Latest Articles of Journal of Computational Chemistry


TopP–S: Persistent homology‐based multi‐task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility 10.1002/jcc.25213 2018-04-06 Aqueous solubility and partition coefficient are important physical properties of small molecules. Accurate theoretical prediction of aqueous solubility and partition coefficient plays an important role in drug design and discovery. The prediction accuracy de...
TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems 10.1002/jcc.25181 2018-03-23 We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molec...
Cover Image, Volume 39, Issue 12 10.1002/jcc.25210 2018-03-15 Molecular dynamics (MD) simulations provide insights into biological mechanisms. Existing MD visualization programs do not implement many of the advanced rendering algorithms common in the film and video-game industries. In contrast, the open-source program B...
Dispersion interactions between neighboring Bi atoms in (BiH3)2 and Te(BiR2)2 10.1002/jcc.25209 2018-03-13 Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR2)2 molecules (R = ...
Can we predict the structure and stability of molecular crystals under increased pressure? First‐principles study of glycine phase transitions 10.1002/jcc.25198 2018-03-12 The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goa...
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package 10.1002/jcc.25187 2018-03-12 Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseas...
Real‐space grid representation of momentum and kinetic energy operators for electronic structure calculations 10.1002/jcc.25208 2018-03-08 We show that the central finite difference formula for the first and the second derivative of a function can be derived, in the context of quantum mechanics, as matrix elements of the momentum and kinetic energy operators on discrete coordinate eigenkets defi...
Theoretical study of nitrogen‐doped graphene nanoflakes: Stability and spectroscopy depending on dopant types and flake sizes 10.1002/jcc.25206 2018-03-05 As nitrogen‐doped graphene has been widely applied in optoelectronic devices and catalytic reactions, in this work we have investigated where the nitrogen atoms tend to reside in the material and how they affect the electron density and spectroscopic properti...
Azobenzene‐bridged diradical janus nucleobases with photo‐converted magnetic properties between antiferromagnetic and ferromagnetic couplings 10.1002/jcc.25207 2018-03-05 We computationally design a series of azobenzene (AB)‐bridged double radicalized nucleobases, a novel kind of diradical Janus‐type nucleobases, and explore their spin coupling characteristics. Calculations prove that such diradical Janus‐bases not only normal...
Accurate lattice energies of organic molecular crystals from periodic turbomole calculations 10.1002/jcc.25205 2018-03-05 Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom‐centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non‐covalentl...

TopP–S: Persistent homology‐based multi‐task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility

10.1002/jcc.25213

2018-04-06

Aqueous solubility and partition coefficient are important physical properties of small molecules. Accurate theoretical prediction of aqueous solubility and partition coefficient plays an important role in drug design and discovery. The prediction accuracy de...

TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems

10.1002/jcc.25181

2018-03-23

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molec...

Cover Image, Volume 39, Issue 12

10.1002/jcc.25210

2018-03-15

Molecular dynamics (MD) simulations provide insights into biological mechanisms. Existing MD visualization programs do not implement many of the advanced rendering algorithms common in the film and video-game industries. In contrast, the open-source program B...

Dispersion interactions between neighboring Bi atoms in (BiH3)2 and Te(BiR2)2

10.1002/jcc.25209

2018-03-13

Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR2)2 molecules (R = ...

Can we predict the structure and stability of molecular crystals under increased pressure? First‐principles study of glycine phase transitions

10.1002/jcc.25198

2018-03-12

The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goa...

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

10.1002/jcc.25187

2018-03-12

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseas...

Real‐space grid representation of momentum and kinetic energy operators for electronic structure calculations

10.1002/jcc.25208

2018-03-08

We show that the central finite difference formula for the first and the second derivative of a function can be derived, in the context of quantum mechanics, as matrix elements of the momentum and kinetic energy operators on discrete coordinate eigenkets defi...

Theoretical study of nitrogen‐doped graphene nanoflakes: Stability and spectroscopy depending on dopant types and flake sizes

10.1002/jcc.25206

2018-03-05

As nitrogen‐doped graphene has been widely applied in optoelectronic devices and catalytic reactions, in this work we have investigated where the nitrogen atoms tend to reside in the material and how they affect the electron density and spectroscopic properti...

Azobenzene‐bridged diradical janus nucleobases with photo‐converted magnetic properties between antiferromagnetic and ferromagnetic couplings

10.1002/jcc.25207

2018-03-05

We computationally design a series of azobenzene (AB)‐bridged double radicalized nucleobases, a novel kind of diradical Janus‐type nucleobases, and explore their spin coupling characteristics. Calculations prove that such diradical Janus‐bases not only normal...

Accurate lattice energies of organic molecular crystals from periodic turbomole calculations

10.1002/jcc.25205

2018-03-05

Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom‐centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non‐covalentl...