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.     

可见光驱动丰产金属卟啉类配合物催化的二氧化碳选择性还原反应

随着能源短缺和环境问题日益突出, 寻找清洁和可再生能源来替代化石燃料是本世纪科学家面临的最紧迫的任务之一. 为了实现我国“双碳”战略目标, 利用太阳能将二氧化碳(CO₂)转化为清洁燃料和化学品是实现社会可持续发展的途径之一. 催化剂是CO₂光还原技术的核心组成部分, 其可以吸附气态CO₂分子, 在可见光照射下将CO₂还原为一氧化碳(CO)、 甲酸(HCOOH)、 甲醇(CH₃OH)或甲烷(CH₄)等能源小分子. 目前, 新型CO₂还原光催化体系的开发取得了很好的进展. 本文综合评述了近年来均相及非均相丰产金属卟啉类催化剂在光催化CO₂还原中的研究进展, 并对在金属卟啉均相催化剂作用下, CO₂光还原为CO或CH₄的反应机理分别进行了介绍, 还讨论了金属卟啉基多孔有机聚合物与卟啉有机金属框架在光催化CO₂方面的重要应用. 最后, 对可见光驱动卟啉类金属配合物催化的CO₂还原的发展前景进行了展望.     

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.     

Toward efficient catalysts for electrochemical CO2 conversion to C2 products

With impressive progress in carbon capture and renewable energy, carbon dioxide (CO₂) conversion into useful chemicals has become a potential tool against climate change. Electrochemical CO₂ conversion into C₂ products (ethylene and ethanol) is an especially economically promising approach and an active research area. Nonetheless, catalyst layer design for CO₂ conversion is challenging because of the complex CO₂-to-C₂ reaction pathways. In this review, we highlight key ideas in catalyst layer design for CO₂ conversion to C₂ in the past few years. We identify three fundamental principles to control catalyst selectivity—local CO₂ and CO concentration, local pH, and intermediate–catalyst interaction. To achieve these goals, we introduce design strategies for both catalytic materials and overall catalyst layer morphology.     

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.     

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.     

Strong and Superhydrophobic Wood with Aligned Cellulose Nanofibers as a Waterproof Structural Material†

Lightweight structural materials are important for the energy efficiency of applications, particularly those in the building sector. Here, inspired by nature, we developed a strong, superhydrophobic, yet lightweight material by simple in situ growth of nano‐SiO₂ and subsequent densification of the wood substrate. In situ generation of SiO₂ nanoparticles both inside the wood channels and on the wood surfaces gives the material superhydrophobicity, with static and dynamic contact angles of 159.4^o and 3^o, respectively. Densification of the wood to remove most of the spaces among the lumen and cell walls results in a laminated, dense structure, with aligned cellulose nanofibers, which in turn contributes to a high mechanical strength up to 384.2 MPa (7‐times higher than natural wood). Such treatment enables the strong and superhydrophobic wood (SH‐Wood) to be stable and have excellent water, acid, and alkaline resistance. The high mechanical strength of SH‐Wood combined with its excellent structural stability in harsh environments, as well its low density, positions the strong and superhydrophobic wood as a promising candidate for strong, lightweight, and durable structural materials that could potentially replace steel.     

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.