yusuke1997/dblp-id-title huggingface dataset:
Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer
Partial atomic multipoles for internally consistent microelectrostatic calculations
Using support vector machine to predict beta- and gamma-turns in proteins
Characterization of chalcogen bonding interactions via an in-depth conceptual quantum chemical analysis
Substituent effects on the Bergman cyclization of (Z)-1, 5-hexadiyne-3-enes: a systematic computational study
A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level
Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure
Molecular dynamics simulation of organic glass formers: I. ortho-terphenyl and 1, 3, 5-tri-naphthyl benzene
Orbital energies and nuclear forces in DFT: Interpretation and validation
Water order profiles on phospholipid/cholesterol membrane bilayer surfaces
Erratum: Proton solvation in protic and aprotic solvents [J. Comput. Chem. 37, 2015 1082-1091]
Fault-tolerant quantum chemical calculations with improved machine-learning models
Thermodynamic Molecular Mechanics Force Field: Modified QCFF Program
Symmetrizer: Algorithmic determination of point groups in nearly symmetric molecules
PAPER - Accelerating parallel evaluations of ROCS
Ab initio parametrized MM3 force field for the metal-organic framework MOF-5
Cover Image, Volume 39, Issue 13
The para-didehydropyridine, para-didehydropyridinium, and related biradicals - a contribution to the chemistry of enediyne antitumor drugs
Electrophilicity index revisited
Efficient calculation of short-range Coulomb energies
Alanine boronic acid functionalized UiO-66 MOF as a nanoreactor for the conversion of CO 2 into formic acid
An improved nucleic acid parameter set for the GROMOS force field
DOIT: a program to calculate thermal rate constants and mode-specific tunneling splittings directly from quantum-chemical calculations
Modeling the interactions between polyoxometalates and their environment
Big data analysis of ab Initio molecular integrals in the neglect of diatomic differential overlap approximation
Rhodium catalyzed hydroformylation of olefins
A comparative analysis of symmetric diketopyrrolopyrrole-cored small conjugated molecules with aromatic flanks: From geometry to charge transport
A perturbation-based super-CI approach for the orbital optimization of a CASSCF wave function
Design of screening libraries biased for pharmaceutical discovery
Dynamics of flexible cycloalkanes. Ab initio and DFT study of the conformational energy hypersurface of cyclononane
Coordination chemistry of Zn2+ with Sal(ph)en ligands: Tetrahedral coordination or penta-coordination? a DFT analysis
A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues
Force-field parametrization based on radial and energy distribution functions
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery
SwissParam: A fast force field generation tool for small organic molecules
On hidden anisotropy of formally charged fragments
The Mechanism of Nitrite Reductase
QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)
Fast and accurate generation of ab initio quality atomic charges using nonparametric statistical regression
An algorithm to delineate and integrate topological basins in a three-dimensional quantum mechanical density function
Conformational splitting: A more powerful criterion for dead-end elimination
A rigorous and optimized strategy for the evaluation of the Boys function kernel in molecular electronic structure theory
sigma and pi contributions to the induced magnetic field: Indicators for the mobility of electrons in molecules
Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations
Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm
Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data
Accelerating VASP electronic structure calculations using graphic processing units
Distinguishing between keto-enol and acid-base forms of firefly oxyluciferin through calculation of excited-state equilibrium constants
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1
Electronic structure, magnetic properties, and mixed valence character of Ce 2 Ni 3 Si 5 from first principles calculations
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
Adsorption of benzene, fluorobenzene and meta-di-fluorobenzene on Cu(110): A computational study
Resonance revisited: A consideration of the calculation of cyclic conjugation energies
Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands
Adsorption of small molecules on helical gold nanorods: A relativistic density functional study
The Electronic Strucure of Weakley Bound Systems. I. Rare-Gas Bimolecular Cations
MoleculaRnetworks : An integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation
Modeling the structure-property relationships of nanoneedles: A journey toward nanomedicine
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations
Adsorption of single Cu atoms at differently stabilized polar ZnO surfaces: An ab initio study
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs
A reliable and efficient first principles-based method for predicting p K a values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and p K a values predicted more accurately?
A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility
Implementation of atomic basis set composed of 1s Gaussian and 1s Slater-type orbitals to carry out quantum mechanics molecular calculations
An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions
Bond indices in solids: Extended analytical model
Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm
Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations
Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations
Use of test particle calculations for the derivation of van der Waals parameters used in force fields
Predicting the activity of methoxyphenol derivatives antioxidants: II - Importance of the nature of the solvent on the mechanism, a DFT study
Principal Component Analysis of Dipeptides
Simple tests for density functional methods
Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects
Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations
Combined ab initio and density functional study of ring chain tautomerism in benzofurazan-1-oxide
Analyzing the electric response of molecular conductors using "electron deformation" orbitals and occupied-virtual electron transfer
Multiple pathways in conformational transitions of the alanine dipeptide: An application of dynamic importance sampling
NBO 6.0 : Natural bond orbital analysis program
Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantum
An appreciation
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules
Automated discovery of chemically reasonable elementary reaction steps
GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
A molecular mechanics force field for rhodium(I) carbonyl phosphine complexes and its application on the oxidative addition reactions of these complexes
A computational foray into the mechanism and catalysis of the adduct formation reaction of guanine with crotonaldehyde
A systematic study of minima in alanine dipeptide
A theoretical description of charge reorganization energies in molecular organic P-type semiconductors
Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains
Variation of atomic charges on proton transfer in strong hydrogen bonds: The case of anionic and neutral imidazole-acetate complexes
Understanding reactivity with Kohn-Sham molecular orbital theory: E2-SN2 mechanistic spectrum and other concepts
Comparison of ab initio and density functional methods for vibrational analysis of TeCl4
A semiempirical long-range corrected exchange correlation functional including a short-range Gaussian attenuation (LCgau-B97)
Geometrical and optical benchmarking of copper guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols
Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory
A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols
Rational Design of Electronically Labile Dinuclear Fe and Co complexes with 1, 10-Phenanthroline-5, 6-Diimine: A DFT study
MSINDO parameterization for third-row transition metals
DFT calculations on the electronic structures of BiOX (X = F, Cl, Br, I) photocatalysts with and without semicore Bi 5 d states
New ways to boost molecular dynamics simulations
Pressure tensor for electrostatic interaction calculated by fast multipole method with periodic boundary condition
Correlation energy, correlated electron density, and exchange-correlation potential in some spherically confined atoms
Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations
Ruthenium complexes bearing nile red chromophore and one of its derivative: Theoretical evaluation of PDT-related properties
Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations
On the O2 binding of Fe-porphyrin, Fe-porphycene, and Fe-corrphycene complexes
Quantum chemical topology at the spin-orbit configuration interaction level: Application to astatine compounds
Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase - A contribution from quantum chemical studies
Alder-ene reaction: Aromaticity and activation-strain analysis
High-level ab initio versus DFT calculations on (H2O2)2 and H2O2-H2O complexes as prototypes of multiple hydrogen bond systems
BAND NN: A Deep Learning Framework for Energy Prediction and Geometry Optimization of Organic Small Molecules
Hydrolysis of cyclic phosphates by ribonuclease A: A computational study using a simplified ab initio quantum model
Examination of the structures, energetics, and vibrational frequencies of small sulfur-containing prototypical dimers, (H2S)2 and H2O/H2S
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers
First-principles lattice dynamics calculations of the phase boundary between beta-Si 3 N 4 and gamma-Si 3 N 4 at elevated temperatures and pressures
The valence bond calculations for conjugated hydrocarbons having 24-28 -electrons
Toward deformation densities for intramolecular interactions without radical reference states using the fragment, atom, localized, delocalized, and interatomic (FALDI) charge density decomposition scheme
Force field for copper clusters and nanoparticles
Theoretical study of the reactions CF 3 CH 2 OCHF 2 + OH/Cl and its product radicals and parent ether(CH 3 CH 2 OCH 3 ) with OH
To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC
How to obtain statistically converged MM/GBSA results
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model
Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes
A dynamic lattice searching method for fast optimization of Lennard-Jones clusters
Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5
Mechanistic insights into N-Bromosuccinimide-promoted synthesis of imidazo[1, 2-a]pyridine in water: Reactivity mediated by substrates and solvent
Density functional theory of the Cu A -like Cu 2 S 2 diamond core in Cu 2II(NGuaS) 2 Cl 2
Theoretical study on selectivity trends in ( N -heterocyclic carbene)-Pd catalyzed mizoroki-heck reactions: Exploring density functionals methods and molecular models
Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure
A fast method for large-scale De Novo peptide and miniprotein structure prediction
Heuristic control of kinetic energy in dynamic reaction coordinate calculations
Molecular integrals over the gauge-including atomic orbitals. II. The Breit-Pauli interaction
A parallel distributed data CPHF algorithm for analytic Hessians
Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics
Physical Significance of Descriptors to Predict the Band Center of High-Entropy Nanoalloys
Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy
A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations
Diffuse functions in natural bond orbital analysis
Ab initio prediction of the structure and vibration-rotation spectroscopic properties of Na 2 OH and K 2 OH
Prediction of protein secondary structure content by artificial neural network
Weighted least square analysis method for free energy calculations
Comparative studies on group III σ-hole and π-hole interactions
A comparative computationally study about the defined m(II) pincer hydrogenation catalysts (m = fe, ru, os)
Probing the structural and electronic effects to stabilize nonplanar forms of thioamide derivatives: A computational study
An Improved Algorithm for the Analystical Computation of Solvent-Excluded Volume. The Treatment of Singulatities in Solvent-Accessible Surface Area and Volume Functions
First-Principles Calculations of Phonons and Thermodynamic Properties of Zr(Hf)S2-Based Nanotubes
First-principles investigation of A-B intersite charge transfer and correlated electrical and magnetic properties in BiCu 3 Fe 4 O 12
Reaction mechanisms of dissociative chemisorption of HI, I 2 , and CH 3 I on a magic cluster Al - 13
Review of Relativistic Effects in Chemistry Part A: Theory and Techniques
Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM
Fragment-based similarity searching with infinite color space
Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry
RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I
Solvent effects on glycine II. Water-assisted tautomerization
Enantiomerization of five-membered-heterocycle-embedded helicenes: A DFT study
Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface
Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3
Hexahalogenated and their mixed benzene derivatives as prototypes for the understanding of halogen···halogen intramolecular interactions: New insights from combined DFT, QTAIM-, and RDG-based NCI analyses
Spin-component-scaled double hybrids: An extensive search for the best fifth-rung functionals blending DFT and perturbation theory
Conformers of dehydrogenated glycine isomers
New insights on the bridge carbon-carbon bond in propellanes: A theoretical study based on the analysis of the electron localization function
Automatic molecular structure perception for the universal force field
Chemical bonding of HF, HCl, and H 2 O onto YF 3 surfaces: Quantification by first principles
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning
MBO(N)D: A multibody method for long-time molecular dynamics simulations
Trans-philicity (trans-influence/trans-effect) ladders for square planar platinum(II) complexes constructed by 35Cl NMR probe
Response to "comment on density functional theory study of 1, 2-dioxetanone decomposition in condensed phase"
Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution
A computational study on the capability of borane-cyclic boryl anion adducts to act as hydrogen atom donors
Direct-list algorithm for configuration interaction calculations
Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F . tularensis enoyl-ACP reductase (FabI)
Electron pairing and chemical bonds: Pair localization in ELF domains from the analysis of domain averaged Fermi holes
Toward force fields for atomistic simulations of iridium-containing complexes
Surface-enhanced Raman scattering of M2 -pyrazine-M2 (M = Cu, Ag, Au): Analysis by natural perturbation orbitals and density functional theory functional dependence
Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA
TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method
Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon-carbon interactions
Erratum: Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study
Mechanistic study of the Ni-catalyzed hydroalkylation of 1,3-dienes: The origins of regio- and enantioselectivities and a further rational design
The Role of Gold in Modifying the Structural Stabilities, Superhalogen Properties, and Double Aromaticity of Cyclic Carbon Clusters: Insights From AuC 20 - and AuC 20
MDLab: A molecular dynamics simulation prototyping environment
SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity
Electron localization function from density components
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
Highly accurate biomolecular electrostatics in continuum dielectric environments
An ab initio-based global potential energy surface for the SH3 system and full-dimensional state-to-state quantum dynamics study for the H2 + HS → H2S + H reaction
Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations
Electronic structure of iron(II)-porphyrin nitroxyl complexes: Molecular mechanism of fungal nitric oxide reductase (P450nor)
Ab Initio calculations of the stabilization energies of the conformational and the structural isomers of C3H7X where X = F, Cl, and Br
VESPA: A new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods
Gaussian Multipoles in Practice: Electrostatic Energeis for Intermolecular Potentials
DFT study of the mechanism of hydroamination of ethylene with ammonia catalyzed by diplatinum(II) complexes: Inner- or outer-sphere?
Gradients for configuration interaction energies with spin-orbit coupling in a semiempirical framework
Efficient "On-the-Fly" calculation of Raman Spectra from Ab-Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water
Boron based intramolecular heterocyclic frustrated Lewis pairs as organocatalysts for CO2 adsorption and activation
Fitting continuum wavefunctions with complex Gaussians: Computation of ionization cross sections
Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions
A critical comparison of search algorithms applied to the optimization of protein side-chain conformations
Identifying essential pairwise interactions in elastic network model using the alpha shape theory
Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase
A new algorithm to handle finite nuclear mass effects in electronic calculations: The ISOTOPE program
The adaptive hierarchical expansion of the kinetic energy operator
Estimating π binding energy of N-Heterocyclic carbenes: The role of polarization
Electrostatic Bonding Models: A Test on Group 1 and 2 Complexes with H 2 , NH 3 , H 2 S, Ph 3 , and Related Liquids
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
Four-component relativistic DFT calculations of 77 Se NMR chemical shifts: A gateway to a reliable computational scheme for the medium-sized organoselenium molecules
Development of a multipopulation parallel genetic algorithm for structure solution from powder diffraction data
Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis
Toward accurate relative energy predictions of the bioactive conformation of drugs
Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation
Theoretical study of Aun clusters (n = 1-5) deposited on a rutile TiO2 (110) slab, concerning structure and stability
Ab initio calculation of dynamic polarizability and dielectric constant of carbon and silicon cubic crystals
Statistical mechanical prediction of ligand perturbation to RNA secondary structure and application to riboswitches
The role of the long-range exchange corrections in the description of electron delocalization in aromatic species
Quantum chemical studies on structures and spectra of 2, 5-distyrylpyrazine (DSP) laser dye
An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides
Efficient compression of molecular dynamics trajectory files
Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ
Electron pairing and chemical bonds. Electron fluctuation and pair localization in ELF domains
CH/pi hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: An ab initio fragment molecular orbital study
Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules
Toward high-performance computational chemistry: II. A scalable self-consistent field program
The orientation and distance-dependence analysis of the electron transfer reactivity: An electron correlation level investigation of Mn2+(H2O)2/Mn3+(H2O)2 system
Effect of metal ions on radical type and proton-coupled electron transfer channel: sigma-Radical vs pi-radical and sigma-channel vs pi-channel in the imide units
Vibrational frequency scale factors for density functional theory and the polarization consistent basis sets
From explicit to implicit density functionals
Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory
The finite-size effect on the transport properties in edge-modified graphene nanoribbon-based molecular devices