Article
Physics, Multidisciplinary
Xi-An Chen, Shifang Li, Jin Li, Chaoyu He, Tao Ouyang, Chunxiao Zhang, Chao Tang, Jianxin Zhong
Summary: Due to the existence of various allotropes and strong spin-oribital coupling effects, two-dimensional bismuth materials have attracted great research interest. Currently, first-principles calculations based on the hybrid functional HSE06 or GW methods are commonly used to calculate accurate electronic properties. However, these calculations are time-consuming, especially for large unit-cell systems and high-throughput calculations with numerous structures. To address this, a general and transferable Slater-Koster tight-binding (TB) model based on the Bi sp(3)d(5) hybridization was proposed, which accurately calculates the electronic properties of different 2D Bi allotropes. The TB model shows excellent transferability and accuracy, facilitating future numerical studies on electronic properties of 2D Bi allotropes with different structures efficiently.
Article
Chemistry, Inorganic & Nuclear
Raad Chegel, Somayeh Behzad, Ying Wang, Jinrong Xu
Summary: The study investigates the thermoelectric properties of bilayer SiC under bias voltage using a tight binding model and formulas, revealing that the thermal properties of biased bilayer SiC vary with temperature and bias voltage. The bias voltage leads to changes in the band gap, affecting the electrical and thermal behaviors of bilayer SiC.
SOLID STATE SCIENCES
(2021)
Article
Chemistry, Physical
James Goff, Yu Zhang, Christian Negre, Andrew Rohskopf, Anders M. N. Niklasson
Summary: A shadow molecular dynamics scheme for flexible charge models is proposed, which derives the shadow Born-Oppenheimer potential from a coarse-grained approximation of range-separated density functional theory. The atomic potential and force terms are modeled by the linear atomic cluster expansion (ACE), providing a computationally efficient alternative to machine learning methods. The proposed scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) and provides stable dynamics with reduced computational overhead.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Computer Science, Interdisciplinary Applications
Yixiao Chen, Linfeng Zhang, Han Wang, E. Weinan
Summary: DeePKS-kit is an open-source software package for developing machine learning based energy and density functional models. It supports multiple methods and provides simple and customized tools. The paper also provides an example of developing a chemically accurate model for water clusters.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Worasak Sukkabot
Summary: The electronic and optical characteristics of CdSbulk/CdSe nanoshells and CdSbulk/CdSe/CdS quantum-well nanoshells with experimentally synthesized structures were determined using the atomistic tight-binding model. The optical band gaps become narrow with increasing CdSe layer thicknesses due to quantum confinement, while encapsulating CdSe layers on CdSbulk/CdSe nanoshells mainly promote optical properties. The stokes shift and radiative lifetimes of CdSbulk/CdSe/CdS quantum-well nanoshells are greater than those of CdSbulk/CdSe nanoshells, with enhancements observed with increasing CdSe layer thicknesses.
MATERIALS SCIENCE IN SEMICONDUCTOR PROCESSING
(2023)
Article
Materials Science, Multidisciplinary
Qiangqiang Gu, Shishir Kumar Pandey, Rajarshi Tiwari
Summary: Spin-orbit coupling (SOC) drives interesting and non-trivial phenomena in solid-state physics, ranging from topological to magnetic to transport properties. We provide a simple yet effective computational approach to estimate the onsite SOC strength, which combines ab-initio and tight-binding calculations. Our method demonstrates wide applicability and high sensitivity by accurately estimating SOC strength in materials with varying SOC strengths and the number of SOC active ions. This approach can readily be applied to a wide range of materials.
COMPUTATIONAL MATERIALS SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Alireza Mostafaei, Ebrahim Heidari Semiromi
Summary: This study focuses on the electronic structure of a class of MXene monolayers named M2XT2, and provides an accurate description using a parameterized minimal tight-binding model. The results show that this model effectively describes the electronic structure of these materials over a wide energy range.
Article
Physics, Multidisciplinary
Qile Li, Jackson S. Smith, Yuefeng Yin, Chutian Wang, Mykhailo Klymenko, Jared H. Cole, Nikhil Medhekar
Summary: Bismuth, with its unique properties, has been used as a prototype material to study topological electronic structures. By developing tight-binding models based on first-principles calculations, it has been shown that these models can accurately reproduce the electronic and topological features of two-dimensional bismuth allotropes. The models provide insight into the physical origin of novel band topology and perturbation effects in bismuth allotropes, serving as a starting point for exploring electron/spin transport and electromagnetic response in low-dimensional topological devices.
NEW JOURNAL OF PHYSICS
(2021)
Article
Engineering, Electrical & Electronic
Worasak Sukkabot
Summary: This study investigated the electronic, optical, and magnetic properties of Mn-doped ZnSe nanocrystals using the atomistic tight-binding theory with sp-d exchange interaction. Results showed that magnetic fields split the spin-degenerate states and optical band gaps were reduced with increasing diameters due to the quantum confinement effect. Zeeman splittings were enhanced with increasing magnetic fields, while g-factor values were decreased. The study provides a better understanding of magnetically-doped semiconductor nanocrystals and their potential applications in spintronics.
MATERIALS SCIENCE IN SEMICONDUCTOR PROCESSING
(2022)
Article
Engineering, Chemical
Jianxiong Kang, Yanni An, Jiwei Xue, Xiao Ma, Jiuzhou Li, Fanfan Chen, Sen Wang, He Wan, Chonghui Zhang, Xianzhong Bu
Summary: The electronic structure of the galena surface was investigated using first-principle calculation. The results showed that galena is a p-type semiconductor with a direct band gap. During the formation of galena, the 3p orbital of S and the 6p orbital of Pb played a primary role. Additionally, the surface properties of galena were influenced by the transfer of electrons from the 6p orbital of Pb to the 3p orbital of S.
Article
Computer Science, Artificial Intelligence
Johannes Gedeon, Jonathan Schmidt, Matthew J. P. Hodgson, Jack Wetherell, Carlos L. Benavides-Riveros, Miguel A. L. Marques
Summary: This article presents a solution to the problems in density functional theory, namely the explicit dependency of the functionals on the particle number and the derivative discontinuity at integer particle numbers. They propose training a neural network as a universal functional that exhibits piece-wise linearity between integer particle numbers and reproduces the derivative discontinuity of the exchange-correlation energy.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Physical
S. D. Borisova, S. Eremeev, G. G. Rusina, E. Chulkov
Summary: The structure and magnetic properties of small Cr clusters, Cr-3 and Cr-4, adsorbed on the Cu(111) surface have been investigated using DFT calculations, while their vibrational properties have been studied within calculations based on TBSMA. The magnetic ordering in the Cr clusters significantly affects their crystal structure and symmetry, influencing the vibrational modes of the clusters and nearest neighbor copper atoms. The vibrational modes select potentially possible structures of Cr-3 and Cr-4, prohibiting the lowest total energy cluster structure as dynamically unstable.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Physics, Condensed Matter
Sejoong Kim
Summary: We propose optimized tight-binding (TB) models with atomic orbitals to enhance ab initio TB models truncated from full density functional theory (DFT) Hamiltonian based on localized orbitals. The optimization retains qualitative features of the original Hamiltonian and reduces quantitative deviations in overall band structures between the ab initio TB model and the full DFT Hamiltonian. We demonstrate the optimization process using semiconducting and metallic Janus transition metal dichalcogenides monolayers in the 2 H configuration, showing differences in electronic structures between the truncated TB model and the original full Hamiltonian, and how much the optimization can mitigate the quantitative loss caused by truncation. We also elaborate the optimization process to accurately reproduce local electronic properties and extend the discussions to TB models including spin-orbit interactions.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2023)
Article
Chemistry, Multidisciplinary
Meiyi Jiang, Kun Yang, Hongjing Yu, Li Yao
Summary: Through density functional theory calculations, the effects of different metal oxides adsorbed on the anatase TiO2 (101) surface were studied, indicating that a small amount of CuO increases the reactivity of the catalyst, but the overall catalytic effect is inferior to those with FeO or MnO. Catalysts containing FeO are more stable than those with only CuO or MnO, with higher FeO adsorption ratio leading to increased stability of the catalyst structure.
JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS
(2021)
Article
Spectroscopy
Yi-Wei Fan, Huai-Qian Wang, Hui-Fang Li
Summary: The study on hydrated clusters Co(H2O)(n)(-) in gas phase using DFT coupled with stochastic kicking method reveals that the global minimum structure of Co(H2O)(n)(-) exhibits a low-symmetry pattern. The Co- ion tends to be located at the vertex site of the water molecular clusters to reduce repulsion with O atom. These results demonstrate that the formation of these low-lying isomers is determined by the delicate balance between ion-water and water-water interactions.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Multidisciplinary
Xiao Li, Marc Muniz, Karlun Chun, Jonathan Tai, Francesca Guerra, Darrin M. York
Summary: This article introduces a series of active-learning activities and a gamified approach to develop students' representational competence about atomic orbitals and engage students in learning their properties. The activities focus on exploring the relationship between spatial properties and quantum numbers of atomic orbitals and utilize the Orbital Explorer website for visualization and analysis. These activities are suitable for both in-person and remote teaching settings.
JOURNAL OF CHEMICAL EDUCATION
(2022)
Article
Chemistry, Multidisciplinary
Xiao Li, Marc Muniz, Karlun Chun, Jonathan Tai, Francesca Guerra, Darrin M. York
Summary: This article introduces an online suite of tools that help develop students' representational competence about atomic orbitals. The tools include Orbital Explorer, which allows visualization and interactive investigation of atomic orbital properties, and BingOrbital, a chemistry educational gamification design resembling Bingo. The tools aim to reinforce students' recognition of atomic orbitals and have been applied as engaging retrieval practice tools.
JOURNAL OF CHEMICAL EDUCATION
(2022)
Article
Biochemistry & Molecular Biology
Tushar Aggarwal, William A. Hansen, Jonathan Hong, Abir Ganguly, Darrin M. York, Sagar D. Khare, Enver Cagri Izgu
Summary: Researchers have redesigned an archaeal DNA polymerase to exhibit a new activity of catalyzing the formation of internucleotidyl N-P linkages. This unnatural enzyme activity was enabled by a key substitution in the active site, which enhanced the positioning of a 3'-amino nucleophile. Further modifications of the protein-nucleic acid interface yielded a variant with DNA-dependent NP-DNA polymerase activity, which was utilized for the synthesis of DNA-NP-DNA copolymers. This study provides insights into substrate fidelity and latent promiscuity in enzymes.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Timothy J. Giese, Jinzhe Zeng, Solen Ekesan, Darrin M. York
Summary: This paper presents a fast, accurate, and robust approach for determining free energy profiles and kinetic isotope effects of RNA reactions with the inclusion of nuclear quantum effects. The approach utilizes deep potential range correction (DPRc) and quantum mechanical/molecular mechanical (QM/MM) simulations to achieve high accuracy in tuning QM and QM/MM interactions. The method is demonstrated through the calculation of free energy profiles of RNA cleavage reactions and reactions involving thio-substitutions, showing close agreement with ab initio calculations and the superior performance compared to other methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Solen Ekesan, Erika McCarthy, David A. Case, Darrin M. York
Summary: Electrostatic interactions play a crucial role in the structure and function of RNA, particularly in the recruitment of metal ions for catalysis. This study investigates the electrostatic features and their relation to the binding of monovalent and divalent metal ions in metal-dependent ribozymes and an engineered DNAzyme. The findings demonstrate the importance of RNA electrostatics in catalysis, including the structural integrity of the active state, pK(a) tuning, and electrostatic stabilization of the transition state.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian C. C. J. C. Ebert, Paul Labute, Kenneth M. Merz, Darrin M. York
Summary: We propose a framework for optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for softcore potentials. The framework is implemented and tested in the GPU-accelerated AMBER software suite. The optimized pathways integrate important features such as smoothstep functions, power scaling of interactions, LJ pairwise form, and smoothing of the potential at the nonbonded cutoff boundary. The pathways demonstrate superior numerical stability and minimal variance of free energy estimates compared to traditional methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jinzhe Zeng, Yujun Tao, Timothy J. Giese, Darrin M. York
Summary: We introduce the QD7 pi-v1.0 model for accurately modeling the internal energy of drug molecules. This model combines a quantum mechanical/machine learning potential correction with a high-level deep-learning potential. It outperforms other semiempirical and machine learning potentials in handling electrostatic interactions and charge/protonation state changes. The QD pi model is highly accurate in various molecular interactions and shows excellent performance in relative protonation/deprotonation energies and tautomers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Tai-Sung Lee, Hsu-Chun Tsai, Abir Ganguly, Darrin M. York
Summary: We propose an alchemical enhanced sampling method called ACES, implemented in the GPU-accelerated AMBER free energy MD engine. The method creates an enhanced sampling state by reducing or eliminating certain potential energy terms and interactions, while maintaining terms that limit the need for extensive phase space sampling. This enhanced sampling state is connected to the real state through a Hamiltonian replica exchange framework, resulting in a counterdiffusion of states. The ACES method has been successfully applied to various test cases and demonstrated superior performance compared to traditional MD and alternative enhanced sampling methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Benjamin Weissman, Solen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J. Giese, Erika McCarthy, Michael E. Harris, Darrin M. York, Joseph A. Piccirilli
Summary: Ribonucleases and small nucleolytic ribozymes both catalyze RNA strand cleavage through 2'-O-transphosphorylation, but their mechanisms involve distinct transition states. In this study, we demonstrate that hepatitis delta virus ribozyme catalysis proceeds through a dissociative, metaphosphate-like transition state, in contrast to the associative transition states observed with other enzymes. These findings provide evidence for a unique ribozyme active site design that modulates the RNA cleavage pathway.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Suhyun Yoon, Edward Ollie, Darrin M. York, Joseph A. Piccirilli, Michael E. Harris
Summary: Psr is an important experimental system for defining RNA catalysis and designing valuable tools in biotechnology. The rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood.
Article
Chemistry, Physical
Jinzhe Zeng, Yujun Tao, Timothy J. Giese, Darrin M. York
Summary: Modern semiempirical electronic structure methods have potential applications in drug discovery for accurately modeling biological and drug-like molecules. Comparisons were made between different methods, and the hybrid quantum mechanical/machine learning potentials, especially the QD pi model, showed the most robust performance for tautomers and protonation states relevant to drug discovery.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Timothy J. Giese, Darrin M. York
Summary: We used the modified Bigeleisen-Mayer equation to calculate kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions. The modified equation includes the ratio of vibrational frequencies and the effect of isotopic substitution on the activation free energy. We developed a practical method to estimate the frequency ratio correction directly from umbrella sampling, which avoids the need for normal mode analysis. This method provides a new tool for calculating kinetic isotope effects in complex chemical reactions in the condensed phase.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yuqing Xu, Michael E. Harris, Darrin M. York, Kin-Yiu Wong
Summary: RNA strand cleavage can be catalyzed by both ribozymes and hydroxide or hydronium ions. Experiments showed that cleavage of the 5'-linked nucleoside and isomerization between 3',5'- and 2',5'-phosphodiesters occur under acidic conditions, while only cleavage reaction is observed under basic conditions. A path-integral approach was used to reveal the reaction mechanisms under acidic conditions, and the proposed mechanisms can also be supported by experimental pH-rate profiles.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Erika McCarthy, Soelen Ekesan, Timothy J. Giese, Timothy J. Wilson, Jie Deng, Lin Huang, David M. J. Lilley, Darrin M. York
Summary: By using simulations and calculations, we have elucidated the mechanism of methyl transfer catalyzed by a methyltransferase ribozyme. We have identified two transition states and a rate-controlling step, and predicted the activity-pH profile of the reaction.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Organic
Solen Ekesan, Darrin M. York
Summary: The pistol ribozyme (Psr) is a recently discovered class of nucleolytic ribozymes that catalyze RNA self-cleavage. This study investigates the mechanism of Psr and proposes different roles for G42 and G40 as general bases. The findings provide new insights and suggest further experimental tests to solve the mystery of proton abstraction in the pistol ribozyme.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)