Conformational flexibility in hydrated sugars: the glycolaldehyde-water complex

Unravelling the structural features of monosaccharide glyceraldehyde upon mono-hydration by quantum chemistry and rotational spectroscopy

Water is a fundamental molecule for life, and investigating its interaction with monosaccharides is of great interest in order to understand its influence on their conformational behavior. In this study, we report on the conformational landscape of monosaccharide glyceraldehyde, the simplest aldose sugar, in the presence of a single water molecule in the gas phase. This investigation was performed using a combination of Fourier transform microwave spectroscopy and theoretical calculations. Out of the nine calculated conformers, only the lowest energy conformer was experimentally observed and characterized. Interestingly, the presence of water was found to induce structural features in the lowest energy conformer of the glyceraldehyde monomer, with water positioned between the alcohol groups. To analyze this interaction further, non-covalent interaction plots were employed to map the intermolecular interactions in the observed species. Additionally, natural bond orbital analysis was conducted to study the effects of charge transfer in the monohydrate system. Furthermore, topological analysis based on Bader's Atoms in Molecules theory was performed to gain insights into the observed complex. The results of all three analyses consistently showed the formation of relatively strong hydrogen bonds between water and glyceraldehyde, leading to the formation of a seven-member ring network.

Gas-phase hydration of nopinone: the interplay between theoretical methods and experiments unveils the conformational landscape

The structure of microsolvated nopinone formed in the supersonic jet expansion is investigated in the gas phase. The rotational spectra of nopinone(H₂O)_n (n = 1, 2, 3) were analysed by means of Fourier transform microwave spectroscopy. In the present study, three monohydrates, two dihydrates and two trihydrates were observed and characterized. The observed structures are the lowest energy conformers predicted by quantum chemical calculations. In all the observed hydrates of nopinone, water was found to be linked to the ketone group (C[double bond, length as m-dash]O) with a strong hydrogen bond (O_NOPH_W) and finishing with a dispersive one (O_WH_NOP). The structure of nopinone was found to alter the structure of water dimer and water trimer, which make nopinone be surrounded with a chain of water molecules. A remarkable decrease in the H-bonding length was observed when the number of attached water molecules is increased. Different DFT and ab initio calculations at the equilibrium structure allowed the identification of the observed conformers. Evaluation of the B3LYP-D3 and ωB97X-D results revealed deficiencies in reproducing the structure of one observed monohydrated structure while MP2 and M06-2X reproduce all the three observed structures. A comparison with similar bicyclic ketones highlights how a small change in the bicyclic ring leads to different effects in the microsolvation of biogenic VOCs. This study presents the first step of molecular aggregation to understand the atmospheric formation of aerosols at the molecular scale.

Steric effects on two inequivalent methyl internal rotations of 3,4-dimethylfluorobenzene

The microwave spectrum of 3,4-dimethylfluorobenzene was measured using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range from 2.0 to 26.5 GHz with the goal of quantifying steric effects on barriers to internal rotation of the two inequivalent methyl groups. Due to these torsional motions, splittings of all rotational transitions into quintets were observed and fitted with residuals close to measurement accuracy. The experimental work was supported by quantum chemical calculations, and the B3LYP-D3BJ/6-311++G(d,p) level of theory yielded accurate optimized geometry parameters to guide the assignment. The three-fold potential values of 456.20(13) cm^-1 and 489.78(15) cm^-1 for the methyl groups at the meta and para position, respectively, deduced from the experiments are compared with the predicted values and those of other toluene derivatives.

Conformational sampling and large amplitude motion of methyl valerate

The microwave spectrum of the fruit ester methyl valerate was recorded using two molecular jet Fourier transform spectrometers covering the frequency range from 2 to 40 GHz. Quantum chemical calculations yielded 11 minima for the anti ester configuration, among them two were identified in the experimental spectrum. The methyl group in the methoxy moiety undergoes internal rotation, leading to torsional splittings of all rotational transitions into doublets. The barrier to internal rotation of the methoxy methyl group was deduced to be 417.724(70) cm-1 and 418.059(27) cm-1 for the C1 and the Cs conformer, respectively, essentially the same values as those in methyl alkanoates with shorter alkyl chains, which are methyl acetate, methyl propionate and methyl butyrate. Geometry parameters such as the rotational and centrifugal distortion constants could be determined with very high accuracy. Optimisations at different levels of theory were performed for a comparison with the experimental results. The MP2/6-311++G(d,p) level of theory failed to calculate reliable rotational constants to guide the assigment of the C1 conformer, while the MP2/cc-pVDZ level fully succeeded.

Insights into the existing form of glycolaldehyde in methanol solution: an experimental and theoretical investigation

Glycolaldehyde (HOCH₂CHO, GA), the simplest molecule containing both hydroxyl and aldehyde groups, is structurally the most elementary member of the monosaccharide sugars, which may provide new clues for probing the origin of life on planets like the Earth.

Understanding (coupled) large amplitude motions: the interplay of microwave spectroscopy, spectral modeling, and quantum chemistry

A large variety of molecules contain large amplitude motions (LAMs), inter alia internal rotation and inversion tunneling, resulting in tunneling splittings in their rotational spectrum. We will present the modern strategy to study LAMs using a combination of molecular jet Fourier transform microwave spectroscopy, spectral modeling, and quantum chemical calculations to characterize such systems by the analysis of their rotational spectra. This interplay is particularly successful in decoding complex spectra revealing LAMs and providing reference data for fundamental physics, astrochemistry, atmospheric/environmental chemistry and analytics, or fundamental researches in physical chemistry. Addressing experimental key aspects, a brief presentation on the two most popular types of state-of-the-art Fourier transform microwave spectrometer technology, i.e., pulsed supersonic jet expansion–based spectrometers employing narrow-band pulse or broad-band chirp excitation, will be given first. Secondly, the use of quantum chemistry as a supporting tool for rotational spectroscopy will be discussed with emphasis on conformational analysis. Several computer codes for fitting rotational spectra exhibiting fine structure arising from LAMs are discussed with their advantages and drawbacks. Furthermore, a number of examples will provide an overview on the wealth of information that can be drawn from the rotational spectra, leading to new insights into the molecular structure and dynamics. The focus will be on the interpretation of potential barriers and how LAMs can act as sensors within molecules to help us understand the molecular behavior in the laboratory and nature.

Water Triggers Hydrogen-Bond-Network Reshaping in the Glycoaldehyde Dimer

Carbohydrates are ubiquitous biomolecules in nature. The vast majority of their biomolecular activity takes place in aqueous environments. Molecular reactivity and functionality are, therefore, often strongly influenced by not only interactions with equivalent counterparts, but also with the surrounding water molecules. Glycoaldehyde (Gly) represents a prototypical system to identify the relevant interactions and the balance that governs them. Here we present a broadband rotational‐spectroscopy study on the stepwise hydration of the Gly dimer with up to three water molecules. We reveal the preferred hydrogen‐bond networks formed when water molecules sequentially bond to the sugar dimer. We observe that the dimer structure and the hydrogen‐bond networks at play remarkably change upon the addition of just a single water molecule to the dimer. Further addition of water molecules does not significantly alter the observed hydrogen‐bond topologies.

VMS-ROT: A New Module of the Virtual Multifrequency Spectrometer for Simulation, Interpretation, and Fitting of Rotational Spectra

The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical-chemical properties "hidden" in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment. In the present work, we introduce VMS-ROT, a new module of VMS that has been specifically designed to deal with rotational spectroscopy. This module offers an integrated environment for the analysis of rotational spectra: from the assignment of spectral transitions to the refinement of spectroscopic parameters and the simulation of the spectrum. While bridging theoretical and experimental rotational spectroscopy, VMS-ROT is strongly integrated with quantum-chemical calculations, and it is composed of four independent, yet interacting units: (1) the computational engine for the calculation of the spectroscopic parameters that are employed as a starting point for guiding experiments and for the spectral interpretation, (2) the fitting-prediction engine for the refinement of the molecular parameters on the basis of the assigned transitions and the prediction of the rotational spectrum of the target molecule, (3) the GUI module that offers a powerful set of tools for a vis-à-vis comparison between experimental and simulated spectra, and (4) the new assignment tool for the assignment of experimental transitions in terms of quantum numbers upon comparison with the simulated ones. The implementation and the main features of VMS-ROT are presented, and the software is validated by means of selected test cases ranging from isolated molecules of different sizes to molecular complexes. VMS-ROT therefore offers an integrated environment for the analysis of the rotational spectra, with the innovative perspective of an intimate connection to quantum-chemical calculations that can be exploited at different levels of refinement, as an invaluable support and complement for experimental studies.

Gas-phase conformational preference of the smallest saccharide (glycolaldehyde) and its hydrated complexes with bridged hydrogen bonding

Glycoaldehyde (GA, HOCH₂CHO) is the simplest sugar unit of the carbohydrates and the only sugar to have been detected in interstellar space to date.

Rotational spectroscopy of the atmospheric photo-oxidation product o-toluic acid and its monohydrate

o-Toluic acid, a photo-oxidation product in the atmosphere, and its monohydrate were characterized in the gas phase by pure rotational spectroscopy. High-resolution spectra were measured in the range of 5-14 Hz using a cavity-based molecular beam Fourier-transform microwave spectrometer. Possible conformers were identified computationally, at the MP2/6-311++G(2df,2pd) level of theory. For both species, one conformer was identified experimentally, and no methyl internal rotation splittings were observed, indicative of relatively high barriers to rotation. In the monomer, rocking of the carboxylic acid group is a large amplitude motion, characterized by a symmetrical double-well potential. This and other low-lying out-of-plane vibrations contribute to a significant (methyl top-corrected) inertial defect (-1.09 amu Å(2)). In the monohydrate, wagging of the free hydrogen atom of water is a second large amplitude motion, so the average structure is planar. As a result, no c-type transitions were observed. Water tunneling splittings were not observed, because the water rotation coordinate is characterized by an asymmetrical double-well potential. Since the minima are not degenerate, tunneling is precluded. Furthermore, a concerted tunneling path involving simultaneous rotation of the water moiety and rocking of the carboxylic acid group is precluded, because the hilltop along this coordinate is a virtual, rather than a real, saddle-point. Inter- and intramolecular non-covalent bonding is discussed in terms of the quantum theory of atoms in molecules. The percentage of o-toluic acid hydrated in the atmosphere is estimated to be about 0.1% using statistical thermodynamics.

Molecular recognition in glycolaldehyde, the simplest sugar: two isolated hydrogen bonds win over one cooperative pair

Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C₂-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase.

Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.

A theoretical model study on the cyclic reaction of 4-hydroxybutanal catalyzed by Brønsted acid

For a theoretical model study on the cyclic reaction of 4-hydroxybutanal (4-OH-BL), we have examined five assumed reaction pathways (I–V) by performing the B3LYP calculations in the gas phase and self-consistent isodensity polarized continuum model (SCIPCM)-B3LYP calculations in aqueous solution. Pathways II (4-OH-BL + H+), III (4-OH-BL + H3O+), and IV (4-OH-BL + H3O+ + H2O) represent three models for the cyclic reaction catalyzed by Brønsted acids. The present study leads to the following conclusions concerning the five pathways (mainly on the basis of the calculation results in the solution). The high barrier along pathway I (with no catalyst) implies that the reaction does not occur without a catalyst, and the extremely large stabilization energy of the intermediate implies that pathway II is not a realistic model for the reaction catalyzed by Brønsted acid. Along pathway III, there are two intermediates and a transition state in between, and they are 10–16 kcal/mol lower in energy than the reactants (4-OH-BL + H3O+). Along pathway IV, there is only one intermediate, and it is 20.6 kcal/mol lower in energy than the reactants (4-OH-BL + H3O+ + H2O). Pathways III and IV are predicted to be feasible. Energetically, pathway IV is more favourable than pathway III and it is considered as a rational model for the cyclic reaction of 4-OH-BL catalyzed by Brønsted acid. Our calculations for pathway V (catalyzed by H2O) indicate that the water molecule may also serve as a catalyst for the cyclic reaction. The transition state along pathway V is 20.0 kcal/mol higher in energy than the reactants (4-OH-BL + H2O), and one can clearly see the “proton wire” in its structure. Our calculations show strong solvent effects on energetics of the charged intermediates along pathways II, III, and IV.