A5100423946- Protein Structure and Dynamics
- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Photochemistry and Electron Transfer Studies
- Click Chemistry and Applications
- Monoclonal and Polyclonal Antibodies Research
- Protein Interaction Studies and Fluorescence Analysis
- Alzheimer's disease research and treatments
- Chemical Thermodynamics and Molecular Structure
- Antibiotic Resistance in Bacteria
- Mass Spectrometry Techniques and Applications
- Metal-Catalyzed Oxygenation Mechanisms
- Fluorine in Organic Chemistry
- Chemical Synthesis and Analysis
- Natural product bioactivities and synthesis
- Genomics and Phylogenetic Studies
- Free Radicals and Antioxidants
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Computational Drug Discovery Methods
- Photosynthetic Processes and Mechanisms
- Crystallography and molecular interactions
- Electrochemical Analysis and Applications
University of Nebraska–Lincoln
2010-2025
Chinese Academy of Medical Sciences & Peking Union Medical College
2024
Henan University of Science and Technology
2024
University of South China
2023
Xijing Hospital
2021
Jilin University
2021
Sun Yat-sen University Cancer Center
2021
Sun Yat-sen University
2010-2021
Union Hospital
2021
Jinan University
2021
A discussion of many the recently implemented features GAMESS (General Atomic and Molecular Electronic Structure System) LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These include fragmentation methods such as fragment molecular orbital, effective potential orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, resolution identity second order perturbation theory. Many new coupled cluster theory have been in GAMESS, multiple levels density functional/tight...
Abstract Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced mainly rely multiple sequence alignments (MSAs) inputs to learn the co-evolution information from homologous sequences. Nonetheless, searching MSAs protein databases is time consuming, usually taking tens of minutes. Consequently, we attempt explore limits fast by using only primary structures proteins. Our proposed method,...
Significance Quantitative characterization of hydrophobicity amino acid side chains in protein environment has important implications to the understanding hydrophobic effects and their role folding. Numerous parameters were developed previously determine residues. However, these scales are not always correlated consistently. Here, we constructed artificial planar peptide networks composed unified chains, considering both primary β-sheet secondary structure protein. Using molecular dynamics...
Ferroelectric materials are characterized by spontaneous electric polarization that can be reversed inverting an external field. Owing to their unique properties, ferroelectric have found broad applications in microelectronics, computers, and transducers. Water molecules dipolar thus alignment of water is conceivable when freezes into special forms ice. Although the ice XI has been proposed exist on Uranus, Neptune, or Pluto, evidence a fully proton-ordered still elusive. To date, existence...
Abstract Anisotropic Bi 2 Te 3 ‐based thermoelectric materials have drawn extensive interest in the past decades. Here, n‐type 2.7 Se 0.3 films with superhigh figure of merit are developed through anisotropy control via tuning an external electric field and deposition anisotropy. It is found that angle interplanar grain boundaries between (0 1 5) 11) planes can be tuned by applied field, which leads to strengthened electron mobility simultaneously maintains low lattice thermal conductivity....
Abstract A computational methodology for protein pK a predictions, based on ab initio quantum mechanical treatment of part the and linear Poisson–Boltzmann equation bulk solvent, is presented. The method used to predict interpret values five carboxyl residues (Asp7, Glu10, Glu19, Asp27, Glu43) in serine protease inhibitor turkey ovomucoid third domain. All predicted are within 0.5 pH units experiment, with root‐mean‐square deviation 0.31 units. We show that decreased observed some primarily...
The (3+2)-cycloaddition reaction involving oxyallyl cations has proven to be a versatile and efficient approach for the construction of five-membered carbo- heterocycles, which are prevalent frameworks in natural products pharmaceuticals. following article will provide brief summary recent disclosures on this process featuring chemo-, regio- diastereoselective cycloadditions with both electron-rich electron-deficient 2π partners. 1 Introduction 2 Heteroatom-Substituted Oxyallyl Cations 3...
Understanding the catalytic mechanism of histone deacetylases can greatly benefit development targeted therapies that are safe and effective. Combined quantum mechanical molecular (QM/MM) Møller-Plesset second-order perturbation theory (MP2) geometry optimizations performed to investigate deacetylation reaction a tetrapeptide catalyzed by human Histone Deacetylase 8. A three-step is identified: first step formation negatively charged tetrahedral intermediate via nucleophilic addition...
Analytic gradient of the combined conductorlike polarizable continuum model (CPCM) and time-dependent density functional theory method is derived implemented. Due to use fixed points with variable areas tessellation scheme, excited state potential energy surfaces (PESs) are rigorously continuous smooth. The CPCM/TD-B3LYP used study an analog photoactive yellow protein chromophore, anionic thiomethyl p-coumaric acid (TMpCA−). Although may not be accurate in predicting solvent effect on...
The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined mechanical and molecular (QM/MM) calculations with induced dipole fields surface charge continuum solvation models. QM methods include Hartree–Fock method, density functional theory method (DFT), generalized valence bond multiconfiguration self-consistent Møller–Plesset perturbation time-dependent DFT method. dipoles of the MM atoms charges model are self-consistently variationally determined...
Antibiotic-resistant bacteria are a great threat to human health and food safety there is an urgent need understand the mechanisms of resistance for combating these bacteria. In current study, comparative proteomic methodologies were applied identify Escherichia coli K-12 outer membrane (OM) proteins related kanamycin resistance. Mass spectrometry western blotting results revealed that OM TolC, Tsx OstA up-regulated, whereas MipA, OmpA, FadL OmpW down-regulated in kanamycin-resistant E....
Abstract Model quality evaluation is a crucial part of protein structural biology. How to distinguish high-quality models from low-quality models, and assess which have relatively incorrect regions for improvement, are remain challenge. More importantly, the assessment multimer hot topic structure prediction. In this study, we propose GraphCPLMQA, novel approach evaluating residue-level model that combines graph coupled networks embeddings language models. The GraphCPLMQA consists encoding...
The burial of hydrophobic side chains in a protein core generally is thought to be the major ingredient for stable, cooperative folding. Here, we show that, snow flea antifreeze (sfAFP), stability and cooperativity can occur without core, α-helices or β-sheets. sfAFP has low sequence complexity with 46% glycine an interior filled only backbone H-bonds between six polyproline 2 (PP2) helices. However, folds kinetically two-state manner moderately stable at room temperature. We believe that...
Using ab initio methods, we investigate the structural evolution of a family gold−sulfide cluster anions (AumSn−). We show that this clusters exhibits simple size-evolution rules and novel hollow polyhedron structures. The highly stable AumSn− species such as Au6S4−, Au9S5−, Au9S6−, Au10S6−, Au11S6−, Au12S8−, Au13S8− detected in recent ion mobility mass spectrometry experiment Au25(SCH2CH2Ph)18 (Angel et al. ACS Nano2010, 4, 4691) are found to possess either quasi-tetrahedron, pyramidal,...
Linear response and variational treatment are formulated for Hartree-Fock (HF) Kohn-Sham density functional theory (DFT) methods combined discrete-continuum solvation models that incorporate self-consistently induced dipoles charges. Due to the treatment, analytic nuclear gradients can be evaluated efficiently these discrete continuum models. The forces torques on point charges using simple electrostatic formulas as permanent charges, in accordance with nature of methods. Implementation...
The 1,3-dipolar cycloaddition reaction between an alkene and a tetrazole represents one elegant rare example of fluorophore-forming bioorthogonal chemistry. This is attractive for imaging applications in live cells that requires less intensive washing steps and/or needs spatiotemporal resolutions. In the present work, as effort to improve fluorogenic property alkene-tetrazole reaction, aromatic (styrene) was investigated dipolarophile. Over 30-fold improvement quantum yield product achieved...
Abstract Benzobicyclo[3.2.1]octane is a cage‐like unique motif containing bicyclo[3.2.1]octane structure fused with at least one benzene ring. It found in various natural products that exhibit structural complexities and important biological activities. The total synthesis of possessing this challenging has received considerable attention, great advances have been made field during the past 15 years. This review summarizes thus far achieved chemical syntheses synthetic studies compounds...
A novel "long chain" toxin BmP09 has been purified and characterized from the venom of Chinese scorpion Buthus martensi Karsch. The is composed 66 amino acid residues, including eight cysteines, with a mass 7721.0 Da. Compared B. Karsch AS-1 as Na(+) channel blocker (7704.8 Da), an exclusive difference in sequence by oxidative modification at C terminus. sulfoxide Met-66 terminus brought peptide dramatic switch toaK(+) blocker. Upon probing targets on isolated mouse adrenal medulla...
Formulas for evaluating analytic energy gradient are derived combined time-dependent density functional theory (TDDFT) and polarizable force field methods that incorporate dipole polarizability tensors linearly induced point dipoles. The Z-vector method determining relaxed one-particle difference matrix in regular TDDFT is extended to include of the mutual polarization excited state can be formulated by using density-induced dipoles transition All forces torques involving efficiently...
The formation of like-ion pairs, Na(+)-Na(+) and Cl(-)-Cl(-), in aqueous solution was studied by high-level ab initio methods, classical molecular dynamics (MD), QM/TIP5P, QM/EFP MD (quantum mechanics/effective fragment potential dynamics). Ab calculations on model clusters revealed that the Na(+)(H2O)nNa(+) (n = 2-4) were significantly more stabilized bridged waters than corresponding Cl(-)(H2O)nCl(-) clusters. simulations also predicted a clear local minimum near 3.6 Å only for pair,...