yusuke1997/dblp-id-title huggingface dataset:
Rational design of the nickel-borane complex for efficient hydrogenation of styrene
Density functional based vibrational study of conformational isomers: Molecular rearrangement of benzofuroxan
Gating energetics of a voltage-dependent K + channel pore domain
Wavelet formulation of the polarizable continuum model
Ability of the PM3 quantum-mechanical method to model inter molecular hydrogen bonding between neutral molecules
The effect of basis set superposition error on the convergence of intermolecular interaction energies for deprotonated complexes
An improved SCPF scheme for polarization energy calculations
Fast construction of assembly trees for molecular graphs
Performance of density functional theory for describing hetero-metallic active-site motifs for methane-to-methanol conversion in metal-exchanged zeolites
Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin
Bonding contribution to restricted internal rotations in saccharides
Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase
Configuration interaction and density functional study of the influence of lithium cation complexation on vertical and adiabatic excitation energies of enones
Gravitational smoothing as a global optimization strategy
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures
Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors
Topological studies on IRC paths of X+H2XH+H reactions
A new approach for second-order perturbation theory
Chemometric study of liquid water simulations. I. The parameters of the TIP4P model potential
Computation of internal coordinates, derivatives, and gradient expressions: torsion and improper torsion
Efficient parametrization of complex molecule-surface force fields
Gaussian basis set of double zeta quality for atoms K through Kr: Application in DFT calculations of molecular properties
Interaction of two functional groups through the benzene ring: Theory and experiment
Comparison of Potential-Derived Charge and Atomic Multipole Models in Calculating Electrostatic Potentials and Energies of Some Muleic Acid Bases and Pairs
The active E4 structure of nitrogenase studied with different DFT functionals
Cover Image, Volume 41, Issue 7
Atomistic Simulation of Structural and Mechanical Properties of the AMgF3 (A = K, Rb, and Cs) Compounds Under Hydrostatic Pressure
Ab initio simulation of chemical shift effects from metal ion binding in Bacitracin A
Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops
Cuby: An integrative framework for computational chemistry
Implementation of the Bethe-Salpeter equation in the TURBOMOLE program
Analysis of the core-repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems
Electronic excitations of green fluorescent proteins: Protonation states of chromophore model compound in solutions
Impact of dielectric constant of solvent on the formation of transition metal-ammine complexes
Coral: QSPR modeling of rate constants of reactions between organic aromatic pollutants and hydroxyl radical
U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [ n ]helicenes and Phe-Gly-Phe tripeptide
Molecular surface generation using marching tetrahedra
Method of calculating band shape for molecular electronic spectra
Computerized implementation of higher-order electron-correlation methods and their linear-scaling divide-and-conquer extensions
D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations
UNO DMRG CAS CI calculations of binuclear manganese complex Mn(IV)2O2(NHCHCO2)4: Scope and applicability of Heisenberg model
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm
Analytic second derivatives for the efficient electrostatic embedding in the fragment molecular orbital method
Many-body effects on structure and dynamics of aqueous ionic solutions- Erratum
Analysis of pseudo jahn-teller distortion based on natural bond orbital theory: Case study for silicene
Ab initio determination of the electric multipole moments and static (hyper)polarizability of HCCX, X = F, Cl, Br, and I
Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
Adsorption of proteins onto charged surfaces: A Monte Carlo approach with explicit ions
GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters
Probability Density Analysis Reveals Substantial Differences Between the Dinitrogen and Acetylene Triple Bonds
Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions
Systematic quantum chemical study of DNA-base tautomers
Hybridized particle swarm algorithm for adaptive structure training of multilayer feed-forward neural network: QSAR studies of bioactivity of organic compounds
The application of cholesky decomposition in valence bond calculation
Explicit factorization of external coordinates in constrained statistical mechanics models
Machine learning assisted analysis of equivalent circuit usage in electrochemical impedance spectroscopy applications
Selective descriptor pruning for QSAR/QSPR studies using artificial neural networks
Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
Ab initio study of C4H3 potential energy surface and reaction of ground-state carbon atom with propargyl radical
Reconstruction of atomistic details from coarse-grained structures
Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N
Use of effective core potentials for ab initio calculations on molecular siloxanes and silicates
Covalent versus ionic bonding in alkalimetal fluoride oligomers
Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties
A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules
Pipek-Mezey localization of occupied and virtual orbitals
Electron probability distribution in AIM and ELF basins
Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation
Multiscale enhanced sampling of intrinsically disordered protein conformations
Electronic properties for small tin clusters Sn n ( n <= 20) from density functional theory and the convergence toward the solid state
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation
Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF
Advances in vibrational configuration interaction theory - part 2: Fast screening of the correlation space
Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates
Automation of AMOEBA polarizable force field for small molecules: Poltype 2
Implementation of the finite field perturbation method in the CRYSTAL program for calculating the dielectric constant of periodic systems
NIAS-Server 2.0: A versatile complementary tool for structural biology studies
Modeling the effect of substituents on the electronically excited states of indole derivatives
Small molecule-mediated control of hydroxyapatite growth: Free energy calculations benchmarked to density functional theory
Symmetry groups for unit cells in solids
The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules
Preface of Carlo Adamo's virtual special issue
Performance analysis of the double-iterated Kalman filter for molecular structure estimation
Electric field effects on the performance of a candidate multipole molecular switch: A quantum computational study
Correlation method for variance reduction of Monte Carlo integration in RS-HDMR
Solid-state reaction as a mechanism of 1T &[LEFT RIGHT ARROW]; 2H transformation in MoS 2 monolayers
Assessing the role of Hartree-Fock exchange, correlation energy and long range corrections in evaluating ionization potential, and electron affinity in density functional theory
Polarizable continuum models provide an effective electrostatic embedding model for fragment-based chemical shift prediction in challenging systems
A comparison of techniques for calculating protein essential dynamics
Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments
A comparison of conformational energies calculated by several molecular mechanics methods
Neural network-based prediction of transmembrane -strand segments in outer membrane proteins
Inhibitor docking screened by the modified SAFE_p scoring function: Application to cyclic urea HIV-1 PR inhibitors
An efficient parallel algorithm for the calculation of unrestricted canonical MP2 energies
Inexpensive vibrational anharmonicities from estimated derivatives: Diatomic molecules
Adatom mediated adsorption of N-heterocyclic carbenes on Cu(111) and Au(111)
Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model
Calculation of amino acid pKaS in a protein from a continuum electrostatic model: Method and sensitivity analysis
Mechanistic Study of Unprecedented Highly Regioselective Hydrocyanation of Terminal Alkynes: Insight into the Origins of the Regioselectivity and Ligand Effects
Integrated Modeling Program, Applied Chemical Theory (IMPACT)
Normal Coordinates-Finite Elements Calculation of 3D Vibrational Energy Levels: Hanon-Heiles and Eckart Potentials, H3+ Molecule
Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems
Parametrization of the GMIPp for the study of stacking interactions
Hybrid density functional studies of a bacteriopheophytin a model and its anion radical form: Geometry, spin densities, and hyperfine couplings
DC24: A new density coherence functional for multiconfiguration density-coherence functional theory
On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a posteriori BSSE correction schemes
Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO 3
Cover Image, Volume 40, Issue 19
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms
Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding
Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses
PDECO: Parallel differential evolution for clusters optimization
A comparative view on the potential acting on an electron in a molecule and the electrostatic potential through the typical halogen bonds
Characterization of force fields for lipid molecules: Applications to crystal structures
Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids
Understanding of bonding and mechanical characteristics of cementitious mineral tobermorite from first principles
Density functional theory-based electrochemical models for the oxygen reduction reaction: Comparison of modeling approaches for electric field and solvent effects
Structures and vibrational frequencies of vanadium (V) oligomers: An ab initio study using effective core potentials
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints
LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques
Vibrational spectral signatures of peptide secondary structures: N -methylation and side chain hydrogen bond in cyclosporin A
An approach based on genetic algorithms and machine learning coupled for studying alloy and molecular clusters by optimizing quantum energy surfaces
Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor
Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics
SDOVS: A solvent dipole ordering-based method for virtual screening
Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT
Optimized infrared spectrum of ( H 2 O ) m : ( H C N ) n mixtures
Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding
Estimating the ligand-binding affinity via λ-dependent umbrella sampling simulations
Theoretical studies on four-membered ring compounds with NF 2 , ONO 2 , N 3 , and NO 2 groups
A Force Field for Monosaccharides and (1->4) Linked Polysaccharides
Consistent modifications of SINDO1: I. Approximations and parameters
Investigation of the distinction between van der Waals interaction and chemical bonding based on the PAEM-MO diagram
An ETS-NOCV-based computational strategies for the characterization of concerted transition states involving CO2
A posteriori localization of many-body excited states through simultaneous diagonalization
Theoretical investigations on 1, 2-ethanediol: The problem of intramolecular hydrogen bonds
Compatibility of correlation-consistent basis sets with a hybrid Hartree-Fock/density functional method
An analytical approach for computing franck-condon integrals of harmonic oscillators with arbitrary dimensions
Cover Image, Volume 41, Issue 2
Pattern recognition and massively distributed computing
DSPMP: Discriminating secretory proteins of malaria parasite by hybridizing different descriptors of Chou's pseudo amino acid patterns
Internal-to-cartesian back transformation of molecular geometry steps using high-order geometric derivatives
On the nature of the pi -> pi* ionic excited states: The V state of ethene as a prototype
A molecular mechanics model for imatinib and imatinib: kinase binding
Quantum mechanics and quasiclassical study of the H/D+FO -> OH/OD+F, HF/DF+O reactions: Chemical stereodynamics
Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone
Chemical reactivity in the framework of pair density functional theories
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect
Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods
Molecular Mechanics (MM3) Calculations on Alkyl Radicals
Methyl dynamics in crystalline amino acids: MD and NMR
New all-atom force field for molecular dynamics simulation of an AlPO 4 -34 molecular sieve
Bay-type H···H "bonding" in cis-2-butene and related species: QTAIM versus NBO description
Theoretical study concerning the reactivity of imine derivatives of polycyclic aromatic hydrocarbons
Iso-guanine quintet complexes coordinated by mono valent cations (Na + , K + , Rb + , and Cs + )
Blue-shifting hydrogen bond in the benzene-benzene and benzene-naphthalene complexes
A massively parallel multireference configuration interaction program: The parallel COLUMBUS program
Crystal structure predictions using five space groups with two independent molecules. The case of small organic acids
Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors
prepareforleap: An automated tool for fast PDB-to-parameter generation
Publisher's note: Sir John A. Pople, 1925-2004
Modal dynamics of proteins in water
Computational analyses of singlet-singlet and singlet-triplet transitions in mononuclear gold-capped carbon-rich conjugated complexes
Lattice models of peptide aggregation: Evaluation of conformational search algorithms
Atomistic insight into chondroitin-6-sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
Relativistic correlating basis sets for 57 La and 89 Ac
Libcint: An efficient general integral library for Gaussian basis functions
OPEP: A tool for the optimal partitioning of electric properties
Molecular basis of calcium binding by polyguluronate chains. Revising the egg-box model
Symmetry measures of the electron density
IMPACT-4CCS: Integrated Modeling and Prediction Using Ab Initio and Trained Potentials for Collision Cross Sections
Cover Image, Volume 40, Issue 21
Sulfide release and rebinding in the mechanism for nitrogenase
Insights on selenium and tellurium diaryldichalcogenides: A benchmark DFT study
Resonance Raman spectra and excited state properties of methyl viologen and its radical cation from time-dependent density functional theory
Rapid sampling of all-atom peptides using a library-based polymer-growth approach
Block deformation analysis: Density matrix blocks as intramolecular deformation density
Energetic analyses of chair and boat conformations of maleimide substituted cyclohexane derivatives
Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation
Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices
Exploration of density functional methods for one-electron reduction potential of nitrobenzenes
Free Energy of Solvation of a Small Lennard-Jones Particle
A solvation-free-energy functional: A reference-modified density functional formulation
Comparison of methods to estimate the free energy of solvation: Importance in the modulation of the affinity of 3-benzazepines for the D 1 receptor
A comparative study of various computational approaches in calculating the structure of pyridoxal 5 r -phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment
Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions
Optimizing efficiency of perturbative Monte Carlo method
Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures
Efficient pole-search algorithm for dynamic polarizability: Toward alternative excited-state calculation for large systems
An Application of the Reaction Field Theory to Hydrated Metal Cations in the Framework of the MNDO, AM1, and OM3 Methods
On the kinetic mechanism of the hydrogen abstraction reactions of the hydroxyl radical with CH 3 CF 2 Cl and CH 3 CFCl 2 : A dual level direct dynamics study
A computational methodology for accurate predictions of rate constants in solution: Application to the assessment of primary antioxidant activity
Rationalization of the behavior of M2(CH3CS2)4I (M = Ni, Pt) chains at room temperature from periodic density functional theory and ab initio cluster calculations
Syn and anti aryl nitrenium ions
Alkaline hydrolysis of ethylene phosphate: An ab initio study by supermolecule model and polarizable continuum approach
Meshed tert-butyl gears on a quasirigid backbone
Theoretical investigations on geometrical and electronic structures of silver clusters
Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features
A full-pivoting algorithm for the Cholesky decomposition of two-electron repulsion and spin-orbit coupling integrals
Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein
DynamO: a free σ( N ) general event-driven molecular dynamics simulator
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic
Modeling high pressure reactivity in unsaturated systems: Application to dimethylacetylene
QM/QM docking method based on the variational finite localized molecular orbital approximation
A computational investigation on the sequential rearrangement mechanism of 2-allyl-2, 4, 5-hexatrienaldehyde involving [1, 5]-hydrogen migration and 8pi-electrocyclization
Definitive heat of formation of methylenimine, CH2NH, and of methylenimmonium ion, CH2NH2+, by means of W2 theory
The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube
Enthalpies of formation of monoderivatives of hydrocarbons: Interaction of polar groups with an alkyl group
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem
Comprehensive relativistic ab initio and density functional theory studies on PtH, PtF, PtCl, and Pt(NH3)2Cl2
Infinite basis set extrapolation for double hybrid density functional theory 1: Effect of applying various extrapolation functions
Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry-adapted cluster/configuration interaction methodology
Quantitative computer simulations of biomolecules: A snapshot
Estimating relative free energies from a single ensemble: Hydration free energies
A QM/MM study on the aqueous solvation of the tetrahydroxouranylate [UO2(OH)4]2- complex ion
Thermochemical stabilities, electronic structures, and optical properties of C 56 X 10 (X = H, F, and Cl) fullerene compounds
Covalent hydration energies for purine analogs by quantum chemical methods
FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data
Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions
A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models
A density functional study of the glycine molecule: Comparison with post-Hartree-Fock calculations and experiment
Stochastic molecular optimization using generalized simulated annealing
Linear augmented Slater-type orbital method for free standing clusters
Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges
Geometrical and optical benchmarking of copper(II) guanidine-quinoline complexes: Insights from TD-DFT and many-body perturbation theory (part II)
G2 ab initio calculations on three-membered rings: Role of hydrogen atoms
Development of a Flexible-Monomer Two-Body Carbon Dioxide Potential and Its Application to Clusters up to (CO 2 ) 13
DFT, DLPNO-CCSD(T), and NEVPT2 benchmark study of the reaction between ferrocenium and trimethylphosphine
Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines
RPA(D) and HRPA(D): Two new models for calculations of NMR indirect nuclear spin-spin coupling constants
New insights into the meaning and usefulness of principal component analysis of concatenated trajectories
Parameterization of a reactive force field using a monte carlo algorithm
Sensitivity of coupled cluster electronic properties on the reference determinant: Can Kohn-Sham orbitals be more beneficial than Hartree-Fock orbitals?
Understanding the ring current effects on magnetic shielding of hydrogen and carbon nuclei in naphthalene and anthracene