Mechanism for the gas‐phase reaction between OH and 3‐methylfuran: A theoretical study

The mechanism for the OH + 3‐methylfuran reaction has been studied via ab initio calculations to investigate various reaction pathways on the doublet potential energy surface. Optimizations of the reactants, products, intermediates, and transition structures are conducted using the MP2 level of theory with the 6‐311G(d,p) basis set. The single‐point electronic energy of each optimized geometry is refined with G3MP2 and G3MP2B3 calculations. The theoretical study suggests that the OH + 3‐methylfuran reaction is dominated by the formation of HC(O)CH?C(CH₃)CHOH (P7) and CH(OH)CH?C(CH₃)C(O)H (P9), formed from two low‐lying adducts, IM1 and IM2. The direct hydrogen abstraction pathways and the S_N2 reaction may play a minor or negligible role in the overall reaction of OH with 3‐methylfuran. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

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.     

亚烷基锡烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet alkylidenestannylene and ethylene has been investigated with MP2/3-21 G^* and B3LYP/3-21 G* methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//MP2/3-2 IG^* and CCSD(T)//B3LYP/3-21G^* methods, respectively. The results show that the dominant reaction pathway of the cycloaddition is that an intermediate (INT) is firstly formed between the two reactants through a barrier-free exothermic reaction of 39.7 kJ/mol, and the intermediate then isomerizes to a four-membered ring product (P2.1) via a transition state TS2.1 with a barrier of 66.8 kJ/mol.     

Gas-phase acidity, bond dissociation energy and enthalpy of formation of fluorine-substituted benzenes: A theoretical study

A variety of theoretical methods have been used to study the gas-phase acidity of benzene and its eleven fluorine-substituted derivatives: fluorobenzene, three isomers of difluorobenezene, three isomers of trifluorobenzene, three isomers of tetrafluorobenzene and 1,2,3,4,5-pentafluorobenzene. The high-level ab initio methods, G3//B3-LYP and CBS-QB3, are shown to reproduce experimental data to within an average of 1.9 and 1.4 kcal mol⁻¹, respectively. Of the lower-cost methods studied, M05-2X and MP2 showed the best overall performance with mean absolute deviations of just 1.2 and 1.1 kcal mol⁻¹, respectively. The effect of substitution and position on the acidity of the protons in the various compounds are studied and the structure-reactivity trends in these heterolytic C-H bond dissociation energies (BDEs) are compared with the corresponding homolytic C-H BDEs for the same species.     

Use of cluster expansion techniques in quantum chemistry. A linear response model for calculating energy differences

In this paper we have reviewed the theoretical framework of the coupled-cluster (cc) based linear response model as a tool for directly calculating energy differences of spectroscopic interest like excitation energy (ee), ionisation potential (ip) or electron affinity (ea). In this model, the ground state of a many-electron system is described as in a coupled cluster theory for closed shells. The electronic ground state is supposed to interact with an external photon field of frequencyw, and the poles of the linear response function as a function ofw furnish with the elementary excitations of the system. Depending on the general form of the coupling term chosen, appropriate difference energies like ee, ip or EA may be generated. Pertinent derivations of the general working equations are reviewed, and specific details as well as approximations for ee, ip or ea are indicated. It is shown that the theory bears a close resemblance to the equation of motion (eom) method but is superior to the latter in that the ground state correlation is taken to all orders and may be looked upon as essentially a variant of renormalisedtda. A perturbative analysis elucidating the underlying perturbative structure of the formulation is also given which reveals that the theory has a hybrid structure: the correlation terms are treated akin to an open shellmbpt, while the relaxation terms are treated akin to a Green function theory. A critique of the methodvis-a-vis other cc-based approaches for difference energies forms the concluding part of our review.     

G3(QCI)模型化学方法

建立了非微扰外推模式下的几种G3(QCI)方法：G3(QCI/fu1)、G3(QCI/fu2)、G3(QCI/ful)//B3PW91和G3(QCI/fu2)//B3PW91.其中,电子能量用QCISD(T,FC)/G3large直接计算,芯电子相关能分别在MP2/6-31G(d)和MP2/6-31G(d,p)级别上计算,对125个G2-1 test set 的计算结果表明,总体精度与G3和G3 //B3LYP相当;平均绝对偏差分别为4.370、4.389、4.061和4.022kJ mol-1,相应G3和G3//B3LYP分别为4.27和4.05kJ mol-1.文章提出的方法排除了G3中外推办法的不确定因素,且更适用于非平衡几何构型体系能量的定量计算。     

过氧硝酸乙酰酯分解反应的速率常数

在G3MP2B3结构优化和能量计算的基础上, 采用RRKM理论和疏松过渡态模型重新估算了过氧硝酸乙酰酯(PAN)的热分解反应PAN→CH₃C(O)OO+NO₂(R1)的反应速率常数, 得到与实验值吻合的结果.用同样的模型计算了PAN→CH₃C(O)O+NO₃(R2)的反应速率常数. 结果表明, 在相同的反应条件下, R1是主要的分解通道, R2是次要通道, R2的反应速率常数比R1的小两个数量级.     

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.     

CH_3自由基和O（~3P）反应机理的量子化学研究

用分子轨道从头计算MP2（full）方法和密度泛函理论（DFT）中的B3LYP方法 研究了CH_3自由基和三线态O原子反应的微观机理，优化得到了反应途径上的反应 物、过渡态、中间体和产物的几何构型，通过振动分析对过渡态和中间体构型进行 了确认，在G3不平上计算了能量，同时用经典过渡态理论对该反应的绝对速率常数 进行了理论计算。研究结果表明：CH_3自由基与O（~3P）反应有四条不同的放热反 应通道，主反应通道为IM1→TS1→CH_2O + H，同时反应可彻底裂解生成CO, H_2 及H。     

Composite Correlated Molecular Orbital Theory Calculations of Ring Strain for Use in Predicting Polymerization Reactions

Strained ring systems play an important role in synthesis and can be characterized by the ring strain energy (RSE). The RSE of 3, 4, 5, and 6 membered saturated and unsaturated ring systems containing N, O, P, and S heteroatoms and H, F, SiMe₃, and SO₂Me substituents were calculated at the G3(MP2) composite correlated molecular orbital theory level using up to 5 models to predict the RSE. Generally, the RSE decreased as ring size increased with a substantial decrease from 4 to 5 membered rings. Replacement of a ring CH₂ with P or S reduced the RSE, consistent with less angle strain. The RSE for unsaturated systems were generally greater than for saturated systems due to increased angle strain. No general trends were found with respect to substituent effects. The RSE values suggest that 3-pyrroline and 2-pyrroline and their derivatives may be able to support ring opening metathesis polymerization and warrant further study.     

均三氮苯类除草剂结构与活性的理论研究

利用Gaussian03程序包中的B3LYP方法,选择6-31G基组对均三氮苯类除草剂及类似衍生物2-(4-溴苄氨基)-4-甲基-6-三氟甲基-1,3,5-三氮苯进行了量子化学计算,从理论上讨论了它们的空间结构、电子结构特征与活性的关系.计算结果表明:三氮苯环与N(7)和N(8)原子形成了共轭结构,分子活性大小与LUMO轨道的得电子能力以及在LUMO轨道中占主要成分的原子有重要关系.N(7)和N(8)连接单个具有推电子能力的基团,有利于生物活性的提高.对于2-(4-溴苄氨基)-4-甲基-6-三氟甲基-1,3,5-三氮苯中,N(8)和C(9)是重要的活性部位,和传统的均三氮苯类除草剂分子相比,与D1蛋白上不同的氨基酸残基发生了键合作用.     

Accessing the applicability of polarized protein‐specific charge in linear interaction energy analysis

The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein‐specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β‐secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic‐potential‐based charge fitting methods via a dual‐step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design. © 2014 Wiley Periodicals, Inc.     

thermocalc — A poor man's approach to computational thermochemistry

We present thermocalc, a Perl module to perform the automated calculation of atomization energies and heats of formation for lists of molecules. The methods used are based on density functional theory and second‐order perturbation theory to ensure that data sets of medium sized to large molecules can be run at reasonable throughput rates. The quantum chemical calculations are performed using the program package TURBOMOLE in a three‐step protocol. In a first step, a pre‐optimization of the structure and a zero‐point energy calculation are performed. As second step, a geometry optimization is being carried out, and the last step is a single point energy calculation. The level of theory used in the different steps can be modified by the user to allow for customized protocols. The performance of example protocols is investigated on different test sets of molecules. In the course of this work, a simple, but efficient one‐parameter correction term based on the shared electron numbers has been developed, which reduces the error of calculated heats of formation significantly. © 2012 Wiley Periodicals, Inc.     

Quantum-chemical investigation of the electrophile affinity of molecules of five-membered heterocycles with one hetero-atom and some model systems

Quantum-chemical calculations have been made of the energy characteristics of the molecules of pyrrole, furan, thiophene, and selenophene, the simplest derivatives of N, O, S, and Se with sp³-and sp²-hybridized C atoms and heteroatoms, and also of the products of addition of proton and certain other electrophiles to these molecules. The calculations were carried out by HF, B3LYP, and MP2 methods with the 6−31+G(d) basis set with corrections to the energy of zero-point vibrations. It was shown that the values of the affinity of the nitrogen-containing systems towards the electrophile were significantly greater than for their analogs, derivatives of chalcogens, while the relative stability of the onium states of the latter depends both on the hybridization of the heteroatoms, and also on the nature of the electrophile. Analysis of the obtained results made it possible to build a stability series of the onium compounds and to interpret the special features of the positional selectivity in electrophilic substitution reactions of five-membered heteroaromatic compounds with one heteroatom. Dedicated to the remarkable heterocyclic chemist Aleksandr Fedorovich Pozharskii on his 70th jubilee. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1645–1654, November, 2008.     

A theoretical study of the dihydrogen molecule confined inside carbon nanotubes

The aim of this work is to better understand the interaction between the confined dihydrogen molecule and armchair (2,2), (3,3) (4,4), (5,5), and (6,6) single‐walled carbon nanotubes (SWNT) using Restricted Hartree–Fock (RHF) and Density Functional Theory (DFT) methods using B3LYP and CAM‐B3LYP functionals. Depending on the calculation method and its orientation inside the nanotube, H₂ binds differently. We found that H? H bond length increases when H₂ is trapped in CNT (2,2) and decreases for CNT (3,3) and (4,4). The characteristics of confined H₂ in (5,5) and (6,6) nanotubes are similar to H₂ in a free state. © 2013 Wiley Periodicals, Inc.     

An empirical scheme for evaluating in situ bond energy from MNDO data

The in situ bond energy is evaluated from the resonance integral contribution to energy with a correction term of monatomic energy obtained from MNDO calculation. The sum of the in situ bond energies in a molecule is expected to be equal to its atomization energy. Root-mean-square error of heat of formation calculated from in situ bond energy for seventy nine molecules containing hydrogen, carbon, nitrogen, oxygen, and fluorine amounts to 5.5 kcal/mol. Correlations of in situ bond energy with contributional bond energy, bond dissociation energy, isolated stretching frequency, and bond length are performed and discussed.     

A DFT and AIM analysis of the spin–spin couplings across the hydrogen bond in the 2‐fluorobenzamide and related compounds

In 1975 a large number of coupling constants were measured in 2‐fluorobenzamide labeled with ¹⁵N. Some of them were assigned to couplings through intramolecular N? H···F hydrogen bonds (HBs). These couplings change dramatically when CDCl₃ is replaced by DMSO‐d₆. In this theoretical paper we provide density functional theory (DFT) calculations that justify the existence of a weak HB in the absence of solvent, while solvents that act as HB acceptors break down the intramolecular hydrogen bond (IMHB) of 2‐fluorobenzamide. Atoms in molecules (AIM) analyses and Steiner‐Limbach plots were used to analyze the structure of the compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical Study of Weakly Bound Dimers between Hydrogen Fluoride and Some Polar Molecules

Weakly bound linear and bent dimers, FH—X (where X = CO, OC, CNH, NCH, N₂O and ON₂), are investigated using the DFT B3LYP and ab initio MP2 methods with the same basis sets (6–311++G(3df,2pd)). The strengths of the H—C or H—N H‐bonds in dimers FH—CO, FH—CNH, and FH—N₂O are compared with those of the H—O or H—N H‐bonds in dimers FH—OC, FH—NCH, and FH—ON₂. The results obtained for the H‐bond distances, the elongation effect of the HF bond, the red shift of the HF stretching frequency, and the energy difference between the dimer and the charge transfer reveal that the H‐bonds of the first group of dimers are stronger than those of the second. The Gibbs energies calculated for the six dimer formations indicate that the weakly bound dimers are unstable at room temperature (T = 298 K) (FH—X's → FH + X's, ΔG < 0).     

Electronic structures and reactivities of iodinating agents in the gas phase and in solutions: A density functional study

The electronic and spatial structures of a broad spectrum of neutral compounds with X-Hal (X = N, O, Cl; Hal = Cl, Br, I) bonds and their protonated forms and of different electronic states of triiodide cation, I₃ ⁺, were determined from density functional B3LYP/6 311G* quantum chemical calculations. The effects of the structure of these compounds on the parameters of electrophilic reactivity were revealed and the thermochemical characteristics of homolytic and heterolytic X-Hal bond dissociation and of iodine transfer in hydroxyl-containing solvents were calculated. Due to low homolytic bond dissociation energies of X-I, the formation of molecular iodine and triiodide cation I₃ ⁺ becomes thermodynamically favorable and the cation should act as iodinating agent alternative to acylhypoiodites and N-iodoimides. The solvation effects of MeOH and CH₂Cl₂ on the X-Hal bond homolysis and heterolysis were determined using the PCM model. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1280–1288, August, 2006.