1. General introduction 2. The separation of nuclear and electronic motion 3. The electronic hamiltonian 4. Interactions arising from nuclear magnetic and electric moments 5. Angular momentum theory and spherical tensor algebra 6. Electronic and vibrational states 7. Derivation of the effective hamiltonian 8. Molecular beam magnetic and electric resonance 9. Microwave and far-infrared magnetic resonance 10. Pure rotational spectroscopy 11. Double resonance spectroscopy Appendices.

https://physicstoday.scitation.org/doi/pdf/10.1063/1.1878342

Rotational Spectroscopy of Diatomic Molecules

ConspectusThe carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly.These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found t...

http://pubs.acs.org/doi/pdf/10.1021/acs.accounts.7b00121

The n→π* Interaction

Terahertz biophotonics as a tool for studies of dielectric and spectral properties of biological tissues and liquids

Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.

/pdf/role-of-tautomerism-in-rna-biochemistry-4l65qfw4bz.pdf

Role of tautomerism in RNA biochemistry

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

The combination of Fourier transform microwave spectroscopy in a pulsed supersonic jet with laser ablation has made beta-alanine amenable to a structural study in the gas phase. Two new conformers of beta-alanine have been identified together with the two previously observed by McGlone and Godfrey [J. Am. Chem. Soc. 1995, 117, 1043]. The comparison between the experimental rotational and 14N nuclear quadrupole coupling constants and those calculated ab initio provide a definitive test for molecular structures and confirm unambiguously the identification of all conformers. For the two most abundant conformers, an intramolecular hydrogen bond between the amino group and carbonyl oxygen (N-H...O=C) is established, and the COOH adopts a cis-COOH configuration. The next conformer in order of abundance presents an O-H...N intramolecular hydrogen bond with a trans configuration for the COOH group. The high sensitivity of the experiment has allowed us to detect for the first time a conformer uniquely stabilized by an n-pi* hyperconjugative interaction between the nucleophile N: of the amino group and the pi* orbital at the carbonyl group. Partial conformational relaxation has been observed in the supersonic expansion.

The shape of beta-alanine.

The conformational preferences of the simplest amine neurotransmitter 2-phenylethylamine have been investigated using molecular beam Fourier transform microwave (MB-FTMW) spectroscopy. Two new conformers have been observed together with the two previously reported by Godfrey et al. [J. Am. Chem. Soc., 1995, 117, 8204]. The 14N nuclear quadrupole hyperfine structure has been resolved for all four conformers. Comparison of the experimental rotational and quadrupole coupling constants with those calculated theoretically provides a conclusive test for the identification of all conformers. The two most stable conformers present a gauche (folded) disposition of the alkyl-amine chain and are stabilised by a weak NH⋯π interaction between the amino group and the aromatic ring. The other two conformers show an anti (extended) arrangement of the alkyl-amine chain. Tunnelling splittings have been observed in the spectrum of one of the anti conformers. The post expansion relative abundances in the supersonic jet have been also investigated and related to the conformer energies.

/pdf/conformational-study-of-2-phenylethylamine-by-molecular-beam-41bcxymw1n.pdf

Conformational study of 2-phenylethylamine by molecular-beam Fourier transform microwave spectroscopy

The Fourier transform microwave spectra of the hydrated forms of the tautomeric pair 2-pyridinone/2-hydroxypyridine (2PO/2HP) have been investigated in a supersonic expansion. Three hydrated specie...

Tautomerism and microsolvation in 2-hydroxypyridine/2-pyridone.

Microwave spectroscopy has been applied to characterize the conformations adopted in the gas phase by a small peptide derived from alanine, N-acetyl-L-alaninamide (Ac-Ala-NH2). This compound was vaporized by laser ablation and shown to exist as a mixture of Ceq7 and C5 conformers stabilized by a CO⋯HN intramolecular hydrogen bond closing a seven- or a five-membered ring, respectively. The complicated quadrupole hyperfine structure originated from two 14N nuclei has been completely resolved for both species and the derived nuclear quadrupole coupling constants have been used to determine the Ramachandran angles that describe their molecular shapes.

The alanine model dipeptide Ac-Ala-NH2 exists as a mixture of Ceq7 and C5 conformers

The neutral form of the unnatural amino acid phenylglycine was vaporized by laser ablation, and the presence of two conformers was detected in a supersonic expansion by Fourier transform microwave spectroscopy. Both conformers were unequivocally identified by comparison of their experimental rotational and quadrupole coupling constants with those calculated ab initio. The most stable conformer is stabilized by intramolecular hydrogen bonds N-H...O=C, N-H...pi (with the closest C-C bond in the aromatic ring), and a cis-COOH interaction. The other conformer exhibits a O-H...N hydrogen bond between the hydrogen atom of the hydroxyl group and the lone pair at the nitrogen atom.

Vanessa Cortijo

Papers

The shape of beta-alanine.

Conformational study of 2-phenylethylamine by molecular-beam Fourier transform microwave spectroscopy

Tautomerism and microsolvation in 2-hydroxypyridine/2-pyridone.

The alanine model dipeptide Ac-Ala-NH2 exists as a mixture of Ceq7 and C5 conformers

The Conformers of Phenylglycine