IR cavity ringdown spectroscopy and density functional theory calculation of pyrrole-diethyl ketone clusters: impacts of carbon-chain flexibility on the diversity of N-H⋯OC hydrogen bonds.

Abstract

The N-H⋯OC hydrogen bond (H-bond) plays a key role in stabilizing the geometry and energy of biomolecules such as protein folding and DNA double strand. To investigate N-H⋯OC H-bonds in a microscopic view, we apply IR cavity ringdown spectroscopy (IR-CRDS) and density functional theory (DFT) calculation to pyrrole-diethyl ketone (Py-Dek) clusters in the gas phase. Dek exhibits a pentane carbon chain, which provides various conformations such as anti, gauche, and their mixtures. An introduction of the carbon-chain flexibility to Py-Dek clusters is expected to cause a diversity of the N-H⋯OC H-bond formation. In the observed IR spectra, there are seven prominent bands of the NH stretches due to Py-Dek clusters. These bands are classified into three groups: one for Py1-Dek1, two for Py1-Dek2, and four for Py2-Dek1. Stable structures and their harmonic frequencies obtained by DFT calculations provide the proper NH band assignments and appropriate cluster structures. Py1-Dek1 exhibits a single isomer, which is formed by an ordinary N-H⋯OC H-bond between Py and anti-conformation of Dek (Dek(a)) with a linear carbon-chain. Py1-Dek2 shows two isomeric structures, in which both isomers are commonly constructed by the N-H⋯OC H-bond for the first Dek and by the stacking interaction between π electrons of Py and the second Dek. Both isomers exhibit the Dek(a) for the stacking interaction, but are distinguished between Dek(a) and gauche-conformation Dek (Dek(g)) for the N-H⋯OC H-bond. Py2-Dek1 shows a triangular cyclic structure, which is formed by the N-H⋯OC H-bond, the N-H⋯π H-bond, and the stacking interaction between Py and Dek. The observed four bands are assigned to two N-H⋯OC and two N-H⋯π H-bonds for two isomeric structures due to Dek(a) and Dek(g). Not only smaller clusters but also higher hetero-tetramers are characterized based on the architecture of smaller clusters. In particular, Py2-Dek(a)2(I) was the first to be found with a highly symmetric (Ci) cyclic structure. Calculated potential energy surfaces of Py-Dek clusters shed light on the impact of Dek flexibility on N-H⋯OC H-bond diversity. Selective formation of isomeric structures for Py-Dek clusters is discussed in terms of a mechanism of a two- and three-body collision process in a supersonic expansion.