yusuke1997/dblp-id-title huggingface dataset:
Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
Hybrid Monte Carlo: An Efficient Algorithm for Condensed Matter Simulation
Absorption and emission properties of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (M = Al, Ga, In) and correlations with molecular electrostatic potential
Parallel internally contracted multireference configuration interaction
Deriving effective mesoscale potentials from atomistic simulations
Ecoupling server: A tool to compute and analyze electronic couplings
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes
Chemical shift driven geometry optimization
Time-dependent quantum study of the kinetics of the H( 2 S) + FO( 2 II) -> OH( 2 II) + F( 2 P) reaction
Analytical quadrature method using recurrence formulas for two-electron integrals of frequency-dependent Breit interaction
An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase
A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides, acetamides, and N -methylformamides
Theoretical study of the internal elimination reactions of xanthate precursors
Global and local indices for characterizing biomolecular flexibility and rigidity
New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue
Direct hydride transfer in the reaction mechanism of quinoprotein alcohol dehydrogenases: a quantum mechanical investigation
A formula and numerical study on Ewald 1D summation
Comparison of Hartree-Fock and Kohn-Sham determinants as wave functions
Cover Image, Volume 40, Issue 32
Benzdiynes revisited: ab initio and density functional theory
A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges
Protonation enthalpies in fluorosulfonic acid using ab initio self-consistent reaction field theory
Formation of Stone-Wales edge: Multistep reconstruction and growth mechanisms of zigzag nanographene
The influence of the metal cations and microhydration on the reaction trajectory of the N3 [LEFT RIGHT ARROW] O2 thymine proton transfer: Quantum mechanical study
On the stability and chemical bond of noble gas halide cations NgX+ (Ng = He - Rn; X = F - I)
On relativistic effects in ground state potential curves of Zn 2 , Cd 2 , and Hg 2 dimers. A CCSD(T) study
Prediction of refractive index of vinyl polymers by using density functional theory
Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence
A tessellationless integration grid for the polarizable continuum model reaction field
Structure and intermolecular interactions in ionic liquid 1-ethyl-3-methylimidazolium bromide and its aqueous solutions investigated by vibrational spectroscopy and quantum chemical computations
Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules
Investigation of binding features: Effects on the interaction between CYP2A6 and inhibitors
Ab initio molecular dynamics study of intersystem crossing dynamics for MH 2 (M = Si, Ge, Sn, Pb) on spin-pure and spin-mixed potential energy surfaces
Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment
Small-Amplitude Protein Conformational Dynamics: Second Order Analytic Relation between Cartesian Coordinates and Dijedral Angles
Enhanced sampling in explicit solvent by deep learning module in FSATOOL
Long-range corrected density functionals combined with local response dispersion: A promising method for weak interactions
Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases
Algorithm to evaluate rate constants for polyatomic chemical reactions. I. Theory and computational details
DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF 3 Br
Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach
First principles study of gallium cleaning for hydrogen-contaminated α-Al 2 O 3 (0001) surfaces
Fluxional bonds in quasi-planar and half-sandwich (M = K, Rb, and Cs)
A theoretical investigation of the excited states of OCLO radical, cation, and anion using the CASSCF/CASPT2 method
Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies
Molecular mechanics (MM3) calculations on lithium amide compounds
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
A Genuine Hydrocarbon Ion Pair More Stable Than Its Covalent Counterpart. A Computational Study
Composition-induced structural transitions in mixed Lennard-Jones clusters: Global reparametrization and optimization
Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules
Linear combination of Lanczos vectors: A storage-efficient algorithm for sparse matrix eigenvector computations
Electronic ground states and vibrational frequency shifts of diatomic ligands in heme adducts
A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function
A bulk adjusted linear combination of atomic orbitals (BA-LCAO) approach for nanoparticles
Chemically modified fullerene derivatives as photosensitizers in photodynamic therapy: A first-principles study
Implementation and application of helix-helix distance and crossing angle restraint potentials
H/D isotope effect on charge-inverted hydrogen-bonded systems: Systematic classification of three different types in H 3 XH ... YH 3 (X = C, Si, or Ge, and Y = B, Al, or Ga) with multicomponent calculation
RAQET: Large-scale two-component relativistic quantum chemistry program package
Investigation of challenging spin systems using Monte Carlo configuration interaction and the density matrix renormalization group
Anisotropic charge carrier transport of optoelectronic functional selenium-containing organic semiconductor materials
Ab initio calculations of the interaction potentials and thermodynamic functions for ArN and ArN +
RNA secondary structure prediction using a self-consistent mean field approach
Dependence of the rate constants on the treatment of internal rotation modes: The reaction OH + CH3SH CH3S + H2O as an example
Ab initio molecular orbital study on the structures and energetics of CH3OH(H2O)n and CH3SH(H2O)n in the gas phase
Reduced-cost sparsity-exploiting algorithm for solving coupled-cluster equations
Ann Efficient Approach to Calculation of Zero-Flux Atimic Surfaces and Generation of Atimic Intergration Data
Half metallic properties of LaSrVMoO 6
A self-organizing algorithm for molecular alignment and pharmacophore development
CHARMM force field for protonated polyethyleneimine
Prediction of possible crystal structures for C-, H-, N-, O-, and F-containing organic compounds
Theoretical study on the mechanism of the gas-phase reaction of diborane(3) anion with carbon disulfide
Elucidating the binding mechanism of thione-containing mercaptopurine and thioguanine drugs to small gold clusters
Minimal molecular surfaces and their applications
Density Functional Theory and Moleculer Clusters
Exploring the role of mean-field potentials and short-range wave function behavior in the adiabatic connection
Techniques for the compression of sequences of integer numbers and real numbers with fixed absolute precision
On the nature of interactions in the F 2 OXe ... NCCH 3 complex: Is there the Xe(IV)-N bond?
Erratum: Properties of atoms in electronically excited molecules within the formalism of TDDFT [J. Comput Chem. 2014, 35, 820-828]
A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers
Shape-based virtual screening with volumetric aligned molecular shapes
Study of solvent effects by means of averaged solvent electrostatic potentials obtained from molecular dynamics data
Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question
Fast non-iterative calculation of solvation energies for water and non-aqueous solvents
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane
Intramolecular chelation of Zn2+ by - and -mercaptocarboxamides. A parallel ab initio and polarizable molecular mechanics investigation. Assessment of the role of multipole transferability
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods
Intramolecular interactions of L-phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules
Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids
Translation of STO charge distributions
Three-site and five-site fixed-charge water models compatible with AMOEBA force field
TANGO: A high through-put conformation generation and semiempirical method-based optimization tool for ligand molecules
Double hybrids and time-dependent density functional theory: An implementation and benchmark on charge transfer excited states
Accurate estimation of correlation energies using locally dense basis sets
Accurate and fast treatment of large molecular systems: Assessment of CEPA and pCCSD within the local pair natural orbital approximation
Application of explicitly correlated Gaussian functions for calculations of the ground state of the beryllium atom
Use of statistical measures for analyzing RNA secondary structures
Q-Dock LHM : Low-resolution refinement for ligand comparative modeling
FA(I): Au+ and FA(II): Cu+ laser activity and photographic sensitization at the low coordinated surfaces of AgBr ab initio calculations
Coriolis coupling and nonadiabaticity in chemical reaction dynamics
Quantifying electro/nucleophilicity by partitioning the dual descriptor
Zinc-Homocysteine binding in cobalamin-dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies
Docking Flexible Molecules: A Case Study of Three Proteins
Optimization of a molecular mechanics force field for polyoxometalates based on a genetic algorithm
Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909
Lewis acid stabilized group 13-15 element analogs of ethylene
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
On the kinematics of protein folding
Constructing a multidimensional free energy surface like a spider weaving a web
Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions
Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins
Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: Development and implementation of the continuous fractional component move
A novel parallel algorithm for large-scale Fock matrix construction with small locally distributed memory architectures: RT parallel algorithm
A new computer program for QSAR-analysis: ARTE-QSAR
Single-Walled ZnSe Nanotubes for High-Performance Photodetectors: A Computational Prediction
A neural network potential based on pairwise resolved atomic forces and energies
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer
Secondary structure analysis of peptides with relevance to iron-sulfur cluster nesting
Validation of critical points in the electron density as descriptors by building quantitative structure-property relationships for the atomic polar tensor
On the performance of some aromaticity indices: A critical assessment using a test set
GNN-DDAS: Drug discovery for identifying anti-schistosome small molecules based on graph neural network
The ab initio limit quartic force field of BH3
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides
Hydrogen bond energy estimation (H-BEE) in large molecular clusters: A Python program for quantum chemical investigations
Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations
Ab initio studies of counterion effects in molecular quantum-dot cellular automata
Structural basis of BMP-2 and BMP-7 interactions with antagonists Gremlin-1 and Noggin in Glioblastoma tumors
Wave functions derived from experiment. V. Investigation of electron densities, electrostatic potentials, and electron localization functions for noncentrosymmetric crystals
Study of absorption and emission spectra of substituted terthiophene compounds by methods of theoretical chemistry
Force field for platinum binding to adenine
Calculation of Molecular Geometries, Relative Conformational Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Function Theory
Loop problem in proteins: Developments on Monte Carlo simulated annealing approach
Study of the cold charge transfer state separation at the TQ1/PC 71 BM interface
Electronic and geometric structure analysis of neutral and anionic metal nitric chalcogens: The case of MNX series (M=Li, Na, Be and X=O, S, Se, Te)
Stochastic proximity embedding
Hybrid organic-inorganic CH 3 NH 3 PbI 3 perovskite building blocks: Revealing ultra-strong hydrogen bonding and mulliken inner complexes and their implications in materials design
Plane-wave density functional theory investigation of adsorption of 2, 4, 6-trinitrotoluene on al-hydroxylated (0001) surface of (4 × 4) α-alumina
Electronic structure and optical properties of isolated and TiO2-grafted free base porphyrins for water oxidation: A challenging test case for DFT and TD-DFT
Experimental and theoretical study of the polarized infrared spectra of the hydrogen bond in 3-thiophenic acid crystal
Energetics and spectroscopic studies of CNO (-) (H 2 O) n clusters and the temperature dependencies of the isomers: An approach based on a combined recipe of parallel tempering and quantum chemical methods
Adsorption integral equation via complex approximation with constraints: kernel of general form
Pseudopericyclic design drives antara-antara [1, 5] methylene sigmatropic shifts from a stepwise to a concerted mechanism
Serenity: A subsystem quantum chemistry program
New accurate benchmark energies for large water clusters: DFT is better than expected
Optimization of RI-MP2 Auxiliary Basis Functions for 6-31G** and 6-311G** Basis Sets for First-, Second-, and Third-Row Elements
Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix
Electronic structure and bonding studies on triple-decker sandwich complexes with a P 6 middle ring
Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution
Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine
Comparative study of density functionals for the description of lithium-graphite intercalation compounds
Influence of the presence of small gas molecules in the structure of comblike polyacrylates: A Monte Carlo study
Solvent effects: 6. A comparison between gas phase and solution acidities
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules
Saving time and energy with oversubscription and semi-direct Møller-Plesset second order perturbation methods
Direct ab initio dynamics study on the rate constants and kinetic isotope effect for the reactions of H atoms with GeDn(CH3)4-n (n = 1-4)
New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates
Effective prediction of SnO 2 conduction band edge potential: The key role of surface oxygen vacancies
Electronic processes in NO dimerization on Ag and Cu clusters: DFT and MRMP2 studies
First example of the correlated calculation of the one-bond tellurium-carbon spin-spin coupling constants: Relativistic effects, vibrational corrections, and solvent effects
On the basis-set dependence of local and integrated electron density properties: Application of a new computer program for quantum-chemical density analysis
A density functional theory investigation on the mechanism and kinetics of dimethyl carbonate formation on Cu 2 O catalyst
Using Gaussian model to improve biological sequence comparison
A Molecular modeling study of the changes of some steric properties of the precatalysts during the olefin metathesis reaction
Peptide reagent design based on physical and chemical properties of amino acid residues
Application to nonlinear optical properties of the RSX-QIDH double-hybrid range-separated functional
The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents ( λ 3 -iodanes): Facing the limit of the stationary quantum chemical approach
Comprehensive analysis of chemical bonding in boron clusters
An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation
An automated approach for the parameterization of accurate intermolecular force-fields: Pyridine as a case study
In silico prediction of deleterious single amino acid polymorphisms from amino acid sequence
Theoretical study on the gas-phase reaction mechanism between rhodium monoxide and methane for methanol production
Interdependence of ICD rates in paired quantum dots on geometry
Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance
A quick solvation energy estimator based on electronegativity equalization
The Role of Computational Chemistry in the Experimental Determination of the Dipole Moment of Molecules in Solution
Partial atomic charges and their impact on the free energy of solvation
Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L-tryptophan in aqueous solution
Two faces of triel bonds in boron trihalide complexes
Distance dependency and minimum amino acid alphabets for decoy scoring potentials
Green's function study of the one-electron and shake-up ionization spectra of unsaturated hydrocarbon cage compounds
Predicting helical hairpins from sequences by Monte Carlo simulations
Chemically intuitive indices for charge-transfer excitation based on SAC-CI and TD-DFT calculations
Support vector machine based training of multilayer feedforward neural networks as optimized by particle swarm algorithm: Application in QSAR studies of bioactivity of organic compounds
Modern Electronic Structure Theory
Algorithm to test the structural plausibility of a proposed elementary reaction
Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi
Numerical calculation of molecular surface area. II. Speed of calculation
A self-consistent coulomb bath model using density fitting
Theoretical mechanistic study on the radical-molecule reactions of cyanomethylidyne with PH3, H2S, and HCl
An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization
Dead-end elimination for multistate protein design
Diatropicity of tetraazanaphthalenes
Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system
Newton-Raphson Optimization of the Explicitly Correlated Gaussian Functions for Calculations of the Ground State of the Helium Atom
FEREBUS: Highly parallelized engine for kriging training
EXAT: EXcitonic analysis tool
Accurate heats of formation of polycyclic saturated hydrocarbons predicted by using the XYG3 type of doubly hybrid functionals
Structural interconnections and the role of heptagonal rings in endohedral trimetallic nitride template fullerenes
Dichroism of plasmonic chiral nanoalloys by rational design
Semidirect MP2 gradient evaluation on workstation computers: The MPGRAD program
Rational design of pincer-nickel complexes for catalytic cyanomethylation of benzaldehyde: A systematic DFT study
Geometry optimization of molecular structures in solution by the polarizable continuum model
Dynamic covalent bond from first principles: Diarylbibenzofuranone structural, electronic, and oxidation studies
The reHISS Three-Range Exchange Functional with an Optimal Variation of Hartree-Fock and Its Use in the reHISSB-D Density Functional Theory Method
Density functional theory study of a molecular allosteric switch for 2, 2'-bipyridyl-3, 3'-15-crown-5
H ··· H model potential for exchange-repulsion energy of methane dimer
Density Functional Studies of Coenzyme NADPH and Its Oxidized Form NADP+: Structures, UV-Vis Spectra, and the Oxidation Mechanism of NADPH
General method for symmetry orbitals and tensors in electronic structure calculations
IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files
Etomica : An object-oriented framework for molecular simulation
Hybrid supermolecule-polarizable continuum approach to solvation: Application to the mechanism of the Stevens rearrangement
Long-range corrected functionals satisfy Koopmans' theorem: Calculation of correlation and relaxation energies
Extension of SCF and DFT versions of chemical Hamiltonian approach to N interacting subsystems and an algorithm for their efficient implementation
Clustering one million molecular structures on GPU within seconds
Monte carlo configuration interaction applied to multipole moments, ionisation energies and electron affinities
Calculation of free energy landscapes: A histogram reweighted metadynamics approach
In silico study suggests potential drugs that target CD151 to treat breast cancer and glioblastoma
Role of nonlocal exchange in molecular crystals: The case of two proton-ordered phases of ice
EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
Unveiling gas-phase oxidative coupling of methane via data analysis
Structure and spectroscopy of water-fluoride microclusters: A combined genetic algorithm and DFT-based study
Haptic quantum chemistry
Electronic structure of CO - An exercise in modern chemical bonding theory
"Quasi flexible" automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of Delta Delta G of complexation and 1 H-NMR NOE correlation
Vibalizer : A free, web-based tool for rapid, quantitative comparison and analysis of calculated vibrational modes
Relativistic state-specific multireference perturbation theory incorporating improved virtual orbitals: Application to the ground state single-bond dissociation
Modeling a halogen dance reaction mechanism: A density functional theory study
Why does electron sharing lead to covalent bonding? A variational analysis
OBGMX: A web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field
Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains
Mechanism and rate constants of the CH2 + CH2CO reactions in triplet and singlet states: A theoretical study
Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models