Determination of the sign of the order parameter from MAS spectra of oriented molecules

The use of the intensities of the spinning sidebands in the magic-angle spinning spectra of oriented molecules is proposed for the determination of the signs of the order parameters. The method is demonstrated for benzene and chloroform oriented in nematic phases of liquid crystals. On the basis of the theoretical expressions derived for the various order sidebands, the applicability of the method for different experimental conditions is discussed.

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Electronic absorption and emission spectroscopic investigations of the interaction of the fullerenes, C60 and C70, with amines and aromatic molecules

Electronic absorption spectroscopy and fluorescence spectroscopy have been used to investigate the interaction of the fullerenes C60 and C70 with diethylaniline, and with aromatic solvents such as benzene. C60 interacts weakly with aromatic amines in the ground state while C70 does not interact at all. Steady state fluorescence emission and lifetime measurements show that both C60 and C70 form excited state complexes (exciplexes) with the amines in non-aromatic solvents such as methylcyclohexane, but not in benzene. In benzene, only fluorescence quenching is observed due to the interaction between the π systems of the aromatic solvent and the fullerene in the ground state. This is also borne out by the systematic study of solvent effects on the absorption and emission spectra of the fullerenes.

Application of a modified z-cosy experiment for the analysis of spectra of oriented molecules - the spectrum of cis,cis-mucanonitrile

NMR spectra of cis,cis-mucanonitrile oriented in a liquid crystal have been analysed using the connectivity information obtained from a modified Z-COSY experiment which provided crucial clues for the starting parameters for the iterative analysis. The proton spectra with and without C-13 satellites and the C-13 spectra have thus been interpreted. The indirect spin-spin couplings required for the analyses have been obtained from the corresponding isotropic spectra. The H-1-H-1 and C-13-H-1 dipolar couplings so obtained have been utilized to determine the relative internuclear distances. The results indicate that the molecule is planar. (C) 1994 Academic Press, Inc.

Factors contributing to phantom bonds in inorganic molecules: Interpretations and predictions

The validity of various qualitative proposals for interpreting and predicting the existence of short contacts between formally non-bonded atoms, as in cyclodisiloxane and related inorganic ring systems, is critically evaluated. The models range from simple considerations of geometric constraints, lone pair repulsions and pi-complex formation to proposals such as the unsupported pi-bond model and the sigma-bridged-pi bond concept. It is pointed out that a unified description based on a combination of closed and open 3-centre 2-electron bonds is possible. The role of hybridisation is emphasized in the short phantom bond computed in an earlier model system. These insights are used to predict structures with exceptionally short Si..Si and B..B phantom bonds. The proposals are confirmed by ab initio calculations.

Use of L matrix to obtain reliable ab initio force constants of polyatomic molecules: ethylene as a test system

Direct use of experimental eigenvalues of the vibrational secular equation on to the ab initio predicted eigenvector space is suggested as a means of obtaining a reliable set of intramolecular force constants. This method which we have termed RECOVES (recovery in the eigenvector space) is computationally simple and free from arbitrariness. The RECOVES force constants, by definition, reproduce the experimental vibrational frequencies of the parent molecule exactly. The ab initio calculations were carried out for ethylene as a test molecule and the force constants obtained by the present procedure also correctly predict the vibrational frequencies of the deuterated species. The RECOVES force constants for ethylene are compared with those obtained by using the SQM procedure.

Evidence for supramolecular organization of alkane and surfactant molecules in the process of forming mesoporous silica

Investigations of the pore expansion in mesoporous silica in the presence of n-alkanes suggest a cooperative organization of the surfactant and alkane molecules, involving additivity of chain lengths.

New triquinane-based host molecules : binding with diamines

Synthesis of several shape-specific hosts through heteroaromatic annulation on cis,syn,cis-triquinanedione 1 and X-ray crystal structure determination of one of them, 4a, is reported. Preliminary results of complexation between cleft 5a and diamines are reported.

First-order hyperpolarizabilities of octupolar aromatic molecules: symmetrically substituted triazines

The first hyperpolarizabilities of some symmetrically substituted triazines have been measured and compared with those of the corresponding symmetrically substituted benzenes. The octupolar triazines have higher quadratic polarizabilities than the corresponding octupolar benzenes. The triazine ring seems to be a better central acceptor than the benzene ring, but if it acts as a donor as in sym-triphenyl triazine, the nonlinearity improves further.

The stretching of single poly-ubiquitin molecules: Static versus dynamic disorder in the non-exponential kinetics of chain unfolding

Static disorder has recently been implicated in the non-exponential kinetics of the unfolding of single molecules of poly-ubiquitin under a constant force Kuo, Garcia-Manyes, Li, Barel, Lu, Berne, Urbakh, Klafter, and Fernandez, Proc. Natl. Acad. Sci. U. S. A. 107, 11336 (2010)]. In the present paper, it is suggested that dynamic disorder may provide a plausible, alternative description of the experimental observations. This suggestion is made on the basis of a model in which the barrier to chain unfolding is assumed to be modulated by a control parameter r that evolves in a parabolic potential under the action of fractional Gaussian noise according to a generalized Langevin equation. The treatment of dynamic disorder within this model is pursued using Zwanzig's indirect approach to noise averaging Acc. Chem. Res. 23, 148 (1990)]. In conjunction with a self-consistent closure scheme developed by Wilemski and Fixman J. Chem. Phys. 58, 4009 (1973); ibid. 60, 866 (1974)], this approach eventually leads to an expression for the chain unfolding probability that can be made to fit the corresponding experimental data very closely. (C) 2011 American Institute of Physics.

Weak molecular complexes as studied by NMR spectroscopy of oriented molecules

Weak molecular interactions such as those in pyridine-iodine, benzene-iodine and benzene-chloroform systems oriented in thermotropic liquid crystals have been studied from the changes of the order parameters as a result of complex formation. The results indicate the formation of at least two types of charge transfer complexes in pyridine-iodine solutions. The pi-complexes in benzene-chloroform and benzene-iodine mixtures have also been detected. No detectable changes in the inter-proton distances in these systems were observed.

Molecular-dynamics studies of systems of confined dumbbell molecules

We present the results of molecular-dynamics simulations of systems of dumbbell molecules confined by parallel molecular walls. We have carried out systematic studies of three cases: freezing, steady flows, and stick-slip friction. We find that the molecular orientational degrees of freedom cause the surface layers to deviate from a planar configuration. Nevertheless, steady flows, in a channel as narrow as 15 molecular sizes, display continuum behavior. A range of mechanisms in the dynamics of the freezing of a confined fluid is found, as a function of the wall-fluid interactions and the bond length of the dumbbell molecules. The simple order-disorder transition associated with stick-slip motion in the presence of a layer of monoatomic lubricant molecules is supplanted by more complex behavior due to rotational degrees of freedom of the diatomic molecules.