Anharmonic vibrational frequencies for closed‐shell molecules computed with CCSD(T)‐F12b/aug‐cc‐pVTZ differ from significantly more costly composite energy methods by a mean absolute error (MAE) of 7.5 cm−1 per fundamental frequency. Comparison to a few available gas phase experimental modes, however, actually lowers the MAE to 6.0 cm−1. Open‐shell molecules have an MAE of nearly a factor of six greater. Hence, open‐shell molecular anharmonic frequencies cannot be as well‐described with only explicitly correlated coupled cluster theory as their closed‐shell brethren. As a result, the use of quartic force fields and vibrational perturbation theory can be opened to molecules with six or more atoms, whereas previously such computations were limited to molecules of five or fewer atoms. This will certainly assist in studies of more chemically interesting species, especially for atmospheric and interstellar infrared spectroscopic characterization.
The cyclopropenylidenyl carbene, c-(C)C3H2, should make for an excellent probe of unidentified infrared bands. It has a dipole moment of roughly 5.0 D making it easily detectable rotationally from the ground. Furthermore, it has vibrational frequencies computed here with proven and high-level quantum chemical methods that line up rather well with the typical C−H stretch, C−C stretch, out-of-plane wag, etc., bins delineated for polycyclic aromatic hydrocarbon fundamental frequencies. For instance, the bright C = C stretches are predicted to be at 5.474 and 6.394 μm, in line with the aromatic infrared bands observed toward various astrophysical regions and within the range of the EXES instrument on board the Stratospheric Observatory for Infrared Astronomy. As a result, potential radioastronomical detection of this molecule could be followed with IR analysis leading to a rare two-pronged analysis for this hydrocarbon, which should shed light onto the nature of currently unattributed IR features.
Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvent, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness towards designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an X-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an X-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. Also, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.
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