Kirkwood-Buff (KB) solution theory is a means to obtain certain thermodynamic derivatives from knowledge of molecular distributions. In actual practice the required integrals over radial distribution functions suffer inaccuracies due to finite-distance truncation effects and their use in closed systems. In this work we discuss how best to minimize these inaccuracies under traditional KB theory. In addition we implement a method for calculating KB quantities in molecular simulations with periodic boundary conditions and particularly within the canonical ensemble. The method is based on a finite-Fourier-series expansion of molecular concentration fluctuations and leads to more reliable results for a given computational effort. The procedure is validated and compared to the original method for a nonideal liquid mixture of Lennard-Jones particles intended to imitate a real system, carbon tetrafluoride, and methane.
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http://dx.doi.org/10.1103/PhysRevE.80.051203 | DOI Listing |
Int J Biol Macromol
January 2025
Institute of Chemistry and Center for Computing in Engineering and Science - CCES, Universidade Estadual de Campinas (UNICAMP), Brazil. Electronic address:
The β-glucosidase enzyme is a glycosyl hydrolase that breaks down the β-1,4 linkage of cellobiose. It is inhibited by glucose at high concentrations due to competitive inhibition. However, at lower glucose concentrations, the glucose-tolerant β-glucosidase from Humicola insolens (BGHI) undergoes stimulation.
View Article and Find Full Text PDFJ Chem Phys
July 2024
Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA.
Alcohol/alkane solutions widely used in chemical synthesis and as transportation fuels are highly non-ideal due to the nanoscale clustering of the amphiphilic alcohol molecules within the nonpolar alkanes. Besides impacting reactivity, such as combustion, non-ideal solutions are likely to exhibit unusual solvation dynamics on ultrafast time scales arising from the structurally heterogeneous nature of molecular-scale association. Using a convenient transition metal carbonyl vibrational probe [(C5H5)Mn(CO)3, CMT], linear absorption and nonlinear two-dimensional infrared (2D-IR) spectroscopy reveal composition-dependent solvation dynamics as reported by the frequency fluctuation correlation function in a series of ethanol/heptane solutions.
View Article and Find Full Text PDFJ Phys Chem B
June 2024
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
Mixing two solvents can sometimes make a much better solvent than expected from their weighted mean. This phenomenon, called synergistic solvation, has commonly been explained via the Hildebrand and Hansen solubility parameters, yet their inability in other solubilization phenomena, most notably hydrotropy, necessitates an alternative route to elucidating solubilization. While, recently, the universal theory of solubilization was founded on the statistical thermodynamic fluctuation theory (as a generalization of the Kirkwood-Buff theory), its demand for experimental data processing has been a hindrance for its wider application.
View Article and Find Full Text PDFMAbs
April 2024
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
Understanding factors that affect the clustering and association of antibodies molecules in solution is critical to their development as therapeutics. For 19 different monoclonal antibody (mAb) solutions, we measured the viscosities, the second virial coefficients, the Kirkwood-Buff integrals, and the cluster distributions of the antibody molecules as functions of protein concentration. Solutions were modeled using the statistical-physics Wertheim liquid-solution theory, representing antibodies as Y-shaped molecular structures of seven beads each.
View Article and Find Full Text PDFJ Chem Phys
September 2023
Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark.
Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell.
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