Article
Mathematics, Applied
Zhan Chen, Yuanzhen Shao
Summary: In the past decade, variational implicit solvation models (VISM) have been successful in predicting solvation energy. However, existing VISMs lack the uniqueness of an energy minimizing solute-solvent interface, hindering the study of important interface properties. To address this, a new constrained VISM is introduced and rigorously analyzed. The model examines the existence, uniqueness, and regularity of the energy minimizing interface, and derives a necessary condition for a sharp solute-solvent interface. Experimental validation and numerical implementation demonstrate accurate solvation energy calculations.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2023)
Article
Chemistry, Physical
Daniel A. Olaya-Munoz, Juan P. Hernandez-Ortiz, Monica Olvera de la Cruz
Summary: Controlling the aggregation of dielectric particles can be achieved by adjusting their geometry and contact surface.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Stefan D. Search, Christopher D. Cooper, Elwin van't Wout
Summary: The Poisson-Boltzmann equation is a useful tool to study electrostatics in molecular systems. This paper presents a generalized expression of the boundary integral representation of the implicit solvent model, which leads to new ways of computing the electrostatic potential. It also proposes a strategy to build efficient preconditioners for the resulting systems, improving the convergence of the linear solver. The authors perform benchmark tests on different formulations and preconditioners, focusing on time to solution, matrix conditioning, and eigenvalue spectrum. The results suggest that the optimal choice depends on the problem size, with simpler direct formulations being faster for small molecules and more involved second-kind equations being better for larger problems. The paper also introduces a fast Calderon preconditioner for first-kind formulations, which shows promise for future analysis.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Tiejun Xiao, Yun Zhou
Summary: Continuum theories, such as the energy-scaled Debye-Huckel (ESDH) theory, are useful in computing the electrostatic solvation free energy (ESFE) in ionic fluids. This study demonstrates the applicability of ESDH theory to molecules of complex geometries and charge distributions, with accurate predictions of ESFE in a molten salt system compared to molecular dynamics simulation results. The research sheds light on accurately predicting ESFE in ionic fluids using phenomenological continuum theories.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Chemistry, Multidisciplinary
John M. Herbert
Summary: This review discusses the theory and implementation of implicit solvation models based on continuum electrostatics, emphasizing on theory and methods rather than applications. The article also describes numerical techniques for implementing the equations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2021)
Article
Agricultural Engineering
Weixian Wang, Yi Kong, Jianjun Peng, Bin Li, Huanfei Xu
Summary: This paper studied the solubilization effect of three ionic liquids and three choline chloride-based deep eutectic solvents for xylan using molecular dynamics method. The results showed that all six solvents had good solubility for xylan and the solubilization mechanisms of the two green solvents were similar, based on the strong hydrogen bond between the anion and the hydroxyl group on the xylan model. The addition of water formed a new hydrogen bonding network, which enhanced the interaction of xylan with choline chloride/urea and promoted dissolution.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Loizos Savva, James A. Platts
Summary: Conventional and accelerated molecular dynamics simulations of alpha-Synuclein were performed to evaluate the impact of different starting conformations, solvation environments, and force field combinations. The study found that the choice of force field and solvent significantly influenced the size and secondary structure reproduction of alpha-Synuclein, with acceptable results obtained using ff03ws force field and OBC implicit solvent model.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Sanghamitra Sengupta, Jan Versluis, Huib J. Bakker
Summary: In this study, we investigated the influence of sodium chloride (NaCl) on the interface properties of water and dodecyl sulfate (DS-) surfactant using vibrational sum-frequency generation spectroscopy. We observed a highly nonlinear dependence of the O-H stretch vibrations of oriented water molecules on the NaCl concentration at the interface. This nonlinear dependence can be explained by the screening effects of the electric field of surface-bound DS- ions and the Coulomb repulsion between the headgroups of DS- ions in the surface plane. Within a limited concentration range of NaCl (10-100 mM), the latter effect significantly increased the signal of oriented water, indicating a two-dimensional hydrophobic collapse of the surfactant layer.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Materials Science, Paper & Wood
Joel A. Sanchez-Badillo, Marco Gallo, Jose G. Rutiaga-Quinones, Pablo Lopez-Albarran
Summary: This study investigated the solvent behavior of a set of imidazolium-based ionic liquids around a crystallite model of cellulose I beta through molecular dynamics simulations. Results showed that the ionic liquids can disrupt the external chains of the cellulose crystallite and affect its properties such as density and vaporization enthalpy, contributing to cellulose preconditioning. Solvation free energy calculations for the cellulose chain revealed a specific trend among the different ionic liquids in their capacity for cellulose preconditioning.
Article
Chemistry, Physical
Carolina Cruz, Enrique Lomba, Alina Ciach
Summary: This study investigates the concentration fluctuations in an electrolyte confined between electrodes formed by parallel graphene layers. The effect of proximity to the demixing transition on electric double layers is analyzed and compared to theoretical predictions. The results show that lowering temperature enhances capacitance for dilute ionic solutions near the demixing transition, while higher ionic concentrations have a less noticeable effect. Additionally, the shape of the capacitance changes, exhibiting a maximum at the potential of zero charge and symmetric maxima for positive and negative voltages.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Mario S. Valdes-Tresanco, Mario E. Valdes-Tresanco, Pedro A. Valiente, Ernesto Moreno
Summary: gmx_MMPBSA is a new tool for performing end-state free energy calculations from GROMACS molecular dynamics trajectories, offering various options including binding free energy calculations with different solvation models, stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Additionally, promising methodologies for calculating relative binding free energies have been implemented.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
Priya Kumari, Raju Poddar
Summary: This study explores the binding affinity and a method to enhance the catalysis activity of nitrilase enzyme through computational approaches. Four mutants were generated and rigorously tested for stability and interaction with ligand. Mutants 2 and 3 showed better affinity towards acrylamide, indicating improved catalysis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Physical
Davide Castaldo, Soran Jahangiri, Alain Delgado, Stefano Corni
Summary: This work extends the variational quantum eigensolver to simulate solvated systems on quantum computers. The algorithm is generalized to treat non-linear molecular Hamiltonians in order to account for the solute-solvent interaction. The results show that including solvation effects does not impact the algorithmic efficiency. Noiseless simulations and calculations on simulated noisy quantum hardware yield computed solvation free energies in fair agreement with classical calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Polymer Science
Jonas Landsgesell, David Beyer, Pascal Hebbeker, Peter Kosovan, Christian Holm
Summary: This study investigates the swelling properties of weak polyelectrolyte gels using a hierarchy of models. The results show that particle-based models are the most accurate in predicting gel swelling, but field-based models can also reasonably explain the experimental trends.
Article
Chemistry, Physical
Lucie da Rocha, Antonio M. Baptista, Sara R. R. Campos
Summary: This study analyzed the binding and distribution of ions around beta-lactoglobulin using a constant-pH MD method and compared it with the Poisson-Boltzmann model and experimental data. The findings showed good agreement between the CpHMD simulations and the nonlinear form of the PB model, and the pH-dependent trends of counterions and co-ions were as expected.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
