Article
Chemistry, Physical
Aran Lamaire, Maarten Cools-Ceuppens, Massimo Bocus, Toon Verstraelen, Veronique Van Speybroeck
Summary: Although many molecular dynamics simulations treat atomic nuclei as classical particles, it is necessary to consider nuclear quantum effects (NQEs) when studying proton transfer reactions. In this study, quantum free energy profiles for three typical proton transfers, which properly include NQEs using the path integral formalism, are constructed. The computational cost of the simulations is reduced by using machine learning potentials. The results show a significant deviation between classical/quasi-classical centroid free energy profiles and the exact quantum free energy profile for proton transfers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Tatsuya Joutsuka, Koji Ando
Summary: This paper proposes a method for simplifying free energy calculations of proton transfers by using adiabatic MD trajectories and umbrella sampling with geometric coordinates. The calculated free-energy profile is able to reproduce the more accurate results obtained by free-energy perturbation.
Article
Chemistry, Multidisciplinary
Amir Peyman Soleymani, Marcia Reid, Jasna Jankovic
Summary: This research implements an epoxy-free ultramicrotome technique on beginning-of-life (BOL) and end-of-life (EOL) samples of proton exchange membrane fuel cells (PEMFCs) to observe and analyze the electrode structure in detail. Using transmission electron microscopy (TEM) and electron tomography (TEM), images of the ionomer network, carbon particles' structure, and Pt distribution are obtained, providing insights into their structural changes over time.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Physical
Xi Xu, Yang Yang
Summary: This study developed a cNEO-DFT method with good descriptive performance for molecular vibrational frequencies, which can better include nuclear quantum effects. By using the analytic Hessian, the vibrational frequencies of a series of small molecules were computed, and it was found that cNEO-DFT significantly outperforms conventional DFT in describing vibrational frequencies in regular polyatomic molecules.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Niklas von Wolff, Marc Robert
Summary: Electron serves as the ultimate redox reagent for building and reshaping molecular structures. Understanding and controlling the parameters involved in dissociative electron transfer (DET) reactivity and its coupling with proton transfer are crucial for enhancing selectivity, kinetics, and energy efficiency in molecular chemistry. Various applications, such as photoredox catalysis, CO2 reduction, and alcohol oxidation, highlight the broad range of processes encompassed by DET pathways and demonstrate the importance of studying the driving force-rate relationships for future developments in energy efficient catalytic schemes in redox organic chemistry.
Article
Chemistry, Physical
A. Coretti, T. Baird, R. Vuilleumier, S. Bonella
Summary: A new algorithm for efficient and fully time-reversible integration of orbital-free density functional theory (OFDFT) based molecular dynamics is presented. The algorithm adapts to the recently introduced Mass-Zero (MaZe) constrained dynamics and ensures adiabatic separation between nuclear and electronic degrees of freedom. The efficiency and accuracy of the algorithm are demonstrated through calculations of liquid sodium's static and dynamic properties.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Chenghan Li, Gregory A. Voth
Summary: The study introduces accurate and transferable reactive molecular dynamics models derived from constrained density functional theory, which can be used for proton dissociation reactions of amino acids in both aqueous and protein environments, showing potential for widespread application.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Pingping Sun, Devesh R. Kripalani, Weijie Chi
Summary: This study systematically investigated the excited-state intramolecular proton transfer (ESIPT) effect of three 3-thiolflavone derivatives containing sulfur-hydrogen bonds. The presence of intramolecular sulfur-hydrogen bonds was confirmed through bond length analysis, interaction energy calculations, and infrared vibrational spectra. It was found that the electron-withdrawing group stabilizes the tautomer, while the electron-donating group reduces the energy barrier of the ESIPT reaction. Additionally, the substituent group determines the excited-state electronic properties of keto tautomers, with the electron-withdrawing group significantly reducing the radiation rate and the electron-donating group leading to bright emission.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Review
Chemistry, Inorganic & Nuclear
Dopil Kim, Minjung Kang, Hyeonbin Ha, Chang Seop Hong, Min Kim
Summary: Metal-organic frameworks (MOFs) are emerging materials with fine tunability, making them a good platform for target-specific utilization. Various functional groups can be introduced onto the organic ligands, and positional isomerism can help elucidate the effects of each substituent on the linkers.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Engineering, Mechanical
Chuanda Wang, Guoke Huang, Fei Li, Guorui Yu, Hui Yi, Haijun Peng
Summary: This paper proposes a method of constrained optimal tuning to suppress rotor vibration and blade track spread. By adjusting the length of the pitch rods as control inputs, the vibration and track spread can be effectively reduced.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2023)
Article
Chemistry, Physical
Xi Xu
Summary: Solvent effects are crucial for simulating chemical and biological processes in solutions. In this study, a combination of constrained nuclear-electronic orbital density functional theory and a dielectric continuum solvation model is used to simultaneously consider nuclear quantum effects and solvent effects. By applying this new approach to the formate ion, accurate descriptions of the vibrational frequency of the C-H stretch and the solvatochromic shift are achieved.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Javier Carmona-Espindola, Jose L. Gazquez
Summary: The perturbative approach based on Taylor series expansion around the ground state, introduced as an alternative to variational constrained density functional theory, provides energy differences close to variational values and shows minimal dependence on exchange-correlation energy functional and basis set. The method evaluates first and second order corrections using information from the ground state calculation and determines the Lagrange multiplier value based on charge transfer. The results indicate practical independence from the choice of energy functional and small variations with respect to the basis set.
THEORETICAL CHEMISTRY ACCOUNTS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jacob D. Story, Shahnaz Ghahremani, Sevgi Gokce Kafali, Shu-Fu Shih, Kelsey J. Kuwahara, Kara L. Calkins, Holden H. Wu
Summary: This study improved MRI acquisition and analysis methods for quantifying pancreatic fat in children. By using free-breathing MRI and characterizing the spatial heterogeneity of pancreatic fat fraction, the researchers were able to relate it to clinical markers and obtained meaningful results.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Biology
Matthew J. Tudball, Rachael A. Hughes, Kate Tilling, Jack Bowden, Qingyuan Zhao
Summary: Many partial identification problems can be addressed by deriving asymptotically valid confidence intervals for the optimal value. We applied this method to the problem of selection bias and showed that incorporating population-level auxiliary information can lead to more informative results. Simulation studies and a motivating example further support the development and application of our method.
Article
Chemistry, Physical
Chenghan Li, Gregory A. Voth
Summary: Ab initio molecular dynamics (AIMD) is a popular approach for modeling complicated systems. However, its computational cost limits its application for large-scale simulations. This paper presents a computational approach that combines machine learning with path integral contraction schemes, achieving significant acceleration while maintaining accuracy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biophysics
Zhi Yue, Chenghan Li, Gregory A. Voth
Summary: The structure of a Cl-/H+ antiporter mutants displays a novel backbone arrangement which challenges the traditional view that Cl-/H+ antiporters do not undergo large conformational motions. The mutant substitution significantly impacts the local structure and dynamics, but does not represent the behavior of the wild-type ClC-ec1. Continuous constant-pH molecular dynamics reveals the proton-coupled dynamics of ClC-ec1 and suggests a higher complexity for intracellular H+ transfer in Cl-/H+ antiporters.
BIOPHYSICAL JOURNAL
(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
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
Chenghan Li, Junjie Yang, Xing Zhang, Garnet Kin-Lic Chan
Summary: The practical description of disordered chemical reactions involving multiple species at multiple sites is currently a challenge due to high computational cost and scaling. The gradient theory of multi-fragment density matrix embedding theory is introduced as a potential computational framework for modeling such processes at the correlated electron level. The derivation, implementation, validation, and application of the gradient theory are presented.
JOURNAL OF CHEMICAL PHYSICS
(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, Physical
Sijia Chen, Zhefu Li, Gregory A. Voth
Summary: Molecular dynamics simulation and enhanced free energy sampling were used to study the hydrophobic solute transfer across the water-oil interface in the presence of different electrolytes. It was found that hydronium cation can stabilize the hydrophobic solute in the aqueous phase and at the oil-water interface, while sodium cation tends to salt out the solute. The hydronium cation showed an affinity to the solute in acidic conditions, acting like a surfactant.
JOURNAL OF PHYSICAL CHEMISTRY B
(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
Chemistry, Physical
Yuxing Peng, Alexander J. Pak, Aleksander E. P. Durumeric, Patrick G. Sahrmann, Sriramvignesh Mani, Jaehyeok Jin, Timothy D. Loose, Jeriann Beiter, Gregory A. Voth
Summary: The bottom-up approach to coarse-graining is an important method for building computational models to simulate large-scale and complex phenomena. OpenMSCG is a modularized open-source software that provides a collection of successful bottom-up coarse-graining methods. It allows users to derive coarse-grained models from fine-grained simulation data, improving the reliability, reproducibility, and sharing of the models.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
John H. Hack, Xinyou Ma, Yaxin Chen, James P. Dombrowski, Nicholas H. C. Lewis, Chenghan Li, Harold H. Kung, Gregory A. Voth, Andrei Tokmakoff
Summary: This study reveals the protonation behavior of zeolite Bronsted acid sites in the presence of water, showing that full deprotonation of the acid sites can occur with two or more water molecules, with a deprotonation energy of 1.6 kcal/mol. Experimental measurements and molecular dynamics simulations provide insight into the proton structure and hydration dependence of the acid sites, demonstrating that the excess charge remains relatively localized between two oxygen atoms across the range of hydration levels.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Bohak Yoon, Gregory A. Voth
Summary: In this study, the reaction mechanisms responsible for carbamate formation during CO2 capture by amino acid ionic liquids were investigated using explicit ab initio molecular dynamics. The results revealed a two-step reaction pathway involving the formation of a zwitterion and a kinetically facile intermolecular proton transfer. The enhanced intermolecular interaction between the zwitterion and serine was found to significantly reduce the free-energy barriers, facilitating the proton transfer and governing the overall CO2 capture mechanism. This work provides valuable insight into the mechanistic and kinetic features of these reactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(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
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)