Article
Chemistry, Multidisciplinary
Paul B. Calio, Chenghan Li, Gregory A. Voth
Summary: This study examines the hydrated excess proton in water, concluding that a distorted and dynamic Eigen cation is the most prevalent species of hydrated proton in aqueous acid solutions of dilute to moderate concentration.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Florian N. Bruenig, Manuel Rammler, Ellen M. Adams, Martina Havenith, Roland R. Netz
Summary: The study investigates the spectroscopic signatures of excess protons in HCl solutions using ab initio simulations and THz experiments, identifying two contributions beyond the normal-mode scenario that reflect proton-waiting and proton-transfer processes.
NATURE COMMUNICATIONS
(2022)
Article
Spectroscopy
Kazuki Inoue, Masanari Okuno
Summary: Hyper-Raman spectra of concentrated hydrochloric acid solutions were reported for the first time. The spectra reflected the presence of chloride anions solvated in water. Unlike infrared spectroscopy, the Hyper-Raman spectra were insensitive to excess protons in water and did not show any signature of a proton continuum or shoulders on the bending mode of H2O. Additionally, a sharp Hyper-Raman signal at around 500 cm(-1) was observed in the 532 nm excited spectra, indicating a photochemical reaction.
JOURNAL OF RAMAN SPECTROSCOPY
(2022)
Article
Multidisciplinary Sciences
Mailis Lounasvuori, Yangyunli Sun, Tyler S. Mathis, Ljiljana Puskar, Ulrich Schade, De-En Jiang, Yury Gogotsi, Tristan Petit
Summary: This study investigates the hydration structure of protons intercalated in Ti3C2Tx MXene layers and finds that it differs from protons in bulk water. This finding has important implications for characterizing chemical species in energy storage and conversion applications.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Christopher Arntsen, Chen Chen, Paul B. Calio, Chenghan Li, Gregory A. Voth
Summary: In this work, molecular dynamics simulations of a hydrated excess proton in water were analyzed to study the occurrence of concerted hopping events and rattling events in proton transport. The results showed that rattling events are more common than concerted hopping events, contrary to previous suggestions. By applying a filter to the trajectory, misleading effects of simple rattling were removed, leading to a reduction in multiple hopping events. Comparing filtered and unfiltered trajectories, agreement with experimental values for proton hopping time and Eigen-Zundel interconversion time was found.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Ye Tian, Jiani Hong, Duanyun Cao, Sifan You, Yizhi Song, Bowei Cheng, Zhichang Wang, Dong Guan, Xinmeng Liu, Zhengpu Zhao, Xin-Zheng Li, Li-Mei Xu, Jing Guo, Ji Chen, En-Ge Wang, Ying Jiang
Summary: The nature of hydrated proton on solid surfaces has been visualized using cryogenic qPlus-based atomic force microscopy. Eigen cations self-assemble into monolayer structures with local order, while Zundel cations form long-range ordered structures stabilized by nuclear quantum effects. It is found that Zundel configuration is preferred over Eigen on Pt(111), but such preference is absent on Au(111).
Article
Chemistry, Physical
Joani Mato, Soohaeng Yoo Willow, Jasper C. Werhahn, Sotiris S. Xantheas
Summary: By using Mg+ metal, we were able to extend the size range of aqueous clusters and extrapolate to the bulk limit of the solvated electron's vertical detachment energy (VDE) to a value exceeding 3,200, which is significantly larger than previous experimental or theoretical measurements. We established a relationship between the VDE and the energy difference between Mg+(H2O)(n) and Mg2+(H2O)n systems, as well as the metal's second ionization potential. The extrapolated bulk VDEs for the localized surface electron in semiempirical and ab initio calculations were found to be in excellent agreement with the experimental results.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Polymer Science
Jihao Wang, Jia Chen, Zhiyang Xu, Xiaozhen Yang, Seeram Ramakrishna, Yong Liu
Summary: Fuel cells rely on proton exchange membranes (PEMs) for their operation. This study used dissipative particle dynamics to investigate the hydration morphology of several perfluorosulfonic acid (PFSA) membranes. The results showed that increasing water content improved water dispersion, and different chemical structures of the membranes had varying water cluster sizes and dispersion capabilities.
JOURNAL OF APPLIED POLYMER SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Jakob Heller, Wai Kit Tang, Ethan M. Cunningham, Ephrem G. Demissie, Christian van der Linde, Wing Ka Lam, Milan Oncak, Chi-Kit Siu, Martin K. Beyer
Summary: Infrared multiple photon spectroscopy was used to probe the structure of hydrated singly charged aluminum ions. The Al-H vibration frequency is highly sensitive to the hydrogen bonding network, and the hydride can act as a double hydrogen bond acceptor. The onset of hydrogen bonding and disappearance of the free Al-H stretch coincides with the onset of hydrogen evolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Inorganic & Nuclear
James Louis-Jean, Paul M. Forster, Samundeeswari Mariappan Balasekaran, Chien Thang Pham, Frederic Poineau
Summary: The crystal structure of the [Co(NH3)(6)](2)[ReF6](3)center dot 3H(2)O salt has been reported, consisting of [Co(NH3)(6)](3+) cations, [ReF6](2-) anions, and co-crystallized water molecules with slightly distorted octahedra. Infrared spectra of (I) show characteristic vibration bands of the cation, anion, and co-crystallized H2O molecules, while UV-Visible analyses indicate that the cation absorption dominates the spectra.
JOURNAL OF FLUORINE CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kyoko Fujita, Hiroyuki Ohno
Summary: Hydrated ionic liquid is a mixture of ionic liquid and water, which allows for the design of unique aqueous electrolyte solutions. The properties of hydrated ionic liquids, such as polarity, viscosity, ion mobility, and hydrogen bonding ability, can be controlled by adjusting the water content. This mixture provides a similar environment to that of living cells and has potential as effective solvents for biomolecules. In this account, we summarize the basic properties, recent results, and future aspects of hydrated ionic liquids.
Article
Chemistry, Physical
Austin O. Atsango, Tobias Morawietz, Ondrej Marsalek, Thomas E. Markland
Summary: The transport of excess protons and hydroxide ions in water is crucial for many important chemical and biological processes. Traditional simulation methods are prohibitively expensive for accurately modeling the associated transport mechanisms. In this study, machine-learned potentials (MLPs) are developed to simulate the transport of excess protons and hydroxide ions at a fraction of the cost of traditional methods, while still reproducing the trends observed in ab initio simulations. These simulations provide insights into the role of hypercoordination in the transport mechanism of hydroxide ions and support the asymmetry in diffusion between excess protons and hydroxide ions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Haibei Huang, Lijuan Xue, Gang Lu, Shibo Cheng, Yuxiang Bu
Summary: We investigate the structures of hydrated electrons (e(aq)(-)) in clathrate hydrates (CHs), a solid phase of water. Using various computational methods, we find that e(aq)(-) can form a node in CHs, which is a H2O defect composed of four unsaturated hydrogen bonds. The guest molecules in CHs can alter the electronic structure of the e(aq)(-)@node, leading to experimentally observed optical absorption spectra. These findings extend our understanding of hydrated electrons in porous aqueous systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biophysics
Masaru Tanaka, Shigeaki Morita, Tomohiro Hayashi
Summary: This review emphasizes the crucial role of water molecules in biointerfacial interactions, particularly the indicator function of intermediate water for the bioinertness of material surfaces. Analyzing the states of water can provide novel insights and help develop new experimental models for understanding protein adsorption in a wide range of materials, especially those used in biomedical applications.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Chemistry, Physical
Marco Nava, Nancy Makri
Summary: The study reveals that proton transfer is driven by the oscillation of the oxygen pair and primarily occurs at single-well or nearby low-barrier configurations. Tunneling and zero-point energy significantly accelerate the proton transfer dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
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, 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, Physical
Kambham Devendra Reddy, Rajib Biswas
Summary: In this study, theoretical vibrational spectroscopy was used to investigate the solvation structure of TMAO in water. The Netz force field was found to be more accurate compared to other classical force fields. The results showed that TMAO forms stronger hydrogen bonds with water compared to water-water interactions. Additionally, a strong orientational correlation was observed in the hydrophilic region but not in the hydrophobic region.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Albin Joy, Rajib Biswas
Summary: In this study, the additional stability conferred by the copper ion on azurin was explored using REMD data. It was found that holo azurin had a higher denaturation temperature compared to apo azurin, indicating an additional thermal stability induced by the copper ion. The unfolding pathway of apo azurin was similar to that of holo azurin, with certain beta-sheets being more stable. The strong hydrophobic interactions among apolar residues in the protein core contributed to the high stability of both apo and holo forms.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
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
Chemistry, Physical
Kambham Devendra Reddy, Rajib Biswas
Summary: Understanding the microscopic solvation structure of TMAO in water using theoretical vibrational spectroscopy reveals that the Netz force field provides better agreement with experimental results compared to other classical force fields. The redshift of the O-H stretching frequency suggests stronger hydrogen bonding between TMAO and water compared to water-water. Furthermore, a strong orientational correlation of the O-H stretching frequencies is observed in the hydrophilic region of TMAO, while it is absent in the hydrophobic region. These findings are supported by hydrogen-bond analysis and local structure index data.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Kambham Devendra Reddy, Rajib Biswas
Summary: The presence of external solutes affects the local structure and dynamics of water, with the nature and extent of these modifications depending on several factors, especially the chemical nature of the solute. The effects of hydrophobic substances on water structure and dynamics have attracted significant attention in biological systems. This study focuses on examining the microscopic arrangement of solvation shells around the hydrophobic solute methane. Using tetrahedral order, local structural index, and van Hove self-correlation function, we obtain a quantitative understanding of these arrangements. We observe a slight increase in the structural order of water molecules in methane's first solvation shell, similar to that of low-temperature water. We also find that the water molecules facing methane have lower structural order compared to bulk water. Additionally, the water molecules in the first solvation shell around methane exhibit relatively slower orientational relaxation.
JOURNAL OF CHEMICAL SCIENCES
(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)