Photographic investigations in molecular spectroscopy

The determination of the energy levels and the probabilities of transition between them, by the formal analysis of observed electronic, vibrational, and rotational band structures, forms the direct goal of all investigations of molecular spectra, but the significance of such data lies in the possibility of relating them theoretically to more concrete properties of molecules and the radiation field. From the well developed electronic spectra of diatomic molecules, it has been possible, with the aid of the non-relativistic quantum mechanics, to obtain accurate moments of inertia, molecular potential functions, electronic structures, and detailed information concerning the coupling of spin and orbital angular monenta with the angular momentum of nuclear rotation. The silicon fluori1e molecule has been investigated in this laboratory, and is found to emit bands whose vibrational and rotational structures can be analyzed in this detailed fashion.

Like silicon fluoride, however, the great majority of diatomic molecules are formed only under the unusual conditions of electrical discharge, or in high temperature furnaces, so that although their spectra are of great theoretical interest, the chemist is eager to proceed to a study of polyatomic molecules, in the hope that their more practically interesting structures might also be determined with the accuracy and assurance which characterize the spectroscopic determinations of the constants of diatomic molecules. Some progress has been made in the determination of molecule potential functions from the vibrational term values deduced from Raman and infrared spectra, but in no case can the calculations be carried out with great generality, since the number of known term values is always small compared with the total number of potential constants in even so restricted a potential function as the simple quadratic type. For the determination of nuclear configurations and bond distances, however, a knowledge of the rotational terms is required. The spectra of about twelve of the simpler polyatomic molecules have been subjected to rotational analyses, and a number of bond distances are known with considerable accuracy, yet the number of molecules whose rotational fine structure has been resolved even with the most powerful instruments is small. Consequently, it was felt desirable to investigate the spectra of a number of other promising polyatomic molecules, with the purpose of carrying out complete rotational analyses of all resolvable bands, and ascertaining the value of the unresolved band envelopes in determining the structures of such molecules, in the cases in which resolution is no longer possible. Although many of the compounds investigated absorbed too feebly to be photographed under high dispersion with the present infrared sensitizations, the location and relative intensities of their bands, determined by low dispersion measurements, will be reported in the hope that these compounds may be reinvestigated in the future with improved techniques.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

I. Spectroscopic observation of discrete sites in simple liquids. II. Infrared intensity perturbations of hydrogen halide fundamentals in liquid xenon. III. Rotation of HCl in solid rare gases.

Part I

The spectrum of dissolved mercury atoms in simple liquids has been shown to be capable of revealing information concerning local structures in these liquids.

Part II

Infrared intensity perturbations in simple solutions have been shown to involve more detailed interaction than just dielectric polarization. No correlation has been found between frequency shifts and intensity enhancements.

Part III

Evidence for perturbed rotation of HCl in rare gas matrices has been found. The magnitude of the barrier to rotation is concluded to be of order of 30 cm^(-1).