yusuke1997/dblp-id-title huggingface dataset:
Theoretical studies on the structure and protonation of Cu(II) complexes of a series of tripodal aliphatic tetraamines: Good correlations with the experimental data
Exploration of Carbon Allotropes with Four-membered Ring Structures on Quantum Chemical Potential Energy Surfaces
Tuning the metal-ligand bond in the σ-complexes of stannylenes and azabenzenes
Stability, electronic, and optical properties of two-dimensional phosphoborane
Development of machine learning models based on molecular fingerprints for selection of small molecule inhibitors against JAK2 protein
Interaction between ions and substituted buckybowls: A comprehensive computational study
PSIXAS : A Psi4 plugin for efficient simulations of X-ray absorption spectra based on the transition-potential and Δ-Kohn-Sham method
Solvent effects on the NMR parameters of H2S and HCN
Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity
Anion substitution in zinc chalcogenides
Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids
A novel predictive model for formation enthalpies of Si and Ge hydrides with propane- and butane-like structures
TmoleX - A graphical user interface for TURBOMOLE
Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide
molSimplify: A toolkit for automating discovery in inorganic chemistry
Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective
MLatom: A program package for quantum chemical research assisted by machine learning
Incorporating the excluded solvent volume and surface charges for computing solvation free energy
Gas-phase and liquid-state properties of esters, nitriles, and nitro compounds with the OPLS-AA force field
Corrigendum: Ion strength limit of computed excess functions based on the linearized poisson-boltzmann equation
Ab initio ground-state potential energy function and vibration-rotation energy levels of imidogen, NH
Theoretical approach to the mechanism of reactions between halogen atoms and unsaturated hydrocarbons: The Cl + propene reaction
Probing the free energy landscape of the FBP28WW domain using multiple techniques
Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK
On the computation of frequency-dependent molecular magnetizabilities via dynamical charge and current electron densities
Chemical reactivity indexes in density functional theory
Using pseudo amino acid composition to predict protein structural class: Approached by incorporating 400 dipeptide components
Systematic errors in DFT calculations of haloalkane heats of formation
Molecular mechanics calculations on carbonyl compounds. II. Open-chain ketones
First-principles and molecular-dynamics study of structure and bonding in perovskite-type oxynitrides AB O 2 N ( A = Ca, Sr, Ba; B = Ta, Nb)
Temperature-dependent structural fluctuation and its effect on the electronic structure and charge transport in hybrid perovskite CH3NH3PbI3
Reaction of hypochlorous acid with imidazole: Formation of 2-chloro- and 2-oxoimidazoles
How reliable is DFT in predicting relative energies of polycyclic aromatic hydrocarbon isomers? comparison of functionals from different rungs of jacob's ladder
DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water
Semiautomatic sequence-specific assignment of proteins based on the tertiary structure - The program st2nmr
Force Field Calculations (MM3) on Glyoxal, Quinones, and Related Compounds
Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins
Exploring chemical reactivity of complex systems with path-based coordinates: Role of the distance metric
Focused grid-based resampling for protein docking and mapping
Assessment of density functional methods for reaction energetics: Iridium-catalyzed water oxidation as case study
Conformational distributions of helical perfluoroalkyl substances and impacts on stability
The MC-DFT approach including the SCS-MP2 energies to the new minnesota-type functionals
Automatic parameterization of force fields for liquids by simplex optimization
Importance of Madelung potential in quantum chemical modeling of ionic surfaces
Identification of thermostabilizing mutations for a membrane protein whose three-dimensional structure is unknown
Energy minimization of mixed argon-xenon microclusters using a genetic algorithm
Improving the predictive quality of time-dependent density functional theory calculations of the X-ray emission spectroscopy of organic molecules
A method to calculate the one-electron reduction potentials for nitroaromatic compounds based on gas-phase quantum mechanics
Indexing and mapping of proteins using a modified nonlinear Sammon projection
Accurate double many-body expansion potential energy surface by extrapolation to the complete basis set limit and dynamics calculations for ground state of NH 2
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside
Triacylglyceride melting point determination using coarse-grained molecular dynamics
Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD
An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfaces
Charge distributions for molecular dynamics simulations from self-consistent polarization method
Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators
Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function?
Efficient implementation of restricted active space configuration interaction with the hole and particle approximation
The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation
Theoretical Analysis of the Role of the Solvent on the Reaction on the Reaction Mechanismus: One-Step versus Two-Step Ketene-Imine Cycloaddition
A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine
Accurate ab initio potential energy surface, rovibrational energy levels and resonance interactions of triplet ( X ~ 3 B 1 ) methylene
First-principles calculations of the stability and electronic properties of the PbTiO 3 (110) polar surface
Density functional theory studies on molecular geometry, spectroscopy, HOMO-LUMO and reactivity descriptors of titanium(IV) and oxidozirconium(IV) complexes of phenylacetohydroxamic acid
Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study
A cascaded QSAR model for efficient prediction of overall power conversion efficiency of all-organic dye-sensitized solar cells
Extremely localized nonorthogonal orbitals by the pairing theorem
Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges
Guidelines for presentation of methodological choices in the publication of computational results: Ab initio electronic structure calculations
Comment on "A stationary-wave model of enzyme catalysis" by Carlo Canepa
Zinc oxide nanoclusters and their potential application as CH4 and CO2 gas sensors: Insight from DFT and TD-DFT
Fragmentation at sp2 carbon atoms in fragment molecular orbital method
Theoretical investigation of structure and electronic properties in Cisplatin-citrate complexes
Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers
Quantum mechanical assessment on the optical properties of capsanthin conformers
Solids modeled by ab initio crystal field methods, part 22: The Fock matrix transformed supermolecule model and the structure determination of D-erythronic acid-3, 4-carbonate
Derivation of fused-sphere molecular surfaces from properties of the electrostatic potential distribution
Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type
Accurate thermochemistry at affordable cost by means of an improved version of the JunChS-F12 model chemistry
Developing a variation of 3D-QSAR/MD method in drug design
Rearrangement of azirine intermediates to nitriles: Theoretical study of cleavage of 3, 4-dihydro-1aH-azirine[2, 3-c]pyrrol-2-one to cyanoketene-formaldimine complex
Towards improved FAIRness of the ThermoML Archive
Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities
Self-consistent field calculations using two-body density functionals for correlation energy component: I. Atomic systems
Noncovalent Complexes of the Noble-Gas Atoms: Analyzing the Transition from Physical to Chemical Interactions
A refined cavity construction algorithm for the conductor-like screening model
Is GVB-CI superior to CASSCF?
Bowl-shaped hydrocarbons related to C60
Transition metal dimers as potential molecular magnets: A challenge to computational chemistry
On the origin of photodynamic activity of hypericin and its iodine-containing derivatives
Quantitative structure-activity relationships for phenyl triazolinones of protoporphyrinogen oxidase inhibitors: A density functional theory study
Correlated motions analysis from molecular dynamics trajectories: Statistical accuracy on the determination of canonical correlation coefficients
Truncation of small matrix elements based on the Euclidean norm for blocked data structures
Intermolecular interactions of the extended recognition site of VIM-2 metallo-β-lactamase with 1, 2, 4-triazole-3-thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio QC
Free energy landscapes of prototropic tautomerism in pyridoxal 5′-phosphate schiff bases at the active site of an enzyme in aqueous medium
Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins
Reduction potential calculations of the Fe-S clusters in Thermus thermophilus respiratory complex I
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence quality of the lanthanides La-Lu for solid-state calculations
Thermodynamic Stability in Transition Metal-Hydrogen Dications: Potential Energy Curves, Spectroscopic Parameters, and Bonding for VH 2 +
A versatile AMBER-Gaussian QM/MM interface through PUPIL
Density functional theory study of the oxidation of methanol to formaldehyde on a hydrated vanadia cluster
Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation
Automated error control in divide-and-conquer self-consistent field calculations
Modeling the spectral properties of poly(x-phenylenediamine) conducting polymers using a combined TD-DFT and electrostatic embedding approach
Conformational analysis: A new approach by means of chemometrics
Visualizing dispersion interactions through the use of local orbital spaces
Alignment of molecules by the Monte Carlo optimization of molecular similarity indices
Molecular adsorption on coinage metal subnanoclusters: A DFT+D3 investigation
Multiple grid methods for classical molecular dynamics
Minimum sequence requirements for selective RNA-ligand binding: A molecular mechanics algorithm using molecular dynamics and free-energy techniques
Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium
Maintaining solvent accessible surface area under rotamer substitution for protein design
Comparison of two simulation methods to compute solvation free energies and partition coefficients
Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites
Implemenation of a Parallel Direct SCF Algorithm on Distributed Memory Computers
Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
Bonding and metastability for Group 12 dications
VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model
Testing the ONIOM G2R3 model against donor-acceptor dissociation energies of group 13-15 complexes: Accuracy comparable to CCSD(T)/aug-CC-pVTZ at a fraction of the resource cost
DFT study on the catalytic decomposition of hydrogen peroxide by iron complexes of nitrilotriacetate
Aromatic and magnetic properties in a series of heavy rare earth-doped Ge 6 cluster anions
Assessment of range-separated exchange functionals and nonempirical functional tuning for calculating the static second hyperpolarizabilities of streptocyanines
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
Ab initio SCF and Møller - plesset studies on hexafluorides of selenium and tellurium
What I like about Hückel theory
Phase stability and mechanical properties of rhenium borides by first-principles calculations
A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory
Recognition of tandem sialic acid residues by CD38: A theoretical study
Application of the thin-shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics
Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi
Alcohols, ethers, carbohydrates, and related compounds. III. The 1, 2-dimethoxyethane system
Ratio control variate method for efficiently determining high-dimensional model representations
Optimizing energy functions for protein-protein interface design
Fast docking using the CHARMM force field with EADock DSS
ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways
Theoretical study of lithium ionic conductors by electronic stress tensor density and electronic kinetic energy density
Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces
Modification of the integral isoconversional method to account for variation in the activation energy
A surface site interaction point methodology for macromolecules and huge molecular databases
Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)
Computation of determinant expansion coefficients within the graphically contracted function method
Ab initio molecular orbital study on structures and energetics of CH3O-(H2O)n and CH3S-(H2O)n in gas phase
Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model
A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family
Ab initio /GIAO-CCSD(T) 13 C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C 6 H13+ and C 7 H15+
Docking to heme proteins
Paired orbitals for different spins equations
Automated first-principles mapping for phase-change materials
Portably parallel construction of a configuration-interaction wave function from a matrix-product state using the Charm++ framework
GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water
Mechanistic details of metal-free cyclization reaction of organophosphorus oxide with alkynes mediated by 2, 6-lutidine and Tf2O
SurfKin: An ab initio kinetic code for modeling surface reactions
Optimized Slater-type basis sets for the elements 1-118
MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups
Multibaric-multithermal ensemble molecular dynamics simulations
Cover Image, Volume 40, Issue 9
Classical force field parameters for the heme prosthetic group of cytochrome c
Formation pathways of DMSO 2 in the addition channel of the OH-initiated DMS oxidation: A theoretical study
Fermi-Löwdin orbital self-interaction corrected density functional theory: Ionization potentials and enthalpies of formation
Nonlinear optical properties DFT calculations of polyacethylene and copolymers models substituted with aldimines chromophores as side chains
Computational predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models
Efficient Implementation of Cluster Expansion Models in Surface Kinetic Monte Carlo Simulations with Lateral Interactions: Subtraction Schemes, Supersites, and the Supercluster Contraction
Comparison of enzyme polarization of ligands and charge-transfer effects for dihydrofolate reductase using point-charge embedded ab initio quantum mechanical and linear-scaling semiempirical quantum mechanical methods
Relating Trp-Glu dipeptide fluorescence to molecular conformation: The role of the discrete chi 1 and chi 2 angles
Improving the Wang-Landau algorithm for polymers and proteins
FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
Electron group functions for the analysis of the electronic structures of molecules
Description of excited states in [Re(Imidazole)(CO) 3 (Phen)] + including solvent and spin-orbit coupling effects: Density functional theory versus multiconfigurational wavefunction approach
SODOCK: Swarm optimization for highly flexible protein-ligand docking
Atoms-in-molecules analysis for planewave DFT calculations - A numerical approach on a successively interpolated charge density grid
Calculations of solid-state 43 Ca NMR parameters: A comparison of periodic and cluster approaches and an evaluation of DFT functionals
Modulation of membrane permeability by carbon dioxide
Multireference calculations for ring inversion and double bond shifting in cyclooctatetraene
Cover Image, Volume 40, Issue 22
Continuum in the X-Z - Y weak bonds: Z= main group elements
Structure and stability of supramolecular crown ether complexes
Predicting the halogen-n (n = 3-6) synthons to form the "windmill" pattern bonding based on the halogen-bonded interactions
New strontium titanate polymorphs under high pressure
Solvatochromic shifts of Br 2 and I 2 in water cages of type 5 12 , 5 12 6 2 , 5 12 6 3 , and 5 12 6 4
A noniterative mean-field QM/MM-type approach with a linear response approximation toward an efficient free-energy evaluation
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins
Crystal structures and P-T phase diagrams of SrC 2 O 5 and BaC 2 O 5
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations
Can large active-space CASSCF calculation make sense to the reaction analysis of iron complex? A benchmark study of methane oxidation reaction by FeO+
Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities
Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield
Lantern-type dinickel complexes: An exploration of possibilities for nickel-nickel bonding with bridging bidentate ligands
Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes
On the geometry dependence of tuned-range separated hybrid functionals
New reaction simulator LUMMOX and its application for prediction of catalytic activities
Noncatalytic bromination of benzene: A combined computational and experimental study
Wavelet transform analysis of ab initio molecular dynamics simulation: Application to core-excitation dynamics of BF 3
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility
Internal dynamics of a globular protein in water
Estimating and modeling charge transfer from the SAPT induction energy
Role of the surface heterogeneity in adsorption of hydrogen ions on metal oxides: Theory and simulations
Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods
Interpretation and Automatic Generation of Fermi-Orbital Descriptors
Theoretical study of lanthanide-based in vivo luminescent probes for detecting hydrogen peroxide
NMR chemical shielding surface of N-Acetyl-N-Methylalaninamide: A density functional study
Drug efficiency indices for improvement of molecular docking scoring functions
Circular dichroic constrained structure optimization of homoalanine peptides
Quadruple chemical bonding in the diatomic anions TcN-, RuC-, RhB-, and PdBe-
SIMPRE: A software package to calculate crystal field parameters, energy levels, and magnetic properties on mononuclear lanthanoid complexes based on charge distributions
Carbon nanotube, graphene, nanowire, and molecule-based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory
Accelerating molecular dynamic simulation on the cell processor and Playstation 3
The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A
Protein structure prediction: Combining de novo modeling with sparse experimental data
Unraveling pnicogen bonding cooperativity: Insights from molecular electrostatic potential analysis
Complexes of 4-substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding
Geometric measures of large biomolecules: Surface, volume, and pockets
B, N-co-doped graphene-supported Ir and Pt clusters for methane activation and C─C coupling: A density functional theory study
Understanding the Role of Surface Oxygen in Hg Removal on Un-Doped and Mn/Fe-Doped CeO2(111)
Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics
Accurate relativistic adapted Gaussian basis sets for hydrogen through xenon without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models
Toward amino acid typing for proteins in FFLUX
Comprehensive Analysis of Deuterium Isotope Effects on Ionic H 3 O +... π Interactions Using Multi-Component Quantum Mechanics Methods
An object-oriented library for computational protein design
On the Origin of the Rotational Barrier in Ethane
Substitution effect on the geometry and electronic structure of the ferrocene
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing
How good is a Broyden-Fletcher-Goldfarb-Shanno-like update Hessian formula to locate transition structures? Specific reformulation of Broyden-Fletcher-Goldfarb-Shanno for optimizing saddle points
A stress tensor and QTAIM perspective on the substituent effects of biphenyl subjected to torsion
Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy
Uncovering Clar's aromatic -sextet rule in the Hubbard model using Maximum Probability Domain Partitions