yusuke1997/dblp-id-title huggingface dataset:
Efficient prediction for high precision CO-N2 potential energy surface by stacking ensemble DNN
Interplay between two spin states determines the hydroxylation catalyzed by P450 monooxygenase from Trichoderma brevicompactum
Standard grids for high-precision integration of modern density functionals: SG-2 and SG-3
Electronegativity estimator built on QTAIM-based domains of the bond electron density
The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields
Efficiency of the multicanonical simulation method as applied to peptides of increasing size: The heptapeptide deltorphin
Vibrational Raman optical activity of pi-conjugated helical systems: Hexahelicene and heterohelicenes
The reactivity of the trapping reaction of the benzene-bridged boron/phosphorus-based frustrated Lewis pair with difluorocarbene and its group 14 analogs: A theoretical investigation
Consideration of data load time on modern processors for the Verlet table and linked-cell algorithms
Calculation of the interaction energy in a localized representation for a trimer (Ne 3 ) system
A potential function for computer simulation studies of proton transfer in acetylacetone
Determining the role of the underlying orbital-dependence of PBE0-DH and PBE-QIDH double-hybrid density functionals
Molecular dynamics studies of the solubility behavior of carbon dioxide (CO 2 ), difluoromethane (R-32), 1-chloro-3,3,3-trifluoropropene (R-1233zd(E)) and 2,3,3,3-tetrafluoro-1-propene (R-1234yf) in pentaerythritol tetra(2-ethylhexanoate) (PEB8), pentaerythritol tetrabutyrate (PEC4) and pentaerythritol tetraoctanoate (PEC8)
Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design
Identification and thermodynamic treatment of several types of large-amplitude motions
Development and optimization of a novel genetic algorithm for identifying nanoclusters from scanning transmission electron microscopy images
Role of stereoelectronic features of imine and enamine in ( S )-proline catalyzed mannich reaction of acetaldehyde: An in silico study
Computational Insights Into Corrosion Inhibition Mechanism: Dissociation of Imidazole on Iron Surface
An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer
Mechanistic Study of LIDT Reduction in KH 2 PO 4 With Y i Predicted by Density Functional Theory
Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes
An ab initio theoretical study of electronic structure and properties of 2-deoxyguanosine in gas phase and aqueous media
Calculation of affinities of peptides for proteins
Electronic structure and thermodynamics of V2O3 polymorphs
Role of the anomeric effect in methanediamines in the gas phase and aqueous solutions
Efficient exploration of conformational space using the stochastic search method: application to -peptide oligomers
Ab initio and DFT studies on hydrolyses of phosphorus halides
The dramatic effect of NH 3 co-ligation on the FE + -assisted activation of carbon dioxide in the gas phase: From bare metal ions to complexes
A theoretical investigation on optimal structures of ethane clusters (C 2 H 6 ) n with n ≤ 25 and their building-up principle
Giant Dipole Moments: Remarkable Effects Mono-, Di-, and Tri- Hydrated 5,6-Diaminobenzene-1,2,3,4-Tetracarbonnitrile
Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function
Iterative diagonalization for orbital optimization in natural orbital functional theory
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation
Molecular caps for full quantum mechanical computation of peptide-water interaction energy
Molecular mechanisms from reaction coordinate graph enabled multidimensional free energies illustrated on water dimer hydrogen bonding
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity
On closed-shell interactions between heavy main-group elements
Acetalization and thioacetalization of cabonyl compounds: A case study based on global and local electrophilicity descriptors
Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force
Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets
CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS
DFT/TD-DFT investigation on Ir(III) complexes with N -heterocyclic carbene ligands: Geometries, electronic structures, absorption, and phosphorescence properties
Hydrogen-bond networks in finite ice nanotubes
Complete maps of molecular-loop conformational spaces
Theoretical exploration of the reactivity of cellulose models under non-thermal plasma conditions - mechanistic and NBO studies
New parallel algorithm for MP2 energy gradient calculations
Interaction between alkyl radicals and single wall carbon nanotubes
Systematic evaluation and refinement of existing all-atom force fields for the simulation of liquid acetonitrile
Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules
Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method
Stochastic simulation of physicochemical processes performance over supported metal nanoparticles
van der Waals host-guest complexes: Can one predict complexation selectivity of neutral guests by a cryptophane? MD-FEP studies in gas phase and chloroform solution
On the highest oxidation states of the actinoids in AnO 4 molecules (An = Ac - Cm): A DMRG-CASSCF study
Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers
An atoms-in-molecules characterization of the nature of the OO bond in peroxides and nitroxide dimers
Computational Study of Complexation in LiH:nNH 3 ( n = 1-4) Clusters: An Interplay Among Hydrogen, Dihydrogen, and Lithium Bonds
Statistical analysis of the estimation of distance measures
Parallel pseudospectral electronic structure: I. Hartree-Fock calculations
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design
A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm
Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, " by Jason Wagoner and Nathan A. Baker
Theoretical investigation of novel carbazole-fluorene based D-π-A conjugated organic dyes as dye-sensitizer in dye-sensitized solar cells (DSCs)
Probing the reactivity of microhydrated α-nucleophile in the anionic gas-phase S N 2 reaction
Computational chemistry development of a unified free energy Markov model for the distribution of 1300 chemicals to 38 different environmental or biological systems
Nature of the water/aromatic parallel alignment interactions
Properties of atoms in electronically excited molecules within the formalism of TDDFT
Interpretation of ANN-based QSAR models for prediction of antioxidant activity of flavonoids
A generalized higher order kernel energy approximation method
A molecular dynamics study of a fully zwitterionic copolymer/ionic liquid-based electrolyte: Li+ transport mechanisms and ionic interactions
Generation of basis sets with high degree of fulfillment of the Hellmann-Feynman theorem
Dcdftbmd: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum Mechanical Molecular Dynamics Simulations
Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes
Some case studies on application of " r m 2 " metrics for judging quality of quantitative structure-activity relationship predictions: Emphasis on scaling of response data
Recurrent Neural Network/Machine Learning Predictions of Reactive Channels in H + + C 2 H 4 at E Lab = 30 eV: A Prototype of Ion Cancer Therapy Reactions
Theoretical study on the gas phase reaction of propargyl alcohol with hydroxyl radical
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
Computational study of the process of hydrogen bond breaking: The case of the formamide-formic acid complex
Basis-set completeness profiles in two dimensions
Conformational searching methods for small molecules. III. Study of stochastic methods available in SYBYL and MACROMODEL
Barrier heights for H-atom abstraction by HO . 2 from n -butanol - A simple yet exacting test for model chemistries?
CoTCNQ as a Catalyst for CO 2 Electroreduction: A First Principles r 2 SCAN Meta-GGA Investigation
New Tabu Search based global optimization methods outline of algorithms and study of efficiency
Excitation energy transfer pathways in light-harvesting proteins: Modeling with PyFREC
To Be or Not to Be: Demystifying the 2nd-Quantized Picture of Complex Electronic Configuration Patterns in Chemistry with Natural Poly-Electron Population Analysis
Molecular dynamics study of a new metastable allotropic crystalline form of gallium - supertetrahedral gallium
Gradient tabu search
Substitution effects on olefin epoxidation catalyzed by Oxoiron(IV) porphyrin π-cation radical complexes: A dft study
Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks
First Principles Calculations Toward Understanding SERS of 2, 2′-Bipyridyl Adsorbed on Au, Ag, and Au-Ag Nanoalloy
Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation
Configuration space partitioning and matrix buildup scaling for the vibrational configuration interaction method
Constant pH molecular dynamics in generalized Born implicit solvent
Terminal end-on coordination of dinitrogen versus isoelectronic CO: A comparison using the charge displacement analysis
A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways
Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation
Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons
Geometries, electronic structures, and bonding properties of endohedral Group-14 Zintl clusters TM@E10 (TM = Fe, Co, Ni; E = Ge, Sn, Pb)
Using correlated parameters for improved ranking of protein-protein docking decoys
Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria
A massively multicore parallelization of the Kohn-Sham energy gradients
From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins
Interatomic exchange-correlation interaction energy from a measure of quantum theory of atoms in molecules topological bonding: A diatomic case
A quantum-chemical perspective on the laser-induced alignment and orientation dynamics of the CH3X (X = F, Cl, Br, I) molecules
Influence of the solvent on the Lewis acidity of antimony pentahalides and group 13 Lewis acids toward acetonitrile and pyridine
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model
Distorted silicon hydrides - a comparative study with various density functionals
Pteros: Fast and easy to use open-source C++ library for molecular analysis
Molecular Mechanics (MM3) Parameterization of Hydroxylamine and Methyl Derivatives
Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index
Quantum wave packet and quasiclassical trajectory studies of the reaction H( 2 S) + CH(X 2 Π; v = 0, j = 1) → C( 1 D) + H 2 (X 1 Σg+): Coriolis coupling effects and stereodynamics
Insights into the solubility of γ D-crystallin from multiscale atomistic simulations
Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms
Effects of entropy on the gas-phase pyrolysis of ethyl N , N -dimethylcarbamate
Generalized gradient approximation adjusted to transition metals properties: Key roles of exchange and local spin density
Electron localizability for hexagonal element structures
Relativistic effects and the halogen dependencies in the 13C chemical shifts of CH4-nIn, CH4-nBrn, CCl4-nIn, and CBr4-nIn (n=0-4)
The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2)
Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements
BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method
QUILD: QUantum-regions interconnected by local descriptions
Ab Initio energetics of Si‒O bond cleavage
Theoretical study on the mechanism of the 1CHCl + NO reaction
Time-dependent coupled-cluster calculations of polarizabilities and dispersion energy coefficients
Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence with polarization quality of the sixth period for solid-state calculations
Structure, stability, and nature of bonding in carbon monoxide bound EX3+ complexes (E = group 14 element; X = H, F, Cl, Br, I)
Assessment of programs for ligand binding affinity prediction
Transition polarizability model of induced resonance Raman optical activity
The structure and stability of Si60 and Ge60 cages: A computational study
A model hamiltonian tuned toward high level ab initio calculations to describe the character of excitonic states in perylenebisimide aggregates
Combined NMR three-bond scalar coupling measurements and QM calculations to calculate OH-rotamer equilibrium of polyalcohols
Approach to regiochemistry using local softness in 1, 3-dipolar cycloadditions
A polarizable ellipsoidal force field for halogen bonds
Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures
Systematic study of the effect of HSE functional internal parameters on the electronic structure and band gap of a representative set of metal oxides
Computational mechanistic studies on persulfate assisted p-phenylenediamine polymerization
Combining frozen-density embedding with the conductor-like screening model using Lagrangian techniques for response properties
Reply to 'comment on "extending hirshfeld-I to bulk and periodic materials"'
The physical nature of the ultrashort spike-ring interaction in iron maiden molecules
Revised CHARMM force field parameters for iron-containing cofactors of photosystem II
Replica sub-permutation method for molecular dynamics and monte carlo simulations
Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy Landscape
The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin
Free energy change estimation: The Divide and Conquer MBAR method
Mapping the correlations between bandgap, HOMO, and LUMO trends for meta substituted Zn-MOFs
Molecular structures of the two most stable conformers of free glycine
Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules - Preliminary validations of a polarizable potential by ab initio quantum chemistry
Van Der Waals heterogeneous layer-layer carbon nanostructures involving π···H-C-C-H···π···H-C-C-H stacking based on graphene and graphane sheets
IBIsCO: A molecular dynamics simulation package for coarse-grained simulation
Promising insights in parallel grid-based algorithms for quantum chemical topology
New functionalities in the GROMOS biomolecular simulation software
Molecular dynamics of 18-crown-6 complexes with alkali-metal cations and urea: Prediction of their conformations and comparison with data from the cambridge structural database
Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions
The structure, properties, and nature of HArF-HOX (X = F, Cl, Br) complex: An ab initio study and an unusual short hydrogen bond
A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O CH2O + CH3
Size-guided multi-seed heuristic method for geometry optimization of clusters: Application to benzene clusters
Revision of the GROMOS 56A6 CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains
GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity
Density functional investigation and bonding analysis of pentacoordinated iron complexes with mixed cyano and carbonyl ligands
Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination
Erratum: NBO 6.0: Natural bond orbital analysis program
SIMPRE1.2: Considering the hyperfine and quadrupolar couplings and the nuclear spin bath decoherence
Q-Chem 2.0: a high-performance ab initio electronic structure program package
Constraint structure optimization to a specific minimum using ionization energy
The nitrogen edge-doped effect on the static first hyperpolarizability of the supershort single-walled carbon nanotube
An environmental pseudopotential approach to molecular interactions: Implementation in MOLPRO
Exploring the limits of gradient corrections in density functional theory
Ab-initio simulations of materials using VASP: Density-functional theory and beyond
A theoretical ab initio study on the H2NO + O3 reaction
Vibrational averaging of the chemical shift in crystalline α-glycine
Reliable radical stabilization energies from diffusion Monte Carlo calculations
Multidimensional persistence in biomolecular data
A DLPNO-CCSD(T) benchmarking study of intermolecular interactions of ionic liquids
Toward an automated analysis of exchange pathways in spin-coupled systems
Toward the identification of molecular cogs
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. Part 3. Application to electrochemical systems comprising second-order chemical reactions
Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations
High-dimensional model representations generated from low order terms - lp-RS-HDMR
Critical evaluation of search algorithms for automated molecular docking and database screening
A consensus procedure improving solvent accessibility prediction
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions
Toward the understanding of the environmental effects on core ionizations
Ground and excited state charge transfer at aqueous nanodiamonds
Evolutionary conservation of amino acids contributing to the protein folding transition state
Comparison of line search minimization algorithms for exploring topography of multidimensional potential energy surfaces: Mg + Ar n case
Accurate integration over atomic regions bounded by zero-flux surfaces
Theoretical modeling of the heme group with a hybrid QM/MM method
Stability of the hydration layer of tropocollagen: A QM study
Density functional study on the reaction mechanism of palladium-catalyzed addition of cyanoboranes to alkynes
Chemical mechanism of surface-enhanced raman scattering spectrum of pyridine adsorbed on Ag cluster: Ab initio molecular dynamics approach
Calculation of relative binding affinities of fructose 1, 6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method
Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations
Molecular dynamic simulations, GIAO-NMR and TD-DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution
Hydration of selenolate moiety: Ab initio investigation of properties of O-H⋯Se(-) hydrogen bonds in CH3Se(-)⋯(H2O)n clusters
Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace
Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes
Simple algorithm for isothermal-isobaric molecular dynamics
Single determinant N-representability and the kernel energy method applied to water clusters
Polarizable force field parameterization and theoretical simulations of ThCl4-LiCl molten salts
Geometric Molecular Similarity from Volume-Based Distance Minimization Application to Saxitoxin and Tetrodotoxin
Ab Initio Study of Low-Lying Electronic States of the PF2 Radical
A computational chemist approach to gas sensors: Modeling the response of SnO 2 to CO, O 2 , and H 2 O Gases
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space
Extensive theoretical studies on the low-lying electronic states of indium monochloride cation, InCl +
A high-level ab initio study of the N 2 + N 2 reaction channel
BinderSpace : A package for sequence space analyses for datasets of affinity-selected oligonucleotides and peptide-based molecules
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling
Energy-based prediction of amino acid-nucleotide base recognition
Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen-storage catalyst: A classical and ab initio molecular simulation study
Information on Gas-Phase Diatomic Molecules from Magnetically Induced Current Densities
Computational insights into the S 3 transfer reaction: A special case of double group transfer reaction featuring bicyclically delocalized aromatic transition state geometries
Quantum Master Equation Approach to Singlet Fission Dynamics in Pentacene Linear Aggregate Models: Size Dependences of Excitonic Coupling Effects
Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10-electron hydrides
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations
Is large-scale ab initio Hartree-Fock calculation chemically accurate? Toward improved calculation of biological molecule properties
Energy and spectroscopic parameters of neutral and cations isomers of the C n H 2 ( n = 2-6) families using high-level ab-initio approaches
Imine hydrosilylation using an iron complex catalyst: A computational study
Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models
Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing
Methodology of predicting approximate shapes and size distribution of micelles: Illustration for simple models
An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
Continuous symmetry analyses: C nv and D n measures of molecules, complexes, and proteins
SARS-CoV protease inhibitors design using virtual screening method from natural products libraries