yusuke1997/dblp-id-title huggingface dataset:
Studying the Protein Thermostabilities and Folding Rates by the Interaction Energy Network in Solvent
Linear regression model of DNA sequences and its application
Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents
Generalized simulated annealing applied to protein folding studies
Reaction rates in a theory of mechanochemical pathways
Trajectory on-the-fly molecular dynamics approach to tunneling splitting in the electronic excited state: A case of tropolone
Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations
Significant nonlinear-optical switching capacity in atomic clusters built from silicon and lithium: A combined ab initio and density functional study
Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method
Application of the dressed time-dependent density functional theory for the excited states of linear polyenes
Assessment of free energy predictors for ligand binding to a methyllysine histone code reader
Geometry optimization in density functional methods
PyDEF 2.0: An Easy to Use Post-treatment Software for Publishable Charts Featuring a Graphical User Interface
Is the Stereomutation of Methane Possible?
Proton affinities of maingroup-element hydrides and noble gases: Trends across the periodic table, structural effects, and DFT validation
All-electron scalar relativistic basis sets for the elements Rb-Xe
Ab initio crystal structure prediction - I. Rigid molecules
Effect of methylation on relative energies of tautomers and on the intramolecular proton transfer barriers of protonated nitrosamine: A MR-CISD study
Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking
Can we predict the structure and stability of molecular crystals under increased pressure? First-principles study of glycine phase transitions
Parallel computation of second derivatives of RHF energy on distributed memory computers
Exploring the Structure and Stability of Cholesterol Dimer Formation in Multicomponent Lipid Bilayers
Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models
Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics
Numerical interpretation of molecular surface field in dielectric modeling of solvation
An ab initio potential energy surface and vibrational energy levels of ZnH 2
Probing gas adsorption in MOFs using an efficient ab initio widom insertion Monte Carlo method
Computational protein design: Software implementation, parameter optimization, and performance of a simple model
Performance of parallel TURBOMOLE for density functional calculations
An algorithm for three-dimensional Voronoi S-network
Ab Initio quantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties
G2 study of triplet [H4, Si, P]+ potential energy surface: Mechanism for reaction of P+ (3P) with silane
Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach
Efficient computation of root mean square deviations under rigid transformations
Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations
Harmonic vibrational frequencies: Scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets
Efficiency of the algorithms for the calculation of Slater molecular integrals in polyatomic molecules
Substituent effects on heats of formation, group interactions, and detonation properties of polyazidocubanes
Methods for refining interactively established models of ribosomal RNA towards a physico-chemically plausible structure
The correlation of proton affinities with atomic charges and electronegativities for the group 14 to 17 hydrides
Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation
Multi-zinc-expanded graphene patches: Tetraradical versus diradical character
Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space
Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics
Analytical excited state forces for the time-dependent density-functional tight-binding method [Journal of Computational Chemistry 28, 2589]
Electron localization and delocalization indices for solids
Confined polyelectrolytes: The complexity of a simple system
A comparative quantum chemical study of the ruthenium catalyzed olefin metathesis
Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules
Lone pairs mapping by Laplacian of 3He NMR chemical shift
CSiGaAl2-/0 and CGeGaAl2-/0 having planar tetracoordinate carbon atoms in their global minimum energy structures
Theoretical investigation of the ethylene dimer: Interaction energy and dipole moment
The effect of electron correlation on the conformational space of melatonin
Structural, electronic, bonding, and elastic properties of NH 3 BH 3 : A density functional study
Unexpectedly strong anion-π interactions on the graphene flakes
Solvation in octanol: parametrization of the continuum MST model
Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets
Computational Probing of Schleyer's Hyperconjugative Aromaticity in a Novel Designed Anion Acceptor
Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library
On the performance of composite schemes in determining equilibrium molecular structures
CATKINAS: A large-scale catalytic microkinetic analysis software for mechanism auto-analysis and catalyst screening
QM/MM calculation of solvent effects on absorption spectra of guanine
Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments
Conformational preferences of N -methoxycarbonyl proline dipeptide
A CASSCF-CASPT2 study of the excited-state intramolecular proton transfer reaction in 1-amino-3-propenal using different active spaces
Analysis of the Ring-Form Tautomers of Psicose with MM3(92)
On the centrality of vertices of molecular graphs
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3
Multigrid solution of the Poisson - Boltzmann equation
High-level ab initio calculations on HGeCl and the equilibrium geometry of the Ã 1 A" state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeCl
Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids
Toward a global maximization of the molecular similarity function: Superposition of two molecules
Lattice modeling: Accuracy of energy calculations
Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution
A coarse-grained MARTINI-like force field for DNA unzipping in nanopores
Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: Weighted core-valence correlation consistent basis sets for the 4 d elements Y-Pd
Performance of plane-wave-based LDA+ U and GGA+ U approaches to describe magnetic coupling in molecular systems
Reference program for molecular calculations with Slater-type orbitals
On the Existence of SH 3 , and TeH 3 : Discrepanticies between All-Electron and Pseudopotential Calculations
Strategies to model the near-solute solvent molecular density/polarization
Bond length and the electron density at the bond critical point: X-X, Z-Z, and C-Z bonds (X = Li-F, Z = Na-Cl)
Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units
Stochastic generator of chemical structure. 4. Building polymeric systems with specified properties
Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441
Parametrization of macrolide antibiotics using the force field toolkit
A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package
Electron density deformations provide new insights into the spectral shift of rhodopsins
The influence of peripheral ligand bulk on nitrogen activation by three-coordinate molybdenum complexes - A theoretical study using the ONIOM method
Computational Assessment of MLCT versus MC Stabilities in First-to-Third-Row d6 Pseudo-Octahedral Transition Metal Complexes
An Examination of a Density Functional/Molecular Mechanical Coupled Potential
Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study
Prediction of human cytochrome P450 2B6-substrate interactions using hierarchical support vector regression approach
Similarity measures based on Gaussian-type promolecular electron density models: Alignment of small rigid molecules
New dimension indices for the characterization of the solvent-accessible surface
Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces
Full four-component relativistic calculations of NMR shielding and indirect spin-spin coupling tensors in hydrogen halides
An extended dead-end elimination algorithm to determine gap-free lists of low energy states
Transferable Semiempirical Quadratic Force Fields: The Case of Polythiophene and Shorter Oligomers
First-principles modeling of hafnia-based nanotubes
A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias
Theoretical modulation of the color of light emitted by firefly oxyluciferin
Vibrational projection analysis: New tool for quantitatively comparing vibrational normal modes of similar molecules
Novel topological index for research on structure-property relationships of complex organic compounds
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
Computational study of static first hyperpolarizability of donor-acceptor substituted ( E )-benzaldehyde phenylhydrazone
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines
Reactivity index based on orbital energies
Proton-coupled electron transfer of the phenoxyl/phenol couple: Effect of Hartree-Fock exchange on transition structures
Cluster size convergence for the energetics of the oxygen evolving complex in PSII
TD-DFT study on the sensing mechanism of a fluorescent chemosensor for fluoride: Excited-state proton transfer
Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction
A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid-vapor interface of water
Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro
Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA
Royal crown-shaped electride Li3-N3-Be containing two superatoms: New knowledge on aromaticity
Conformational analysis of arginine in gas phase - A strategy for scanning the potential energy surface effectively
Cassandra: An open source Monte Carlo package for molecular simulation
Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations
Path Integral Molecular Dynamics Methods: Application to Neon
Development of minimized mixing molecular orbital method for designing organic ferromagnets
Theoretical investigations on structure, density, detonation properties, and sensitivity of the derivatives of PYX
Theoretical insights on the electron doping and Curie temperature in La-doped Sr 2 CrWO 6
Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes
Isomerization of stilbene using enforced geometry optimization
Ab initio determination of the infrared phosphine torsion spectrum in vinylphosphine with ZPE correction
Cover Image, Volume 39, Issue 19
QSARINS-chem: Insubria datasets and new QSAR/QSPR models for environmental pollutants in QSARINS
Comparative studies of quasi-relativistic density functional methods for the description of lanthanide and actinide complexes
Interconversion behavior of the CH bond in the CH radical cation: Ab initio molecular dynamics study
Computational studies on electron and proton transfer in phenol-imidazole-base triads
Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields
Molecular mechanics and dynamics of biomolecules using a solvent continuum model
Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown
An electronic structure theory investigation of the physical chemistry of the intermolecular complexes of cyclopropenylidene with hydrogen halides
Treatment of multibody interactions in molecular simulations of systems with general bond networks
Core-shell potential-derived point charges
Judicious design functionalized 3D-COF to enhance CO2 adsorption and separation
The interaction of thiocyanate with peptides - A computational study
Molecular sensing using armchair graphene nanoribbon
Quantum correction to the pair distribution function
PyCDFT : A Python package for constrained density functional theory
Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory
Benchmark ab initio proton affinity and gas-phase basicity of α-alanine based on coupled-cluster theory and statistical mechanics
Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential
Equation-of-motion orbital-optimized coupled-cluster doubles method with the density-fitting approximation: An efficient implementation
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver
The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code
Acylation and deacylation mechanism and kinetics of penicillin G reaction with Streptomyces R61 DD -peptidase
Water polarizability in condensed phase: Ab initio evaluation by cluster approach
Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin
The Becke Fuzzy Cells Integration Scheme in the Amsterdam Density Functional Program Suite
Comparison of the Molecular Mechanics+Generalized Born/Surface Area and the Ab Initio+Monte Carlo Simulation Methods in Estimating Conformational Equilibria in Aqueous Solution
The Jahn-Teller and pseudo-Jahn-Teller effects in the anion photoelectron spectroscopy of B3 cluster
Reaction pathways of propene pyrolysis
Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities
Physical insight into the entropy-driven ion association
Unorthodox uses of Bennett's acceptance ratio method
Predicting hydration energies for multivalent ions
Ab initio study of hydrogen bonding in the phenol-water system
Searching for saddle points of potential energy surfaces by following a reduced gradient
Unveiling the Antiferromagnetic Properties of Cr 2 Pb n ( n = 3-20) Clusters
Potential Energy Surfaces for Rh-CO from DFT Calculations
Efficient algorithm for conformational search of macrocyclic molecules
Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields
Delocalization-ratio analysis of 3-center bonding in position-space for closo -boranes and related systems: Approaching the styx picture and beyond
Cover Image, Volume 40, Issue 24
Effect of inclusion of electron correlation in MM3 studies of cyclic conjugated compounds
Blue shifts of the C-H stretching vibrations in hydrogen-bonded and protonated trimethylamine. Effect of hyperconjugation on bond properties
Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds
McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal: A theoretical investigation of the concerted and stepwise mechanisms
Infrared and Raman active vibrational modes in MoS2-based nanotubes: Symmetry analysis and first-principles calculations
Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material
Iterative Atomic Charge Partitioning of Valence Electron Density
Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-x Ni x O 8- x (x = 1, 2, 3)
Anionic behavior and single-molecule crystal in fullerene confinements: A contribution from DFT energy decomposition and cooperativity analyses
Solvation effects in SINDO1: Application to organic molecules
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates
Building cavities in a fluid of spherical or rod-like particles: A contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model
A theoretical study of CO adsorption on gold by Hückel theory and density functional theory calculations
Amide-pi interactions between formamide and benzene
Identification of novel inhibitors for Prp protein of Mycobacterium tuberculosis by structure based drug design, and molecular dynamics simulations
The reactions of Cr(CO) 6 , Fe(CO) 5 , and Ni(CO) 4 with O 2 yield viable oxo-metal carbonyls
Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations
A complex Gaussian approach to molecular photoionization
Red and blue shifted hydridic bonds
Stabilization in neutral bicyclic sulfoxide compounds
Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH CH2CN + H2O
A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations
Electronic structure of the strongly correlated electron system plutonium hexaboride: A study from single-particle approximations and many-body calculations
Analytical methods for calculating Continuous Symmetry Measures and the Chirality Measure
Algorithms for Clustering Molecular Dynamics Confogurations
Gaseous reaction mechanism of C2F radical with water
A complete set of self-consistent charge density-functional tight-binding parametrization of zinc chalcogenides (ZnX; X=O, S, Se, and Te)
How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?
An augmented effective core potential basis set for the calculation of molecular polarizabilities
A first-order system least-squares finite element method for the Poisson-Boltzmann equation
The coupling constant polarizability and hyperpolarizabilty of 1 J (NH) in N -methylacetamide, and its application for the multipole spin-spin coupling constant polarizability/reaction field approach to solvation
Rate constants for hydrogen abstraction reactions by the hydroperoxyl radical from methanol, ethenol, acetaldehyde, toluene, and phenol
Pairwise decomposition of an MMGBSA energy function for computational protein design
mHDFS-HoF: A generalized multilevel homodesmotic fragment-separation reaction based program for heat-of-formation calculation for acyclic hydrocarbons
Theoretical strategies toward stabilization of singlet remote N-heterocyclic carbenes
Upack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules
On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states
Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules
Quantum chemical insights into the aggregation induced emission phenomena: A QM/MM study for pyrazine derivatives
GROMACS: Fast, flexible, and free
Rigid-CLL: Avoiding constant-distance computations in cell linked-lists algorithms
Energy Minimization of Peptide Ananlogues Using Genetic Algorithms
Temperature effects on the branching dynamics in the model ambimodal (6 + 4)/(4 + 2) intramolecular cycloaddition reaction
Correcting charge distribution in reduced Li-molecule pair for computational screening of battery solvents
Development of a general quantum-chemical descriptor for steric effects: Density functional theory based QSAR study of herbicidal sulfonylurea analogues
Conformational energies for 2-substituted butanes
Calculation of the excited states properties of LH1 complex of Thermochromatium tepidum
Proton solvation in protic and aprotic solvents
Conformational memories with variable bond angles
Relativistic density functional approach to open shells
Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources
Automated selection of optimal Gaussian fits to arbitrary functions in electronic structure theory
Current density analysis of electron transport through molecular wires in open quantum systems
On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model
Charge redistribution effect on the properties of charge transfer complexes HnRXY and HnRX2 (X, Y = F, Cl, Br, I; R = O, S, N, P)
Toward accurate modeling of structure and energetics of bulk hexagonal boron nitride
CHARMM force field and molecular dynamics simulations of protonated polyethylenimine
Can an OH radical form a strong hydrogen bond? A theoretical comparison with H 2 O
Voronoi-based detection of pockets in proteins defined by large and small probes
Time-dependent quantum study of H ( 2 S ) + FO ( 2 Pi) -> OH ( 2 Pi) + F ( 2 P ) reaction on the 1 3 A ' and 1 3 A " states
Toward Similarity Measures for Macromolecular Bodies: MEDLA Test Calculations for Substituted Benzene Systems
Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient
Linear polarizabilities and second hyperpolarizabilities of streptocyanines: Results from broken-Symmetry DFT and new CCSD(T) benchmarks
New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations
Ab-initio multireference study of an organic mixed-valence Spiro molecular system
Basis set approach to solution of poisson equation for small molecules immersed in solvent
Structural and Electronic Property Changes of the Nucleic Acid Bases upon Base Pair Formation
Theoretical density functional theory studies on interactions of small biologically active molecules with isolated heme group
Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions
A highly efficient hybrid method for calculating the hydration free energy of a protein
XGBoost-based intelligence yield prediction and reaction factors analysis of amination reaction
Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol
A polarizable, charge transfer model of water using the drude oscillator
Molecular mechanics calculations of -diketonate, aqua, and aqua-diketonate complexes of lanthanide ions using Gillespie-Kepert model
Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion