yusuke1997/dblp-id-title huggingface dataset:
A charge-scaling implementation of the variational electrostatic projection method
Comparison of the FeO2+ and FeS2+ complexes in the cyanide and isocyanide ligand environment for methane hydroxylation
High-spin versus broken symmetry - Effect of DFT spin density representation on the geometries of three diiron (III) model compounds
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
New basis sets for the evaluation of interaction-induced electric properties in hydrogen-bonded complexes
DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
Cover Image, Volume 40, Issue 16
Preconditioners for Distance Matrix Algorithms
B-spline method for energy minimization in grid-based molecular mechanics calculations
Nonlinear mapping of massive data sets by fuzzy clustering and neural networks
Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space
New combining rules for rare gas van der waals parameters
SVMtm: Support vector machines to predict transmembrane segments
A combined ab initio and Franck-Condon factor simulation study on the photodetachment spectrum of ScO 2 -
Computing ionization states of proteins with a detailed charge model
JACOB: An enterprise framework for computational chemistry
ePharmer: An integrated and graphical software for pharmacophore-based virtual screening
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures
An enantioselective study of β-cyclodextrin and ionic liquid-β-cyclodextrin towards propranolol enantiomers by molecular dynamic simulations
Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere
Relativistic Gaussian functions for atoms by fitting numerical results with adaptive nonlinear least-square algorithm
Coordination of noble gases by alkali-metal-like superatom cation Be 3 B +
Importance of model size in quantum mechanical studies of DNA intercalation
DFT insights into LaFeO 3 with Mn substitution: A promising path to energy-efficient magneto-optical applications
Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected and BSSE-corrected potential energy hypersurfaces
Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions
Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O H2O + OH
Monte Carlo simulations of biomolecules: The MC module in CHARMM
The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides
Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion
On the formation of smaller p -block endohedral fullerenes: Bonding analysis in the E@C 20 (E = Si, Ge, Sn, Pb) series from relativistic DFT calculations
TS-tools: Rapid and automated localization of transition states based on a textual reaction SMILES input
Reformulating the entropic contribution in molecular docking scoring functions
Bonding character of intermediates in on-surface Ullmann reactions revealed with energy decomposition analysis
On the efficiency of VBSCF algorithms, a comment on "An efficient algorithm for energy gradients and orbital optimization in valence bond theory"
Direct CI method in restricted configuration spaces
A Rapid Method for Calculating Derivatives of Solvent Accessible Surface Areas of Molecules
Host-guest interactions between octa acid and cations/nucleobases
Prodock: Software package for protein modeling and docking
Assessment of the parallelization approach of d2_cluster for high-performance sequence clustering
From Antipsychotic to Neuroprotective: Computational Repurposing of Fluspirilene as a Potential PDE5 Inhibitor for Alzheimer's Disease
Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems
MM3 parameterization for the BN dative bond
Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS-CoV-2 pathway
The reliability of DFT methods to predict electronic structures and minimum energy crossing point for [Fe IV O](OH) 2 models: A comparison study with MCQDPT method
Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics
Describing electron correlation effects in the framework of the elongation method - Elongation-MP2: Formalism, implementation and efficiency
Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective
A path integral molecular dynamics study on intermolecular hydrogen bond of acetic acid-arsenic acid anion and acetic acid-phosphoric acid anion clusters
Consistent gaussian basis sets of Triple-Zeta valence with polarization quality for solid-State Calculations
Dispersion interactions between neighboring Bi atoms in (BiH3)2 and Te(BiR2)2
Photodissociation and formation of an ion-pair in CH 2 FCl (HCFC-31)
The behavior of benzene confined in a single wall carbon nanotube
Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide
On the Calculation of Ab Initio Quantum Molecular Similarities for Large Systems: Fitting the Electron Density
A multilayered approach to approximating solute polarization
Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations
Improved convergence in dual-topology free energy calculations through use of harmonic restraints
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator
The Iterative Protein Redesign and Optimization (IPRO) suite of programs
Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules
Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations
Molecular conformations from distance matrices
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units
Finding optimal finite field strengths allowing for a maximum of precision in the calculation of polarizabilities and hyperpolarizabilities
On-the-path random walk sampling for efficient optimization of minimum free-energy path
New energy terms for reduced protein models implemented in an off-lattice force field
Possible molecular hydrogen formation mediated by the radical cations of anthracene and pyrene
Ab Initio Calculation of Molar Volumes: Compariso with Experiment and Use in Solvation Models
Computation of cavity shapes, sizes, and plasticities
A new unconventional halogen bond C-X--H-M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study
Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands
Franck-Condon simulation of the photoelectron spectrum of AsCl 2 and the photodetachment spectrum of AsCl
Molecular mechanics (MM3) parameterization for oxocarbenium ions
Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms
A theoretical study of fullerene-ferrocene hybrids
Towards excitation energies and (hyper)polarizability calculations of large molecules. Application of parallelization and linear scaling techniques to time-dependent density functional response theory
Molecular mechanics (MM4) calculations on conjugated hydrocarbons
Ab initio conformational analysis of cyclooctane molecule
Geometric similarity between protein-RNA interfaces
A dispersion-corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone-wales defects
Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle
Nature of bonding in the sulfuryl group
Interaction between Carbon Dioxide and Naphthalene: A Molecular Modeling Approach
Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess
Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids: A quantitative study
Non long-range corrected density functionals incorrectly describe the intensity of the CH stretching band in polycyclic aromatic hydrocarbons
Thermal Effect on Positive Patterned Self-Assembled Monolayer Grown from a Droplet of Alkanethiol
He 2 ++ molecular ion in a strong time-dependent magnetic field: A current-density functional study
Conformation Energy around the N(sp 3 ) - O Single Bond
Porting ONETEP to graphical processing unit-based coprocessors. 1. FFT box operations
Re-evaluation of the bond length-bond strength rule: The stronger bond is not always the shorter bond
Relativistic energy-consistent pseudopotentials - Recent developments
Theoretical study on the mechanism of the 3CH2 + NO2 reaction
Polarizable model potential function for nucleic acid bases
Gilbert N. Lewis and the chemical bond: The electron pair and the octet rule from 1916 to the present day
Radial quadrature for multiexponential integrands
Anisotropy of Atom-Atom Repulsions
A kinetics study of ligand substitution reaction on dinuclear platinum complexes: Stochastic versus deterministic approach
Force field parameters for the simulation of modified histone tails
First-principles prediction on electronic and magnetic properties of hydrogenated AlN nanosheets
Ab initio molecular orbital study of OH-(H2O)n in the gas phase
Features of CPB: A Poisson-Boltzmann solver that uses an adaptive cartesian grid
Rotational barrier in phosphatriafulvene: An MCSCF study
The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N 2 -N 2 collisions
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field" Journal of Computational Chemistry(2004) 25(9) 1157-1174
π-π interaction of quinacridone derivatives
FALDI-based criterion for and the origin of an electron density bridge with an associated (3, -1) critical point on Bader's molecular graph
Screening seven-electron boron-centered radicals for dinitrogen activation
Solvation properties of N -acetyl-β-glucosamine: Molecular dynamics study incorporating electrostatic polarization
On the applicability of density functional theory to manganese-based complexes with catalytic activity toward water oxidation
New QM/MM implementation of the DFTB3 method in the gromacs package
Connectivity and binding-site recognition: Applications relevant to drug design
Spin density accuracy and distribution in azido Cu(II) complexes: A source function analysis
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
Assessing the attractive/repulsive force balance in axial cyclohexane C-H ax ···Y ax contacts: A combined computational analysis in monosubstituted cyclohexanes
The vertical excitation energies and a lifetime of the two lowest singlet excited states of the conjugated polyenes from C2 to C22: Ab initio, DFT, and semiclassical MNDO-MD simulations
A force-field description of short-range repulsions for high density alkane molecular dynamics simulations
Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm
Exchange-correlation effects in interatomic energies for pure density functionals and their application to the molecular energy prediction
Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin
Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution
Model parameters for simulation of physiological lipids
Divide-and-conquer, pattern matching, and relaxation methods in interpretation of 2-D NMR spectra of polypeptides
1 H and 13 C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory
Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems
Hydrogen-hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods
Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges
Quantum chemical investigation of electronic transitions of mitorubrin azaphilones
Real-time time-dependent density functional theory using density fitting and the continuous fast multipole method
thermocalc - A poor man's approach to computational thermochemistry
Hydrogen bonding and solvatochromatic shift of the lowest 1(n, *) excitation of s-tetrazine in its hydrated clusters and dilute solutions
Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory
AMBER force-field parameters for guanosine triphosphate and its imido and methylene analogs
Evaluation of a new series of pyrazole derivatives as a potent epidermal growth factor receptor inhibitory activity: QSAR modeling using quantum-chemical descriptors
Cover Image, Volume 41, Issue 22
Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex
Globally convergent computation of chemical equilibrium composition
Full rate constant matrix contraction method for obtaining branching ratio of unimolecular decomposition
Continuous symmetry measures for complex symmetry group
Ab initio multireference calculation of electronic spectra of the osmium complexes, [Os(bpy) 3 ] 2 + and [Os(phen) 3 ] 2 +
Chemical reactivity predictions: Use of data mining techniques for analyzing regioselective azidolysis of epoxides
The parallel implementation of configuration-selecting multireference configuration interaction method
Relativistic effects in HgHe and HgXe CCSD(T) ground state potential curves. Low-density viscosity simulations of Hg: Xe mixture
A semiempirical free energy force field with charge-based desolvation
Sodium chloride's effect on self-assembly of diphenylalanine bilayer
An electron repulsion integral compression algorithm
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi
Computational gibberellin-binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor
Stability of functionalized corannulene cations [R-C 20 H 10 ] + : An influence of the nature of R-Group
A new algorithm for construction of coarse-grained sites of large biomolecules
Comparison of the capillary wave method and pressure tensor route for calculation of interfacial tension in molecular dynamics simulations
Accurate Ab initio potential energy surface and vibration-rotation energy levels of hydrogen peroxide
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles
Direct determination of discrete harmonic bath parameters from molecular dynamics simulations
The bonding picture in hypervalent XF 3 (X = Cl, Br, I, At) fluorides revisited with quantum chemical topology
Distributed data parallel coupled-cluster algorithm: Application to the 2-hydroxypyridine/2-pyridone tautomerism
Revisiting the thermochemistry of chlorine fluorides
Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach
Statistical analysis of electronic excitation processes: Spatial location, compactness, charge transfer, and electron-hole correlation
Molecular dynamics of minimal B-DNA
Extending Hirshfeld-I to bulk and periodic materials
A universal scale of aromaticity for pi-organic compounds
Self-Similarity of solvent-accessible surfaces of biological and synthetical macromolecules
Property-oriented basis sets for computation of atomization energies
Geometry optimization using generalized, chemically meaningful constraints
Characterization of bonding modes in metal complexes through electron density cross-sections
Theoretical study on the reaction CX 3 + SiH(CH 3 ) 3 (X = H, F)
Conformational and energetic properties of the ammonia dimer - comparison of post-Hartree - Fock and density functional methods
Evaluation of reactivity for nitroxide radical trapping by correlation analysis using steric substituent parameter (S)
Pareto optimization in computational protein design with multiple objectives
Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
18-electron rule and the 3c/4e hyperbonding saturation limit
An ab initio molecular orbital study of intramolecular hydrogen bonding in ortho-substituted arylamides: Implications for the parameterization of molecular mechanics force fields
Expedited analysis of DFT outputs: Introducing moanalyzer
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Metallic monoboronyl compounds: Prediction of their structure and comparison with the cyanide analogues
Ground-state potential energy functions and vibration-rotation energy levels of beryllium lithium and its cation
Vibrational center-ligand couplings in transition metal complexes
Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids
The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY)
cclib: A library for package-independent computational chemistry algorithms
Stabilization of group 14 elements E = C, Si, Ge by hetero-bileptic ligands cAAC, MCOn with push-pull mechanism
A QTAIM-based energy partitioning for understanding the physical origin of conformational preferences: Application to the Z effect in O=C-X-R and related units
Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions
Theoretical investigations of NMR chemical shifts and reactivities of oxovanadium(v) compounds
Efficient parameterization of torsional terms for force fields
Quantum chemical exploration of formaldehyde clusters (H2CO)n (n = 2-4)
A Ring-Bracing Approach to Computer-Assisted Ligand Design
Data-driven and constrained optimization of semi-local exchange and nonlocal correlation functionals for materials and surface chemistry
Efficiency of perturbation-selection and its orbital dependence in the SAC-CI calculations for valence excitations of medium-size molecules
Correlated response calculations of the spin-orbit interaction contribution to nuclear spin-spin couplings
Cycloaddition reactions via " on water " protocol reactions: A density functional theory study
Theoretical description of solvent effects on fluorescence spectra of bulky charge transfer compound DMA-DMPP
Path-integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher-order trotter factorizations
Isothiirane: A Molecular Structure Dilemma Resolved
Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of metal-organic frameworks
New vibrational self-consistent field program for large molecules
Atom-atom partitioning of total (super)molecular energy: The hidden terms of classical force fields
Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
Thermodynamics and kinetics of initial gas phase reactions in chemical vapor deposition of titanium nitride. Theoretical study of TiCl4 ammonolysis
Multiple classifier integration for the prediction of protein structural classes
Theoretical simulation of CO 2 capture in organic cage impregnated with polyoxometalates
Enhanced stability of the model mini-protein in amino acid ionic liquids and their aqueous solutions
Towards protein folding with evolutionary techniques
Hartree-Fock exchange fitting basis sets for H to Rn
Incorporating structural characteristics for identification of protein methylation sites
Multicanonical parallel simulations of proteins with continuous potentials
Semiempirical implementation of strictly localized geminals for analysis of molecular electronic structure
Atomic transferability within the exchange-correlation density
Martini coarse-grained model for polyethylenimine
Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers
The density polarization reveals directions of electron displacements due to the substituent effect: Analysis performed on a metal-organic Mo-Oxo catalyst
A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N‒H···O˭C and C‒H···O˭C hydrogen-bonded complexes
Partial hessian fitting for determining force constant parameters in molecular mechanics
Systematic and statistical error in histogram-based free energy calculations
Theoretical study of the microhydration of mononuclear and dinuclear uranium(VI) species derived from solvolysis of uranyl nitrate in water
Multistate active spaces from local CAS-SCF molecular orbitals: The photodissociation of HFCO as an example
Application of the Shape Group Method to Conformation Processes: Shape and Conjugation Changes in the Conformers of 2-Phenyl Pyrimidine
Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins
CO bonding in hexa- and pentacoordinate carboxy-neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study
Theoretical study on the ring-opening isomerization reaction mechanism of the ring isomers of N 8 H 8
Origin of intrinsic 3 10 -helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field
Time-dependent density functional theory study of the optical properties of tetrahedral aluminum nanoparticles
Parallelization of a multiconfigurational perturbation theory
Performance evaluation of the zero-multipole summation method in modern molecular dynamics software
Applicability of the WKB Method in Asymmetric Double Wells with Degenerate and Nondegenerate Minima
Hyperconjugative effects on carbon - Carbon bond lengths in molecular mechanics (MM4)
How does a hydrocarbon staple affect peptide hydrophobicity?
Generalized linear response method: Application to hydration free energy calculations
Producing chemically accurate atomic Gaussian process regression models by active learning for molecular simulation
Predicting stability limits for pure and doped dicationic noble gas clusters undergoing coulomb explosion: A parallel tempering based study
A fast parallel clustering algorithm for molecular simulation trajectories
Application of ab initio theory to QSAR study of 1, 4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures
LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm
Bridging gold: B-Au-B three-center-two-electron bonds in electron-deficient B 2 Au n -/0 ( n = 1, 3, 5) and mixed analogues