yusuke1997/dblp-id-title huggingface dataset:
Analysis of electronic structures and chemical bonding of metal-rich compounds. I. Density functional study of Pt metal, LiPt 2 , LiPt, and Li 2 Pt
Ab initio study of the mechanism of the atmospheric reaction: NO2 + O3 NO3 + O2
Reversible peptide folding: Dependence on molecular force field used
Effect of the damping function in dispersion corrected density functional theory
Relaxed energetic maps of kappa-carrabiose: A DFT study
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
Bond paths between distant atoms do not necessarily indicate dominant interactions
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations
An efficient parallel algorithm for the calculation of canonical MP2 energies
A dual-level state-specific time-dependent density-functional theory
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure
Linear Dependency in the Refinement of Force Constants with the Jacobian Method
Assessment of the orbital-optimized coupled-electron pair theory for thermochemistry and kinetics: Improving on CCSD and CEPA(1)
Thermodynamics and kinetics of large-time-step molecular dynamics
Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table
Monte-Carlo model for the hydrogenation of alkenes on metal catalyst
Implementation of renormalized excitonic method at ab initio level
Electronic and geometric structure analysis of neutral and anionic alkali metal complexes of the CX series (X = O, S, Se, Te, Po): The case of M(CX) n = 1-4 (M = Li, Na) and their dimers
Yoink: An interaction-based partitioning API
Impact of Structure on Excitation Energies and S 1 -T 1 Energy Gaps of Asymmetrical Systems of Interest for Inverted Singlet-Triplet Gaps
Tunable model promoters in DFT simulations of catalysts
Cover Image, Volume 40, Issue 29
Free-energy calculations of the host-guest association in grafted supramolecular assemblies
The Lewis legacy: The chemical bond - A territory and heartland of chemistry
A two-scale approach to electron correlation in multiconfigurational perturbation theory
Cover Image, Volume 39, Issue 32
Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols
Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
Donor→acceptor coordination interactions in 1, 3-bis(NHC)triazenyl Cations: An electronic structure analysis
Parallel MP2-energy evaluation: Simulated shared memory approach on distributed memory parallel machines
A comprehensive analysis of charge transfer effects on donor-pyrene (bridge)-acceptor systems using different substituents
Partitioning the motion in molecular dynamics simulations into characteristic modes of motion
Artificial neural network-based drug design for diabetes mellitus using flavonoids
Kinetic energy decomposition scheme based on information theory
DelPhi Suite: New Developments and Review of Functionalities
Assessment of quantum-chemical methods for electronic properties and geometry of signaling biomolecules
Dual-level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical
Ab initio study of the positronation of the CaO and SrO molecules including calculation of annihilation rates
Feshbach resonances in D + HD(v = 1, j = 0) reaction at low collision energies
Theoretical study and rate constant calculation for the reactions of SH (SD) with Cl2, Br2, and BrCl
Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil
Molecular mechanics (MM4) calculations on alkenes
SuSMoST: Surface Science Modeling and Simulation Toolkit
A distance geometry heuristic for expanding the range of geometries sampled during conformational search
Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method
The Relation Between the Excited Electronic States of Acene Radical Cations and Neutrals - A Computational Analysis
A chirality-based metrics for free-energy calculations in biomolecular systems
Magnetic properties of CrMnGe n ( n = 3-20) clusters
Acceleration of a QM/MM-QMC simulation using GPU
Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function
Ion strength limit of computed excess functions based on the linearized Poisson-Boltzmann equation
Multiscale simulation of pollution gases adsorption in porous organic cage CC3
Extended method for adiabatic mode reordering
Corrected small basis set Hartree-Fock method for large systems
Atomistic hybrid particle-field molecular dynamics combined with slip-springs: Restoring entangled dynamics to simulations of polymer melts
Communications on quantum similarity (2): A geometric discussion on holographic electron density theorem and confined quantum similarity measures
Understanding cross-boundary events in ONIOM QM: QM' calculations
Are accurate computations of the 13 C′ shielding feasible at the DFT level of theory?
Temperature dependence of vibrational modes of CH3‒C≡C(ads) and I(ads) coadsorbed on Ag(111): Ab initio molecular dynamics approach
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields
Mechanistic study on the coupling reaction of CO2 with propylene oxide catalyzed by (CH3)4PI·MgCl2
Structural stability and phase transition in OsC and RuC
Fluxional Bonds in Planar B19-, Tubular Ta@B20-, and Cage-Like B39-
Interactions of the "piano-stool" [ruthenium(II)(η 6 -arene)(quinolone)Cl] + complexes with water; DFT computational study
SONHICA (Simple optimized non-HIerarchical Cluster Analysis): A new tool for analysis of molecular conformations
Bonding analysis of planar hypercoordinate atoms via the generalized BLW-LOL
Charge optimization of the interface between protein kinases and their ligands
Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters
Looking for some free energy? Call JEFREE (...)
Molecular mechanical study of halogen bonding in drug discovery
Transition state theory with Tsallis statistics
Melting of icosahedral nickel clusters under hydrostatic pressure
CHAMPION: Chalmers hierarchical atomic, molecular, polymeric and ionic analysis toolkit
Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions
Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4
Trimeric cluster of lithium amidoborane - the smallest unit for the modeling of hydrogen release mechanism
The influence of relativistic effects on nuclear magnetic resonance spin-spin coupling constant polarizabilities of H2O2, H2S2, H2Se2, and H2Te2
Dismantlement of ammonia upon interaction with Be n ( n ≤ 10) clusters
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
Local-scaling transformation version of density functional theory: Application to atoms and diatomic molecules
Hydrogen splitting by pyramidalized 13-15 donor-acceptor cryptands: A computational study
Observations concerning the treatment of long-range interactions in molecular dynamics simulations
Ab initio simulation of the IR spectra of pyrope, grossular, and andradite
An economic prediction of refinement coefficients in wavelet-based adaptive methods for electron structure calculations
Mono- and Poly- Ligated Complexes of Zn 2+ : An Ab Initio Analysis of the Metal-Ligand Interaction Energy
Assessment of Free Energies From Electrostatic Embedding Density Functional Tight Binding-Based/Molecular Mechanics in Periodic Boundary Conditions
New procedure to evaluate aromaticity at the density functional theory, Hartree-Fock, and post-self-consistent field levels
A survey of recent developments in ab initio valence bond theory
Madelung fields from optimized point charges for ab initio cluster model calculations on ionic systems
Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase
The development of an artificial organic networks toolkit for LabVIEW
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems
Assessment of linear finite-difference Poisson-Boltzmann solvers
Orbital-orthogonality constraints and basis-set optimization
First-principles calculations on thermodynamic properties of BaTiO3 rhombohedral phase
A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation
nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations
van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads
Development of a force field for Li 2 SiF 6
Development of polyphosphate parameters for use with the AMBER force field
Ethylene coordination, insertion, and chain transfer at a cationic aluminum center: A comparative study with Ab Initio correlated level and density functional methods
Quantum chemistry applied to the mechanisms of transition metal containing enzymes - Cytochrome c oxidase, a particularly challenging case
New insights in chemical reactivity from quantum chemical topology
Two-step evaluation of binding energy and potential energy surface of van der Waals complexes
Using chiral molecules as an approach to address low-druggability recognition sites
Efficient treatment of the effect of vibrations on electrical, magnetic, and spectroscopic properties
Sampling protein conformations and pathways
Gas adsorption in Mg-porphyrin-based porous organic frameworks: A computational simulation by first-principles derived force field
Benson group additivity values of phosphines and phosphine oxides: Fast and accurate computational thermochemistry of organophosphorus species
Structure and stability of B+13 clusters
Liquid properties of dimethyl ether from molecular dynamics simulations using Ab Initio force fields
Guide to tuning the chalcone molecular properties based on the push-pull effect energy scale created via the molecular tailoring approach
Analytical hessian fitting schemes for efficient determination of force-constant parameters in molecular mechanics
Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields
When anomeric effects collide
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3
Modeling of magic water clusters (H 2 O) 20 and (H 2 O) 21 H + with the PM3 quantum-mechanical method
Extracting the mechanisms and kinetic models of complex reactions from atomistic simulation data
Investigation on the individual contributions of N-H***O=C and C-H***O=C interactions to the binding energies of beta-sheet models
Web services as applications' integration tool: QikProp case study
Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent
CHARMM: The biomolecular simulation program
Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations
Theoretical study on structures and stabilities of [H, Ge, C, N]
Homolytic Versus Heterolytic Bond Breaking in Functionalized [R-C20H10]+ Systems
Proton affinities of polybenzenoid aromatic hydrocarbons and those with five-membered rings
A novel graphical representation of protein sequences and its application
Derication of Class II Force Fields. I. Methology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules
A comparison between parallelization approaches in molecular dynamics simulations on GPUs
Asymmetrization effects on structures and populations of the ground state of dipolar donor-acceptor-substituted molecular organic NLO materials
Alpha sphere filter method: Application of pseudomolecular descriptors in virtual screening of 2D chemical structures
Benzenoid rings resonance energies and local aromaticity of benzenoid hydrocarbons
Performance of time-dependent density functional and Green functions methods for calculations of excitation energies in radicals and for Rydberg electronic states
Comment on Using quaternions to calculate RMSD [J. Comp. Chem. 25, 1849 (2004)]
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules
Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system
Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation
Quantum monte carlo study of the retinal minimal model C5H6NH2+
The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion
Global double hybrids do not work for charge transfer: A comment on "Double hybrids and time-dependent density functional theory: An implementation and benchmark on charge transfer excited states"
Ab initio characterization of size dependence of electronic spectra for linear anionic carbon clusters C n - ( n = 4-17)
Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations
Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators
Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules
molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software
HolT Hunter: Software for identifying and characterizing low-strain DNA holliday triangles
From acetylene complexes to vinylidene structures: The GeC 2 H 2 system
Density functional theory and CCSD(T) evaluation of ionization potentials, redox potentials, and bond energies related to zirconocene polymerization catalysts
Error Evaluation in the Disign of a Special-Purpose Processor That Calculates Nonbonded Forces in Molecular Dynamics Simulations
Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules
Theoretical investigations of Rh-catalyzed asymmetric 1, 4-addition to enones using planar-chiral phosphine-olefin ligands
FACTS: Fast analytical continuum treatment of solvation
Efficient implementation of the interacting quantum atoms energy partition of the second-order Møller-Plesset energy
Multi-level quantum monte Carlo wave functions for complex reactions: The decomposition of α-hydroxy-dimethylnitrosamine
Kinetics and Thermodynamics of Reactions Involving Criegee Intermediates: An Assessment of Density Functional Theory and Ab Initio Methods Through Comparison with CCSDT(Q)/CBS Data
External fields in conceptual density functional theory
Highly asymmetric electrolytes in the primitive model: Hypernetted chain solution in arbitrary spatial dimensions
A pH-dependent computational approach to the effect of mutations on protein stability
DFT approach to calculate electronic transfer through a segment of DNA double helix
An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution
Electronic and structural properties of Lin@Be2B8 (n = 1-14) and Lin@Be2B36 (n = 1-21) nanoflakes shed light on possible anode materials for Li-based batteries
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
Development of non-bonded interaction parameters between graphene and water using particle swarm optimization
Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory
Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers
Spin-orbit effects on structures of closed-shell polyatomic molecules containing heavy atoms calculated by two-component Hartree-Fock method
Improved model core potentials for the second- and third-row transition metals
Interstitial carbon defects in silicon. A quantum mechanical characterization through the infrared and Raman spectra
Cover Image, Volume 41, Issue 17
Dynamics of large proteins through hierarchical levels of coarse-grained structures
Quantum monte carlo vibrational dynamics in a property-based interaction potential scheme for weakly bound clusters
FRAGMENTISE: A user-friendly, cross-platform tool to create and analyze comprehensive small-molecule fragment databases
Improving the description of solvent pairwise interactions using local solute/solvent three-body functions. The case of halides and carboxylates in aqueous environment
Tuning ultrafast time-evolution of photo-induced charge-transfer states: A real-time electronic dynamics study in substituted indenotetracene derivatives
Implementation of Artificial Intelligence for Automatic Drug Design. I. Stepwise Computation of the Interactive Drug-Design Sequence
The RTAM electronic bibliography, version 17.0, on relativistic theory of atoms and molecules
Determination of substitutional sites in heterocycles from the topological analysis of the electron localization function (ELF)
Efficient linear algebra routines for symmetric matrices stored in packed form
PyRETIS: A well-done, medium-sized python library for rare events
Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches
Energy density analysis for second-order Møller-Plesset perturbation theory and coupled-cluster theory with singles and doubles: Application to C 2 H 4 -CH 4 complexes
"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets
MOPED: Method for optimizing physical energy parameters using decoys
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution
Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID)
Accompanying coordinate expansion formulas derived with the solid harmonic gradient
Nonadiabatic quantum dynamics in O( 3 P)+H 2 →OH+H: A revisited study
Application of Genetic Algorithms in Molecular Modeling
A computational mechanistic study on the formation of aryl sulfonyl fluorides via Bi(III) redox-neutral catalysis and further rational design
A new release of MOPAC incorporating the INDO/S semiempirical model with CI excited states
Conformers of gaseous protonated glycine
Cover Image, Volume 41, Issue 13
Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering
Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes
Effect of ZrS 2 load single/dual-atom catalysts on the hydrogen evolution reaction: A first-principles study
Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s
First-principles based theoretical investigation of impact of polyolefin structure on photooxidation behavior
Ab initio QM/MM dynamics of H3O+ in water
A flexible implementation of frozen-density embedding for use in multilevel simulations
Accelerating AIREBO: Navigating the Journey from Legacy to High-Performance Code
Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT
Multicanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction
Limitations of density functional theory in application to degenerate states
General molecular mechanics approach to transition metal complexes
On the Meaning of De-Excitations in Time-Dependent Density Functional Theory Computations
The importance of aromatic-type interactions in serotonin synthesis: Protein-ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase
The statistical significance of selected sense-antisense peptide interactions [J. Comp. Chem. 33, 1440-1447]
Magnetic exchange interactions in binuclear and tetranuclear iron(III) complexes described by spin-flip DFT and Heisenberg effective Hamiltonians
Update of the ATTRACT force field for the prediction of protein-protein binding affinity
Continuous symmetry measures: Finding the closest C2-symmetric object or closest reflection-symmetric object using unit quaternions
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach
Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
Essential dynamics for the study of microstructures in liquids
Chemical graph theory and n -center electron delocalization indices: A study on polycyclic aromatic hydrocarbons
New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanine
Generation of crystal structures of acetic acid and its halogenated analogs
Photodissociation of Cr(CO) 4 bpy $$ \mathrm{Cr}{\left(\mathrm{CO}\right)}_4\mathrm{bpy} $$ : A Non-Adiabatic Dynamics Investigation
Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions
Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
Incorporating support vector machine for identifying protein tyrosine sulfation sites
Simultaneous parametrization of torsional and third-neighbor interaction terms in force-field development: The LLS-SC algorithm
Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers
PhAST: Pharmacophore alignment search tool
QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface
A fast and Space-Efficient boundary element method for computing electrostatic and hydration effects in large molecules
Generation and characterization of low-energy structures in atomic clusters
Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies
ST-analyzer: A web-based user interface for simulation trajectory analysis
Voronoi cell: New method for allocation of space among atoms: Elimination of avoidable errors in calculation of atomic volume and density
On the axial chirality of leucoindigo
Software package SIMPRE - Revisited
Performance of the OP correlation functional in relation to its formulation: Influence of the exchange component and the effect of incorporating same-spin correlations
Elucidating protein secondary structure with circular dichroism and a neural network
Acceleration of self-consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function
Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results?
Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water
Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part III. Effect of lattice vibrations