Intricate Conformational Tunneling in Carbonic Acid Monomethyl Ester

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Theoretical Characterization of Carbonic Acid Clusters in the UV

Two theoretical structural motifs are proposed to match two experimental solid carbonic acid UV spectra from previous literature ( Astron. Astrophys. 2021, 646, A172): a linear ribbon structure as a single octamer and nonplanar orientations of carbonic acid clusters. The latter have some contribution from approximated amorphous solid carbonic acid in the form of 40 different clusters of 8 carbonic acid molecules ensemble-averaged together, but unoptimized pairs of optimized dimers oriented perpendicular to one another give the strongest intensities of lower energy UV transitions. The linear ribbon structure's predicted spectrum computed with CAM-B3LYP/6-311G(d,p) agrees well with Experimental Solid B─the β-carbonic acid experimental data in the UV region. Meanwhile, the 40 amorphous clusters are built with a randomization script, and the electronically excited states are calculated with both CAM-B3LYP/6-311G(d,p) and ωB97XD/6-311G(d,p). The resulting theoretical spectrum is constructed by employing a Boltzmann distribution of the intensities and artificially broadening the simulated spectra. The nonplanar dimer pairs are computed with CAM-B3LYP and B3LYP with the 6-311G(d,p) basis set. The results of the amorphous simulation weakly correspond with the Experimental Solid A spectrum, but the fully nonplanar motif matches the experiment much more convincingly. As a result, the previous work appears to have observed the traditional crystalline phase of solid carbonic acid in Experimental Solid B, whereas the nonplanar orientations of the carbonic acids in the clusters appear to correlate with Experimental Solid A. This spectral classification will aid in future laboratory work exploring the role that carbonic acid can play in low temperature, low pressure desorbed environments with potential application to astrochemistry.

Characterization of the Simplest Thiolimine: The Higher Energy Tautomer of Thioformamide

As sulfur‐containing organic molecules thioamides and their isomers are conceivable intermediates in prebiotic chemistry, for example, in the formation of amino acids and thiazoles and resemble viable candidates for detection in interstellar media. Here, we report the characterization of parent thioformamide in the solid state via single‐crystal X‐ray diffraction and its photochemical interconversion to its hitherto unreported higher energy tautomer thiolimine in inert argon and dinitrogen matrices. Upon photogeneration, four conformers of thiolimine form, whose ratio depends on the employed wavelength. One of these conformers interconverts due to quantum mechanical tunneling with a half‐life of 30–45 min in both matrix materials at 3 and 20 K. A spontaneous reverse reaction from thiolimine to thioformamide is not observed. To support our experimental findings, we explored the potential energy surface of the system at the AE‐CCSD(T)/aug‐cc‐pCVTZ level of theory and computed tunneling half‐lives with the CVT/SCT approach applying DFT methods.

Biological concepts for catalysis and reactivity: empowering bioinspiration

Biological systems provide attractive reactivity blueprints for the design of challenging chemical transformations. Emulating the operating mode of natural systems may however not be so easy and direct translation of structural observations does not always afford the anticipated efficiency. Metalloenzymes rely on earth-abundant metals to perform an incredibly wide range of chemical transformations. To do so, enzymes in general have evolved tools and tricks to enable control of such reactivity. The underlying concepts related to these tools are usually well-known to enzymologists and bio(inorganic) chemists but may be a little less familiar to organometallic chemists. So far, the field of bioinspired catalysis has greatly focused on the coordination sphere and electronic effects for the design of functional enzyme models but might benefit from a paradigm shift related to recent findings in biological systems. The goal of this review is to bring these fields closer together as this could likely result in the development of a new generation of highly efficient bioinspired systems. This contribution covers the fields of redox-active ligands, entatic state reactivity, energy conservation through electron bifurcation, and quantum tunneling for C-H activation.

Hydrogen-Atom Tunneling in Metaphosphorous Acid

Metaphosphorous acid (HOPO), a key intermediate in phosphorus chemistry, has been generated in syn- and anti-conformations in the gas phase by high-vacuum flash pyrolysis (HVFP) of a molecular precursor ethoxyphosphinidene oxide (EtOPO→C₂ H₄ +HOPO) at ca. 1000 K and subsequently trapped in an N₂ -matrix at 2.8 K. Unlike the two conformers of the nitrogen analogue HONO, the anti-conformer of HOPO undergoes spontaneous rotamerization at 2.8 K via hydrogen-atom tunneling (HAT) with noticeable kinetic isotope effects for H/D (>10⁴ for DOPO) and ¹⁶ O/¹⁸ O (1.19 for H¹⁸ OPO and 1.06 for HOP¹⁸ O) in N₂ -matrices.

Alpha-Carbonic Acid Revisited: Carbonic Acid Monomethyl Ester as a Solid and its Conformational Isomerism in the Gas Phase

In this work, earlier studies reporting α‐H₂CO₃ are revised. The cryo‐technique pioneered by Hage, Hallbrucker, and Mayer (HHM) is adapted to supposedly prepare carbonic acid from KHCO₃. In methanolic solution, methylation of the salt is found, which upon acidification transforms to the monomethyl ester of carbonic acid (CAME, HO‐CO‐OCH₃). Infrared spectroscopy data both of the solid at 210 K and of the evaporated molecules trapped and isolated in argon matrix at 10 K are presented. The interpretation of the observed bands on the basis of carbonic acid [as suggested originally by HHM in their publications from 1993–1997 and taken over by Winkel et al., J. Am. Chem. Soc. 2007 and Bernard et al., Angew. Chem. Int. Ed. 2011] is inferior compared with the interpretation on the basis of CAME. The assignment relies on isotope substitution experiments, including deuteration of the OH‐ and CH₃‐ groups as well as ¹²C and ¹³C isotope exchange and on variation of the solvents in both preparation steps. The interpretation of the single molecule spectroscopy experiments is aided by a comprehensive calculation of high‐level ab initio frequencies for gas‐phase molecules and clusters in the harmonic approximation. This analysis provides evidence for the existence of not only single CAME molecules but also CAME dimers and water complexes in the argon matrix. Furthermore, different conformational CAME isomers are identified, where conformational isomerism is triggered in experiments through UV irradiation. In contrast to earlier studies, this analysis allows explanation of almost every single band of the complex spectra in the range between 4000 and 600 cm⁻¹.

Riddles of the structure and vibrational dynamics of HO3 resolved near the ab initio limit

The hydridotrioxygen (HO₃) radical has been investigated in many previous theoretical and experimental studies over several decades, originally because of its possible relevance to the tropospheric HO_x cycle but more recently because of its fascinating chemical bonding, geometric structure, and vibrational dynamics. We have executed new, comprehensive research on this vexing molecule via focal point analyses (FPA) to approach the ab initio limit of optimized geometric structures, relative energies, complete quartic force fields, and the entire reaction path for cis-trans isomerization. High-order coupled cluster theory was applied through the CCSDT(Q) and even CCSDTQ(P) levels, and CBS extrapolations were performed using cc-pVXZ (X = 2-6) basis sets. The cis isomer proves to be higher than trans by 0.52 kcal mol^-1, but this energetic ordering is achieved only after the CCSDT(Q) milestone is reached; the barrier for cis → trans isomerization is a minute 0.27 kcal mol^-1. The FPA central r_e(O-O) bond length of trans-HO₃ is astonishingly long (1.670 Å), consistent with the semiexperimental r_e distance we extracted from microwave rotational constants of 10 isotopologues using FPA vibration-rotation interaction constants (α_i). The D₀(HO-O₂) dissociation energy converges to a mere 2.80 ± 0.25 kcal mol^-1. Contrary to expectation for such a weakly bound system, vibrational perturbation theory performs remarkably well with the FPA anharmonic force fields, even for the torsional fundamental near 130 cm^-1. Exact numerical procedures are applied to the potential energy function for the torsional reaction path to obtain energy levels, tunneling rates, and radiative lifetimes. The cis → trans isomerization occurs via tunneling with an inherent half-life of 1.4 × 10^-11 s and 8.6 × 10^-10 s for HO₃ and DO₃, respectively, thus resolving the mystery of why the cis species has not been observed in previous experiments executed in dissipative environments that allow collisional cooling of the trans-HO₃ product. In contrast, the pure ground eigenstate of the cis species in a vacuum is predicted to have a spontaneous radiative lifetime of about 1 h and 5 days for HO₃ and DO₃, respectively.

S–H rotamerizationviatunneling in a thiol form of thioacetamide

Rotamerization of the S–H groupviahydrogen tunneling is reported for the first time.

Conformational changes underlying variation in the structural dynamics of materials confined at the nanometric scale

Herein, it was shown that the equilibration phenomenon observed in Ben-IBU is related to thecis–translike conformational variation within the molecule induced most likely by the processes taken place at the interface.