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

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

Exploring epigenetic marks by analysis of noncovalent interactions

Producción CientíficaEpigenetic marks are modest chemical modifications on DNA and histone proteins that regulate the activation or silencing of genes through modulation of the intermolecular interactions between the DNA strands and the protein machinery. The process is complex and not always well understood. One of the systems studied in greater detail is the epigenetic mark on H3K9: lysine 9 of histone 3. The degree of methylation or acetylation of this histone is linked to silencing or activation of the corresponding gene, but it is not clear which effect each mark has in gene expression. We shed light on this particular methylation process by using density functional theory (DFT) calculations. First, we built a model consisting of a DNA double strand containing three base pairs and a sequence of three amino acids of the histone's tail. Then, we computed the modulation introduced into the intermolecular interactions by each epigenetic modification: from mono- to trimethylation and acetylation. The calculations show that whereas acetylation and trimethylation result in a reduction of the DNA-peptide interaction; non-, mono-, and dimethylation increase the intermolecular interactions. Such observations compare well with the findings reported in the literature, and highlight the correlation between the balance of intermolecular forces and biological properties, simultaneously advancing quantum-mechanical studies of large biochemical systems at molecular level through the use of DFT methods.Ministerio de Economía, Industria y Competitividad - Fondo Europeo de Desarrollo Regional (grants PGC2018-098561-B and UNLR-094E2C-225)Gobierno Vasco (grant IIT62-19

A combined spectroscopic and theoretical study of propofol center dot (h2o)(3)

Contains fulltext : 103321.pdf (publisher's version ) (Open Access

Molecular beam Fourier transform microwave spectrum of the dimethylether-xenon complex: tunnelling splitting and 131Xe quadrupole coupling constants

The rotational spectra of three isotopomers of the complex dimethyl ether–Xe (132Xe, 129Xe, 131Xe) have been measured by molecular beam Fourier transform microwave spectroscopy. An evenly spaced doubling of ca. 0.2 MHz, due to the internal rotation of the dimethyl ether subunit in the complex, has been observed for the lc-type transitions. The corresponding vibrational spacing, D01, has been determined to be 105(1) and 106(1) kHz for the 132Xe and 129Xe species, respectively. This datum has been useful to size the tunnelling barrier of Xe from above to below the COC plane. The nuclear quadrupole coupling constants of the 131Xe ðI ¼ 3=2Þ species have been precisely determined, vaa ¼ 4:57ð3Þ, vbb ¼ 2:93ð3Þ, and vcc ¼ 1:64ð3Þ MHz, respectively. These values indicate that the nuclear contributions to the field electric gradient at the Xe nucleus are smaller than the electronic ones

Bifurcated CH2•••O and (C-H)2•••F-C Weak Hydrogen Bonds: The Oxirane–Difluoromethane Complex

The oxirane-difluorometane molecular complex is stabilized by two bifurcated weak hydrogen bond, CH2×××O and CH2×××F. The binding energy of the complex has been estimated to be 9.6 kJ mol-1 from the DJ centrifugal distortion parameter

Conformational equilibrium of formanilide: detection of the pure rotational spectrum of the tunnelling cis conformer

Formanilide has been investigated by molecular beam Fourier transform microwave spectroscopy. The rotational spectra of two conformers, with the formyl hydrogen cis or trans with respect to the phenyl group have been measured. Their relative energy has been estimated to be 350150 cm1, the trans form being more stable. In the cis species the plane of the pseudo-peptidic group forms an angle of 34.7(5) (equilibrium value) with the ring. The two equivalent configurations, corresponding to the \ufe or \u2013 sign, are tunnelling through a barrier to planarity of 152(2) cm1