Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

Development of spin‐dependent relativistic open‐shell Hartree–Fock theory with time‐reversal symmetry (I): The unrestricted approach

An open‐shell Hartree–Fock (HF) theory for spin‐dependent, two‐component relativistic calculations, termed the Kramers‐unrestricted HF (KUHF) method, is developed. The present KUHF method, which is formulated as a relativistic counterpart of nonrelativistic UHF, is based on quaternion algebra and partly uses time‐reversal symmetry. The fundamental characteristics of KUHF are discussed in this study. From numerical assessments, it was revealed that KUHF gives a corresponding solution to nonrelativistic UHF; furthermore, KUHF properly describes spin‐orbit interactions. In addition, KUHF can improve the self‐consistent field convergence behavior in spin‐dependent calculations, for example, for f‐block elements.     

Performance of the elongation method with larger basis sets

The elongation method proposed by Imamura serves as a theoretical model for polymerization processes. It can now be used together with larger basis sets, Hartree–Fock and density functional methods from the Gaussian 94 package with direct self‐consistent field (SCF). This allows electronic structure calculation of elongating clusters with an efficiency superior to full cluster calculations and a precision superior to previous versions of our elongation method. Performance and accuracy compared with full cluster calculations on a regular polymer using the BLYP/6‐31G(d, p) method. Interaction energies of water and hydrogen fluoride polymers of increasing length are compared between HF, BLYP methods and 4‐31G, 6‐31G(d, p) basis sets: Diffuse and polarization functions have a large influence on the interaction energy on both polymers. Local density of states are calculated for different cluster lengths. They are in good agreement with full cluster calculations. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 35–47, 1999     

Kernel energy method: Basis functions and quantum methods

The kernel energy method (KEM) has been illustrated with peptides and has been shown to reduce the computational difficulty associated with obtaining ab initio quality quantum chemistry results for large biological compounds. In a recent paper, the method was illustrated by application to 15 different peptides, ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate Hartree–Fock (HF) molecular energies within the model, using Slater‐type orbital (STO)‐3G basis functions. A question arises concerning whether the results obtained from the use of KEM are wholly dependent on the STO‐3G basis functions that were employed, because of their relative simplicity, in the first applications. In the present work, it is shown that the accuracy of KEM does not depend on a particular choice of basis functions. This is done by calculating the ground‐state energy of a representative peptide, ADPGV7B, containing seven amino acid residues, using seven different commonly employed basis function sets, ranging in size from small to medium to large. It is shown that the accuracy of the KEM does not vary in any systematic way with the size or mathematical completeness of the basis set used, and good accuracy is maintained over the entire variety of basis sets that have been tested. Both approximate HF and density functional theory (DFT) calculations are made. We conclude that the accuracy inherent in the KEM is not dependent on a particular choice of basis functions. The first application, to 15 different peptides mentioned above, employed only HF calculations. A second question that arises is whether the results obtained with the use of KEM will be accurate only within the HF approximation. Therefore, in the present work we also study whether KEM is applicable across a variety of quantum computational methods, characterized by differing levels of accuracy. The peptide, Zaib4, containing 74 atoms, was used to calculate its energy at seven different levels of accuracy. These include the semi‐empirical methods, AM1 and PM5, a DFT B3LYP model, and ab initio HF, MP2, CID, and CCSD calculations. KEM was found to be widely applicable across the spectrum of quantum methods tested. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Vibrational spectra and conformations of 1,4-cyclohexadiene and its oxygen analogues: ab initio and density functional calculations

The vibrational spectra and ring-puckering potential energy functions of 1,4-cyclohexadiene, 4H-pyran and 1,4-dioxin have been examined using a density functional theory (DFT) method as well as the Hartree–Fock (HF) and second-order Møller–Plesset (MP2) methods. The calculated vibrational frequencies and potential energy functions of those molecules have been compared with previously reported experimental data and MM3 results. For all three molecules, the DFT method using Becke's three-parameter functional (B3LYP) has led to the prediction of more accurate vibrational frequencies than the HF and MP2 methods. The enlargement of the basis set at the B3LYP levels has improved the accuracy of calculated vibrational frequencies. In particular, the C–O–C=C torsional force field parameters obtained from the B3LYP method have correctly predicted the ring-puckering potential energy functions of the oxygen-containing analogues, 4H-pyran and 1,4-dioxin, which could not be done by the MM3 method.     

密度泛函理论与Hartree-Fock方法混合处理中的稳态相关能校正

本文分析了通常的Hartree-Fock(HF)相关能定义和密度泛函理论(DFT)中的相关能定义的等价性条件。认为在参考电子密度与真实密度相差很大时两种定义是不等价的, 严格的DFT相关能比HF相关能(绝对值)要大。而在DFT与HF混合处理中得到的相关能比HF相关能(绝对值)要小, 两者之差相当于稳态相关能。实际计算表明, 通过合理地选择组态, 采用有限CI可以求得这一差值。本文描绘了双原子分子H2(X^1∑g^+), HF(X^1∑^+), N2(X^1∑g^+)的势能曲线, 结果比完全CISD和MP4的曲线还要好。H2的离解能是0.17a.u., 逼近实验值0.1747a.u..。     

Electron correlation in the interacting quantum atoms partition via coupled‐cluster lagrangian densities

The electronic energy partition established by the Interacting Quantum Atoms (IQA) approach is an important method of wavefunction analyses which has yielded valuable insights about different phenomena in physical chemistry. Most of the IQA applications have relied upon approximations, which do not include either dynamical correlation (DC) such as Hartree‐Fock (HF) or external DC like CASSCF theory. Recently, DC was included in the IQA method by means of HF/Coupled‐Cluster (CC) transition densities (Chávez‐Calvillo et al., Comput. Theory Chem. 2015, 1053, 90). Despite the potential utility of this approach, it has a few drawbacks, for example, it is not consistent with the calculation of CC properties different from the total electronic energy. To improve this situation, we have implemented the IQA energy partition based on CC Lagrangian one‐ and two‐electron orbital density matrices. The development presented in this article is tested and illustrated with the H₂, LiH, H₂O, H₂S, N₂, and CO molecules for which the IQA results obtained under the consideration of (i) the CC Lagrangian, (ii) HF/CC transition densities, and (iii) HF are critically analyzed and compared. Additionally, the effect of the DC in the different components of the electronic energy in the formation of the T‐shaped (H₂)₂ van der Waals cluster and the bimolecular nucleophilic substitution between F^– and CH₃F is examined. We anticipate that the approach put forward in this article will provide new understandings on subjects in physical chemistry wherein DC plays a crucial role like molecular interactions along with chemical bonding and reactivity. © 2016 Wiley Periodicals, Inc.     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

CO在Cu/ZnO上吸附的簇模型研究

采用DFT方法和HF方法对CO在Cu／ZnO催化剂上的Zn（Ⅱ）和Cu（Ⅰ）表面位上的吸附行为进行了比较研究.结果表明：HF方法给出了较弱的M-CO（M＝Zn（Ⅱ），Cu（Ⅰ））表面吸附键描述，但无法正确预测其强弱顺序，MP2方法与DFT方法则给出与实验事实一致的描述.文章还对CO／铜基催化剂吸附体系的IR光谱进行了合理的理论预测.     

Towards a photophysical model for 5-hydroxyflavone

The photophysics of the 5-hydroxyflavone (5HF) molecule has been revised. Conversely to what has been hitherto reported, the proton-transfer fluorescence of 5HF has been recorded under xenon lamp excitation in cyclohexane, hexane, ethanol, ethyl ether, 2-methyl-2-propanol, and dimethylsulfoxide at room temperature. The 5HF fluorescence spectra only exhibit one emission band centered at ca. 700 nm. A small photoreaction quantum yield of 10(-5)-10(-6) denotes the great photostability exemplified by 5HF in hydrocarbon solvent, ethanol, and dimethylsulfoxide. This great photostability is predominantly explained owing to an internal conversion process from the first excited singlet state 1(pi,pi*)1 (S1), which has a repulsive (proton-transfer) potential energy curve with respect to the stretching of the OH bond and only one energy minimum for the proton-transfer tautomer. The S1'-S0' energy gap proves to be small because of important modifications found in the molecular geometry of 5HF upon photoexcitation. A computational strategy, based upon theoretical calculations at the B3LYP density functional theory (DFT) and time-dependent DFT levels, supports the experimental spectroscopic evidence. Also an abnormal singlet-triplet splitting for a pi,pi* configuration has been found in 5HF.     

Molecular (hyper)polarizabilities computed by pseudospectral methods

We have developed algorithms based on pseudospectral (PS) ab initio electronic structure methods for solving the first- and second-order Hartree-Fock/Kohn-Sham equations and evaluating molecular polarizabilities and first- and second-order hyperpolarizabilities in the spin-restricted and spin-unrestricted formalisms at the Hartree-Fock (HF) and density functional theory (DFT) levels. We carry out calculations on 50 small molecules to test the accuracy of the PS approach. Our results demonstrate that the molecular polarizability alpha computed by the PS method is essentially identical to the value obtained from conventional methods for both HF and DFT calculations, while the first-order hyperpolarizability beta and second-order hyperpolarizability gamma have mean unsigned percentage differences of 1.26% and 0.62% (HF) and 0.78% and 0.65% (DFT), respectively. We also present CPU timing comparisons between the PS and conventional methods at the 6-31 G(**) level for 14 molecules having 185 to 1185 basis functions. The timing results show that the PS method is 25 (PS-HF) and 13 (PS-DFT) times faster than the conventional method for a system with 500 basis functions. The PS methods are found scale as N(2.70) (PS-HF) and N(2.40) (PS-DFT), while the conventional methods scale as N(2.93) (PRISM-HF) and N(2.87) (PRISM-DFT), where N is the number of basis functions.     

Molecular structure and vibrational spectra of γ-oxo [1,1′-biphenyl]-4-butanoic acid (fenbufen) and its interaction with ofloxacin

The Fourier transform Raman and Fourier transform infrared spectra of fenbufen (γ-oxo [1,1′-biphenyl]-4-butanoic acid) were recorded in the solid phase. The gas-phase structure and conformational properties of fenbufen were determined by quantum-chemical calculations (HF and DFT/B3LYP with 6-311++G(d,p) basis set). The harmonic wave numbers were calculated by the density functional theory (DFT) calculations with B3LYP functional and 6-311++G(d,p) basis set, and the scaled values were in good agreement with the majority of the experimental observations. A complete assignment of the fundamentals was proposed based on the total energy distribution (TED) calculation. The possible interaction between fenbufen and ofloxacin which is a synthetic antimicrobial agent was investigated. The changes observed in some bands of mixed drug indicated that there is an interaction between the two drug molecules.     

Basis set and method dependence in quantum theory of atoms in molecules calculations for covalent bonds

The influence of various small- and medium-size basis sets used in Hartree-Fock (HF) and density functional theory (DFT)/B3LYP calculations on results of quantum theory of atoms in molecules based (QTAIM-based) analysis of bond parameters is investigated for several single, double, and triple covalent bonds. It is shown that, in general, HF and DFT/B3LYP methods give very similar QTAIM results with respect to the basis set. The smallest 6-31G basis set and DZ-quality basis sets of Dunning type lead to poor results in comparison to those obtained by the most reliable aug-cc-pVTZ. On the contrary, 6-311++G(2df,2pd) and in a somewhat lesser extent 6-311++G(3df,3pd) basis sets give satisfactory values of QTAIM parameters. It is also demonstrated that QTAIM calculations may be sensitive for the method and basis set in the case of multiple and more polarized bonds.     

Geometric and chelation influences on the electronic structure and optical properties of tetra(carboxylic acid)phenyleneethynylene dyes

A quantum-chemical study on the consequences of geometric modification and chelation on the electronic structure and optical properties of a tetra(carboxylic acid)phenyleneethynylene dye, of interest for chemical sensing applications, is presented. Rotation within the central biphenylene and complexation with divalent metal ions--in particular Cu2+--lead to notable changes in the absorption and emission profiles. Calculations at both the density functional theory (DFT) and Hartree-Fock (HF) levels are used to evaluate geometric potential energy surfaces for rotation within the central biphenylene unit; HF coupled with configuration interaction singles (HF-CIS) is used to investigate the first excited state of the dye. Time-dependent DFT (TDDFT) calculations are employed to assess changes in optical absorption and fluorescence as a function of geometry and chelation.     

Evaluation of DFT methods for computing the interaction energies of homomolecular and heteromolecular dimers of monosubstituted benzene

We present density functional theory (DFT) interaction energies for the sandwich and T‐shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree–Fock (HF) and second‐order Møller–Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene–dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

环己烯分子2b和3a轨道的电子动量谱学研究

The electron momentum profile for inner valence orbitals 2b and 3a of cyclohexene (C6H10) was firstly studied by the binary (e,2e) electron momentum spectroscopy (EMS), at the impact energy of 1200 eV plus binding energy using symmetric non-coplanar kinematics. The complete valence shell binding energy spectrum of C6H10 was also obtained. The experimental momentum profile of the summed orbitals was compared with Hartree Fock (HF) and density functional theory (DFT) methods with various basis sets. The experimental measurement was well described by the HF and DFT calculations except for the low-p region (p<0.25 a.u.). Experimental small “turn-up” effects of momentum profile in the low-p region could be due to the distorted wave effects.     

Theoretical Studies on the Thermodynamic Properties and Detonation Performances of Bicyclic Nitramines： TNAD Isomers

1 INTRODUCTION Nowadays, HEDMs have been receiving heated attention because of their superior explosive per- formances to the currently used materials. Searching for novel HEDMs to meet the future demands has become one of the most activated regions and seems to be never ending. As is well known, nitramines have important applications in both civilian and military fields for a long time. This group of com- pounds is still a source of explosives or propellants that possess predominantl…