molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software

The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup . © 2018 Wiley Periodicals, Inc.     

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     

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.     

PhotochemCAD 2: a refined program with accompanying spectral databases for photochemical calculations

The PhotochemCAD program has been revised extensively. Calculations can be performed using eight modules (oscillator strength, transition dipole moment and natural radiative lifetime, Förster energy transfer, multicomponent analysis, blackbody radiator, artificial spectrum creation, transmission calculation, and analysis of energy transfer among linear multichromophore arrays). The user interface has been streamlined to facilitate visual display, operation of the various modules, input of user data via a wizard and output of spectra and calculations. The database of absorption and fluorescence spectra has been expanded to 150 photochemically relevant compounds. A database of solar spectra has been added. The program runs under Windows and is equipped with extensive literature references and help features, including a tutorial section with video files.     

GammaLab: a suite of programs for k0-NAA and gamma-ray spectrum analysis

The GammaLab is a collection of computer codes, written in MATLAB, for performing calculations involved in k ₀ neutron activation analysis. The main features of the program include calibrations including energy-channel, energy-FWHM and energy-efficiency for different geometries, background subtraction, nuclide identification, spectral interference correction, elemental concentration and limit of detection determination. The data input is taken from two files one is the spectrum file stored in IAEA ASCII format and other is report file containing peak energy and peak area data. The information about sample, irradiation and counting conditions, background spectra are retrieved from QAQCData database. GammaLab takes nuclear data such as gamma lines, emission probabilities, half-lives, and k ₀ factors from NucData database. The sample results which contain elemental concentrations with uncertainties are stored in the QAQCData database. The program has been evaluated by analyzing several hundred spectra and results were found satisfactory.     

pyVib, a computer program for the analysis of infrared and Raman optical activity

A new program called pyVib has been developed as a tool for the analysis of Gaussian (Gaussian 03, Gaussian Inc., Pittsburgh, PA) outputs of vibrational absorption (IR), Raman as well as vibrational optical activity (VOA) spectra calculations. This program has been designed to help the computational chemistry practitioner in the task of analyzing and visualizing molecular vibrations and cross sections. In particular, the analysis of absorption and scattering cross sections can be done using new tools such as group coupling matrices (GCMs) and atomic contribution patterns (ACPs) as either 2D or 3D representations, respectively (Hug, Chem Phys 2001, 264, 53). It reads the Hessian, the atomic polar tensors (APTs), the atomic axial tensors (AATs) (Nafie, J Chem Phys 1983, 79, 4950), and the gradients of the various polarizability tensors involved in VOA calculations and stored in Gaussian fchk ascii files. pyVib is capable of picking suitably chosen atoms or group of atoms for evaluating the contribution of each atom or defined groups of atoms to the calculated VOA scattered intensities. All the results generated by pyVib can be visualized in real-time but can also be transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the visualization by other graphical user interfaces (GUIs).This program is coded in Python and used the visualization toolkit (VTK) library. It is freely available under the terms of the general GNU public license (GPL) for Linux platforms.     

NADA: A versatile PC based program for neutron activation data analysis

We have developed a PC based program for neutron activation data analysis using the FORTRAN and C languages. The routines are based on creating files associated with conventional ORTEC hardware and output software. The main features of the program include radionuclide identification, and the use of semi-automatic integration or the peak fitting SAMPO routine. Other developments are hard and soft copy records for detailed sample identification and particular irradiation, decay and counting procedures. Flux variations, high deadtime corrections, counting geometries, spectral and nuclear interferences, as well as uranium fission interferences are also automatically accounted for. The data output includes concentration values in %, ppm, g or ppb units with associated errors, while detection limits for each individual sample are indicated. Further data output can easily be generated which can be imported to most spreadsheet programs for various statistical uses. A future implementation to the program will include batch-file processing and automated self-absorption calculations for geological samples.     

MEPSIM: A computational package for analysis and comparison of molecular electrostatic potentials

Summary MEPSIM is a computational system which allows an integrated computation, analysis, and comparison of molecular electrostatic potential (MEP) distributions. It includes several modules. Module MEPPLA supplies MEP values for the points of a grid defined on a plane which is specified by a set of three points. The results of this program can easily be converted into MEP maps using third-parties graphical software. Module MEPMIN allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values, and all the geometrical relationships between them (distances, angles, and dihedral angles). Module MEPCOMP computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes the similarity. Module MEPCONF performs the same process as MEPCOMP, considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. The most recently developed module, MEPPAR, is another modification of MEPCOMP in order to compute the MEP similarity between two molecules, but only taking into account a particular plane. The latter module is particularly useful to compare MEP distributions generated by systems of aromatic rings. MEPSIM can use several wavefunction computation approaches to obtain MEP distributions. MEPSIM has a menu type interface to simplify the following tasks: creation of input files from output files of external programs (GAUSSIAN and AMPAC/MOPAC), setting the parameters for the current computation, and submitting jobs to the batch queues of the computer. MEPSIM has been coded in FORTRAN and its current version runs on VMS/VAX computers.     

KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results†

Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas‐phase molecular thermodynamic properties (offering hindered rotor treatment), thermal equilibrium constants, transition state theory rate coefficients (transition state theory (TST), variational transition state theory (VTST)) including one‐dimensional (1D) tunnelling effects (Wigner, and Eckart) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate constants, for elementary reactions with well‐defined barriers. KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front‐end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the graphical user interface and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D plots, exporting images and data files. These features make this program also well‐suited to support and enhance students learning and can serve as a very attractive courseware, taking the teaching content directly from results in molecular and kinetic modelling. © 2013 Wiley Periodicals, Inc.     

Valence : A Massively Parallel Implementation of the Variational Subspace Valence Bond Method

This work describes the software package, Valence , for the calculation of molecular energies using the variational subspace valence bond (VSVB) method. VSVB is an ab initio electronic structure method based on nonorthogonal orbitals. Important features of practical value include high parallel scalability, wave functions that can be constructed automatically by combining orbitals from previous calculations, and ground and excited states that can be modeled with a single configuration or determinant. The open-source software package includes tools to generate wave functions, a database of generic orbitals, example input files, and a library build intended for integration with other packages. We also describe the interface to an external software package, enabling the computation of optimized molecular geometries and vibrational frequencies. © 2019 Wiley Periodicals, Inc.     

Software for localization and visualization of cavities in crystal structures and supramolecular assemblies

This paper describes the CAVITY software for a personal computer (AT/XT). The software is designed for seeking interstices, channels, and cavities in structures, calculating the volumes of closed cavities, constructing cross sections of cavities by the planes given by the crystallographic indices hkl or by the coordinates of points lying in the planes. The cavities and their cross sections may be visualized and stored as graphical files. The program calculates the distances between any points on the “cavity walls” and inside or outside the cavity as well as the nearest environment for any point inside the cavity. The data are input as a SHELX or ASCII file with Cartesian atomic coordinates.     

MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.     

Elektronentheorie auf dem Smartphone

We introduce a new tool for the performance of Hueckel molecular orbital calculations on a smartphone using a simple graphical input. It produces all routine output expected from a Hueckel calculation. Advanced users may also study things like Moebius rings, hetero systems, or Pauli‐antisymmetry constraints in monocycles. In short, in addition to its main use in teaching, the app can also be employed for fast estimate in research, be it only to assess whether the application of state‐of‐the‐art quantum chemical calculations may be warranted.     

ExcelAutomat 1.3: Fragment analysis based on the distortion/interaction-activation strain model

The distortion/interaction-activation strain model (D/I-ASM), a fragment analysis method, is applied to study the structure–reactivity relationship in reactions. The application of D/I-ASM involves the generation of input files for points along a reaction profile, submission of input files to a quantum software package, processing of parameters from the resulting output files and generation of graphical plots. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667) provides a framework and library in Visual Basic for Application programming language to process such files. New routines were written in ExcelAutomat 1.3 to facilitate processing of files for D/I-ASM. The worksheet “ASM” was included where initial parameters needed can be defined. The routines for D/I-ASM were tested successfully on bimolecular nucleophilic substitution, cycloaddition, and barrierless reactions. The automation of fragment analysis by ExcelAutomat 1.3 is compatible with Microsoft Excel and LibreOffice Calc. The extensible tool processes files from Gaussian and GAMESS-US packages. © 2018 Wiley Periodicals, Inc.     

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.     

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.