yusuke1997/dblp-id-title huggingface dataset:
Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water
Thermodynamic calculations for molecules with asymmetric internal rotors - application to 1, 3-butadiene
Interpretation of molecular electron transport in ab initio many-electron framework incorporating zero-point nuclear motion effects
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies
On the aromaticity and stability of benzynes in the ground and lowest-lying triplet excited states
Molecular dynamics simulation studies of liquid acetonitrile: New six-site model
A theoretical study of topomerization of imine systems: Inversion, rotation or mixed mechanisms?
Revised model core potentials of s-block elements
Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects
Are Ba 11 Cd 6 Sb 12 and Sr 11 Cd 6 Sb 12 Zintl phases or not? A density-functional theory study
A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
Electron density analysis of large (molecular and periodic) systems: A parallel implementation
Implementation of pi-pi interactions in molecular dynamics simulation
RASPT2 study of the valence excited states of an iron-porphyrin-carbonyl model complex
Theoretical study on the [Si, C, N, O] potential energy surface
Application of the Multple Computer Automated Structure Evaluation Methodology to a Qantitative Structure-Activity Relationship Study of Acidity
Controlling the strong field fragmentation of ClCHO+ using two laser pulses -an ab initio molecular dynamics simulation
Interactions between chlorinated dioxins and a positively charged molecular probe: New molecular interaction potential
Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs
Singlet/triplet exciton dissociation and charge recombination in donor-acceptor ThQs-C60/PDIxCN2 complexes
Ab Initio Orbital Studies of Nonidentity Allyl Transfer Reactions
New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics
Interaction energy of Cl 2 and Br 2 with H 2 O: Exchange, dispersion and density the crucial ingredients
Chloride ion conduction without water coordination in the pore of ClC protein
p K A in proteins solving the Poisson-Boltzmann equation with finite elements
Hash Codes for the Indentification and Classification of Molecular Structure Elements
Density functional theory study of mechanism of epoxy-carboxylic acid curing reaction
Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor
Efficiency of random search procedures along the silicon cluster series: Si n ( n = 5-10, 15, and 20)
Efficient representation of the linear density-density response function
Density functional studies of cation-water complexes
Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers
Identification of novel inhibitors of SARS-CoV-2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation
libKEDF: An accelerated library of kinetic energy density functionals
Electrostatic polarization is critical for the strong binding in streptavidin-biotin system
PathOpt - A global transition state search approach: Outline of algorithm
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study
Specific interactions between lactose repressor protein and DNA affected by ligand binding: Ab initio molecular orbital calculations
Decision Trees for the Recognition of Metal-Centered Chirality in Coordination Complexes
Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver
Rapid evaluation of two-center two-electron integrals
On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment
How hot? Systematic convergence of the replica exchange method using multiple reservoirs
In situ data analytics and indexing of protein trajectories
MOCASSIN: Metropolis and kinetic Monte Carlo for solid electrolytes
Analysis of the genetic algorithm method of molecular conformation determination
Ion flux through membrane channels - An enhanced algorithm for the Poisson-Nernst-Planck model
Prediction of physicochemical properties of organic molecules using van der Waals surface electrostatic potentials
Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes
Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis
Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions
Density functional study of structural, electronic, and optical properties of small bimetallic ruthenium-copper clusters
Comment On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states [by J. M. Anglada, E. Besalú, J. M. Bofill, and R. Crehuet, J Comput Chem 2001, 22, 4, 387-406]
Hartree-Fock instabilities and electronic properties
Analysis of the Updated Hessian Matrices for Locating Transition Strucutres
EVEBAT: A fast strategy for the examination of the empty space in polymer matrices
Revealing noncovalent interactions in quantum crystallography: Taurine revisited
Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands
A new molecular mechanics force field for the oxidized form of blue copper proteins
Working tools for theoretical chemistry: Polanyi, eyring, and debates over the "semiempirical method"
Molecular mechanics calculations (MM3) on sulfones
The structure and chemical bonding in the N 2 -CuX and N 2 ***XCu (X = F, Cl, Br) systems studied by means of the molecular orbital and Quantum Chemical Topology methods
Probing the electronic structure, chemical bonding, and excitation spectra of [CuE]+/0/- (E = 14 group element) diatomics employing DFT and ab initio methods
Unraveling Solvent and Substituent Effects in the Photodynamics of Light-Dependent Microtubule Inhibitors for Cancer Phototherapy
MARVEL analysis of high-resolution rovibrational spectra of 13 C 16 O 2
Prediction of lattice energy of benzene crystals: A robust theoretical approach
Ring inversion in 1, 4, 7 cyclononatriene and analogues: Ab initio and DFT calculations and topological analysis
Molecular mechanics (MM4) study of amines
Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character
Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study
A potential with low point charges for pure siliceous zeolites
Evaluation the synergistic antitumor effect of methotrexate-camptothecin codelivery prodrug from self-assembly process to acid-catalyzed both drugs release: A comprehensive theoretical study
Theoretical investigation on the photophysical properties of N-heterocyclic carbene iridium (III) complexes (fpmb) x Ir(bptz) 3- x ( x = 1-2)
Dative and electron-sharing bonding in transition metal compounds
The helix-inversion mechanism in double-stranded helical oligomers bridged by rotary cyclic boronate esters
Strategies for an efficient implementation of the Gauss-Bessel quadrature for the evaluation of multicenter integral over STFs
Vibrational anharmonic calculations in solution: Performance of various DFT approaches
Comment on "Extending hirshfeld-i to bulk and periodic materials"
Complete active space analysis of a reaction pathway: Investigation of the oxygen-oxygen bond formation
Modeling peptide binding to anionic membrane pores
Computational Study of the Hydrolysis of Degradable Polysaccharide Biomaterials: Subtituent Effects on the Hydrolytic Mechanism
Theoretical dynamic studies on the reactions of CH 3 C(O)CH 3- n Cl n ( n = 0-3) with the chlorine atom
Harmonic Analysis of Large Systems. I. Methodology
Metal Dimers-Doped h-BN Structures as Novel Toxic Gases Sensors With Enhanced Sensitivity Properties: An ADFT Study
Exploring the potential energy surface of retinal, a comparison of the performance of different methods
Evaluation of the electron momentum density of crystalline systems from ab initio linear combination of atomic orbitals calculations
Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose-1, 6-bisphosphatase inhibitors
Performance of DFT in modeling electronic and structural properties of cobalamins
ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms
Improving the Q2MM method for transition state force field modeling
Large scale peptide screening against main protease of SARS CoV-2
Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry
Multiscale fast summation of long-range charge and dipolar interactions
The Use of Fraga's Potential with AMI Atomic Point Charges in the Evaluation of Spectral Shifts: Application to TICT Molecules
Separation of hydrocarbon mixture of neopentane and n-hexane using NaY zeolite: Large distinct diffusivity
High-Precision Atomic Computations from Finite Element Techniques: Second-Order Correlation Energeis for Be, Ca, Sr, Cd, Yb, and Hg
Simple position and orientation preconditioning scheme for minimum energy path calculations
Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine
Quantum chemical calculation of Henry constants of diatomic molecules in faujasite-type zeolites
Corrigendum: Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory (Part II)
Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches
Exploring potential energy hypersurfaces for triple symmetric inversion in 3-azabicyclo[3.3.1]nonan-9-one and its N-methyl derivative
Heats of Formation of Organic Molecules Calculated from AB Initio Theory and a Group Equivalent Scheme: Alkenes
Charge donation to and dearomatization of benzene attending complexation: DFT estimates of binding energies of TpMXO(L) with benzene, for Tp = hydridotris(pyrazolyl) borate, MXO = MoNO, ReCO, and WNO, and L = ammonia, N-methylimidazole, pyridine, phosphine, methyl isocyanide, and carbon monoxide
TITAN: A Code for Modeling and Generating Electric Fields - Features and Applications to Enzymatic Reactivity
Nonadiabatic scattering of NO off Au3 clusters: A simple and robust diabatic state manifold generation method for multiconfigurational wavefunctions
Agreement between experiment and hybrid DFT calculations for OH bond dissociation enthalpies in manganese complexes
Phase diagrams of the Ziff-Gulari-Barshad model on random networks
Cyclic voltammetry modeling, geometries, and electronic properties for metallofullerene complexes with µ 3 - eta 2 : eta 2 : eta 2 -C 60 bonding mode
Shape and size effects in pi-pi interactions: Face-to-face dimers
Performance of the COSMO solvation model for photoacidity and basicity in water
Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions
Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: II
Theoretical study of ionization and one-electron oxidation potentials of N -heterocyclic compounds
Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods
Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients
First-principles calculations on the four phases of BaTiO 3
Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry
Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer
Carbonyl insertion reaction into the PtC bond in heterobimetallic Pt(SnCl3)(PH3)2(CO)(CH3) compound: Theoretical study
Calculating p K a values for substituted phenols and hydration energies for other compounds with the first-order fuzzy-border continuum solvation model
Molecular tailoring approach as tool for revealing resonance-assisted hydrogen bond: Case study of Z-pyrrolylenones with the NH⋯OС intramolecular hydrogen bond
A density functional theory study of the dimers of HX (X = F, Cl, and Br)
Predicting core level binding energies shifts: Suitability of the projector augmented wave approach as implemented in VASP
Effect of available volumes on radial distribution functions
Density-functional theory (DFT) and time-dependent DFT study of the chemical and physical origins of key photoproperties of end-group derivatives of a nonfullerene acceptor molecule for bulk heterojunction organic solar cells
Theoretical studies on thermally activated delayed fluorescence mechanism of a series of organic light-emitting diodes emitters comprising 2, 7-diphenylamino-9, 9-dimethylacridine as electron donor
A Theoretical study on the charge and discharge states of Na-ion battery cathode material, Na1+xFePO4F
Rationalizing Nuclear Overhauser Efect Data for Compounds Adopting Multiple-Solution Conformations
QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
Revisiting the generator coordinate approximation for calculating the ro-vibrational energies of H
MCDP: an advanced tool to simulate comb-like polymers
Extension of QM/MM docking and its applications to metalloproteins
Site specificity of the alpha C-H bond dissociation energy for a naturally occurring beta-hairpin peptide - An ab initio study
Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study
A computational analysis of interaction energies in methane and neopentane dimer systems
Relationship between orbital energy gaps and excitation energies for long-chain systems
Full configuration interaction algorithm on a massively parallel architecture: Direct-list implementation
Consensus bond-charge increments fitted to electrostatic potential or field of many compounds: Application to MMFF94 training set
The Natural Atomic Orbital Point Charge Model for PM3: Multipole Moments and Molecular Electrostatic Potentials
CHIMERA: A software tool for reaction rate calculations and kinetics and thermodynamics analysis
Molecular dynamics analysis of Mg2+-dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis
Conformational fluctuations and electronic properties in myoglobin
Computation of vertical excitation energies of retinal and analogs: Scope and limitations
Comment on the paper "Extensive Theoretical Studies of a New Energetic Material: Tetrazino-Tetrazine-Tetraoxide (TTTO)" by Xinli Song, Jicun Li, Hua Hou, and Baoshan Wang
Prediction of LUMO Energy and Rate Constant by Comparative Molecular Field Analysis(CoMFA)
An efficient second-order poisson-boltzmann method
Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system
A dimensionless reaction coordinate for quantifying the lateness of transition states
Hybrid density functional theory for -stacking interactions: Application to benzenes, pyridines, and DNA bases
Supplementary d and f functions in molecular wave functions: Optimum and nonoptimum exponents
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models
Introducing Pep McConst - A user-friendly peptide modeler for biophysical applications
The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α-alkenoyl ketene-( S, S )-acetals: Hydrogen bonding and electrostatic interactions
Deep learning for computational chemistry
Reversible Hydrogen Storage by Planar Hypercoordinate Hydrogen Clusters
Conformational energies of microsolvated Na+ clusters with protic and aprotic solvents from GFNn-xTB methods
Microsecond dynamics of H10N7 influenza neuraminidase reveals the plasticity of loop regions and drug resistance due to the R292K mutation
Retardation of setting of plaster of Paris by organic acids: Understanding the mechanism through molecular modeling
Calculation of the inner-shell contribution to the correlation energy through DLPNO-CEPA/1 and scaled same-spin second-order Møller-Plesset perturbation theory
Representation of DNA environment: Spiral staircase distribution function
NLOPredict: Visualization and data analysis software for nonlinear optics
PSI3: An open-source Ab Initio electronic structure package
Variation of the optical properties with size and composition of small, isolated CdxSey+ clusters
Interplay between tetrel and triel bonds in RC 6 H 4 CN⋯MF 3 CN⋯BX 3 complexes: A combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study
Maximum probability domains from Quantum Monte Carlo calculations
Cover Image, Volume 41, Issue 19
Rapid determination of RMSDs corresponding to macromolecular rigid body motions
Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia
Geometry of Pyrazole: A Test for Ab Initio Calculations
Comprehensive method based on model free method and IKP method for evaluating kinetic parameters of solid state reactions
Algorithms for exact counting of energy levels of spectroscopic transitions at different temperatures
Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane
Exploring self-organization of molecular tether molecules on a gold surface by global structure optimization
Extensive theoretical study on electronically excited states and predissociation mechanisms of sulfur monoxide including spin-orbit coupling
Conformational analysis of thiopeptides: (, ) maps of thio-substituted dipeptides
Solvation effects on reaction profiles by the polarizable continuum model coupled with the Gaussian density functional method
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
GARLEEK: Adding an extra flavor to ONIOM
Theoretical study of methane adsorption and C─H bond activation over Fe-embedded graphene: Effect of external electric field
Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods
Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex
β -sheets mediate the conformational change and allosteric signal transmission between the As LOV2 termini
The role of -type nonbonding orbitals for spin-orbit induced NMR chemical shifts: DFT study of 13C and 19F shifts in the series CF3IFn (n=0, 2, 4, 6)
The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide
MNDO parameters for helium: Optimization, tests, and application to endohedral fullerene - helium complexes
Why many semiempirical molecular orbital theories fail for liquid water and how to fix them
Distance and exposure dependent effective dielectric function
Exact rotamer optimization for protein design
Practical modeling of molecular systems with symmetries
Computational investigation of pyrazinamide drugs and its transition metal complexes using a DFT approach
The effect of iron and copper impurities on the wettability of sphalerite (110) surface
Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations
The total Position Spread in mixed-valence compounds: A study on the H4+ model system
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units
A systematic sequence of relativistic approximations
Chiral force constants: Recommendations for the presentation of internal coordinate force constants
Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase
Correlation functional in screened-exchange density functional theory procedures
Eliminating symmetry problems in electronegativity equalization and correcting self-interaction errors in conceptual DFT
Parallelization of the deMon2k code
All-electron density functional calculation on insulin with quasi-canonical localized orbitals
Unrolr: Structural analysis of protein conformations using stochastic proximity embedding
Activation barriers for DNA alkylation by carcinogenic methane diazonium ions
Conformation, hydration, and ligand exchange process of ruthenium nitrosyl complexes in aqueous solution: Free-energy calculations by a combination of molecular-orbital theories and different solvent models
Fluorine as a Lewis acid: A symmetry-adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH3 complex
Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials
Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water
Germanium, carbon-germanium, and silicon-germanium triangulenes
A new GROMOS force field for hexopyranose-based carbohydrates
Potential derived charges using a geodesic point selection scheme
Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins
Cool walking: A new Markov chain Monte Carlo sampling method
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO
Parameterizing elastic network models to capture the dynamics of proteins
The eigenvalue problem in phase space
Investigation of chemical bond characteristics, thermal expansion coefficients and bulk moduli of alpha-R 2 MoO 6 and R 2 Mo 2 O 7 (R = rare earths) by using a dielectric chemical bond method
The comparison of structure, nature of bond, and electronic transitions in [M(η5-Cp)(η5-C60Me5)] (M = Fe2+, Ru2+, Os2+) hybrids and corresponding metallocenes; a theoretical study
A theoretical investigation into gallic acid pyrolysis
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field
A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo
The implementation of a fast and accurate QM/MM potential method in Amber
Constraining the electron densities in DFT method as an effective way for ab initio studies of metal-catalyzed reactions
Performance enhancements for GROMACS nonbonded interactions on BlueGene
QSAR of antilipid peroxidative activity of substituted benzodioxoles using chemometric tools
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
Symmetry classification of electron and phonon states in TiO 2 -based nanowires and nanotubes