yusuke1997/dblp-id-title huggingface dataset:
Can Water Trigger Room-Temperature Formation of Benzofuran-2(3H)-one Scaffolds From Vinyldiazene Derivatives? Computational Insights Into an Unusual Cyclization
Parameterization of the ReaxFF reactive force field for a proline-catalyzed aldol reaction
Is the spin-orbit coupling important in the prediction of the 51 V hyperfine coupling constants of V IV O 2+ species? ORCA versus Gaussian performance and biological applications
New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases
Reaction mechanism of Ru(II) piano-stool complexes: Umbrella sampling QM/MM MD study
The dynamics of the calcium-induced chain-chain association in the polyuronate systems
A partition function algorithm for nucleic acid secondary structure including pseudoknots
Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover
Mono-silicon isoelectronic replacement in CAl4: van't hoff/le bel carbon or not?
Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms
Calculation of rotational partition functions by an efficient Monte Carlo importance sampling technique
2, 5-Dimethoxy-1, 4-bis[2-(2, 4-dimethoxyphenyl) ethenyl]benzene studied by quantum chemical calculations and single crystal X-ray diffraction
An Empirical Force Field I. Alkanes
A quantum chemistry study: A new kind of boron nitrides
Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason?
Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer
HCVpred : A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors
A group center overlap based approach for "3D QSAR" studies on TIBO derivatives
Dipole moments of molecules with multi-reference character from optimally tuned range-separated density functional theory
Three-dimensional visualization of the first hyperpolarizability tensor
Simple models for nonpolar solvation: Parameterization and testing
On the stability of metal-aminoacid complexes in water based on water-ligand exchange reactions and electronic properties: Detailed study on iron-glycine hexacoordinated complexes
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation
GRID: A high-resolution protein structure refinement algorithm
W4-17: A diverse and high-confidence dataset of atomization energies for benchmarking high-level electronic structure methods
A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems
ESCAPE: A novel approach for a fast estimation of dynamic correlation energies: Application to large organic molecules
SIESTA-SIPs: Massively parallel spectrum-slicing eigensolver for an ab initio molecular dynamics package
Combined DFT, QCISD(T), and G2 mechanism investigation for the reactions of carbon monophosphide CP with unsaturated hydrocarbons allene CH 2 CCH 2 and methylacetylene CH 3 CCH
Following the evolution of excited states along photochemical reaction pathways
Ab Initio spectroscopic characterization of borane, BH, in its X1Σ+ electronic state
A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard-Jones clusters
Docking macromolecules with flexible segments
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation
Mode-tracking based stationary-point optimization
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study
Corrigendum: Competition between Hydrogen and Halogen Bonding in Halogenated 1-Methyluracil: Water Systems
Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine
Comparison of density functional theory models' ability to reproduce experimental 13C-NMR shielding values
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function
A Density Functional Treatment of Organolithium Compounds: Comparison to Ab Initio, Semiempirical, and Epreimental Results
Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations
Semiempirical GGA-type density functional constructed with a long-range dispersion correction
An efficient molecular docking using conformational space annealing
The general setting for the zero-flux condition: The lagrangian and zero-flux conditions that give the heisenberg equation of motion
Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics
Energetic and topological analyses of the oxidation reaction between Mon (n = 1, 2) and N2O
Concerted versus stepwise proton transfer reactions in the [2, 2′-bipyridyl]-3-3′-diol molecule: A static and dynamic ab-initio investigation
Interactions of CO2 with cluster models of metal-organic frameworks
Theoretical comparative studies on transport properties of pentacene, pentathienoacene, and 6, 13-dichloropentacene
An unbiased population-based search for the geometry optimization of Lennard-Jones clusters: 2 leq N leq 372
Program for analyzing knots represented by polygonal paths
Tl(I)-the strongest structure-breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study
Ionic bonding of lanthanides, as influenced by d- and f-atomic orbitals, by core-shells and by relativity
Identifying promising metal-organic frameworks for heterogeneous catalysis via high-throughput periodic density functional theory
ALMOST: An all atom molecular simulation toolkit for protein structure determination
Structure of Disiloxane: A Semiempirical and Post-Hartree-Fock Study
X-PLORing Extrarisomal Peptide Folding during Synthesis
Batch tautomer generation with MolTPC
Dispersion in the Mott insulator UO 2 : A comparison of photoemission spectroscopy and screened hybrid density functional theory
Jahn-Teller distortion, octahedra rotations and orbital ordering in perovskites: KScF 3 as a model system
Thoughts about density functional theory in 1998
PaDEL-DDPredictor: Open-source software for PD-PK-T prediction
RNA conformational sampling. I. Single-nucleotide loop closure
Scalable molecular dynamics with NAMD
Molecular rectification in triangularly shaped graphene nanoribbons
Estimations of FH···X hydrogen bond energies from IR intensities: Iogansen's rule revisited
A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[ N ]arenes as carriers for Bosutinib and Sorafenib
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
A novel strategy to determine protein structures using exclusively residual dipolar coupling
Evaluating electronic structure methods for accurate calculation of 19 F chemical shifts in fluorinated amino acids
Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model
Extended Koopmans' theorem at the second-order perturbation theory
The valence and Rydberg excited states of CH 2 : A theoretical exploration
Theoretical investigations of the reactivities of four-membered N-heterocyclic carbene analogues of the group 13 elements
Exploring possible reaction pathways for the o-atom transfer reactions to unsaturated substrates catalyzed by a [Ni-NO 2 ] ↔ [Ni-NO] redox couple using DFT methods
A computational study of the role of hydrogen bonds in SN1 and E1 reactions
Chalcogen atom effect on the intersystem crossing kinetic constant of oxygen- and sulfur disubstituted heteroporphyrins
Polarized basis sets for accurate calculations of static and dynamic electric properties of molecules
GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations
Conformational analysis of the HIV-1 virus reverse transcriptase nonnucleoside inhibitors: TIBO and nevirapine
ErratumAdaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
Chemical information from the source function
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability
Ab Initio Calculations of the Ultraviolet Resonance Raman Spectra of Uracil
Structural evolution and electronic properties of pure and semiconductor atom doped in clusters: Inn-, InnSi-, and InnGe- (n = 3-16)
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints
Conductor-like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO
X2-PEC: A Neural Network Model Based on Atomic Pair Energy Corrections
Cover Image, Volume 39, Issue 10
Calculation of photoionization differential cross sections using complex Gauss-type orbitals
Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2
New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue
Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules
Reaction pathways and projection operators: Application to string methods
Mechanistic Insight on Ethanol Driven Swelling and Disruption of Cholesterol Containing Biomimetic Vesicles From Coarse-Grained Molecular Dynamics
COX-2 Inhibitor Prediction With KNIME: A Codeless Automated Machine Learning-Based Virtual Screening Workflow
Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator
The numerical evaluation of Slater integrals on graphics processing units
Typical aromatic noncovalent interactions in proteins: A theoretical study using phenylalanine
Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor: Structure, dynamics, and comparison with the experimental data
Revisiting the extrapolation of correlation energies to complete basis set limit
Implementation of dynamical nucleation theory with quantum potentials
Encapsulation effect of π-conjugated quaterthiophene on the radial breathing and tangential modes of semiconducting and metallic single-walled carbon nanotubes
(σ 3 , λ 5 )-phosphoranes versus (σ 3 , λ 3 )-thiaphosphiranes: Quantum chemical investigation of products of phosphaalkene sulfurization
Error vector choice in direct inversion in the iterative subspace method
Ab initio molecular orbital study of energies and conformers of 3, 4-dihydro-1, 2-dithiin, 3, 6-dihydro-1, 2-dithiin, 4H-1, 3-dithiin, and 2, 3-dihydro-1, 4-dithiin
Development of a restricted Hartree - Fock program INDMOL on PARAM: A highly parallel computer
Dendrimer building toolkit: Model building and characterization of various dendrimer architectures
An incremental isoconversional method for kinetic analysis based on the orthogonal distance regression
The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability
The quest for a bidirectional auxetic, elastic, and enhanced fracture toughness material: Revisiting the mechanical properties of the BeH 2 monolayers
Sequence-based prediction of protein-peptide binding sites using support vector machine
Accurate and efficient determination of higher roots in diagonalization of large matrices based in function restricted optimization algorithms
Selective oxidation of styrene on an oxygen-adsorbed Cu(111): A comparison with Au(111)
Ab initio investigation of the diels-alder reaction between 2H-phosphole and phosphaethene: A model for phosphole dimerization
Theoretical mechanistic study on the radical-molecule reaction of CHCl2/CCl3 with NO2
Quantitative investigation of bonding characteristics in ternary Zintl anions: Charge and energy analysis of [Sn 2 E 15 2 (ZnPh)] - (E 15 = Sb, Bi) and [Sn 2 Sb 5 (ZnPh) 2 ] 3-
Conformational behavior of simple furanosides studied by optical rotation
Symmetry operation measures
An averaged polarizable potential for multiscale modeling in phospholipid membranes
Theoretical study of structure of alkali metal cyanates and isocyanates and their related ion pair SN2 reactions
Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides
An improvement of the resolution of the identity approximation for the formation of the Coulomb matrix
Calculating core-level excitations and x-ray absorption spectra of medium-sized closed-shell molecules with the algebraic-diagrammatic construction scheme for the polarization propagator
Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models
Fully relativistic description of static magnetic hyperfine interaction in magnetic and nonmagnetic solids
Erratum: Tuning aromaticity in trigonal alkaline earth metal clusters and their alkali metal salts
Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model
Cover Image, Volume 40, Issue 8
First-principles conformational analysis of the C36H36 spheriphane, a prototype hydrocarbon host cage
GUIDE: A GUI for automated quantum chemistry calculations
Incorporation of Bond-Length Constraints in Monte Carlo Simulations of Cyclic and Linear Molecules: Conformational Sampling for Cyclic Alkanes as Test Systems
Two- and one-photon absorption spectra of aqueous thiocyanate anion highlight the role of symmetry in the condensed phase
Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase
Evolution of the linker in microhydrated hydrogen dinitrate anions: From H+ to H5O2+
When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms
Static and frequency dependent polarizabilities and hyperpolarizabilities of H2Sn
A polynomial version of the generator coordinate Dirac-Fock method
Examining the Impact of Local Constraint Violations on Energy Computations in DFT
Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods
Computational convergence of electronic structure calculations of transition metal ligand complexes
Optimization of a molecular mechanics force field for type-II polyoxometalates focussing on electrostatic interactions: A case study
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes
Pseudosymmetry analysis of molecular orbitals
Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si)
Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction
An ant colony pairwise alignment based on the dot plots
σ-holes and π-holes: Similarities and differences
Stepwise basis set selection
Combined QM/MM study of the opsin shift in bacteriorhodopsin
A radial probability density function for analysis of canonical molecular orbitals
Developing multisite empirical force field models for Pt(II) and cisplatin
Phonon spectra, electronic, and thermodynamic properties of WS 2 nanotubes
Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge-charge flux-dipole flux model
Bayesian inference of conformational state populations from computational models and sparse experimental observables
Aromaticity, quantum multimolecular polyhedra, and quantum QSPR fundamental equation
Ab initio study on the electronic structures of styrene in the Franck-Condon region
SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach
GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments
Advanced techniques for constrained internal coordinate molecular dynamics
An efficient method for computing the QTAIM topology of a scalar field: The electron density case
Updated Hessian Matrix and the Restricted Step Method for Locating Transition Structures
A combinatorial study of inverse Heusler alloys by first-principles computational methods
Relative stability of the 3A2, 1A2, and 1A1 states of phenylnitrene: A difference-dedicated configuration interaction calculation
Erratum: "iVI: An iterative vector interaction method for large eigenvalue problems" [J. Comput. Chem. 38 2481 (2017)]
Polygonal current models for polycyclic aromatic hydrocarbons and graphene sheets of various shapes
Parallel Implementation of a Mesh-Based Density Functional Electronic Structure Code
Kinetics of radical-molecule reactions in aqueous solution: A benchmark study of the performance of density functional methods
Effect of nonproximate atomic substitution on excited state intramolecular proton transfer
Reaction mechanism of methanol decomposition on Pt-based model catalysts: A theoretical study
On the importance of excited state dynamic response electron correlation in polarizable embedding methods
Molecular dynamics with restrictions derived from optical spectra
Accurate description of van der Waals complexes by density functional theory including empirical corrections
Erratum: On-the-path random walk sampling for efficient optimization of minimum free energy path
Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers
Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry
Time-dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen-bonded complexes
Unusual Conformational-Determining Interactions in Oxymethylpyridines: An Ab Initio Study and an Improved Method for Refining Molecular Mechanics Parameters
Theoretical investigations of the substituent effect on the opto-electronic properties of the linearly fused napthadithiophene-based molecules
Cover Image, Volume 40, Issue 11
A real space picture of the role of steric effects in SN2 reactions
Origin-independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method
Hydrogen abstraction reactions of OH radicals with CH 3 CH 2 CH 2 Cl and CH 3 CHClCH 3 : A mechanistic and kinetic study
Theoretical study of quinolines-I2 intermolecular interaction and implications on dye-sensitized solar cell performance
Local protein backbone folds determined by calculated NMR chemical shifts
The role of macrocyclic ligands in the peroxo/superoxo nature of Ni-O2 biomimetic complexes
Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory
Similarity recognition of molecular structures by optimal atomic matching and rotational superposition
PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints
Investigating charge transport in molecular switches with neural networks
SCC-DFTB parameters for simulating hybrid gold-thiolates compounds
Multipole moments for embedding potentials: Exploring different atomic allocation algorithms
Reoptimized interaction parameters for the peptide-backbone model compound N -methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol
Vibrational corrections to geometries of transition metal complexes from density functional theory
Performance of Fast Multipole Methods for Calculating Electrostatic Interactions in Biomacromolecular Simulations
First principle studies on structural, elastic, electronic, optical, and thermoelectric properties of new perovskite TlTaO 3 : For renewable energy applications
Discovery of a series of silicon-based ferrimagnets in CrMnSi n ( n = 4-20) clusters
A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy
One-electron images in real space: Natural adaptive orbitals
Exploring the conformational space of cobalt(III)-salen catalyst for CO2/epoxide copolymerization: Effect of quaternary ammonium salts on preference of alternative isomers
DFT potentials from a chemical perspective: Anatomy of electron (de)localization in molecules and crystals
Refinement of the application of the GROMOS 54A7 force field to β-peptides
Conformational preferences of endohedral metallofullerenes on Ag, Au, and MgO surfaces: Theoretical studies
Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide
On the Analytical Calculation o van der Waals Surfaces and Volumes: Some Numerical Aspects
Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins
Conformational Analysis of Jet-Cooled Tryptohan Analogs and Histamine Using the MM3(94) Force Field: Comparison with Experiment
Electronic state of small and large cavities for methane hydrate
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
New parallel optimal-parameter fast multipole method (OPFMM)
Analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment
Record Atomistic Simulation of Crystalline Silicon: Bridging Microscale Structures and Macroscale Properties
Controlled-advancement rigid-body optimization of nanosystems
Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions
Molecular modeling for Cu(II)-aminopolycarboxylate complexes: Structures, conformational energies, and ligand binding affinities
Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques
Comparing distance metrics for rotation using the k -nearest neighbors algorithm for entropy estimation
Prediction of GFP spectral properties using artificial neural network
Computation of the physio-chemical properties and data mining of large molecular collections
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
A novel hybrid method named electron conformational genetic algorithm as a 4D QSAR investigation to calculate the biological activity of the tetrahydrodibenzazosines
Integrating quantum and molecular mechanics
New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures
Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods
Regioselectivity in cycloaddition reaction between phosphaacetylene and diazomethane: An ab initio study
Which density functional is close to CCSD accuracy to describe geometry and interaction energy of small non-covalent dimers? A benchmark study using gaussian09
Diabatic ordering of vibrational normal modes in reaction valley studies
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens
Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water
Combining machine learning and quantum mechanics yields more chemically aware molecular descriptors for medicinal chemistry applications
A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium
The equivalent potential of water for electronic structure of aspartic acid