Search Results - "The journal of physical chemistry. B"

Developing a Fully Glycosylated Full-Length SARS-CoV‑2 Spike Protein Model in a Viral Membrane by Woo, Hyeonuk, Park, Sang-Jun, Choi, Yeol Kyo, Park, Taeyong, Tanveer, Maham, Cao, Yiwei, Kern, Nathan R, Lee, Jumin, Yeom, Min Sun, Croll, Tristan I, Seok, Chaok, Im, Wonpil

“…This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First,…”
Get full text

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States by Piana, Stefano, Donchev, Alexander G, Robustelli, Paul, Shaw, David E

“…Many proteins can be partially or completely disordered under physiological conditions. Structural characterization of these disordered states using…”
Get full text

Superhydrophobic Surfaces: Insights from Theory and Experiment by Parvate, Sumit, Dixit, Prakhar, Chattopadhyay, Sujay

“…Biomimetic nanosurfaces with distinct wettability and versatility have found special enthusiasm in both fundamental research and industrial applications. With…”
Get full text

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations by Zheng, Wenwei, Dignon, Gregory L, Jovic, Nina, Xu, Xichen, Regy, Roshan M, Fawzi, Nicolas L, Kim, Young C, Best, Robert B, Mittal, Jeetain

“…The formation of membraneless organelles in cells commonly occurs via liquid–liquid phase separation (LLPS) and is in many cases driven by multivalent…”
Get full text

Does SARS-CoV‑2 Bind to Human ACE2 More Strongly Than Does SARS-CoV? by Nguyen, Hoang Linh, Lan, Pham Dang, Thai, Nguyen Quoc, Nissley, Daniel A, O’Brien, Edward P, Li, Mai Suan

“…The 2019 novel coronavirus (SARS-CoV-2) epidemic, which was first reported in December 2019 in Wuhan, China, was declared a pandemic by the World Health…”
Get full text

Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV‑2 RNA-Dependent RNA Polymerase by Zhang, Leili, Zhou, Ruhong

“…Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for…”
Get full text

Effects of pH and Oxidants on the First Steps of Polydopamine Formation: A Thermodynamic Approach by Salomäki, Mikko, Marttila, Lauri, Kivelä, Henri, Ouvinen, Tuomo, Lukkari, Jukka

“…We present a general thermodynamic top-down analysis of the effects of oxidants and pH on dopamine oxidation and cyclization, supplemented with UV–vis and…”
Get full text

Mechanisms of Airborne Infection via Evaporating and Sedimenting Droplets Produced by Speaking by Netz, Roland R

“…For estimating the infection risk from virus-containing airborne droplets, it is crucial to consider the interplay of all relevant physical-chemical effects…”
Get full text

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types by Klauda, Jeffery B, Venable, Richard M, Freites, J. Alfredo, O’Connor, Joseph W, Tobias, Douglas J, Mondragon-Ramirez, Carlos, Vorobyov, Igor, MacKerell, Alexander D, Pastor, Richard W

“…A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and…”
Get full text

1.14CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations by Dodda, Leela S, Vilseck, Jonah Z, Tirado-Rives, Julian, Jorgensen, William L

“…The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations of free energies of hydration. For a set of 426 neutral molecules,…”
Get full text

Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials by John, S. T, Csányi, Gábor

“…We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free…”
Get full text

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”? by Cui, Qiang, Pal, Tanmoy, Xie, Luke

“…QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including…”
Get full text

Structure of Lipid Nanoparticles Containing siRNA or mRNA by Dynamic Nuclear Polarization-Enhanced NMR Spectroscopy by Viger-Gravel, Jasmine, Schantz, Anna, Pinon, Arthur C, Rossini, Aaron J, Schantz, Staffan, Emsley, Lyndon

“…Here, we show how dynamic nuclear polarization (DNP) NMR spectroscopy experiments permit the atomic level structural characterization of loaded and empty lipid…”
Get full text

Hydrogenation of CO2 on ZnO/Cu(100) and ZnO/Cu(111) Catalysts: Role of Copper Structure and Metal–Oxide Interface in Methanol Synthesis by Palomino, Robert M, Ramírez, Pedro J, Liu, Zongyuan, Hamlyn, Rebecca, Waluyo, Iradwikanari, Mahapatra, Mausumi, Orozco, Ivan, Hunt, Adrian, Simonovis, Juan P, Senanayake, Sanjaya D, Rodriguez, José A

“…The results of kinetic tests and ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) show the important role played by a ZnO–copper interface in the…”
Get full text

Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water by Li, Pengfei, Song, Lin Frank, Merz, Kenneth M

“…Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is…”
Get full text

Polariton-Mediated Electron Transfer via Cavity Quantum Electrodynamics by Mandal, Arkajit, Krauss, Todd D, Huo, Pengfei

“…We investigate the polariton-mediated electron transfer reaction in a model system with analytic rate constant theory and direct quantum dynamical simulations…”
Get full text

Identification of Clathrate Hydrates, Hexagonal Ice, Cubic Ice, and Liquid Water in Simulations: the CHILL+ Algorithm by Nguyen, Andrew H, Molinero, Valeria

“…Clathrate hydrates and ice I are the most abundant crystals of water. The study of their nucleation, growth, and decomposition using molecular simulations…”
Get full text

Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations by Celebi, Alper T, Vlugt, Thijs J. H, Moultos, Othonas A

“…Deep eutectic solvents (DESs) are a new generation of green solvents, which are considered an environmentally friendly alternative to ionic liquids and…”
Get full text

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model by Laury, Marie L, Wang, Lee-Ping, Pande, Vijay S, Head-Gordon, Teresa, Ponder, Jay W

“…A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust…”
Get full text

Current Status of the AMOEBA Polarizable Force Field by Ponder, Jay W, Wu, Chuanjie, Ren, Pengyu, Pande, Vijay S, Chodera, John D, Schnieders, Michael J, Haque, Imran, Mobley, David L, Lambrecht, Daniel S, DiStasio, Robert A, Head-Gordon, Martin, Clark, Gary N. I, Johnson, Margaret E, Head-Gordon, Teresa

“…Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but…”
Get full text