Article
Biochemistry & Molecular Biology
Ruben D. Parra, Slawomir J. Grabowski
Summary: In this paper, density functional theory and wave function theory calculations were used to investigate the strength and nature of the C-X···N bond interaction as a function of the number of cyano groups. The results showed that the strength of the C-X···N interaction increased significantly and in a non-additive fashion with the number of CN groups, and the nature of the interaction was revealed through the atoms in molecules approach.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nanoscience & Nanotechnology
B. Akdim, C. Woodward, S. Rao, E. Antillon
Summary: Recent studies have shown that chemically-complex solid-solution alloys produce equilibrium dislocations at high temperatures, leading to kinks and pinning points that significantly increase strength. Atomistic studies and chemical analysis can help understand the effects of different alloy compositions on dislocation formation.
SCRIPTA MATERIALIA
(2021)
Article
Spectroscopy
Wojciech Pietrus, Rafal Kurczab, Rafal Kafel, Ewa Machalska, Justyna Kalinowska-Tluscik, Adam Hogendorf, Marek Zylewski, Malgorzata Baranska, Andrzej J. Bojarski
Summary: The study explores the direct and indirect effect of fluorine on hydrogen bond patterns, revealing that a fluorine substituent decreases the strength and frequency of N-H···N hydrogen bonds while increasing the acidity of CH protons, enhancing weaker interactions. Furthermore, the position of fluorine in the aromatic ring strongly influences the C-F bond length and the stability of the N-H bond.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Physical
Amelie A. Ehrhard, Lucas Gunkel, Sebastian Jager, Arne C. Sell, Yuki Nagata, Johannes Hunger
Summary: The conformational states of thioureas in solution have been characterized using vibrational spectroscopy, revealing different N-H stretching bands in the infrared spectra. CF3-substituted DPTU is shown to favor the trans-trans conformation, allowing for donating two hydrogen bonds to the reactive substrate. However, only one N-H group forms a strong hydrogen bond to the substrate's carbonyl group, while the second N-H group only weakly interacts with the substrate.
Article
Biochemistry & Molecular Biology
Jeffrey Plante, Beth A. Caine, Paul L. A. Popelier
Summary: Predicting the aqueous pK(a) of carbon acids is challenging due to insufficient experimental data, but using atom-type feature vectors can help reduce prediction errors. Incorporating knowledge from multiple models into a general model has shown to improve predictions compared to using literature experimental data alone.
Article
Chemistry, Multidisciplinary
Rui Liu, Rui Wang, Danhui Li, Yu Zhu, Xinrui Yang, Zhigang Wang
Summary: The cooperative effect is important in understanding the interactions of hydrogen bonds. Through high-precision ab initio calculations, it is shown that intermolecular H-bonded systems with different donor and acceptor atoms exhibit structural changes predicted by the cooperative effect upon compression. However, when the donor and acceptor are the same, the structural changes are different. Further analysis reveals that the failure of the cooperative effect has boundaries and is related to the H-bond strength.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Physical
Aziz Habibi-Yangjeh, Hadi Basharnavaz
Summary: DFT computations were used to investigate the adsorption performance of hydrogen molecules over transition metals embedded graphitic carbon nitride, showing that Os-embedded gCN has superior interaction with H-2 molecules. The maximum storage number of adsorbed H-2 molecules was found to be 6. Adsorption of H-2 molecules converted the semi-conductive behavior of the systems to a conductive state.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2021)
Article
Chemistry, Physical
Mukesh Singh, Alok Shukla, Brahmananda Chakraborty
Summary: In this study, the hydrogen-storage properties of Zr-decorated g-graphyne monolayer were investigated using Density Functional Theory (DFT). The results predict that each Zr atom can adsorb up to seven H2 molecules with a hydrogen gravimetric density of 7.95 wt% and a desorption temperature of 574 K, making it suitable for fuel-cell applications. The strong attachment between decorated Zr atom and graphyne sheet is due to charge transfer, while hydrogen molecules adsorb on Zr decorated graphyne through Kubas type of interactions. The stability of Zr+g-graphyne was confirmed through ab-initio molecular dynamics simulations. Overall, these findings suggest that Zr functionalized on g-graphyne could be a promising solid-state hydrogen storage material.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Spectroscopy
Zhen Wang, Yugao Xu, Wenqin Li, Tao Lu, Gang Feng
Summary: In this study, the 1,4-pentadien-3-ol and its monohydrate were characterized using microwave spectroscopy and theoretical computations. The research revealed the characteristics of hydrogen bonds in the compounds.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Yuehui Li, Yantao Shi, Xuedan Song, Zhengyan Zhao, Naitian Zhang, Ce Hao
Summary: In this study, the state and dynamic equilibrium of glycolaldehyde in methanol solution were systematically investigated. It was found that glycolaldehyde hemiacetal (GAHA) is the dominant component in methanol solution, with more than 90% abundance. The study provides important insights into the analysis of sugars and related compounds in biochemical reactions.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
Luis E. Gonzalez, David J. Gonzalez
Summary: The static and dynamic properties of several bulk liquid 4d transition metals near their respective melting points have been evaluated using ab-initio molecular dynamics simulations. The results demonstrate the existence of ordered structures and special collective excitations, and further study several transport coefficients.
INTERNATIONAL JOURNAL OF REFRACTORY METALS & HARD MATERIALS
(2022)
Article
Engineering, Chemical
Chun Yuan Chot, Ace Christian Serron, Chong Siang Yaw, Ai Kah Soh, Joey D. Ocon, Meng Nan Chong
Summary: The functional MoO3 photoanode with self-photorechargeability was synthesized through aerosol-assisted chemical vapour deposition, and the Pt co-catalyst in Pt-mediated MoO3 photoanode was found to significantly improve charge density for photoelectrochemical water oxidation under non-irradiated condition. The presence of Pt co-catalyst inhibited the recombination of photogenerated charge carriers, leading to a substantial enhancement in both current and charge densities of the Pt/MoO3 photoanode.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2021)
Article
Chemistry, Physical
Shuo Cao, Gang Zhao, Dehua Wang
Summary: Using fully ab initio molecular dynamics simulations, this study investigates the inherent structure of water and its temperature dependence. The results reveal three types of translational ordering in the second oxygen coordination shell, leading to the classification of local structures in water into three types. These findings provide ab initio evidence for the mixture model of water and shed light on the temperature dependence of its inherent structure.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Matthieu Micoulaut, Hugo Flores-Ruiz, Annie Pradel, Andrea Piarristeguy
Summary: This study investigates the structure of a typical binary amorphous telluride GeTe2 using first-principles molecular dynamics simulations. It reveals soft tetrahedra structures and increased angular bending motion, especially in Ge-rich materials, which may be crucial for understanding phase-change phenomena. The findings offer insights into the unique characteristics of binary Ge tellurides compared to lighter chalcogenides and their relevance for phase-change behavior.
PHYSICA STATUS SOLIDI-RAPID RESEARCH LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Sergei Vlassov, Dmitry Bocharov, Boris Polyakov, Mikk Vahtrus, Andris Sutka, Sven Oras, Veronika Zadin, Andreas Kyritsakis
Summary: In this critical review, we address the issue of the vast disagreement in reported elastic moduli values for nanostructures made of the same material. As a case study, we focus on ZnO nanowires, which have been extensively studied due to their remarkable physical properties and potential applications. Despite considering the same growth direction and crystal structure, there is a significant variation in reported Young's modulus values, ranging from 20 to 800 GPa. This work provides a critical overview and thorough analysis of existing experimental and theoretical studies in order to identify the most significant sources of errors and reliable results.
NANOTECHNOLOGY REVIEWS
(2023)
Article
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The ultimate goal of this series of articles is to establish a better correspondence between the dynamics of fine-grained (FG) and coarse-grained (CG) models. By utilizing the excess entropy scaling relationship, the authors show that FG and CG counterparts follow the same universal scaling relationship. They develop a new theory to calculate excess entropies for both FG and CG systems, taking into account entropy representability. Applying the excess entropy scaling idea to liquid water and methanol systems, they find that the scaling exponents remain unchanged during the coarse-graining process, indicating universality of the scaling behavior for the same underlying molecular systems. Furthermore, they demonstrate that missing entropy plays a crucial role in accelerating CG dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The first paper of this series demonstrated the scalability of excess entropy for both fine-grained and coarse-grained systems. However, a more precise determination of the scaling relationship was not possible due to its semi-empirical nature. In this second paper, an analytical scaling relation for excess entropy is derived for bottom-up coarse-grained systems. By constructing effective hard sphere systems at the single-site resolution, the dynamics and excess entropy of the target coarse-grained systems can be accurately approximated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Sijia Chen, Gregory A. Voth
Summary: Molecular dynamics simulation is used to study the properties of the air-liquid interface of a common room temperature ionic liquid. The effects of electronic polarizability and scaled-charge ions on the interface properties are investigated.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Jaehyeok Jin, Gregory A. Voth
Summary: Systematic bottom-up coarse-graining is a useful approach for exploring different length and time scales in molecular systems. However, the configuration dependence of coarse-grained interactions limits their applicability. In this study, a statistical mechanical theory is proposed to design coarse-grained interactions across different configurations and conditions. By identifying classical coarse-grained free energy surfaces for characteristic configurations and quantifying the coupling interaction between them, the theory accurately captures the underlying potential of mean force in coarse-grained variables and offers a new protocol for multiscale model design.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Manish Gupta, Alexander J. Pak, Gregory A. Voth
Summary: Researchers use molecular dynamics simulations to reveal the molecular mechanism of HIV-1 capsid formation, including the role of IP6. This study shows that IP6 initially promotes curvature generation by trapping pentameric defects and shifts the assembly behavior towards kinetically favored outcomes. Additionally, IP6 can stabilize metastable capsid intermediates and induce structural pleomorphism in mature capsids.
Article
Biophysics
Arpa Hudait, James H. Hurley, Gregory A. Voth
Summary: In the late stages of the HIV-1 life cycle, the membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. The release of the virion requires the interaction between Gag lattice and ESCRT machinery at the viral budding site, followed by the assembly of downstream ESCRT-III factors. However, the molecular details of upstream ESCRT assembly dynamics remain unclear. In this study, molecular simulations were used to investigate the interactions between Gag, ESCRT-I, ESCRT-II, and membrane, revealing the mechanisms by which upstream ESCRTs assemble at the viral budding site.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Aleksander E. P. Durumeric, Gregory A. Voth
Summary: Bottom-up CG molecular dynamics models, parameterized using complex effective Hamiltonians, are often optimized to approximate high dimensional data from atomistic simulations. However, human validation of these models may not differentiate between the CG model and the atomistic simulations. We propose using classification to estimate high dimensional errors and utilizing explainable machine learning to convey this information to scientists. This approach is demonstrated using Shapley additive explanations and two CG protein models, and may be valuable for assessing the accuracy of allosteric effects in CG models at the atomistic level.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Patrick G. Sahrmann, Timothy D. Loose, Aleksander E. P. Durumeric, Gregory A. Voth
Summary: In this work, a new method is proposed to improve the accuracy of coarse-grained (CG) models of biomolecules by incorporating virtual particles as latent variables. The virtual particle interactions are optimized through a gradient descent algorithm aided by machine learning, capturing solvent-mediated behavior and higher-order correlations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Huong T. Kratochvil, Laura C. Watkins, Marco Mravic, Jessica L. Thomaston, John M. Nicoludis, Noah H. Somberg, Lijun Liu, Mei Hong, Gregory A. Voth, William F. DeGrado
Summary: Selective proton transport through proteins is essential for cellular functions. Static protein structures have shown interruptions in proton conduction pathways, which may be overcome by the formation of transient water wires. Molecular dynamics simulations were performed to design transmembrane channels with stable water pockets and apolar segments capable of forming flickering water wires, which successfully conducted protons with high selectivity over ions. These studies have implications for understanding proton conduction mechanisms and engineering proton-conductive materials.
Article
Multidisciplinary Sciences
Kun Wang, Chia-Wei Lee, Xuewu Sui, Siyoung Kim, Shuhui Wang, Aidan B. Higgs, Aaron J. Baublis, Gregory A. Voth, Maofu Liao, Tobias C. Walther, Robert V. Farese
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Daniel Beckett, Gregory A. Voth
Summary: Microtubules (MTs) are large cytoskeletal polymers composed of α(3-tubulin heterodimers that undergo stochastic polymerization and depolymerization processes. Depolymerization involves the hydrolysis of guanosine triphosphate (GTP), which is favored in the MT lattice compared to the free heterodimer. This study used extensive simulations to investigate the GTP hydrolysis mechanism in different lattice states. The results revealed the catalytic role of α:E254 and demonstrated that GTP hydrolysis is variable with lattice state and slower at the MT tip.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Sijia Chen, Gregory A. Voth
Summary: Molecular dynamics simulations were conducted to investigate the effects of electronic polarizability and scaled-charge ions on the properties of the room temperature ionic liquid (RTIL) air-liquid interface. Three different force fields were used and it was found that the nonpolarizable force field with scaled-charge ions provided a simple cure for the over-ordered structures and sluggish dynamics predicted by the nonpolarizable force field with united ion charges. However, this model failed to accurately reproduce the results of the polarizable force field at the interface due to inappropriate scaling of charges near the interface.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Timothy D. Loose, Patrick G. Sahrmann, Thomas S. Qu, Gregory A. Voth
Summary: Machine learning has become mainstream in coarse-grained molecular modeling and simulation, with deep learning improving accuracy. However, using neural networks as coarse-grained force fields is slower and requires large amounts of data for training. This paper addresses the data-hunger trap by incorporating equivariant convolutional operations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Jiangbo Wu, Weizhi Xue, Gregory A. Voth
Summary: KMC-CG is a generalized coarse-graining method that removes sequence-dependent constraints, allowing for the discovery of more physically optimal CG mappings and better capture of the structural, dynamic, and functional domains of large biomolecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jaehyeok Jin, Jisung Hwang, Gregory A. Voth
Summary: Coarse-grained interactions determined via bottom-up methodologies can accurately reproduce the structural correlations observed in fine-grained systems. However, their limited extensibility due to complex many-body correlations is a challenge. In this study, we propose an alternative approach that combines perturbation theory and Gaussian basis functions to improve both accuracy and transferability of coarse-grained models. Our findings provide a solid foundation for constructing transferable bottom-up coarse-grained models of liquids with enhanced extensibility.
JOURNAL OF CHEMICAL PHYSICS
(2023)