yusuke1997/dblp-id-title huggingface dataset:
Molecular mechanics-based measures of steric effects: Customized code to compute Ligand repulsive energies
Quantum chemistry in parallel with PQS
iVI-TD-DFT: An iterative vector interaction method for exterior/interior roots of TD-DFT
Realistic nuclear charge distribution model function for analytic nuclear attraction integrals in Gaussian basis functions
New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions
Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?
Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms
Quantum mechanical study of regioselectivity of radical additions to substituted olefins
Contracted Schrödinger equation in quantum phase-space
Dynamics and structural changes of small water clusters on ionization
An automated method for graph-based chemical space exploration and transition state finding
A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error
Theoretical study and rate constants calculation for the reactions of SiH 3 radical with SiH 3 CH 3 and SiH 2 (CH 3 ) 2
Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges
Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3, 3, 3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory
Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal
The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
Insight into spin-orbital interaction using MCSCF method: A special analysis of the 1Σg+ electronic state in C2 and the linear polyacetylenic C4 and C6
Complementary version of fermion coupled coherent states method and gram-schmidt algorithm: Theory and applications for electronic states of and
STAAR: Statistical analysis of aromatic rings
A strategy to find minimal energy nanocluster structures
Quantum chemical study of the autoxidation of ascorbate
A Cost-Effective Computational Strategy for the Electronic Layout Characterization of a Second Generation Light-Driven Molecular Rotary Motor in Solution
Molecular Mechanics Calculations (MM2 and MM3) on Enamines and Aniline Derivatives
A nonredundant structure dataset for benchmarking protein-RNA computational docking
Performance of the VBSCF method for pericyclic and π bond shift reactions
A computational study on the hydrogen adsorption capacity of various lithium - Doped boron hydrides
Ab initio calculations on the and states of AlNC and simulation of the AlNC - emission spectra
A theoretical study of imine hydrocyanation catalyzed by halogen-bonding
Multiscale modeling of stochastic dynamics processes with MBN Explorer
Molecular dynamics simulation of single wall carbon nanotubes polymerization under compression
Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation, multi-Fock algorithm, and pseudodiagonalization
Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions
Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene
Reply to comment on the paper "An efficient Algorithm for Energy Gradients and Orbital Optimization in Valence Bond Theory"
Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha 3 W - A large-scale Monte Carlo study
Oligovalent link atoms in embedding calculations
Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of förster theory
Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure
Partially linearized external models to active-space coupled-cluster through connected hextuple excitations
Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations
A multilayered representation, quantum mechanical and molecular mechanics study of the CH 3 F + OH - reaction in water
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
DJMol: An open-source modeling platform for computational chemistry and materials science with a Python interpreter
Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca 2+ -ATPase
A first-principles DFT study of UN bulk and (001) surface: Comparative LCAO and PW calculations
MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries
Expanding Molecular Dynamics Simulations to the NMR Time Scale. I. Studies of Conformational Interconversions of 1, 1-Difluoro-4.4-Dimethylcycloheptane Using MM3-MD
An efficient method by combining different basis sets and SAPT levels
An efficient algorithm for energy gradients and orbital optimization in valence bond theory
Interplay between anion-pi and hydrogen bonding interactions
Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods
Rotamer optimization for protein design through MAP estimation and problem-size reduction
IDEA: Interface dynamics and energetics algorithm
First-principle calculations on CO oxidation catalyzed by a gold nanoparticle
Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites
Definitive thermochemistry and kinetics of the interconversions among conformers of n -butane and n -pentane
Neutral gold clusters studied by the isothermal Brownian-type molecular dynamics and metadynamics molecular dynamics simulations
Interaction potential models for bulk Zns, Zns nanoparticle, and Zns nanoparticle-PMMA from first-principles
Continuous similarity measure between nonoverlapping X-ray powder diagrams of different crystal modifications
Interatomic potential models for natural apatite crystals: Incorporating strontium and the lanthanides
Improved solutions to the one-center McMurchie - Davidson tree search problem
General atomic and molecular electronic structure system
Accurate potential energy surfaces for hydrogen abstraction reactions: A benchmark study on the XYG3 doubly hybrid density functional
Adjustment of born-oppenheimer electronic wave functions to simplify close coupling calculations
AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers
Hybrid density functional study on the electronic structures and properties of P3HT-PbS and P3HT-CdS hybrid interface for photovoltaic applications
Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach
Development of the cyclic cluster approach for ionic systems
Convergence of electric field and electric field gradient versus atomic basis sets in all-siliceous and Mg substituted phillipsites
Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size
Mechanism of the O2(1Δg) generation from the Cl2/H2O2 basic aqueous solution explored by the combined ab initio calculation and nonadiabatic dynamics simulation
Photocatalytic properties of graphene-supported titania clusters from density-functional theory
Comprehensive ab initio quantum mechanical and molecular orbital (MO) analysis of cisplatin: Structure, bonding, charge density, and vibrational frequencies
B3LYP calculations on bishomoaromaticity in substituted semibullvalenes*
Disentanglement of orthogonal hydrogen and halogen bonds via natural orbital for chemical valence: A charge displacement analysis
Application of a BOSS - Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions
Strain in nonclassical silicon hydrides: An insight into the "ultrastability" of sila-bi[6]prismane (Si 18 H 12 ) cluster with the endohedrally trapped silicon atom, Si 19 H 12
Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
Kinetics and equilibrium of multicomponent adsorption on chiraly templated surfaces
An Analytical Algorithm for the Rapid Determination of the Solvent Accessibility of Points in a Three-Dimensional Lattice around a Solute Molecule
Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations
Decoding energy decomposition analysis: Machine-learned Insights on the impact of the density functional on the bonding analysis
Electron transfer reactivity of O2+O2- system in low-spin coupling: Ab Initio study at electron correlation level
Computational protein design: The proteus software and selected applications
Cover Image, Volume 39, Issue 15
Van der Waals effects between hydrogen and first-row atoms in molecular mechanics (MM3/MM4)
The topology of the Coulomb potential density. A comparison with the electron density, the virial energy density, and the Ehrenfest force density
"Solved and unsolved problems of structural chemistry" by Milan Randić, Marjana Novič, and Dejan Plavšić CRC Press, Boca Raton, 2016, XX+472 pp. ISBN 13-978-1-4987-1151-7
The performance of nonhybrid density functionals for calculating the structures and spin states of Fe(II) and Fe(III) complexes
Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices
Rational design of iron catalysts for C-X bond activation
Calculation of chemical reaction energies using the AM05 density functional
Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients
A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents
ERKALE - A flexible program package for X-ray properties of atoms and molecules
Excited states of OsO 4 : A comprehensive time-dependent relativistic density functional theory study
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster
Algorithms for Constrained Molecular Dynamics
Density functional finite cluster method for polarizability of large BeN three-dimensional systems
Half-numerical evaluation of pseudopotential integrals
Loop-erased self-avoiding random walks in four and five dimensions
Improved p K a prediction: Combining empirical and semimicroscopic methods
Roles of proteins in the electron transfer in the photosynthetic reaction center of Rhodopseudomonas viridis: bacteriopheophytin to ubiquinone
Nature of hydration shells of a polyoxy-anion with a large cationic centre: The case of iodate ion in water
State-specific multireference perturbation theory with improved virtual orbitals: Taming the ground state of F 2 , Be 2, and N 2
Structural diradical character
Cover Image, Volume 41, Issue 20
Performance of efficient minimization algorithms as applied to models of peptides and proteins
A metropolis Monte Carlo method for analyzing the energetics and dynamics of lipopolysaccharide supramolecular structure and organization
Parallel direct SCF and gradient program for workstation clusters
Basic ingredients of free energy calculations: A review
Molecular dynamics for proteins: Performance evaluation on massively parallel computers based on mesh networks using a space decomposition approach
TD-DFT study of BIPS spiropyran: Effects of functionals and high-polarity solvent on C spiro O bond dissociation and recovery
A critical evaluation of several global optimization algorithms for the purpose of molecular docking
Self-consistent field method for open-shell systems within the density-matrix functional theory
Electronic structure, chemical bonding, and finite-temperature magnetic properties of full Heusler alloys
Intruder states in multireference perturbation theory: The ground state of manganese dimer
Molecular mechanics (MM4) calculations on carbonyl compounds. I-IV - Erratum
Basis set and correlation effects in the calculation of accurate gas phase dimerization energies of two M+2 to give M2+4 (M = S, Se)
Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics
Excited state properties, fluorescence energies, and lifetimes of a poly(fluorene-phenylene), based on TD-DFT investigation
Persistent homology for the quantitative prediction of fullerene stability
Conformational analysis of synthetic neolignans active against leishmaniasis, using the molecular mechanics method (MM2)
Can substituted allenes be highly efficient leaving groups in catalytic processes? A computational investigation
Redox-active ligands as a challenge for electronic structure methods
Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes. IV. Dihydrophospholophosphole isomers
How much tetraradical character is present in the Si 6 Ge 9 cluster?
Unusual Sb-Sb bonding in high temperature thermoelectric materials
QSARINS: A new software for the development, analysis, and validation of QSAR MLR models
Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid
Adsorption of CO on oxygen preadsorbed neutral and charged gas phase Pd 4 clusters: A density functional study
Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics
Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules
Discovery of new beta-D-galactosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening
Experimental and theoretical electron density of intermediates in palladium-phenanthroline catalyzed carbonylation of amines and reductive carbonylation of nitroarenes
Unraveling the effect of aromaticity for the dynamics of excited states of single benzene fluorophores
Theoretical prediction regarding structural and thermodynamical characteristics of stable CH 3 PO 2 isomers and unimolecular decomposition mechanisms of species CH 3 P(=O) 2 , CH 3 O-P=O, and CH 2 =P(=O)OH
Guidelines for publication of research results from force-field calculations
A DFT and kinetic study: Is it possible to prepare epoxides without catalysts using the in-situ generated peroxy radicals or peroxides by one-step method?
Energy minimizations with a combination of two knowledge-based potentials for protein folding
Modeling disordered morphologies in organic semiconductors
Density functional theory studies on the dissociation energies of metallic salts: relationship between lattice and dissociation energies
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins
Merck molecular force field. IV. conformational energies and geometries for MMFF94
Registering the Amica electronic structure code in the Extensible Computational Chemistry Environment
Inductive effects in radicals calculated from DFT energies; substituted bicyclo[2.2.2]octan-1-yloxy radicals
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins
Assessing search strategies for flexible docking
Nature of partial sigma bond
Erratum: A convective replica-exchange method for sampling new energy basins
Linear scaling approaches to quantum macromolecular similarity: Evaluating the similarity function
Stable, aromatic, and electrophilic azepinium ions: Design using quantum chemical methods
Stability of Two-Dimensional Crystalline Aggregates of a PRotein Studied by Molecular Dynamics
Comprehensive investigation of electronic structure, phonon spectrum and thermoelectric performance of LuMSb (M = Ni, Pd, Pt) half Heusler compounds from first principles
Beyond the MNDO model: Methodical considerations and numerical results
Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water
Specific empirical free energy function for automated docking of carbohydrates to proteins
Using the gini coefficient to measure the chemical diversity of small-molecule libraries
Time-averaged predictions of folded and misfolded peptides using a reduced physicochemical model
First principles investigation on the ultra-incompressible and hard TaN
Bulk properties from finite cluster calculations. VIII. Benchmark calculations of the efficiency of extrapolation methods for the HF and MP2 energies of polyacenes
Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal?
Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: Development of the molecular mechanics-based program ACE and application to asymmetric epoxidation reactions
Transport of hydrated nitrate and nitrite ions through graphene nanopores in aqueous medium
A new approach to global minimization
Computational modeling of tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone derivatives: An atomistic drug design approach using Kier-Hall electrotopological state (E-state) indices
All-electron LCAO calculations of the LiF crystal phonon spectrum: Influence of the basis set, the exchange-correlation functional, and the supercell size
All-body concept and quantified limits of cooperativity and related effects in homodromic cyclic water clusters from a molecular-wide and electron density-based approach
Theoretical study on the molecular structures of X-, α-, and β-types of lithium phthalocyanine dimer
Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization
Beryllium bonding with noble gas atoms
Oxygen versus sulfur: Structure and reactivity of substituted arsine oxides and arsine sulfides
Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: A theoretical study of enzyme inhibition
Mechanism of methylacetylene bisselenation catalyzed by palladium complex from density functional study
Improving efficiency of semi-direct møller-plesset second-order perturbation methods through oversubscription on multiple nodes
Search of truncation of ( N -1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via fock-space coupled cluster approach
Multigrid high-order mesh refinement techniques for composite grid electrostatics calculations
The Electronic Strucure of Weakley Bound Systems. II. NeX + and ArX + (X=H 2 O, HCI, and HF) Bimolecular Cations
ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces
Deciphering excited state properties utilizing algebraic diagrammatic construction schemes of decreasing order
Quantum-mechanical and molecular mechanics conformational analysis of 1, 5-cyclooctadiene
Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response
Anticooperativity of FH···Cl- hydrogen bonds in [FH)nCl]- clusters (n = 1...6)
Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model
Effects of oxidative adsorbates and cluster formation on the electronic structure of nanodiamonds
A novel method for enzyme design
High throughput selection of organic cathode materials
Ab initio structure and vibration-rotation dynamics of germylene, GeH2
Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation
Quantum mechanical charge field molecular dynamics simulation of the TiO 2+ ion in aqueous solution
Efficient inclusion of receptor flexibility in grid-based protein-ligand docking
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
PyGlobal: A toolkit for automated compilation of DFT-based descriptors
Efficient singular-value decomposition of the coupled-cluster triple excitation amplitudes
Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening
Fast Ewald sums for general van der Waals potentials
Theoretical study on the carbon nanomaterial-supported Pt complex electrocatalysts for efficient and selective chlorine evolution reaction
Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network
MembrFactory: A Force Field and composition Double Independent Universal Tool for Constructing Polyamide Reverse Osmosis Membranes
Point atomic multipole moments for simulation of electrostatic potential and field in all-siliceous zeolites
The role of electric field on decomposition of CL-20/HMX cocrystal: A reactive molecular dynamics study
Identifying the O 2 diffusion and reduction mechanisms on CeO 2 electrolyte in solid oxide fuel cells: A DFT + U study
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package
Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate p K a shifts of protein residues
DFT study of the carbon- and nitrogen-pivot lariat crown ethers and their complexes with alkali metal cations: Na + , K +
Investigation of excited-state properties of fluorene-thiophene oligomers by the SAC-CI theoretical approach
An orbital localization criterion based on the theory of fuzzy atoms
Heats of formation of organic molecules calculated by density functional theory: II. Alkanes
QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation
Using quaternions to calculate RMSD
Chemistry with ADF
VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers
Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results
The isomers of ionized ethane
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence with polarization quality of the fifth period for solid-state calculations
From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg-Coxeter fullerenes up to C 980
A QTAIM and stress tensor investigation of the torsion path of a light-driven fluorene molecular rotary motor
An adaptive treecode for computing nonbonded potential energy in classical molecular systems
Multiscale geometric modeling of macromolecules II: Lagrangian representation
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions
Curvature correction for microiterative optimizations with QM/MM electronic embedding
The nature of structure and bonding between transition metal and mixed Si-Ge tetramers: A 20-electron superatom system