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     

Registering the Amica electronic structure code in the extensible computational chemistry environment

We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.     

UCSF Chimera--a visualization system for exploratory research and analysis

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.     

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.     

Nitrogen as a probable problematic factor of computational chemistry: A benchmarking study

In the present study, theoretical IR frequencies and geometric parameters of triamterene, furosemide, and triamterene-furosemide salt were investigated. ORCA software was handled for commonly used BLYP, B3LYP, and HF (combined with various basis sets including 6-31G**, def2-SVP, cc-pVDZ, and pcseg-1 basis sets) calculations. Theoretical IR frequencies and geometric parameters of triamterene and furosemide were compared with the corresponding experimental data. In addition, theoretical geometric parameters of triamterene-furosemide salt were, as well, compared with the corresponding experimental data. Based on these comparisons, the performances of computational methods/basis sets were measured. As a result of this study, it was discovered that the studied computational approaches were generally successful in the prediction of molecular geometries and IR frequencies of the target molecules. When IR and geometry data were more deeply investigated, it was observed that there were problems specific to nitrogen atoms. The computed geometry and IR of amine and sulphonamide nitrogen atoms’ bonds strongly disagreed with the experimental data. Similar disagreements were also observed for sulphur, oxygen, and cyclic hydrogen atoms but the level of disagreements was lower.     

Real‐time quantum chemistry

Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or molecular assemblies—especially linear and sublinear scaling techniques are devoted to the accomplishment of this goal. However, as many chemical reactions are rather local, they usually involve only a limited number of atoms so that models of about 200 (or even less) atoms embedded in a suitable environment are sufficient to study their mechanisms. Thus, the system size does not need to be enlarged, but remains constant for reactions of this type that can be described by less than 200 atoms. The question then arises how fast one can obtain the quantum chemical results. This question is not directly answered by linear‐scaling techniques. In fact, ideas such as haptic quantum chemistry (HQC) or interactive quantum chemistry require an immediate provision of quantum chemical information which demands the calculation of data in “real time.” In this perspective, we aim at a definition of real‐time quantum chemistry, explore its realm and eventually discuss applications in the field of HQC. For the latter, we elaborate whether a direct approach is possible by virtue of real‐time quantum chemistry. © 2012 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.     

JACOB: An enterprise framework for computational chemistry

Here, we present just a collection of beans (JACOB): an integrated batch‐based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user‐specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application‐programming interface provides a set of generic tools for processing large‐scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob . © 2013 Wiley Periodicals, Inc.     

Theoretical evaluation of sensitivity and thermal stability for high explosives based on quantum chemistry methods: A brief review

Over the past 20 years, a number of scientists have conducted numerous fundamental investigations based on quantum chemistry theory into various mechanistic processes that seems to contribute to the sensitivity of energetic materials. A large number of theoretical methods that have been used to predict their mechanical and spark sensitivity are summarized in this article, in which the advantages and disadvantages of these methods, together with their scope of use are clarified. In addition, the theoretical models for thermal stability of explosives are briefly introduced as a supplement. It has been concluded that the current ability to predict sensitivity is merely based on a series of empirical rules, such as simple oxygen balance, molecular properties, and the ratios of C and H to oxygen for different classes of explosive compounds. These are valid only for organic classes of explosives, though some special models have been proposed for inorganic explosives, such as azides. An exact standard for sensitivity should be established experimentally by some new techniques for both energetic compounds and their mixtures. © 2013 Wiley Periodicals, Inc.     

Supramolecular chemistry

The article discusses molecular recognition and overviews the key concepts -storage and retrieval of chemical information by molecular structures, supramolecular reagents and catalysts, molecular transport, semiochemistry and self assembly. The prospects of controlling supramolecular architecture through engineered molecular recognition and design of ‘programmed systems’ controlled by molecular information are also discussed.     

Exchange and correlation in density functional theory and quantum chemistry

The nature of exchange, dynamic correlation (DC) and left–right correlation (LRC) is considered in density functional theory and wavefunction‐based quantum chemistry. The presence of LRC in approximate exchange density functionals is highlighted and the separation of LRC and DC is considered. For H₂, the Heitler–London approach is shown to include the essential elements of exchange and LRC. The arguments are illustrated by a comparison of Gaussian orbital s‐optimised Heitler–London and OPTX potential energy curves. They agree well near equilibrium, but differ at large distances due to the inability of the OPTX form to describe the dissociation process. LRC and DC values determined using the two approaches are compared. The influence of higher angular momentum functions in the Heitler–London approach is then investigated (commonly called self‐consistent valence bond); the agreement with OPTX degrades, leading to a larger value of LRC and a smaller value of DC at H₂ equilibrium. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Ab initio calculations of the structure and harmonic force fields for the amine forms of dinitramine and methyldinitramine. Vibrational spectra and their interpretation using a scaling procedure

Ab initio geometries and vibrational spectra have been calculated for the amine structures of dinitramine and methyldinitramine, HN(NO₂)₂ and CH₃N(NO₂)₂. It is shown at the RHF and MP2 levels with the use of the 6-31G^* and 6-31G^** basis sets that these molecules have different symmetries in their equilibrium states,C _sandC ₁ respectively. The quantum chemical RHF/6-31G^* force fields were scaled with the set of transferable factors previously obtained by the authors to assign the available experimental vibrational bands and predict the positions of bands for the unmeasured spectral regions. Some common patterns of the geometrical parameters, vibrational spectra, and force fields of the simplest nitramines are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2135–2147, November, 1995.The authors are grateful to the Russian Foundation for Basic Research (Project No. 93-03-4410) and to the International Science Foundation (Grant No. MQXOOO) for financial support of works fulfilled at the Department of Chemistry, M. V. Lomonosov Moscow State University. The authors also acknowledge the support of the Scientific Technical Program Universities of Russia.     

Identification of ligands for the Tau exon 10 splicing regulatory element RNA by using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry (DCC) to identify ligands for the stem-loop structure located at the exon 10-5'-intron junction of Tau pre-mRNA, which is involved in the onset of several tauopathies including frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). A series of ligands that combine the small aminoglycoside neamine and heteroaromatic moieties (azaquinolone and two acridines) have been identified by using DCC. These compounds effectively bind the stem-loop RNA target (the concentration required for 50% RNA response (EC(50)): 2-58 μM), as determined by fluorescence titration experiments. Importantly, most of them are able to stabilize both the wild-type and the +3 and +14 mutated sequences associated with the development of FTDP-17 without producing a significant change in the overall structure of the RNA (as analyzed by circular dichroism (CD) spectroscopy), which is a key factor for recognition by the splicing regulatory machinery. A good correlation has been found between the affinity of the ligands for the target and their ability to stabilize the RNA secondary structure.     

共轭烯烃的分子几何构型、电子结构和生成热的DMM和AM1、PM3的比较研究

运用Ｄｅｌｆｔ分子力学（ＤＭＭ）力场和程序以及半经验分子轨道ＡＭ１和ＰＭ３方法计算研究了丁二烯、苯、甲苯、联苯、苯乙烯、富烯、、环辛四烯、［２，２］对环烷和菲等１０个共轭烯烃分子的几何构型、电子结构和生成热．ＤＭＭ计算的几何构型和生成热与实验结果相吻合，电荷分布结果与从头计算结果较接近．ＡＭ１和ＰＭ３计算的几何构型较好，但计算的生成热与实验结果偏差较大．ＰＭ３计算值比ＡＭ１的稍好．     

分散剂对水焦浆成浆性影响的量子化学研究

为高效利用半焦资源,选择适宜的水焦浆分散剂以提高兰炭制备水焦浆的性能,本研究以陕北半焦及四种不同分散剂(腐植酸钠SH、木质素磺酸钠SLS、十二烷基磺酸钠SDS和一种自制衣康酸型分散剂IPMS)为研究对象,探讨了不同添加剂对水焦浆成浆特性的影响。利用Material Studio(MS)软件计算了分散剂的结构参数及半焦与分散剂间的相互作用能,从量子化学角度对分散剂的作用进行探讨,并与制浆实验结果进行比较。结果表明,加入分散剂可有效降低液体表面张力,增大半焦颗粒表面电负性,从而增强颗粒间静电排斥作用使得浆体更加稳定。相同制备条件下,分散剂IPMS制备水焦浆时效果较优,在剪切速率为100 s~(-1)时,其表观黏度为625 mP·s,7 d析水率仅为2.38%且无硬沉淀。通过计算机模拟得出吸附过程中分散剂的氧原子向半焦的羟基一侧靠近,产生电荷转移,四种分散剂活性大小顺序为IMPS SH SLS SDS,IMPS与半焦相互作用的吸附作用较强与实验结果一致。证明了采用量子化学计算结合实验数据可以对水焦浆分散剂的性能进行评价,为浆体燃料制备技术及新型药剂的设计开发提供了理论基础。     

Bayesian inference of conformational state populations from computational models and sparse experimental observables

We present a Bayesian inference approach to estimating conformational state populations from a combination of molecular modeling and sparse experimental data. Unlike alternative approaches, our method is designed for use with small molecules and emphasizes high‐resolution structural models, using inferential structure determination with reference potentials, and Markov Chain Monte Carlo to sample the posterior distribution of conformational states. As an application of the method, we determine solution‐state conformational populations of the 14‐membered macrocycle cineromycin B, using a combination of previously published sparse Nuclear Magnetic Resonance (NMR) observables and replica‐exchange molecular dynamic/Quantum Mechanical (QM)‐refined conformational ensembles. Our results agree better with experimental data compared to previous modeling efforts. Bayes factors are calculated to quantify the consistency of computational modeling with experiment, and the relative importance of reference potentials and other model parameters. © 2014 Wiley Periodicals, Inc.     

Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions

Ab initio and molecular mechanics studies of LiPF₆ and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li⁺/PF₆^? complexes obtained from quantum chemistry revealed a preference for C_3V symmetry structures for Li⁺–P separations under 2.8 Å, C_2V symmetry for Li⁺–P in the range of 2.8–3.3 Å and C_4V symmetry for Li⁺–P separations larger than 3.3 Å. Electron correlation effects were found to make an insignificant contribution to binding in the Li⁺/PF₆^? complex. By contrast, analogous studies of PF₆^?/PF₆^? and PF₆^?/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF₆ melts was parameterized to reproduce the geometries and energies of Li⁺/PF₆^?, PF₆^?/PF₆^?, PF₆^?/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF₆ melts were performed to validate this quantum chemistry‐based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF₆ solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001     

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/).