Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

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.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

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.     

Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles

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.     

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

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.     

Geometric analysis of anharmonic downward distortion following paths

A mathematical aspect of the anharmonic downward distortion following (ADDF) path is discussed. The ADDF method is utilized as an automated reaction path search method, which can explore transition state geometries on a potential energy surface from a potential minimum. We show that the maximum number of the ADD stationary paths intersecting the potential minimum is 2^{f + 1} ? 2 , where f denotes the degree of freedom of the system. We also show that the bifurcation of the ADD stationary path is essential to detect all the transition states connected from a given minimum. The ADDF computation is demonstrated for a H₂O molecule in which pitchfork bifurcation is observed.     

Analysis of Non-innocence of Phosphaquinodimethane Ligands when Charge and Aromaticity Come into Play

Several phosphaquinodimethanes and their M(CO)₅ complexes (M=Cr, Mo, W) and model derivatives have been theoretically investigated regarding the quest of non-innocence. Computed structural and electronic properties of the P-Me/NH₂ substituted phosphaquinodimethanes and tungsten complexes revealed an interesting non-innocent ligand behaviour for the radical anion complexes with distonic ion character and a strong rearomatization of the middle phenyl ring. The latter was further probed taking also geometric aromaticity (HOMA) and quinoid distortion parameters (HOMQc) into account, as well as NICS(1). Furthermore, the effect of the P-substitution was investigated for real (or plausible) complexes and their free ligands focusing on the resulting aromaticity at the middle phenyl ring and vertical one-electron redox processes. The best picture of ligand engagement in redox changes was provided by representing NICS(1) values versus HOMA and the new geometric distortion parameter HOMQc8.     

空间遥感测绘光学系统研究综述

将遥感技术应用到测绘当中是现代地质测绘技术的发展趋势,随着光学载荷分辨率的不断提高,遥感测绘已经成为社会发展和国民经济发展的重要保障。光学载荷决定了测绘空间遥感器的分辨率、测绘精度、卫星平台体积与重量,是遥感器的核心部分。本文对高成像质量透射光学系统、同轴三反光学系统、离轴三反系统等常用的空间遥感测绘光学系统的结构形式和光学性能分别进行了介绍,并对处于研发阶段的新型空间反射光学系统的结构形式和光学性能进行了展望。分析认为,根据不同的应用环境和技术指标,合理选用不同种类的遥感测绘光学系统,可以最大程度利用平台资源,满足遥感测绘需求。     

Electronic structures of NbGen−/0/+ (n = 1–3) clusters from multiconfigurational CASPT2 and density matrix renormalization group-CASPT2 calculations

Density functional theory and multiconfigurational CASPT2 and density matrix renormalization group DMRG-CASPT2 have been employed to study the low-lying states of NbGe_n^−/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 NbGe_n⁻ (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.     

Benchmark approach to search of cost-effective and accurate density functional for homolytic cleavage of C─Mg bond of Grignard reagent

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.     

High Compression‐Induced Conductivity in a Layered Cu–Br Perovskite

We show that the onset pressure for appreciable conductivity in layered copper‐halide perovskites can decrease by ca. 50 GPa upon replacement of Cl with Br. Layered Cu–Cl perovskites require pressures >50 GPa to show a conductivity of 10^?4 S cm^?1, whereas here a Cu–Br congener, (EA)₂CuBr₄ (EA=ethylammonium), exhibits conductivity as high as 2×10^?3 S cm^?1 at only 2.6 GPa, and 0.17 S cm^?1 at 59 GPa. Substitution of higher‐energy Br 4p for Cl 3p orbitals lowers the charge‐transfer band gap of the perovskite by 0.9 eV. This 1.7 eV band gap decreases to 0.3 eV at 65 GPa. High‐pressure X‐ray diffraction, optical absorption, and transport measurements, and density functional theory calculations allow us to track compression‐induced structural and electronic changes. The notable enhancement of the Br perovskite's electronic response to pressure may be attributed to more diffuse Br valence orbitals relative to Cl orbitals. This work brings the compression‐induced conductivity of Cu‐halide perovskites to more technologically accessible pressures.