Effects of mixing between short-chain and branched-chain alcohols in protonated clusters

On the influence of solvent on the stereoselectivity of glycosylation reactions

Methodology development in carbohydrate chemistry entails the stereoselective formation of C-O bonds as a key step in the synthesis of oligo- and polysaccharides. The anomeric selectivity of a glycosylation reaction is affected by a multitude of parameters, such as the nature of the donor and acceptor, activator/promotor system, temperature and solvent. The influence of different solvents on the stereoselective outcome of glycosylation reactions employing thioglucopyranosides as glycosyl donors with a non-participating protecting group at position 2 has been studied. A large change in selectivity as a function of solvent was observed and a correlation between selectivity and the Kamlet-Taft solvent parameter π* was found. Furthermore, molecular modeling using density functional theory methodology was conducted to decipher the role of the solvent and possible reaction pathways were investigated.

Infrared spectroscopy and theoretical structure analyses of protonated fluoroalcohol clusters: the impact of fluorination on the hydrogen bond networks

To explore the impact of fluorination on the hydrogen bond networks of protonated alkylalcohols, infrared spectroscopy and theoretical computations of protonated 2,2,2-trifluoroethanol clusters, H⁺(TFE)_n, (n = 4-7), were performed. It has been demonstrated that the development of the hydrogen bond networks from a linear type to cyclic types occurs in this size region for the protonated alkylalcohol clusters. In contrast, infrared spectroscopy of H⁺(TFE)_n in the OH/CH stretch region clearly indicated that the linear type structures are held in the whole size range, irrespective of temperature of the clusters. The extensive stable isomer structure search of H⁺(TFE)_n based on our latest sampling approach supported the strong preference of the linear type hydrogen bond networks. Detailed analyses of the free OH stretching vibrational bands evidenced the intra- and intermolecular OH⋯FC interactions in the clusters. In addition, infrared spectra of protonated clusters of 2,2-difluoroethanol, 2,2-difluoropropanol, and 3,3,3-trifluoropropanol were measured for n = 4 and 5, and their spectra also indicated the effective inhibition of the cyclic hydrogen bond network formation by the fluorination.

Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning

We propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in ab initio methods to train a deep-learning machine learning (ML) model using SchNet.

How many methanol molecules effectively solvate an excess proton in the gas phase? Infrared spectroscopy of H+(methanol)n-benzene clusters

An excess proton in a hydrogen-bonded system enhances the strength of hydrogen bonds of the surrounding molecules. The extent of this influence can be a measure of the number of molecules effectively solvating the excess proton. Such extent in methanol has been discussed by the observation of the π-hydrogen-bonded OH stretch bands of the terminal sites of protonated methanol clusters, H⁺(methanol)_n, in benzene solutions, and it has been concluded that ∼8 molecules effectively solvate the excess proton (Stoyanov et al., Chem. Eur. J. 2008, 14, 3596-3604). In the present study, we performed infrared spectroscopy of H⁺(methanol)_n-benzene clusters in the gas phase. The cluster size and hydrogen-bonded network structure are identified by the tandem mass spectrometric technique and the comparison of the observed infrared spectra with density functional theory calculations. Though changes of the preferred hydrogen bond network type occur with the increase of cluster size in the gas phase clusters, the observed size dependence of the π-hydrogen bonded OH frequency agrees well with that in the benzene solutions. This means that the observations in both the gas and condensed phases catch the same physical essence of the excess proton solvation by methanol.

Structures of Pyridine-Water Clusters Studied with Infrared-Vacuum Ultraviolet Spectroscopy

The infrared (IR) spectra of the O-H stretching vibrations of pyridine-water clusters (Pyd)_m(H₂O)_n, with m, n = 1-4, have been investigated with infrared-vacuum ultraviolet (VUV) spectroscopy under a jet-cooled condition. The time-of-flight mass spectrum of (Pyd)_m(H₂O)_n⁺ by VUV ionization at ∼9 eV showed an unusual intensity pattern with very weak ion signals for m = 1 and 2 and stronger signals for m ≥ 3. This unusual mass pattern was explained by a drastic structural change of (Pyd)_m(H₂O)_n upon the VUV ionization, which was followed by the elimination of water molecules. Among the recorded IR spectra, only one spectrum monitored, (Pyd)₂⁺ cation, showed a well-resolved structure. The spectrum was analyzed by comparing with the simulated ones of possible stable isomers of (Pyd)₂(H₂O)_n, which were obtained with quantum-chemical calculations. Most of the calculated (Pyd)₂(H₂O)_n clusters had the characteristic structure in which H₂O or (H₂O)₂ forms a hydrogen-bonded bridge between two pyridines to form the π-stacked (Pyd)₂, and an additional H₂O molecule(s) extends the H-bonded network. The π-stacked (Pyd)₂(H₂O)_n moiety is very stable and is thought to exist as a local structure in a pyridine/water mixed solution. The Fermi resonance between the O-H stretch fundamentals and the overtones of the O-H bending vibrations in (Pyd)_m(H₂O)_n was found to be less pronounced in the case of (Pyd)_m(NH₃)_n studied previously.

Size of the hydrogen bond network in liquid methanol: a quantum cluster equilibrium model with extensive structure search

Studies have debated what is a favorable cluster size in liquid methanol. Applications of the quantum cluster equilibrium (QCE) model on a limited set of cluster structures have demonstrated the dominance of cyclic hexamers in liquid methanol. In this study, we examined the aforementioned question by integrating our implementation of QCE with a molecular-dynamics-based structural searching scheme. QCE simulations were performed using a database comprising extensively searched stable conformers of (MeOH)n for n = 2-14, which were optimized by B3LYP/6-31+G(d,p) with and without the dispersion correction. Our analysis indicated that an octamer structure can contribute significantly to cluster probability. By reoptimizing selected conformers with high probability at the MP2 level, we found that the aforementioned octamer became the dominant species due to favorable vibrational free energy, which was attributed to modes of intermolecular vibration.

IR-VUV spectroscopy of pyridine dimers, trimers and pyridine-ammonia complexes in a supersonic jet

The infrared spectra of the C-H stretching vibrations of (pyridine)m, m = 1-3, and the N-H stretching vibrations of (pyridine)m-(NH3)n, m = 1, 2; n = 1-4, complexes were investigated by infrared (IR)-vacuum ultraviolet (VUV) spectroscopy under jet-cooled conditions. The ionization potential (IP0) of the pyridine monomer was determined to be 74 546 cm-1 (9.242 eV), while its complexes showed only smooth curves of the ionization thresholds at ∼9 eV, indicating large structural changes in the ionic form. The pyridine monomer exhibits five main features with several satellite bands in the C-H stretching region at 3000-3200 cm-1. Anharmonic calculations including Fermi-resonance were carried out to analyze the candidates of the overtone and combination bands which can couple to the C-H stretching fundamentals. For (pyridine)2 and (pyridine)3, most C-H bands are blue-shifted by 3-5 cm-1 from those of the monomer. The structures revealed by random searching algorithms with density functional methods indicate that the π-stacked structure is most stable for (pyridine)2, while (pyridine)3 prefers the structures stabilized by dipole-dipole and C-Hπ interactions. For the (pyridine)m-(NH3)n complexes, the mass spectrum exhibited a wide range distribution of the complexes. The observed IR spectra in the N-H stretching vibrations of the complexes showed four main bands in the 3200-3450 cm-1 region. These features are very similar to those of (NH3)n complexes, and the bands are assigned to the anti-symmetric N-H stretching band (ν3), the symmetric N-H stretching (ν1) band, and the first overtone bands of the N-H bending vibrations (2ν4). The anharmonic calculations including the Fermi-resonance between ν1 and 2ν4 well reproduced the observed spectra.