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1.
Hui Li Dmitri G. Fedorov Takeshi Nagata Kazuo Kitaura Jan H. Jensen Mark S. Gordon 《Journal of computational chemistry》2010,31(4):778-790
The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
2.
Fedorov DG Kitaura K Li H Jensen JH Gordon MS 《Journal of computational chemistry》2006,27(8):976-985
3.
3-(二氰亚甲基)-5,5-二甲基-1-(3-[9-(2-乙基-己基)-咔唑基]-乙烯基)环己烷(DCDHCC)是一种用于光电器件中的有机染料,它具有良好的发光特性.我们使用含时密度泛函方法(TD-PBE0,TD-BMK和TD-M06)以及极化连续模型(PCM)计算了该材料在溶剂中的吸收和发射特性.计算中使用了线性响应(LR)、态定(SS)两种溶剂模型和6-31G(d)、6-31+G(d,p)两种基组.计算了DCDHCC在苯、四氢呋喃和丙酮溶剂中的吸收和发射光谱,并与实验观测进行了比较.结果表明:对于吸收光谱的计算,杂化函数的影响大于基组和溶剂模型,在三种函数中BMK更适于研究DCDHCC的吸收光谱;而对于发射光谱,基组的影响最大,基组通过影响激发态构型从而影响发射光谱,对于激发态构型的优化需要使用6-31+G(d,p)基组.我们希望这些研究能对今后设计类似的发光分子有帮助. 相似文献
4.
Ajay Chaudhari Prabhat K. Sahu Shyi‐Long Lee 《International journal of quantum chemistry》2005,101(1):67-72
Hydrogen‐bonded formaldehyde oligomers (dimer to pentamer) are studied using density functional theory (DFT), the B3LYP method, and the 6‐311+G* basis set. Many‐body interaction energies are obtained to study the contribution of many‐body terms to binding energy. The basis set superposition error (BSSE)‐corrected total energies are ?229.08170, ?343.61410, ?458.16660, and ?572.70901 hartrees for dimer, trimer, tetramer, and pentamer, respectively, with corresponding binding energies ?2.55, ?4.86, ?6.99, and ?9.49 kcal/mol. Two‐body energies have been found to contribute significantly to the total binding energy in dimer to pentamer, whereas higher‐order interaction energies are negligible. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 相似文献
5.
采用密度泛函理论B3LYP/6-31+G(d,p)方法对氯化乙基吡啶([EPy]Cl)、溴化乙基吡啶([EPy]Br)的离子对进行了结构优化和频率分析, 并利用自洽反应场(SCRF)的导体极化连续模型(CPCM)考察了离子液体液相下的结构及相互作用. 得到了两种离子液体的离子对在气相、液相下最稳定结构及气相红外光谱特征值, 两种离子液体的离子对结构存在相似性, 红外光谱特征值与文献值比较吻合. 应用自然键轨道(NBO)理论分析了离子对中原子电荷分布及电荷转移情况, 结果证明两种离子液体中阴阳离子间除了静电相互作用外还存在着氢键作用. 通过对比气相及液相下的几何参数、相互作用能及NBO分析结果, 发现液相下阴阳离子的相互作用明显降低. 液相环境抵消了大部分阴阳离子间的静电作用, 导致液相下阴阳离子间相互作用的减小. 相似文献
6.
The 96 pKa values of 85 carboxylic acids in aqueous solution were calculated with the density functional theory method at the level of B3LYP/6‐31+G(d,p) and the polarizable continuum model (PCM) was used to describe the solvent. In the calculations of pKa values, the dissociation Gibbs free energies were directly calculated using carboxylic acid dissociation reactions in aqueous solution, i. e., no thermodynamic cycle was employed, which is different from the previous literatures. A highly significant correlation of R2=0.95 with a standard deviation (SD) of 0.36 between the experimental pKa values and the calculated dissociation Gibbs free energies [ΔG(calc.)] was found. The slope of pKa vs. (G(calc.)/(20303RT) is only 47.6% of the theoretically expected value, which implies that the ΔG(calc.) value from the theoretical calculation is larger than the actual one for all 85 carboxylic acids studied. Thus, by adding the 0.476 scaling‐factor into the slope, we can derive a reliably procedure that can reproduce the experimental pKa values of carboxylic acids. The pKa values furnished by this procedure are in good agreement with the experimental results for carboxylic acids in aqueous solution. 相似文献
7.
Roberto Cammi 《Journal of computational chemistry》2015,36(30):2246-2259
A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported. © 2015 Wiley Periodicals, Inc. 相似文献
8.
Christian Silvio Pomelli Jacopo Tomasi Maurizio Cossi Vincenzo Barone 《Journal of computational chemistry》1999,20(16):1693-1701
A new computational strategy for the building of molecular cavities (named DefPol) has been linked to the most recent implementation of the polarizable continuum model (PCM) for the representation of solvent effects on physicochemical properties of large molecules. Free energies, analytical gradients, and Hessians can be computed in this framework in the rigid cavity approximation. Coupling DefPol cavities with a number of other recent improvements of the standard algorithm (e.g., effective use of symmetry, iterative procedures with linear scaling) significantly enlarges the dimensions of systems amenable to refined computations and strongly reduces the gap between computations for isolated molecules and in solution. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1693–1701, 1999 相似文献
9.
We present a detailed study of harmonic vibrational frequencies obtained with the self-consistent charge density functional tight-binding (SCC-DFTB) method. Our testing set comprises 66 molecules and 1304 distinct vibrational modes. Harmonic vibrational frequencies are computed using an efficient analytical algorithm developed and coded by the authors. The obtained results are compared to experiment and to other theoretical findings. Scaling factor for the SCC-DFTB method, determined by minimization of mean absolute deviation of scaled frequencies, is found to be 0.9933. The accuracy of the scaled SCC-DFTB frequencies is noticeably better than for other semiempirical methods (including standard DFTB method) and approximately twice worse than for other well established scaled ab initio quantum chemistry methods (e.g., HF, BLYP, B3LYP). Mean absolute deviation for the scaled SCC-DFTB frequencies is 56 cm(-1), while standard deviation is 82 cm(-1), and maximal absolute deviation is as large as 529 cm(-1). Using SCC-DFTB allows for substantial time savings; computational time is reduced from hours to seconds when compared to standard ab initio techniques. 相似文献
10.
Dedachi K Hirakawa T Fujita S Khan MT Sylte I Kurita N 《Journal of computational chemistry》2011,32(14):3047-3057
Thermolysin (TLN) is a metalloprotease widely used as a nonspecific protease for sequencing peptide and synthesizing many useful chemical compounds by the chemical industry. It was experimentally shown that the activity and functions of TLN are inhibited by the binding of many types of amino acid dipeptides. However, the binding mechanisms between TLN and dipeptides have not been clarified at the atomic and electronic levels. In this study, we investigated the binding mechanisms between TLN and four dipeptides. Specific interactions and binding free energies (BFEs) between TLN and the dipeptides were calculated using molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital (FMO) methods. The molecular systems were embedded in solvating water molecules during calculations. The calculated BFEs were qualitatively consistent with the trend of the experimentally observed inhibition of TLN activity by binding of the dipeptides. In addition, the specific interactions between the dipeptides and each amino acid residue of TLN or solvating water molecules were elucidated by the FMO calculations. 相似文献
11.
William H. Stevenson Michael J. McQuaid 《International journal of quantum chemistry》2010,110(7):1376-1393
Aqueous‐phase dissociation constants (Ka) for the conjugate acids of a series of 2‐azidoethanamine bases: R1N(R2)CH2CH2N3 ( 1 , R1 = CH3, R2 = H; 2 , R1 = CH3, R2 = CH3; 3 , R1 = CH2CH3, R2 = CH2CH3; 4 , R1/R2 = CH2CH2CH2CH2 ; 5 , R1/R2 = CH2CH2OCH2CH2 ; 6 , R1 = CH2CH3, R2 = CH2CH2N3) were measured and found to fall between those for analogous unfunctionalized and cyano‐functionalized ethanamines. To explore the possibility of a relationship existing between the constants and molecular geometry, a theoretically based study was conducted. In it, the Gibbs free energies of aqueous‐phase (equilibrium) conformers of the bases and their conjugate acids were determined via a density functional theory/polarizable continuum model method. The results indicate that an attractive interaction between the amine and azide groups that underlies the lowest‐energy gas‐phase conformer of 2 is negated in an aqueous environment by solvent–solute interactions. The magnitudes of the free energy changes of solvation and −TS (entropic) energies of the conformers of the 2‐azidoethanamines and their conjugate acids are observed to correlate with the magnitude of the separation between the conformers' amine and azide groups. However, those correlations are not by themselves sufficient to predict the relative free energies of a molecule's conformers in an aqueous environment. That insufficiency is due to the influence of the correlations being mitigated by three other parameters that arise within the thermodynamic framework employed to compute the observable. The nature of those parameters is discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 相似文献
12.
1,2,3-三氮杂苯－(水)3复合物多体相互作用 总被引：5，自引：0，他引：5
The interaction between 1,2,3-triazine and three water molecules was studied using density functional theory B3LYP method at 6-31-t＋＋G^＊＊ basis set. Various structures for 1,2,3-triazine-（water）n （n= 1, 2, 3） complex were investigated and the different lower energy structures were reported. Many-body analysis was also carded out to obtain relaxation energy and many-body interaction energy （two, three, and four-body）, and the most stable conformer has the basis set superposition error corrected interaction energy of -- 102.61 kJ/mol. The relaxation energy, two- and three-body interactions have significant contribution to the total interaction energy whereas four-body interaction was very small for 1,2,3-triazine-（water）3 complex. 相似文献
13.
Shulei Zhao Zhengyu Zhou Wenjuan Wang Hongkun Ma 《International journal of quantum chemistry》2007,107(4):1015-1026
Six stationary points of alaninamide have been located on the potential surface energy (PES) at the B3LYP/6‐311++G(2d,2p) level of theory both in the gas phase and in aqueous solution. In the aqueous solution, to take the water solvent effect into account, the polarizable continuum model (PCM) method has been used. Accurate geometric structures and their relative stabilities have been investigated. The results show that the intramolecular hydrogen bond plays a very important role in stabilizing the global minimum of the alaninamide. Moreover, the consistent result in relative energy using high‐level computations, including the MP2 and MP3 methods with the same basis set [6‐311++G(2d,2p)], indicates that the B3LYP/6‐311++G(d,p) level may be applied to the analogue system. More importantly, the optical rotation of the optimized conformers (both in the gas phase and in aqueous solution) of alaninamide have been calculated using the density functional theory (DFT) and Hartree–Fock (HF) method at various basis sets (6‐31+G*, 6‐311++G(d,p), 6‐311++G(2d,2p) and aug‐cc‐pvdz). The results show that the selection of the computation method and the basis set in calculation has great influence on the results of the optical rotations. The reliability of the HF method is less than that of DFT, and selecting the basis set of 6‐311++G(2d,2p) and aug‐cc‐pvDZ produces relative reliable results. Analysis of the computational results of the structure parameters and the optical rotations yields the conclusion that just the helixes in molecules caused the chiral molecules to be optical active. The Boltzmann equilibrium distributions for the six conformers (both in the gas phase and in the aqueous solution) are also carried out. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 相似文献
14.
15.
Wang FT Chen L Tian CJ Meng Y Wang ZG Zhang RQ Jin MX Zhang P Ding DJ 《Journal of computational chemistry》2011,32(15):3264-3268
The adsorption of six free radicals (FRs) respectively on a graphene fragment was studied using a density functional tight‐binding method with the inclusion of an empirical dispersion term in total energy. The results indicate that the different interaction paths between the FRs and the graphene lead to different forms of physical (PA) or chemical adsorptions (CA). The CA appears only in the condition where some of the nonhydrogen atoms are closer to the graphene, with the deformation occurring in the latter. The charge transfer increases with the increase in adsorption energy in every FR‐graphene system. Although the deformation in the graphene is negligible in all PA cases, the FR is closer to the graphene and the graphene deformation is clearer in all CA cases, with all atomic displacements being larger than 0.1 Å. Our findings are useful not only for FR scavenging but also for studying the interaction between general molecules and material surfaces. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 相似文献
16.
Hiroaki Nishizawa Yoshifumi Nishimura Masato Kobayashi Stephan Irle Hiromi Nakai 《Journal of computational chemistry》2016,37(21):1983-1992
The linear‐scaling divide‐and‐conquer (DC) quantum chemical methodology is applied to the density‐functional tight‐binding (DFTB) theory to develop a massively parallel program that achieves on‐the‐fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC‐DFTB potential energy surface are implemented to the program called DC‐DFTB‐K. A novel interpolation‐based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC‐DFTB‐K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC‐DFTB‐K program, a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. 相似文献
17.
New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs. 相似文献
18.
An efficient version of the polarizable continuum model for solvation has been implemented in the Gaussian density-functional-based code called deMon. Solvation free energies of representative compounds have been calculated as a preliminary test. The hydration effects on the reaction profile of the Cl−+CH3Cl→ClCH3+Cl− reaction and the thermodynamics of the Menschutkin reaction have also been investigated. Finally, the conformational behavior of the 1,2-diazene cis–trans isomerization process in water was examined. Comparisons between the results obtained and the available experimental data and previous theoretical computations have been made. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 290–299, 1998 相似文献
19.
S. Chiodo G. N. Chuev S. E. Erofeeva M. V. Fedorov N. Russo E. Sicilia 《International journal of quantum chemistry》2007,107(2):265-274
The solvent response on the solute is calculated by the reference interaction site model (RISM) and by the polarizable continuum model (PCM) methods. The linearized RISM technique is developed to treat free energies of atomic and polyatomic ions in water. An empirical repulsive bridge is used for the RISM calculations. The solvent electrostatic potential is approximated by a linear dependence on the solute atomic charges. For a series of monovalent polyatomic cations and anions, the method provides free energies deviating by few percent from the experimental data. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 相似文献
20.
This paper addresses the issue of accurately describing the structures and properties of electronically excited systems embedded in an environment, through multiscale approaches combining quantum-mechanical (QM) and polarizable classical representations of the system and environment, respectively. Such approaches represent an efficient strategy and allow to effectively study the excited states of molecular systems in the condensed phase, still maintaining the computational efficiency and the physical reliability of the ground-state calculations. The most important theoretical and computational aspects of the coupling between the QM system and the polarizable environment are presented and discussed. Even if these approaches already reached an evident degree of maturity, they can still be subject to further development, in order to achieve their full potential. This perspective presents an overview of the state of the art of these strategies, showing the fields of applicability and indicating the current limitations, which need to be overcome in future developments. 相似文献