yusuke1997/dblp-id-title huggingface dataset:
Surface electronic structure calculations using the MBJLDA potential: Application to Si(111)2 × 1
Delineating Protein-Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple-Walker Umbrella Sampling Simulations
Comparison between self-guided langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations
Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity
Calculation of clustered eigenvalues of large matrices using variance minimization method
DFT and Ab initio direct dynamics studies on the hydrogen abstraction reactions of chlorine atoms with CH4-nFn (n = 1-3)
A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
Are most of the stationary points in a molecular association minima? Application of Fraga's potential to benzene-benzene
Optimized Monte Carlo sampling in forward-backward semiclassical dynamics
BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study
Aqueous Diels-Alder reactions for thermochemical storage and heat transfer fluids identified using density functional theory
Introduction of steered molecular dynamics into UNRES coarse-grained simulations package
Simulation of the infrared spectra of amorphous silicon alloys
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum
Mechanism of Ampicillin Hydrolysis by New Delhi Metallo-β-Lactamase 1: Insight From QM/MM MP2 Calculation
Identification of small molecule aggregators from large compound libraries by support vector machines
KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results
MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust
Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water
Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA
Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation
On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials
Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method
Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins
Static hyperpolarizability of the van der Waals complex CH 4 ‒N 2
On the accurate estimation of free energies using the jarzynski equality
Water PMF for predicting the properties of water molecules in protein binding site
Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic
A fast pairwise evaluation of molecular surface area
Phenylene vinylene oligomers studied by theoretical methods: Joint analysis of computational and x-ray results of the configurational isomers of 1, 4-bis[2-(3, 4, 5-trimethoxyphenyl)ethenyl]benzene
Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
Density functional theory investigation of Cu(I)- and Cu(II)-curcumin complexes
Empirical prediction of protein p K a values with residue mutation
Remarks on the Use of the Apparent Surface Charges /ASC) Methods in Solvation Problems: Iterative versus Matrix-Inversion Procedures and the Renormalization of the Apparent Charges
Theoretical study of reaction of trifluoromethyl radical with hydroxyl and hydrogen radicals
Martini Force Field for Protonated Polyethyleneimine
Software news and updates
Complete graph conjecture for inner-core electrons: Homogeneous index case
Bis-μ-oxo and μ-η 2 : η 2 -peroxo dicopper complexes studied within (time-dependent) density-functional and many-body perturbation theory
Ab initio and DFT studies of the thermal rearrangement of trimethylsilyl(methyl)silylene: Remarkable rearrangements of silicon intermediates
Molecular basis of RNA recognition by TBP of HIV-1 from multiple molecular dynamics simulations and energy predictions
Using steered molecular dynamic tension for assessing quality of computational protein structure models
Cover Image, Volume 40, Issue 26
Controlling the oxidative addition of aryl halides to Au(I)
Explicit proton transfer in classical molecular dynamics simulations
Accurate prediction of heats of formation by a combined method of B3LYP and neural network correction
Ab initio theory for treating local electron excitations in molecules and its performance for computing optical properties
Reduction of OH vibrational frequencies in amino acids by positron attachment
Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n -octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method
A systematic first-principles investigation of the structural, electronic, mechanical, optical, and thermodynamic properties of Half-Heusler ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) for spintronics and optoelectronics applications
Structure and properties of the aluminum borates Al(BO 2 ) n and Al(BO 2 ) n - , ( n = 1-4)
Exploring the reactivity of framework vanadium, niobium, and tantalum sites in zeolitic materials using DFT reactivity descriptors
Artificial neural networks-based approach to design ARIs using QSAR for diabetes mellitus
Hydrodynamic modeling of diffusion tensor properties of flexible molecules
Efficient geometry optimization of molecular clusters
Implementation of Reaction Field Methods in Quantum Chemistry Computer Codes
Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking
A reaction route network for methanol decomposition on a Pt(111) surface
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics
Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery
Free energy of micellization of dodecyl phosphocholine (DPC) from molecular simulation: Hybrid PEACH-BAR method
Description of core excitations by time-dependent density functional theory with local density approximation, generalized gradient approximation, meta-generalized gradient approximation, and hybrid functionals
Lattice representations of globular proteins: How good are they?
A theoretical study on the structures and energetics of hypothetical TiM(NCN)3 compounds of the 3d transition metals
CHARMM-GUI 10 years for biomolecular modeling and simulation
Empirical force-field and ab initio calculations on delocalized open chain cations
CRYSPLOT: A new tool to visualize physical and chemical properties of molecules, polymers, surfaces, and crystalline solids
SDA 7: A modular and parallel implementation of the simulation of diffusional association software
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme
Cover Image, Volume 39, Issue 20
A Structural Model of Nitro-Porphyrin Dyes Based on Spectroscopy and Density Functional Theory
Mechanistic and kinetic investigations of N 2 H 4 + OH reaction
Ab initio study of the high-temperature phase transition in crystalline GeO 2
Allostery of the two-state model of hemoglobin studied by ECEPP energy minimization
A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations
Development of glycyl radical parameters for the OPLS-AA/L force field
Cover Image, Volume 41, Issue 26
A two-step reaction scheme leading to singlet carbene species that can be detected under matrix conditions for the reaction of Zr( 3 F) with either CH 3 F or CH 3 CN
GARANT-a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra
A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs
Fullerene faraday cage keeps magnetic properties of inner cluster pristine
Automated reaction path searches for spin-forbidden reactions
Application of artificial neural network and global optimization techniques for high throughput modeling of the crystal structure of stannites and kesterites
Formulation of a new and simple nonuniform size-modified poisson-boltzmann description
Conformational analysis of the tyrosine dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model
The subspace iteration method in protein normal mode analysis
Structures and stability of lithium monosilicide clusters SiLi n ( n = 4-16): What is the maximum number, magic number, and core number for lithium coordination to silicon?
Predicting reduction potentials of 1, 3, 6-triphenyl fulvenes using molecular electrostatic potential analysis of substituent effects
Density functional tight binding-based free energy simulations in the DFTB+ program
On the FUnctional Representation of Bond Energy Functions
Mesoscopic model for mechanical characterization of biological protein materials
MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates
New ab initio potential energy surfaces for both the ground (X̃ 1 A′) and excited (Ã 1 A″) electronic states of HSiCl and the absorption and emission spectra of HSiCl/DSiCl
Similarity of RNA secondary structures
Modeling of phytochrome absorption spectra
A new strategy of outlier detection for QSAR/QSPR
A theoretical study on fullerene-dizincocene hybrids
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
Conformational dependence of electrostatic potential-derived charges: Studies of the fitting procedure
Study of Cl - (H 2 O) n ( n = 1-4) using basin-hopping method coupled with density functional theory
Theoretical study on the low-lying electronic states of NiH and NiAt
Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems
Dynamic Charge Equilibration-Morse stretch force field: Application to energetics of pure silica zeolites
A scalable parallel Monte Carlo method for free energy simulations of molecular systems
Quasi-degenerate perturbation theory with general multiconfiguration self-consistent field reference functions
Atomic Neural Network for Calculation of Solvation Free Energies in Organic Solvents
Keto-enol tautomerism from the electron delocalization perspective
Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations
Fast density matrix-based partitioning of the energy over the atoms in a molecule consistent with the hirshfeld-I partitioning of the electron density
Development and evaluation of a generic evolutionary method for protein-ligand docking
Theoretical evidence for bond stretch isomerism in Grubbs olefin metathesis
Regional self-interaction correction of density functional theory
Reliability of computed molecular structures
Automated Search of Minimum Free-Energy Path by Umbrella Integration
A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase
Theoretical insights into the nature of Pt‒Sn bond: Reevaluating the bonding/back-bonding properties of trichlorostannate with comparison to the cyano ligand
Hydration of copper(II) amino acids complexes
Optimizing Computational Parameters for Nuclear Electronic Orbital Density Functional Theory: A Benchmark Study on Proton Affinities
QM/MM refinement and analysis of protein bound retinoic acid
Reducing CAS-SDCI space. Using selected spaces in configuration interaction calculations in an efficient way
Relativistic Gaussian basis sets for molecular calculations: Fully optimized single-family exponent basis sets for HHg
Diffusion Monte Carlo Calculations of Zero-Point Energies of Methanol and Deuterated Methanol
Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer
Foreword to the special issue on machine learning/artificial intelligence
How to find an optimum cluster size through topological site properties: MoS x model clusters
ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water
Prediction of the reduction potential in transition-metal containing complexes: How expensive? For what accuracy?
Using Huffman coding method to visualize and analyze DNA sequences
Modeling spin relaxation in complex radical systems using MolSpin
Ab initio prediction of 15N-NMR chemical shift in -boron nitride based on an analysis of connectivities
129 Xe NMR chemical shift in Xe@C 60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent
A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability
Effect of ligand binding on the intraminimum dynamics of proteins
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution
Insights into the electronic structure and mechanism of norcarane hydroxylation by OxoMn(V) porphyrin complexes: A density functional theory study
Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: Focus on correlation with experiment
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes
The relationship between peptide plane rotation (PPR) and similar conformations
A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics
Aluminum oxo-fluoride clusters: A first principle investigation of stability, synthetic considerations, and the interaction with water
Electronic structure, sodium diffusion and redox potentials of low-symmetry NaMFe(MoO4)3 (M = Mg, Ni)
How reliable are GIAO calculations of 1 H and 13 C NMR chemical shifts? A statistical analysis and empirical corrections at DFT (PBE/3z) level
Massively parallel quantum chemical density matrix renormalization group method
Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials
Mechanistic aspects of the dehydration and dehydrohalogenation of halo-hydroxyformaldoxime conformers. A quantum chemical model study
Electron affinities of heavier phosphoryl and thiophosphoryl halides APX 3 (A = O, S and X = Br, I)
High-quality protein backbone reconstruction from alpha carbons using gaussian mixture models
Molecular quantum similarity measures as an alternative to log P values in QSAR studies
Docking of small ligands to low-resolution and theoretically predicted receptor structures
The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis
Surface chemistry of oxygen on aluminum - Performance of the density functionals: PBE, PBE0, M06, and M06-L
Communication through molecular bridges: Different bridge orbital trends result in common property trends
T-cell epitopes of the La/SSB autoantigen: Prediction based on the homology modeling of HLA-DQ2/DQ7 with the insulin-B peptide/HLA-DQ8 complex
Evaluation of the restricted virtual space approximation in the algebraic-diagrammatic construction scheme for the polarization propagator to speed-up excited-state calculations
Nature of the ring-closure process along the rearrangement of octa-1, 3, 5, 7-tetraene to cycloocta-1, 3, 5-triene from the perspective of the electron localization function and catastrophe theory
A quantitative analysis of light-driven charge transfer processes using voronoi partitioning of time dependent DFT-derived electron densities
Implementation of the direct SCF and RPA methods on loosely coupled networks of workstations
Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages
Shared-memory parallelization of the TURBOMOLE programs AOFORCE, ESCF, and EGRAD: How to quickly parallelize legacy code
Efficiency of simulated annealing for peptides with increasing geometrical restrictions
Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points
Metal-thiolate bonds in bioinorganic chemistry
Predicting 15N amide chemical shifts in proteins. I. An additive model for the backbone contribution
Molecular symmetry and ab initio calculations. II. Symmetry-Matrix and symmetry-Supermatrix in the Dirac-Fock method
Crystal structure predictions for acetic acid
An approximate diatomics in molecules formulation of generalized valence bond theory
Energy-based automatic determination of buffer region in the divide-and-conquer second-order Møller-Plesset perturbation theory
Achieving Pressure Consistency in Mechanochemical Simulations of Chemical Reactions Under Pressure
Explainable artificial intelligence in the design of selective carbonic anhydrase I-II inhibitors via molecular fingerprinting
Catalytic performance of bis(imino)pyridine Fe/Co complexes toward ethylene polymerization by 2D-/3D-QSPR modeling
Relative basicities of carboxylate lone pairs in aqueous solution
Bonding and 13C-NMR properties of coinage metal tris(ethylene) and tris(norbornene) complexes: Evaluation of the role of relativistic effects from DFT calculations
Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets
Density functional study of isomerization of fluoro- and chloroformaldehyde radical cations
A new nonempirical tuning scheme with single self-consistent field calculation: Comparison with global and IP-tuned range-separated functional
Registration, orientation, and similarity of molecular electrostatic potentials through multipole matching
Placevent : An algorithm for prediction of explicit solvent atom distribution - Application to HIV-1 protease and F-ATP synthase
Structural dissimilarity sampling with dynamically self-guiding selection
A first-principles study on the existence and structures of the lighter alkaline-earth pernitrides
SDOCK: A global protein-protein docking program using stepwise force-field potentials
A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid
Common vertex matrix: A novel characterization of molecular graphs by counting
OOPSE: An object-oriented parallel simulation engine for molecular dynamics
SAnDReS 2.0: Development of machine-learning models to explore the scoring function space
Continuous medium theory for nonequilibrium solvation: II. Interaction energy between solute charge and reaction field and single-sphere model for spectral shift
WebProp: Web interface for ab initio calculation of molecular one-electron properties
Geometric analysis of anharmonic downward distortion following paths
New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes
Corrigendum: Differential geometric analysis of alterations in MH α-helices
Loop entanglement of semicrystalline polyethylene in amorphous region: Diamond lattice approach
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects
How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules
Pair interaction energy decomposition analysis
The location of transition states: A comparison of Cartesian, Z-matrix, and natural internal coordinates
Multidimensional scaling and visualization of large molecular similarity tables
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software
A graph-based short-cut to low-energy structures
Halogen in materials design: Chloroammonium lead triiodide perovskite (ClNH3PbI3) a dynamical bandgap semiconductor in 3D for photovoltaics
Insights into the mechanism of methionine oxidation catalyzed by metal (Cu 2+ , Zn 2+ , and Fe 3+ ) - Amyloid beta (Abeta) peptide complexes: A computational study
TGMin: An efficient global minimum searching program for free and surface-supported clusters
Investigation of the complete encapsulation process of the noble gases by cryptophanes
Intramolecular interactions in sterically crowded hydrocarbon molecules
Photoelectron spectra, penning ionization electron spectra, and character of canonical molecular orbitals
Anomerization reaction of bare and microhydrated d-erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal
Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule
Effective protein conformational sampling based on predicted torsion angles
AIMD-Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter-System Crossing in Photocatalytic Chromophores
Probing vibrational coupling via a grid-based quantum approach - an efficient strategy for accurate calculations of localized normal modes in solid-state systems
Rapid evaluation of the binding energies between peptide amide and DNA base
Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches
Force field development for organic molecules: Modifying dihedral and 1- n pair interaction parameters
The strength and selectivity of perfluorinated nano-hoops and buckybowls for anion binding and the nature of anion-π interactions
Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons
Noncovalent interactions in supramolecular complexes: A study on corannulene and the double concave buckycatcher
Folding funnels: The key to robust protein structure prediction
Description of peptide and protein secondary structures employing semiempirical methods
Spin-inversion mechanisms in O2 binding to a model heme compound: A perspective from nonadiabatic wave packet calculations
Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline
Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO-MST Continuum Solvation Model
Calculation of X-ray scattering intensities by means of the coupled cluster singles and doubles model
Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein
A comparative study of molecular dynamics in Cartesian and in internal coordinates: Dynamical instability in the latter caused by nonlinearity of the equations of motion
Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge
Solvatochromism and preferential solvation of Brooker's merocyanine in water-methanol mixtures
Linearity condition for orbital energies in density functional theory (III): Benchmark of total energies
A configuration-based heatbath-CI for spin-adapted multireference electronic structure calculations with large active spaces