Article
Chemistry, Multidisciplinary
Adi Cohen, Thomas M. Brenner, Johan Klarbring, Rituraj Sharma, Douglas H. Fabini, Roman Korobko, Pabitra K. Nayak, Olle Hellman, Omer Yaffe
Summary: Lead-based halide perovskite crystals exhibit strongly anharmonic structural dynamics, which may be the reason behind their exceptional photovoltaic properties. Cs2AgBiBr6, a lead-free alternative, has been studied as well but does not show the same photovoltaic activity. By comparing Cs2AgBiBr6 and CsPbBr3, it is found that their expression of anharmonic behavior differs significantly.
ADVANCED MATERIALS
(2022)
Article
Chemistry, Physical
Bogdan A. Marekha, Johannes Hunger
Summary: The hydrophobicity and denaturation efficiency of urea can be modified by alkylation. In this study, the hydration of 1-methylurea was investigated using infrared spectroscopy. The results showed that 1-methylurea has little effect on the hydrogen-bond distribution of water but slows down the rotational dynamics and hydrogen-bond fluctuation dynamics of water molecules in its hydration shell. Further alkylation does not necessarily affect the rotational dynamics of additional water molecules. Ureas that have a similar effect on water's hydrogen-bond fluctuation dynamics exhibit a similar protein denaturation tendency.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Applied
Hui Liu, Qian Li, Di Zhao, Miao Zhang, Shuai Jiang, Chunbao Li
Summary: The study found that myoglobin's structural characteristics changed after sodium chloride treatment, with hydrophobic amino acids exposed and phenylalanine binding becoming more stable, resulting in reduced digestibility.
Article
Chemistry, Multidisciplinary
Shurong Yuan, Bernet E. Meijer, Guanqun Cai, Richard J. C. Dixey, Franz Demmel, Martin T. Dove, Jiaxun Liu, Helen Y. Playford, Helen C. Walker, Anthony E. Phillips
Summary: This study resolves the long-standing controversy on the origin of entropy change in ammonium sulfate, a simple inorganic salt. It shows that the entropy arises from low-frequency librations of ammonium ions, suggesting that vibrational entropy is equally important as configurational entropy in the search for molecular materials with large entropy changes.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Chemistry, Physical
Prakash Govindaraj, Kathirvel Venugopal
Summary: This study investigates the feasibility of BiSI chalcohalide for thermoelectric conversion through first principles computations. The results show that BiSI exhibits stable mechanical and lattice dynamical properties, as well as high power factor and low thermal conductivity, indicating its potential for room-to-mid temperature applications.
JOURNAL OF ALLOYS AND COMPOUNDS
(2022)
Article
Chemistry, Physical
Ahmed A. A. Ali, Falk Hoffmann, Lars Schaefer, Frans A. A. Mulder
Summary: Nuclear magnetic resonance (NMR) spin relaxation and molecular dynamics (MD) simulations are important methods for studying the internal dynamics of proteins. This study establishes a computational framework to extract cross correlation relaxation parameters of methyl groups in proteins from MD simulations and successfully obtains results consistent with experimental data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Physics, Applied
Zhi W. Hua, Tan Zheng, Jing X. Sang, Xiao F. Xu, Bin H. Wu, Lian F. Wei
Summary: Vanadium dioxide (VO2) undergoes a phase transition from the monoclinic phase to the rutile phase near 340 K at ambient pressure, with potential device applications. The study calculates the phonon properties of the two phases of VO2 using the TDEP method and constructs a resistance-temperature phase diagram, indicating the stability of the rutile phase. The research provides evidence that anharmonicity in the lattice dynamics of VO2 is significant.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Multidisciplinary Sciences
Yi Xia, Dale Gaines II, Jiangang He, Koushik Pal, Zhi Li, Mercouri G. Kanatzidis, Vidvuds Ozolins, Chris Wolverton
Summary: We propose a first-principles model of minimum lattice thermal conductivity (rmin L ) based on a unified theoretical treatment of thermal transport in crystals and glasses. This model reveals a universal behavior of rmin L in crystals, which is independent of structural complexity and bounded within a range from & SIM;0.1 to & SIM;2.6 W/(m K) at high temperatures. By studying the underlying physics, we find that the importance of different heat transport channels depends strongly on the degree of disorder, and propose an approximation method for diffuson-dominated rmin L in complex and disordered compounds. Furthermore, we validate our model by extending predictions to all compounds within the Inorganic Crystal Structure Database (ICSD) using graph network and random forest machine learning models.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biophysics
Malgorzata Nattich-Rak, Agata Pomorska, Piotr Batys, Zbigniew Adamczyk
Summary: The adsorption kinetics of myoglobin molecules on mica and silica surfaces were studied under varying salt concentrations and pH conditions. Results show that at pH 3.5, myoglobin molecules form stable single molecule layers, while adsorption kinetics at higher pH levels are slower.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Review
Biochemistry & Molecular Biology
Lars Erichsen, Chantelle Thimm, Simeon Santourlidis
Summary: Methyl group metabolism plays a crucial role in cellular methylation reactions and DNA methylation, which are essential for various cellular functions. Stable and proper metabolic processes are important to prevent deficiencies and erosion of the methylome, as alterations can lead to epigenetic and genetic perturbations causing diverse disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Stefan Hofbauer, Marcello Pignataro, Marco Borsari, Carlo Augusto Bortolotti, Giulia Di Rocco, Gianina Ravenscroft, Paul G. Furtmuller, Christian Obinger, Marco Sola, Gianantonio Battistuzzi
Summary: The autosomal dominant striated muscle disease myoglobinopathy is caused by a single point mutation in human myoglobin, leading to increased reactivity towards hydrogen peroxide, enhanced tendency to form high-molecular-weight aggregates, and accelerated heme bleaching. These effects contribute to impaired oxygen binding capacity and faster heme dissociation, ultimately impacting the pathological symptoms of myoglobinopathy.
Article
Physics, Multidisciplinary
Kasra Farain, Daniel Bonn
Summary: The question of when dense granular materials start to flow under stress has not been resolved. A simple equation based on frictional aging of the granular packing is developed and tested, resulting in a nonmonotonic stress-strain relation independent of shear rate. This relation helps understand the quasistatic deformations and solid-to-liquid transition of aging granular media. It also explains the flow history dependence of mechanical properties and sensitivity to initial preparation of granular media.
PHYSICAL REVIEW LETTERS
(2023)
Article
Polymer Science
Xin Ning Zhang, Cong Du, Yan Jie Wang, Li Xin Hou, Miao Du, Qiang Zheng, Zi Liang Wu
Summary: The molecular structure of supramolecular hydrogels significantly affects their mechanical and viscoelastic behaviors. Increasing the number of alpha-methyl groups in the hydrogel composition can transition the gel from an elastic to a glassy state. The presence of methyl groups on the carboxylic acid unit enhances the stability of the hydrogel more significantly than on the acrylamide unit.
Article
Nanoscience & Nanotechnology
Xiangzhou Zhu, Sebastian Caicedo-Davila, Christian Gehrmann, David A. Egger
Summary: This study theoretically characterizes the vibrational interactions among atoms in the prototypical cubic CsPbBr3 and reveals the interlocking motion of neighboring Cs-Br atoms and the important local structural fluctuations on an atomic scale.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Materials Science, Multidisciplinary
Cameran Beg, John Kieffer
Summary: Atomic transport properties in a simple two-component solid-state material were investigated using molecular dynamics simulations. The model system consists of a carbon lattice element that supports a solute, interacting with carbon and itself via Lennard-Jones potentials. The size of the solute species was systematically varied while the system volume remained constant. The results show a causal relationship between structural instabilities, internal pressure, vibrational properties, and an increase in diffusivity of the mobile species.
COMPUTATIONAL MATERIALS SCIENCE
(2023)
Article
Biophysics
Rupesh Agarwal, Utsab R. Shrestha, Xiang-Qiang Chu, Loukas Petridis, Jeremy C. Smith
BIOPHYSICAL JOURNAL
(2020)
Article
Chemistry, Physical
Rupesh Agarwal, Micholas Dean Smith, Jeremy C. Smith
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemistry & Molecular Biology
Christopher M. Topham, Jeremy C. Smith
Summary: The study investigates the binding interactions between the E-base and thymine and uracil bases, finding significant strain energy in systems containing a beta-alanine linker, while the E-base swings away from the target bases into the solvent in systems containing a 3-trans olefin linker. Additionally, calculations on a novel 2-cis olefin linker design suggest potential simultaneous hydrogen bonding with the thymine 4-oxo group, circumvention of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Chemistry, Physical
Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova, Jeremy C. Smith, Isabella Daidone
Summary: The catalytic reaction in the SARS-CoV-2 main protease is activated by a proton transfer, with inhibitors reducing the free energy cost to reach the charge-separated state of the active-site dyad. Specific water molecules play a crucial role in enhancing or reducing the thermodynamic feasibility of the proton transfer reaction.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Rajitha T. Rajeshwar, Moumita Saharay, Jeremy C. Smith, Marimuthu Krishnan
Summary: The study focuses on the fast side-chain dynamics and conformational entropy changes during protein binding, demonstrating that significant flexibility changes are unlikely after ligand binding and establishing a linear correlation between O-axis(2) and conformational entropy changes for protein-ligand complexes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Medicinal
Bhagyesh Varvdekar, Akshay Prabhakant, Marimuthu Krishnan
Summary: Terahertz protein vibrations are sensitive reporters of protein structure and interactions. The study highlights the significant role of protein-ligand and solvent interactions in modulating low-frequency protein vibrations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Sree Kavya Penneru, Moumita Saharay, Marimuthu Krishnan
Summary: Bacterial cellulase enzymes are potential candidates for the efficient production of bioethanol from cellulosic biomass. CelS is a microbial enzyme that cleaves cellulose into cellobiose. This study investigates the mechanism of substrate dynamics and product expulsion in CelS through molecular dynamics simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Shaunak Badani, Marimuthu Krishnan
Summary: RENS is a computational technique that achieves extensive configurational sampling from a sequence of equilibrium and nonequilibrium MD simulations without modifying the potential energy surface. Unlike REMD, RENS uses nonequilibrium heating and cooling simulations to improve acceptance probability with only a few replicas.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Viswanathan Gurumoorthy, Utsab R. Shrestha, Qiu Zhang, Sai Venkatesh Pingali, Eric T. Boder, Volker S. Urban, Jeremy C. Smith, Loukas Petridis, Hugh O'Neill
Summary: c-Src kinase is a non-receptor tyrosine kinase that phosphorylates signaling proteins in cancers. This study focuses on the N-terminal disordered region (SH4UD) and its interactions with other domains of c-Src kinase. The results show that the presence of SH4UD leads to structural changes in the regulatory domains (SH3-SH2), indicating the importance of the disordered region for allosteric interactions. This study provides insights that may aid in the development of therapeutic interventions targeting the regulatory domains of c-Src kinase.
Article
Chemistry, Multidisciplinary
Luoxi Tan, Haden L. Scott, Micholas Dean Smith, Sai Venkatesh Pingali, Hugh M. O'Neill, Jennifer L. Morrell-Falvey, John Katsaras, Jeremy C. Smith, Brian H. Davison, James G. Elkins, Jonathan D. Nickels
Summary: Biofuels are crucial for sustainable energy and optimizing their production is a societal and economic imperative. Reducing the toxicity of co-solvents can improve the efficiency of biofuel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Physical
Mood Mohan, Micholas Dean Smith, Omar Demerdash, Michelle K. Kidder, Jeremy C. Smith
Summary: Understanding the physical properties of ionic liquids is crucial for various industrial and research applications, but experimental screening can be challenging and expensive. Previous research has shown that combining quantum-mechanics-based property prediction tools with machine learning approaches can help screen and design ionic liquids with desired properties. However, the most appropriate machine learning approach is still unclear.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Mood Mohan, Micholas Dean Smith, Omar N. Demerdash, Blake A. Simmons, Seema Singh, Michelle K. Kidder, Jeremy C. Smith
Summary: Ionic liquids (ILs) have unique solvent properties, but it is unrealistic to experimentally determine their physicochemical properties. To address this issue, we developed machine learning models to predict the surface tension and speed of sound of ILs, which showed excellent agreement with experimental observations. This study paves the way for the development of machine learning models for predicting IL properties.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Nikhil Jakhar, Akshay Prabhakant, Marimuthu Krishnan
Summary: UV radiation-induced DNA damages, particularly the cyclobutane pyrimidine dimer (CPD) lesions, have adverse effects on genome integrity and cellular function. Rad4/XPC protein is responsible for recognizing and repairing CPD lesions, but the molecular mechanism behind this process has been elusive. By using enhanced sampling and molecular dynamics simulations, this study investigates the mechanism and energetics of lesion recognition by Rad4/XPC. The findings shed light on the sequence of events and their potential coupling, providing important insights into understanding UV-related skin disorders and cancers and facilitating the development of novel therapeutic strategies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Medicinal
Rupesh Agarwal, T. Rajitha Rajeshwar, Jeremy C. Smith
Summary: Structure-based virtual high-throughput screening is commonly used in early-stage drug discovery. This study evaluated the performance of three docking protocols on 173 RNA-small molecule crystal structures. The results showed that Vina and rDock are both applicable for projects without known ligand-protein structures, but their performance is relatively poor compared to protein-target docking methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)