Article
Chemistry, Physical
Jan Dockal, Martin Lisal, Filip Moucka
Summary: This article develops and studies polarizable microscopic models and force fields for molecular simulations of alkali halide electrolyte aqueous solutions, their crystals, and phase equilibria. The refined force fields accurately predict the properties of crystals and aqueous solutions, making them suitable for various applications.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo
Summary: Accuracy and transferability are key properties of molecular mechanical force fields. Polarizable force fields are thought to have advantages in modeling atomic polarization effects. This study assessed the transferability of the electrostatic parameters in polarizable Gaussian multipole (pGM) models and found that they showed improved transferability compared to additive models. The observation that pGM models have better accuracy and transferability than additive models highlights the importance of intramolecular polarization effects. Overall, this study shows that pGM models possess accuracy and transferability, making them suitable for modeling polarization-sensitive biological systems and processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Malgorzata Bogunia, Adam Liwo, Cezary Czaplewski, Joanna Makowska, Artur Gieldon, Mariusz Makowski
Summary: Hydrophobic interactions, the aggregation of nonpolar particles in a polar solvent, are crucial for complex processes like protein folding. This study used molecular dynamics simulations to investigate the hydrophobic association of adamantane and hexane under various conditions and determined the thermodynamic properties associated with their formation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Review
Chemistry, Multidisciplinary
Kateryna Goloviznina, Zheng Gong, Agilio A. H. Padua
Summary: This article discusses the importance of using molecular dynamics simulation and theoretical chemistry tools to study ionic liquids and eutectic solvents, as well as the use of polarizable force fields to describe their interactions and conformations. The development of polarizable force fields is a combination of science and art, with the main challenge being how to handle the diversity in chemical structures and interactions to build a model that can represent solutions, mixtures, and material interfaces effectively.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Multidisciplinary Sciences
Lianghao Guo, Wenfei Bo, Kaicheng Wang, Shaomeng Wang, Yubin Gong
Summary: The study investigates the interaction of terahertz waves with ions in nerve cell channels and its potential effects. It finds that terahertz radiation can generate electromagnetic radiation in calcium channels and accelerate the transport of calcium ions. These findings provide a theoretical basis for the future application of terahertz waves in neurological treatments.
Article
Chemistry, Multidisciplinary
Sergiy Markutsya, Austin Haley, Mark S. Gordon
Summary: This study combines multiple coarse-graining methods to develop a CG model that accurately predicts the structure and dynamics properties of water, achieving good results in experiments.
Article
Chemistry, Physical
Ajay Muralidharan, Arun Yethiraj
Summary: Ion-pairing plays a crucial role in electrolyte solutions, and accurately estimating ion-pairing is valuable for designing and screening new electrolytes. In this study, we propose an efficient cluster model to estimate the ion-pair potential-of-mean-force between ionic solutes in electrolytes, utilizing an enhanced sampling approach to achieve high efficiency and accuracy.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo
Summary: Molecular modeling at the atomic level is widely used in biological systems. However, additive force fields that rely on fixed atom-centered partial charges cannot accurately simulate polarization effects. This study presents PyRESP, a Python program that parameterizes atomic multipole moments by reproducing the ab initio electrostatic potential around molecules, catering to the needs of force field parameterizations in molecular modeling.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Yan Li, Ye Liu, Boya Yang, Guohui Li, Huiying Chu
Summary: A polarizable atomic multipole force field (FF) for the molecular dynamic simulation of cholesterol is proposed, based on the AMOEBA model. The proposed FF utilizes electronic parameters calculated from ab initio calculations to represent charge distribution, and models many-body polarization using distributed atomic polarizabilities. The feasibility of the proposed FF is validated through molecular dynamics (MD) simulations of bilayers composed of different cholesterol concentrations and comparisons with experimental values.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Aditi Khot, Brett M. Savoie
Summary: Coarse-grained molecular dynamics (CGMD) simulations address critical lengthscales and timescales in chemical and material applications. The development of black-box CGMD methodologies similar to density functional theory for electronic structure is still lacking. Machine learning (ML)-based CGMD potentials show promise in simplifying model development, but they have yet to outperform physics-based CGMD methods. In this study, λ-learning models are explored to combine the advantages of both approaches. The λ-models outperform ML-only CGMD models and provide essentially free gains in reproducing atomistic properties. However, neither the λ-learning models nor the ML-only models significantly outperform elementary pairwise models in reproducing atomistic properties due to the large irreducible force errors associated with coarse-graining.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Szabolcs Goger, Almaz Khabibrakhmanov, Ornella Vaccarelli, Dmitry V. Fedorov, Alexandre Tkatchenko
Summary: The quantum Drude oscillator (QDO) is an efficient coarse-grained approach used to model electronic and optical response properties of atoms and molecules. An optimized parametrization (OQDO) is presented in this study, where the parameters are fixed using only dipolar properties. The OQDO accurately reproduces atomic polarization potentials and multipolar dispersion coefficients for the periodic table of elements and small molecules, showing great potential in the development of next-generation quantum-mechanical force fields for (bio)molecular simulations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Physics, Multidisciplinary
Simone Benaglia, Manuel R. Uhlig, Jose Hernandez-Munoz, Enrique Chacon, Pedro Tarazona, Ricardo Garcia
Summary: This study demonstrates that the generation of 3D maps is dependent on the polarization of the tip, with differently charged tips revealing different density distributions. Experimental data reproduce key findings of the theory.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Joshua A. Rackers, Roseane R. Silva, Zhi Wang, Jay W. Ponder
Summary: A new empirical potential, the HIPPO force field, has been developed for efficient molecular dynamics simulation of water, balancing a wide range of water properties across different conditions. This model explicitly correlates water structure, dynamics, and thermodynamics with ab initio energy decomposition, offering comparable accuracy to previous polarizable atomic multipole force fields. The HIPPO water model can serve as a cornerstone for developing similarly detailed physics-based models for other molecular species.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Hidefumi Naito, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga
Summary: Through molecular simulation, it has been found that the strength of hydrophobic interaction varies with the molecular size following a power law, which is different from the cubic power law observed in the second virial coefficients of gases.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Van A. Ngo, Ramesh K. Jha
Summary: The SARS-CoV-2 virus interacts with the human receptor ACE2 for invasion, showing stronger anchoring in ACE2 compared to the related SARS-CoV from 2003. This results in a reduced dissociation rate from the human receptor, potentially aiding in the development of diagnostics and therapeutics for combatting the pandemic.
Article
Chemistry, Multidisciplinary
Allan Jay P. Cardenas, Bojana Ginovska, Neeraj Kumar, Jianbo Hou, Simone Raugei, Monte L. Helm, Aaron M. Appel, R. Morris Bullock, Molly O'Hagan
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2016)
Article
Biochemistry & Molecular Biology
Adam J. Comish, Bojana Ginovska, Adam Thelen, Julio C. S. da Silva, Thereza A. Soares, Simone Raugei, Michel Dupuis, Wendy J. Shaw, Eric L. Hegg
Article
Chemistry, Physical
Yongsoon Shin, Wei Liu, Birgit Schwenzer, Sandeep Manandhar, Dylan Chase-Woods, Mark H. Engelhard, Ram Devanathan, Leonard S. Fifield, Wendy D. Bennett, Bojana Ginovska, David W. Gotthold
Article
Chemistry, Multidisciplinary
Truong Ba Tai, Minh Tho Nguyen
CHEMICAL COMMUNICATIONS
(2016)
Article
Chemistry, Inorganic & Nuclear
Arnab Dutta, Bojana Ginovska, Simone Raugei, John A. S. Roberts, Wendy J. Shaw
DALTON TRANSACTIONS
(2016)
Article
Chemistry, Inorganic & Nuclear
Matthew L. Reback, Bojana Ginovska, Garry W. Buchko, Arnab Dutta, Nilusha Priyadarshani, Brandon L. Kier, Monte L. Helm, Simone Raugei, Wendy J. Shaw
JOURNAL OF COORDINATION CHEMISTRY
(2016)
Article
Chemistry, Physical
Dang Thi Tuyet Mai, Long Van Duong, Truong Ba Tai, Minh Tho Nguyen
JOURNAL OF PHYSICAL CHEMISTRY A
(2016)
Article
Chemistry, Physical
Vu Thi Thu Huong, Truong Ba Tai, Jyh-Chiang Jiang, Minh Tho Nguyen
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Chemistry, Multidisciplinary
Truong Ba Tai, Minh Tho Nguyen
Article
Chemistry, Physical
Pham Vu Nhat, Truong Ba Tai
CHEMICAL PHYSICS LETTERS
(2018)
Article
Chemistry, Physical
Truong Ba Tai, LiAo Cao, Felix Mattelaer, Geert Rampelberg, Fatemeh S. M. Hashemi, Jolien Dendooven, J. Ruud van Ommen, Christophe Detavernier, Marie-Francoise Reyniers
JOURNAL OF PHYSICAL CHEMISTRY C
(2019)
Article
Chemistry, Physical
Truong Ba Tai, Jihoon Son, Hyeyoung Shin
Summary: In this study, we theoretically investigated the reaction mechanisms during the atomic layer deposition (ALD) of HfO2 thin film on silicon (Si) surface. We found that controlling the concentration of hydroxyl groups on the surface is crucial for enhancing the activity of the ligand-exchange reactions (LERs) and promoting HfO2-ALD.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Physical
Yujin Jung, Hyeyoung Shin, Se-Woong Baek, Truong Ba Tai, Benjamin Scheffel, Olivier Ouellette, Margherita Biondi, Sjoerd Hoogland, F. Pelayo Garcia de Arquer, Edward H. Sargent
Summary: Solution-processed semiconducting materials have potential for high-performance, low-cost, and flexible energy conversion devices. By using a library of surface ligands with different functions, the photophysical mismatch at the colloidal quantum dot (CQD)/organic interface was addressed, resulting in improved charge transfer efficiency. Hybrid CQD/organic heterojunction solar cells showed record photocurrent density and near-unity broadband quantum efficiency.
ACS ENERGY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Phu Cuong Nguyen, My Tuyen Thi Nguyen, Ba Tai Truong, Dae-Ryeol Kim, Sujin Shin, Ju-Eun Kim, Kyu-Been Park, Ji-Hyun Park, Phuong Lan Tran, So-Young Ban, Jaehan Kim, Jong-Tae Park
Summary: This study aimed to develop an efficient method to produce high-purity inotodiol from Chaga mushroom and evaluate its physicochemical properties and biological activities. A new method with high purity (>97%) and purification yield (33.6%) was developed by optimizing the extraction and purification solvents. Inotodiol exhibited distinctive physicochemical properties compared to cholesterol and lanosterol, and a nonionic surfactant-based microemulsion was developed to improve its bioavailability. The microemulsion showed effectiveness in oral delivery and potential applications in functional food, cosmetic, and pharmaceutical industries.
Article
Chemistry, Physical
Truong Ba Tai, Pham Vu Nhat
CHEMICAL PHYSICS LETTERS
(2017)
