Isoenergetic Conformers Research Articles

Structures, vibrational frequencies, and infrared spectra of the hexa-hydrated benzene clusters

The water hexamer is known to have a number of isoenergetic structures. The first experimental identification of the O–H stretching vibrational spectra of the water hexamer was done in the presence of benzene. It was followed by the identification of the pure water hexamer structure by vibration-rotational tunneling (VRT) spectroscopy. Although both experiments seem to have located only the Cage structure, the structure of the benzene–water hexamer complex is not clearly known, and the effect of benzene in the water hexamer is unclear. In particular, it is not obvious how the energy difference between nearly isoenergetic water hexamer conformers changes in the presence of benzene. Thus, we have compared the benzene complexes with four low-lying isoenergetic water hexamers, Ring, Book, Cage, and Prism structures, using ab initio calculations. We also investigated the effects of the presence of benzene on the structures, harmonic vibrational frequencies, and infrared (IR) intensities for the four low-lying energy conformers. There is little change in the structure of the water hexamer upon its interaction with the benzene molecule. Hence the deformation energies are very small. The dominant contribution to the benzene–water cluster interaction mainly comes from the π–H interactions between benzene and a single water molecule. As a result of this π–H interaction, O–Hπ bond length increases and the corresponding stretching vibrational frequencies are redshifted. The IR spectral features of both (H2O)6 and benzene–(H2O)6 are quite similar. From both the energetics and the comparison of calculated and experimental spectra of the benzene–(H2O)6, the water structure in these complexes is found to have the Cage form. In particular, among the four different Cage structures, only one conformer matches the experimental O–H vibrational frequencies.

Structures, energies, vibrational spectra, and electronic properties of water monomer to decamer

The correlation of various properties of water clusters (H2O)n=1–10 to the cluster size has been investigated using extensive ab initio calculations. Since the transition from two dimensional (2-D) (from the dimer to pentamer) to 3-D structures (for clusters larger than the hexamer) is reflected in the hexamer region, the hexamer can exist in a number of isoenergetic conformers. The wide-ranging zero-point vibrational effects of the water clusters having dangling H atoms on the conformational stability by the O–H flapping or proton tunneling through a small barrier (∼0.5 kcal/mol) between two different orientations of each dangling H atom are not large (∼0.1) kcal/mol). Large dipole moments (>2.5 D) are found in the dimer and decamer, and significant dipole moments (∼2 D) are observed in the monomer, hexamer, and nonamer. The polarization per unit monomer rapidly increases with an increasing size of the cluster. However, this increase tapers down beyond the tetramer. The O–H vibrational frequencies serve as sensitive indicators of the status of proton donation (“d”) and acceptance (“a”) (i.e., the structural signature of H-bond type) for each water monomer in the cluster. In general, the magnitudes of the O–H frequencies (ν) for each cluster can be arranged in the following order: ν3da (single donor–single acceptor) ≅ν3daa (single donor–double acceptor) >ν3dda (double donor–single acceptor) >ν1dda>ν1da> (or ≅) ν1daa. The increase in the cluster size has a pronounced effect on the decrease of the lower frequencies. However, there are small changes in the higher frequencies (ν3da and ν3daa). The intensities of ν1daa and ν1da are very high, since the increased atomic charges can be correlated to the enhanced H-bond relay effect. On the other hand, the intensities of the ν1dda modes are diminished by more than half. Most of the above data have been compared to the available experimental data. Keeping in view the recent experimental reports of the HOH bending modes, we have also analyzed these modes, which show the following trend: ν2dda>ν2daa≅ν2da. The present study therefore would be useful in the assignments of the experimental O–H stretching and HOH bending modes.

Conformationally controlled p K-switching in membrane proteins: One more mechanism specific to the enzyme catalysis?

Internal proton displacements in several membrane photosynthetic enzymes are analyzed in relation to general mechanisms of enzymatic catalysis. In the bacterial photosynthetic reaction center (RC) and in bacteriorhodopsin (BR), carboxy residues (Glu-212 in the RC L-subunit and Asp-96 in BR) serve as indispensable intrinsic proton donors. Both carboxyls are protonated prior to the proton-donation step, because their p K values are shifted to ≥12.0 by the interaction with the protein and/or substrate. In both cases, the proton transfer reactions are preceded by conformational changes that, supposedly, let water interact with the carboxyls. These changes switch over the p K values of the carboxyls to ≤6.0 and 7.1 in the RC and BR, respectively. The sharp increase in the proton-donating ability of the carboxyls drives the reaction cycles. This kind of catalytic mechanism, where a strong general acid or base emerges, when needed, as a result of a conformational change can be denoted as a conformationally controlled p K-switching. Generally, the ability of enzymes to go between isoenergetic conformations that differ widely in the reactivity of the catalytic group(s) may be of crucial importance to the understanding of enzymatic catalysis. Particularly, the p K-switching concept could help to reconcile the contradictory views on the functional protonation state of the redox-active tyrosine Y Z in the oxygen-evolving photosystem II. It is conceivable that Y Z switches its p K from ∼4.5 to ≥10.0 upon the last, rate-limiting step of water oxidation. By turning into a strong base, tyrosine assists then in abstracting a proton from the bound substrate water and helps to drive the dioxygen formation.

Is Arginine Zwitterionic or Neutral in the Gas Phase? Results from IR Cavity Ringdown Spectroscopy

Is Arginine Zwitterionic or Neutral in the Gas Phase? Results from IR Cavity Ringdown Spectroscopy

The microwave spectrum and OH internal rotation dynamics of gauche-2,2,2-trifluoroethanol

The microwave spectra of CF3CH2OH and CF3CH2OD have been investigated from 5 to 26 GHz with a pulsed-nozzle Fourier-transform microwave spectrometer and from 26 to 42 GHz with an electric resonance optothermal spectrometer. Tunneling of the OH proton between the two isoenergetic gauche conformations splits the observed transitions into two tunneling components. An effective rotation-tunneling Hamiltonian is used to fit the aan both isotopomers to better than 5 and 13 kHz for the OH and OD forms, respectively. The tunneling splittings determined from the fits for the OH and OD isotopomers are 5868.6952(16) and 208.5037(42) MHz, respectively. A structural analysis using the moments of inertia of the OH and OD isotopomers determines that the hydroxyl hydrogen is directed toward the fluorine with a F...H separation of 2.561(1) Å and a dihedral angle of φ(CCOH)=68.97(6)°. The observed tunneling splittings are fit to a double-minimum potential, giving gauche–gauche tunneling barriers of 763 and 720 cm−1 and OH torsional fundamental frequencies of 364 and 271 cm−1 for CF3CH2OH and CF3CH2OD, respectively. The uncertainties shown in parentheses throughout the paper are one standard deviation.

Structural characterization of syndiotactic 1,2‐poly(4‐methyl‐1,3‐pentadiene)

Abstract4‐Methyl‐1,3‐pentadiene was polymerized with the MAO/CpTiCl3 (MAO: methyl‐aluminoxane, Cp: Cyclopentadienyl) system to yield a highly stereoregular syndiotactic 1,2‐polymer. Fiber diffraction patterns indicate two crystalline modifications: a major one with a repeat of 11.73 Å and minor amounts of a zig‐zag planar polymorph (axial repeat 5.05 Å). Energy calculations account for three nearly isoenergetic conformations: the more stable one, with repeat of 11.65Å, is (T6G2T2G2) analogous to the one recently reported for syndiotactic poly(propylene) (Chatani et al., 1991).

Ab initio studies of the conformations of methylamine and ethylenediamine: interaction forces affecting the structural stability

The structures and conformational energies of methylamine and ethylenediamine have been studied extensively with ab initio molecular orbital theory. For methylamine, there are good linear relationships among the C-N bond length, cosine of the H-C-N-H dihedral angle, and conformational energy. For ethylenediamine which has numerous multiminima, we studied the stereoelectronic effect, steric effect, intramolecular hydrogen bonding, repulsion between hydrogens, and repulsion between lone-pair electrons. The major factor determining the conformational stabilities of the multiminima is found to be the stereoelectronic effect. The partial hydrogen bonding, though weak, contributes to the structural stability so that two isoenergetic gauche conformers become the lowest energy structures

Counter-ion effects in cationic dyes: photophysics and photochemistry of a macrocyclic dimer of dimethylindocarbocyanine

The spectroscopic behavior of a series of salts, comprising a macrocyclic bis-cyanine dication ( 1) and various anions, was studied in hydrocarbon and ethanol solution. In benzene solution, the nature of the anion controls the properties of the cyanine. Molecular modeling reveals that there are two nearly isoenergetic conformations for 1. The calculations show that in benzene solution anions are positioned above and below the mean plane of 1. When the anion is small, for example trifluoroacetate, it does not perturb the structure of the cyanine. In contrast, when the anion is large, for example, tetrakis-perfluorophenyl borate, it distorts the structure of the cyanine and modifies its spectroscopic properties due to a change in excitonic interaction.

The Energy Landscapes and Motions of Proteins

Recent experiments, advances in theory, and analogies to other complex systems such as glasses and spin glasses yield insight into protein dynamics. The basis of the understanding is the observation that the energy landscape is complex: Proteins can assume a large number of nearly isoenergetic conformations (conformational substates). The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.

Conformational equilibria of the l-iduronate residue in non-sulphated di-, tetra- and hexa-saccharides and their alditols derived from dermatan sulphate

The conformation of the L-iduronate residue in non-sulphated di-, tetra- and hexa-saccharides and their alditol derivatives derived from rooster comb dermatan sulphate was investigated by 400 MHz 1H-n.m.r. spectroscopy. The ratio of conformational isomers is obtained by the average spin-spin coupling constants of a mixture of nearly isoenergetic conformers (1C4, 4C1 and 2S0). The non-reducing terminal L-iduronate residue in the tetrasaccharides (I-H-I-H and I-H-G-H) and their alditols (I-H-I-H-ol and I-H-G-H-ol) is in equilibrium with three conformers (1C4, 30%; 4C1, 40%; 2S0, 30%) of nearly equal population. Whereas the internal L-iduronate residue in the tetrasaccharides (I-H-I-H and G-H-I-H) exists as an equilibrium mixture of 1C4 (54%) and 2S0 (42-44%) conformers, that of their alditols (I-H-I-H-ol and G-H-I-H-ol) is in equilibrium between 2S0 conformer (66%) and 1C4 conformer (28%). The conformational population for the internal L-iduronate residue 2I in the hexasaccharide (3I-H-2I-H-1I-H) is also calculated and compared with that for the L-iduronate residue in native dermatan sulphate, which was calculated on the basis of the spin-spin coupling constants reported by Gatti, Casu, Torri & Vercellotti [(1979) Carbohydr. Res. 68, c3-c7].

Emission spectroscopy evidenvce for the existence of rotamers in solutions of trans-diarylethylenes and related compounds

A large variety of trans-1,2-diarylethylenes and 2,6-distyrl naphthalenes exhibit a pronounced variation in their emission spectra with the wavelength of excitation. (The aryl group can be phenyl, substituted phenyl, naphthyl, pyridyl, quinolyl, phenanthryl or anthryl.) The most reasonable working hypothesis seems to be that in solution these compounds exist as mixtures of two or three almost isoenergetic rotational conformers involving the quasi-single bonds. The conformers have slightly different absorption and emission spectra. Compounds in which such conformers cannot be postulated or are expected to be far from isoenergetic do not exhibit the phenomena. In some cases the modifications also differ in their emission decay times and emission yields and can be distinguished by time-resolved emission spectroscopy. We are not aware of the application of other physical methods to prove the existence of such conformers in these compounds.

Temperature dependence of photoisomerization. Part VIII. Excited-state behaviour of 1-naphthyl-2-phenyl- and 1,2-dinaphthyl-ethylenes and their photocyclisation products, and properties of the latter

The main deactivation pathways of excited trans-isomers of the title compounds in dilute solutions are fluorescence and trans→cis conversion, those of excited cis-isomers are cis→trans and cis→ DHP conversion (DHP = 4a,4b-dihydrophenanthrene derivative, the photocyclisation product) and fluorescence, while those of excited DHP are DHP →cis conversion and, in some cases, fluorescence. The quantum yields of fluorescence and of the photoconversions were measured as a function of temperature, in alicyclic and aliphatic hydrocarbon solvents. The relative contributions of these deactivation paths vary sharply with the temperature and the compound, in the above series. In all compounds trans→cis, cis→trans(with one exception), and cis→ DHP photoconversions are slowed down sharply at low temperatures, while DHP →cis is attenuated on cooling only in the 2-naphthyl derivatives. Only in these three compounds was DHP fluorescence observed. The critical increments calculated by an ‘Arrhenius treatment’ of the variation of these quantum yields with temperature amount to 2–10 kcal mol–1, and may indicate the existence of potential barriers on the way from the excited starting molecules to the final product. In the three 2-naphthyl derivatives, the ratio [trans]/[DHP] resulting from the reactions transâ†�cis*→ DHP was found to vary sharply with the wavelength of the exciting light (313,334, and 366 nm). This effect is explained as being due to selective excitation of the various more or less isoenergetic conformers of these compounds which exist in solution. Some of these conformers were observed to give rise to hitherto unknown types of DHPs and their oxidation products, again as a function of the wavelength of the exciting light. The structure of all DHPs formed via photocyclisation of the cis-isomers was proved, and their complete u.v. and visible absorption spectra determined, by dehydrogenation with atomic iodine to the corresponding benzo- or dibenzo-phenanthrenes. The proton n.m.r. spectrum of the DHPs derived from two dinaphthyl derivatives was determined, and signals were assigned to 4a-and 4b-H. Photodehydrogenation of DHPs involving excited DHP and ground-state oxygen or iodine was also observed. The thermal ring opening reaction DHP →cis was measured over a wide temperature range. The critical increments calculated therefrom were in the range 13–27 kcal mol–1.

A case of conformational isomorphism in polymers. The crystal structure of isotactic poly-(S)-3-methylpentene-1

Fibres of P(S) 3MP1 were studied by X-ray analysis. The polymer crystallizes in a tetragonal unit cell; a = b - 13·35 ± 0·10 A ̊ , c = 6·80 ± 0·05 A ̊ ; space group 14 1. The structure is described in terms of a statistical disorder of the optically active side groups, which assume randomly two different almost isoenergetic conformations. An unusual case of conformational isomorphism is involved, not previously found in polymer structures.

Conformational Flexibility of Choline Derivatives

CHOLINERGIC substrates have been found in a gauche conformation (G), skewed about the Cα–Cβ bond of the (CH3)3N+–CH2–CH2–O cholinic fragment in a number of crystal structures1–11. Sulphur and selenium isologues, on the other hand, with the (CH3)3N–CH2–CH2–(S,Se) group, are normally in the extended trans conformations (T)10,12,13. In agreement with the assumption that the reduced spectrum of biological activity of many rigid analogues and Cα or Cβ substituted derivatives of acetylcholine can be partially ascribed to the reduction in conformational flexibility14–17, a theoretical investigation18 predicted the existence of four almost isoenergetic conformations TTTT, TGTT, TTGT and TGGT about the ψ0, ψ1, ψ2 and ψ3 internal rotation angles schematically represented in Fig. 1.