Article
Biochemistry & Molecular Biology
Ai Shinobu, Suyong Re, Yuji Sugita
Summary: Molecular dynamics (MD) simulations are used to study biological processes, but conventional methods are not effective for slow dynamics. Researchers applied a two-dimensional replica-exchange MD method and optimized the simulation protocols to achieve accurate results and good random sampling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Yuzhu Lu, Chuangang Ning
Summary: This study reports the energy-difference measurement of a salt-water complex and discovers three isomers for both the negatively charged and neutral complexes. These results can serve as a benchmark for the development of theoretic methods for weakly bound complexes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Engineering, Chemical
Sepideh Niazi, Heidi S. Nygard, Bruno Reis, Moritz to Baben
Summary: Thermochemical databases for aqueous and high-temperature salt solutions have been developed separately in the past few decades. However, there is increasing interest in highly concentrated aqueous solutions and the hydrolysis of salt melts, bridging the gap between the two communities. This study consistently models the liquid phase between H2O, HCl, KOH, and KCl, covering a wide range of temperatures. The modeling successfully represents phase diagrams and heat of reactions using the Calphad technique.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Chemistry, Medicinal
Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill
Summary: The study developed the MELD-Bracket method for efficient affinity ranking of structurally diverse small molecule ligands in structure-based drug discovery. The method was tested on multiple protein systems and showed a balanced accuracy and computational efficiency in ranking different ligands.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Jinzen Ikebe, Munenori Suzuki, Aya Komori, Kaito Kobayashi, Tomoshi Kameda
Summary: This paper presents a method called MSPER for enhancing the regioselectivity of substrate reaction sites by destabilizing binding poses for byproducts while maintaining those for target products. Applying MSPER to cytochrome P450 CYP102A1 (BM3) and two substrates resulted in successfully enhancing the regioselectivity for four target products with different reaction sites.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Inorganic & Nuclear
Pingfan Wu, Yu Wang, Weizhou Chen, Xunliang Hu, Bo Huang, Zicheng Xiao
Summary: This study illustrates the influence of organic ligands on magnetic structure and behavior using a mixed-valence Lindqvist-type hexavanadate as a research platform. The introduction of organic ligands can modify the crystal packing manners of the derivatives, leading to changes in the interaction between magnetic units. The work demonstrates that organic functionalization can significantly affect the magnetism of polyoxometalates by adjusting the distance and location of the magnetic fractions.
INORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Ameya Harmalkar, Jeffrey J. Gray
Summary: Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility can hinder accurate predictions. Recent advances include enhanced sampling techniques and internal coordinate formulations to address the issue of protein backbone flexibility.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Physical
Elizabeth G. Christensen, Ryan P. Steele
Summary: The gas-phase clusters of the hydrated Cu(II) cation with 2-8 water molecules were investigated using ab initio quantum chemistry. The isomer structures, energies, and vibrational spectra were computed to gain insights into the behavior of the Cu2+ hydrate and its interaction with the surrounding water network. The results demonstrate the flexibility of Cu(II) ions in terms of their electronic, chemical, and structural properties.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biology
Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou
Summary: This study developed generative autoencoders that can learn from short molecular dynamics simulations and generate full conformational ensembles of intrinsically disordered proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biophysics
Aparna Vilas Dongre, Sudip Das, Asutosh Bellur, Sanjeev Kumar, Anusha Chandrashekarmath, Tarak Karmakar, Padmanabhan Balaram, Sundaram Balasubramanian, Hemalatha Balaram
Summary: By stabilizing the succinimide residue, protein flexibility is reduced, leading to increased hyperthermostability. Mechanisms such as electrostatic shielding, n -> pi* interactions, and hydrogen bonding prevent water access to the succinimide residue, stabilizing the protein conformation.
BIOPHYSICAL JOURNAL
(2021)
Review
Construction & Building Technology
Binyu Lei, Patrick Janssen, Jantien Stoter, Filip Biljecki
Summary: Many challenges hinder the design and implementation of digital twins and are rarely discussed. Social and legal issues are often overlooked as well. Through a literature review and expert survey, we identify the challenges of operating digital twins in the urban context. The most severe challenges appear to be related to interoperability and practical value.
AUTOMATION IN CONSTRUCTION
(2023)
Article
Chemistry, Multidisciplinary
Daniele Rosa-Gastaldo, Marion Pupier, Giorgi Meshvildishvili, Jasmine Viger-Gravel, Thomas Burgi
Summary: Ligand and metal exchange reactions are important for shaping the properties of metal nanoclusters, and understanding the dynamics of the ligand monolayer is crucial for functionalization. Through experiments and simulations, we determined the activation parameters for an intracluster ligand rearrangement in specific clusters, revealing that the process does not involve metal-sulfur bond breaking and follows a first-order rate law, different from collisional ligand exchange.
Article
Engineering, Mechanical
Adwait Sharma, C. S. Manohar
Summary: This paper investigates the evaluation of the reliability integral in the presence of complicating features of limit state functions. It proposes the use of particle splitting framework and an improved Markov chain Monte Carlo sampler with replica exchange strategy to enhance the detection and exploration of important regions of failure. The application of bootstrap technique to deduce the sampling variance of the estimator of the probability of failure is also developed. Several examples in structural mechanics are presented to compare the performance of the proposed method with existing methods.
PROBABILISTIC ENGINEERING MECHANICS
(2023)
Article
Chemistry, Physical
Kai Diao, Shunping Shi, Yong Song, Leilei Tang, Jiabao Hu, Jing Jiang, Zhanjiang Duan, Deliang Chen
Summary: The structural evolution, adsorption energy, and mechanism of hydrogen evolution reaction of Be-n clusters with n = 5-9 were studied. It was found that except for the Be-7 cluster, the beryllium clusters with n = 5-9 showed higher point group symmetry. The Be-9@H2O complex released the greatest energy. The hydrogen evolution reaction in Be-n + H2O (n = 5-9) is exothermic, and all transition states, intermediate stages, and products have energies lower than the equilibrium constant. Breaking the O-H bond in the Be-n@H2O (n = 5-9) complex releases more energy and results in a change in the cluster structure, especially in the Be-7 + H2O reaction.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Immunology
Martin Kulke, Felix Nagel, Lukas Schulig, Norman Geist, Marcel Gabor, Julia Mayerle, Markus M. Lerch, Andreas Link, Mihaela Delcea
Summary: The study identified two main binding states of the inhibitor to the complex, explicitly relating the influence of the mutation site to conformational changes in the active site of trypsin. Based on the results, a hypothesis was formulated that explains the development of chronic pancreatitis through accelerated digestion of the mutant by trypsin.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Chemistry, Physical
Honglin Ma, Hongwei Jin, Yanli Li, Bilian Ni, Yi Li, Shuping Huang, Wei Lin, Yongfan Zhang
Summary: This study investigated the SHG response difference between two novel interpenetrated MOFs (M1 and M2) by performing first-principles calculations. The results showed that the structural transformation from M2 to M1 was energetically favorable, and M1 with the most tightly packed structure had the largest dielectric constant. The presence of the DMF guest had a small effect on the optical anisotropy of the system. Due to the different coordination environments of Zn atoms, M1 showed more significant optical anisotropy and a wider range of phase matchability compared to M2.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Biochemistry & Molecular Biology
Brodie L. Ranzau, Kartik L. Rallapalli, Mallory Evanoff, Francesco Paesani, Alexis C. Komor
Summary: Base editors are genome editing tools that modify nucleobases in DNA to enable precise base conversions. Adenine base editors convert A.T base pairs to G.C base pairs by using an adenosine deaminase enzyme. Previous experiments showed that the wild-type TadA enzyme had no activity on DNA, but we demonstrated that it can perform base editing in both bacterial and mammalian cells.
Article
Chemistry, Physical
Xuanyu Zhu, Marc Riera, Ethan F. Bull-Vulpe, Francesco Paesani
Summary: Using the MB-pol theoretical/computational framework, we have introduced a new family of data-driven many-body potential energy functions (PEFs) for water, named MB-pol(2023). By employing larger training sets and adopting sophisticated machine-learned representations, the MB-pol(2023) PEFs achieve sub-chemical accuracy in modeling hexamer isomers and outperform existing PEFs in describing water clusters in the gas phase. Moreover, the MB-pol(2023) PEFs show remarkable agreement with experimental results for various properties of liquid water, improving upon the original MB-pol PEF and closing the gap with experimental measurements.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Thomas M. Rayder, Filip Formalik, Simon M. Vornholt, Hilliary Frank, Seryeong Lee, Maytham Alzayer, Zhihengyu Chen, Debabrata Sengupta, Timur Islamoglu, Francesco Paesani, Karena W. Chapman, Randall Q. Snurr, Omar K. Farha
Summary: Carbon capture, storage, and utilization (CCSU) is an opportunity to reduce carbon emissions and combat global climate change. Metal-organic frameworks (MOFs) have shown great potential as effective CO2 sorbents in CCSU through gas adsorption. Understanding the properties of MOF pores and their dynamic behavior during sorption can lead to the development of more efficient CCSU materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yanli Li, Dengning Chen, Zhongpu Fang, Hegen Zhou, Jia Zhu, Yi Li, Shuping Huang, Wei Lin, Yongfan Zhang
Summary: First-principles calculations were used to investigate the reaction mechanisms of CO2 conversion to methanol over supported copper clusters. The adsorption and migration of hydrogen atoms were found to significantly impact the catalytic activity. The size of the cluster was found to influence the rate-limiting steps and the formate pathway was favored on large copper clusters.
JOURNAL OF CO2 UTILIZATION
(2023)
Article
Chemistry, Physical
Yuanhui Pan, Ching-Hwa Ho, Francesco Paesani, Raja Ghosh
Summary: Covalent organic frameworks (COFs) are 2D organic materials with unique electronic and transport properties. In this study, the impact of interlayer stacking arrangements on the electronic structure and coherence of polarons in donor-acceptor COFs was investigated through density functional theory and multiparticle Holstein formalism simulations. It was found that the stacking arrangement significantly influences the transport properties, with varying behavior from metallic to highly localized states. The extent of charge delocalization is sensitive to the type and precise arrangement of interlayer stacking and donor-acceptor fragments in the COF structure. The results suggest that interlayer interactions can aid in enhancing charge delocalization and guide the design of new COF structures for potential applications in organic electronics.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
Marc Riera, Christopher Knight, Ethan F. Bull-Vulpe, Xuanyu Zhu, Henry Agnew, Daniel G. A. C. Smith, Andrew Simmonett, Francesco Paesani
Summary: MBX is a C++ library that implements many-body potential energy functions (PEFs) within the many-body energy (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be used as a standalone package or integrated with other molecular simulation software as an energy/force engine. It allows for classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations combining conventional force fields and MB-nrg PEFs for diverse systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Ruihan Zhou, Marc Riera, Francesco Paesani
Summary: We introduce a data-driven many-body energy potential energy function (MB-nrg PEF) to accurately describe the energetics and structural properties of N-methylacetamide (NMA), as well as the NMA-water interactions. The results show that the MB-nrg PEF is able to accurately represent many-body effects in both gas and liquid phases, making it a promising molecular model for predictive simulations of biomolecular systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Materials Science, Multidisciplinary
Jierui Zhang, Francesco Paesani, Martina Lessio
Summary: Studies have shown that incorporating hydrophilic functional groups into the UiO-66 metal-organic framework (MOF) can improve its water uptake ability at low relative humidity (RH). This computational study provides insights into the adsorption mechanism of water in UiO-66 and its functionalized derivatives, revealing the preferential interaction sites and the formation of localized water clusters inside the octahedral pores. The presence of functional groups allows water to cluster in the pores at lower RH, making the MOF a more efficient water harvester.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Yang Yang, Junmin Peng, Huilin Tao, Zhou Yang, Yidong Hou, Wei Lin, Jinshui Zhang
Summary: The development of efficient catalysts is crucial for the photocatalytic ozonation process used in organic wastewater treatment. However, the influence of exposed facets and surface defects of the catalyst on the performance of photocatalytic ozonation is not well-studied. In this study, ZnO nanocomposites with different preferentially exposed crystal facets were synthesized and used for the photocatalytic ozonation of phenol. The results showed that the exposed {0001} facets and oxygen vacancies helped in the separation and transfer of photogenerated charges and improved the adsorption and activation of ozone molecules on the catalyst surface, leading to higher TOC removal rate.
ENVIRONMENTAL SCIENCE-NANO
(2023)
Article
Chemistry, Physical
Honglin Ma, Hongwei Jin, Yanli Li, Bilian Ni, Yi Li, Shuping Huang, Wei Lin, Yongfan Zhang
Summary: This study investigates the underlying causes of the significant difference in second harmonic generation (SHG) response between two novel metal-organic frameworks (MOFs). It is found that the tightly packed structure of the M1 compound leads to a larger dielectric constant and a favorable phase-matching feature, resulting in a strong SHG response at 950 nm. In contrast, the phase-mismatched behavior of the M2 compound with sevenfold interpenetration leads to a weak SHG signal.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Shaohua Liu, Yi Li, Yongfan Zhang, Wei Lin
Summary: Nanoribbon construction and modification with functional groups have been used to enhance the performance of photocatalysts. This study uses density functional theory (DFT) calculations to assess the electron absorption capacity of different nanoribbon structures in the photocatalytic CO2 reduction reaction. The results show that edge-modified nanoribbons have a significantly reduced band gap and an optimized CO2 reduction process.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yuanyuan Hu, Ting Wu, Yi Li, Yongfan Zhang, Wei Lin
Summary: Doping of selenium improves the photocatalytic activity and electronic structure of melon carbon nitride. In this study, the CO2 reduction performance of selenium-doped melon carbon nitride (Se-doped melon CN) is investigated using density functional theory calculations. Cobalt clusters loaded on the Se-doped melon CN surface significantly improve CO2 activation, favoring the formation of the 8-electron product, CH4. Overall, this work provides insights into the CO2 reduction mechanism on Se-doped melon CN with cobalt as the co-catalyst.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Bo Su, Yuehua Kong, Sibo Wang, Shouwei Zuo, Wei Lin, Yuanxing Fang, Yidong Hou, Guigang Zhang, Huabin Zhang, Xinchen Wang
Summary: The study successfully synthesized an infrared-ignited photocatalyst with efficient CO2 conversion activity on the TiN surface using Ru species, which achieved CO2 polarization and activation through the formation of surface HO-RuN5-Ti Lewis pair sites, and significantly enhanced the separation and transfer of photoinduced charges.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Yabing Zeng, Jie Yu, Yi Li, Yongfan Zhang, Wei Lin
Summary: In this study, density functional theory calculations were performed to investigate the microscopic mechanism of CO2 hydrogenation to methanol over Cd-doped ZrO2 catalyst. The results showed that Cd doping promoted the generation of oxygen vacancies and activated the stable adsorption configurations of CO2. Additionally, the dominant reaction pathway from CO2 to methanol via formate intermediate was revealed.
JOURNAL OF CHEMICAL PHYSICS
(2023)
