr(OSiMe(3))](CO)(PR(3))(2) (M = Ir and Rh). By a comparison of the ΔG°(++) and ΔG° values, the M-BO (M = Ni, Pd, Ir, and Rh) bonding nature, and the interaction energy between [MBrCl(CO)(PR(3))(2)](+) and BO(-) with those of the platinum system, MBrCl(BO)(CO)(PR(3))(2) (M = Ir and Rh) is predicted to be a good candidate for a stable oxoboryl complex. 相似文献
12.
Combined quantum mechanics/molecular mechanics molecular dynamics simulations have been carried out to study the cleavage of the carbon–chlorine bond in 1,2-dichloroethane catalysed by haloalkane dehalogenase from Xanthobacter Autotrophicus GJ10. The process has been compared with an adequate counterpart in aqueous solution, the nucleophilic attack of acetate anion on 1,2-dichloroethane. Within the limitations of the model, mainly due to the use of a semiempirical Hamiltonian, our results reproduce the magnitude and characteristics of the catalytic effect. Comparisons of the enzymatic and in solution potentials of mean force reveal that, irrespective of the reference state, the enzyme shows a larger affinity for the transition state. The origin of this increased affinity is found in the differences in the electrostatic pattern created by the environment in aqueous solution and in the enzyme.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail 相似文献
13.
The hydration of mesityl oxide (MOx) was investigated through a sequential quantum mechanics/molecular mechanics approach.
Emphasis was placed on the analysis of the role played by water in the MOx syn–anti equilibrium and the electronic absorption spectrum. Results for the structure of the MOx–water solution, free energy of solvation
and polarization effects are also reported. Our main conclusion was that in gas-phase and in low-polarity solvents, the MOx
exists dominantly in syn-form and in aqueous solution in anti-form. This conclusion was supported by Gibbs free energy calculations in gas phase and in-water by quantum mechanical calculations
with polarizable continuum model and thermodynamic perturbation theory in Monte Carlo simulations using a polarized MOx model.
The consideration of the in-water polarization of the MOx is very important to correctly describe the solute–solvent electrostatic
interaction. Our best estimate for the shift of the π–π* transition energy of MOx, when it changes from gas-phase to water solvent, shows a red-shift of −2,520 ± 90 cm−1, which is only 110 cm−1 (0.014 eV) below the experimental extrapolation of −2,410 ± 90 cm−1. This red-shift of around −2,500 cm−1 can be divided in two distinct and opposite contributions. One contribution is related to the syn → anti conformational change leading to a blue-shift of ~1,700 cm−1. Other contribution is the solvent effect on the electronic structure of the MOx leading to a red-shift of around −4,200 cm−1. Additionally, this red-shift caused by the solvent effect on the electronic structure can by composed by approximately 60 %
due to the electrostatic bulk effect, 10 % due to the explicit inclusion of the hydrogen-bonded water molecules and 30 % due
to the explicit inclusion of the nearest water molecules. 相似文献
14.
Michael Meyer Gerd Wohlfahrt Jörg Knäblein Dietmar Schomburg 《Journal of computer-aided molecular design》1998,12(5):425-440
The complex structure of glucose oxidase (GOX) with the substrate glucose was determined using a docking algorithm and subsequent molecular dynamics simulations. Semiempirical quantum chemical calculations were used to investigate the role of the enzyme and FAD co-enzyme in the catalytic oxidation of glucose. On the basis of a small active site model, substrate binding residues were determined and heats of formation were computed for the enzyme substrate complex and different potential products of the reductive half reaction. The influence of the protein environment on the active site model was estimated with a point charge model using a mixed QM/MM method. Solvent effects were estimated with a continuum model. Possible modes of action are presented in relation to experimental data and discussed with respect to related enzymes. The calculations indicate that the redox reaction of GOX differs from the corresponding reaction of free flavins as a consequence of the protein environment. One of the active site histidines is involved in substrate binding and stabilization of potential intermediates, whereas the second histidine is a proton acceptor. The former one, being conserved in a series of oxidoreductases, is also involved in the stabilization of a C4a-hydroperoxy dihydroflavin in the course of the oxidative half reaction. 相似文献
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17.
Chunli Yan Zhilong Xiu Xiaohui Li Hu Teng Ce Hao 《Journal of inclusion phenomena and macrocyclic chemistry》2007,58(3-4):337-344
The inclusion interaction between quercetin and β-cyclodextrin (β-CD) binding site has been investigated, based on PM3 and
ONIOM2 methods. The obtained results clearly indicate that the orientation in which the B ring of the guest molecule located
near the secondary hydroxyls of the β-CD cavity is preferred in the binding energy. Moreover, Analyses regarding the complex
structures suggest that one hydrogen bond between 7-hydroxy group (OH) of quercetin and 6-OH of β-CD is formed. This hydrogen
bond interaction plays an important role in the bound quercetin/β-CD complex. 相似文献
18.
Charge-transfer complex study by chemical force spectroscopy: a dynamic force spectroscopic approach
Gil R Guillerez MG Poulin JC Schulz E 《Langmuir : the ACS journal of surfaces and colloids》2007,23(2):542-548
Charge-transfer interaction, as a reversible and rapid phenomenon, was evidenced by force microscopy. Pull-off forces were measured between a tip grafted with a trinitrofluorenone derivative and a surface functionalized with an electron-rich aromatic anthracene compound in a dodecane environment. The effect of the sweep time on the measured interaction forces is described, together with an extensive study of a competitive influence of free aromatic molecules in dodecane diluted solutions. These forces depend on the nature of the competitor and its concentration as well as on the velocity of tip/sample separation. 相似文献
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20.
The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- and medium-size molecules in gas phase has currently become a routine optimization process, as it has been implemented in many electronic structure packages. However, optimization of conical intersections of small- and medium-size molecules in solution or macromolecules remains inefficient, even poorly defined, due to large number of degrees of freedom and costly evaluations of gradient difference and nonadiabatic coupling vectors. In this work, based on the sequential quantum mechanics and molecular mechanics (QM/MM) and QM/MM-minimum free energy path methods, we have designed two conical intersection optimization methods for small- and medium-size molecules in solution or macromolecules. The first one is sequential QM conical intersection optimization and MM minimization for potential energy surfaces; the second one is sequential QM conical intersection optimization and MM sampling for potential of mean force surfaces, i.e., free energy surfaces. In such methods, the region where electronic structures change remarkably is placed into the QM subsystem, while the rest of the system is placed into the MM subsystem; thus, dimensionalities of gradient difference and nonadiabatic coupling vectors are decreased due to the relatively small QM subsystem. Furthermore, in comparison with the concurrent optimization scheme, sequential QM conical intersection optimization and MM minimization or sampling reduce the number of evaluations of gradient difference and nonadiabatic coupling vectors because these vectors need to be calculated only when the QM subsystem moves, independent of the MM minimization or sampling. Taken together, costly evaluations of gradient difference and nonadiabatic coupling vectors in solution or macromolecules can be reduced significantly. Test optimizations of conical intersections of cyclopropanone and acetaldehyde in aqueous solution have been carried out successfully. 相似文献