An Accurate Molecular Structure of Phenyl, the Simplest Aryl Radical

Precise Equilibrium Structure of Benzene

Recent advances in gas-phase structure determination afford outstanding agreement between the CCSD(T)/cc-pCVTZ-corrected semi-experimental (reSE) equilibrium structures and their corresponding best theoretical estimates (BTEs) of the equilibrium structures (re) based upon corrections to the CCSD(T)/cc-pCV5Z geometries for the aromatic heterocycles pyrimidine and pyridazine. Herein, that same analysis is extended to the fundamental aromatic molecule benzene, using published experimental spectroscopic data for a total of 11 available isotopologues. The incorporation of rotational constants from all of these isotopologues and CCSD(T) corrections to address the impacts of both the vibration-rotation interaction and electron-mass distribution results in a highly precise and accurate reSE structure. The CCSD(T)/cc-pCV5Z optimized geometry has been further corrected to address a finite basis set, untreated electron correlation, relativistic effects, and a breakdown of the Born-Oppenheimer approximation. This analysis achieves outstanding agreement between the re (BTE) and reSE structural parameters of benzene to a highly satisfying level (0.0001 Å), an agreement that surpasses our recently published structures of the aforementioned nitrogen-substituted benzene analogues. The D6h geometry of benzene is now known to an unprecedented precision: RC-C = 1.3913 (1) Å and RC-H = 1.0809 (1) Å. The mutual agreement between theory and experiment presented in this work validates both, substantially resolving all discrepancies between the reSE and theoretical re structures available in the literature.

Coupled Cluster Characterization of 1-, 2-, and 3-Pyrrolyl: Parameters for Vibrational and Rotational Spectroscopy

Pyrrolyl (C₄H₄N) is a nitrogen-containing aromatic radical that is a derivative of pyrrole (C₄H₅N) and is an important intermediate in the combustion of biomass. It is also relevant for chemistry in Titan's atmosphere and may be present in the interstellar medium. The lowest-energy isomer, 1-pyrrolyl, has been involved in many experimental and theoretical studies of the N-H photodissociation of pyrrole, yet it has only been directly spectroscopically detected via electron paramagnetic resonance and through the photoelectron spectrum of the pyrrolide anion, yielding three vibrational frequencies. No direct measurements of 2- or 3-pyrrolyl have been made, and little information is known from theoretical calculations beyond their relative energies. Here, we present an ab initio quantum chemical characterization of the three pyrrolyl isomers at the CCSD(T) level of theory in their ground electronic states, with an emphasis on spectroscopic parameters relevant for vibrational and rotational spectroscopy. Equilibrium geometries were optimized at the CCSD(T)/cc-pwCVTZ level of theory, and the quadratic, cubic, and partial quartic force constants were evaluated at CCSD(T)/ANO0 for analysis using second-order vibrational perturbation theory to obtain harmonic and anharmonic vibrational frequencies. In addition, zero-point-corrected rotational constants, electronic spin-rotation tensors, and nuclear hyperfine tensors are calculated for rotational spectroscopy. Our computed structures and energies agree well with earlier density functional theory calculations, and spectroscopic parameters for 1-pyrrolyl are compared with the limited existing experimental data. Finally, we discuss strategies for detecting these radicals using rotational and vibrational spectroscopy on the basis of the calculated spectroscopic constants.

The formation of PBDFs from the ortho-disubstituted phenol precursors: A comprehensive theoretical study on the PBDD/Fs formation from 2,4,6-tribromophenol

Bromophenols are known as direct precursors of the notorious polybrominated dibenzo-p-dioxin/dibenzofurans (PBDD/Fs). There is a long-held viewpoint that only the more toxic dioxin-type products could be formed from the ortho-disubstituted phenols, totally contrary to the experimental observations that both PBDDs and PBDFs are generated. To tackle the issue, the gaseous formation mechanism of PBDD/Fs from 2,4,6-tribromophenol (TBP), a typical ortho-disubstituted phenol, was investigated in this study. Firstly, the reactions between TBP and the active H radical produce three key radical species including the bromophenoxyl radical, the substituted phenyl radical and phenoxyl diradical. The self- and cross-combinations of these radical species and TBP yield not only the dioxin-type products 1,3,6,8-TeBDD and 1,3,7,9-TeBDD, but also the brominated dibenzofurans 1,3,6,8-TeBDF and 2,4,6,8-TeBDF. Notably, the reactions involving the phenyl C sites in the substituted phenyl and phenoxyl diradicals are demonstrated to be both thermodynamically and kinetically more favorable than those involving the bromophenoxyl radical and the TBP molecule. Most importantly, the findings of the present work are of great importance as it provides feasible pathways to form less toxic dibenzofuran-type products from the ortho-disubstituted phenols. These results will improve the understanding of the PBDD/Fs formation mechanism from phenol precursors.

Theory meets experiment for elucidating the structure and stability of non-covalent complexes: water–amine interaction as a proof of concept

A joint experimental-theoretical spectroscopic investigation has focused on a better understanding of the nature of weak, non-covalent interactions in amine-water model systems.

The Hunt for Elusive Molecules: Insights from Joint Theoretical and Experimental Investigations

Rotational spectroscopy is an invaluable tool to unambiguously determine the molecular structure of a species, and sometimes even to establish its very existence. This article illustrates how experimental and theoretical state-of-the-art tools can be used in tandem to investigate the rotational structure of molecules, with particular emphasis on those that have long remained elusive. The examples of three emblematic species-gauche-butadiene, disilicon carbide, and germanium dicarbide-highlight the close, mutually beneficial interaction between high-level theoretical calculations and sensitive microwave measurements. Prospects to detect other elusive molecules of chemical and astronomical interest are discussed.

Steric and Electronic Effects of Electrochemically Generated Aryl Radicals on Grafting of the Graphite Surface

Grafting of aryl radicals generated by electrochemical reduction of aryldiazonium salts has been extensively studied on various surfaces. However, there exists two unclear aspects; the first one is the generality of the blocking ability of simple functional groups toward multilayer growth, and the second one is the electronic impact of substituent groups of aryl radicals on grafting efficiency. To address these aspects, we have studied the electrochemical functionalization of graphite using aryldiazonium salts having electron-donating or electron-withdrawing groups at the 3,4,5-positions. Atomic force microscopy investigation of the functionalized surfaces revealed the formation of monolayers for all aryldiazonium salts, and thus, nitro, carboxy, ester, methyl, and methoxy groups at the 3,4,5-positions of the benzene ring suppress polyaryl growth. The degree of grafting estimated by scanning tunneling microscopy imaging and Raman spectroscopy of the functionalized surfaces depends on the electronic state of the aryl radicals, in which the radicals with electron-donating groups show a high degree of functionalization, whereas those with electron-withdrawing groups exhibit a low degree of functionalization. We discuss several possibilities that affect grafting density. Though there are several factors, we hypothesize that one factor to explain the observed reactivity trend is the electronic property of the aryl radicals, namely, the relative position of the singly occupied molecular orbital energy levels of the aryl radicals with respect to the graphite Fermi energy level.

Theoretical study on the formation mechanism of polychlorinated dibenzothiophenes/thianthrenes from 2-chlorothiophenol molecules

Homogeneous formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs), sulfurated compounds analogous to polychlorinated dibenzo-p-dioxin/dibenzofurans (PCDD/Fs), has been well-documented to occur via radical-radical coupling reactions from chlorinated thiophenol precursors. However, the current understanding of the formation mechanism of PCDT/TAs is exclusively limited to the inherent point of view that chlorothiophenoxy radicals act as the only required intermediates for PCDT/TAs. This study investigates reaction pathways for the formation of PCDT/TAs involving two new types of radical species, i.e., substituted phenyl radicals and substituted thiophenoxyl diradicals. Taking 2-chlorothiophenol (2-CTP) as a model compound for chlorothiophenols, we found that apart from the mostly discussed chlorothiophenoxy radicals, substituted phenyl radicals and substituted thiophenoxyl diradicals could also be readily formed via the reaction of 2-CTP with H radicals. Furthermore, direct self- and cross-coupling of these radicals can result in the formation of PCDT/TAs, including 1-monochlorothianthrene (1-MCTA), 1,6-dichlorothianthrene (1,6-DCTA), 4,6-dichlorodibenzothiophene (4,6-DCDT) and 1,6-dichlorodibenzothiophene (1,6-DCDT). The pathways proposed in this work are proven to be both thermodynamically and kinetically favorable. Particularly, comparisons were made between the formation mechanisms of sulfurated and oxygenated dioxin systems from an energetic point view, showing that replacing oxygen with sulfur atoms greatly reduces the activation barriers of the rate-controlling steps involved in the PCDT/TA formation processes compared with those involved for PCDD/Fs. The calculated results in this work may improve our understanding of the formation mechanism of PCDT/TAs from chlorothiophenol precursors and should be informative to environmental scientists.

Can Carbamates Undergo Radical Oxidation in the Soil Environment? A Case Study on Carbaryl and Carbofuran

Radical oxidation of carbamate insecticides, namely carbaryl and carbofuran, was investigated with spectroscopic (electron paramagnetic resonance [EPR] and UV-vis) and theoretical (density functional theory [DFT] and ab initio orbital-optimized spin-component scaled MP2 [OO-SCS-MP2]) methods. The two carbamates were subjected to reaction with ^•OH, persistent DPPH^• and galvinoxyl radical, as well as indigenous radicals of humic acids. The influence of fulvic acids on carbamate oxidation was also tested. The results obtained with EPR and UV-vis spectroscopy indicate that carbamates can undergo direct reactions with various radical species, oxidizing themselves into radicals in the process. Hence, they are prone to participate in the prolongation step of the radical chain reactions occurring in the soil environment. Theoretical calculations revealed that from the thermodynamic point of view hydrogen atom transfer is the preferred mechanism in the reactions of the two carbamates with the radicals. The activity of carbofuran was determined experimentally (using pseudo-first-order kinetics) and theoretically to be noticeably higher in comparison with carbaryl and comparable with gallic acid. The findings of this study suggest that the radicals present in soil can play an important role in natural remediation mechanisms of carbamates.

Theoretical study on the formation mechanism of pre-intermediates for PXDD/Fs from 2-Bromophenol and 2-Chlorophenol precursors via radical/molecule reactions

This study investigates reaction pathways for the formation of pre-PXDD/F intermediates via a radical/molecule mechanism. Thermodynamic and kinetic parameters for the combination reactions of 2-bromophenol (2-BP) and 2-chlorophenol (2-CP) precursors with key radical species including the phenoxy radicals, the phenyl radicals and the phenoxyl diradicals were calculated in detail. The couplings of phenoxy radicals with 2-B(C)P tend to produce pre-PXDD intermediates of halogenated o-phenoxyphenol. The combinations of phenyl and phenoxyl diradicals with 2-B(C)P produce two types of structures, i.e., dihydroxybiphenyl and o-phenoxyphenyl, which exclusively act as prestructures of PXDFs. These condensation reactions, especially those involving the phenyl C atom sites in phenyl and phenoxyl diradicals, are proven to be both thermodynamically and kinetically favorable and are nearly comparable with the corresponding steps involved in the radical/radical reactions. Most importantly, reactions of phenyl and phenoxyl diradicals with halogenated phenols solely lead to the formation of PXDFs, which to some extent provides a plausible explanation for the high PXDF-to-PXDD ratios in the real environment. Therefore, our study reveals the pivotal role of the radical/molecule mechanism in homogeneous gas-phase PXDD/F formation, especially in PXDF formation. The present results fill in a knowledge gap that has hitherto existed regarding dioxin formation and improve our understanding of PXDD/F formation characteristics in the environment.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route

The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.