QM/MM: what have we learned,where are we,and where do we go from here?

This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM. Contribution to the Proceedings of the 10th Electronic Computational Chemistry Conference     

生物质平台化合物电催化制备高值燃料与化学品研究进展

生物质是一类丰富的可再生碳基资源, 有望代替传统化石资源生产燃料和化学品, 受到了广泛关注和研究. 近年来, 电催化作为一种绿色高效的转化策略, 成为生物质催化转化的重要研究方向之一, 具有巨大的应用前景. 本文总结了生物质平台化合物电催化制备高附加值燃料与化学品的研究进展, 根据反应类型重点介绍了电催化氧化、 还原和偶联反应, 对催化反应过程和机理进行了阐述, 并对电催化生物炼制的前景进行了展望.     

金属-有机框架衍生的多功能光催化剂

在光催化过程中,光催化剂被太阳能激发产生光生电子和空穴,来实现环境净化或能量转换,是应对全球变暖和能源短缺的有效途径之一.然而,光催化技术面临的主要瓶颈问题是光生载流子的低分离效率和高反应能垒.而催化剂本身的特性对这一点起到了决定性的作用.因此,催化剂的合理设计和改性是提高光催化效率的关键.金属有机框架(MOFs)是一...     

锌酶的计算模拟:挑战与最新进展

锌酶在人体中分布非常广泛,种类繁多,是当前最受关注的金属酶之一。由于在锌配位结构上的多样性以及Zn²⁺饱和的d轨道带来的“光谱寂静”性,导致许多实验研究手段受限。计算模拟在锌酶的研究中发挥着越来越重要的作用,已经成为不可或缺的研究工具。现代量子化学计算模拟方法,特别是被视为研究生物大分子体系非常有效的QM/MM组合方法,目前已经被广泛应用于探讨复杂多变的锌配位结构以及锌酶催化反应机理。通过在QM/MM水平下开展的分子动力学模拟,可以揭示锌酶体系中结构与功能间的相互关系。此外,分子力场方法在锌酶研究中同样发挥了不可替代的作用,由于传统力场普遍无法正确描述锌配位结构,因此,锌酶分子力场的开发具有迫切的现实意义。本文总结了近年来锌酶计算模拟领域的最新进展,提出了锌酶计算研究中还有待解决的一些问题。     

Developing adaptive QM/MM computer simulations for electrochemistry

We report the development of adaptive QM/MM computer simulations for electrochemistry, providing public access to all sources via the free and open source software development model. We present a modular workflow‐based MD simulation code as a platform for algorithms for partitioning space into different regions, which can be treated at different levels of theory on a per‐timestep basis. Currently implemented algorithms focus on targeting molecules and their solvation layers relevant to electrochemistry. Instead of using built‐in forcefields and quantum mechanical methods, the code features a universal interface, which allows for extension to a range of external forcefield programs and programs for quantum mechanical calculations, thus enabling the user to readily implement interfaces to those programs. The purpose of this article is to describe our codes and illustrate its usage. © 2016 Wiley Periodicals, Inc.     

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).     

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.     

Structure-breaking effects of solvated Rb(I) in dilute aqueous solution--an ab initio QM/MM MD approach

Structural properties of the hydrated Rb(I) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at the double-zeta HF quantum mechanical level. The first shell coordination number was found to be 7.1, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and theta-angle distributions allowed the full characterization of the hydration structure of the Rb(I) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions, as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes, and rate constants were also analyzed. The mean ligand residence time for the first shell was determined as tau = 2.0 ps.     

Recent progress in MXene and graphene based nanocomposites for microwave absorption and electromagnetic interference shielding

There is widespread use of telecommunication and microwave technology in modern society, and raised the electromagnetic interference (EMI) issue to alarming situation due to apprehensive demand and growth of 5G technology undesirably disturbing the human health. The two dimensional (2D) materials including graphene and MXenes are already been used for variety of electronic devices due to their exceptional electrical, mechanical, optical, chemical, and thermal properties. MXene is composed of metal carbides, in which mainly metals are the building blocks for dielectrics, semiconductors, or semimetals. However, the strong interfaces with electromagnetic waves (EM) are variable from terahertz (THz) to gigahertz (GHz) frequency levels and are widely used in EMI and Microwave absorption (MA) for mobile networks and communication technologies. The use of different organic materials with metal, organic, inorganic fillers, polymers nanocomposite and MXene as a novel material has been studied to address the recent advancement and challenges in the microwave absorption mechanism of 2D materials and their nanocomposites. In this concern, various techniques and materials has been reported for the improvement of shielding effectiveness (SE), and theoretical aspects of EMI shielding performance, as well stability of 2D materials particularly MXene, graphene and its nanocomposites. Consequently, various materials including polymers, conducting polymers, and metal–organic frameworks (MOF) have also been discussed by introducing various strategies for improved MA and control of EMI shieling. Here in this comprehensive review, we summarized the recent developments on material synthesis and fabrication of MXene based nanocomposites for EMI shielding and MA. This research work is a comprehensive review majorly focuses on the fundamentals of EMI/MA.  The recent developments and challenges of the MXene and graphene based various structures with different polymeric composites are described in a broader perspective.     

Modelling of Enzyme Properties in Organic Solvents

 In this article we review how molecular modeling techniques can be used to shed some light on the influence of organic solvents on the molecular characteristics of proteins and enzymes. Molecular dynamic simulations on bovine pancreas trypsin inhibitor, chymotrypsin, and subtilisin make it possible to get a deeper understanding into how increased intramolecular interactions improve conformational rigidity, thus explaining the lower reactivity and the higher thermostability of enzymes in non-aqueous media. The application of thermodynamics-based models allows first qualitative predictions on the selectivity of many reaction types; however, the application of quantum mechanical/molecular mechanical methods is required for the development of quantitative models of actual reactivity patterns.     

Engineering Metal–Organic Framework Catalysts for C−C and C−X Coupling Reactions: Advances in Reticular Approaches from 2014–2018

Metal–organic frameworks (MOFs) are a class of crystalline porous materials that have been actively used for several industrial and synthetic applications. MOFs are spatially and geometrically extrapolated coordination polymers with intriguing properties such as tunable porosity and dimensionality. In terms of their catalytic efficiency, MOFs combine the easy recoverability of heterogeneous catalysts with the increased selectivity of biological catalysts. It is therefore not surprising that a lot of work on optimizing MOF catalysts for organic transformations has been carried out over the past decade. In this review, recent developments in MOF catalysis are summarized, with special attention being paid to C−C, C−N, and C−O coupling reactions. The influence of pore size, pore environment, and load on catalytic activity is described. Post-synthetic stabilization techniques and host–guest interactions in caged MOF scaffolds are detailed. Mechanistic aspects pertaining to the use of MOFs in asymmetric heterogeneous catalysis are highlighted and categorized.     

Added-Value Chemicals from Lignin Oxidation

Lignin is the second most abundant component, next to cellulose, in lignocellulosic biomass. Large amounts of this polymer are produced annually in the pulp and paper industries as a coproduct from the cooking process—most of it burned as fuel for energy. Strategies regarding lignin valorization have attracted significant attention over the recent decades due to lignin’s aromatic structure. Oxidative depolymerization allows converting lignin into added-value compounds, as phenolic monomers and/or dicarboxylic acids, which could be an excellent alternative to aromatic petrochemicals. However, the major challenge is to enhance the reactivity and selectivity of the lignin structure towards depolymerization and prevent condensation reactions. This review includes a comprehensive overview of the main contributions of lignin valorization through oxidative depolymerization to produce added-value compounds (vanillin and syringaldehyde) that have been developed over the recent decades in the LSRE group. An evaluation of the valuable products obtained from oxidation in an alkaline medium with oxygen of lignins and liquors from different sources and delignification processes is also provided. A review of C₄ dicarboxylic acids obtained from lignin oxidation is also included, emphasizing catalytic conversion by O₂ or H₂O₂ oxidation.     

Synthesis and Adsorption/Catalytic Properties of the Metal Organic Framework CuBTC

CuBTC (Copper(II) benzene-1,3,5-tricarboxylate) is one of the most well characterized and widely studied metal organic framework (MOF) structures for potential use in industrial applications due to its relatively easy synthesis and excellent textural and physicochemical properties. In this comprehensive review, a different perspective on MOF materials for future sustainability is presented by critically examining the recent works that have considered the synthesis and adsorption/catalytic applications of CuBTC as a model case.     

Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations

Scaling factors for atomic charges derived from the RM1 semiempirical quantum mechanical wavefunction in conjunction with CM1 and CM3 charge models have been optimized by minimizing errors in absolute free energies of hydration, ΔG_hyd, for a set of 40 molecules. Monte Carlo statistical mechanics simulations and free energy perturbation theory were used to annihilate the solutes in gas and in a box of TIP4P water molecules. Lennard–Jones parameters from the optimized potentials for liquid simulations‐all atom (OPLS–AA) force field were utilized for the organic compounds. Optimal charge scaling factors have been determined as 1.11 and 1.14 for the CM1R and CM3R methods, respectively, and the corresponding unsigned average errors in ΔG_hyd relative to experiment were 2.05 and 1.89 kcal/mol. Computed errors in aniline and two derivatives were particularly large for RM1 and their removal from the data set lowered the overall errors to 1.61 and 1.75 kcal/mol for CM1R and CM3R. Comparisons are made to the AM1 method which yielded total errors in ΔG_hyd of 1.50 and 1.64 kcal/mol for CM1A*1.14 and CM3A*1.15, respectively. This work is motivated by the need for a highly efficient yet accurate quantum mechanical (QM) method to study condensed‐phase and enzymatic chemical reactions via mixed QM and molecular mechanical (QM/MM) simulations. As an initial test, the Menshutkin reaction between NH₃ and CH₃Cl in water was computed using a RM1/TIP4P‐Ew/CM3R procedure and the resultant ΔG^?, ΔG_rxn, and geometries were in reasonable accord with other computational methods; however, some potentially serious shortcomings in RM1 are discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

碳量子点-金属有机骨架复合材料的合成和应用

金属-有机骨架材料(MOF)与碳量子点(CD)的复合材料CD@MOF是一种应用范围很广的新型材料。本文介绍了MOF和CD@MOF复合材料的合成方法和复合材料在各领域中的应用,并对其未来发展作出了展望。     

An updated review of metal–organic framework materials in photo(electro)catalytic applications: From CO2 reduction to wastewater treatments

This review summarizes recent advances in the development of metal–organic framework (MOF) materials, focusing on their photocatalytic and photoelectrocatalytic activities for different applications, such as CO₂ reduction, water splitting, elimination of inorganic contaminants, and degradation of organic pollutants. In each section, the first applications described focus on the photocatalysts developed using MOF materials. Meanwhile, the latest are centered on photoelectrode applications using these materials. The last advances in the synthesis process are discussed in terms of improvement in electron transfer and charge separation, which enhance the activity of the photo (electro)catalysts. Finally, some insights about the upcoming applications of MOF materials are provided.