烷基氟化物热消除反应的理论研究-1

用RHF从头计算法研究了氟代乙烷消除氟化氢反应的取代基效应．对所有构型均采用能量梯度法在3-21G基级水平上进行了优化，过渡态的构型用振动分析确认．计算结果表明，对所讨论的基团-F，-CH_3，－CN，－NH_2，在α位和β位取代，均对过渡态的结构有一定的影响，电荷分布表明，标题反应的过渡态为部分极化的四元环过渡态．－F在α位和β位的取代均使氟代烷1－2消除氟化氢反应的活化位垒升高，且前者的活化位垒高于后者；－CN在α位的取代使反应的活化位垒升高，在β位的取代使反应的活化位垒降低．－CH_3和-NH_2在α位的取代使反应的活化位垒降低，在β位的取代使反应的活化位垒升高，只是-NH_2的效应强于-CH_3．这些结果与由实验结果推测的结论一致表明，本消除反应与其它卤代烷的消除反应有显著的差别．     

Estimation of n-Octanol/water Partition Coefficients （lgKow） and the Aqueous Solubility （-lgSw） of all PCDF Congeners by Density Functional Theory

1 INTRODUCTION As is widely known, PCDFs together with poly- chlorinated dibenzo-p-dioxins (PCDDs) and poly- chlorinated biphenyls (PCBs) have been included in many blacklists, such as “persistent organic pol- lutants (POPs)” and suspected “environmental en- docrine disruptors (EEDs)”. This is because PC- DFs are chemically and thermally stable and com- plex PCDF mixtures are generally resistant to bio- degradation. Although the concentration of these chemicals is quite low o…     

A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.     

Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters

Hydrogen bond interaction properties of backbone uracil was studied in crystalline structure of 5-nitrouracil. To this aim the electric field gradient tensors were calculated at the level of density functional theory in two single (non-hydrogen bonded) and cluster (hydrogen-bonded four-molecule) models of 5-nitrouracil. The electric field gradient tensors at the sites of O-17, N-14, and H-2 nuclei were converted to the experimentally measurable nuclear quadrupole resonance spectroscopy parameters, quadrupole coupling constant and asymmetry parameter. The results indicated different hydrogen bond interaction properties at the sites of various nuclei and also the protective role of ?NO₂ group for contribution of O1 to hydrogen bond interactions in comparison with uracil. The density functional theory calculations were performed using GAUSSIAN 98 package employing B3LYP method and 6-311G** and 6-311++G** basis sets.     

Vibrational Analysis for Decomposition Reactions of Fluorochloromethanol and Its Isomers

All species involved the multichannel decomposition reaction system of fluorochloromethanol and its isomers have been optimized utilizing a GAUSSIAN98 procedure package at B3LYP/6-311++G* level. After zero-point energy calibration, the potential energy surface is determined. The reactant CHFClOH has 12 reaction channels including five nonbarrier pathways. For its isomers CH₂FOCl and CH₂ClOF, there are four and two channels, respectively. Vibrational analysis is employed to elucidate the reaction mechanism.     

An algorithm for geometry optimization without analytical gradients

A numerical algorithm for locating both minima and transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is based on the RFO method of Simons and coworkers and is effectively the numerical version of an analytical algorithm (OPT = EF) previously published in this journal. The algorithm is designed to make maximum use of external second derivative information obtained from prior optimizations at lower levels of theory. It can be used with any wave function for which an energy can be calculated and is about two to three times faster than the default DFP algorithm (OPT = FP) supplied with GAUSSIAN 82.     

Aromatic behavior of three membered rings

The aromatic behavior of three membered ring compounds has been analyzed by mean of GAUSSIAN94 theoretical calculations at B3LYP//6-311++G(2d,p) level. Diamagnetic exaltation values obtained from magnetic susceptibilities as well as NICS show the expected aromatic character of the cyclopropyl cation, but the correspondent anion also shows aromatic behavior. This unexpected result is analyzed as well as the character of the other three membered ring derivatives.     

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.     

Conformational and NBO analysis on cis and trans isomers of methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylate

The cis and trans-methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylates were prepared and ¹H and ¹³C NMR spectra were recorded for both isomers. Conformational and NBO analysis were carried out for the cis and trans isomers. Conformer structures were pre-optimized using the hybrid method B3LYP along with the 6-311+G(d) basis set. Frequency calculations were employed to confirm the structures as minimum points. Potential energy surfaces (PES) were built at the same level of theory. Geometries obtained from DFT calculations were used to perform NBO analysis by the NBO 3.1 module in GAUSSIAN 03. The results obtained through theoretical calculations revealed that the shielding observed at C1 for the trans isomer can be attributed to carbomethoxy γ-effect, together with the hyperconjugative effect, while only hyperconjugative effects were found to explain the shielding of C3. The higher chemical shift value of C3 of the cis isomer was attributed to the carbonyl substituent, which plays an important role by capturing part of the electronic density in C3.     

A comparison of the HAM/3 semiempirical method with the MINDO/3 and CNDO/2 semiempirical methods and the GAUSSIAN 70 ab initio method; a comparison of ionization potential calculations and experimental photoelectron spectra of some imines and diimines

Molecular orbital calculations have been performed on eight molecules (containing 16–80 electrons) using the GAUSSIAN 70, MINDO/3, CNDO/2 and HAM/3 programs. The molecules contain nitrogen—nitrogen (diimines) or carbon—nitrogen (imines) double bonds. A comparison of the results of each method with experimental photoelectron data and an analysis of the cost effectiveness indicates that the HAM/3 method will prove a useful tool for photoelectron spectroscopists.     

Are donor–acceptor self organised aromatic systems NLO (non-linear optical) active?

This contribution to the understanding of non-linear optical (NLO) properties of organic systems is concentrated on donor–acceptor aromatic systems such as [2]catenanes. We report accurate ab initio quantum chemical calculations of the first static hyperpolarizability (β) of donor–acceptor aromatic systems containing naphthalene and anthracene as electron donors and pyromellitimide and naphthadiimide as electron acceptors. We investigate the NLO effect when the donor acceptor units are not connected through a bridge. In this kind of system the electronic communication between donor and acceptor is solely due to through space charge transfer mechanism. Geometries of all molecular systems were optimised at the Hartree–Fock level with STO-3G minimal basis set and with the 3-21G split valence basis and finally with 6-31G basis set using GAUSSIAN 98W. The first static hyperpolarizabilities of these molecular systems were calculated using Hartree–Fock level using 6-31G basis set using GAUSSIAN 98W. To understand the possibility of developing these systems as NLO materials we have also calculated the linear and nonlinear optical properties of bridged donor–acceptor systems. The study suggested that these unconnected donor–acceptor systems equivalent to some [2]catenanes reported in literature in general have little influence on the first static hyperpolarizability, however, the linked macro cyclic systems may have potential applications in the development of non-linear optical materials.     

A conceptual realization of stationary points using the Hessian matrix

In this study we use surface-fitting equations to generate the energy and its first derivative in terms of two torsional angles in the methanediol model, using GAUSSIAN 88 at the 4-31G level of approximation. The Hessian matrix is further used to locate the stationary points, and a Gaussian fit of the absolute values of the sum of the eigenvalues of the Hessian is used in order to generate a surface in which all the stationary points are identified.     

Hydrogen Bonds of Peptide Group in Four Acetamide Derivatives: DFT Study of Oxygen and Nitrogen NQR and NMR Parameters

A computational study was conducted to examine hydrogen bond (HB) properties of peptide group in four derivatives of acetamide by density functional theory (DFT) calculations of nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) parameters at the sites of oxygen and nitrogen nuclei of peptide groups. The available crystalline structures of four derivatives; 2,2,2-trifluoro-N-(2-hydroxy-5-nitrophenyl)acetamide, N-(2-acetylphenyl)acetamide, 2-chloro-N-(4-nitrophenyl) acetamide, and N-(4-fluorophenyl)acetamide were obtained from literature. Following the influence of HB interactions, calculations were done on non-hydrogen bonded (single) and hydrogen bonded (cluster) models of derivatives. The results revealed different behaviors of peptide group in contributing to HB interactions in different derivative structures. HB interactions are the strongest in 2-chloro-N-(4-nitrophenyl)acetamide. However, the strengths of HB interactions in all of the four derivatives are still less than that of acetamide. The calculations are done at the level of B3LYP method and 6-311++G** standard basis set using GAUSSIAN 98 package of program.     

Comparison of CBS-QB3, CBS-APNO, G2, and G3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water

The GAUSSIAN 2, GAUSSIAN 3, complete basis set-QB3, and complete basis set-APNO methods have been used to calculate DeltaH( composite function) and DeltaG( composite function) values for ionic clusters of hydronium and hydroxide ions complexed with water. Results for the clusters H3O+(H2O)n and OH-(H2O)n, where n=1-4 are reported in this paper, and compared against experimental values contained in the National Institutes of Standards and Technology (NIST) database. Agreement with experiment is excellent for the three ab initio methods for formation of these clusters. The high accuracy of these methods makes them reliable for calculating energetics for the formation of ionic clusters containing water. In addition this allows them to serve as a valuable check on the accuracy of experimental data reported in the NIST database, and makes them useful tools for addressing unresolved issues in atmospheric chemistry.     

A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands

The Comparative Molecular Field Analysis (CoMFA) was developed to investigate a three-dimensional quantitative structure activity relationship (3D-QSAR) model of ligands for the sigma 1 receptor. The starting geometry of sigma-1 receptor ligands was obtained from the Tripos force field minimizations and conformations were decided from DISCOtech using the SYBYL 6.8. program. The structures of 48 molecules were fully optimized at the ab initio HF/3-21G* and semiempirical AM1 calculations using GAUSSIAN 98. The electrostatic charges were calculated using several methods such as semiempirical AM1, density functional B3LYP/3-21G*, and ab initio HF/3-21G*, MP2/3-21G* calculations within GAUSSIAN 98. Using the optimized geometries, the CoMFA results derived from the HF/3-21G method were better than those from AM1. The best CoMFA was obtained from HF/3-21G* optimized geometry and charges (R2 = 0.977). Using the optimized geometries, the CoMFA results derived from the HF/3-21G methods were better than those from AM1 calculations. The training set of 43 molecules gave higher R2 (0.989-0.977) from HF/3-21G* optimized geometries than R2 (0.966-0.911) values from AM1 optimized geometries. The test set of five molecules also suggested that HF/3-21G* optimized geometries produced good CoMFA models to predict bioactivity of sigma 1 receptor ligands but AM1 optimized geometries failed to predict reasonable bioactivity of sigma 1 receptor ligands using different calculations for atomic charges.     

ChemInform Abstract: Structures and Bonding of Auropolyboroenes [Au2(B4)xB3]‐, [Au2(B4)xB2]2‐ and [Au2(B4)xB]+(x = 2, 3): Comparison with Dihydride Polyboroenes.

Equilibrium structures of title ions are determined by DFT calculations (TPSS with the τ‐dependent gradient‐corrected functional as implemented in the GAUSSIAN09 code).     

Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM‐MD simulation”

We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011 , 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN‐03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open‐source codes more generally. © 2012 Wiley Periodicals, Inc.     

卤代PNNO的磁性及相变温度

采用量子化学GAUSSIAN 92 UHF PM3方法对卤素取代的PNNO进行研究, 讨论了它的磁性及电子结构, 并用自旋波理论预测了其二聚物的磁性相变温度(Tc), 与用同样方法得到的对位硝基取代的PNNO相变温度比较, 发现卤代PNNO有更高的相变温度。     

An efficient UMP2 program

Timings are reported for 6-31G*/UMP2 calculations on planar allene, twisted ethylene, cyclopropenyl anion, allyl, ethyl, isopropyl and CF₃ radicals performed by means of the programs GAUSSIAN 80 and HONDO UMP2. The comparison of the two programs is used for pointing out several factors affecting the speed of MP2 calculations.