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Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study
Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study
Abstract Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic di...
Adatom mediated adsorption of N‐heterocyclic carbenes on Cu(111) and Au(111)
Adatom mediated adsorption of N‐heterocyclic carbenes on Cu(111) and Au(111)
Abstract The adsorption of N-heterocyclic carbenes (NHCs) on Cu(111) and Au(111) surfaces is studied with density-function...
Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility
Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility
Abstract Dynamics of protein cavities associated with protein fluctuations and conformational plasticity is essential for ...
A tiny charge‐scaling in the OPLS‐AA + L‐OPLS force field delivers the realistic dynamics and structure of liquid primary alcohols
A tiny charge‐scaling in the OPLS‐AA + L‐OPLS force field delivers the realistic dynamics and structure of liquid primary alcohols
Abstract We carry out molecular dynamics simulations for pure liquid primary alcohols ranging from methanol to 1-decanol u...
Tuning the quasi‐harmonic treatment of crystalline ionic liquids within the density functional theory
Tuning the quasi‐harmonic treatment of crystalline ionic liquids within the density functional theory
Abstract Five ionic liquids are selected for benchmarking the performance of quasi-harmonic density functional theory (DFT...
Mechanistic study of cobalt(I)‐catalyzed asymmetric coupling of ethylene and enynes to functionalized cyclobutanes
Mechanistic study of cobalt(I)‐catalyzed asymmetric coupling of ethylene and enynes to functionalized cyclobutanes
Abstract Density functional theory (DFT) calculations have been performed to gain insight into the reaction mechanism of t...
Using projection operators with maximum overlap methods to simplify challenging self‐consistent field optimization
Using projection operators with maximum overlap methods to simplify challenging self‐consistent field optimization
Abstract Maximum overlap methods are effective tools for optimizing challenging ground- and excited-state wave functions u...
BF3‐Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2‐siloxy‐1‐propene
BF3‐Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2‐siloxy‐1‐propene
Abstract The Mukaiyama aldol reaction is a powerful tool for the construction of the carbon–carbon bond and the for...
Taking the Monte‐Carlo gamble: How not to buckle under the pressure!
Taking the Monte‐Carlo gamble: How not to buckle under the pressure!
Abstract Consistent buckling distortions of a large membrane patch (200 × 200 Å) are observ...
Distance geometry and protein loop modeling
Distance geometry and protein loop modeling
Abstract Due to the role of loops in protein function, loop modeling is an important problem in computational biology. We ...
CellSys: An open‐source tool for building initial structures for bio‐membranes and drug‐delivery systems
CellSys: An open‐source tool for building initial structures for bio‐membranes and drug‐delivery systems
Abstract Since phospholipids are the most important components in the structure of biomembranes, they deserve to be consid...
Computational study on noncovalent interactions between (n, n) single‐walled carbon nanotubes and simple lignin model‐compounds
Computational study on noncovalent interactions between (n, n) single‐walled carbon nanotubes and simple lignin model‐compounds
Abstract Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of—to this...
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Abstract Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a tr...
Benchmark study on deep neural network potentials for small organic molecules
Benchmark study on deep neural network potentials for small organic molecules
Abstract There has been tremendous advancement in machine learning (ML) applications in computational chemistry, particula...
XGBoost‐based intelligence yield prediction and reaction factors analysis of amination reaction
XGBoost‐based intelligence yield prediction and reaction factors analysis of amination reaction
Abstract Buchwald-Hartwig amination reaction catalyzed by palladium plays an important role in drug synthesis. In the last...
Maximal occupation by bases of π‐hole bands surrounding linear molecules
Maximal occupation by bases of π‐hole bands surrounding linear molecules
Abstract Linear molecules such as CO2 contain a positive π-hole ring that surrounds C on the molecule's equator. Qua...
Picture‐word order compound protein interaction: Predicting compound‐protein interaction using structural images of compounds
Picture‐word order compound protein interaction: Predicting compound‐protein interaction using structural images of compounds
Abstract Identifying potential associations between proteins and compounds is significant and challenging in the drug disc...
Computer‐aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution
Computer‐aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution
Abstract The recently developed efficient protocol combining implicit and explicit, accurate quantum-mechanical modeling o...
Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules
Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules
Abstract Traditionally, substituents are described not by their intrinsic properties, but by their effect elsewhere in a m...
Efficient prediction for high precision CO‐N2 potential energy surface by stacking ensemble DNN
Efficient prediction for high precision CO‐N2 potential energy surface by stacking ensemble DNN
Abstract High-dimensional potential energy surface (PES) for van der Waals systems with spectroscopic accuracy, is of grea...
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation
Abstract The effect of a static electric (E)-field and an unchirped and chirped laser pulse field on the cycl[3.3.3]azine ...
Strategies for the optimization of the structure of crystalline compounds
Strategies for the optimization of the structure of crystalline compounds
Abstract When different proposals exist (or can reasonably be formulated) for the size of the unit cell (in terms of numbe...
An inexpensive density functional theory‐based protocol to predict accurate 19F‐NMR chemical shifts
An inexpensive density functional theory‐based protocol to predict accurate 19F‐NMR chemical shifts
Abstract Thanks to its advantages, 19F-NMR is an increasingly popular technique for the structural characterization of F-c...
Assessment of the van der Waals, Hubbard U parameter and spin‐orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters
Assessment of the van der Waals, Hubbard U parameter and spin‐orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters
Abstract The coinage-metal clusters possess a natural complexity in their theoretical treatment that may be accompanied by...
FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program
FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program
Abstract Molecular dynamics simulation is important in the computational study of the biomolecules. In this paper, we upgr...
ParaCopasi: A package for parallel biochemical simulation and analysis
ParaCopasi: A package for parallel biochemical simulation and analysis
Abstract Biochemical simuflation and analysis play a significant role in systems biology research. Numerous software tools...
CIFDock: A novel CHARMM‐based flexible receptor–flexible ligand docking protocol
CIFDock: A novel CHARMM‐based flexible receptor–flexible ligand docking protocol
Abstract Docking studies play a critical role in the current workflow of drug discovery. However, limitations may often ar...
The effect of midbond functions on interaction energies computed using MP2 and CCSD(T)
The effect of midbond functions on interaction energies computed using MP2 and CCSD(T)
Abstract In this article we use MP2 and CCSD(T) calculations for the A24 and S66 data sets to explore how midbond function...
Thermostabilization mechanisms in thermophilic versus mesophilic three‐helix bundle proteins
Thermostabilization mechanisms in thermophilic versus mesophilic three‐helix bundle proteins
Abstract The engineered three-helix bundle, UVF, is thermostabilized entropically due to heightened, native-state dynamics...
The Ad‐MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA
The Ad‐MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA
Abstract A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistic...
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