yusuke1997/dblp-id-title huggingface dataset:
An electron density based analysis to establish the electronic adiabaticity of proton coupled electron transfer reactions
Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin
Computing p K A values of hexa-aqua transition metal complexes
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
Hydrogen-hydrogen bonding: The current density perspective
Erratum: analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment
Photophysical properties of heavy atom containing tetrasulfonyl phthalocyanines as possible photosensitizers in photodynamic therapy
Accurate van der Waals force field for gas adsorption in porous materials
Competitive diamond-like and endohedral fullerene structures of Si 70
On the interaction of Mo and Mo2 with NH3, C2H4, and C3H6
Neural graph distance embedding for molecular geometry generation
Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds
Analysis of the convergence of the general coupling operator method for one-configuration-type wave functions
Modeling -lactam interactions in aqueous solution through combined quantum mechanics-molecular mechanics methods
Approaching bulk limit for three-dimensional solids via the cyclic cluster approximation: Semiempirical INDO study
Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH
Applying efficient implicit nongeometric constraints in alchemical free energy simulations
Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study
Design and training of a neural network for predicting the solvent accessibility of proteins
Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors
Ylidic radical-molecule reactions
Three-residue loop closure in proteins: A new kinematic method reveals a locus of connected loop conformations
How accurate can Kohn-Sham density functional be for both main-group and transition metal reactions
Discrepancy in the near-solute electric dipole moment calculated from the electric field
Systematic Interaction Analysis of Anti-Human Immunodeficiency Virus Type-1 Neutralizing Antibodies with High Mannose Glycans Using Fragment Molecular Orbital and Molecular Dynamics Methods
Four faces of the interaction between ions and aromatic rings
Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form
Algorithm to Infer the Strucutres of Molecular Formulas within a Reaction Pathway
Next-generation QTAIM for scoring molecular wires in E-fields for molecular electronic devices
Interesting properties of Thomas-Fermi kinetic and Parr electron-electron-repulsion DFT energy functional generated compact one-electron density approximation for ground-state electronic energy of molecular systems
Approximate expressions and the relationship between pyramidalization (out-of-plane deformation) characteristics of trigonal centers
Benchmarking approximate density functional theory. I. s/d excitation energies in 3d transition metal cations
MARVEL Analysis of High-Resolution Rovibrational Spectra of 16 O 13 C 18 O
Modified calculations of hydrocarbon thermodynamic properties
Application of the multiensemble sampling to the hydration free energy
Reduced-size polarized basis sets for calculations of molecular electric properties. II. Simulation of the Raman spectra
Restrained point-charge models for disaccharides
Application of a High-Performance, Special-Purpose Computer, GRAPE-2A, to Molecular Dynamics
Combining the biased and unbiased sampling strategy into one convenient free energy calculation method
A new force field for simulating phosphatidylcholine bilayers
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map
Automated preparation of nanoscopic structures: Graph-based sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates
Two-electron integrations in the Quantum Theory of Atoms in Molecules with correlated wave functions
Structural evolution of small gold clusters doped by one and two boron atoms
Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes
Mechanistic insights on DBU catalyzed β -amination of nbs to chalcone driving by water: Multiple roles of water
Path integral Brownian chain molecular dynamics: A simple approximation of quantum vibrational dynamics
Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P 2 ) 2 and (PCCP) 2
Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility
Infia - program for rotational analysis of linear molecule spectra
Computation of the binding affinities of catechol- O -methyltransferase inhibitors: Multisubstate relative free energy calculations
GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field
Erratum - An ab initio force field for the cofactors of bacterial photosynthesis
Halogen bonding in mono- and dihydrated halobenzene
Electronic properties of tricoordinated phosphorus in hexagonal phosphininium compounds and molecular aromaticity
Starting SCF calculations by superposition of atomic densities
Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations
Ab initio potential energy surface and vibration-rotation energy levels of silicon dicarbide, SiC 2
Multigrid solver for the reference interaction site model of molecular liquids theory
Structural, electronic, and magnetoresponsive properties of triangular lanthanide clusters and their free-standing nitrides
Parallel implementation of a protein structure refinement algorithm
Structure and properties of iron oxide clusters: From Fe 6 to Fe 6 O 20 and from Fe 7 to Fe 7 O 24
Generalized Prediction of Enthalpies of Formation Using DLPNO-CCSD(T) Ab Initio Calculations for Molecules Containing the Elements H, C, N, O, F, S, Cl, Br
Topological analysis of electron density in depleted homopolar chemical bonds
Cumulative and discrete similarity analysis of electrostatic potentials and fields
FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program
Stiffness and energy conservation in molecular dynamics: An improved integrator
Determination of atomic valence indices from population analyses at correlated level
MD-based CD calculations for the assignment of the absolute axial configuration of the naphthylisoquinoline alkaloid dioncophylline A
New Approach to the Semiempirical Calcualtion of Atomic Charges for Polypeptides and Large Molecular Systems
Predicting whether aromatic molecules would prefer to enter a carbon nanotube: A density functional theory study
An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes
Electronic, bonding, and optical properties of 1d [CuCN] n ( n = 1-10) chains, 2d [CuCN] n ( n = 2-10) nanorings, and 3d [Cu n (CN) n ] m ( n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods
k- Nearest neighbors optimization-based outlier removal
Insights on protein-DNA recognition by coarse grain modelling
A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
New algorithm for tensor contractions on multi-core CPUs, GPUs, and accelerators enables CCSD and EOM-CCSD calculations with over 1000 basis functions on a single compute node
Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase
Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine
Density functional studies of AnF6 (An=U, Np, and Pu) and UF6-nCln (n=1-6) using hybrid functionals: geometries and vibrational frequencies
Origin of the "endo rule" in Diels-Alder reactions
Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force field
Molecular properties and tautomeric equilibria of isolated flavins
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes
Atom equivalents for converting DFT energies calculated on molecular mechanics structures to formation enthalpies
Protein sequence threading, the alignment problem, and a two-step strategy
Influence of intrinsic defects on the properties of zinc oxide
Deep generative models for ligand-based de novo design applied to multi-parametric optimization
Computational design of S -nitrosothiol "Click" reactions
General methodology in two dimensions for classical simulation of reactive and nonreactive events on ab initio potential energy surfaces
A diagonalization-free optimization algorithm for solving Kohn-Sham equations of closed-shell molecules
HF/6-31G* energy surfaces for disaccharide analogs
Short-time Fourier transform analysis of ab initio molecular dynamics simulation: Collision reaction between CN and C 4 H 6
Behavior of counterpoise correction in many-body molecular clusters of organic compounds: Hartree-Fock interaction energy perspective
Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study
DFT studies on the mechanism of Ag 2 CO 3 -catalyzed hydroazidation of unactivated terminal alkynes with TMS-N 3 : An insight into the silver(I) activation mode
Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
Predictions of photophysical properties of phosphorescent platinum(II) complexes based on ensemble machine learning approach
Unified QSAR and network-based computational chemistry approach to antimicrobials, part 1: Multispecies activity models for antifungals
Theoretical study for the reaction of CH 3 OCl with Cl atom
A method to calculate the weights of nbo electronic structures from Moffitt's theorem
Continuum and discrete calculation of fractional contributions to solvation free energy
A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations
Modeling large protein-glycosaminoglycan complexes using a fragment-based approach
Analytical calculation of pressure for confined atomic and molecular systems using the eXtreme-Pressure Polarizable Continuum Model
Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic NimCun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters
Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns
Role of the variable active site residues in the function of thioredoxin family oxidoreductases
Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field
Towards a transferable nonelectrostatic model for continuum solvation: The electrostatic and nonelectrostatic energy correction model
Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues
Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach
Ab initio investigation of excited state charge transfer pathways in differently capped bithiophene cages
Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?
Libkrylov: A modular open-source software library for extremely large on-the-fly matrix computations
First-order relativistic corrections to MP2 energy from standard gradient codes: Comparison with results from density functional theory
Kinetic mechanism of the hydrogen abstraction reactions of the chlorine atoms with CH 3 CF 2 Cl and CH 3 CFCl 2 : A dual level direct dynamics study
Revisit of large-gap Si16 clusters encapsulating group-IV metal atoms (Ti, Zr, Hf)
Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach
Chemical structures from the analysis of domain-averaged fermi holes. Nature of the Mn-Mn bond in bis(pentacarbonylmanganese)
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
How the substituents in corannulene and sumanene derivatives alter their molecular assemblings and charge transport properties? - A theoretical study with a dimer model
WATsite: Hydration site prediction program with PyMOL interface
A theoretical study on keto-enol tautomerization involving simple carbonyl derivatives
PKA17 - A Coarse-Grain Grid-Based Methodology and Web-Based Software for Predicting Protein pK a Shifts
Ground and excited electronic structures of electride and alkalide units: The cases of Metal-Tren, -Azacryptand, and -TriPip222 complexes
Insulator-metal transition driven by pressure and B-site disorder in double perovskite La2CoMnO6
Aluminabenzene-based Lewis superacids and weakly coordinating anions
Cage-size effects on the encapsulation of P 2 by fullerenes
Theoretical investigations on thallium halides: Relativistic and electron correlation effects in T1 X and T1 X 3 compounds ( X &[DOUBLE BOND];F, C1, Br, and I)
Counting the cyclocized polyphenacenes
In silico evaluation of proposed biosynthetic pathways for the unique dithiolate ligand of the H-cluster of [FeFe]-hydrogenase
Study of protein fluctuation with an effective inter-C atomic potential derived from average distances between amino acids in proteins
Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids
Massive docking of flexible ligands using environmental niches in parallelized genetic algorithms
Direct dynamics study on the reaction of acetaldehyde with ozone
A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them
Predicting antibiotic resistance in complex protein targets using alchemical free energy methods
Theoretical study of the vertical excited states of benzene, pyrimidine, and pyrazine by the symmetry adapted cluster - Configuration interaction method
Effect of interprotein polarization on protein-protein binding energy
3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins
On the sensitivity of computed partial charges toward basis set and (exchange-)correlation treatment
Tuning aromaticity in trigonal alkaline earth metal clusters and their alkali metal salts
Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes
Mechanistic aspects of the synthesis of seven-membered internal nitronates via stepwise [4 + 3] cycloaddition involving conjugated nitroalkenes: Molecular Electron Density Theory computational study
Assessment of the performance of density-functional methods for calculations on iron porphyrins and related compounds
Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model
Ab Initio molecular dynamics study of ethylene adsorption onto Si(001) surface: Short-time fourier transform analysis of structural coordinate autocorrelation function
Towards the design of novel boron- and nitrogen-substituted ammonia-borane and bifunctional arene ruthenium catalysts for hydrogen storage
MC(JBW): Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules
Analysis of the bond-valence method for calculating 29 Si and 31 P magnetic shielding in covalent network solids
Quantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferase
CONDON 3.0: An Updated Software Package for Magnetochemical Analysis-All the Way to Polynuclear Actinide Complexes
Do anionic titanium dioxide nano-clusters reach bulk band gap? A density functional theory study
The high electron mobility for spin-down channel of two-dimensional spin-polarized half-metallic ferromagnetic EuSi 2 N 4 monolayer
Reviews in Computational Chemistry, Volume 7
Domain-based local pair natural orbital methods within the correlation consistent composite approach
Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets
A New Optimization Technique for Artificial Neural Networks Applied to Prediction of Force Constants of Large Molecules
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Ab-initio study of initial atmospheric oxidation reactions of C3 and C4 alkanes
A Theoretical Study on Crossings Among Electronically Excited States and Laser Cooling of Group VIA (S, Se, and Te) Hydrides
Empirical formulation and parameterization of cation-π interactions for protein modeling
Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d 4
Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials
Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules
Local current analysis on defective zigzag graphene nanoribbons devices for biosensor material applications
Numerical characterization of DNA sequences based on the k-step Markov chain transition probability
Study of Localized Molecular Orbitals Using Group Theory Methods and Its Approach to the Many-Electron Correlation Problem. IV. The Symmetry-Adaptation of Many-Center Integrals and Hamiltonian Matrix Elements in MCSCF Calculations
A comparison between two massively parallel algorithms for Monte Carlo computer simulation: An investigation in the grand canonical ensemble
Odd-even effects in the homologous series of alkyl-cyanobiphenyl liquid crystals: A molecular dynamic study
Molecular design of a "molecular syringe" mimic for metal cations using a 1, 3-alternate calix[4]arene cavity
An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averages
Assessment of local coupled cluster methods for excited states of BODIPY/Aza-BODIPY families
Rational determination of charge distributions for free energy calculations
Theoretical calculations of β-lactam antibiotics. V. AM1 calculations of hydrolysis of cephalothin in gaseous phase and influence of the solvent
Computational methods for conformational analysis of unsymmetrical 1, 3-diamines: 3-aminotropanes
QM/MM study of catalytic methyl transfer by the N 5 -glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides
Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation
A hydration study of (1->4) and (1->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations
Fourier transform convolution integrals applied to generalized Born molecular volume
Implicit solvation in domain based pair natural orbital coupled cluster (DLPNO-CCSD) theory
A numerically stable restrained electrostatic potential charge fitting method
Conformational transitions of cyclic D, L-peptides
Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials
Adaptive lambda schemes for efficient relative binding free energy calculation
Electronic structures and chemical bonding in 4d transition metal monohalides
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins
Triazene Proton Affinities: A Comparison between Density Functional, Hartree-Fock, and Post-Hartree-Fock Methods
Quasirelativistic study of 125Te nuclear magnetic shielding constants and chemical shifts
Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations
Modification of the Wiener index 4
Reinforcement learning for in silico determination of adsorbate - substrate structures
New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds
Water solvent effects using continuum and discrete models: The nitromethane molecule, CH 3 NO 2
Toward direct determination of conformations of protein building units from multidimensional NMR experiments I. A theoretical case study of For-Gly-NH2 and For-L-Ala-NH2
Ab initio quality properties for macromolecules using the ADMA approach
Commentaries on quantum similarity (1): Density gradient quantum similarity
A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions
Systematic prediction of the products and intermediates of isotopic labeling in reaction pathway studies
2D representation of protein secondary structure sequences and its applications
Outer electronic shell visualization by NMR chemical shift laplacian of a helium probe
Aromatic-backbone interactions in model alpha-helical peptides
Libra: An open-Source "methodology discovery" library for quantum and classical dynamics simulations
Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane
Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions
A tiny charge-scaling in the OPLS-AA + L-OPLS force field delivers the realistic dynamics and structure of liquid primary alcohols
Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction
Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method
Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides
MOLSIM: A modular molecular simulation software
Density functional theory for efficient ab initio molecular dynamics simulations in solution
Fast generation of molecular surfaces from 3D data fields with an enhanced "marching cube" algorithm
A theoretical survey on the structures, energetics, and isomerization pathways of the B 5 O radical
Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important
The origins of the directionality of noncovalent intermolecular interactions
Bonding, aromaticity, and structure of trigonal dianion metal clusters
Tinned: A symbolic library for response theory and high-order derivatives
Free energy calculations, enhanced by a gaussian ansatz, for the "chemical work" distribution
In Silico screening for agonists and blockers of the β 2 adrenergic receptor: Implications of inactive and activated state structures
A greener catalyst for hydroboration of imines - external electric field modify the reaction mechanism