omplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspectiv

Author(s)

Martinez, Leandro ^{[1, 2]}

Affiliation

^[1] Univ Estadual Campinas, Inst Chem, Campinas, SP - Brazil

^[2] Univ Estadual Campinas, Ctr Computat Engn & Sci, Campinas, SP - Brazil

• Document type: Journal article
• Source: JOURNAL OF MOLECULAR LIQUIDS; v. 347, FEB 1 2022.
• Web of Science Citations: 0

Abstract

Distribution functions are used to investigate the interactions between the components of condensed-phase systems, while allowing the computation of thermodynamic properties that can be probed experimentally. Radial distribution functions are the most fundamental and easily understood of these distributions, but fail to provide a molecular picture of the interactions when one or all species have complex shapes. On the other hand, regardless of the complexity of the molecular structures involved, minimum-distance distribution functions (MDDFs) can provide a molecular viewpoint on solute-solvent contacts. Here, we describe the ComplexMixtures.jl package, which provides a practical implementation of MDDFs and corresponding Kirkwood-Buff integrals to analyze Molecular Dynamics and Monte-Carlo simulations. Examples are provided for the study of macromolecules in solutions of multiple cosolvents, homogeneous systems, polymer solvation by organic solvents and lipid bilayer interactions with disruptive agents. The distribution functions can be examined using tools to assess the contributions of each atom, group of atoms, and amino acid residues, for example. ComplexMixtures.jl is free software and is compatible with the most common molecular simulation trajectory formats. The software is available as a Julia package with a com- prehensive documentation at: http://m3g.iqm.unicamp.br/ComplexMixtures. (C) 2021 Elsevier B.V. All rights reserved. (AU)

• FAPESP's process: 10/16947-9 - Correlations between dynamics, structure and function in protein: computer simulations and algorithms
• Grantee: Leandro Martinez
• Support Opportunities: Regular Research Grants
• FAPESP's process: 18/14274-9 - Protein Structure Determination from Distance Constraints Derived from Chemical Cross-linking: Computational Methods and Applications
• Grantee: Leandro Martinez
• Support Opportunities: Regular Research Grants
• FAPESP's process: 18/24293-0 - Computational methods in optimization
• Grantee: Sandra Augusta Santos
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC