Describing chain-like assembly of ethoxygroup-functionalized organic molecules on Au(111) using high-throughput simulations

Due to the low corrugation of the Au(111) surface, 1,4-bis(phenylethynyl)-2,5-bis(ethoxy)benzene (PEEB) molecules can form quasi interlocked lateral patterns, which are observed in scanning tunneling microscopy experiments at low temperatures. We demonstrate a multi-dimensional clustering approach to quantify the anisotropic pair-wise interaction of molecules and explain these patterns. We perform high-throughput calculations to evaluate an energy function, which incorporates the adsorption energy of single PEEB molecules on the metal surface and the intermolecular interaction energy of a pair of PEEB molecules. The analysis of the energy function reveals, that, depending on coverage density, specific types of pattern are preferred which can potentially be exploited to form one-dimensional molecular wires on Au(111).

The Study of the Influence of Chemical Nature of Functional Groups in Oligomeric and Low--Molecular Modifiers on the Rheological Properties of the Epoxy Oligomer

The influence of chemical nature of modifier functional groups on the level of intermolecular interactions in the system "epoxy oligomer ‒ modifier", as well as the structure formation and dynamic viscosity of epoxy oligomer has been studied in detail. Modifying additives in low concentrations contribute to an increase in the degree of structure formation of the epoxy system by increasing the intermolecular interaction between the associates of the epoxydiane oligomer. It was established that the strength of the formed coagulation structures depends both on the compatibility parameter of the modifiers and ED-20, and on their intermolecular interaction energy.

Dataset of Noncovalent Intermolecular Interaction Energy Curves for 24 Small High-Spin Open-Shell Dimers

<div>We introduce a dataset of 24 interaction energy curves of open-shell noncovalent dimers, referred to as the O24x5 dataset. The dataset consists of high-spin dimers up to eleven atoms selected to assure diversity with respect to interactions types: dispersion, electrostatics and induction. The benchmark interaction energies are obtained at the restricted open-shell CCSD(T) level of theory with complete basis set extrapolation aug-cc-pVQZ--> aug-cc-pV5Z.</div>

Dataset of Noncovalent Intermolecular Interaction Energy Curves for 24 Small High-Spin Open-Shell Dimers

<div>We introduce a dataset of 24 interaction energy curves of open-shell noncovalent dimers, referred to as the O24x5 dataset. The dataset consists of high-spin dimers up to eleven atoms selected to assure diversity with respect to interactions types: dispersion, electrostatics and induction. The benchmark interaction energies are obtained at the restricted open-shell CCSD(T) level of theory with complete basis set extrapolation aug-cc-pVQZ--> aug-cc-pV5Z.</div>

MrPIXEL: automated execution of Pixel calculations via the Mercury interface

The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host–guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule–molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

Prediction of Solid Solution Formation among Chemically Similar Molecules Using Calculation of Lattice and Intermolecular Interaction Energy

Several 2-substituted 4-nitrobenzoic acid (NBA) derivatives such as 2-chloro-4-nitrobenzoic acid (2C4NBA), 2-methyl-4-nitrobenzoic acid (2CH34NBA) and 2-hydroxy-4-nitrobenzoic acid (2OH4NBA) were selected as model compounds because of their availability and chemically similar structures, in which the different group/atom (R) does not significantly affect the dominant intermolecular interactions – hydrogen bonds formed by the carboxylic group [1]. Quantum chemical calculations of lattice and intermolecular interaction energy were carried out to identify possible factors, which could be, used in prediction of the formation of solid solutions (SS) in binary systems of chemically similar molecules, in this case - various nitrobenzoic acid derivatives. Meanwhile, crystallization experiments were used to determine the experimental information about formation of solid solutions. The obtained crystalline phases were characterized by combined use of powder X-ray diffraction (XRPD) and differential scanning calorimetry/thermogravimetry (DSC/TG) [2].

Crystal structures and Hirshfeld surface analyses of (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide: lattice energy and intermolecular interaction energy calculations for the former. Corrigendum

In the paper by Gomes et al. [Acta Cryst. (2019), E75, 1403–1410], there was an error and omission in the author and affiliation list.

THEORETICAL STUDY ON THE INTERMOLECULAR INTERACTIONS OF 1,1-DIAMINO-2,2-DINITROETHYLENE WITH NH3 AND H2O

Density Functional Theory (DFT) and dispersion-corrected density functional theory (DFT-D) were used to study the intermolecular interactions of 1,1-diamino-2,2-dinitroethylene FOX-7/NH3and FOX-7/H2O supermolecules. The geometries optimized from DFT and DFT-D methods are similar.Six optimized supermolecules were characterized to be local energy minima on potential energy surfaces without imaginary frequencies. The intermolecular interaction energy (binding energy) was calculated with basis set superposition error (BSSE) correction. The largest corrected intermolecular interaction energy is FOX-7/NH3 (-43.76 kJ×mol-1), indicating that the interaction between FOX-7 and NH3 is stronger than that of FOX-7/H2O. The same conclusion is obtained from the studies on the infrared spectrum and frontier orbitals.

Crystal structures and Hirshfeld surface analyses of (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide: lattice energy and intermolecular interaction energy calculations for the former

The crystal structures of the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide, C20H18N2O6·0.5C2H6OS, and (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide, C17H12N2O3 (4: R = C6H5), are discussed. The non-hydrogen atoms in compound [4: R = (3,4,5-MeO)3C6H2)] exhibit a distinct curvature, while those in compound, (4: R = C6H5), are essential coplanar. In (4: R = C6H5), C—H...O and π–π intramolecular interactions combine to form a three-dimensional array. A three-dimensional array is also found for the hemi-DMSO solvate of [4: R = (3,4,5-MeO)3C6H2], in which the molecules of coumarin are linked by C—H...O and C—H...π interactions, and form tubes into which the DMSO molecules are cocooned. Hirshfeld surface analyses of both compounds are reported, as are the lattice energy and intermolecular interaction energy calculations of compound (4: R = C6H5).