Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Biochemistry & Molecular Biology
Brigitta Elsaesser, Peter Goettig
Summary: Experimental evidence for enzymatic mechanisms is often limited and biased by the methods used. Despite apparent contradictions, opposing views often turn out to be special cases of a more comprehensive and superior concept.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Rajiv K. Kar
Summary: Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
DRUG DISCOVERY TODAY
(2023)
Article
Mathematics, Applied
Yangshuai Wang, Huajie Chen, Mingjie Liao, Christoph Ortner, Hao Wang, Lei Zhang
Summary: Hybrid quantum/molecular mechanics models, known as QM/MM methods, are commonly used in material and molecular simulations to strike a balance between accuracy and computational cost. Adaptive QM/MM coupling methods, with on-the-fly classification of atoms, allow for real-time updates of the QM and MM subsystems as needed. This study proposes a new adaptive QM/MM method for material defect simulations based on a residual from a posteriori error estimator, showcasing its effectiveness through numerical simulations.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2021)
Article
Mathematics, Interdisciplinary Applications
Huajie Chen, Christoph Ortner, Yangshuai Wang
Summary: This paper presents a framework for consistent QM/MM hybrid models of crystalline defects, allowing for general atomistic interactions including traditional and machine-learned interatomic potentials. The authors establish an a priori error estimate for the QM/MM approximations and demonstrate how matching conditions can be used to construct practical machine learned MM potentials for QM/MM simulations.
MULTISCALE MODELING & SIMULATION
(2022)
Review
Physics, Multidisciplinary
O. Lopez-Acevedo, D. Sucerquia
Summary: In this article, the applications of the QM/MM method in the study of interactions between copper, silver, and gold atoms/clusters and biological/organic molecules are reviewed. Various research efforts are highlighted, demonstrating the successful application of the QM/MM method in studying excited state evolution, charge transport, light absorption and emission, and determining atomic structures.
ADVANCES IN PHYSICS-X
(2023)
Article
Spectroscopy
S. Arsenault-Escobar, J. F. Fuentes-Galvez, C. Orellana, S. Bollo, P. Sierra-Rosales, S. Miranda-Rojas
Summary: In this study, we investigated the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA) using spectroscopic, electrochemical, and computational methods. By combining UV-vis experiments with high-level computational models, we were able to determine the proper binding mode at the molecular scale and explain the experimental optical response due to the complex formation. In addition, we used electrochemical measurements to support the results obtained through UV-vis spectroscopy. Our findings showed that TZ is deeply buried in the DNA, as evidenced by the hypochromic effect observed in the absorption spectra.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Biochemical Research Methods
Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu
Summary: ProDESIGN-LE is an accurate and efficient approach to protein sequence design. It uses a transformer to learn the correlation between residue local environments and amino acid types, resulting in designed proteins that fit well with their local environments. Experimental results show that ProDESIGN-LE performs well in designing protein sequences with high solubility and structural similarity to the target structures.
Article
Mathematics, Applied
Xiaocheng Shang
Summary: In this study, a new splitting method for dissipative particle dynamics (DPD) simulations is proposed to improve accuracy and efficiency, particularly in the large friction limit. Various numerical experiments demonstrate the superiority of this new method over popular alternative schemes in the literature for both equilibrium and transport properties.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2021)
Article
Computer Science, Information Systems
Xinyan Zhang, Peng Gao, Sunxiangyu Liu, Kongya Zhao, Guitao Li, Liuguo Yin, Chang Wen Chen
Summary: The study introduces a global-local adjusting dense super-resolution network (GLADSR) to improve image super-resolution performance while reducing parameters and computational cost, using a global-local adjusting module (GLAM) and a separable pyramid upsampling (SPU) module. Extensive experiments demonstrate the superiority of GLADSR over state-of-the-art methods with less parameters and lower computational cost.
IEEE TRANSACTIONS ON MULTIMEDIA
(2021)
Article
Engineering, Civil
Xiangjie Wang, C. S. Cai, Peng Yuan, Guoji Xu, Chao Sun
Summary: This paper aims to improve the efficiency and accuracy of the DSRFG method by modifying the way of discretizing the energy spectra. The grid effects on both the Kraichnan's method and the improved DSRFG method are analyzed theoretically and examined numerically. Results show that the improved DSRFG method is less affected by grid effects and can accurately simulate wind effects on buildings.
ENGINEERING STRUCTURES
(2024)
Article
Materials Science, Multidisciplinary
F. T. Stumpf
Summary: A constitutive framework for mechanical characterization of soft biological tissues is proposed in this work, which can easily include anisotropic and time-dependent behaviors. Improved accuracy and efficiency are achieved through using a higher-order diagonally implicit Runge-Kutta method, making the framework capable of modeling different soft tissues effectively.
MECHANICS OF MATERIALS
(2021)
Review
Chemistry, Multidisciplinary
Himani Sharma, Baddipadige Raju, Gera Narendra, Mohit Motiwale, Bhavna Sharma, Himanshu Verma, Om Silakari
Summary: Computational enzymology is a rapidly developing field that provides deep insights into the process of biological catalysis, aiding in the design of potential inhibitors. The combined quantum mechanics/molecular mechanics approach has gained attention for understanding enzymatic reactions at both structural and energetic levels. It offers a new mechanism for designing potent enzyme inhibitors.
Article
Chemistry, Physical
Yuchen Yuan, Qiang Cui
Summary: Free energy differences are crucial for understanding chemical and biological processes, but direct estimation with quantum mechanics is impractical. A data-driven approach using a deep neural network and enhanced sampling simulations overcomes the challenge of poor configurational overlap between different levels of theory. This approach demonstrates high accuracy and efficiency for both gas phase and condensed phase systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Medicinal
Maciej Spiegel
Summary: This paper provides an overview of the application of computational quantum chemistry in studying the antioxidative nature of chemicals. It summarizes current trends and methods, and is divided into sections corresponding to different stages of research. The paper concludes with remarks and future perspectives based on the remaining elements.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Yuhui Li, Camille Bishop, Kai Cui, J. R. Schmidt, M. D. Ediger, Lian Yu
Summary: Surface diffusion in organic semiconductor glass has been studied and compared with other molecular glasses. The presence of surface mobility gradient and anchoring of surface molecules at different depths are found to significantly influence the surface diffusion behavior. A double-exponential model is proposed to explain the variation in surface diffusion rates.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Kai Cui, Sankar Nair, David S. Sholl, J. R. Schmidt
Summary: Understanding the degradation of nanoporous materials under acid gas exposure is crucial for extending their lifetime and practical applications. Previous theoretical studies focused on isolated point defects, which did not provide enough insights into the long-term bulk material evolution. In this study, a lattice-based kinetic model was developed to simulate the defect propagation and bulk material breakdown in zeolitic imidazolate frameworks (ZIFs). The model accurately reproduced the experimental macroscopic evolution of bulk material properties and provided new insights into the autocatalytic nature of ZIF degradation and the spatial distribution of defects.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Gang Jiang, Huidong Li, Tianjia Cheng, Yuanli Tian, Peizu Liu, Jing Guo, Kai Cui, Ruirui Ma, Xiaodong Ma, Fengjiao Cui, Chen Chen, Yong Hao
Summary: In this study, spontaneous magnetic biochar (SRMC-750) was prepared from municipal sludge and red mud for the adsorption of Cu2+ from wastewater. The experimental results showed that SRMC-750 had a high adsorption capacity and removal efficiency under specific conditions. This study is of great reference value for the development of new methods for wastewater treatment.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Multidisciplinary
R. Dominic Ross, Hongyuan Sheng, Yujia Ding, Aurora N. Janes, Dawei Feng, J. R. Schmidt, Carlo U. Segre, Song Jin
Summary: This study demonstrates the potential of a metal organic framework catalyst called Ni(3)HAB(2) for selective and active two-electron oxygen reduction reaction (2e(-) ORR) in neutral electrolytes. The study also reveals the influence of the catalyst's redox features on the ORR and proposes a hypothesis for the reaction mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Hongyuan Sheng, Aurora N. Janes, R. Dominic Ross, Heike Hofstetter, Kwanpyung Lee, J. R. Schmidt, Song Jin
Summary: This study establishes an efficient cathodic valorization method for glycerol into high-value chemicals using the electro-Fenton process at a stable NiSe2 cathode. The proof-of-concept linear paired electrochemical process achieves high selectivity and conversion of glycerol into the same oxidation products at both NiSe2 cathode and Pt anode.
Article
Chemistry, Physical
Chunyi Li, Zhenzi Yu, Kai Cui, J. R. Schmidt, David S. Sholl, Ryan P. Lively
Summary: In this study, we investigate the adsorption behavior of MIL-125-NH2 in CO2/H2S mixtures and calculate the defect formation energy of the MOF after H2S exposure. The results show that the MOF is stable under dry H2S exposure and exhibits higher selectivity for H2S than predicted. The experimental findings suggest that MIL-125-NH2 has great potential for H2S removal in biogas.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Review
Chemistry, Physical
Hongyuan Sheng, R. Dominic Ross, J. R. Schmidt, Song Jin
Summary: This review summarizes recent developments in metal-compound-based acidic and neutral 2e- ORR catalysts, providing insights into catalyst design rules and mechanistic understanding. The factors influencing H2O2 electrosynthesis are also discussed.
ACS ENERGY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Xuekang Cai, Jingming Zhang, Haishun Ye, Kai Cui, Tingting Hao, Long Yi, Xing Yang
Summary: Researchers have developed ligand-directed sensors (PSMA-Cy7-NBD and PSMA-Py-NBD) that specifically target hydrogen sulfide (H2S) and can be used in vivo. These tools exhibit high specificity and can be selectively transported into prostate cancer cells. By using them, endogenous H2S levels in tumor models can be imaged and downregulated, potentially aiding in the study of H2S cancer biology and related therapies.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Tesia D. Janicki, Mary J. Van Vleet, J. R. Schmidt
Summary: pi-interactions play a crucial role in chemical and biochemical systems, but aromatic molecules pose a challenge for accurate force field development due to their anisotropic electron densities and complex intermolecular interactions. In this study, we demonstrate the effectiveness of our own ab initio MASTIFF force field in accurately modeling aromatic interactions in different phases, using benzene as a proof of concept. Our MASTIFF benzene force field not only accurately predicts liquid phase properties, but also exhibits transferability to gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin that allows customizable anisotropic intermolecular functional forms, which can be used in any molecular dynamics simulation requiring a model for nonspherical atomic features. Overall, our findings highlight the importance of atomic-level anisotropy in advancing next-generation ab initio force field development.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Pawan Kumar, Ehsan Vahidzadeh, Kazi M. Alam, Devika Laishram, Kai Cui, Karthik Shankar
Summary: Solar energy harvesting using semiconductor photocatalysis provides a solution to energy scarcity and environmental pollution. However, current photocatalysts cannot fulfill the requirements for excellent absorption, high quantum efficiency, and photochemical durability simultaneously. This study reports the synthesis of a modified carbon nitride material that can meet the demands for photooxidation reactions. The heterojunction formed by wrapping this material on CdS nanorods exhibits excellent photocatalytic activity.
Article
Chemistry, Applied
Kai Cui, Shuai Guan, Jingyun Liang, Liping Fang, Ruiyan Ding, Jian Wang, Teng Li, Zhan Dong, Xiaohu Wu, Yongquan Zheng
Summary: Understanding the residue fate of fluxapyroxad is crucial for ensuring food safety and protecting human health. This study examined the dissipation, metabolism, accumulation, removal, and risk assessment of fluxapyroxad in cucumbers and cowpeas from field to table. Results from greenhouse-field trials showed that fluxapyroxad dissipated faster in cucumbers than in cowpeas, with M700F008 being the only detected metabolite.
Article
Chemistry, Multidisciplinary
Kai Cui, Alexander V. Soudackov, Matthew C. Kessinger, Jeremiah Xu, Gerald J. Meyer, Sharon Hammes-Schiffer
Summary: The pH dependence of proton-coupled electron transfer (PCET) reactions was studied using a multichannel kinetic model. This model showed that a weak pH dependence can arise from competition among different PCET channels involving various forms of redox species. The model was used to explain the weak pH dependence observed in an electrochemical PCET reaction. The study highlights the importance of considering multiple competing channels in PCET processes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Xin Yuan, Kwanpyung Lee, J. R. Schmidt, Kyoung-Shin Choi
Summary: This study demonstrates that halide adsorption on Cu electrode can effectively suppress the hydrogen atom transfer (HAT) reaction during the reductive upgrading of 5-hydroxymethylfurfural (HMF), leading to enhanced production of 2,5-dimethylfuran (DMF). The identity and concentration of the halide, as well as the reduction conditions, were found to affect the halide adsorption on Cu, and optimal halide coverages were identified to maximize the selectivity for DMF. Experimental and computational results provide a detailed understanding of the effects of halide adsorption at the atomic level.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Inorganic & Nuclear
Xiaofan Jia, Kai Cui, Jose L. Alvarez-Hernandez, Carrie L. Donley, Albert Gang, Sharon Hammes-Schiffer, Nilay Hazari, Sungho Jeon, James M. Mayer, Hannah S. Nedzbala, Bo Shang, Eric A. Stach, Eleanor Stewart-Jones, Hailiang Wang, Alexa Williams
Summary: Three molecular Re hydrides with silatrane functional groups were synthesized for attachment on metal oxide surfaces. These complexes demonstrated similar electronic properties to a control compound and acted as electrocatalysts for CO2 reduction in solution. However, when immobilized on surfaces, the hydride ligand was lost and the complexes degraded. This work exemplifies the challenges of attaching molecular hydride complexes to metal oxide surfaces.
Article
Chemistry, Multidisciplinary
Kai Cui, Alexander V. Soudackov, Matthew C. Kessinger, Jeremiah Xu, Gerald J. Meyer, Sharon Hammes-Schiffer
Summary: The pH dependence of proton-coupled electron transfer (PCET) reactions can be explained by a general, multichannel kinetic model. Multiple sequential and concerted PCET channels, involving different forms of redox species, contribute to a weak pH dependence of PCET apparent rate constants. This model has been used to understand the weak pH dependence observed in an electrochemical PCET reaction involving a ruthenium-based water oxidation catalyst.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)