yusuke1997/dblp-id-title huggingface dataset:
Correlation between thermal conductivity and bond length alternation in carbon nanotubes: A combined reverse nonequilibrium molecular dynamics - Crystal orbital analysis
Electronic structure and physical properties of M i X i clusters (M = B, Al; X = N, P; i = 1, 2, 3): Ab initio study
Krylov subspace accelerated inexact Newton method for linear and nonlinear equations
Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution
A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700
Supplementary d and f functions in molecular wave functions at large and small internuclear separations
After the electronic field: Structure, bonding, and the first hyperpolarizability of HArF
Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach
Novel topological index F based on incidence matrix
RMSD and Symmetry
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches
β-D-Glucopyranose - silver+ (1:1) complex as a small gas molecule scavenger
Extracting hydration sites around proteins from explicit water simulations
DFT and MP2 molecular orbital determination of OH-toluene-O2 isomeric structures in the atmospheric oxidation of toluene
A surface hopping algorithm for nonadiabatic minimum energy path calculations
New density functional parameterizations to accurate calculations of electric field gradient variations among compounds
Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems
Physical achirality in geometrically chiral rotamers of hydrazine and boranylborane molecules
Stochastic model for photoinduced anisotropy
Calculating the Electric Potential of Macromolecules: A Simple Method for Molecular Surface Triangulation
Metadynamics simulations with Bohmian-style bias potential
Real-space grid representation of momentum and kinetic energy operators for electronic structure calculations
In silico prediction and screening of gamma-secretase inhibitors by molecular descriptors and machine learning methods
Toward the description of van der Waals interactions within density functional theory
Foreword to the Special Issue for Hans Lischka
A new protocol for the identification of singlet fission sensitizers through computational screening
An Application of the Miertus-Scrocco-Tomasi Solvation Model in Molecular Mechanics and Dynamics Simulations
Common system setup for the entire catalytic cycle of cytochrome P450 cam in quantum mechanical/molecular mechanical studies
Grand challenges in quantum-classical modeling of molecule-surface interactions
Theoretical studies on the carcinogenicity of polycyclic aromatic hydrocarbons
Toward robust computational electrochemical predicting the environmental fate of organic pollutants
Theoretical analysis of fluoroglycine conformers
New algorithms for iterative matrix-free eigensolvers in quantum chemistry
Hydrogen storage capacity of Be2(NLi)2 cluster with ultra-short beryllium-beryllium distance
A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models
A theoretical study of the reaction of HCO+ with C2H2
On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds
Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase
The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations
Hybrid QM/MM molecular dynamics simulations for an ionic SN2 reaction in the supercritical water: OH- + CH3Cl -> CH3OH + Cl-
A computational method to simulate global conformational changes of proteins induced by cosolvent
A comparison of a direct search method and a genetic algorithm for conformational searching
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation
Bis(azulene) "submarine" metal dimer sandwich compounds (C 10 H 8 ) 2 M 2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations
Cover Image, Volume 40, Issue 20
Durandal: Fast exact clustering of protein decoys
Zinc oxide: A case study in contemporary computational solid state chemistry
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model
Extended N -centered ensemble density functional theory of double electronic excitations
MOVIPAC: Vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations
Electronic fluxes during diels-alder reactions involving 1, 2-benzoquinones: mechanistic insights from the analysis of electron localization function and catastrophe theory
Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model
Efficient calculation of relative binding free energies by umbrella sampling perturbation
Mechanism of β -hairpin formation in AzoChignolin and Chignolin
The role of errors related to DFT methods in calculations involving ion pairs of ionic liquids
Hybrid Unsupervised/Supervised Machine Learning for Identifying Molecular Structural Fingerprints From Ensemble Property
The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis
Graphical approach for defining natural internal coordinates
Cover Image, Volume 41, Issue 21
A new method for the gradient-based optimization of molecular complexes
Transition state theory thermal rate constants and RRKM-based branching ratios for the N(2D) + CH4 reaction based on multi-sState and multi-reference Ab Initio calculations of interest for the titan's chemistry
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
Modified regional self-interaction corrected time-dependent density functional theory for core excited-state calculations
Local conformational dynamics regulating transport properties of a Cl-/H+ antiporter
Efficient implementation of constant pH molecular dynamics on modern graphics processors
Ground and excited state CASPT2 geometry optimizations of small organic molecules
Quantitative symmetry and chirality - A fast computational algorithm for large structures: Proteins, macromolecules, nanotubes, and unit cells
Decomposition Analysis of the Intermolecular Interaction Energies in Thw pi-pi Stacking Complexes: Quinhydrone and N, N, N, N-Tetramethyl-p-Diaminobenzene-Chloranil Complex
A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
Computation of pressure components due to Class II force fields
Automatic parameterization of force field by systematic search and genetic algorithms
Dative quadruple bonds between d 10 transition metals and beryllium in BeM(PMe 3 ) 2 and BeM(CO) 2 (M = Ni, Pd, and Pt) complexes: Transition metal fragments as six-electron donor and two-electron acceptor
Yammp: Development of a molecular mechanics program using the modular programming method
Molecular dynamics simulation study of association in trifluoroethanol/water mixtures
Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field
Electric field-derived point charges to mimic the electrostatics in molecular crystals
Ab initio study of electronic structure and optical properties of heavy-metal azides: TlN 3 , AgN 3 , and CuN 3
Effective Born radii in the generalized Born approximation: The importance of being perfect
Electronic structure of the S 1 state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations
Parametrization of the Becke3-LYP hybrid functional for a series of small molecules using quantum molecular similarity techniques
Probing the bent bonds in cyclopropane systems for gas storage and separation process: A computational study
Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) - (4 × 1) phase transition
Desorption induced by low energy charge carriers on Si(111)-7 × 7: First principles molecular dynamics for benzene derivates
Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks
Selected excitation for CAS-SDCI calculations
A Vibrational Molecular Force Field of Model Compounds with Biological Interest. IV. Parameters for the Different Glycosidic Linkages of Oligoaccharides
Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives
Dependence of the substituent energy on the level of theory
TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible molecules
Divalent NI Compounds: Identifying new Carbocyclic Carbenes to Design Nitreones using Quantum Chemical Methods
Predicting the UV spectrum of polyoxometalates by TD-DFT
Fast force field-based optimization of protein-ligand complexes with graphics processor
Metalophilic interaction in gold halide: Quantum chemical study of AuX (X=F-At)
Natural resonance theory: II. Natural bond order and valency
Resolving coupled pH titrations using alchemical free energy calculations
Gas-phase reactions of SiH n + (n = 1, 2) with NF 3 : A computational investigation on the detailed mechanistic aspects [J. Comp. Chem. 33, 1918-1926]
A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
Mechanistic insights into the role of cyclodextrin in the regioselective radical CH trifluoromethylation of aromatic compounds
Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed-charge Model and the Reference Potential Strategy
Looking for high energy density compounds applicable for propellant among the derivatives of dpo with --n 3 , --ono 2 , and --nno 2 groups
Electronic structure and relative stability of 1: 1 Cu-O 2 adducts from difference-dedicated configuration interaction calculations
Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse-grained molecular dynamics simulations with a weighted histogram analysis method
Excited-state intramolecular proton transfer driven by conical intersection in hydroxychromones
Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method
Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
DFT modeling of reactivity in an ionic liquid: How many ion pairs?
Dipole moment derivatives and integrated intensities for the vibrational transitions of N2 HF
Theoretical study on phosphorescence efficiency and color tuning from orange to blue-green of Ir(III) complexes based on substituted 2-phenylimidazo[1, 2-a]pyridine ligand
Efficient algorithm for expanding theoretical electron densities in canterakis-zernike functions
GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility
Choice of Spin-Orbit Correction Terms in Gaussian Model Chemistries
Complex beryllium amidoboranes: Structures, stability, and evaluation of their potential as hydrogen storage materials
CH 3 NHNH 2 + OH reaction: Mechanism and dynamics studies
Complex molecular assemblies at hand via interactive simulations
Relativistic adapted Gaussian basis sets free of variational prolapse of small and medium size for hydrogen through xenon
Development of new pseudopotential methods: Improved model core potentials for the first-row transition metals
Assessing challenging intra- and inter-molecular charge-transfer excitations energies with double-hybrid density functionals
Computational prediction on the catalytic activity of heterobimetallic complex featuring MMˊ triple bond in acetylene cyclotrimerization: Mechanistic study
Rearrangement of dicarboranyl methyl cation to icosahedral C 3 B 9 H 12 + : An ab initio dynamics view
Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations
A molecular mechanics force field for biologically important sterols
UV-photoexcitation and ultrafast dynamics of HCFC-132b (CF 2 ClCH 2 Cl)
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
Comparative study of global minimum energy conformations of hydrated peptides
Flexible protein-protein docking based on Best-First search algorithm
Electron transfer integral between two zero-overlap states
Ab initio molecular orbital calculations of 3, 4-dihydro-1, 2-dioxin, 3, 6-dihydro-1, 2-dioxin, 4H-1, 3-dioxin (1, 3-diox-4-ene), and 2, 3-dihydro-1, 4-dioxin (1, 4-dioxene)
Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part II. Accurate energy minimization
Computational investigation of functionalized carbenes on dinitrogen activation
Parallel Algorithm for Calculating Ro-Vibrational States of Diatomic Molecules
Reaction of nitrones with silyl ketene acetals: A DFT study
Structural and dynamical properties of the V 3+ ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation
An automated method to find transition states using chemical dynamics simulations
Frenkel-exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems
"First-Principles" kinetic monte carlo simulations revisited: CO oxidation over RuO 2 (110)
Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals
Response of the mechanical and chiral character of ethane to ultra-fast laser pulses
Molybdatricarbaboranes as examples of isocloso metallaborane deltahedra with three carbon vertices
Prediction of hydrocarbon enthalpies of formation by various thermochemical schemes
NUPACK: Analysis and design of nucleic acid systems
Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates
Bonding in the high spin lithium clusters: Non-nuclear attractors play a crucial role
Wave-function frozen-density embedding: Approximate analytical nuclear ground-state gradients
Superacidity of neutral Brfnsted acids in gas phase
Prediction of seebeck coefficient for compounds without restriction to fixed stoichiometry: A machine learning approach
Time-dependent density functional theory study on excited-state dihydrogen bonding O-H***H-Ge of the dihydrogen-bonded phenol-triethylgermanium complex
Study of electronic spectra of free-base porphin and Mg-porphin: Comprehensive comparison of variety of ab initio, DFT, and semiempirical methods
Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model
Electron localizability indicators ELI-D and ELIA for highly correlated wavefunctions of homonuclear dimers. II. N 2 , O 2 , F 2 , and Ne 2
The choice of internal coordinates in complex chemical systems
Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes
Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N 2 intermolecular potential and microwave spectrum
Comparison of different ab initio theoretical models for calculating isodesmic reaction energies for small ring and related compounds
Global cluster geometry optimization by a phenotype algorithm with Niches: Location of elusive minima, and low-order scaling with cluster size
Theoretical study of "protonated pyruvate": A methylhydroxycarbene - carbon dioxide complex - implications for the decarboxylation of pyruvic acid
Chemical bonding: From Lewis to atoms in molecules
Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg 2+ ion models commonly used in biomolecular simulations
Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels
CASSCF and multireference CI with singles and doubles study of low-lying valence and Rydberg states of 2H-tetrazole
Schleyer hyperconjugative aromaticity and Diels-Alder reactivity of 5-substituted cyclopentadienes
Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications
Enhancing the photoresponse by CdSe-Dye-TiO2-based multijunction systems for efficient dye-sensitized solar cells: A theoretical outlook
Highly Efficient Numerical Method for Modeling Mofs Containing Transition Metal Ions
Theoretical study of the internal conversion of sulfoxide precursors of poly-isothianaphthene and related polymers
Chalcogen-mercury bond formation and disruption in model Rabenstein's reactions: A computational analysis
Infrared Spectrum and UV-Triggered Transformations of Matrix-Isolated Meta -Fluorothiophenol Supported by Ground and Excited State Theoretical Calculations
DockoMatic: Automated peptide analog creation for high throughput virtual screening
Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data
Iodido equatorial ligands influence on the mechanism of action of Pt(IV) and Pt(II) anti-cancer complexes: A DFT computational study
Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: An Ab initio fragment molecular orbital study
Computations of the Raman optical activity via the sum-over-states expansions
On the suitability of strictly localized orbitals for hybrid QM/MM calculations
Accelerating molecular dynamic simulation on graphics processing units
Coronavirus phylogeny based on 2D graphical representation of DNA sequence
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. II. Application to systems comprising first-order chemical reactions
Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method
Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins
Adsorption of metadiiodobenzene on Cu(110): A theoretical study
A convective replica-exchange method for sampling new energy basins
Dramatic performance enhancements for the FASTER optimization algorithm
Computational investigations on covalent dimerization/oligomerization of polyacenes: Is it relevant to soot formation?
The role of dispersive forces determining the energetics of adsorption in Ti zeolites
An improved force field for conformational analysis of sulfated polysaccharides
Search for the global minimum structures of AlB 3 H 2 n ( n = 0 - 6) clusters
A density-fitting implementation of the density-based basis-set correction method
Modeling environmental effects on charge density distributions in polar organometallics: Validation of embedded cluster models for the methyl lithium crystal
Spontaneous curvature generation by peptides in asymmetric bilayers
Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy
Ab initio molecular orbital studies for compounds of magnesium
Parallel implementation of gamma-point pseudopotential plane-wave DFT with exact exchange
Cover Image, Volume 41, Issue 15
Perfect planar tetracoordinate carbon in neutral unsaturated hydrocarbon cages: A new strategy utilizing three-dimensional electron delocalization
Efficient optimization of van der Waals parameters from bulk properties
Band gap, Jahn-Teller deformation, octahedra rotation in transition metal perovskites LaTiO 3
Confining CO 2 inside sI clathrate-hydrates: The impact of the CO 2 -water interaction on quantized dynamics
Multipole electrostatics in hydration free energy calculations
Lattice sum calculations for 1/rp interactions via multipole expansions and Euler summation
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds
A parallel tabu search for conformational energy optimization of oligopeptides
Analytical calculation of the solvent-accessible surface area and its nuclear gradients by stereographic projection: A general approach for molecules, polymers, nanotubes, helices, and surfaces
Comprehensive ab initio calculation and simulation on the low-lying electronic states of TlX (X = F, Cl, Br, I, and At)
PACKMOL: A package for building initial configurations for molecular dynamics simulations
Coupled atomic charge selectivity for optimal ligand-charge distributions at protein binding sites
Calculation of stacking geometries by a modified MM2 method
Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study
Long range behavior of high-rank topological multipole moments
Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration
Ab initio description of photoabsorption and electron transfer in a doubly-linked porphyrin-fullerene dyad
Crystal Structure and Properties of Imidazo-Pyridine Ionic Liquids
Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies
Jumping between protein conformers using normal modes
Theoretical comparison of conformational properties of molecules: Conformational probability maps and similarity index
Superposition of waves or densities: Which is the nature of chemical resonance?
Computed versus experimental energy barriers in solution: Influence of the type of the density functional approximation
Uncoupled Hartree-Fock Calculations of the Polarizability and Hyperpolarizabilities of Nitrophenols
Does Basis Set Superposition Error Significantly Affect Post-CCSD( T ) Corrections?
High-order harmonic generation by static coherent states method in single-electron atomic and molecular systems
The Structural, Electronic and Vibrational Properties of LaCrO 3 $$ {}_3 $$ . A Quantum Mechanical Investigation by Using an All Electron Gaussian Type Basis Set and a Full Range Hybrid Functional
Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer
An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model
Computational studies on the mechanism and kinetics of Cl reaction with C 2 H 5 I
Computing Accurate & Reliable Rovibrational Spectral Data for Aluminum-Bearing Molecules
The GROMOS software for biomolecular simulation: GROMOS05
MMFF VI. MMFF94s option for energy minimization studies
Theoretical study of a vanadate peptide complex
The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines
The opsin shift and mechanism of spectral tuning in rhodopsin
Adsorption integral equation via complex approximation with constraints: The Langmuir kernel
Efficient newton-raphson/singular value decomposition-based optimization scheme with dynamically updated critical condition number for rapid convergence of weighted histogram analysis method equations
Systematic study of vibrational frequencies calculated with the self-consistent charge density functional tight-binding method
Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies
Is It Worth Running the Hartree-Fock Calculations With Localized Molecular Orbitals Within the Framework of Variational Coupled Cluster Singles Theory?