We study a system composed of like-charged cylinders and dumbbell-like counterions, with the focus laid on the role of the internal structure of counterions, using Monte Carlo simulations. The dumbbell ions are found to exhibit novel counterion condensation behavior governed by their length. Effective electrostatic interactions mediated between charged parallel cylinders also turn out significantly different from the case of pointlike ions, as a result of the complex interplay between the spatially separated charge distribution in the dumbbell counterions, their orientation, and the curvature of the charged cylinder. We show that at a weak-to-moderate electrostatic coupling strength, where effective like-charge interactions are usually found to be repulsive, the intercylinder interaction can become attractive and display a distinctive sensitivity to the cylinder curvature and dumbbell size, proving the significant effect of ion structure.
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http://dx.doi.org/10.1103/PhysRevLett.121.058001 | DOI Listing |
J Chem Phys
December 2024
Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA.
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)-the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformation, charge, and chemical state of all molecular species-thereby linking the structural state with the chemical/charged state of the system. We investigate how variations in monovalent and divalent salt concentrations, as well as pH, affect the charge distribution across different regions of an NCP and quantify the impact of charge regulation.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
University of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States.
An accurate force field (FF) is the foundation of reliable results from molecular dynamics (MD) simulations. In our recently published work, we developed a protocol to generate atom pair-specific Lennard-Jones (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) parameters in the context of the Drude polarizable FF based on readily accessible quantum mechanical (QM) data to fit condensed phase experimental thermodynamic benchmarks, including the osmotic pressure, diffusion coefficient, ionic conductivity, and solvation free energy, when available. In the present work, the developed protocol is applied to generate NBFIX and NBTHOLE parameters for interactions between monatomic ions (specifically Li, Na, K, Rb, Cs, and Cl) and common functional groups found in proteins and nucleic acids.
View Article and Find Full Text PDFElectrophoresis
November 2024
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
bioRxiv
November 2024
Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP) - the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformations, charges, and chemical states of all molecular species - thereby linking the structural state with the chemical/charged state of the system. We investigate how variations in monovalent and divalent salt concentrations, as well as pH, affect the charge distribution across different regions of an NCP and quantify the impact of charge regulation.
View Article and Find Full Text PDFBiomolecules
November 2024
Institut für Chemie und Biochemie, Freie Universität Berlin, Forschungsbau SupraFab, Altensteinstrasse 23a, 14195 Berlin, Germany.
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