"This repository contains codes, input files, output data, and analyses related to the energy optimization of molecular structures using software such as Gaussian, Orca, PELE, and OPTIM."
Gaussian is a computational chemistry software primarily used by chemists for molecular calculations, the synthesis of organic and inorganic compounds, as well as kinetics studies.
To prepare the input required for the Gaussian software and to analyze the output results from Gaussian, we use the GaussView software.
For downloading, installation, and further guidance regarding the software, please visit the official Gaussian website at ( https://gaussian.com/ ).
A program for finding global minima and calculating thermodynamic properties.
This program employs the basin-hopping algorithm described by Wales and Doye (J. Phys. Chem. A, 101, 5111, 1997) to locate global minima on a potential energy surface. Many potentials are included. The latest version also includes implementations of basin-sampling and parallel tempering, along with free energy basin-hopping, generalised basin-hopping, and grand and semi-grand canonical basin-hopping.
GMIN website ( https://www-wales.ch.cam.ac.uk/GMIN/ ) for further information.
A program for optimizing geometries and calculating reaction pathways
OPTIM includes a variety of methods for locating transition states and characterising the corresponding pathways. OPTIM has analytic first and second derivatives coded for dozens of empirical potentials, and can also treat systems involving periodic boundary conditions and solve general optimization problems, such as least squares fits.
Visit the OPTIM website ( https://www-wales.ch.cam.ac.uk/OPTIM/ ) for further information.
A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
Visit the PATHSAMPLE website ( https://www-wales.ch.cam.ac.uk/PATHSAMPLE/ ) for further information.
For installation and running the software, please visit the Wales group website at ( https://www.ch.cam.ac.uk/group/wales/person/dw34 ).
pele : Python Energy Landscape Explorer.
Tools for global optimization and energy landscape exploration.
Documentation: http://pele-python.github.io/pele/
pele is a python partial-rewriting of GMIN, OPTIM, and PATHSAMPLE: fortran programs written by David Wales of Cambridge University and collaborators (http://www-wales.ch.cam.ac.uk/software.html).
The initial version of Pele was developed by Jacob Stevenson and Stefano Martiniani. ( https://github.com/pele-python/pele )
Currently, the advanced version of this software is being developed by the Martiniani research group at New York University (NYU), incorporating new advancements and features that make it suitable for more complex analyses. ( https://github.com/martiniani-lab/pele )
Orca is a quantum chemistry software used for calculating the electronic structure of molecules and their properties. This program includes modern quantum chemistry methods such as Density Functional Theory (DFT), Multi-Body Perturbation Theory (MP2), Coupled Cluster methods, and semi-empirical approaches. ORCA is widely utilized for studying larger molecules, transition metal complexes, and their spectroscopic properties.
Orca offers a variety of features for quantum chemical computations, including support for various density functional models (DFT) and quantum mechanical methods such as Hartree-Fock, Resolution of Identity MP2 (RI-MP2), and Time-Dependent Density Functional Theory (TDDFT). Additionally, Orca can simulate electronic spectra, molecular structures, molecular thermodynamics, and observable properties.
This software is developed by the University of Technology in Hamburg, Germany, and is used across various fields of chemistry, including computational chemistry, physical chemistry, organic chemistry, and more.
For downloading, installation, and further guidance regarding the software, please visit the official ORCA website at ( https://orcaforum.kofo.mpg.de/app.php/portal ).
PySCF (Python for Strongly Correlated Systems) is an open-source quantum chemistry library designed for advanced computations in molecular and periodic systems. Built on Python, it includes a suite of modules for various tasks such as molecule definition, self-consistent field (SCF) calculations, correlation theories like MP2, CCSD, and multiconfiguration calculations (CASSCF).
For more information and access to PySCF documentation, visit the official website at https://pyscf.org/index.html and the repository at https://github.com/pyscf/pyscf.
Psi4 is an open-source software suite for ab initio simulations in quantum chemistry. This software is designed to perform accurate and efficient calculations of molecular properties and has the capability to execute computations with over 2500 basis functions on multi-core machines. Due to its combination of high performance, user-friendly interface, and support for the Python language, Psi4 is one of the leading tools in the field of computational chemistry.
For more information and access to Psi4 documentation, please visit the official website at www.psicode.org and the repository at https://github.com/psi4/psi4/.