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71.
Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation
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The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. 相似文献
72.
Svitlana V. Shishkina Irina S. Konovalova Sergiy M. Kovalenko Dmitriy V. Kravchenko Natalya D. Bunyatyan 《Acta Crystallographica. Section C, Structural Chemistry》2021,77(1):40-48
Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C11H10N2O2S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure. 相似文献
73.
After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available. 相似文献
74.
Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on 13C and 15N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on 13C chemical shifts are investigated as a possible means of estimating hydrogen bond energies. 相似文献
75.
Density functional theory and multiconfigurational CASPT2 and density matrix renormalization group DMRG-CASPT2 have been employed to study the low-lying states of NbGen−/0/+ (n = 1–3) clusters. With the DMRG-CASPT2 method, the active spaces are extended to a size of 20 orbitals. For most of the states, the CASPT2 relative energies are comparable with the DMRG-CASPT2 results. The leading configuration, bond distances, vibrational frequencies, and relative energies of the low-lying states of these clusters were calculated. The ground states of these clusters were computed to be 3Δ, 4Φ, and 5Φ of NbGe−/0/+; 3A2, 4B1, and 3B1 of cyclic-NbGe2−/0/+; and 1A′, 12A″ and 12A′′ (2E), and 3A″ of tetrahedral-NbGe3−/0/+ isomers. For NbGe cluster, our calculations proposed that the 6∑ is almost degenerate with the 4Φ with the CASPT2 and DMRG-CASPT2 relative energies of 0.05 and 0.06 eV. The adiabatic detachment energies of NbGen− (n = 1–3) clusters were estimated to be 1.46, 1.55, and 2.18 eV by the CASPT2 method. The relevant detachment energies of the anionic ground state and the ionization energies of the neutral ground states are evaluated at the CASPT2 level. 相似文献
76.
Naveen Kosar Khurshid Ayub Mazhar A. Gilani Faheem Shah Tariq Mahmood 《International journal of quantum chemistry》2020,120(4):e26106
Grignard reactions are of importance in organic chemistry for the synthesis β-keto esters and diethyl malonate, alcohols, aldehydes or ketones, monocarboxylic acids, and other organometallic compounds. Generally, the heterolytic dissociation of C─Mg bond in Grignard reagent is the key step in these reactions. Recently, homolytic cleavage of the C─Mg bond in Grignard reagents has been reported in the preparation of stable radicals. These reactive species react with other compounds, which result in the formation of hydrocarbons and their derivatives. Therefore, the study of homolytic cleavage of C─Mg bonds is quite vital to better understand the kinetics and thermodynamics of these reactions. In the current study, a benchmark approach is adopted to find a cost-effective and accurate density functional (DF) for bond dissociation energies measurement of the C─Mg bond of Grignard reagents. Twenty-nine DFs from 13 density functional theory (DFT) classes with three types of basis sets (Pople' 6-31G(d) and 6-311G(d), Dunning's aug-cc-pVDZ, and Karlsruhe' def2-SVP basis sets) are implemented for the measurement of dissociation energies of the C─Mg bond. Theoretical dissociation energy values are compared with experimental reported values of the C─Mg bond of selected Grignard reagents. TPSSTPSS of the meta-GGA class with 6-31G (d) basis set gave accurate results, and its Pearson's correlation is 0.95. SD, root mean square deviation, and mean unsigned error of this method are 2.36 kcal mol−1, 2.33 kcal mol−1, and −0.46 kcal mol−1, respectively. TPSSTPSS of the meta-GGA class is a one-electron, self-interaction, error-free Tao-Perdew-Staroverov-Scuseria functional that performed better with the 6-31G(d) basis set. 相似文献
77.
Aleksandra Bocian Adam Gorczyski Dawid Marcinkowski Grzegorz Dutkiewicz Violetta Patroniak Maciej Kubicki 《Acta Crystallographica. Section C, Structural Chemistry》2020,76(4):367-374
The intermolecular interactions in the structures of a series of Schiff base ligands have been thoroughly studied. These ligands can be obtained in different forms, namely, as the free base 2‐[(2E)‐2‐(1H‐imidazol‐4‐ylmethylidene)‐1‐methylhydrazinyl]pyridine, C10H11N5, 1 , the hydrates 2‐[(2E)‐2‐(1H‐imidazol‐2‐ylmethylidene)‐1‐methylhydrazinyl]‐1H‐benzimidazole monohydrate, C12H12N6·H2O, 2 , and 2‐{(2E)‐1‐methyl‐2‐[(1‐methyl‐1H‐imidazol‐2‐yl)methylidene]hydrazinyl}‐1H‐benzimidazole 1.25‐hydrate, C13H14N6·1.25H2O, 3 , the monocationic hydrate 5‐{(1E)‐[2‐(1H‐1,3‐benzodiazol‐2‐yl)‐2‐methylhydrazinylidene]methyl}‐1H‐imidazol‐3‐ium trifluoromethanesulfonate monohydrate, C12H13N6+·CF3O3S?·H2O, 5 , and the dicationic 2‐{(2E)‐1‐methyl‐2‐[(1H‐imidazol‐3‐ium‐2‐yl)methylidene]hydrazinyl}pyridinium bis(trifluoromethanesulfonate), C10H13N52+·2CF3O3S?, 6 . The connection between the forms and the preferred intermolecular interactions is described and further studied by means of the calculation of the interaction energies between the neutral and charged components of the crystal structures. These studies show that, in general, the most important contribution to the stabilization energy of the crystal is provided by π–π interactions, especially between charged ligands, while the details of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures, a very interesting example of the nontypical F…O interaction was found and its length, 2.859 (2) Å, is one of the shortest ever reported. 相似文献
78.
在全电子相对论BVP86/DNP水平下对CO在Au55,Ag55和Cu55团簇上的吸附进行了比较研究,并考察了电荷对吸附的影响.计算结果表明,CO在Au55团簇上吸附能最大,其次为Cu55团簇,最弱的为Ag55团簇.团簇电荷对C—O键活化和CO与团簇表面原子成键影响较小.金团簇的电荷对吸附能影响较大,而银和铜团簇的电荷对吸附能影响较小.CO吸附到团簇上导致团簇上电子向CO转移.C—O键活化强度与吸附位置密切相关,其中孔位吸附导致C—O键活化程度最大,最弱的为顶位吸附.CO在金团簇上吸附具有较好选择性,而在银和铜团簇上吸附无选择性. 相似文献
79.
采用鞍点截断变分方法和鞍点复数转动技术,计算和分析了锂洞原子双激发共振态[1s(2s2p)3P]2P0的鞍点能量和波函数.计算结果表明这种理论计算方法是获得高精度的能量值的重要保证. 相似文献
80.