DFT Study of Solvent Effects for Some Organic Molecules Using a Polarizable Continuum Model

Forty ionic molecules are studied by DFT (B3LYP, B3P86), MP4 with different basis sets using the PCM/UAHF model within the self-consistent reaction-field method to assess solvent effects. For these molecules, the solvation free energies (ΔG _sol) in water and the dipole moments in vacuoas well as in water are obtained. By comparing the calculated values of ΔG _sol with experimental values and molecular simulation results, it is found that the ΔG _sol values generated by the DFT method are in better agreement with experimental values. Moreover, especially for the B3LYP/6-31+G_∗ level, the results of both ΔG _sol and dipole moments are more accurate considering the lower computational cost. It can be noted that the dipole moments of solutes in water show some increase relative to those in vacuo.     

分子力学在有机化学中的应用

本文评述了近年来分子力学在有机化学中的应用,特别是在有机化学反应和核磁共振中的应用。     

The Calculation for the Molecular Position Electronegativity of Organic Molecules

The molecular position electronegativity (MPEN) is a new concept and based on the auther's studying of group electronegativity^[1,2]. MPEN represents the power of attracting an electron of the center atom situated different molecular environment. MPEN is defined as the electronegativity of the center atom situated different molecular environment and this is affectde by neighbors of the center atom.     

有机链状分子的定域分子轨道的研究

利用Foster-Boys定域化程序和STO-3G ab initio方法,对含有C、H、O、N原子的100多个有机链状分子进行了研究,得到定域分子轨道能量及其相互作用参数。应用这些参数和定域分子轨道模型,对于众多的含有C、H、O、N原子的有机链状分子,可得到相应的正则分子轨道能量及其与定域分子轨道的关系。以此预测它们的电离能,结果与实验值符合较好。     

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.     

Molecular Imprinting of Small Molecules with Organic Silanes: Fluorescence Detection

Abstract

Small molecules, peptides, and proteins can be imprinted using mixtures of organic silanes. Molecular imprints may serve as artificial receptors, i.e., biosensor sensing elements for detection of chemical and biological toxins, drugs, and environmental hazards. One method for detection of imprint-bound molecules is fluorescence. Molecular imprints to N-acetyltryptophanamide (NATA) and fluorescein were prepared, and their respective binding constants determined using steady-state fluorescence spectroscopy. Stern-Volmer fluorescence quenching plots of imprint-bound molecules using potassium iodide (KI) and acrylamide indicate bound molecules are shielded from the solvent environment. Scatchard plot analysis revealed two binding affinities, i.e., aK_d = 0.13 and 2.5 μM for NATA binding to NATA imprints. Interestingly, NATA exhibited higher affinity, i.e., K_d = 1.3 and 35 nM, for the fluorescein imprint. These data support the usefulness of fluorescence techniques in molecular imprint-based detection technology.     

Searching for Small Molecules with an Atomic Sort

The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom‐based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.     

Unbinding Molecular Recognition Force Maps of Localized Single Receptor Molecules by Atomic Force Microscopy

Atomic force microscopy is a technique capable to study biological recognition processes at the single‐molecule level. In this work we operate the AFM in a force‐scan based mode, the jumping mode, where simultaneous topographic and tip–sample adhesion maps are acquired. This approach obtains the unbinding force between a well‐defined receptor molecule and a ligand attached to the AFM tip. The method is applied to the avidin–biotin system. In contrast with previous data, we obtain laterally resolved adhesion maps of avidin–biotin unbinding forces highly correlated with single avidin molecules in the corresponding topographic map. The scanning rate 250 pixel s^?1 (2 min for a 128×128 image) is limited by the hydrodynamic drag force. We are able to build a rupture‐force distribution histogram that corresponds to a single defined molecule. Furthermore, we find that due to the motility of the polymer used as spacer to anchor the ligand to the tip, its direction at rupture does not generally coincide with the normal to the tip–sample, this introduces an appreciable error in the measured force.     

Small Organic Molecules for Direct Aldol Reaction

Since the pioneering finding by List and Barbas III and their coworkers that L-proline could work as a catalyst in the intermolecular direct aldol reaction, the concept of small organic molecules as catalysts has received great attention. However, new organic molecule which have better catalysis ability are reported scarcely. Our groups1 found L-Prolinamides 1 to be active catalysts for the direct aldol reaction of 4-nitrobenaldehyde with neat acetone at room temperature. The enantioselecti…     

量子力学和分子力学组合方法

量子力学和分子力学(QM/MM)组合方法结合了量子力学的精确性和分子力学的高效性,在研究凝聚态中的化学反应及生物大分子的结构和活性等方面发挥着重要作用。本文主要介绍了QM/MM组合方法的基本原理及国内外有关QM/MM组合方法的研究进展。     

A Molecular Mechanics Model for Flavins

Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox-active isoalloxazine system, which is capable of one- and two-electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water–solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin-containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc.     

A New Method for Molecular Mechanics

A promising new method for optimizing molecular structures is described. In place of the terms involving bond angles and torsion angles, used in the force fields of conventional molecular mechanics, two-body central forces between atoms are used exclusively, resulting in a considerable computational advantage. The program STRFIT, using this method has been tested by comparing geometries obtained with those found using the popular molecular mechanics program MM2 (Allinger) for a variety of cyclic and acyclic molecules. For unstrained molecules, the difference in steric energy between geometries refined by STRFIT and MM2 is only a few tenths of a kilocalorie and up to about a kilocalorie for strained molecules. Geometry optimization with STRFIT, to a structure that is slightly higher in energy than the structure arrived at by MM2 starting from the same initial starting geometry, is three to eight times faster. A complete new package of programs for conveniently and rapidly doing molecular mechanics calculations is described. It includes a convenient algorithm for the input of approximate molecular structures, a rapid structure-optimizing module using a pure Central force-field approach, and a drawing program designed for use with a dot-matrix printer or a laser printer.     

有机分子修饰硅表面*

硅作为一种重要的半导体材料,在微电子领域发挥着极其重要的作用。有机分子修饰硅表面是近年来硅表面化学领域的一个研究热点,引起了研究者的广泛重视。以共价键嫁接在硅表面的有机单分子层能形成稳定、高质量的杂化连接,将赋予传统的硅材料更多新的功能,具有许多其它表面难以比拟的优点。本文针对有机分子修饰硅表面的方法、单层膜的表征和应用,对近年来的最新研究进展进行了综述,并对该方向的今后的发展进行了展望。     

Adiabatic Photoreactions of Organic Molecules

An adiabatic photoreaction is a chemical process that occurs entirely on a single excited electronic energy surface. As a rule, most photoreactions of organic molecules start on an excited electronic surface but “jump” to a lower surface somewhere along the reaction coordinate. There are, however, exceptions to this general rule. For example, photoreactions involving small structural changes and minor alterations in covalent bonding (e.g., proton transfer and complex formation) are commonly found to occur adiabatically. The purpose of this review is to survey examples of more complicated adiabatic photoreactions such as fragmentation, electrocyclic rearrangements, and geometrical isomerizations. The concepts employed are presented in an introductory discussion.     

The Fock Matrix Analysis for Atomic Orbitals in Molecular Orbitals II. The Electronic Structure of N2 Molecules

Weinhold's natural hybrid orbitals can be chosen as the molecular adapted atomic orbitals to build the canonical molecular orbitals of N₂ molecules. The molecular Fock matrix expanded in the natural hybrid orbitals can reveal deeper insight of the electronic structure and reaction of the N₂ molecule. For example, the magnitude of F_ab can signify the bonding character of the paired electrons as well as the diradical character of the unpaired electrons for both σ‐ and π‐types. Discarding the concept of the overlap between non‐orthogonal atomic orbitals, the different orbitals for different spins in the unrestricted Hartree‐Fock wavefunction reveal that there are three pairs of opposite spin density flows between two atoms, which proceed until the bonding molecular orbitals form.     

The Synthesis of Organic Molecules of Intrinsic Microporosity Designed to Frustrate Efficient Molecular Packing

Efficient reactions between fluorine‐functionalised biphenyl and terphenyl derivatives with catechol‐functionalised terminal groups provide a route to large, discrete organic molecules of intrinsic microporosity (OMIMs) that provide porous solids solely by their inefficient packing. By altering the size and substituent bulk of the terminal groups, a number of soluble compounds with apparent BET surface areas in excess of 600 m² g^?1 are produced. The efficiency of OMIM structural units for generating microporosity is in the order: propellane>triptycene>hexaphenylbenzene>spirobifluorene>naphthyl=phenyl. The introduction of bulky hydrocarbon substituents significantly enhances microporosity by further reducing packing efficiency. These results are consistent with findings from previously reported packing simulation studies. The introduction of methyl groups at the bridgehead position of triptycene units reduces intrinsic microporosity. This is presumably due to their internal position within the OMIM structure so that they occupy space, but unlike peripheral substituents they do not contribute to the generation of free volume by inefficient packing.     

基于全极化连续介质模型计算溶液分子的第一原理电子结构理论方法的发展和应用

This is a brief review of some recent progress in the development and application of first-principles electronic structure approaches for molecules in solution.In particular,it accounts for the background,theoretical features,and representative applications of a recently developed,truly accurate continuum solvation model which is known as Surface and Volume Polarization for Electrostatics(SVPE) or Fully Polarizable Continuum Model(FPCM) in literature.The FPCM-based first-principles electronic structure approaches have been widely employed to study a variety of chemical and biochemical problems and serve as an integrated part of various computational protocols for rational drug design.Some perspective of the future of the FPCM-based first-principles electronic structure approaches is also given.     

天然五环三萜有机功能分子

天然五环三萜在自然界中广泛存在,由六个异戊二烯单元组成,可以从动植物中分离获取。因具有手性刚性骨架、多反应位点、独特组装性能、良好生物相容性及药理活性,其在超分子化学、智能材料、界面化学、药物传输等领域有着不可忽视的潜力。本文基于课题组近年来在天然五环三萜有机功能分子方面的工作,概述了含甘草次酸和甘草酸骨架的功能小分子和高分子的设计、合成及其在水凝胶、有机凝胶、有机-无机复合凝胶、手性材料、温敏和自愈合材料、农用Pickering乳液、准聚轮烷等方面的应用。