yusuke1997/dblp-id-title huggingface dataset:
The origin of the two-electron/four-centers C-C bond in pi-TCNE 2 2 - dimers: Electrostatic or dispersion?
The DFT route to NMR chemical shifts
Distinguishing and quantifying the torquoselectivity in competitive ring-opening reactions using the stress tensor and QTAIM
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms
CO 2 reduction using aluminum hydride: Generation of in-situ frustrated Lewis pairs and small molecule activation therein
Confinement induced thermodynamic and kinetic facilitation of some Diels-Alder reactions inside a CB[7] cavitand
Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level
Theoretical study on the unimolecular decomposition of thiophenol
CCSD-CTOCD static dipole shielding polarizability for quantification of the chiral NMR effects in oxaziridine derivatives
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins
Theoretical study on reaction mechanism of the fluoromethylene radical with nitrogen dioxide
Assessment of intermolecular interactions at three sites of the arylalkyne in phenylacetylene-containing lithium-bonded complexes: Ab initio and QTAIM studies
Analytical energy gradient evaluation in relativistic and nonrelativistic density functional calculations
Py3BR: A software for computing atomic three-body recombination rates
1, 2-migration in N -phosphano functionalized N -heterocyclic carbenes
Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with distributed memory HEOM (DM-HEOM)
Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ
Electron transfer in the c-type cytochrome subunit of the photosynthetic reaction center of Rhodopseudomonas viridis: ab initio theoretical study
A fast and accurate algorithm for QTAIM integration in solids
QM/MM method for metal-organic interfaces
Theoretical study of the excited-state double proton transfer in the (3-methyl-7-azaindole)-(7-azaindole) heterodimer
Di- and trioxides of triazolotetrazine: Computational prediction of crystal structures and estimation of physicochemical characteristics
Array files for computational chemistry: MP2 energies
Multiwfn: A multifunctional wavefunction analyzer
Support vector machines for predicting HIV protease cleavage sites in protein
Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling
Relation between chemical bonding and exchange coupling approaches to the description of ordering in itinerant magnets
Design of donors with broad absorption regions and suitable frontier molecular orbitals to match typical acceptors via substitution on oligo(thienylenevinylene) toward solar cells
Nonadditive effects in ternary H 2 -cation-PAH systems
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase
Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids
Electronic and chelation effects on the unusual C2-methylation of N -( para -substituted)phenylaziridines with lithium organocuprates
3-D QSAR for intrinsic activity of 5-HT 1A receptor ligands by the method of comparative molecular field analysis
Numerical Evaluation of Three- and Four- Center Bielectronic Integrals Using Exponential- Type Atomic Orbitals
Molecular Mechanics (MM3) Calculations on Azoxy Compounds
Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach
Improved greedy algorithm for protein structure reconstruction
Relativistic Dirac-Fock Calculations for Closed-Shell Molecules
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds
Assessment of density functionals with long-range and/or empirical dispersion corrections for conformational energy calculations of peptides
Systematic stepsize variation: Efficient method for searching conformational space of polypeptides
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution
A metadynamics perspective on the reduction mechanism of the Pt(IV) asplatin prodrug
Graphical approach to analyzing DNA sequences
Maximal probability domains in linear molecules
Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations
Prediction of protein structural class using novel evolutionary collocation-based sequence representation
EQUIPATH - an equilibrial path tracing routine for the use with the program package GAUSSIAN94
Use of molecular dynamics simulations with ab initio SCF calculations for the determination of the deuterium quadrupole coupling constant in liquid water and bond lengths in ice
Jason Wagoner and Nathan A. Baker, "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, "Journal of Computational Chemistry(2004) 25(13) 1623-1629
On the application of the IMOMO (integrated molecular orbital + molecular orbital) method
Joint neighbors approximation of macromolecular solvent accessible surface area
Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the beta 2 -adrenergic receptor
Estimating correlation energy of diatomic molecules and atoms with neural networks
A new parallel method for molecular dynamics simulation of macromolecular systems
A theoretical study of catalytic hydration reactions of ethylene
Quantum Chemical Exploration of Intermolecular Reactions of Acetylene
Influence of core-valence separation of electron localization function
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software
A new hybrid algorithm for finding the lowest minima of potential surfaces: Approach and application to peptides
The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
Improving B3LYP heats of formation with three-dimensional molecular descriptors
A computational study of base-catalyzed reactions between isocyanates and epoxides affording 2-oxazolidones and isocyanurates
Information theoretical measures to analyze trajectories in rational molecular design
Solvent effect on excited state potential energy surfaces of Thioflavin T. Qualitatively different results by TDDFT and SA-2-CASSCF methods
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL)
IGMPlot: A program to identify, characterize, and quantify molecular interactions
LOBSTER: A tool to extract chemical bonding from plane-wave based DFT
Computational protocol for predicting 19F NMR chemical shifts for PFAS and connection to PFAS structure
Theoretical investigation of electron transfer transition in tetracyanoethylene-contained organic complexes
Prion protein conversion triggered by acidic condition: a molecular dynamics study through different force fields
RISMiCal: A software package to perform fast RISM/3D-RISM calculations
A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols
The role of protein "Stability patches" in molecular recognition: A case study of the human growth hormone-receptor complex
Exponential repulsion improves structural predictability of molecular docking
Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits
Simulating enzyme reactions: Challenges and perspectives
Towards design of the smallest planar tetracoordinate carbon and boron systems
On the applicability of cluster models to study the chemical reactivity of carbon nanotubes
Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs
Ionic liquids intercalation in titanium carbide MXenes: A first-principles investigation
Bonding charge density from atomic perturbations
MDockPeP: An ab-initio protein-peptide docking server
tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics
FEW: A workflow tool for free energy calculations of ligand binding
Evaluation of protein-ligand binding free energy focused on its entropic components [J. Comp. Chem. 33, 550-560]
Curvature-weighted nudged elastic band method using the Riemann curvature
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements
An ab initio interpretation in gas phase and aqueous solution of the generalized anomeric effect in ROCR2NR2 (R = H, CH3)
DFT calculations of 57 Fe Mössbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: Applications to methane monooxygenase and ribonucleotide reductase
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
FCclasses3 : Vibrationally-resolved spectra simulated at the edge of the harmonic approximation
Theoretical study and rate constant calculation for reaction of CF 3 CH 2 OH with OH
Acceleration of coarse grain molecular dynamics on GPU architectures
Is coronene better described by Clar's aromatic π-sextet model or by the AdNDP representation?
The hydrogen perturbation in molecular connectivity computations
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics
Implementing dimer metadynamics using gromacs
The second derivative of the electronic energy with respect to the compression scaling factor in the XP-PCM model: Theory and applications to compression response functions of atoms
Utilization of Shape Data in Molecular Mechanics Using a Potential Based on Sherical Harmonic Surfaces
Mechanism of the Non-Kasha Fluorescence in Pyrene
An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis
Periodic trends and complexation chemistry of tetravalent actinide ions with a potential actinide decorporation agent 5-LIO(Me-3, 2-HOPO): A relativistic density functional theory exploration
Calculation and analysis of low frequency normal modes for DNA
A full dimensional grid empowered simulation of the CO2 + CO2 processes
p K a prediction in non-aqueous solvents
Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory
Thermodynamic compatibility of actives encapsulated into PEG-PLA nanoparticles: In Silic o predictions and experimental verification
Use of theoretical descriptors to characterize cation- binding sites in (macro)molecules
Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal
Coordination bonding in dicopper and dichromium tetrakis(μ-acetato)-diaqua complexes: Nature, strength, length, and topology
Evaluation of electroosmotic drag coefficient of water in hydrated sodium perfluorosulfonate electrolyte polymer
Shape Analysis of Hydrogen-Bonded Networks in Solvation Clusters
Cover Image, Volume 40, Issue 27
Reducing I/O costs for the eigenvalue procedure in large-scale configuration interaction calculations
Global optimization of atomic and molecular clusters using the space-fixed modified genetic algorithm method
Implementation of the diagonalization-free algorithm in the self-consistent field procedure within the four-component relativistic scheme
Accurate free energy calculation along optimized paths
Gas-phase reactions of SiH n + ( n = 1, 2) with NF3: A computational investigation on the detailed mechanistic aspects
Polarizable force field for RNA based on the classical drude oscillator
Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis
Pytim: A python package for the interfacial analysis of molecular simulations
Cu2+ in liquid ammonia - The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics
Exchange coupling and magnetic anisotropy in a family of bipyrimidyl radical-bridged dilanthanide complexes: Density functional theory and ab initio calculations
Paths to which the nudged elastic band converges
BonnMag: Computer program for ligand-field analysis of f n systems within the angular overlap model
Global measure of molecular flexibility and shape fluctuations about conformational minima
Gibbs energy minimization in gas + liquid + solid systems
Structures and electron affinities of the di-arsenic fluorides As 2 F n /As 2 F n -( n = 1-8)
Water in Ras Superfamily Evolution
The temperature intervals with global exchange of replicas empirical accelerated sampling method: Parameter sensitivity and extension to a complex molecular system
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
Assessment of DFT Functionals for Structural Determination of Lanthanide(III) Complexes Using Ligand Field Splitting
DFT models for copper(II) bispidine complexes: Structures, stabilities, isomerism, spin distribution, and spectroscopy
Aluminum alkoxy-catalyzed biomass conversion of glucose to 5-hydroxymethylfurfural: Mechanistic study of the cooperative bifunctional catalysis
Consistent modifications of SINDO1: II. Applications to first- and second-row elements
Quantitative characterization of the PC bonds in ylides of phosphorus
Relativistic and electron-correlation effects on magnetizabilities investigated by the Douglas-Kroll-Hess method and the second-order Møller-Plesset perturbation theory
MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface
Extent of structural change during the reaction and its relationship to isoselectivity in polypropylene polymerization with ansa-zirconocene/borate catalyst: A computational study
A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms
Comment on "Martini force field for protonated polyethyleneimine"
Photochemistry in the strong coupling regime: A trajectory surface hopping scheme
Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective
Recasting wave functions into valence bond structures: A simple projection method to describe excited states
Recognition of protein allosteric states and residues: Machine learning approaches
Computational study of conformational preferences of thioamide-containing azaglycine peptides
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters
Density functional theory study with and without COSMO of H2SO4 reactions in an aqueous environment for metal extraction
Improving the heterointerface in hybrid organic-inorganic perovskite solar cells by surface engineering: Insights from periodic hybrid density functional theory calculations
Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br)
Ab initio surface hopping excited-state molecular dynamics approach on the basis of spin-orbit coupled states: An application to the A-band photodissociation of CH3I
Alkali metal atom-aromatic ring: A novel interaction mode realizes large first hyperpolarizabilities of M@AR (M = Li, Na, and K, AR = pyrrole, indole, thiophene, and benzene)
A search algorithm for fixed-composition protein design
Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide
Low-barrier hydrogen bonds: Ab initio and DFT investigation
A theoretical study of solvent effects on tautomerism and electronic absorption spectra of 3-hydroxy-2-mercaptopyridine and 2, 3-dihydroxypyridine
A theoretical study on the alkali metal carboxylate-promoted L-Lactide polymerization
The Molecular Structures and the Absorption Maxima of the H-Chromophores of t he Indigoid Dyes
Practical Machine Learning Strategies. I. Correcting the MMFF Molecular Mechanics Model to More Accurately Provide Conformational Energy Differences in Flexible Organic Molecules
Theoretical study on the rate constants for the C2H5 + HBr C2H6 + Br reaction
Electron localization and delocalization in open-shell molecules
Off-lattice Monte Carlo method with constraints: Long-time dynamics of a protein model without nonbonded interactions
Energy landscape study of water splitting and H2 evolution at a ruthenium(II) pincer complex
Prediction of spectroscopic constants for diatomic molecules in the ground and excited states using time-dependent density functional theory
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular. interactions
Ab Initio and Molecular Mechanics /MM2 and MM3) Calculations of Nonconjugated Positively Charged Nitrogen-Containg Compounds
Investigating Protein-Protein Allosteric Network using Current-Flow Scheme
Blind docking of 260 protein-ligand complexes with EADock 2.0
Molecular dynamics with helical periodic boundary conditions
Theoretical studies on the reactions CH 3 SCH 3 with OH, CF 3 , and CH 3 radicals
A smooth permittivity function for Poisson-Boltzmann solvation methods
Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non-uniform fast fourier transform
Assessment of the applicability of DFT methods to [Cp*Rh]-catalyzed hydrogen evolution processes
Effect of the axial cysteine ligand on the electronic structure and reactivity of high-valent iron(IV) oxo-porphyrins (Compound I): A theoretical study
Dimetallic sulfide endohedral metallofullerene Sc 2 S@C 76 : Density functional theory characterization
A generalized direct-particle-deletion scheme for the calculation of chemical potential and solubilities of small- and medium-sized molecules in amorphous polymers
Investigation of glucose electrooxidation mechanism over N-modified metal-doped graphene electrode by density functional theory approach
Thermochemistry of per- and polyfluoroalkyl substances
Nonlocal Density Functional Calculation of Gas Phase Heats of Formation
Reply to the comment by Sheppard and Henkelman on the nudged elastic band method
Nature of Stoner condition for metallic ferromagnetism
Simulation of the electronic and vibrational structure of hydrogenated amorphous silicon using cluster models
Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data
An algorithm for very high pressure molecular dynamics simulations
Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm
Molecular dynamics study of DNA binding by INT-DBD under a polarized force field
Multiscale Differential Geometry Learning for Protein Flexibility Analysis
Accurate adsorption energies for small molecules on oxide surfaces: CH 4 /MgO(001) and C 2 H 6 /MgO(001)
Automated exploration of stable isomers of H + (H 2 O) n ( n = 5-7) via ab initio calculations: An application of the anharmonic downward distortion following algorithm
Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies
Effect of substitutionally boron-doped single-walled semiconducting zigzag carbon nanotubes on ammonia adsorption
Density Functional Theory Calculations of Structural, Electronic, and Magnetic Properties of the 3d Metal Trifluorides MF3 (M = Ti-Ni) in the Solid State
Effects of lithium on the electronic properties of porous Ge as anode material for batteries
Comment on "Theoretical Investigations on Geometrical and Electronic Structures of Silver Clusters"
PyRETIS 3: Conquering rare and slow events without boundaries
Free energy perturbation and molecular dynamics calculations of copper binding to azurin
Dramatic substituent effects on the mechanisms of nucleophilic attack on Se - S bridges
Total and orbital density-based analyses of molecules revealing long-range interaction regions
A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: Mixed basis set and ONIOM methods combined with a complete basis set extrapolation
Implementation of divide-and-conquer method including Hartree-Fock exchange interaction
Excited state properties, fluorescence energies, and lifetime of a poly(fluorene-pyridine) copolymer, based on TD-DFT investigation
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations
WATGEN: An algorithm for modeling water networks at protein-protein interfaces
XMVB: A program for ab initio nonorthogonal valence bond computations
Treatment of hydrogen bonding in SINDO1
Electronic and magnetic properties of TATA-DNA sequence driven by chemical functionalization
Representations of Shavitt Graphs Within the Graphical Unitary Group Approach
All-atom de novo protein folding with a scalable evolutionary algorithm
Comparing search strategies for finding global optima on energy landscapes
Molecular dynamics simulation in the grand canonical ensemble
Dual-hybrid direct random phase approximation and second-order screened exchange with nonlocal van der Waals correlations for noncovalent interactions
Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model
Intruder state avoidance multireference Møller-Plesset perturbation theory
STOCK: Structure mapper and online coarse-graining kit for molecular simulations
Fast Geometry Optimization Using a Modifed Extended Hückel Method: Results for Molecules Containing H, C, N, O, and F
Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics
Ultrafast Dynamics of Diketopyrrolopyrrole Dimers
Scrutinizing "Invisible" astatine: A challenge for modern density functionals
Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking
Theoretical study of electronic properties of organic photovoltaic materials
Rational designing of 8-hydroxyquinolin-imidazolinone-based fluorescent protein mutants with dramatically red shifted emission: A computational study
Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors
SLIM: An improved generalized Born implicit membrane model
Conformer-RL: A deep reinforcement learning library for conformer generation
Kick: Constraining a stochastic search procedure with molecular fragments
Kylin 1.0: An ab-initio density matrix renormalization group quantum chemistry program
Solvation parameters for amino acids
A computational study of the lowest singlet and triplet states of neutral and dianionic 1, 2-substituted icosahedral and octahedral o-carboranes
Global optimization using bad derivatives: Derivative-free method for molecular energy minimization
Ab initio MO study of selected aluminum and boron chlorides and fluorides: Comparison with 11B NMR spectra of a tetrachloroborate melt
Exploring Inhibition Mechanisms in Wildtype and T315I BCR-ABL1: An In Silico Approach Integrating Virtual Screening, MD Simulations, and MM-GBSA Analysis
Calculation of Binding Energy Differences for Receptor-Ligand Systems Using the Poisson-Boltzmann Method
Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions
Exploring phosphoryl oxygen basicity in U(VI) complexation: A comparative study from trialkyl phosphate to phosphine oxide
Uncertainty of exchange-correlation functionals in density functional theory calculations for lithium-based solid electrolytes on the case study of lithium phosphorus oxynitride
Kinetics for the hydrogen-abstraction of CH4 with NO2
A novel semi-empirical topological descriptor Nt and the application to study on QSPR/QSAR
Mechanism for the reaction of 2-naphthol with N -methyl- N -phenyl-hydrazine suggested by the density functional theory investigations