We report on the noncovalent intermolecular interactions established between the polycyclic aromatic hydrocarbons phenanthrene and phenanthridine with water. Such noncovalent interactions involving ...extended aromatic systems and water molecules are ubiquitous in a variety of chemical and biological systems. Our study provides spectroscopic results on simple model systems to understand the impact that an extended aromatic surface and the presence of a heteroatom have on the nature of the noncovalent interactions established with the solvent. Microhydrated phenanthrene and phenanthridine clusters with up to three water molecules have been observed and unambiguously characterised by means of broadband rotational spectroscopy and quantum chemical calculations. The presence of a nitrogen atom in the backbone of phenanthridine remarkably affects the geometries of the water clusters and the interaction networks at play, with O-H N and C-H O interactions becoming preferred in the phenanthridine-water clusters over the O-H π interactions seen in the phenanthrene-water clusters. The presence of this heteroatom induces nuclear quadrupole coupling, which was used to understand the cooperativity effects found with increasing cluster size. Our results provide important insight to draw a more complete picture of the noncovalent interactions involving solvent molecules and aromatic systems larger than benzene, and they can be significant to enhance our understanding of the aromatic-polar interactions at play in a myriad of chemical and biological contexts.
The influence of a nitrogen atom in the backbone of a PAH was revealed by the hydrated clusters of phenanthrene and phenanthridine in a rotational spectroscopy study. Background image credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA) - ESA/Hubble Collaboration.
Abstract
The rotational spectrum of formamide
2
–H
2
O formed in a supersonic jet has been characterized by Fourier‐transform microwave spectroscopy. This adduct provides a simple model of ...water‐mediated interaction involving the amide linkages, as occur in protein folding or amide‐association processes, showing the interplay between self‐association and solvation. Mono‐substituted
13
C,
15
N,
18
O, and
2
H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three‐body sequential cycle. The two formamide molecules link on one side through an N−H⋅⋅⋅O hydrogen bond and on the other side through a water‐mediated interaction with the formation of C=O⋅⋅⋅H−O and O⋅⋅⋅H−N hydrogen bonds. The analysis of the quadrupole coupling effects of two
14
N‐nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C−N bond lengths with respect to pure formamide.
Examined here are the structures of complexes of benzophenone microsolvated with up to three water molecules by using broadband rotational spectroscopy and the cold conditions of a molecular jet. The ...analysis shows that the water molecules dock sideways on benzophenone for the water monomer and dimer moieties, and they move above one of the aromatic rings when the water cluster grows to the trimer. The rotational spectra shows that the water trimer moiety in the complex adopts an open‐loop arrangement. Ab initio calculations face a dilemma of identifying the global minimum between the open loop and the closed loop, which is only solved when zero‐point vibrational energy correction is applied. An OH⋅⋅⋅π bond and a Bürgi‐Dunitz interaction between benzophenone and the water trimer are present in the cluster. This work shows the subtle balance between water–water and water–solute interactions when the solute molecule offers several different anchor sites for water molecules.
The subtle discrepancy between the experimental and theoretical structures of the Ph2CO‐(H2O)3 complex has been unveiled. An open‐looped structure, instead of the cyclic structure, of the water trimer moiety above one of the π clouds was determined by rotational spectroscopy.
Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for ...molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality.
Structure of Butyl Carbamate and of Its Water Complex in the Gas Phase Pinacho, Pablo; López, Juan Carlos; Kisiel, Zbigniew ...
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
09/2019, Letnik:
123, Številka:
37
Journal Article
Recenzirano
Odprti dostop
The structure of butyl carbamate and of its complex with water generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. Up to 13 low-energy ...conformations of the monomer have been predicted that differ in the relative orientation of the butyl chain and the amide group. However, only three conformations have been observed experimentally. The remaining low-energy conformers are expected to interconvert into the observed rotamers through collisional relaxation processes in the supersonic jet. The values of the COCαCβ dihedral angle observed for the two most stable conformers of butyl carbamate, with extended configurations, can be directly correlated with the values of this angle in the two experimentally observed conformers of the shorter-chain molecule, ethyl carbamate. The less stable form shows a weak CH···OC intramolecular hydrogen bond from the terminal methyl group to the carbamate CO group, stabilizing a folded configuration. For the most stable butyl carbamate monomer the complex with one molecule of water has been observed. In that complex the water molecule attaches to the amide group in a cyclic arrangement using two hydrogen bonds. The results indicate that water does not substantially alter the conformational behavior of butyl carbamate.
We present a rotational spectroscopy study of alpha-methoxy phenylacetic acid in the gas phase. This acid is a derivative of mandelic acid and is used in various organic reactions. The conformational ...landscape of alpha-methoxy phenylacetic acid was explored to gain insight into its intramolecular dynamics. A rich rotational spectrum was obtained using chirped-pulse Fourier transform microwave spectroscopy in the 2-8 GHz range. Five conformers out of six calculated low-energy forms were identified in the spectrum, and the assignment of the
13
C singly substituted isotopologues for the lowest-energy conformer led to its accurate structure determination. Splitting patterns were analyzed and attributed to the internal rotation of a methyl top. The analysis of the non-covalent interactions within the molecule highlights the subtle balance in the stabilization of the different conformers. We thus provide high-level structural and intramolecular dynamics information that is also used to benchmark the performance of quantum-chemical calculations.
Five conformers of the flexible molecule alpha-methoxy phenylacetic acid were identified using rotational spectroscopy. The conformational landscape, internal dynamics, and intramolecular interactions were investigated.
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.
A multi-methodological investigation on the transiently chiral benzyl alcohol reveals a consistent preference for homochiral aggregation from the dimer to the tetramer.
Abstract
The initial stages of the gas‐phase nucleation between CO
2
and monoethanolamine were investigated via broadband rotational spectroscopy with the aid of extensive theoretical structure ...sampling. Sub‐nanometer‐scale aggregation patterns of monoethanolamine‐(CO
2
)
n
,
n
=1–4, were identified. An interesting competition between the monoethanolamine intramolecular hydrogen bond and the intermolecular interactions between monoethanolamine and CO
2
upon cluster growth was discovered, revealing an intriguing CO
2
binding priority to the hydroxyl group over the amine group. These findings are in sharp contrast to the general results for aqueous solutions. In the quinary complex, a cap‐like CO
2
tetramer was observed cooperatively surrounding the monoethanolamine. As the cluster approaches the critical size of new particle formation, the contribution of CO
2
self‐assembly to the overall stability increases.
The initial stages of the gas‐phase nucleation between CO2 and monoethanolamine were investigated via broadband rotational spectroscopy with the aid of extensive theoretical structure sampling. ...Sub‐nanometer‐scale aggregation patterns of monoethanolamine‐(CO2)n, n=1–4, were identified. An interesting competition between the monoethanolamine intramolecular hydrogen bond and the intermolecular interactions between monoethanolamine and CO2 upon cluster growth was discovered, revealing an intriguing CO2 binding priority to the hydroxyl group over the amine group. These findings are in sharp contrast to the general results for aqueous solutions. In the quinary complex, a cap‐like CO2 tetramer was observed cooperatively surrounding the monoethanolamine. As the cluster approaches the critical size of new particle formation, the contribution of CO2 self‐assembly to the overall stability increases.
How does CO2 interact with an alkanolamine in the gas phase? Using rotational spectroscopy, non‐reactive complexes monoethanolamine‐(CO2)n (where n=1–4) were characterized. It was discovered that CO2 has a binding priority to the hydroxyl group over the amine group. This is in sharp contrast to the general results observed in the solution phase.
We report the reinvestigation of the high-resolution rotational spectrum of estradiol. After removing the known spectral lines corresponding to three conformers of estradiol identified in the gas ...phase before, a large number of spectral lines remained unassigned in the spectrum. The observation of remaining lines is a common feature in spectra obtained by broadband rotational spectroscopy. In our reinvestigation, the detection of certain patterns resulted in two new sets of experimental rotational constants. Here we describe a systematic analysis, which together with quantum-chemical computations culminated in the assignment of two estrone conformers, namely exhibiting the
trans
- and the
cis
-arrangement of the hydroxy group attached to the rigid steroid backbone. Estrone and estradiol only differ in two atomic mass units, and they show a dynamic interconversion equilibrium under certain conditions, which might also have been the case in our experiments due to the heating temperature of 195 °C. The results illustrate the potential of high-resolution rotational spectroscopy to discern between structurally related molecules and to provide their gas-phase structures without information beforehand exploiting the benefit of having remaining unassigned rotational transitions in the spectrum.
New unassigned spectral lines were found in a reinvestigation of the rotational spectrum of estradiol-17β. Several possibilities were considered leading to the assignment of the transitions to the steroid molecule estrone, a precursor of estradiol.
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