yusuke1997/dblp-id-title huggingface dataset:
Computational assessment of the use of graphene-based nanosheets as Pt II chemotherapeutics delivery systems
Flexible effective fragment QM/MM method: Validation through the challenging tests
Calculation of binding free energies of inhibitors to plasmepsin II
A reduced-restricted-quasi-Newton-Raphson method for locating and optimizing energy crossing points between two potential energy surfaces
Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area
An estimation method of binding free energy in terms of ABEEMsigmapi/MM and continuum electrostatics fused into LIE method
Optimal use of the recurrence relations for the evaluation of molecular integrals over Cartesian Gaussian basis functions
gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison
Ab initio study of the ground and excited states of HCP and its isomer HPC
A self-consistent Hirshfeld method for the atom in the molecule based on minimization of information loss
Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation
beta-Hairpin prediction with quadratic discriminant analysis using diversity measure
Parallel Computation of the MP2 Energy on Distributed Memory Computers
Conformational analysis of 2, 3, 6, 7-tetrahydroazepines with implications for D 1 -selective benzazepines
Theoretical study on the methyl radical with chlorinated methyl radicals CH 3- n Cl n ( n = 1, 2, 3) and CCl 2
On the Vibrational linear and nonlinear optical properties of compounds involving noble gas atoms: HXeOXeH, HXeOXeF, and FXeOXeF
Exploring the Tl 2 H 2 potential energy surface: A comparative analysis with group 13 systems and experiment
Nature of nonclassical bonds in Closo-Boranes: Nonlinear population analysis approach
Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory
Simulated infrared spectra of triflic acid during proton dissociation
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach
Additive CHARMM Force Field for Pterins and Folates
A randomized kinematics-based approach to pharmacophore-constrained conformational search and database screening
Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model
A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure
Finite-Temperature Dimer Method for Finding Saddle Points on Free Energy Surfaces
Dual-Branch Graph Neural Network for Predicting Molecular Odors and Discovering the Relationship Between Functional Groups and Odors
Predicting experimental electrophilicities from quantum and topological descriptors: A machine learning approach
MVPACK: A package to calculate energy levels and magnetic properties of high nuclearity mixed valence clusters
Predicting redox potentials by graph-based machine learning methods
Peptide models XVI. The identification of selected HCO - L - SER - NH2 conformers via a systematic grid search using ab initio potential energy surfaces
A comparison of predicted and experimental vibrational spectra in some small fluorocarbons
Combining quantum mechanics and interatomic potential functions in ab initio studies of extended systems
Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method
Assessment of the van der Waals, Hubbard U parameter and spin-orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters
New Implementation of a Program to Calculate Correlated Band Structures of Polymers: An Application to the Band Strucutre of Polyparaphenylene (PPP)
Esters flash point prediction using artificial neural networks
Fast determination of the optimal rotational matrix for macromolecular superpositions
Cooperativity and cluster growth patterns in acetonitrile: A DFT study
Predicting adsorption enthalpies on silicalite and HZSM-5: A benchmark study on DFT strategies addressing dispersion interactions
Fanpy: A python library for prototyping multideterminant methods in ab initio quantum chemistry
Systematic sparse matrix error control for linear scaling electronic structure calculations
Parallelization strategies for molecular simulation using the Monte Carlo algorithm
An unconventional ligand-binding mechanism of substrate-binding proteins: MD simulation and Markov state model analysis of BtuF
The VMFCI method: A flexible tool for solving the molecular vibration problem
Electric field convergence versus atomic basis sets in all-siliceous zeolites
stk: A python toolkit for supramolecular assembly
A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: Application to molybdocene-cysteine complexes
Improving description of hydrogen bonds at the semiempirical level: water-water interactions as test case
TGSA: A molecular superposition program based on topo-geometrical considerations
Internal Motions of Carbohydrates as PRobed by Comparative Molecular Modeling and Nuclear Magnetic Resonance of Ethyl beta-Lactoside
Fast summation boundary element method for calculating solvation free energies of macromolecules
Computations on the A-X transition of isoprene-OH-O 2 peroxy radicals
PyFREC 2.0: Software for excitation energy transfer modeling
Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme
A novel approach for designing simple point charge models for liquid water with three interaction sites
Computing free energy hypersurfaces for anisotropic intermolecular associations
Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin
Efficient free energy calculation of water across lipid membranes
Constrained optimization in delocalized internal coordinates
Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: Can the α3 and β2m domains be neglected?
The behavior of transition metal nitrido bonds towards protonation rationalized by means of localized bonding schemes and their weights
Intermolecular potential energy surface for CS 2 dimer
Calculating standard reduction potentials of [4Fe-4S] proteins
Exact and exclusive electron localization indices within QTAIM atomic basins
Conformational energies calculated by the molecular mechanics program CHARMm
Determination of the stereochemistry of natural products from nuclear magnetic resonance data by constrained molecular dynamics
A theoretical study of thermal [1, 3]-sigmatropic rearrangements of 3-trimethylsilyl-1-pyrazoline: Concerted vs. stepwise mechanisms
Nonclassical fullerenes with a heptagon violating the pentagon adjacency penalty rule
CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations
Publisher's Note: "Software News and Updates" section of the Journal of Computational Chemistry
Approximate molecular electrostatic potentials from semiempirical wavefunctions
Modeling adsorption reactions of ammonium perchlorate on rutile and anatase surfaces
Selective oxidation of styrene on an oxygen-adsorbed Au(111): A density functional theory study
Moving of fullerene between potential wells in the external icosahedral shell
Bayesian uncertainty quantification in inverse modeling of electrochemical systems
Excess electron is trapped in a large single molecular cage C 60 F 60
Associative versus dissociative binding of CO to 4 d transition metal trimers: A density functional study
Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations
An assessment of pure, hybrid, meta, and hybrid-meta GGA density functional theory methods for open-shell systems: The case of the nonheme iron enzyme 8R-LOX
Numerical comparisons of three recently proposed algorithms in the protein folding problem
Investigation of the use of density functionals in second- and third-row transition metal dimer calculations
Theoretical and experimental investigation of crown/ammonium complexes in solution
polyGraft 1.0: A program for molecular structure and topology generation of polymer-grafted hybrid nanostructures
Equilibrium between tri- and tetra-coordinate chalcogenuranes is critical for cysteine protease inhibition
Protein alignment: Exact versus approximate. An illustration
Efficient Conformational Space Samling for Nucleosides Using Internal Coordinat Monte Carlo Simulations and a Modified Furanose Description
TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach
Scoring molecular wires subject to an ultrafast laser pulse for molecular electronic devices
The Jahn-Teller effect of the Cr 2+ ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations
Pairwise verlet lists: Combining cell lists and verlet lists to improve memory locality and parallelism
Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation
Determination of the pKa between the active site cysteines of thioredoxin and DsbA
OSPREY 3.0: Open-source protein redesign for you, with powerful new features
Force fields for metallic clusters and nanoparticles
Prediction of Activation Energies of Organic Molecules With at Most Seven Non-Hydrogen Atoms Using Quantum-Chemically Assisted ML
Computational studies on the dimers and the thermal dimerization of norbornadiene
Direct Search for the Molecular Conformation Problem
Ab Initio SCF Calculations on Low-Energy Conformers of Cyclohexaglycine
Identifying native-like protein structures using physics-based potentials
An efficient algorithm for complete active space valence bond self-consistent field calculation
Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations
The QM-MM interface for CHARMM-deMon
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method
Cover Image, Volume 39, Issue 18
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories
Steric effects on alkyl cation affinities of maingroup-element hydrides
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path-search algorithm
Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins
Incorporating the effect of ionic strength in free energy calculations using explicit ions
New approach to free energy of solvation applying continuum models to molecular dynamics simulation
Computation of hydration free energies of organic solutes with an implicit water model
Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-molecules
Combination of the CHARMM27 force field with united-atom lipid force fields
Density functional study of porphyrin distortion effects on redox potential of heme
Generalized solution of interdiffusion problem: Optimal approach for multicomponent bounded systems
PASSerRank: Prediction of allosteric sites with learning to rank
Accelerating wavepacket propagation with machine learning
Adaptation of a fast Fourier transform-based docking algorithm for protein design
Polymer dynamics in torsion space
Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO
A CGenFF-based force field for simulations of peptoids with both cis and trans peptide bonds
Descriptors for amino acids using MolSurf parametrization
Theoretical Study on Adsorption of Halogenated Benzenes on Montmorillonites Modified With M(I)/M(II) Cations
STO and GTO field-induced polarization functions for H to Kr
Fast fragments: The development of a parallel effective fragment potential method
An evaluation of the radial part of numerical integration commonly used in DFT
CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol
A joint study based on the electron localization function and catastrophe theory of the chameleonic and centauric models for the Cope rearrangement of 1, 5-hexadiene and its cyano derivatives
Reply on the 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]
New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation
Structural and static electric response properties of highly symmetric lithiated silicon cages: Theoretical predictions
Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular-orbital method
Evolution of lone pair of excess electrons inside molecular cages with the deformation of the cage in e 2 @C 60 F 60 systems
How the choice of a computational model could rule the chemical interpretation: The Ni(II) catalyzed ethylene dimerization as a case study
A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft
Comment on "Density functional theory study of 1, 2-dioxetanone decomposition in condensed phase"
Molecular dynamics simulation of anticancer drug delivery from carbon nanotube using metal nanowires
Collective motion artifacts arising in long-duration molecular dynamics simulations
Theoretical insights on the inhibition mechanism of a class A Serine Hydrolase by avibactam
Expanding chalcogen bonds in thiophenes to interactions with halogens
Modulating stability of functionalized fullerene cations [R-C60]+ with the nature of R-group
A kernel-based method to determine optimal sampling times for the simultaneous estimation of the parameters of rival mathematical models
A dynamic lattice searching method with constructed core for optimization of large lennard-jones clusters
Fourier transform general formula for systematic potentials
First-principles study of molecular hydrogen dissociation on doped Al 12 X (X = B, Al, C, Si, P, Mg, and Ca) clusters
Sensitivity analysis and uncertainty calculation for dispersion corrected density functional theory
KoBra: A rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings
Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl
The enhanced extended phenomenological kinetics method to deal with timescale disparity problem among different reaction pathways
Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
QSPR modeling of enthalpies of formation for organometallic compounds by SMART-based optimal descriptors
Parameterization of the GPR119 Receptor Agonist AR231453
Oxygen adsorption characteristics on hybrid carbon and boron-nitride nanotubes
Ab initio potential energy surface and vibration-rotation energy levels of germanium dicarbide, GeC2
Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior
Natural transition orbitals for complex two-component excited state calculations
Small molecule activation by sila/germa boryne species
Software news and updates carma: A molecular dynamics analysis program
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction
Quantum chemical comparison of vertical, adiabatic, and 0-0 excitation energies: The PYP and GFP chromophores
Hirshfeld partitioning of the electron density: Atomic dipoles and their relation with functional group properties
Cationic Closo Carboranes - Promising Weakly Coordinating Ions
Prediction of aqueous solubility of drugs and pesticides with COSMO-RS
Computational determination of fundamental pathway and activation barriers for acetohydroxyacid synthase-catalyzed condensation reactions of alpha-keto acids
1, 3-Dipolar cycloadditions of Stone-Wales defective single-walled carbon nanotubes: A theoretical study
Averaged electron densities for averaged conformations
Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method
An efficient first-principle approach for electronic structures calculations of nanomaterials
Genetic Algorithms: A Robust Scheme for Geometry Optimizations and Global Minimum Structure Problems
Performance of density-functional tight-binding models in describing hydrogen-bonded anionic-water clusters
Geometry optimization of metal complexes using natural internal coordinates: Representation of skeletal degrees of freedom
Excited state tracking during the relaxation of coordination compounds
The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics
Loop closure via bond scaling and relaxation
Generation of Kekulé valence structures and the corresponding valence bond wave function
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
Vertical excitation energies for ribose and deoxyribose nucleosides
Accurate prediction of the properties of materials using the CAM-B3LYP density functional
Development and testing of an algorithm for efficient MP2/CCSD(T) energy estimation of molecular clusters with the 2-body approach
Mechanism for large first hyperpolarizabilities of phosphonic acid stilbene derivatives
An inexpensive density functional theory-based protocol to predict accurate 19F-NMR chemical shifts
Understanding topological symmetry: A heuristic approach to its determination
Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations
A computational study of the reactivities of four-membered heavy carbene systems
Temperature dependence of the transport of single-file water molecules through a hydrophobic channel
A fast approximate extension of the interacting quantum atoms energy decomposition to excited states
Communications on quantum similarity, part 3: A geometric-quantum similarity molecular superposition algorithm
A physically meaningful method for the comparison of potential energy functions
Structures, binding energies, temperature effects, infrared spectroscopy of [Mg(NH3)n = 1-10]+ clusters from DFT and MP2 investigations
Semiempirical Study of Compounds with Intramolecular O-H--O Hydrogen Bonds. II. Further Verification of a Modified MNDO Method
Novel dimer based descriptors with solvational computation for QSAR study of oxadiazoylbenzoyl-ureas as novel insect-growth regulators
CAST: A new program package for the accurate characterization of large and flexible molecular systems
Using density based indexes to characterize excited states evolution
Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi
Flexible ligand docking using a robust evolutionary algorithm
Development of modified force field for cation-amino acid interactions: Ab initio-derived empirical correction terms with comments on cation- interactions
Trends of the bonding effect on the performance of DFT methods in electric properties calculations: A pattern recognition and metric space approach on some XY 2 (X = O, S and Y = H, O, F, S, Cl) molecules
Evaluation of protein-ligand binding free energy focused on its entropic components
All-atom simulations of the trimeric spike protein of SARS-CoV-2 in aqueous medium: Nature of interactions, conformational stability and free energy diagrams for conformational transition of the protein
Methane activation by chromium oxide cations in the gas phase: A theoretical study
On the isotropy of induced multipole moments in heavy ion complexes
C library for topological study of the electronic charge density
Cover Image, Volume 40, Issue 15
Structures and properties of lanthanide and actinide complexes by a new density functional approach: Lanthanum, gadolinium, lutetium, and thorium halides as case studies
PDielec: The calculation of infrared and terahertz absorption for powdered crystals
Rapid empirical calculation of the first ( n or π) ionization potential of organic molecules
How the addition of atomic hydrogen to a multiple bond can be catalyzed by water molecules
Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations
Cover Image, Volume 41, Issue 3
Natural bond orbital analysis in the ONETEP code: Applications to large protein systems
Design and parameterization of a stochastic cellular automaton describing a chemical reaction
Rational design of near-infrared absorbing organic dyes: Controlling the HOMO-LUMO gap using quantitative molecular orbital theory
MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers
Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
Collisional Dynamics of Newly Detected Protonated Dicyanoacetylene (NC4NH+$$ {\mathrm{NC}}_4{\mathrm{NH}}^{+} $$) With He at Low Interstellar Temperatures
Acceleration of the GAMESS-UK electronic structure package on graphical processing units
Algorithm to evaluate rate constants for polyatomic chemical reactions. II. Applications
Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary
A practical and efficient method to calculate AIM localization and delocalization indices at post-HF levels of theory
Periodic local MP2 method for the study of electronic correlation in crystals: Theory and preliminary applications
Solving the low dimensional Smoluchowski equation with a singular value basis set
Intra- and intermolecular interactions in crystals of polar molecules. A study by the mixed quantum mechanical/molecular mechanical SCMP-NDDO method
Picture-word order compound protein interaction: Predicting compound-protein interaction using structural images of compounds
Computational investigation into the fluorescence of luciferin analogues
Performance of the semiempirical PM3 (tm) method in the geometry optimization of transition metal complexes
The mechanism of sorbitol dehydration in hot acidic solutions
Prediction of beta-sheet topology and disulfide bridges in polypeptides
Coarse-grained molecular dynamics simulations of protein-ligand binding
Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities
Cover Image, Volume 40, Issue 28
Electron transfer between tryptophan and tyrosine: Theoretical calculation of electron transfer matrix element for intramolecular hole transfer
Transition Structure Modeling by Intersecting Potetntial Energy Surfaces
The Reaction between Bromine and the Water Dimer and the Highly Exothermic Reverse Reaction
Development of molecular cluster models to probe pyrite surface reactivity
Uncovering the hidden reactivity of benzyne/aryne precursors utilized under milder condition: Bonding and stability studies by EDA-NOCV analyses
New developments in the GDIS simulation package: Integration of VASP and USPEX
Comment on "Fast determination of the optimal rotational matrix for macromolecular superpositions" [J. Comp. Chem. 31 1561 (2010)]
N 2 O in small para -hydrogen clusters: Structures and energetics