Rotational spectrum and intramolecular hydrogen bonding in 1,2-butanedithiol

Producción CientíficaThe jet-cooled rotational spectrum of 1,2-butanedithiol was observed in the frequency region 2–8 GHz. Two conformers were detected for the molecule, corresponding to anti- and gauche-carbon molecular skeletons, both featuring a gauche arrangement of the two thiol groups. All 13C and 34S monosubstituted isotopologues were additionally assigned in natural abundance for the most stable anti isomer, while only the two 34S species were detected for the weaker gauche conformation. The structural analysis included ground-state effective structures, isotopic substitution coordinates, B3LYP-D3(BJ) density functional molecular orbital calculations and non-covalent interactions mapping with NCIPlot. The structural data confirm that the two thiol groups synchronize their orientation either parallel or antiparallel to support intramolecular S–H⋯S weak hydrogen bonding, reminiscent of the intramolecular hydrogen bond networks observed in adjacent alcohol groups. DFT calculations on 1,2-butanediol and 1,2-ethanedithiol offered structural comparisons with the title compound.MICIU-FEDER (grant PGC2018- 098561-B-C22) and JCyL (grant VA056G18

Water binding to the atmospheric oxidation product methyl vinyl ketone

Producción CientíficaMethyl vinyl ketone is one of the major oxidation products of isoprene, and therefore, an important precursor of secondary organic aerosol. Understanding its interactions with water is relevant to gain insight into aerosol formation and improve the predictive power of atmospheric chemistry models. The molecular complex formed between methyl vinyl ketone and water has been generated in a supersonic jet and characterized using high-resolution microwave spectroscopy in combination with quantum chemistry calculations. In this study, we show that methyl vinyl ketone interacts with water forming four 1:1 isomers connected by O − H···O and C − H···O hydrogen bond interactions. Water has been found to preferentially bind to the antiperiplanar conformation of methyl vinyl ketone. Evidence of a large amplitude motion arising from the methyl internal rotation has been found in the rotational spectra of the dimer. The threefold methyl internal rotation barrier heights have been further determined and discussed for all the species.Ministerio de Ciencia, Innovación y Universidades (grants PID2020-117925GA-I00 and PGC2018-098561-B-C22

Sulfur hydrogen bonding and internal dynamics in the monohydrates of thenyl mercaptan and thenyl alcohol

Producción CientíficaThe monohydrates of thenyl alcohol and thenyl mercaptan have been probed in a supersonic jet expansion using chirped-pulsed and Fabry-Perot Fourier-transform microwave spectroscopy. The rotational spectra revealed a single isomer for each of the dimers. The thenyl alcohol hydrate is stabilized by an O-H···Ow hydrogen bond between the alcohol and water, with water acting as proton acceptor and additionally engaging in a Ow-H···pi interaction with the thenyl ring. Conversely, water behaves as proton donor in the thenyl mercaptan hydrate, linking to the thiol group though a Ow-H···S hydrogen bond and secondary Ow-H··· interactions to the ring. In both dimers water retains internal mobility, as tunneling doublings in the spectrum confirm an internal rotation motion of water inside the cluster. The experimental results have been complemented with density-functional-theory molecular orbital calculations, binding energy decomposition and a topological analysis of the electronic density, providing a comparative description of the effects of hydrogen bonding of water to the alcohol and thiol groups in the dimers, relevant to understand hydrogen bonding to sulfur centers.MICINN-FEDER (PGC2018-098561- B-C22) and JCyL (grant VA056G18

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.This research was funded by the Spanish Ministerio de Ciencia e Innovación MICINN-FEDER, grants numbers PGC2018-098561-B-C21 and PGC2018-098561-B-C22. The APC were funded by PGC2018-098561-B-C22

Sulfur–arene interactions: the S⋯π and S–H⋯π interactions in the dimers of benzofuran⋯sulfur dioxide and benzofuran⋯hydrogen sulfide

Producción CientíficaNon-covalent interactions between sulfur centers and aromatic rings play important roles in biological chemistry. We examined here the sulfur–arene interactions between the fused aromatic heterocycle benzofuran and two prototype sulfur divalent triatomics (sulfur dioxide and hydrogen sulfide). The weakly-bound adducts were generated in a supersonic jet expansion and characterized with broadband (chirped-pulsed) time-domain microwave spectroscopy. The rotational spectrum confirmed the detection of a single isomer for both heterodimers, consistent with the computational predictions for the global minima. The benzofuran⋯sulfur dioxide dimer exhibits a stacked structure with sulfur closer to benzofuran, while in benzofuran⋯hydrogen sulfide the two S–H bonds are oriented towards the bicycle. These binding topologies are similar to the corresponding benzene adducts, but offer increased interaction energies. The stabilizing interactions are described as S⋯π or S–H⋯π, respectively, using a combination of density-functional theory calculations (dispersion corrected B3LYP and B2PLYP), natural bond orbital theory, energy decomposition and electronic density analysis methods. The two heterodimers present a larger dispersion component, but nearly balanced by electrostatic contributions.National Natural Science Foundation of China (No. 22273009)Ministerio de Ciencia e Innovación (MCIN-AEI) y FEDER (grant PID2021-125015NB-I00)FEDER - Junta de Castilla y León (grants INFRARED IR2021-UVa13 e IR2020-1-UVa02

Chirality-Puckering correlation and intermolecular interactions in Sphingosines: Rotational spectroscopy of jaspine B3 and its monohydrate

Producción CientíficaChirality is determinant for sphingosine biofunctions and pharmacological activity, yet the reasons for the biological chiral selection are not well understood. Here, we characterized the intra- and intermolecular interactions at the headgroup of the cytotoxic anhydrophytosphingosine jaspine B, revealing chirality-dependent correlations between the puckering of the ring core and the formation of amino-alcohol hydrogen bond networks, both in the monomer and the monohydrate. Following the specific synthesis of a shortened 3-carbon side-chain molecule, denoted jaspine B3, six different isomers were observed in a jet expansion using broadband (chirped-pulsed) rotational spectroscopy. Additionally, a single isomer of the jaspine B3 monohydrate was observed, revealing the insertion of water in between the hydroxy and amino groups and the formation of a network of O-H···N-H···Oring hydrogen bonds. The specific jaspine B3 stereochemistry thus creates a double-faced molecule where the exposed lone-pair electrons may easily catalyze the formation of intermolecular aggregates and determine the sphingosine biological properties.Ministerio de Ciencia, Innovación y Universidades - Fondo Europeo de Desarrollo Regional (grant PGC2018-098561-B-C22

π-Stacking Isomerism in Polycyclic Aromatic Hydrocarbons: The 2-Naphthalenethiol Dimer

Producción Científicaπ-Stacking is a common descriptor for face-to-face attractive forces between aromatic hydrocarbons. However, the physical origin of this interaction remains debatable. Here we examined π-stacking in a model homodimer formed by two thiol-substituted naphthalene rings. Two isomers of the 2-naphthalenethiol dimer were discovered using rotational spectroscopy, sharing a parallel-displaced crossed orientation and absence of thiol–thiol hydrogen bonds. One of the isomers presents C2 symmetry, structurally analogous to the global minimum of the naphthalene dimer. The experimental data were rationalized with molecular orbital calculations, revealing a shallow potential energy surface. Noncovalent interactions are dominated by dispersion forces according to SAPT energy decomposition. In addition, the reduced electronic density shows a diffuse and extended region of inter-ring interactions, compatible with the description of π-stacking as a competition between dispersion and Pauli repulsion forces

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

[EN]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 OHMIDLINE HORIZONTAL ELLIPSISO and OHMIDLINE HORIZONTAL ELLIPSIS pi 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.The Gottingen part of the project was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 271107160/SPP1807. We thank M. Lange and E. K. M. M. Sennert for the measurement of the FTIR spectrum and E. Meyer for help with the measurement of the Raman spectrum. Computational resources from the GWDG and the Gottingen Faculty of Chemistry (DFG - 405832858/INST 186/1294-1 FUGG) are acknowledged. We thank the Gottingen chemistry workshops for valuable support. This publication was supported financially by the Open Access Grant Program of the DFG and the Open Access Publication Fund of the University of Gottingen. The Bilbao and Valladolid groups acknowledge funding from the Spanish Ministerio de Ciencia e Innovacion (MICINN-FEDER PGC2018-098561-B-C21 and PGC2018-098561-B-C22). Bilbao's group also thank the SGIKER (UPV/EHU, MICIU-FEDER) for the computational and laser resources. The Hamburg part of this work was financially supported by the Deutsche Forschungsgemeinschaft (SCHN1280/4-2, project number 271359857) in the context of the priority program SPP 1807 "Control of London dispersion interactions in molecular chemistry". P. Pinacho would like to thank the Alexander von Humboldt Foundation for a postdoctoral fellowship

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

Interacciones no covalentes en agregados de tioles y modelos de asociación nucleósido-aminoácido

This thesis contains an experimental and computational investigation of non-covalent interactions in different thiol dimers and DNA-amino acid model complexes. The experiments used chirped-pulse broadband Fourier transform microwave spectroscopy in the cm-wave region (2-8 GHz), providing an accurate structural description of the target compounds. Several quantum mechanical methods including density-functional theory, energy decomposition by symmetry-adapted perturbation theory and topological analyses of the electronic density rationalized the experimental results. The studied thiol systems comprised the weakly-bound homodimers of thiophenol, benzyl mercaptan, 2-phenethyl mercaptan and 2-naphtalenethiol, which were generated in situ in the isolation conditions of a supersonic jet expansion. The thiol dimers were compared to their alcohol counterparts, offering insight into the electronic and structural characteristics of the non-covalent interactions to sulfur centers and, in particular, of the weak dispersive S-H···S hydrogen bond, seldom analysed in the gas phase. Additionally, several biologically relevant model clusters formed by nucleoside dimers and capped amino acids were investigated computationally, in order to improve our understanding of the DNA-amino acid interaction. These models illustrate the influence of sugar puckering in the amino acid conformation and the implication of the hydrogen bonds stabilizing the complexes. The results obtained in the thesis confirm the importance of the chemically specific reductionist approach and the benefits of a synergic combination of rotational data and computational calculations.Esta Tesis contiene una investigación experimental y computacional de interacciones no covalentes en diferentes dímeros de tioles y complejos modelo ADN-aminoácido. Los experimentos han utilizado espectroscopía de microondas de banda ancha con excitación multifrecuencia y transformación de Fourier en la región centimétrica (2-8 GHz). Los resultados experimentales se han racionalizado utilizando diversos métodos mecanocuánticos, incluyendo teoría del funcional de la densidad, descomposición energética por teoría de perturbaciones adaptada en simetría y análisis topológicos de la densidad electrónica. Los tioles estudiados han comprendido los homodímeros débilmente enlazados de tiofenol, bencil mercaptano, 2-fenetil mercaptano y 2-naftalenotiol, que fueron generados in situ bajo condiciones de aislamiento en una expansión de chorro supersónico. Los dímeros de tioles fueron comparados a sus análogos con alcoholes, ofreciendo información sobre las características electrónicas y estructurales de las interacciones no covalentes a grupos de azufre y, en particular, sobre las interacciones dispersivas débiles del enlace de hidrógeno S-H···S, raramente analizado en fase gas. Adicionalmente, se han investigado computacionalmente varios modelos de agregación de relevancia biológica, formados por dímeros de nucleósidos y aminoácidos modelo, con objeto de mejorar nuestro entendimiento de las interacciones ADN-aminoácido. Estos modelos ilustran la influencia del plegamiento de los azúcares en la conformación de los aminoácidos, y la implicación de los enlaces de hidrógeno que estabilizan los complejos. Los resultados obtenidos en la Tesis confirman la importancia de una aproximación reduccionista químicamente selectiva y los beneficios de una combinación sinérgica de datos rotacionales y cálculos computacionales.Departamento de Química Física y Química InorgánicaDoctorado en Químic