The electrocatalytic activity of transition-metal-based compounds is strongly related to the spin states. However, underlying relationship connecting catalytic remains unclear. Herein, we carried out density functional theory calculations on oxygen reduction reaction (ORR) catalyzed by Fe single-atom supported C2N (C2N–Fe) shed light this relationship. It found that change electronic moments and O2 due molecular-catalyst adsorption scales with amount electron transfer from O2, which promotes...

Achieving an effective nitrogen reduction reaction (NRR) under mild conditions is a great challenge for industrial ammonia synthesis. NRR often accompanied by competing hydrogen evolution (HER), which causes extremely low Faraday efficiency. We systematically investigated the reactivity of atom-pair catalysts (APCs) formed 20 transition metal (TM) elements supported N-doped graphene via three pathways. By analyzing correlation among limiting potential, Gibbs free energy, and d-band center,...

Dual-metal-site catalysts (DMSCs) have emerged as a frontier in heterogeneous catalysis, while the underlying relationships connecting their dual-site synergistic effects on catalytic performance remain unclear. Here we present comprehensive first-principles study of O2 activation and CO oxidation series N-coordinated DMSCs. We discovered that N3-coordinated-adjacent dual-metal model has stronger dynamic effects, leading to much higher activity than others investigated. Based this model,...

Abstract Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it computationally intensive, especially for large proteins. To evaluate efficiently and accurately, we, here, propose computation schemes based on coarse‐grained NMA methods. This can be achieved by rescaling results with a specific factor that derived the basis linear correlation protein between standard NMA. Our repeat correctly © 2011 Wiley Periodicals, Inc. J Comput Chem,

In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay–Berne and electric multipole (EMP) potentials, the modeling of nucleic acids. First, comparison has been made between CG atomistic models (AMBER point-charge model) in DNA RNA hairpin structures. The results have demonstrated good quality maintaining acid structures, reproducing dynamics backbone atoms acids, describing hydrogen-bonding interactions base pairs. Second, AMBER yield comparable...

Native defects and nonmetal doping have been shown to be an effective way optimize the photocatalytic properties of Bi2WO6. However, a detailed understanding defect physics in Bi2WO6 has lacking. Here, using Heyd–Scuseria–Ernzerhof hybrid functional calculations, we study formation energies, electronic structures, optical native element (C, N, S, P) into We find that Bi vacancy (Bivac), O (Ovac), S on site (SO), N (NO) can stable depending Fermi level chemical potentials. By contrast,...

Abstract Sodium‐ion batteries (SIBs) have been considered as promising candidates for large‐scale energy storage systems and low‐speed electric vehicles due to abundant sodium resources low cost. Phosphate‐based cathodes stand out their high voltages, structural stability, superior safety, etc. However, large molecular weight limits the overall capacity, compromising density practical applications. Recent advancements in multi‐electron reactions based on transition metal (TM) ions provide a...

Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent polymerase (RdRp) from PV (3Dpol) has been widely employed as an important model for understanding structure-function relationships of DNA polymerases. Many experimental studies kinetics nucleotide incorporation by polymerases suggest that each cycle basically consists six sequential steps: (1) incoming binds to polymerase-primer/template complex; (2) ternary complex (nucleotide-polymerase-primer/template) undergoes...

Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a model for twenty kinds of amino acids and proteins, based on point electric multipole (EMP) potentials. We demonstrate that model, namely GBEMP is able reproduce many key features observed from experimental protein structures (Dunbrack Library) well atomistic force field simulations (using...

Lithium ions experience significantly less resistance when diffusing through the in-channel pathway compared to in-plane migration mechanism.

In our study, we combined classical molecular dynamics (MD) simulations with the simulated annealing (SA) method to explore conformational landscape of water molecules. By using K-means clustering method, processed MD simulation data extract representative samples structures used train a deep potential (DP) model. Our DeePMD showed accuracy in predicting structural properties compared DFT-MD results. Meanwhile, this approach achieves balanced prediction density and self-diffusion...

In this study, we have trained a deep learning (DL) potential for water using training datasets obtained from the DPLibrary (https://dplibrary.deepmd.net/). Subsequently, conducted classical molecular dynamics simulation (DeePMD) and path-integral MD (PI-DeePMD) of liquid based on (DP). Using velocity-velocity auto-correlation function (VVAF) formula, constructed infrared (IR) spectra O-H stretching mode DeePMD trajectories. Our results showed that DeePMD/VVAF approach accurately captured...

Coarse-grained or mesoscopic models of proteins and the corresponding force fields are great importance because they enable us to reduce folding simulation time by several orders magnitude compared all-atom approach and, consequently, reach millisecond scale simulations. In coarse-grained UNRES model for simulations protein structure dynamics, developed our group, each amino acid residue is represented a united side chain peptide group located in middle between two neighboring α-carbon...

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect described by Generalized Kirkwood theory. CG model calibrated using results of all-atom simulations compounds in solution. Instead matching overall effective forces produced atomic models, fundamental intermolecular such as electrostatic, repulsion-dispersion, solvation are represented explicitly at a...

Fluorescence anisotropy (FA) is a homogeneous, ratiometric, and real-time analytical technology. By selective labeling of guanine (G)-quadruplex motif with tetramethylrhodamine (TMR), here, it established that large reduction in FA response can be specifically associated the unfolding → folding transition G-quadruplex structures. On basis fluorescence intensity, polarization lifetime analysis, molecular docking simulation, mechanism was found to labeled fluorophore (TMR) intramolecularly...

Mitochondrial dysfunctions cause numerous human disorders and the development of mitochondria-targeted nanocarriers for drug delivery has aroused great attention. Herein, we report synthesis a liposomal nanohybrid cerasome modified with triphosphonium (TPP) to mitochondrial matrix. The cerasomes were observed possess an average size about 38 nm in diameter, theoretical simulation GBEMP mapping demonstrated that amphiphilic organotrialkoxysilanes stable as bilayer equilibrium conformation...

Here, the mislinked expanded porphyrins singly (labeled A) and doubly B) neo-confused [22]smaragdyrin, boron-dipyrromethenes-based C) D) where both C D include a -BF2 group, are chosen to serve as study objects, theoretical calculations carried out role of group in second-order nonlinear optics (NLO) behaviors. Results highlighted that plays an important for behaviors porphyrins; namely, embedding well enhanced hyper-Rayleigh scattering (HRS) value {βHRS(0;0,0)}, C{βHRS(0;0,0)}A{βHRS(0;0,0)}...

Under O-rich conditions, during the substitution of V by Ce in single negatively charged state (Ce1−V) for m-BiVO₄, no localized is found within calculated band gap so as to improve photocatalysis.

In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that exhibits DFT-level accuracy, and simulation is promising approach modeling structural properties water. Based on trajectories, calculated isotropic Raman spectra O-H stretching mode surface-specific velocity-velocity correlation function (ssVVCF), showing...

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG models (BMW and MARTINI models) as well adopting topology similar to that TIP4P model. model, unit, representing four real molecules, consists virtual site, positively charged particles, van der Waals (vdW) interaction center. Distance constraint is applied bonds formed between vdW center particles. The which carries negative charge, determined locations particles For water, coined...

BM2 channel plays an important role in the replication of influenza virus B. However, few studies attempt to investigate mechanism proton conductance channel, as well drug resistance channel. The first experimental structure protein has recently been solved, enabling us theoretically study systems with different protonation states histidine. By performing molecular dynamics simulations on four His19 residues, we provided our understanding structure, dynamics, and In general, results other...

In this work, we aim at optimizing the performance of anisotropic GBEMP model, which adopts a framework by combining Gay–Berne (GB) potential with an electric multipole (EMP) potential, in simulating DMPC lipid bilayer implicit solvent model. First, parameters were initially obtained fitting to atomistic profiles van der Waals interactions between homodimers molecular fragments while EMP was directly derived from expansion point multipoles predefined sites. Second, GB and for molecule...

In this article, we present a hybrid ENM/MARTINI coarse-grained model and examine the impact of reduced chemical detail on both static dynamic properties by comparing against explicit atomistic simulations. This methodology complements advanced molecular characterization dynamics proteins for medical bioengineering applications developing fundamental understanding how motion characteristics proteins, viruses, their precursors, interactions with environment govern behavior in different...