yusuke1997/dblp-id-title huggingface dataset:
Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules
The Valence Isomers of (CH) 8 and (SiH) 8 : An Ab Inition MO Study
A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: Dynamics of tertiary and quaternary structures
Explicitly correlated frequency-independent second-order green's function for accurate ionization energies
Improved Methods for Semiempirical Solvation Models
Quantum supercharger library: Hyper-parallelism of the Hartree-Fock method
Local perturbations of periodic systems. Chemisorption and point defects by GoGreenGo
A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry
Geometry prediction of bridged zirconocene dichlorides by quantum chemical methods
Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator
Molecular mechanics models for tetracycline analogs
A comparison of neighbor search algorithms for large rigid molecules
Rapidly convergent procedure to solve the density profile equation in the classical density functional theory
Stabilization of activated fragments by shell-wise construction of an embedding environment
The catalytic effect of the NH 3 base on the chemical events in the caryolene-forming carbocation cascade
Application of semiempirical long-range dispersion corrections to periodic systems in density functional theory
On the efficient evaluation of Fourier patterns for nanoparticles and clusters
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
PyFrag 2019 - Automating the exploration and analysis of reaction mechanisms
Thermal isomerizations of vinylcyclopropanes to cyclopentenes
Theoretical investigation into the potential of halogenated methanes to undergo reductive metabolism
Electrostatics for probing lone pairs and their interactions
Quantum chemical topology from tight augmented core densities
Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure-Activity Relationships and Quantum Mechanics Calculations
Cover Image, Volume 41, Issue 16
Hydrolysis mechanism of the cyclohexaborate anion: Unraveling the intricacies
MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes
CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes
Molecular mechanics calculations on carbonyl compounds. IV. Heats of formation
Calculation of solvation free energy using RISM theory for peptide in salt solution
Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: Implications to reactivity and relevance to the nitrogenase problem
Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy
Pyrrolizidine alkaloids necine bases: Ab initio, semiempirical, and molecular mechanics approaches to molecular properties
DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment
Revitalizing Spin Natural Orbital Analysis: Electronic Structures of Mixed-Valence Compounds, Singlet Biradicals, and Antiferromagnetically Coupled Systems
Seminumerical calculation of the Hartree-Fock exchange matrix: Application to two-component procedures and efficient evaluation of local hybrid density functionals
BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential
A chemist's guide to valence bond theory
Appraisal of the Fragments-In-Fragments Method for the Energetics of Individual Hydrogen Bonds in Molecular Crystals
A reference-free stockholder partitioning method based on the force on electrons
Neutral hydrolyses of carbon disulfide: An ab initio study of water catalysis
Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models
A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations
Nonideality in diffusion of ionic and neutral solutes and hydrogen bond dynamics in dimethyl sulfoxide-chloroform mixtures of varying composition
Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin
Parallel Fock matrix construction program for molecular orbital calculation - Specific computer with a hierarchical network
A theoretical study of solvent effect and reaction mechanism of electron transfer reaction between indole side chain and phenol side chain of peptide involving tryptophan and tyrosine
Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations
Assessing energy functions for flexible docking
Further comments on the lack of homoaromaticity in triquinacene
Spectroscopic fingerprints of toroidal nuclear quantum delocalization via Ab Initio path integral simulations
Hydrogenation of 3d-metal oxide clusters: Effects on the structure and magnetic properties
4f fine-structure levels as the dominant error in the electronic structures of binary lanthanide oxides
Theoretical auger electron spectra of polymers by density functional theory calculations using model dimers
Dual-level direct dynamics studies for the reactions of OH radical with bromine-substituted ethanes
Random number generators tested on quantum Monte Carlo simulations
Cover Image, Volume 39, Issue 16
Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions
DFT calculations of quadrupolar solid-state NMR properties: Some examples in solid-state inorganic chemistry
Electron pairing and chemical bonds: Bonding in hypervalent molecules from analysis of Fermi holes
Does alpha-effect exist in E2 reactions? A G2(+) investigation
QM/MM study of the absorption spectra of DsRed.M1 chromophores
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape
Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties
Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence
Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?
Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers
Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians
Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates
Ab initio study on the photochemical behavior of styrene
Molecular and Electronic Structure and Properties of the Single Benzene-Based Fluorophores Containing Guanidine Subunit
Adaptive regularized Gaussian process regression for application in the context of hydrogen adsorption on graphene sheets
Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41
Characterization of dynamics and reactivities of solvated ions by ab initio simulations
Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment
ExcelAutomat 1.3: Fragment analysis based on the distortion/interaction-activation strain model
Theoretical investigation of enantioselectivity of cage-like supramolecular assembly: The insights into the shape complementarity and host-guest interaction
Structural and dynamical properties of methane clathrate hydrates
Kinetics of the hydrogen abstraction reactions of 1, 1- and 1, 2-difluoroethane with hydroxyl radical: an ab initio study
Parameterization and Evaluation of a Flexible Water Model
Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling
Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation
MPI-parallelization of the grid inhomogeneous solvation theory calculation
Suitability of the PM3-derived molecular electrostatic potentials
Topological analysis of electron density distribution taken from a pseudopotential calculation
Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian
Accurate bond dissociation enthalpies by using doubly hybrid XYG3 functional
Force-field modeling through quantum mechanical calculations: Molecular dynamics simulations of a nematogenic molecule in its condensed phases
A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function
Rapid algorithm for computing the electron repulsion integral over higher order Gaussian-type orbitals: Accompanying coordinate expansion method
Aromaticity in linear polyacenes: Generalized population analysis and molecular quantum similarity approach
Accurate lattice energies of organic molecular crystals from periodic turbomole calculations
Theoretical study of sheets formed by -peptides
Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality
Car-Parrinello simulations with a real space method
Protein-protein docking dealing with the unknown
Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions
Modeling UV-Vis spectra of low dimensional materials using electrostatic embedding: The case of CdSe
Long Time Overdamped Langevin Dynamics of Molecular Chains
Relation of the force constant of a bond to the electric field at a nucleus
Effective fragment potential method in Q-CHEM: A guide for users and developers
Reaction mechanism of the CCN radical with nitric oxide
Conformational Study of Dipeptides: A Sensitivity Analysis Approach
Molecular mechanics simulation studies of dienoic hydrocarbons: From alkenes to 1-Palmitoyl-2-linoleoyl-phosphatidylcholines
Efficient solution technique for solving the Poisson-Boltzmann equation
A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations
Advanced Computational Insights Into Cs₂NaScX₆ (X = Cl, Br) ₆ Double Perovskites: Structural Stability, Elastic Properties, and Optical Characteristics for Next-Generation Photovoltaics
Systematic improvement of empirical energy functions in the era of machine learning
Early days of quantum crystallography: A personal account
Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets
Toward efficient generation, correction, and properties control of unique drug-like structures
Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes
Atomic radii: Incorporation of solvation effects
Enhancing protein-ligand binding affinity prediction through sequential fusion of graph and convolutional neural networks
Hydrogen bonding in the mixed HF/HCl dimer: Is it better to give or receive?
Partial rigid-body dynamics in NPT, NPAT and NPT ensembles for proteins and membranes
Nucleic acid sequence design via efficient ensemble defect optimization
Discriminating and understanding molecular crystal polymorphism
Unicorns in the world of chemical bonding models
Coarse-graining of protein structures for the normal mode studies
Relativistic electronic structure theory
Interplay between aromaticity and strain in double group transfer reactions to 1, 2-benzyne
Simulating the full spin manifold of triplet-pair states in a series of covalently linked TIPS-pentacenes
Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters
Thermal dissociation of tripropylamine as the first step in the growth of carbon nanotubes inside AlPO 4 -5 channels
Assessment of theoretical methods for the calculation of methyl cation affinities
Benchmarking of density functionals for a soft but accurate prediction and assignment of 1 H and 13 C NMR chemical shifts in organic and biological molecules
Accurate prediction of dynamic protein-ligand binding using P-score ranking
Dependence of relativistic effects on electronic configuration in the neutral atoms of d- and f-block elements
Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas
Role of bifurcation in the bond shifting of cyclooctatetraene
Is there computational support for an unprotonated carbon in the E4 state of nitrogenase?
Modeling aspects of mechanisms for reactions catalyzed by metalloenzymes
Ab initio and density functional theory study of structures and energies for dimethoxymethane as a model for the anomeric effect
The role of induced current density in Steroelectronic effects: Perlin effect
A computational study of conformational interconversions in 1, 4-dithiacyclohexane (1, 4-dithiane)
Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules
Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential
Photo absorption of p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach
Time-dependent density functional theory study on the electronic excited-state hydrogen-bonding dynamics of 4-aminophthalimide (4AP) in aqueous solution: 4AP and 4AP-(H 2 O) 1, 2 clusters
The SHARK integral generation and digestion system
An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY
Critical Assessment of the DFT + U Approach for the Prediction of Vanadium Dioxide Properties
C3(SINGLE BOND)M Bond contribution to polarizability tensor and 3J(C1M) NMR coupling constant in 1-X-3-M-bicyclo[1.1.1]pentanes
On the Existence of HeHe Bond in the Endohedral Fullerene Hе2@C60
Optimization and dynamics of protein-protein complexes using B-splines
Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions
Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories
Quantum chemical calculation of vibrational spectra of large molecules - Raman and IR spectra for Buckminsterfullerene
Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics
Corrigendum: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain
Superatom molecular orbital in C 80
Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model
Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory
Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: A proton conducting electrolytic component in fuel cells
Robustness in the fitting of molecular mechanics parameters
Application of polarizable ellipsoidal force field model to pnicogen bonds
Application of inverse iteration to 2-dimensional master equations
MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software
Using operators to expand the block matrices forming the Hessian of a molecular potential
Effects of electron correlation and spin projection on rotational barriers of trithiocarbenium ion [C(SH) 3 ] + and Radical Dication [C(SH) 3 ] , 2+
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases
The photoisomerization of 11- cis -retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory
A computational study of unique properties of pillar[ n ]quinones: Self-assembly to tubular structures and potential applications as electron acceptors and anion recognizers
Variationally determined electronic states for the theoretical analysis of intramolecular interaction. II. Qualitative nature of the P‒O bond in phosphine oxides
Discrimination of dynamical system models for biological and chemical processes
Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab Initio study
Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile
The importance of four-membered NHCs in stabilizing Breslow intermediates on benzoin condensation pathway
Mfgnn: Multi-Scale Feature-Attentive Graph Neural Networks for Molecular Property Prediction
Theoretical study on the structure and formation mechanism of [C 6 H 5 M m ] - (M-Ag, Au; m = 1-3)
A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization
Parameterization of a geometric flow implicit solvation model
Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: Models of the iron-iron hydrogenase enzyme active site
Peptide models XXIII. Conformational model for polar side-chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO-L-SER-NH2
Complexes of adamantane-based group 13 Lewis acids and superacids: Bonding analysis and thermodynamics of hydrogen splitting
Some recent techniques for free energy calculations
Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface
Free energy profiles for monomer capture in Grubbs- and SHOP-type olefin polymerization catalysts: A constraint ab initio molecular dynamics study
Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions
Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids
Contrasting electronic requirements for C-H binding and C-H activation in d 6 half-sandwich complexes of rhenium and tungsten
A comparative theoretical study of dipeptide solvation in water
Comparative study of BSSE correction methods at DFT and MP2 levels of theory
Structure and bonding in binuclear metal carbonyls from the analysis of domain averaged Fermi holes. I. Fe 2 (CO) 9 and Co 2 (CO) 8
A combined molecular modeling study on gelatinases and their potent inhibitors
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory
Response to the comment by Wolf Ihlenfeldt on the paper "Indexing molecules with chemical graph identifiers"
Theoretical study on the hydrolysis mechanism of N , N -dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: Water-assisted mechanism and cluster-continuum model
Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs
Ab initio potential energy surface and predicted microwave spectra for ArOCS dimer and structures of ArnOCS (n = 2-14) clusters
CCPE: A Tool to Quickly Extract, Format, and Present the Outputs From Gaussian and VEDA Computational Chemistry Programs
Vertical spectrum of the C2H2+ system. An open shell (SC)2-CAS-SDCI study
Prediction of antibacterial compounds by machine learning approaches
A computational study of the LiH dimer
Rapid estimation of activation enthalpies for cytochrome-P450-mediated hydroxylations
fromage: A library for the study of molecular crystal excited states at the aggregate scale
Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures
Electronic spectra and intersystem spin-orbit coupling in 1, 2- and 1, 3-squaraines
Efficient algorithm for quantitative assessment of similarities among atoms in molecules
An accurate relativistic universal Gaussian basis set for hydrogen through Nobelium without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models
Substrate specificity of cytochrome P450cam for L- and D- norcamphor as studied by molecular dynamics simulations
Molecular understanding of the adhesive interactions between silica surface and epoxy resin: Effects of interfacial water
Calculations on 1, 8-naphthoquinone predict that the ground state of this diradical is a singlet
Benchmarking the thermodynamic analysis of water molecules around a model beta sheet
Spin-orbit coupling of DFT/MRCI wavefunctions: Method, test calculations, and application to thiophene
Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site
Theoretical study on the mechanism of alcohol photooxidation on Nb 2 O 5 surface
Temperature dependence of structure and dynamics of the hydrated Ca 2+ ion according to ab initio quantum mechanical charge field and classical molecular dynamics
A study on orientation and absorption spectrum of interfacial molecules by using continuum model
Tuning Electronic Relaxation of Nanorings Through Their Interlocking
A deeper insight into strain for the sila-bi[6]prismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12
The topology of the Ehrenfest force density revisited. A different perspective based on Slater-type orbitals
Fractional occupation numbers and self-interaction correction-scaling methods with the Fermi-Löwdin orbital self-interaction correction approach
Effect of charge distribution on electrostatic chromophore - protein interactions in Bacteriorhodopsin
Zori 1.0: A parallel quantum Monte Carlo electronic structure package
Multicanonical procedure for continuum peptide models
Thermodynamic properties of Ag2OB2O3 glasses by a modified scale-transformed energy space sampling Monte Carlo method
Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models
FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules
Combining classical molecular dynamics and quantum mechanical methods for the description of electronic excitations: The case of carotenoids
Reconsideration of solvent effects calculated by semiempirical quantum chemical methods
Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2
Formation and infrared spectroscopic characterization of carbon suboxide complexes TM- η 1 -C 3 O 2 and the inserted ketenylidene complexes OCTMCCO (TM=Cu, Ag, Au) in solid neon
Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics
A Molecualr Dynamics Study of the Inhibition of Chicken Dihydrofolate Reductase by a Phenyl Triazine
Novel machine learning insights into the QM7b and QM9 quantum mechanics datasets
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning