yusuke1997/dblp-id-title huggingface dataset:
Computational assessment of electron density in metallo-organic nickel pincer complexes for formation of P-C bonds
DFT study of the cryptand and benzocryptand and their complexes with alkali metal cations: Li + , Na + , K +
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models
Ab initio calculation of structure and transport properties of He...X (X = Zn, Cd, Hg) van der Waals complexes
Quantum Monte Carlo with very large multideterminant wavefunctions
Ab initio studies on isomers of macropolyhedral borane ions [B20H18]n (n = 0, -2, -4)
Optimization of conical intersections using the semiempirical MNDOC-CI method with analytic gradients
Determination of energy minima and saddle points using multireference configuration interaction methods in combination with reduced gradient following: The S0 surface of H2CO and the T1 and T2 surfaces of acetylene
GneimoSim: A modular internal coordinates molecular dynamics simulation package
Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations
Update of the AIM2000-Program for atoms in molecules
New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions
Mono-silicon Isoelectronic Replacement in CAI4: van't Hoff/Le Bel Carbon or Not?
Solubility of aminotriethylene glycol functionalized single wall carbon nanotubes: A density functional based tight binding molecular dynamics study
Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
Notes on quantitative structure-property relationships (QSPR), part 3: Density functions origin shift as a source of quantum QSPR algorithms in molecular spaces
A DFT study on Cu(I) coordination in Cu-ZSM-5: Effects of the functional choice and tuning of the ONIOM approach
Mechanism of some 1: 2 hydrogen transfer reactions through bond variation indices
Direct inversion of the iterative subspace with contracted planewave basis functions
Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces
Inverse Monte Carlo procedure for conformation determination of macromolecules
Molecular dynamics/order parameter extrapolation for bionanosystem simulations
A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack
Pseudodiagonalization-based wavefunction optimization with contracted planewave basis functions
An intramolecular induction correction model of the molecular dipole moment
Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10 1¯0)
Theoretical prediction of closed-shell paramagnetism for scandium and yttrium hydride
The PyPES library of high quality semi-global potential energy surfaces
A valence bond study of the dioxygen molecule
Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy
On the antibacterial photodynamic inactivation mechanism of Emodin and Dermocybin natural photosensitizers: A theoretical investigation
IMOMM: A New Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States
Cover Image, Volume 40, Issue 10
On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n-alkanes
Local electric dipole moments: A generalized approach
Rapid estimation of activation energy in heterogeneous catalytic reactions via machine learning
Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
Time-dependent pair distribution functions based on Smoluchowski equation and application to an electrolyte solution
Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III)
Unified QSAR & network-based computational chemistry approach to antimicrobials. II. Multiple distance and triadic census analysis of antiparasitic drugs complex networks
Force Field Parameters for Sulfates and Sulfamates Based on Ab Initio Calculations: Extensions of AMBER and CHARMm Fields
ZZS similarity tool: The online tool for similarity screening to identify chemicals of potential concern
On the quality of the hardness kernel and the Fukui function to evaluate the global hardness
A computational study of samarium diiodide-induced cyclizations of N -oxoalkyl-substituted methyl indole-3-carboxylates - A rationale of the diastereoselectivity
Beyond ST-246: Unveiling Potential Inhibitors Targeting VP37 Protein in Silico From Herb and Marine Databases
Polarizable protein packing
Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models
A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers
A binary coding method of RNA secondary structure and its application
Semiempirical and DFT computations of the influence of Tb(III) dopant on unit cell dimensions of cerium(III) fluoride
Assessment of long-range corrected density functional theory on the absorption and vibrationally resolved fluorescence spectrum of carbon nanobelts
Charge distribution in the water molecule - A comparison of methods
Self-guided Langevin dynamics via generalized Langevin equation
A fast annealing evolutionary algorithm for global optimization
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
A new procedure for exact ring closure
Ab initio geometry optimization for large molecules
Dipolar 1, 3-cycloaddition of thioformaldehyde S-methylide (CH2SCH2) to ethylene and acetylene. A comparison with (valence) isoelectronic O3, SO2, CH2OO and CH2SO
A Highly Portable Parallel Implementation of AMBER4 Using the Message Passing Interface Standart
Sum and density of states of polyatomic systems with hindered rotors
Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease
A model study of the efficiency of the Asp-His-Ser triad
Unraveling the structure-property relationship of novel thiophene and furan-fused cyclopentadienyl chromophores for nonlinear optical applications
A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections
A Comarative Study of Effective Core Potential and Full-Electron Calculations in Mo Compounds. I. An ANalysis of Topological Properties of Bond Charge Distribution
An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations
The planarity of heteroatom analogues of benzene: Energy component analysis and the planarization of hexasilabenzene
Phasepy: A Python based framework for fluid phase equilibria and interfacial properties computation
Convergence of third order correlation energy in atoms and molecules
Modified Lennard-Jones potentials for nanoscale atoms
Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables
Qcforever2: Advanced Automation of Quantum Chemistry Computations
On reverse Monte Carlo constraints and model reproduction
GPU-accelerated computation of electron transfer
Magic number silicon dioxide-based clusters: Laser ablation-mass spectrometric and density functional theory studies
Similarity analysis of DNA sequences based on the weighted pseudo-entropy
Breaking the polar-nonpolar division in solvation free energy prediction
Ab initio calculations on halogen-bonded complexes and comparison with density functional methods
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules
Full-dimensional coupled-channel statistical approach to atom-triatom systems and applications to H/D + O 3 reaction
Theoretical investigation on the protonation reactions and products of the stable [N, C, C, S] isomers
Cover Image, Volume 41, Issue 18
Hyperconjugative effects in π-hydrogen bonding: Theory and experiment
Theoretical studies on structures and reactivities of organocuprate(I) and organocopper(III) species
Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole
General recurrence-relation generation scheme for molecular integral evaluation
TUNNEX: An easy-to-use wentzel-kramers-brillouin (WKB) implementation to compute tunneling half-lives
Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br)
Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density
Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method
Electric dipole polarity of diatomic molecules
Molecular mechanics studies of acyl halides: II. Vibrational spectra
goChem: A Composable Library for Multi-Scale Computational Chemistry Data Analysis
An open library of relativistic core electron density function for the QTAIM analysis with pseudopotentials
Grid positioning independence and the reduction of self-energy in the solution of the Poisson - Boltzmann equation
Comparison of atomic charges derived via different procedures
Force field parameters for carbohydrates
Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency
SG-0: A small standard grid for DFT quadrature on large systems
Theoretical study of correlations between the coordination structures and catalytic activities in polymer-stabilized au nanocluster catalysts
Iron-sulfur bond covalency from electronic structure calculations for classical iron-sulfur clusters
The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study
lambda-Dynamics free energy simulation methods
MCCE2: Improving protein p K a calculations with extensive side chain rotamer sampling
Quantum chemical rovibrational analysis of aminoborane and its isotopologues
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
Shapelets: Possibilities and limitations of shape-based virtual screening
Exact Gaussian expansions of Slater-type atomic orbitals
Aten - An application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules
On the modeling of arginine-bound carboxylates: A case study with Pyruvate Formate-Lyase
Theoretical study on the Br + CH 3 SCH 3 reaction
Algorithms for computer detection of symmetry elements in molecular systems
Efficient quantification of the importance of contacts for the dynamical stability of proteins
Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds
Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network
Spontaneous segregation on a hybrid chiral surface
Molecular mechanics studies of acyl halides: I. Molecular structures and conformational analysis
Quantum-chemistry based calibration of the alkali metal cation series (Li + -Cs + ) for large-scale polarizable molecular mechanics/dynamics simulations
Binding affinity prediction with different force fields: Examination of the linear interaction energy method
Replicated data and domain decomposition molecular dynamics techniques for simulation of anisotropic potentials
Applying the bioisosterism strategy to obtain lead compounds against SARS-CoV-2 cysteine proteases: An in-silico approach
Toward a rational design of -peptide structures
Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression
Bonding and stability of elusive silaboryne (SiB) and germaboryne (GeB) with donor base ligands
Prediction of conformationally dependent atomic multipole moments in carbohydrates
A Comparative Quatnum Mechanical Study of Bond Separation Energies as a Measure of Cyclic Conjugation
Ab initio periodic study of the conformational behavior of glycine helical homopeptides
A density-functional study of the phase diagram of cementite-type (Fe, Mn) 3 C at absolute zero temperature
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin
Modification of the CHARMM force field for DMPC lipid bilayer
Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force
Molecular modeling of A 1 and A 2A adenosine receptors: Comparison of rhodopsin- and beta 2 -adrenergic-based homology models through the docking studies
Fragments-in-fragments method for efficient and reliable estimates of individual hydrogen bond energies in large molecular clusters
Canonical orbital contributions to the magnetic fields induced by global and local diatropic and paratropic ring currents
The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes
Møller-Plesset perturbation energies and distances for HeC 20 extrapolated to the complete basis set limit
Molecular dynamics simulation of cellobiose in water
MORMIN: A quasi-Newtonian energy minimizer fitting the nuclear overhauser data
The effect of midbond functions on interaction energies computed using MP2 and CCSD(T)
Novel bi-transition metallic encapsulated naphthalene-like Si 20 prismatic cage: A DFT investigation
Parametrization of a Force Field for Studying Some Beta Lactams
PGA: A new particle swarm optimization algorithm based on genetic operators for the global optimization of clusters
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design
Accuracy of finite-difference harmonic frequencies in density functional theory
Electronic and ligating properties of carbocyclic carbenes: A theoretical investigation
A Kirkwood-Buff derived force field for amides
Water exchange dynamics of manganese(II), cobalt(II), and nickel(II) ions in aqueous solution
A kinematic view of loop closure
On the Use of PDB X-Ray Crystal Structures as Force Field Target and Validation Data for Pyranose Ring Puckering
Rapid parameterization of small molecules using the force field toolkit
Erratum: "A solvation-free-energy functional: A reference-modified density functional formulation" [J. Comput. Chem 36, 1359-1369]
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features
Theoretical mechanistic study on the reaction of CN radical with HNCN
Accurate prediction of proton chemical shifts. I. Substituted aromatic hydrocarbons
Basis set error estimation for DFT calculations of electronic g-tensors for transition metal complexes
Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?
Accurate prediction of basicity in aqueous solution with COSMO-RS
Multiparticle moves in acceptance rate optimized monte carlo
Isolated pentagon rule violating endohedral metallofullerenes explained using the Hückel rule: A statistical mechanical study of the C 84 Isomeric Set
A simple representation of energy matrix elements in terms of symmetry-invariant bases
Toward prediction of the precatalyst activation mechanism through the cross-coupling reactions: Reduction of Pd(II) to Pd(0) in precatalyst of the type Pd-PEPPSI
The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties
Practical aspects of computational chemistry calculations through PC networks: the RAMSES-Beowulf implementation
Critical reevaluation of proximity effects in the barton oxidation and related intramolecular reactions
BF3-Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2-siloxy-1-propene
Parallel Direct Implementations of Second-Order Perturbation Theories
Quantum cluster equilibrium theory applied to liquid ammonia
Van der Waals Effects on semiconductor clusters
Steered molecular dynamics simulations for uncovering the molecular mechanisms of drug dissociation and for drug screening: A test on the focal adhesion kinase
Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table
Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study
Implementation of real-time TDDFT for periodic systems in the open-source PySCF software package
Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling
Nudged elastic stiffness band method: A method to solve kinks problems of reaction paths
Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations
First principles insight into the study of the structural, stability, and optoelectronic properties of alkali-based single halide perovskite ZSnCl 3 (Z = Na/K) materials for photovoltaic applications
Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy
Electronic structures and optical properties of BiOX (X = F, Cl, Br, I) via DFT calculations
Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase
A Fukui function-guided genetic algorithm. Assessment on structural prediction of Si n ( n = 12-20) clusters
NMR 3J(C1, H3) couplings in 1-X-bicyclo[1.1.1]pentanes. FPT-DFT and NBO studies of hyperconjugative interactions and heavy atom substituent effects
Impact of non-empirically tuning the range-separation parameter of long-range corrected hybrid functionals on ionization potentials, electron affinities, and fundamental gaps
Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr
Evaluation of AM1-calculated radical cation ion-neutral complexes
Decoding the reaction mechanism of the cyclocondensation of ethyl acetate2-oxo-2-(4-oxo-4H-pyrido [1.2-a] pyrimidin-3-yl) polyazaheterocycle and ethylenediamine using bond evolution theory
Direct evaluation via forced oscillation method of the electronic state density of sizable clusters
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
A simple method for faster nonbonded force evaluations
A Hammett's analysis of the substituent effect in functionalized diketopyrrolopyrrole (DPP) systems: Optoelectronic properties and intramolecular charge transfer effects
Virtual screening for compounds that mimic protein-protein interface epitopes
Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA
The use of time-averaged 3 J HH restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: Methodology and applications
Coral: QSAR models for acute toxicity in fathead minnow ( Pimephales promelas )
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: On the correlation between crystal water sites, solvent density, and solvent dipole
Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units
Computational chemistry approach for the early detection of drug-induced idiosyncratic liver toxicity
TheRate: Program for ab initio direct dynamics calculations of thermal and vibrational-state-selected rate constants
A versatile method for systematic conformational searches: Application to CheY
Exploring the quality of protein structural models from a Bayesian perspective
Fast approximate methods for calculating nucleic acid base pair interaction energies
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages
Breaking a bottleneck: Accurate extrapolation to "gold standard" CCSD(T) energies for large open shell organic radicals at reduced computational cost
Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra
Electrostatic model for infrared intensities in a spectroscopically determined molecular mechanics force field
Generalized Alteration of Structure and Parameters: A New Method for Free- Energy Perturbations in Systems Containing Flexible Degrees of Freedom
How deeply are core electrons perturbed when valence electrons are spin polarized? The case study of transition metal compounds
How does the NMR thermometer work? Application of combined quantum molecular dynamics and GIPAW calculations into the study of lead nitrate
Quantum crystallography: From the intersection to the union of crystallography and quantum mechanics
Evaluation of electrostatic descriptors for predicting crystalline density
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters
Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics
A computational study of interactions between acetic acid and water molecules
Assessment of density functional approximations for N2 and CO2 physisorption on benzene and graphene
Effective generation of molecular cavities in polarizable continuum model by DefPol procedure
Consistent valence force-field parameterization of bond lengths and angles with quantum chemical ab initio methods applied to some heterocyclic dopamine D3-receptor agonists
Prediction of the properties and thermodynamics of formation for energetic nitrogen-rich salts composed of triaminoguanidinium cation and 5-nitroiminotetrazolate-based anions
Assessment of TD-DFT- and TD-HF-based approaches for the prediction of exciton coupling parameters, potential energy curves, and electronic characters of electronically excited aggregates
Hydrogen bonding and solvent effects on the lowest 1(n, *) excitations of triazines in water
Application of standard DFT theory for nonbonded interactions in soft matter: Prototype study of poly-para-phenylene
Pseudospectral implementations of long-range corrected density functional theory
Pure component spectral reconstruction from mixture data using SVD, global entropy minimization, and simulated annealing. Numerical investigations of admissible objective functions using a synthetic 7-species data set
Efficient mesh refinement for the Poisson-Boltzmann equation with boundary elements
Electronic structure and low temperature thermoelectric properties of In 24 M 8 O 48 (M = Ge 4+ , Sn 4+ , Ti 4+ , and Zr 4+ )
Why is N···Be distance of NH 3 H + ···DBeH shorter than that of NH 3 D + ···HBeH? paradoxical geometrical isotope effects for partially isotope-substituted dihydrogen-bonded isotopomers
BAR-based optimum adaptive steered MD for configurational sampling
Necessity of high-resolution for coarse-grained modeling of flexible proteins
One-electron spin-orbit contribution by effective nuclear charges
HUNTER: A conformational search program for acyclic to polycyclic molecules with special emphasis on stereochemistry
Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields
Constant-NT simulations: Free energy difference method for excess adsorption
SINDO1 Study of the Photoreaction of Tetramethylene Sulfone
Quantum control implemented as combinatorial optimization
Enhancing MM/P(G)BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations
POMSimulator: An open-source tool for predicting the aqueous speciation and self-assembly mechanisms of polyoxometalates
Flexible protein-ligand docking using the Fleksy protocol
Coarse-graining: A procedure to generate equilibrated and relaxed models of amorphous polymers