yusuke1997/dblp-id-title huggingface dataset:
A new extension of classical molecular dynamics: An electron transfer algorithm
Theoretical studies of the reactions of CF 3 CHCLOCHF 2 /CF 3 CHFOCHF 2 with OH radical and Cl atom and their product radicals with OH
Molecular structures and conformations: Experiment and theory
SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies
From C 58 to C 62 and back: Stability, structural similarity, and ring current
Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques
Possible mechanism of BN fullerene formation from a boron cluster: Density-functional tight-binding molecular dynamics simulations
The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
How water molecules modulate the hydration of CO 2 in water solution: Insight from the cluster-continuum model calculations
Quantum chemical modeling of photoadsorption properties of the nitrogen-vacancy point defect in diamond
Adsorption of multivalent alkylthiols on Au(111) surface: Insights from DFT
Analytical method for the representation of atoms-in-molecules densities
Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study
Molecular interaction potential: A new tool for the theoretical study of molecular reactivity
Free energy calculations in globular proteins: Methods to reduce errors
Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model
Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases
Noncovalent interactions between cisplatin and graphene prototypes
Diagnosis of the performance of the state-specific multireference coupled-cluster method with different truncation schemes
New aspects of quantum electrodynamics on electronic structure and dynamics
Fragment-based quantum mechanical calculation of protein-protein binding affinities
Soft-sphere continuum solvation models for nonaqueous solvents
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores
Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors
Accurate prediction of norbornadiene cycle enthalpies by DLPNO-CCSD(T1)/CBS method
MDMS: Software Facilitating Performing Molecular Dynamics Simulations
Correction to "Terminal end-on coordination of dinitrogen vs. isoelectronic CO: A comparison using the charge displacement analysis"
Cover Image, Volume 41, Issue 6
Decoding the components of dynamics in three-domain proteins
Calculation of Relative Free Energy Differrences for the Covalent Hydration of Organic Compounds: A Combined Quantum Mechanical and Free Energy Perturbation Study
Moment expansion of the linear density-density response function
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9
DOT2: Macromolecular docking with improved biophysical models
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
Insights on cyclophosphamide metabolism and anticancer mechanism of action: A computational study
Fulleride-metal η 5 sandwich and multi-decker sandwich complexes: A DFT prediction
Training machine learning potentials for reactive systems: A Colab tutorial on basic models
Cover Image, Volume 39, Issue 17
An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides
A large decoy set of protein-protein complexes produced by flexible docking
Comment on "Superposition of Waves or Densities: Which Is the Nature of Chemical Resonance?" [J. Comput. Chem. 2021 , 42, 412-417]
Cellulose-Builder: A toolkit for building crystalline structures of cellulose
Interaction energy and the shift in OH stretch frequency on hydrogen bonding for the H 2 O -> H 2 O, CH 3 OH -> H 2 O, and H 2 O -> CH 3 OH dimers
Permutationally invariant polynomial representation of polarizability tensor surfaces for linear regression analysis
Comparison of the numerical stability of methods for anharmonic calculations of vibrational molecular energies
Methylation of zebularine investigated using density functional theory calculations
Drug release by pH-responsive molecular tweezers: Atomistic details from molecular modeling
Parallelization of four-component calculations. I. Integral generation, SCF, and four-index transformation in the Dirac-Fock package MOLFDIR
A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins
Ab initio electronic absorption spectra of para -nitroaniline in different solvents: Intramolecular charge transfer effects
Principal coordinate maps of molecular potential energy surfaces
Groupy: An Open-Source Toolkit for Molecular Simulation and Property Calculation
GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations
QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase
Efficient optimization of natural resonance theory weightings and bond orders by gram-based convex programming
The C-terminal self-binding helical peptide of human estrogen-related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists
Notes on quantitative structure-properties relationships (QSPR) part 2: The role of the number of atoms as a molecular descriptor
Rotational barriers of disilane, hexafluorodisilane, and hexamethyldisilane: Ab initio, density functional, and molecular mechanics (MM3) studies
A Noncovalent Binding Strategy to Capture Noble Gases, Hydrogen and Nitrogen
ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity
Arene and functionalized arene based two dimensional organic-inorganic hybrid perovskites for photovoltaic applications
Revisiting the effect of f-functions in predicting the right reaction mechanism for hypervalent iodine reagents
Relativistic correlating basis sets for lanthanide atoms from Ce to Lu
Theoretical study of endohedral metallofullerenes: Sc3-nLanN@C80 (n=0-3)
Performance of DFT+ U method for prediction of structural and thermodynamic parameters of monazite-type ceramics
Structure and stability of coinage metal fluoride and chloride clusters (M n F n and M n Cl n , M = Cu, Ag, or Au; n = 1-6)
The competition of Y⋯o and X⋯n halogen bonds to enhance the group V σ-hole interaction in the NCY⋯o˭PH 3 ⋯NCX and O˭PH 3 ⋯NCX⋯NCY (X, Y˭F, Cl, and Br) complexes
Bond order and valence indices: A personal account
Enhancement of energy decomposition analysis in fragment molecular orbital calculations
Ab initio calculations of intramolecular parameters for a class of arylamide polymers
Comparative study of metal-porphyrins, -porphyrazines, and -phthalocyanines
Origins of relative acidity: First and second period hydrides
Some Challenges of Diffused Interfaces in Implicit-Solvent Models
Quantum-chemical analyses of aromaticity, UV spectra, and NMR chemical shifts in plumbacyclopentadienylidenes stabilized by Lewis bases
Applicability of MNDO techniques AM1 and PM3 to ring-structured polymers
Influence of Ligand Complexity on the Spectroscopic Properties of Type 1 Copper Sites: A Theoretical Study
Molecular energies and properties from density functional theory: Exploring basis set dependence of Kohn - Sham equation using several density functionals
High-precision calculation of Hartree-Fock energy of crystals
Applications of spectral-Representation model as a potential method for Cu clusters
Accurate prediction of proton chemical shifts. II. Peptide analogues
Characterization of two types of intermolecular interactions on halogen monoxide monohydrates
Spin-orbit effects on magnetically induced current densities in the () clusters
Optical response of the Cu 2 S 2 diamond core in Cu2II(NGuaS) 2 Cl 2
Simulation study on functional group-modified Ni-MOF-74 for CH 4 /N 2 adsorption separation
Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study
Horizontal vectorization of electron repulsion integrals
Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument
First-principles pair potentials across the metal-ceramic interface
How stable is a collagen triple helix? An ab initio study on various collagen and beta-sheet forming sequences
Artificial neural networks applied for studying metallic complexes
How resonance assists hydrogen bonding interactions: An energy decomposition analysis
Electron transfer pathways in mixed-valence paracyclophane-bridged bis-triarylamine radical cations
Solving the unimolecular master equation with a weighted subspace projection method
On the Evaluation of the Solvent Polarization Apparent Charges in the Polarizable Contnuum Model: A New Formulation
New space warping method for the simulation of large-scale macromolecular conformational changes
DFT studies using supercells and projector-augmented waves for structure, energetics, and dynamics of glycine, alanine, and cysteine
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
Continuous medium theory for nonequilibrium solvation: IV. Solvent reorganization energy of electron transfer based on conductor-like screening model
First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine
Alchemical free energy calculations via metadynamics: Application to the theophylline-RNA aptamer complex
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information
Symbolic algebra in functional derivative potential calculations
Electron localizability indicators ELI-D and ELIA for highly correlated wavefunctions of homonuclear dimers. I. Li 2 , Be 2 , B 2 , and C 2
Theoretical investigation of unimolecular decomposition channels of furan4
Pivotal Role of Nonmetal Atoms in the Stabilities, Geometries, Electronic Structures, and Isoelectronic Chemistry of Sc3X@C80 (X = C, N, and O)
The flexible alignment of molecular structures using simulated annealing with weighted Lagrangian multipliers
Numerical computations of molecular reactions in associated systems caused by the formation of fractal structures
GaudiMM: A modular multi-objective platform for molecular modeling
Intramolecular CHCcarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding
Two-layer molecular rotors: A zinc dimer rotating over planar hypercoordinate motifs
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
New method for the derivation of net atomic charges from the electrostatic potential
GPGPU for orbital function evaluation with a new updating scheme
Use of symmetric rank-one Hessian update in molecular geometry optimization
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
Fast procedure for reconstruction of full-atom protein models from reduced representations
Recent advances in the structural determination of endohedral metallofullerenes
Analytical density-dependent representation of Hartree - Fock atomic potentials
Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
Thermochemical stabilities of giant fullerenes using density functional tight binding theory and isodesmic-type reactions
Application of zone-folding approach to the first-principles estimation of thermodynamic properties of carbon and ZrS 2 -based nanotubes
Implementation of an algorithm based on the Runge-Kutta-Fehlberg technique and the potential energy as a reaction coordinate to locate intrinsic reaction paths
RNACluster: An integrated tool for RNA secondary structure comparison and clustering
Extended benchmark set for lattice parameters of inorganic solids
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics
Modifying electronic and optical properties of violet phosphorus through variable fluorine coverage
Molecular Dynamics-Assisted Interaction Between HABT and PI3K Enzyme: Exploring Metastable States for Promising Cancer Diagnosis Applications
Projector-Based Quantum Embedding Study of Iron Complexes
MeTA studio: A cross platform, programmable IDE for computational chemist
Analysis in silico of chemical reactivity employing the local hyper-softness in some classic aromatic compounds, boron aromatic clusters and all-metal aromatic clusters
Evaluation of coarse grained models for hydrogen bonds in proteins
Excited state distribution function for probing Herzberg-Teller vibronic coupling using linear optical response theory: Application to glassy pheophytin a
A DFT study on 1, 4-dihydro-1, 4-azaborinine annulated linear polyacenes: Absorption spectra, singlet-triplet energy gap, aromaticity, and HOMO-LUMO energy modulation
A fast scheme to calculate electronic couplings between P3HT polymer units using diabatic orbitals for charge transfer dynamics simulations
Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles
Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems
On the reversible O2 binding of the Fe-porphyrin complex
Genetic training of network using chaos concept: Application to QSAR studies of vibration modes of tetrahedral halides
The performance of the new 6-31G ## basis set: Molecular structures and vibrational frequencies of transition metal carbonyls
Improved semiempirical heats of formation through the use of bond and group equivalents
DFT analysis of the linkage isomerism in penta(ammine)ruthenium(II/III) complexes of benzotriazole: Natural bond orbital method approach and a comprehensive energy decomposition analysis
Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers
Theoretical estimation of the rate of photoinduced charge transfer reactions in triphenylamine C 60 donor-acceptor conjugate
Avoiding the van der Waals endpoint problem using serial atomic insertion
Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3
MSINDO study of large silsesquioxanes
Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
A QM/MM study on the reaction pathway leading to 2-Aceto-2-hydroxybutyrate in the catalytic cycle of AHAS
Molecular dynamics extended for fluctuating networks: Application to water
Molecular dynamics implementation in MSINDO: Study of silicon clusters
Calculation of the vibration frequencies of α-quartz: The effect of Hamiltonian and basis set
Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model
Generation of OPLS-like charges from molecular electrostatic potential using restraints
Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics
Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones
Ladderenes as Covalently Condensed Acetylene: A DFT Investigation of Gold(I)-Catalyzed Mechanism, Substituent Effects and Energy Storage Potential
Extensive theoretical studies of a new energetic material: Tetrazino-tetrazine-tetraoxide (TTTO)
Influence of the complete basis set approximation, tight weighted-core, and diffuse functions on the DLPNO-CCSD(T1) atomization energies of neutral H,C,O-compounds
CABS-NMR - De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes
Atomic Radii Scales and Electron Properties Deduced from the Charge Density
A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein
Theoretical Investigation of the Relative Stabilites of XSSX and X 2 SS Isomers (X=F, C1, H, and CH 3
Stability of N 4 2- -based sandwich-like energetic complexes [N 4 TiN 4 ] 2- : Effect of spins and counterions
Analytic atomic gradients in the fermi-löwdin orbital self-interaction correction
Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a
Power transformations improve interpolation of grids for molecular mechanics interaction energies
A CAS study on S-loss and O-loss dissociation mechanisms of the SO 2 + ion in the C , D , and E states
Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure
A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS
Explicitly Correlated Gaussian Functions with r2n, 12 Factors for Calculations of the Ground State of the Helium Atom
Coupled-cluster frozen-density embedding using resolution of the identity methods
Calculations of frequency-dependent molecular magnetizabilities with quasi-relativistic time-dependent generalized unrestricted Hartree-Fock method
Computer-aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution
QTAIM n -center delocalization indices as descriptors of aromaticity in mono and poly heterocycles
Systematic studies on the computation of nuclear magnetic resonance shielding constants and chemical shifts: The density functional models
Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids
Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: A steered molecular dynamics simulation route
De novo generation of optically active small organic molecules using Monte Carlo tree search combined with recurrent neural network
Path integral theory: An improved simulation for the forces in semiclassic systems
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies
Cover Image, Volume 39, Issue 11
A labeling scheme for young tableaux spanning representations of permutation group S(N)
Collisions of ideal gas molecules with a rough/fractal surface. A computational study
Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions
Determination of C- Terminal Structure of Human C-Ha-Ras Oncogenic Protein
Coherent Excitation of the CH Stretching Vibrations in C 2 H 4 + : The Role of the Derivative Coupling Studied by the Quantum Ehrenfest Method
Transport properties of graphene nanoribbon-based molecular devices
Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface
The performance of exchange - correlation functionals in describing electron density parameters of saddle point structures along chemical reactions
State-of-the-art computations of dipole moments using analytic gradients of high-level density-fitted coupled-cluster methods with focal-point approximations
A novel method for protein-ligand binding affinity prediction and the related descriptors exploration
Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine
Theoretical determination of electron affinity and ionization potential of DNA and RNA bases
Extensive theoretical study on the low-lying electronic states of silicon monofluoride cation including spin-orbit coupling
Simulations of optically switchable molecular machines for particle transport
Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model
Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules
Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape
Theoretical prediction of Ni(I)-catalyst for hydrosilylation of pyridine and quinoline
Monomeric adenine decay dynamics influenced by the DNA environment
A new iterative linear integral isoconversional method for the determination of the activation energy varying with the conversion degree
Electronic reorganization: Origin of sigma trans promotion effect
Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work
Electronic structure benchmark calculations of inorganic and biochemical carboxylation reactions
The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations
DFT-predicted structural, vibrational, and bonding properties of XSiO and X2SiO (X=F, Cl, or Br) molecules
Is molecular alignment an indispensable requirement in the MIA-QSAR method?
A Boundary-Integral Approach for the Poisson-Boltzmann Equation with Polarizable Force Fields
LUMPAC lanthanide luminescence software: Efficient and user friendly
Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: An ab initio study
Molecular simulations to delineate functional conformational transitions in the HCV polymerase
Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation
Theoretical characterizations of HAsXH (X = N, P, As, Sb, and Bi) isomers in the singlet and triplet states
Proton affinities of deoxyribonucleosides via the ONIOM-ccCA methodology
Reduced-size polarized basis sets for calculations of molecular electric properties. I. The basis set generation
Cover Image, Volume 40, Issue 13
Solid-state quantum chemistry with ΘΦ (ThetaPhi): Spin-liquids, superconductors, and magnetic superstructures made computationally available
Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum-chemical calculations
A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack
Analysis and prediction of protein folding rates using quadratic response surface models
Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation
Electron transfer between biphenyl and biphenyl anion radicals: Reorganization energies and electron transfer matrix elements
Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals
Computational study on nature of transition structure for oxygen transfer from dioxirane and carbonyloxide
Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)
FFLUX molecular simulations driven by atomic Gaussian process regression models
An ab initio study of heterodienophiles addition to 2, 3-diaza-1, 3-butadiene: An example of endo-lone-pair effect on the reaction energy barrier
Computational design of organometallic oligomers featuring 1, 3-metal-carbon bonding and planar tetracoordinate carbon atoms
PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions
Limiting factors in the accuracy of DFT calculation for redox potentials
Reverse mapping method for complex polymer systems
Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability