Odorant Binding Proteins Facilitate the Gas-Phase Uptake of Odorants Through the Nasal Mucus

Mammalian odorant binding proteins (OBPs) have long been suggested to transport hydrophobic odorant molecules through the aqueous environment of the nasal mucus. While the function of OBPs as odorant transporters is supported by their hydrophobic beta-barrel structure, no rationale has been provided on why and how these proteins facilitate the uptake of odorants from the gas phase. Here, a multi-scale computational approach validated through available high-resolution spectroscopy experiments reveals that the conformational space explored by carvone inside the binding cavity of porcine OBP (pOBP) is much closer to the gas than the aqueous phase, and that pOBP effectively manages to transport odorants by lowering the free energy barrier of odorant uptake. Understanding such perireceptor events is crucial to fully unravel the molecular processes underlying the olfactory sense and move towards the development of protein-based biomimetic sensor units that can serve as artificial noses.

Exploring the conformational landscape through rotational spectroscopy and computational modelling: The tunneling dynamics in 2,6-diethylphenol

Phenol and some of its derivatives exhibit interesting tunneling motions consisting of two groups of transitions separated by a few hundred MHz. Recently, one of its derivatives, 2,6-di-tert-butylphenol, has shown additional hyperfine tunneling components, the origin of which remains unclear. In this work, another member of the family, 2,6-diethylphenol, has been investigated through its rotational spectrum. The jet-cooled broadband chirped-pulse Fourier transform microwave spectra in the 2-8 GHz frequency region revealed the presence of two conformers. The comparison with the equilibrium structure obtained by computational calculations at the B3LYP-D3(BJ)/Def2-TZVP level validates the structural determination and the orientation of the lateral ethyl groups. Additional observation of all the singly-substituted 13C isotopologues for the most stable ones allowed the determination of the substitution structure by means of the Kraitchman equations. Both conformers exhibited tunneling that was reproduced using an advanced 1D model, which provides an estimate of the barrier height for both conformers.

Binary conformers of a flexible, long-chain fluoroalcohol: dispersion controlled selectivity and relative abundances in a jet

The complex conformational panorama of binary 4,4,4-trifluoro-1-butanol (TFB) aggregates was investigated using chirped-pulse Fourier transform microwave spectroscopy, aided by conformational searches using CREST (Conformer-Rotamer Ensemble Sampling Tool) and quantum chemistry calculations. From nearly 1500 initial dimer geometries, 16 most stable binary candidates were obtained within a relative energy window of ∼4 kJ mol-1. Rotational spectra of five binary conformers were experimentally observed in supersonic expansion and assigned. Interestingly, three out of the five observed binary conformers are composed solely of monomer conformers, which were not observed in their isolated gas phase forms in jet expansion. In addition, an observed dimer that is made exclusively of the most stable TFB monomer subunits does not correspond to the global minimum. The intricate kinetically and thermodynamically controlled dimer formation mechanisms are discussed, and a modified kinetic-thermodynamic model was developed, providing conformational abundances that are in good agreement with the experiment. Subsequent non-covalent interaction analyses reveal that the observed conformers are held together by one primary O-H⋯O hydrogen bond and secondary intermolecular C-H⋯O, C-H⋯F, and/or O-H⋯F interactions, as well as C-H⋯H-C London dispersion interactions between the methylene groups. Further symmetry-adapted perturbation theory analyses of the TFB dimer conformers and related alcohol dimers reveal a considerable rise in dispersion contributions with increasing n-alkyl carbon chain length and highlight the role of dispersion interactions in preferentially stabilizing the global minimum of the TFB dimer.

The Structure of 2,6-Di-tert-butylphenol-Argon by Rotational Spectroscopy

The molecular structure of a van der Waals-bonded complex involving 2,6-di-tert-butylphenol and a single argon atom has been determined through rotational spectroscopy. The experimentally derived structural parameters were compared to the outcomes of quantum chemical calculations that can accurately account for dispersive interactions in the cluster. The findings revealed a π-bound configuration for the complex, with the argon atom engaging the aromatic ring. The microwave spectrum reveals both fine and hyperfine tunneling components. The main spectral doubling is evident as two distinct clusters of lines, with an approximate separation of 179 MHz, attributed to the torsional motion associated with the hydroxyl group. Additionally, each component of this doublet further splits into three components, each with separations measuring less than 1 MHz. Investigation into intramolecular dynamics using a one-dimensional flexible model suggests that the main tunneling phenomenon originates from equivalent positions of the hydroxyl group. A double-minimum potential function with a barrier of 1000 (100) cm-1 effectively describes this extensive amplitude motion. However, the three-fold fine structure, potentially linked to internal motions within the tert-butyl group, requires additional scrutiny for a comprehensive understanding.

Revealing Internal Rotation and 14N Nuclear Quadrupole Coupling in the Atmospheric Pollutant 4-Methyl-2-nitrophenol: Interplay of Microwave Spectroscopy and Quantum Chemical Calculations

The structure and interactions of oxygenated aromatic molecules are of atmospheric interest due to their toxicity and as precursors of aerosols. Here, we present the analysis of 4-methyl-2-nitrophenol (4MNP) using chirped pulse and Fabry-Pérot Fourier transform microwave spectroscopy in combination with quantum chemical calculations. The rotational, centrifugal distortion, and ¹⁴N nuclear quadrupole coupling constants of the lowest-energy conformer of 4MNP were determined as well as the barrier to methyl internal rotation. The latter has a value of 106.4456(8) cm^-1, significantly larger than those from related molecules with only one hydroxyl or nitro substituent in the same para or meta positions, respectively, as 4MNP. Our results serve as a basis to understand the interactions of 4MNP with atmospheric molecules and the influence of the electronic environment on methyl internal rotation barrier heights.

Hydrogen Bonding in the Dimer and Monohydrate of 2-Adamantanol: A Test Case for Dispersion-Corrected Density Functional Methods

Weakly-bound intermolecular clusters constitute reductionist physical models for non-covalent interactions. Here we report the observation of the monomer, the dimer and the monohydrate of 2-adamantanol, a secondary alcohol with a bulky ten-carbon aliphatic skeleton. The molecular species were generated in a supersonic jet expansion and characterized using broadband chirped-pulse microwave spectroscopy in the 2–8 GHz frequency region. Two different gauche-gauche O-H···O hydrogen-bonded isomers were observed for the dimer of 2-adamantanol, while a single isomer was observed for the monomer and the monohydrate. The experimental rotational parameters were compared with molecular orbital calculations using density functional theory (B3LYP-D3(BJ), B2PLYP-D3(BJ), CAM-B3LYP-D3(BJ), ωB97XD), additionally providing energetic and electron density characterization. The shallow potential energy surface makes the dimer an interesting case study to benchmark dispersion-corrected computational methods and conformational search procedures.

Torsional chirality and molecular recognition: the homo and heterochiral dimers of thenyl and furfuryl alcohol

Furfuryl alcohol and thenyl alcohol contain a labile torsional chiral center, producing transiently chiral enantiomers interconverting in the nanosecond time-scale. We explored chiral molecular recognition using the weakly-bound intermolecular dimers of both alcohols, freezing stereomutation. Supersonic jet broadband microwave spectroscopy revealed homo and heterochiral diastereoisomers for each alcohol dimer and the structural characteristics of the clusters. All dimers are primarily stabilized by a moderately intense O-H⋯O hydrogen bond, but differ in the secondary interactions, which introduce additional hydrogen bonds either to the ring oxygen in furfuryl alcohol or to the π ring system in thenyl alcohol. Density-functional calculations (B2PLYP-D3(BJ)/def2-TZVP) show no clear preferences for a particular stereochemistry in the dimers, with relative energies of the order 1-2 kJ mol^-1. The study suggests opportunities for the investigation of chiral recognition in molecules with torsional barriers in between transient and permanent interconversion regimes.

2,2,3,3,3-pentafluoro-1-propanol and its dimer: structural diversity, conformational conversion, and tunnelling motion

Rotational spectra of the 2,2,3,3,3-pentafluoro-1-propanol (PFP) were measured using cavity and chirped pulse Fourier transform microwave spectrometers. Of the nine possible PFP configurations which include four mirror-imaged pairs and an...

Rovibronic signatures of molecular aggregation in the gas phase: subtle homochirality trends in the dimer, trimer and tetramer of benzyl alcohol

Molecular aggregation is of paramount importance in many chemical processes, including those in living beings. Thus, characterization of the intermolecular interactions is an important step in its understanding. We describe here the aggregation of benzyl alcohol at the molecular level, a process governed by a delicate equilibrium between OH⋯O and OH⋯π hydrogen bonds and dispersive interactions. Using microwave, FTIR, Raman and mass-resolved double-resonance IR/UV spectroscopic techniques, we explored the cluster growth up to the tetramer and found a complex landscape, partly due to the appearance of multiple stereoisomers of very similar stability. Interestingly, a consistently homochiral synchronization of transiently chiral monomer conformers was observed during cluster growth to converge in the tetramer, where the fully homochiral species dominates the potential energy surface. The data on the aggregation of benzyl alcohol also constitute an excellent playground to fine-tune the parameters of the most advanced functionals.

Molecular Recognition, Transient Chirality and Sulfur Hydrogen Bonding in the Benzyl Mercaptan Dimer

The homodimers of transiently chiral molecules offer physical insight into the process of molecular recognition, the preference for homo or heterochiral aggregation and the nature of the non-covalent interactions stabilizing the adducts. We report the observation of the benzyl mercaptan dimer in the isolation conditions of a supersonic jet expansion, using broadband (chirped-pulse) microwave spectroscopy. A single homochiral isomer was observed for the dimer, stabilized by a cooperative sequence of S-H···S and S-H···π hydrogen bonds. The structural data, stabilization energies and energy decomposition describe these non-covalent interactions as weak and dispersion-controlled. A comparison is also provided with the benzyl alcohol dimer.

Structures and hydrogen bonding of 1,7-dioxaspiro[5.5]undecane and its hydrates

The conformations of 1,7DSU and its stepwise solvation by up to 5 water molecules were explored using supersonic-jet Fourier transform microwave spectroscopy with the supplement of theoretical calculations. Experimentally, the rotational spectra of the most stable structures of the monomer, monohydrate and dihydrate were observed and assigned. The characteristics of the stability and intermolecular interaction topologies of the 1,7DSU monomer and its hydrated clusters were obtained by CREST conformational sampling followed by B3LYP-D3(BJ)/def2-TZVP geometrical optimizations and MP2/aug-cc-pVTZ single-point energy calculations. The first water molecule links to the 1,7DSU monomer through an O_wH⋯O hydrogen bond. The water molecules tend to aggregate with each other and form cyclic structures for the n = 2-5 clusters. The interactions between water and the 1,7DSU monomer as well as those between water and water were revealed. The analyses of non-covalent interactions and the natural bond orbital suggest that the O_wH⋯O_1,7DSU, O_wH⋯O_w, and CH⋯O_w hydrogen bonds play a prominent role in structural stability.

Interaction topologies of the SO chalcogen bond: the conformational equilibrium of the cyclohexanolSO2 cluster

The conformational landscape of the cyclohexanolSO2 cluster was revealed in the gas phase using chirped-pulsed broadband rotational spectroscopy and quantum chemical calculations. Four isomers stabilized by a dominant SO chalcogen bond and cooperative C-HO[double bond, length as m-dash]S and O-HO[double bond, length as m-dash]S secondary weak hydrogen bonds were observed, with a near-parallel orientation of the S[double bond, length as m-dash]O and O-H bonds. Isomers formed by equatorial-gauche cyclohexanol are more stable than the isomers containing axial cyclohexanol. The multiple conformations of cyclohexanol and the versatile binding properties of SO2, simultaneously operating as nucleophile and electrophile through its π-holes and non-bonding electrons lead to a complex conformational behavior when the cluster is formed. The long (2.64-2.85 Å) attractive SO interaction between SO2 and cyclohexanol is mainly electrostatic and the contribution of charge transfer is obvious, with an NBO analysis suggesting that the strength of the SO interaction is nearly two orders of magnitude larger than the hydrogen bonds. This study provides molecular insights into the structural and energetic characteristics that determine the formation of pre-nucleation clusters between SO2 and a volatile organic compound like cyclohexanol.

Characterizing the lone pair⋯π–hole interaction in complexes of ammonia with perfluorinated arenes

Stronger and more flexible lone pair⋯π–hole interaction of ammonia with respect to water in complexes with perfluorinated arenes.