Journal of Computational Chemistry

doi: 10.1002/jcc.26619pmid: N/A

Levina, Elena O.; Khrenova, Maria G.; Astakhov, Andrey A.; Tsirelson, Vladimir G.

doi: 10.1002/jcc.26858pmid: 35411548

The equilibrium between keto and enol forms in acetylacetone and its derivatives is studied using electron delocalization indices and delocalization tensor density. We demonstrate how electron delocalization governs the equilibrium between keto and enol forms. The less stable enols have more distinct double and single bond character in the CCC fragment, while electron delocalization in this fragment is more pronounced in more stable enols. Looking for the origin of such behavior, we considered the one‐electron potentials entering the Euler equation for the electron density. We found that electron delocalization is mainly governed by the static exchange potential, which depends on the three‐dimensional atomic structure. It, however, does not distinguish differences in electron delocalization in more and less stable enols, the effect arising from the kinetic exchange contribution, which reflects spin‐dependent effects in the electron motion. The local depletion of kinetic exchange in the conjugated fragment yields the enhanced electron delocalization along the CCC bonds in more stable enols. Thus, a combination of considered descriptors allowed us to reveal the influence of electron delocalization on the equilibrium between keto and enol forms and showed the significant features of this phenomenon.

Sülzner, Niklas; Haberhauer, Julia; Hättig, Christof; Hellweg, Arnim

doi: 10.1002/jcc.26864pmid: 35460090

In this contribution we extent the use of the conductor‐like screening model for realistic solvation (COSMO‐RS) to the prediction of pKa values in acetone, a commonly used dipolar aprotic solvent. For this, we calculated the Gibbs free energy of dissociation of 120 organic acids (nine acrylic acids, 87 benzoic acids, nine phenols, and 15 benzenesulfonamides) using COSMO‐RS at the two levels BP‐TZVP and BP‐TZVPD‐FINE and determined the parameters for a linear free energy relation for the pKa prediction by performing linear fits to experimental values. Our results suggest that the data set dissects into two groups, with the phenols being different from the other three subsets. The acrylic and benzoic acids and the sulfonamides can be treated together and yield an excellent linear correlation (r2>0.95) with an RMSD of only ~0.3. The slope is found to be significantly smaller than the theoretical value (1/RTln10), only 45% of it, which is in accordance with findings in the literature. The phenols, however, while similarly well correlated in their own subset with an RMSD of 1.7–1.9, exhibit a slope larger than one. We discuss both a higher uncertainty in the reference values as well as physical origins as possible reasons.

Kraus, Jakob; Kortus, Jens

doi: 10.1002/jcc.26865pmid: 35460103

Thermodynamic and kinetic information on the first two steps of gallic acid pyrolysis, a decarboxylation followed by a dehydrogenation, is obtained based on density functional theory and quantum chemistry. For the kinetics, transition states are identified with the help of the climbing image nudged elastic band method. Both reactions exhibit two transition states. One of them is related to the rotation of OH groups, and the other one is related to the breaking and forming of bonds. The gallic acid pyrolysis as a whole is judged to be endothermal, and it changes from endergonic to exergonic between 500 and 750 K. The second reaction, the dehydrogenation of pyrogallol, is identified as the rate‐determining step of gallic acid pyrolysis, with reaction rate constants below 1 s−1 for temperatures below 1250 K.

Bae, Gyun‐Tack; Aikens, Christine M.

doi: 10.1002/jcc.26868pmid: 35426447

The plasmonic properties of tetrahedral aluminum nanoparticles have been investigated using time‐dependent functional theory (TDDFT) calculations. The excitation energies are calculated for tetrahedral aluminum nanoparticles (Aln, n = 10–120) with different charge states. The BP86/DZ model is used to perform geometric optimization calculations for these clusters. The SAOP/DZ and LB94/DZ levels of theory have been used for the excitation energy calculations of these tetrahedral aluminum clusters. The absorption peaks are red‐shifted upon increasing the size of the aluminum nanoparticles.

Wassenaar, Pim N. H.; Rorije, Emiel; Vijver, Martina G.; Peijnenburg, Willie J. G. M.

doi: 10.1002/jcc.26859pmid: 35403727

Screening and prioritization of chemicals is essential to ensure that available evaluation capacity is invested in those substances that are of highest concern. We, therefore, recently developed structural similarity models that evaluate the structural similarity of substances with unknown properties to known Substances of Very High Concern (SVHC), which could be an indication of comparable effects. In the current study the performance of these models is improved by (1) separating known SVHCs in more specific subgroups, (2) (re‐)optimizing similarity models for the various SVHC‐subgroups, and (3) improving interpretability of the predicted outcomes by providing a confidence score. The improvements are directly incorporated in a freely accessible web‐based tool, named the ZZS similarity tool: https://rvszoeksysteem.rivm.nl/ZzsSimilarityTool. Accordingly, this tool can be used by risk assessors, academia and industrial partners to screen and prioritize chemicals for further action and evaluation within varying frameworks, and could support the identification of tomorrow's substances of concern.

Gehlhaar, Daniel K.; Luty, Brock A.; Cheung, Philip P.; Litman, Andy H.; Owen, Robert M.; Rose, Peter W.

doi: 10.1002/jcc.26862pmid: 35394655

Pfizer's Crystal Structure Database (CSDB) is a key enabling technology that allows scientists on structure‐based projects rapid access to Pfizer's vast library of in‐house crystal structures, as well as a significant number of structures imported from the Protein Data Bank. In addition to capturing basic information such as the asymmetric unit coordinates, reflection data, and the like, CSDB employs a variety of automated methods to first ensure a standard level of annotations and error checking, and then to add significant value for design teams by processing the structures through a sequence of algorithms that prepares the structures for use in modeling. The structures are made available, both as the original asymmetric unit as submitted, as well as the final prepared structures, through REST‐based web services that are consumed by several client desktop applications. The structures can be searched by keyword, sequence, submission date, ligand substructure and similarity search, and other common queries.