yusuke1997/dblp-id-title huggingface dataset:
Multireference space without first solving the configuration interaction problem
Molecular polarizabilities and induced dipole moments in molecular mechanics
A First-Principle Study Investigating the Half-Metallic and Mechanical Properties of Double Halide Perovskites Rb 2 OsX 6 (X = cl, Br, and I) for Spintronic Applications
Modeling adsorbate-induced property changes of carbon nanotubes
Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime
The ring current model of the pentaprismane molecule
6-31G* basis set for third-row atoms
PyRETIS 2: An improbability drive for rare events
Reaction energy benchmarks of hydrocarbon combustion by Gaussian basis and plane wave basis approaches
Determination of Net Atomics Charges Using a Modified Partial Equalization or Orbital Electronegativity Method. IC. Application to Hypervalent Sulfur and Phosphorus-Containing Molecules
Construction of direct Z-Scheme photocatalysts for overall water splitting using two-dimensional van der waals heterojunctions of metal dichalcogenides
Analytical Approach to Very Large Benzenoid Polymers
A new Lamarckian genetic algorithm for flexible ligand-receptor docking
Molecular tailoring approach in conjunction with MP2 and Ri-MP2 codes: A comparison with fragment molecular orbital method
Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators
Erratum: Search of truncation of (N-1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via fock space coupled cluster approach
Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations
Reconsideration on hydrogen bond strengthening or cleavage of photoexcited coumarin 102 in aqueous solvent: A DFT/TDDFT study
The Influence of the Solvation on the Bonding of Molecular Complexes of Diatomic Halogens With Nitrogen-Containing Donors and Their Stability With Respect to the Heterolytic Halogen-Halogen Bond Splitting
Intramolecular electronic communication in a dimethylaminoazobenzene-fullerene C 60 dyad: An experimental and TD-DFT study
Theoretical rationalization for reduced charge recombination in bulky carbazole-based sensitizers in solar cells
The parameterization and validation of generalized born models using the pairwise descreening approximation
Docking small ligands in flexible binding sites
The ENUF method - Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application
Organometallic chemistry of fullerenes: 2- and 5-()complexes
In silico prediction of drug solubility: 4. Will simple potentials suffice?
SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation
Effective atomic charges in alanine dipeptide
Semiempirical configuration interaction calculations for ru-centered dyes
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water
QMCube (QM3): An all-purpose suite for multiscale QM/MM calculations
Portable, parallel transformation: Distributed-Memory approach
Second-order state-specific multireference Møller Plesset perturbation theory: Application to energy surfaces of diimide, ethylene, butadiene, and cyclobutadiene
Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model
Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations
A general, recursive, and open-ended response code
Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach
Use of exchange maximization to generate starting vectors for self-consistent field calculations on metal cluster/adsorbate systems
Development of Coarse-Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm
PVM-AMBER: A Parallel Implementation of the AMBER Molecular Mechanics Package for Workstation Clusters
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions
Editors' note
An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase
Ab initio coupled Hartree-Fock study of the Bloembergen effect on paramagnetic systems: SiH3 radical
The performance of low-cost commercial cloud computing as an alternative in computational chemistry
Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem
Electron correlation: The many-body problem at the heart of chemistry
Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study
Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations
Method for free-energy calculations using iterative techniques
Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study
A local interpolation scheme using no derivatives in potential sampling: Application to O(1D) + H2 system
Structures and Stabilization Energies of Methyl Anions with Main Group Stubstituens from the First Five Periods
Source function and plane waves: Toward complete bader analysis
Ability of fullerenes to act as 6 ligands in transition metal complexes. A comparative PM3(tm)-density functional theory study
Searching new structures of beryllium-doped in small-sized magnesium clusters: Be2MgnQ (Q = 0, -1; n = 1-11) clusters DFT study
Valence bond theory for chemical dynamics
BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system
Quantum chemical characterization of the cytosine: 2-Aminopurine base pair
Interaction of graphene with antipsychotic drugs: Is there any charge transfer process?
A computational study of photochemical isomerization reactions of thiophenes
QuanPol: A full spectrum and seamless QM/MM program
Non-Born-Oppenheimer dynamics calculations using the coherent switching with decay of mixing method
Density functional theory study of the free and tetraprotonated spheroidal macrotricyclic ligands and the complexes with halide anions: F - , Cl - , Br -
Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations
Electronic couplings for singlet fission: Orbital choice and extrapolation to the complete basis set limit
Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions
PharmRF: A machine-learning scoring function to identify the best protein-ligand complexes for structure-based pharmacophore screening with high enrichments
Comment on "Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory"
Effects of multidimensional tunneling in the kinetics of hydrogen abstraction reactions of O (3P) with CH3OCHO
Use of locally dense basis sets for nuclear magnetic resonance shielding calculations
Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR
Chemical Bond Overlap Descriptors From Multiconfiguration Wavefunctions
MATCH: An atom-typing toolset for molecular mechanics force fields
Comment on the validation of continuum electrostatics models
irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules - a GPU solver using the fast multipole method and statistical thermodynamics
Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
Gradient gravitational search: An efficient metaheuristic algorithm for global optimization
Ensemble QSAR: A QSAR method based on conformational ensembles and metric descriptors
A generator of protein folding kinetics states for the diffusion-collision model
New paint and a new engine
MNDO-PM3 study on model cytochrome P450-mediated desulfuration of thiophosphoryl trifluoride, trimethylphosphine sulfide, and trimethyl phosphorothionate
Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations
Effect of Na + , Mg 2+ , and Zn 2+ chlorides on the structural and thermodynamic properties of water/ n -heptane interfaces
An Improved Molecular Modeling Method for the Prediction of Enantioselectivity
INDO calculations of small copper clusters and CO adsorbed on copper(100) surfaces
Finite element approach to the electrostatics of macromolecules with arbitrary geometries
Control of delocalization and structural changes by means of an electric field
Interplay between halogen bond and lithium bond in MCN-LiCN-XCCH (M = H, Li, and Na; X = Cl, Br, and I) complex: The enhancement of halogen bond by a lithium bond
Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination
The role of radial nodes of atomic orbitals for chemical bonding and the periodic table
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
Can the hybrid meta GGA and DFT-D methods describe the stacking interactions in conjugated polymers?
High-throughput molecular simulations of SARS-CoV-2 receptor binding domain mutants quantify correlations between dynamic fluctuations and protein expression
Computational alanine scanning mutagenesis - An improved methodological approach
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides
A combined semiempirical-DFT study of oligomers within the finite-chain approximation, evolution from oligomers to polymers
S N 1-S N 2 and S N 2-S N 3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides
Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives
Electronic structure of Li 1,2,3 +,0,- and nature of the bonding in Li 2,3 +,0,-
Aggregation propensities of proteins with varying degrees of disorder
Relativistic adapted Gaussian basis sets free of variational prolapse of small and medium size for cesium through radon
RI-MP3 calculations of biomolecules based on the fragment molecular orbital method
Molecular mechanics models for the image charge, a comment on "including image charge effects in the molecular dynamics simulations of molecules on metal surfaces"
An enhanced Monte Carlo outlier detection method
Cluster expansion models for flexible-backbone protein energetics
Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices
An improved Poisson-Nernst-Planck ion channel model and numerical studies on effects of boundary conditions, membrane charges, and bulk concentrations
Photophysical properties of donor (D)-acceptor (A)-donor (D) diketopyrrolopyrrole (A) systems as donors for applications to organic electronic devices
Evaluation of density functional theory for a large and diverse set of organic and inorganic equilibrium structures
Molecules for materials: Germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeHn- (n = 0-4) and Ge2Hn/Ge2Hn- (n = 0-6)
Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy-based fragmentation method
Torque and atomic forces for Cartesian tensor atomic multipoles with an application to crystal unit cell optimization
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
The statistical significance of selected sense-antisense peptide interactions
Comparison of electron density properties in frozen and relaxed electronic distributions
A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets
Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities
Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations
Benchmark study of popular density functionals for calculating binding energies of three-center two-electron bonds
Localized basis orbitals: Minimization of 2-electron integrals array and orthonormality of basis set
Accurate dynamical structure factors from ab initio lattice dynamics: The case of crystalline silicon
Quantitative structure-property relationship modeling of Grätzel solar cell dyes
Coarse-grained model of nucleic acid bases
Phage-like packing structures with mean field sequence dependence
Optimization and application of lithium parameters for PM3
Normalization of the Fox - Goodwin algorithm to calculate scattering matrices in an adiabatic basis at low and high collision energies
Micellar polymerization: Computer simulations by dissipative particle dynamics
Natural resonance theory. I. General formalism
A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank
A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field
Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method
Interactions of the "piano-stool" [ruthenium(II) (eta 6 -arene)(en)CL] + complexes with water and nucleobases; ab initio and DFT study
σ-Hole intermolecular interactions between carbon oxides and dihalogens: Ab-initio investigations
Techniques for geometry optimization: A comparison of cartesian and natural internal coordinates
Computational alanine scanning of the 1: 1 human growth hormone-receptor complex
A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions
Quantum dynamics of vibration-vibration energy transfer for vibrationally excited HF colliding with H2
Using fractal to solve the multiple minima problem in molecular mechanics calculation
Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters
Atoms in molecules interpretation of the anomeric effect in the O-C-O unit
Atomic forces for geometry-dependent point multipole and Gaussian multipole models
An analytical bond-order potential for carbon
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis
PyUNIxMD: A Python-based excited state molecular dynamics package
Description of noncovalent interactions involving π-system with high precision: An assessment of RPA, MP2, and DFT-D methods
Conformation and Reactivity of a-Oxo-Ketenes: Ab Initio and Semiempirical /AM1, PM3) Calculations
Computational tool to model the packing of polycyclic chains: Structural analysis of amorphous polythiophene
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations
Using the fast fourier transform in binding free energy calculations
Performance of density functionals for modeling vapor liquid equilibria of CO 2 and SO 2
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure
A mountaineering strategy to excited states: Accurate vertical transition energies and benchmarks for substituted benzenes
Comparing the performance of TD-DFT and SAC-CI methods in the description of excited states potential energy surfaces: An excited state proton transfer reaction as case study
Binding energies of five molecular pincers calculated by explicit and implicit solvent models
Impact of Mn on the solution enthalpy of hydrogen in austenitic Fe-Mn alloys: A first-principles study
Theoretical study on the OH + CH 3 NHC(O)OCH 3 reaction
Systematic study of the boundary composition in Poisson Boltzmann calculations
Testing standard basis sets for direct ionizations: H + + H at E Lab = 0.1-100 keV
Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations
Estimating reaction parameters in mechanism-enabled population balance models of nanoparticle size distributions: A Bayesian inverse problem approach
GalaxyDock2: Protein-ligand docking using beta-complex and global optimization
Predicted solution structure of zymogen human coagulation FVII
Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids
Windock: Structure-based drug discovery on windows-based PCs
Quantum effects on the stability of the He5I2 van der Waals conformers
Conformational ensembles and sampled energy landscapes: Analysis and comparison
Exploration of potential inhibitors for tuberculosis via structure-based drug design, molecular docking, and molecular dynamics simulation studies
Mechanisms of norbornadiene dimerization to Binor-S using cationic Co I , Rh I , and Ir I catalysts
8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: A molecular dynamics study
On the ion-pair dissociation mechanisms in the small NaCl·(H2O)6 cluster: A perspective from reaction path search calculations
Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean
Conformational dependence of the electrostatic potential-derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution
Vibrational computations beyond the harmonic approximation: Performances of the B3LYP density functional for semirigid molecules
Monte Carlo Study of Lipid Membranes: Simulation of Diparmitoyl-phosphatidylcholine Bilayers in Gel and Liquid-Crystalline Phases
Investigation of water substitution at RuII complexes by conceptual density function theory approach
A new method for empirical force field calculations on localized and delocalized carbocations
Is tetrahedral H 4 2+ a minimum? Anomalous behavior of popular basis sets with the standard p exponents on hydrogen
Nucleus-independent chemical shift analysis of the electronic states of the (CO) 4 , (CS) 4 , and (CSe) 4 molecules
Electronic and vibrational linear and nonlinear polarizabilities of Li@C 60 and [Li@C 60 ] +
Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach
DIRECT-ID: An automated method to identify and quantify conformational variations - application to β 2 -adrenergic GPCR
Topological analysis of chemical bonding in the layered FePSe3 upon pressure-induced phase transitions
Model of twelve properties of a set of organic solvents with graph-theoretical and/or experimental parameters
Transformation of organic sulfur and its functional groups in nantong and laigang coal under microwave irradiation
Quality of correlating functions generated from commonly used basis sets
Increase Docking Score Screening Power by Simple Fusion With CNNscore
Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD
Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect
GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics
Molecules under external electric field: On the changes in the electronic structure and validity limits of the theoretical predictions
Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype
Efficient extraction of free energy profiles from nonequilibrium experiments
Computational study of epoxy-amine reactions
Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study
Multireference perturbation theory with optimized partitioning. II. Applications to molecular systems
The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems
Adapted Gaussian basis sets for atoms Cs to Lr based on the generator coordinate Hartree-Fock method
One- and multidimensional conformational free energy simulations
Insights into the mechanism of [3+2] cycloaddition reactions between N-benzyl fluoro nitrone and maleimides, its selectivity and solvent effects
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin
Comparison of group 14 elements in sp3 and sp2 environment by fragment structure energy analysis
Multipolar electrostatics for proteins: Atom-atom electrostatic energies in crambin
Improving ligand-ranking of AutoDock Vina by changing the empirical parameters
A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour
Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase
Elongation method for electronic structure calculations of random DNA sequences
Molecular mechanics study of transannular amine-ketone (NC˭O) interaction in medium-sized heterocycles
Systematic derivation of implicit solvent models for the study of polymer collapse
Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer
Solving the Finite-Difference, Nonlinear, Poisson-Boltzmann Equation under a Linear Approach
Vectorizable algorithm for green function and many-body perturbation methods
Two-electron integral evaluation on the graphics processor unit
Polarization energies in the fragment molecular orbital method
Halogen bonds with benzene: An assessment of DFT functionals
Range-separated density functional theory using multiresolution analysis and quantum computing
Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals
Normal-mode driven exploration of protein domain motions
Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack
Assessment of the OLYP and O3LYP density functionals for first-row transition metals
Photochemistry of CH3Mn(CO)5: A multiconfigurational ab initio study
Accurate quantum-chemical description of gold complexes with pyridine and its derivatives
CORAL: Quantitative structure-activity relationship models for estimating toxicity of organic compounds in rats
Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field
Chemical structures from the analysis of domain-averaged Fermi holes: Multiple metalmetal bonding in transition metal compounds
A hybrid approach combining energy density analysis with the interaction energy decomposition method