Assessment of four strain energy decomposition methods for phase field fracture models using quasi-static and dynamic benchmark cases

Strain energy decomposition methods in phase field fracture models separate strain energy that contributes to fracture from that which does not. However, various decomposition methods have been proposed in the literature, and it can be difficult to determine an appropriate method for a given problem. The goal of this work is to facilitate the choice of strain decomposition method by assessing the performance of three existing methods (spectral decomposition of the stress or the strain and deviatoric decomposition of the strain) and one new method (deviatoric decomposition of the stress) with several benchmark problems. In each benchmark problem, we compare the performance of the four methods using both qualitative and quantitative metrics. In the first benchmark, we compare the predicted mechanical behavior of cracked material. We then use four quasi-static benchmark cases: a single edge notched tension test, a single edge notched shear test, a three-point bending test, and a L-shaped panel test. Finally, we use two dynamic benchmark cases: a dynamic tensile fracture test and a dynamic shear fracture test. All four methods perform well in tension, the two spectral methods perform better in compression and with mixed mode (though the stress spectral method performs the best), and all the methods show minor issues in at least one of the shear cases. In general, whether the strain or the stress is decomposed does not have a significant impact on the predicted behavior.

How electron-deficient Cp ligand facilitates Rh-catalyzed annulations with alkynes

The mechanism and origin of CpX ligand effects on Rh-catalyzed annulations with alkynes were investigated by using DFT calculations and the approach of energy decomposition analysis (EDA). The results reveal...

A Comprehensive In Silico Perspective For Discovery of Novel Inhibitory Candidates Targeting Versatile Transcriptional Repressor MBD2

Genome methylation is a key epigenetic mechanism in various biological events such as development, cellular differentiation, cancer progression, aging, and iPSC reprogramming. Crosstalk between DNA methylation and regulation in gene expression is employed through MBD2, known as reader of DNA methylation and suggested as a drug target. Despite its magnitude of significance and rationale of nomination, a scarcely limited number of druggable ligands has been detected so far. Hence, we screened a comprehensive compound library, and then certain of them were subjected to computational docking analysis by targeting the methylated DNA-binding domain of human MBD2. We could detect reasonable binding energies and docking residues presumably located in druggable pockets. Docking results were also validated via MD simulation and per-residue energy decomposition calculation. Drug-likeness of tested ligands was assessed through ADMET prediction in order to foresee off-target side effects for future studies. Herein, on the basis of collaborating approaches such as molecular docking, MD simulation, energy decomposition, and ADMET prediction, notably two compounds named CID3100583 and 8,8-Ethylenebistheophylline, have become prominent as novel candidates, possibly disrupting MBD2MBD–DNA interaction. Hereby, these compounds exhibit a promising usage potential in a wide range of implementations from cancer treatment to somatic cell reprogramming protocols.

Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2+2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed.

Path-Dependency of Energy Decomposition Analysis & the Elusive Nature of Bonding

Here, we provide evidence of the path-dependency of the energy components of the energy decomposition analysis scheme, EDA, by studying a set of thirty-one closed-shell model systems with D2h symmetry point group. For each system, we computed EDA components from nine different pathways and numerically showed that the relative magnitudes of the components differ substantially from one path to the other. Not surprisingly, yet unfortunately, the most significant variations in the relative magnitudes of the EDA components appear in the case of species with bonds within the grey zone of covalency and ionicity. We further discussed that the role of anions and their effect on arbitrary Pauli repulsion energy components affects the nature of bonding defined by EDA. The outcome variation by the selected partitioning scheme of EDA might bring arbitrariness when a careful comparison is overlooked.

Unravelling the Interactions of Magnetic Ionic Liquids by Energy Decomposition Schemes: Towards a Transferable Polarizable Force Field

This work aims at unravelling the interactions in magnetic ionic liquids (MILs) by applying Symmetry-Adapted Perturbation Theory (SAPT) calculations, as well as based on those to set-up a polarisable force field model for these liquids. The targeted MILs comprise two different cations, namely: 1-butyl-3-methylimidazolium ([Bmim]+) and 1-ethyl-3-methylimidazolium ([Emim]+), along with several metal halides anions such as [FeCl4]−, [FeBr4]−, [ZnCl3]− and [SnCl4]2− To begin with, DFT geometry optimisations of such MILs were performed, which in turn revealed that the metallic anions prefer to stay close to the region of the carbon atom between the nitrogen atoms in the imidazolium fragment. Then, a SAPT study was carried out to find the optimal separation of the monomers and the different contributions for their interaction energy. It was found that the main contribution to the interaction energy is the electrostatic interaction component, followed by the dispersion one in most of the cases. The SAPT results were compared with those obtained by employing the local energy decomposition scheme based on the DLPNO-CCSD(T) method, the latter showing slightly lower values for the interaction energy as well as an increase of the distance between the minima centres of mass. Finally, the calculated SAPT interaction energies were found to correlate well with the melting points experimentally measured for these MILs.