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
Chemistry, Physical
Shaowei Li, Yuanzhe Li, Pengpeng Bai, Yonggang Meng, Yu Tian
Summary: In this study, the interfacial frictional behavior between charged colloidal probes and a gold electrode was investigated using electrochemical atomic force microscopy. It was found that the surface charges and potentials have an impact on the friction behavior, which can be attributed to the rearrangement of hydrated ions and water molecules. At positive potential, hydrogen bonds formed between negatively charged microspheres and gold surface increased friction, whereas positively charged microspheres relied on hydrated Cl- ions for hydrogen bonding. At negative potential, lubrication by hydrated Na+ ions reduced friction and facilitated superlubricity.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Yawen Miao, Kai Chen, Xu Zhang, Zhijun Xu, Xiaoning Yang
Summary: Studying the interaction of ionized two-dimensional graphene oxide (GO) nanosheets at the air-water interface revealed that GO nanosheets with the same negative charge can attract each other at the interface, in contrast with repulsive interaction in the bulk phase. This attractive interaction is attributed to an enhanced solvation force arising from shared bridge water structure at the interface between negatively charged GO sheets.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Multidisciplinary
Ciera M. Wentworth, Alexander C. Castonguay, Pepijn G. Moerman, Caleb H. Meredith, Rebecca Balaj, Seong Ik Cheon, Lauren Zarzar
Summary: This study reports emulsions with a behavior opposite to the typical one where solubilization decreases the interfacial tension and leads to droplet attraction. By adjusting the oil chemical structure, nonionic surfactant structure, and surfactant concentration, three regimes corresponding to droplet attraction, repulsion, or inactivity are identified.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Justyna D. Krys, Dominik Gront
Summary: Understanding protein structure and dynamics is crucial for investigating biological processes. We propose a novel hydrogen bond energy function for coarse-grained simulations, which accurately recognizes hydrogen bonds and identifies β-sheet structures in amyloid peptide simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Chemistry, Physical
Olivera Drecun, Cecilia Bernardini, Misbah Sarwar, Alberto Striolo
Summary: This study investigates the interactions and agglomeration of γ-alumina nanoparticles in water and salt solutions. Molecular dynamics simulations are used to characterize surface effects, and dynamic light scattering experiments are conducted to study agglomeration at the macroscale. The results highlight the capability of molecular simulations to explain macroscopic observations.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(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)
Article
Energy & Fuels
Liu Chenwei, Zhou Chenru, Li Mingzhong, Tong Shikun, Qi Minhui, Wang Zhiyuan
Summary: This study measured the interaction forces between methane hydrate particles at high pressure using a custom-built high-pressure micromechanical force device. It found that the cohesion forces between hydrate particles increase with contact time and decrease with annealing time and subcooling. The adhesion forces between hydrate particles and water droplets are much stronger and are influenced by subcooling and contact time. This study provides insights into the agglomeration mechanism of hydrates in gas pipelines and contributes to evaluating hydrate plugging risk.
Article
Engineering, Chemical
Ting Long, Hongguan Wu, Chongzhi Qiao, Bo Bao, Shuangliang Zhao, Honglai Liu
Summary: A theoretical study on the potential of mean force between nanoparticles in nanochannels under confinement effects was conducted. The short-ranged attraction between nanoparticles was found to be enhanced by nano-confinement, and the strength of attraction can be moderated by adjusting various factors. This study offers theoretical guidance for the development of efficient particle separation methods in nanochannel-based devices.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Multidisciplinary Sciences
Andri Sharma, Rajeev Kapri, Abhishek Chaudhuri
Summary: This study investigates the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a spatially varying driving force. It is found that the asymmetric shape of the channel leads to non-monotonic features in the total translocation time as a function of the channel apex angle. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions. Additionally, the stiffness of the polymer affects both the translocation time and the features of the waiting time distributions.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Chengwei Zhang, Jing Huang
Summary: The organization of genomes in space and time dimension is crucial for gene expression and regulation. Through explicit-solvent all-atom simulations under physiological conditions, the effective interactions between nucleosomes can be revealed at an atomic level, aiding in the construction of a coarse-grained model for chromatin. Free energy landscapes derived from umbrella sampling simulations are consistent with recent experimental and simulation results, providing valuable insights into the interactions between nucleosomes in solution.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Microbiology
Yuqi Li, Zhenxiang Meng, Yao Xu, Qicheng Shi, Yuping Ma, Min Aung, Yanfen Cheng, Weiyun Zhu
Summary: Anaerobic fungi in the digestive tract of herbivores play a critical role in the rumen ecosystem by degrading lignocellulosic materials and producing metabolic products such as H-2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products to produce methane. The interaction between anaerobic fungi and methanogens is important for understanding microbial relationships in the rumen, as they stimulate each other's growth and metabolic pathways.
Article
Chemistry, Multidisciplinary
Andraniek Evadgian, Ambadasu Bharatha, Damian Cohall
Summary: Barbados has a rich tradition of using medicinal plants, especially among the older population with chronic noncommunicable diseases. This study aims to identify possible interactions between popular herbal remedies used for high blood pressure and conventional antihypertensive drugs in Barbados.
Article
Chemistry, Physical
Aditya Koneru, Henry Chan, Sukriti Manna, Troy D. Loeffler, Debdas Dhabal, Andressa A. Bertolazzo, Valeria Molinero, Subramanian K. R. S. Sankaranarayanan
Summary: In this study, an improved formalism and parameterization of the BKS model were introduced using a multireward reinforcement learning approach. The model accurately predicts the structure, energetics, and properties of silica polymorphs and outperforms existing empirical models. A machine-learned ML-BKS model was also introduced, which captures the experimental structure and properties of silica polymorphs and amorphous silica.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Rui Ma, Feng Wang, Yuanhao Chang, Senbo Xiao, Niall J. English, Jianying He, Zhiliang Zhang
Summary: In this study, large-scale molecular simulations were used to investigate the adhesion of hydrates on solid surfaces, focusing on the atomistic structures of the intermediate layer and their impact on adhesion. The results revealed that the structure of the intermediate layer is a competitive equilibrium of induced growth from both sides, regulated by the content of guest molecules. By comparing the fracture behaviors of hydrate-solid surface systems with different intermediate structures, it was found that the adhesion strength is determined by the lattice areal density of water structure and the adsorption of guest molecules on the interface. Further analysis of adhesion strength distribution showed significant differences in adhesion among different water structures like ice and hydrate, with ice having approximately five times the adhesion strength compared to the lowest hydrate adhesion strength, consistent with experimental results.
Biographical-Item
Chemistry, Physical
Henry S. Ashbaugh, Dilipkumar Asthagiri, Thomas L. Beck, Susan B. Rempe
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Dilipkumar N. Asthagiri, Michael E. Paulaitis, Lawrence R. Pratt
Summary: The quasi-chemical theory QCT provides a practical way to calculate and conceptual framework for molecular hydration phenomena. It can be viewed from multiple perspectives, such as regularization of statistical thermodynamic problems, emphasis on solute neighborship characteristics, or inclusion of accurate electronic structure descriptions. The theory has been successfully applied to a wide range of solutes with different chemical complexities, providing guidance on necessary approximations and simplifications for calculations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Correction
Chemistry, Physical
Philip M. Singer, Arjun Valiya Parambathu, Xinglin Wang, Dilip Asthagiri, Walter G. Chapman, George J. Hirasaki, Marc Fleury, Kalina Ranguelova
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Editorial Material
Chemistry, Physical
Arjun Valiya Parambathu, Thiago J. Pinheiro dos Santos, Walter G. Chapman, Dilipkumar N. Asthagiri
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Review
Chemistry, Multidisciplinary
Diego T. Gomez, Lawrence R. Pratt, Dilipkumar N. Asthagiri, Susan B. Rempe
Summary: This article reviews the quasi-chemical theory (QCT) used to evaluate the hydration free energies of ions, with a focus on anions such as halides. The study finds that QCT provides good agreement with experimental results and accurate numerical values for the inner-shell contribution. However, there may be issues when evaluating the outer-shell contribution for heavily hydrated, less effectively shielded ions. Sampling inner-shell structures from bulk solutions can improve the accuracy.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Physical
Rohan S. Adhikari, Arjun Valiya Parambathu, Walter G. Chapman, Dilipkumar N. Asthagiri
Summary: Calculating the hydration free energy of macromolecules has always been a challenge, but with the development of molecular quasi-chemical theory (QCT), it is now possible to calculate it within all-atom simulations. This study compares the results obtained using QCT with predictions from implicit solvent models and reveals the importance of cooperativity in hydration. The deviations between implicit and explicit solvent results highlight the limitations of additive models.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Arjun Valiya Parambathu, Walter G. Chapman, George J. Hirasaki, Dilipkumar Asthagiri, Philip M. Singer
Summary: In this study, atomistic MD simulations were used to investigate the effects of nanoconfinement on the 1H NMR relaxation times T1 and T2 of heptane in kerogen. The results show that confinement plays an important role in reducing T1 by -3 orders of magnitude, in agreement with experimental measurements. For T2, confinement breaks spatial isotropy and gives rise to residual dipolar coupling, leading to a -5 orders of magnitude reduction compared to bulk heptane. Using the simulated T2, the surface relaxivity was calibrated to predict the pore-size distribution of organic nanopores in kerogen without additional experimental data.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Polymer Science
Winnie H. Shi, Rohan S. Adhikari, Dilipkumar N. Asthagiri, Amanda B. Marciel
Summary: We studied the influence of charge block length on the structure and behavior of polyampholyte chains using SAXS and molecular simulations. By synthesizing polyampholytes with different lengths of glutamic acid and lysine blocks, we found that longer blocks tend to induce phase separation. The addition of NaCl affected the phase behavior in a manner dependent on the charge block length. Our findings suggest the importance of electrostatic interactions and hydrogen bonding in phase separation and offer insights for intracellular condensates and material design.
Article
Chemistry, Physical
Chase E. Herman, Arjun Valiya Parambathu, Dilipkumar N. Asthagiri, Abraham M. Lenhoff
Summary: Electrostatic interactions in proteins are influenced not only by ionic charges but also by their chemical identities. This study investigates the varying strength of association of different monovalent molecular ions in protein-protein and protein-ligand interactions. A nonpolarizable model captures trends with cations, but not anions, while a continuum correction model considering electronic polarizability captures both trends at the cost of fidelity to the underlying ion-pair association energy landscape. A polarizable model proves crucial in capturing experimentally suggested trends for both cations and anions, altering the free energy landscape and configurational sampling.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Polymer Science
Winnie H. Shi, Rohan S. Adhikari, Dilipkumar N. Asthagiri, Amanda B. Marciel
Summary: In this study, the effect of charge block length on the conformation and phase behavior of polyampholyte chains was investigated using small-angle X-ray scattering (SAXS) and molecular simulations. The results showed that as the block size increased, the polyampholyte chains tended to phase separate. The addition of NaCl resulted in a salting-in effect in the phase separated polyampholytes, which was dependent on the charge block length. Fourier-transform infrared (FTIR) spectroscopy revealed the disruption of intramolecular hydrogen bonds upon the addition of NaCl, indicating the involvement of electrostatic interactions and hydrogen bonding in the phase behavior. SAXS spectra showed minimal dependence of charge block length on the radius of gyration (Rg) for soluble polyampholytes under no-added salt conditions, but local chain stiffening was found to be dependent on charge block length. With increasing NaCl, all polyampholytes expanded and behaved as neutral or swollen chains in good solvent conditions, consistent with electrostatic screening. Molecular simulations were in qualitative agreement with the experiments. The implications of this study for understanding intracellular condensates and material design were also highlighted.
Article
Chemistry, Physical
Arjun Valiya Parambathu, Walter G. Chapman, George J. Hirasaki, Dilipkumar Asthagiri, Philip M. Singer
Summary: This study investigates the effects of nanoconfinement on the 1H NMR relaxation times (T1 and T2) of heptane in kerogen using atomistic MD simulations. The results show that confinement plays an important role in reducing T1 by three orders of magnitude, in agreement with experimental measurements of heptane dissolved in kerogen. In addition, confinement breaks spatial isotropy and gives rise to residual dipolar coupling, leading to a five orders of magnitude reduction in T2. The simulated T2 is used to calibrate the surface relaxivity and predict the pore-size distribution of the organic nanopores in kerogen.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Thiago J. Pinheiro J. dos Santos, Arjun Valiya Parambathu, Carla C. Fraenza, Casey Walsh, Steve G. Greenbaum, Walter G. Chapman, Dilip Asthagiri, Philip M. Singer
Summary: In this study, the effects of temperature and concentration on r(1) of the Gd3+-aqua complex were investigated using molecular dynamics simulations and measurements. By expanding the autocorrelation function and determining the thermal activation energies, new insights into the molecular-scale physics of r(1) were revealed.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Philip M. Singer, Arjun Valiya Parambathu, Thiago J. Pinheiro dos Santos, Yunke Liu, Lawrence B. Alemany, George J. Hirasaki, Walter G. Chapman, Dilip Asthagiri
Summary: Atomistic molecular dynamics simulations were used to predict the T-1 relaxation of water caused by paramagnetic Gd3+ ions in solution at 25 degrees C. The simulations agreed closely with measurements within a certain frequency range, showing potential for predicting r(1) in chelated Gd3+ contrast agents for clinical MRI.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)