yusuke1997/dblp-id-title huggingface dataset:
Computerized evaluation of mean residence times in multicompartmental linear system and pharmacokinetics
A simple model of planar membrane: An integral equation investigation
Modeling the nitrogenase FeMo cofactor with high-spin Fe 8 S 9 X + (X=N, C) clusters. Is the first step for N 2 reduction to NH 3 a concerted dihydrogen transfer?
A new approximate method for the stochastic simulation of chemical systems: The representative reaction approach
Application of a ligand-based theoretical approach to derive conversion paths and ligand conformations in CYP11B2-mediated aldosterone formation
The α-effect exhibited in gas-phase S N 2@N and S N 2@C reactions
Fast clustering of equivalent structures in crystal structure prediction
AutoMeKin2021: An open-source program for automated reaction discovery
Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene
Photodeactivation paths in norbornadiene
Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes
About the calculation of exchange coupling constants in polynuclear transition metal complexes
Suitability of Available Interatomic Potentials for Sn to Model Its 2D Allotropes
Toward a less costly but accurate calculation of the CCSD(T)/CBS noncovalent interaction energy
Conformational analysis of HIV protease inhibitors. I. Rotation of the amide group adjacent to the P′ 1 decahydroisoquinoline ring system in ro 31-8959 and related systems
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Geomerty-Dependent Atomic Charges: Methodology and Application to Alkanes, Aldehydes, Ketones, and Amides
Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility
Barrier heights of hydrogen-transfer reactions with diffusion quantum monte carlo method
Local deformations of polymers with nonplanar rigid main-chain internal coordinates
Parameters for molecular dynamics simulations of iron-sulfur proteins
Cover Image, Volume 41, Issue 9
The barrier to the methyl rotation in C is -2-butene and its isomerization energy to T rans -2-butene, revisited
Single electron densities: A new tool to analyze molecular wavefunctions
Kinetics of the OH+HCl→H2O+Cl reaction: Rate determining roles of stereodynamics and roaming and of quantum tunneling
Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS-QB3 composite method and their consequences in DFT benchmark studies
Theoretical elucidation of the rhodium-catalyzed [4 + 2] annulation reactions
Development of the force field parameters for phosphoimidazole and phosphohistidine
Dissecting the concave-convex π-π interaction in corannulene and sumanene dimers: SAPT(DFT) analysis and performance of DFT dispersion-corrected methods
Web servers and services for electrostatics calculations with APBS and PDB2PQR
Comparison of methods for deriving atomic charges from the electrostatic potential and moments
Clarification of Some Bonding Concepts: Virial Theorem, Electron Pair Repulsion, and Rotational Barriers
Ab Initio direct classical trajectory investigation on the S N 2 reaction of F - with NH 2 F: Nonstatistical central barrier recrossing dynamics
An effective method for accurate prediction of the first hyperpolarizability of alkalides
ESES: Software for Eulerian solvent excluded surface
A Q-learning method based on coarse-to-fine potential energy surface for locating transition state and reaction pathway
Canonical Numerical Methods for Molecular Dynamics Simulations
Rehybridization as a general mechanism for maximizing chemical and supramolecular bonding and a driving force for chemical reactions
SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs
A coupled-cluster study on the noble gas binding ability of metal cyanides versus metal halides (metal = Cu, Ag, Au)
Residue-centric modeling and design of saccharide and glycoconjugate structures
BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials
Universal solvation model based on conductor-like screening model
Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies
Spin states in polynuclear clusters: The [Fe2O2] core of the methane monooxygenase active site
Development and use of an atomistic CHARMM-based forcefield for peptoid simulation
Benchmark calculations of the adsorption of aromatic molecules on graphene
Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory
Conformational searching of transition metal compounds
Analytical First Derivatives of the SCF Energy for the Conductor-Like Polarizable Continuum Model With Non-Static Radii
Fitting complex potential energy surfaces to simple model potentials: Application of the simplex-annealing method
Fast and accurate computation schemes for evaluating vibrational entropy of proteins
Modeling halogen bonding with planewave density functional theory: Accuracy and challenges
Regioselective multistep reconstructions of half-saturated zigzag carbon nanotubes
Empirical van der Waals corrections to solid-state density functional theory: Iodine and phosphorous containing molecular crystals
Ab initio and molecular mechanics (MM2 and MM3) calculations of positively charged conjugated nitrogen-containing compounds
Monosilicon-substituted cyanoacetylene: A computational study
Energy transfer between Si nanocrystals and protoporphyrin molecules as a function of distance, orientation and size
Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls
Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials?
Remarkable shifts of Csp2-H and O-H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes
Recognizing five molecular ligand-binding sites with similar chemical structure
Instanton rate constant calculations using interpolated potential energy surfaces in nonredundant, rotationally and translationally invariant coordinates
Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level
Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux
Valence energy correction for electron reactive force field
ChemNetworks: A complex network analysis tool for chemical systems
DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse steroids
Efficient electronic integrals and their generalized derivatives for object oriented implementations of electronic structure calculations
A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices
A self-contained and portable density functional theory library for use in Ab Initio quantum chemistry programs
Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes
DIESEL-MP2: A new program to perform large-scale multireference-MP2 computations
A computational study of the crystal and electronic structure of the room temperature organometallic ferromagnet V(TCNE) 2
AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites
Metabolic-intermediate complex formation with cytochrome P450: Theoretical studies in elucidating the reaction pathway for the generation of reactive nitroso intermediate
Theoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations
New parallel software (P_Anhar) for anharmonic vibrational calculations: Application to (CH3Li)2
Relevance of the DFT method to study expanded porphyrins with different topologies
Mechanistic Study of the Carbonylation of Aziridines to β-Lactams: Alkylation, Solvent and Molecular NaBr and MgO Clusters Catalysts Effects
Ab initio compact group model potentials for describing environment effects in cluster calculations
Ionization, intrinsic basicity, and intrinsic acidity of unsaturated diols of astrochemical interest: 1,1- and 1,2-ethenediol: A theoretical survey
Comparison of many-particle representations for selected-CI I: A tree based approach
A free energy calculation study of the effect of HF substitution on binding affinity in ligand-antibody interactions
Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers
Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis
AOMadillo: A program for fitting angular overlap model parameters
Modeling the polychromism of oxide minerals: The case of alexandrite and cordierite
On the Accuracy of Density Functionals and Theiro Basis Set Dependence: An Extensive Study on the Main Group Homonuclear Diatomic Molecules Li 2 to Br 2
Accurate prediction of the enthalpies of formation for xanthophylls
Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers
SeqDPI: A 1D-CNN approach for predicting binding affinity of kinase inhibitors
Relativistic corrections to magnetic properties
A Computational Analysis of the Intrinsic Plasticity of Five-Coordinate Cu(II) Complexes and the Factors Leading to the Breakdown of the Orbital Directing Effect in Paddlewheel Secondary Building Units
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM
TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility
Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method
Opto-electronic and thermophysical characteristics of A 2 TlAgF 6 (A = Rb, Cs) for green technology applications
Accurate prediction of thermodynamic properties of alkyl peroxides by combining density functional theory calculation with least-square calibration
Economical treatments of relativistic effects and electron correlation in WH6
Systematic Study of Selected Diagonalization Methods for Configuration Interaction Matrices
AGGREGATES: Finding structures in simulation results of solutions
Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach
A coarse-grained approach to NMR-data-assisted modeling of protein structures
GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-Dependent Density-Functional Tight-Binding
Extending spin-symmetry projected coupled-cluster to large model spaces using an iterative null-space projection technique
Hydrogen bonds of OCNH motif in rings in drugs: A molecular electrostatic potential analysis
Second derivatives in generalized Born theory
Encapsulation of Mg2 inside a C60 cage forms an electride
Rate coefficients for the reaction of OH with CF 3 CH 2 CH 3 (HFC-263fb) between 200 and 400 K: Ab initio , DFT, and transition state theory calculations
Prediction of Henry's law constant of benzene derivatives using quantum chemical continuum-solvation models
Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis
Conformational analysis of HIV-1 protease inhibitors: 2. Thioproline P1 Residue in the potent inhibitor KNI-272
Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical
Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH 3 ) 2 Cl 4 ] by methyl thiolate anion
Insulin mimetic peptide S371 folds into a helical structure
Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application
PICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels
RedMD - Reduced molecular dynamics package
A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s-cis butadiene
Stable conformations of 12-crown-O3N and its Li+ complex in aqueous solution
Understanding the intermolecular Diels-Alder cycloaddition promotion: Activation strain model/energy decomposition analysis model and conceptual density functional theory viewpoints
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer
Ab initio investigation on the ion-associated species and process in Mg(NO 3 ) 2 solution
Charge transport in stacking metal and metal-free phthalocyanine iodides. Effects of packing, dopants, external electric field, central metals, core modification, and substitutions
Structure-based redesign of proteins for minimal T-cell epitope content
Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning
Evolution of chemical bonding and electron density rearrangements during D 3h &[RIGHTWARDS ARROW]; D 3d reaction in monolayered TiS 2 : A QTAIM and ELF study
A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs)
Potential energy function for a photo-switchable lipid molecule
Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima
Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids
A semiclassical initial-value representation for quantum propagator and boltzmann operator
The Mechanism of Cholesterol Modification of Hedgehog Ligand
Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
The Exponents Method for Calculating Equilibrium Concentrations of Complex Species in Solution
Integral transformation with low-order scaling for large local second-order Møller-Plesset calculations
Incremental update of electrostatic interactions in adaptively restrained particle simulations
Tuning Aromaticity, Stability and Radicaloid Character of Periacenes by Chemical BN Doping
Expected degree for RNA secondary structure networks
Heisenberg behavior of some carbon-beryllium compounds: How well truncated-CI approaches work
Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model
Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration
Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces
GEPOL: An Improved Description of Molecular Surfaces. III. A New Algorithm for the Computation of a Silvent- Excluding Surface
Cover Image, Volume 39, Issue 14
Density functional theory studies on the dissociation energies of metallic salts: Relationship between lattice and dissociation energies
Formation pathways of DMSO from DMS-OH in the presence of O 2 and NO x : A theoretical study
SMILES-based optimal descriptors: QSAR analysis of fullerene-based HIV-1 PR inhibitors by means of balance of correlations
A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions
Synthesis, identification, density functional and Hirshfeld surface studies of 2, 2′-disulfanediylbis(tetrahydro-4H-cyclopenta[d][1, 3, 2]dioxaphosphole-2-sulfide)
Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
Tree Parzen estimator for global geometry optimization: A benchmark and database of experimental gas-phase structures of organic molecules
Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes
PyVisA: Visualization and Analysis of path sampling trajectories
Noniterative Doubles Corrections to the Random Phase and Higher Random Phase Approximations: Singlet and Triplet Excitation Energies
New approach to the rapid semiempirical calculation of molecular electrostatic potentials based on the am1 wave function: Comparison with ab initio hf/6-31g* results
Following the density evolution using real time density functional theory and density based indexes: Application to model push-pull molecules
Density functional study of neutral and anionic AlO n and ScO n with high oxygen content
Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV -2
How accurate are TD-DFT excited-state geometries compared to DFT ground-state geometries?
A computational approach for modeling electronic circular dichroism of solvated chromophores
Hydride and halide abstraction reactions behind the enhanced basicity of Be and Mg clusters with nitrogen bases
Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency
ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network
Single- and Three-Photon Ionization of N 2 $$ {N}_2 $$ in Presence of Fano Resonances
Strategies for the optimization of the structure of crystalline compounds
Force constant decomposition for penta-coordinated XH3Cl2- (X = C, Si, Ge) structures
Improved third-order Møller-Plesset perturbation theory
Density functional theory study of calix[4]arene- N -azacrown-5, calix[4]arene- N -phenyl-azacrown-5, and their complexes with alkali-metal cations: Na + , K + , and Rb +
Fitting of nonlinear regressions by orthogonalized power series
Gibbs energy of activation for thermal isomerization of (1Z)-acetaldehyde hydrazone and (1Z)-acetaldehyde N, N-dimethylhydrazone by Gaussian-4 theory and CCSD(T)/CBS computations
Viability of molecular modeling with pentium-based PCs
A combined freeze-and-cut strategy for the description of large molecular systems using a localized orbitals approach
HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides
Can the transition from tunneling to hopping in molecular junctions be predicted by theoretical calculation?
Molecular Dynamics Simulation with a Comtinuum Electrostatic Model of the Solvent
CANADA: Designing nucleic acid sequences for nanobiotechnology applications
Accelerated molecular dynamics simulations of protein folding
Free energy of solvation from molecular dynamics simulations for low dielectric solvents
On the performance of long-range-corrected density functional theory and reduced-size polarized LPol-n basis sets in computations of electric dipole (hyper)polarizabilities of π-conjugated molecules
Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides
Hirshfeld-based intrinsic polarizability density representations as a tool to analyze molecular polarizability
Charge-transfer processes in the assembly of Si n O m neutral clusters
Bond energies for molecules, clusters, and deposit systems
Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective
Understanding chemistry with the symmetry-decomposed Voronoi deformation density charge analysis
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
Deep reinforcement learning in chemistry: A review
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
Evaluation of Chemical Reactivity and Stability of Ionic Liquids Using Ab Initio and COSMO-RS model
Hybrid localized graph kernel for machine learning energy-related properties of molecules and solids
Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations
Prediction of catalytic activities of bis(imino)pyridine metal complexes by machine learning
rhOver: Determination of magnetic anisotropy and related properties for dysprosium(III) single-ion magnets by semiempirical approaches utilizing Hartree-Fock wave functions
A Molecular Mechanics Model for Flavins
MRD-CI Studies of Vertical Excitation Energies of Unsaturated Hydrocarbon Molecules
Improving the efficiency of the NEB reaction path finding algorithm
Comparison of implicit solvent models for the simulation of protein-surface interactions
A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations
Toward an ab initio fragment database for bioisosterism: Dependence of QCT properties on level of theory, conformation, and chemical environment
Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set
Cover Image, Volume 41, Issue 11
Asynchronous replica exchange for molecular simulations
Some practical aspects of free energy calculations from molecular dynamics simulation
Superposition of molecules: Electron density fitting by application of fourier transforms
Searching for stable hept-C 62 X 2 (X = F, Cl, and Br): Structures and stabilities of heptagon-containing C 62 halogenated derivatives
A path from Ih to C1 symmetry for C20 cage molecule
Implicit treatment of solvent dispersion forces in protein simulations
Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution
The Amber biomolecular simulation programs
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites
Adaptive σ aromaticity in the rhenacyclopropene rings
Implementation and performance of the artificial force induced reaction method in the GRRM17 program
Cover Image, Volume 40, Issue 25
A self-adaptive genetic algorithm-artificial neural network algorithm with leave-one-out cross validation for descriptor selection in QSAR study
GAMaterial - A genetic-algorithm software for material design and discovery
Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate
An improved force field (MM4) for saturated hydrocarbons
Single-ended transition state finding with the growing string method
Suitability of density functional methods for calculation of electrostatic properties
A Validation of Cluster Modeling in the Description of Matrix Isolation Spectroscopy
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method
An Empirical Boundary Potential for Water Droplet Simulations
Energetics of [Fe(NCH) 6 ] 2+ via CASPT2 calculations: A spin-crossover perspective
A reactive bond orbital investigation of the Diels-Alder reaction between 1, 3-butadiene and ethylene: Energy decomposition, state correlation diagram, and electron density analyses
The graphical representation of protein sequences based on the physicochemical properties and its applications
Systematic Gaussian basis-set limit using completeness-optimized primitive sets. A case for magnetic properties
Instanton rate constant calculations close to and above the crossover temperature
Molecular mechanics force-field development for amino acid zwitterions
SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies
Dissociation of hydrogen peroxide in water and methanol through a biased molecular dynamics investigation