Article
Crystallography
Jonathon G. Gray, David A. Case
Summary: Replacing traditional geometric restraints with energy gradients derived from force fields can improve the refinement of atomic models for nucleic acids. Solvent screening for charge-charge interactions is important, especially in crowded environments, and newly refined models show improvements in torsion angles and hydrogen-bonding interactions.
Article
Chemistry, Physical
Thomas J. Oweida, Ho Shin Kim, Johnny M. Donald, Abhishek Singh, Yaroslava G. Yingling
Summary: This study assessed the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, and found that the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experimental data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Eric J. M. Lang, Emily G. Baker, Derek N. Woolfson, Adrian J. Mulholland
Summary: We tested a range of standard GB models and protein force fields on a set of designed peptides and found that none of the models accurately predicted the a-helical content for all peptides. These peptides serve as a useful test set for simulation methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Crescenzo Coppa, Andrea Bazzoli, Maral Barkhordari, Alessandro Contini
Summary: This study evaluated the performance of accelerated molecular dynamics (aMD) protocols in predicting the secondary structure of eight peptides, including helical, fi-hairpin, and disordered peptides. The results showed that all three combinations of force fields and solvation models performed well on helical peptides. For fi-hairpins, the ff19SB force field combined with both solvation methods showed good performance, with a slight preference for the TIP3P solvation model. The ff19SB/OPC combination exhibited the best performance on intrinsically disordered peptides. However, the ff14SB/TIP3P combination had a strong bias towards helical peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Thorben Frohlking, Mattia Bernetti, Giovanni Bussi
Summary: This paper presents a novel method that combines the maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models. The method has been applied to study the Karplus parameters for RNA systems, achieving good agreement between simulations and experiments by correcting errors in the forward models and reweighting the sampled structural dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Toshifumi Mori, Norio Yoshida
Summary: The interaction between ATP and disordered proteins plays a crucial role in protein aggregate dissolution and liquid-liquid phase separation. Different water models impact the ATP properties in high concentration, with TIP3P water model leading to excessive ATP aggregation and TIP4P-D and OPC water models promoting ATP-protein interactions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Ruixue Zhu, Zhexin Jiang, Xinxin Zhang, Xiangli Zhong, Congbing Tan, Mingwei Liu, Yuanwei Sun, Xiaomei Li, Ruishi Qi, Ke Qu, Zhetong Liu, Mei Wu, Mingqiang Li, Boyuan Huang, Zhi Xu, Jinbin Wang, Kaihui Liu, Peng Gao, Jie Wang, Jiangyu Li, Xuedong Bai
Summary: In this study, the dynamics of room-temperature polar skyrmions were investigated using in situ scanning transmission electron microscopy. The reversible transformation among different structures was demonstrated, and the electrical manipulation of nanoscale polar skyrmions was discussed. This research provides important insights into the electric field control and potential applications in nanoelectronics.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Valerio Piomponi, Thorben Froehlking, Mattia Bernetti, Giovanni Bussi
Summary: Post-transcriptional modifications are crucial for RNA function, affecting its structure and dynamics. The set of force-field parameters for N-6-methyladenosine developed for AMBER force field cannot accurately describe both paired and unpaired states. New parameters derived using reweighting techniques enable proper description of paired and unpaired m(6)A in both syn and anti conformations, facilitating the investigation of N-6 methylations on RNA structural dynamics through molecular simulations.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Physical
Hao Su, Marten S. G. Ahlquist
Summary: The practical applications of tetravalent metal-based MOFs have gained increased attention recently. A new eight-coordinated tetravalent metal dummy model force field has been proposed, which can accurately describe ion-induced dipole interactions and has been shown to be useful and transferable among MOFs with the same metal-core topology. The modular nature of the model allows for broad applicability to different chemical problems.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Tamilselvan Rajasekaran, Graeme C. Freestone, Rodrigo Galindo-Murillo, Barbara Lugato, Lorena Rico, Juan C. Salinas, Hans Gaus, Michael T. Migawa, Eric E. Swayze, Thomas E. Cheatham, Stephen Hanessian, Punit P. Seth
Summary: The study investigates the impact of restricting rotation around the sugar-phosphate backbone on the hybridization kinetics of modified oligonucleotides. Experimental and molecular dynamics simulation results suggest that backbone-constrained compounds and conformationally preorganized LNA analogues contribute to improving the hybridization properties of modified oligonucleotides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Thermodynamics
Juan He, Xiaosen Li, Zhaoyang Chen, Xiaoliang Huang, Pengfei Shen
Summary: This study investigates the effect of heterogeneous hydrate distribution on hydrate production. The results show that the heterogeneity degree of hydrate distribution influences water and gas production, as well as the temperature loss and sensible heat use ratio. The impact is most significant when the hole combination is 1-2 holes.
Article
Chemistry, Physical
Kye Won Wang, Jumin Lee, Han Zhang, Donghyuk Suh, Wonpil Im
Summary: Implicit solvent models are widely used in various molecular dynamics programs, with CHARMM-GUI's Implicit Solvent Modeler supporting different GB implicit solvent simulations for protein, DNA, RNA, glycan, and ligand systems. Generated systems and input files by ISM produce similar results and show better performance for ligand screening compared to docking. This indicates that ISM is a useful and reliable tool for various implicit solvent simulation applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Young Hyun Kim, Nayeong Kim, Jeong-Min Seo, Jong-Pil Jeon, Hyuk-Jun Noh, Do Hyung Kweon, Jungki Ryu, Jong-Beom Baek
Summary: The study investigated the symmetrical features of benzothiazole-based COFs and their physical/chemical properties by synthesizing two different combinations, and found that COFs with significantly different pore sizes exhibited stronger CO2 adsorption and light-harvesting capabilities.
CHEMISTRY OF MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Xiaohui Wang, Zhe Huai, Zhaoxi Sun
Summary: This paper profiles the energetics and dynamics of four types of popular macrocycles and provides general guidelines on force field parametrization and selection in host-guest modeling.
Article
Chemistry, Physical
Samprita Nandi, Colin Coane, Angel-Emilio Villegas, Angana Ray, Rosa Di Felice
Summary: G-quadruplex is a nucleic acid structure with diverse applications in biology and nanotechnologies. It can be formed in telomeres and other guanine-rich regions, and can be engineered for use in nanodevices. Research shows that manipulating the structure can optimize electron transport efficiency, but the relationship between structure and function is complex and influenced by various factors.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)