Cuby: An integrative framework for computational chemistry

Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high‐level, object‐oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz . © 2016 Wiley Periodicals, Inc.     

cclib: a library for package-independent computational chemistry algorithms

There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.     

Undergraduate women empowering women in computational chemistry: Three perspectives

The undergraduate computational chemistry research group headed by Mauricio Cafiero at Rhodes College has a history of including, promoting, and supporting women in this predominantly male field. Alums of this research group from 2004 to 2019 include nine M.Ds, two science researchers, two Ph.D.s, one secondary teacher, two pharmacists, a physical therapist, two nurses, six current medical school students, and five current science graduate students. They have produced 18 peer-reviewed publications with female undergraduate first authors and over 100 conference presentations, including 9 international conference presentations. While Professor Cafiero does all he can to support these students, he attributes the continuous success of the group in recruiting, retaining, and supporting these women to the students themselves. The students' success and visibility on campus helps to recruit new students. The heavy presence of women in this group provides a strong support system for women who may otherwise feel isolated in a male-dominated field; and these support groups provide models and support for women to overcome common obstacles that women in science face. We will profile three recent graduates who will discuss how the above points affected them during their time in the research group and discuss their experience in the context of some literature on women in Science, Technology, Engineering and Mathematics.     

Engaging undergraduate students in computational chemistry research: A tutorial for new assistant professors

In this article, we provide advice and insights, based on our own experiences, for computational chemists who are beginning new tenure-track positions at primarily undergraduate institutions. Each of us followed different routes to obtain our tenure-track positions, but we all experienced similar challenges when getting started in our new position. In this article, we discuss our approaches to seven areas that we all found important for engaging undergraduate students in our computational chemistry research, including setting up computational resources, recruiting research students, training research students, designing student projects, managing the lab, mentoring students, and student conference participation.     

热力学和计算化学在纳微结构材料构效关系研究与设计中的应用

目前,纳微结构新材料已成为化工过程强化的重要手段之一.金属-有机骨架材料(metal-organic frameworks,MOFs)是由金属离子与有机配体通过配位键自组装而成的新型纳米多孔材料,有望在储气、分离、催化、传感及制药等领域获得广泛应用.本文以MOF材料为例,结合本课题组的工作,介绍了热力学与计算化学在纳微结构材料构效关系研究与设计中的应用.     

Gabedit—A graphical user interface for computational chemistry softwares

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV–visible, infrared, and Raman‐computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color‐coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/ . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Parallelism in computational chemistry

Summary An account is given of experience gained in implementing computational chemistry application software, including quantum chemistry and macromolecular refinement codes, on distributed memory parallel processors. In quantum chemistry we consider the coarse-grained implementation of Gaussian integral and derivative integral evaluation, the direct-SCF computation of an uncorrelated wavefunction, the 4-index transformation of two-electron integrals and the direct-CI calculation of correlated wavefunctions. In the refinement of macromolecular conformations, we describe domain decomposition techniques used in implementing general purpose molecular mechanics, molecular dynamics and free energy perturbation calculations. Attention is focused on performance figures obtained on the Intel iPSC/2 and iPSC/860 hypercubes, which are compared with those obtained on a Cray Y-MP/464 and Convex C-220 minisupercomputer. From this data we deduce the cost effectiveness of parallel processors in the field of computational chemistry.     

Network visualization system for computational chemistry

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces.     

MeTA studio: a cross platform, programmable IDE for computational chemist

The development of a cross-platform, programmable integrated development environment (IDE), MeTA Studio, specifically tailored but not restricted to computational chemists working in the area of quantum chemistry with an emphasis on handling large molecules is presented. The IDE consists of a number of modules which include a visualizer and a programming and collaborative framework. The inbuilt viewer assists in visualizing molecules, their scalar fields, manually fragmenting a molecule, and introduces some innovative but simple techniques for handling large molecules. These include a simple Find language and simultaneous multiple camera views of the molecule. Basic tools needed to handle collaborative computing effectively are also included opening up new vistas for sharing ideas and information among computational chemists working on similar problems. MeTA Studio is an integrated programming environment that provides a rich set of application programming interfaces (APIs) which can be used to easily extend its functionality or build new applications as needed by the users. (http://code.google.com/p/metastudio/).     

An efficient computational model to predict the synthetic utility of heterocyclic arynes

Think before you act: a computational approach is reported for evaluating the synthetic potential of heterocyclic arynes. Routine and rapid calculations of arene dehydrogenation energies and aryne angle distortion predict the likelihood that a given hetaryne can be generated, as well as the degree of regioselectivity expected in a reaction between a given hetaryne and a nucleophilic trapping agent.     

槲皮素、山萘酚与Cu2+配位特性的计算化学解析

在分离介质中添加配位剂可提高分离效率。利用MVD2007软件中的Grid计算程序包,应用分子力场的计算模型模拟了Cu2+与处于 最低能量构象的山萘酚、槲皮素等黄酮类化合物的配位相互作用,得到了Cu2+与山萘酚、槲皮素等分子间的作用力场势能曲面和相对 结合能。通过对山萘酚、槲皮素与Cu2+相对结合能的比较,并与高效液相色谱实验结果进行对照分析,得到的研究结果为Cu2+与山萘酚 的配位结合要优于其与槲皮素的配位结合。模拟计算与实验结果具有很好的相关性。     

Gas‐phase fragmentation of protonated piplartine and its fungal metabolites using tandem mass spectrometry and computational chemistry

Piplartine, an alkaloid produced by plants in the genus Piper , displays promising anticancer activity. Understanding the gas‐phase fragmentation of piplartine by electrospray ionization tandem mass spectrometry can be a useful tool to characterize biotransformed compounds produced by in vitro and in vivo metabolism studies. As part of our efforts to understand natural product fragmentation in electrospray ionization tandem mass spectrometry, the gas‐phase fragmentation of piplartine and its two metabolites 3,4‐dihydropiplartine and 8,9‐dihydropiplartine, produced by the endophytic fungus Penicillium crustosum VR4 biotransformation, were systematically investigated. Proposed fragmentation reactions were supported by ESI‐MS/MS data and computational thermochemistry. Cleavage of the C‐7 and N‐amide bond, followed by the formation of an acylium ion, were characteristic fragmentation reactions of piplartine and its analogs. The production of the acylium ion was followed by three consecutive and competitive reactions that involved methyl and methoxyl radical eliminations and neutral CO elimination, followed by the formation of a four‐member ring with a stabilized tertiary carbocation. The absence of a double bond between carbons C‐8 and C‐9 in 8,9‐dihydropiplartine destabilized the acylium ion and resulted in a fragmentation pathway not observed for piplartine and 3,4‐dihydropiplartine. These results contribute to the further understanding of alkaloid gas‐phase fragmentation and the future identification of piplartine metabolites and analogs using tandem mass spectrometry techniques. Copyright © 2017 John Wiley & Sons, Ltd.     

Serenity: A subsystem quantum chemistry program

We present the new quantum chemistry program Serenity . It implements a wide variety of functionalities with a focus on subsystem methodology. The modular code structure in combination with publicly available external tools and particular design concepts ensures extensibility and robustness with a focus on the needs of a subsystem program. Several important features of the program are exemplified with sample calculations with subsystem density‐functional theory, potential reconstruction techniques, a projection‐based embedding approach and combinations thereof with geometry optimization, semi‐numerical frequency calculations and linear‐response time‐dependent density‐functional theory. © 2018 Wiley Periodicals, Inc.     

Spectral and computational chemistry studies for the optimization of geometry of dioxomolybdenum(VI) complexes of some unsymmetrical Schiff bases as antimicrobial agent

Abstract

This analysis highlights the design, spectroscopic characterization and quantum mechanical calculation of some new dioxomolybdenum(VI) complexes of some dibasic tetradentate Schiff bases. Ligands were derived from mono 5-bromosalicylaldehyde-orthophenylenediamine (^BrSal-OPD) and different 2-hydroxyketone derivatives. The characterization was performed by elemental analysis, FTIR, electronic, ¹H NMR and mass spectra, magnetic and molar conductance studies. Structure of the ligands and complexes were designed depending on experimental data and computational studies. According to all data, distorted octahedral geometry was proposed where oxygen atoms are in cis position. Prepared complexes exhibit moderate antimicrobial properties when evaluated against some pathogenic bacteria and fungi. Pharmacokinetic parameters were calculated to search their biological action, for example, absorption, distribution, metabolism, excretion, and toxicity.     

Amination with Pd-NHC complexes: rate and computational studies involving substituted aniline substrates

The amination of aryl chlorides with various aniline derivatives using the N-heterocyclic carbene-based Pd complexes Pd-PEPPSI-IPr and Pd-PEPPSI-IPent (PEPPSI=pyridine, enhanced precatalyst, preparation, stabilization, and initiation; IPr=diisopropylphenylimidazolium derivative; IPent= diisopentylphenylimidazolium derivative) has been studied. Rate studies have shown a reliance on the aryl chloride to be electron poor, although oxidative addition is not rate limiting. Anilines couple best when they are electron rich, which would seem to discount deprotonation of the intermediate metal ammonium complex as being rate limiting in favour of reductive elimination. In previous studies with secondary amines using PEPPSI complexes, deprotonation was proposed to be the slow step in the cycle. These experimental findings relating to mechanism were corroborated by computation. Pd-PEPPSI-IPr and the more hindered Pd-PEPPSI-IPent catalysts were used to couple deactivated aryl chlorides with electron poor anilines; while the IPr catalysis was sluggish, the IPent catalyst performed extremely well, again showing the high reactivity of this broadly useful catalyst.     

Enantioselective and diastereoselective Tsuji-Trost allylic alkylation of lactones: an experimental and computational study

The Tsuji-Trost protocol has been successfully employed for the allylic alkylation of preformed lactone enolates. It has been demonstrated that this Pd-catalyzed reaction can be carried out in an enantio- and diastereoselective manner. The use of additives, such as LiCl, was found to be crucial for reaching high levels of product selectivity. For one particular pair of reactants, density functional theory was used to investigate the mechanism of the nucleophilic addition. Among the five pathways considered, the reaction between an (allyl)Pd(BINAP) complex and a LiCl-lithium enolate adduct is predicted to be the most likely route for C-C bond formation. LiCl plays a key role as the connecting link between the noble metal and the enolate in the kinetically favored transition state. The computed diastereoselectivity ratio is in good agreement with the experimentally observed value.     

An object-oriented library for computational protein design

Recent advances in computational protein design have established it as a viable technique for the rational generation of stable protein sequences, novel protein folds, and even enzymatic activity. We present a new and object-oriented library of code, written specifically for protein design applications in C(++), called EGAD Library. The modular fashion in which this library is written allows developers to tailor various energy functions and minimizers for a specific purpose. It also allows for the generation of novel protein design applications with a minimal amount of code investment. It is our hope that this will permit labs that have not considered protein design to apply it to their own systems, thereby increasing its potential as a tool in biology. We also present various uses of EGAD Library: in the development of Interaction Viewer, a PyMOL plug-in for viewing interactions between protein residues; in the repacking of protein cores; and in the prediction of protein-protein complex stabilities.