Frequency-comb-referenced molecular spectroscopy in the mid-infrared region

A simple method for absolute frequency measurements of molecular transitions in the mid-infrared region is reported. The method is based on a cw singly-resonant optical parametric oscillator (SRO), which is tunable from 3.2 to 3.45 µm. The mid- infrared frequency of the SRO is referenced to an optical frequency comb through its pump and signal beams. Sub-Doppler spectroscopy and absolute frequency measurement of the P(7) transition of the ν3 band of CH4 are demonstrated.

Single‐gate deep level transient spectroscopy technique

A new deep level transient spectroscopy technique is suggested which allows the deep level parameters to be obtained from a single temperature scan. Using large ratio t2/t1 of the measurement gate positions t1 and t2 and analyzing the steep high‐temperature side of the peak, it is demonstrated that the deep level activation energy can be determined with high accuracy.

Circular dichroism and 13C nuclear magnetic resonance spectroscopy of pennisetin from pearl millet

The conformation and stability of pearl millet prolamin (pennisetin) were examined by using circular dichroism and C-13 nuclear magnetic resonance spectroscopy. The far UV spectrum of pennisetin in 70% (v/v) aqueous ethanol showed the presence of predominant alpha-helical structure and its occurrence in the alpha + beta class of protein. The far and near UV spectra of pennisetin in ethanol: trifluoroethanol also supported this observation. However pennisetin showed the presence of some helical structure in 8 M urea which is known to be a highly unordered structure forming solvent. A decrease in alpha helical content of native pennisetin was observed with rise in temperature from 5-75-degrees-C and this effect of temperature was found to be reversible. A C-13 NMR spectrum of pennisetin in 70% ethanol suggested a high degree of molecular mobility in ethanol. Comparison of the cross polarization spectrum with the single pulse excitation spectrum suggested pennisetin to be a heterogeneous protein.

Ab initio molecular orbital calculations on ion-molecule and ion pair-molecule complexes of the water-lithium cyanide system

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets were performed on a series of ion-molecule and ion pair-molecule complexes for the H2O + LiCN system. Stabilisation energies (with counter-poise corrections), geometrical parameters, internal force constants and harmonic vibrational frequencies were evaluated for 16 structures of interest. Although the interaction energies are smaller, the geometries and relative stabilities of the monohydrated contact ion pair are reminiscent of those computed for the complexes of the individual ions. Thus, interaction of the oxygen lone pair with lithium leads to a highly stabilised C2v structure, while the coordination of water to the cyanide ion involves a slightly non-linear hydrogen bond. Symmetrical bifurcated structures are computed to be saddle points on the potential energy surface, and to have an imaginary frequency for the rocking mode of the water molecule. On optimisation the geometries of the solvent shared ion pair structures (e.g. Li+cdots, three dots, centered OH2cdots, three dots, centered CN−) revealed a proton transfer from the water molecule leading to hydrogen bonded forms such as Li-O-Hcdots, three dots, centered HCN. The variation in the force constants and harmonic frequencies in the various structures considered are discussed in terms of ion-molecular and ion pair-molecule interactions.

Pulsed NMR study of molecular motions and phase transitions in [N(CH3)4]PbX3 (X=Cl, Br, I)

Proton spin—lattice relaxation time (T1) is measured in [N(CH3)4]PbX3 (X=Cl, Br, I) from 300-77 K at 9.75 MHz. All the compounds show discontinuous changes in T1 values (at 256, 270 and 277 K, respectively), indicating phase transitions. Single T1 minimum is observed in all the cases and the T1 variation is explained in terms of [N(CH3)4] and CH3 group dynamics. The activation energy Eα decreases from chloride to iodide (from 4 to 2 kcal/mol). In bromide and iodide, T1 is found to decrease with increase in temperature at higher temperatures, indicating the presence of spin—rotation interaction.

Conformation of polymerizable diacetylenic lecithin, DC8,9PC, by 1H-NMR spectroscopy

Diacetylenic phospholipid, 1,2 bis-(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine (DC8,9PC), forms helices and tubules in addition to liposomes. The diacetylenic moiety responsible for the transformation is probed by 2-D NMR correlated spectroscopy. Chemical shift assignments and the analysis of 2D-COSY measurements were done on the lipid in chloroform-d solution. Based on this analysis, a model for the lipid is proposed. The geometry of the headgroup, glycerol backbone and acyl chains up to three methylenes from glycerol backbone [-(CH2)(3)-] is similar to that of dipalmitoyl phosphatidylcholine. The estimated torsional angle for methylene groups adjacent to diacetylenic moieties suggested an overall tilt of the diacetylenic lipid molecule from the bilayer axis of 25-30 degrees. This tilt could be negative or positive depending on the handedness of the resultant microstructures.

Probing Single and Bilayer Graphene Field Effect Transistors By Raman Spectroscopy

This article is a review of our work related to Raman studies of single layer and bilayer graphenes as a function Fermi level shift achieved by electrochemically top gating a field effect transistor. Combining the transport and in situ Raman studies of the field effect devices, a quantitative understanding is obtained of the phonon renormalization due to doping of graphene. Results are discussed in the light of time dependent perturbation theory, with electron phonon coupling parameter as an input from the density functional theory. It is seen that phonons near and Gamma and K points of the Brillouin zone are renormalized very differently by doping. Further, Gamma-phonon renormalization is different in bilayer graphene as compared to single layer, originating from their different electronic band structures near the zone boundary K-point. Thus Raman spectroscopy is not only a powerful probe to characterize the number of layers and their quality in a graphene sample, but also to quantitatively evaluate electron phonon coupling required to understand the performance of graphene devices.

Constructions of 2D-Metallamacrocycles Using Half-Sandwich Ru-2(II) Precursors: Synthesis, Molecular Structures, and Self-Selection for a Single Linkage Isomer

Coordination-driven self-assembly of oxalato-bridged half-sandwich p-cymene ruthenium complex Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)] (O3SCF3)(2) (1a) with several ditopic donors (L-a-L-d) in methanol affords a series of bi- and tetranuclear metallamacrocycles (2a and 3-5). Similarly, the combination of 2,5-dihydroxy-1,4-benzoquinonato (dhbq)-bridged binuclear complex Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) with a flexible bidentate amide linker (L-a) in 1:1 molar ratio gave the corresponding tetranuclear complex 2b. All the macrocycles were isolated as their triflate salts in high yields and were fully characterized by various spectroscopic techniques. Finally, the molecular structures of all the assemblies were determined unambiguously by single-crystal X-diffraction analysis. Interestingly, the combination of acceptor 1a or 1b with an unsymmetrical linear ditopic donor L-a results in a self-sorted linkage isomeric (head-to-tail) macrocycle (2a or 2b) despite the possibility of formation of two different isomeric macrocycles (head-to-head or head-to-tail) due to different connectivity of the donor. Molecular structures of the complexes 2a and 2b showed tetranuclear rectangular geometry with dimensions of 5.51 angstrom x 13.29 angstrom for 2a and 7.91 angstrom x 13.46 angstrom for 2b. In both cases, two binuclear Ru-2(II) building blocks are connected by a mu-N-(4-pyridyl)isonicotinamide donor in a head-to-tail fashion. Surprisingly, the macrocycle 2a loses one counteranion and cocrystallizes with monodeprotonated 1,3,5-trihydroxybenzene via strong intermolecular pi-pi stacking and hydrogen bonding. The tweezer complex 3 showed strong fluorescence in solution, and it showed fluorescence sensing toward nitroaromatic compounds. A fluorescence study demonstrated a marked quenching of the initial fluorescence intensity of the macrocycle 3 upon gradual addition of trinitrotoluene and exhibits significant fluorescence quenching response only for nitroaromatic compounds compared to various other aromatic compounds tested.

Prediction of nonlocal scaling parameter for armchair and zigzag single-walled carbon nanotubes based on molecular structural mechanics, nonlocal elasticity and wave propagation

Atomic vibration in the Carbon Nanotubes (CNTs) gives rise to non-local interactions. In this paper, an expression for the non-local scaling parameter is derived as a function of the geometric and electronic properties of the rolled graphene sheet in single-walled CNTs. A self-consistent method is developed for the linearization of the problem of ultrasonic wave propagation in CNTs. We show that (i) the general three-dimensional elastic problem leads to a single non-local scaling parameter (e(0)), (ii) e(0) is almost constant irrespective of chirality of CNT in the case of longitudinal wave propagation, (iii) e(0) is a linear function of diameter of CNT for the case of torsional mode of wave propagation, (iv) e(0) in the case of coupled longitudinal-torsional modes of wave propagation, is a function which exponentially converges to that of axial mode at large diameters and to torsional mode at smaller diameters. These results are valid in the long-wavelength limit. (C) 2011 Elsevier Ltd. All rights reserved.

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.

Structure of 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate by X-ray crystallography and F-19-NMR spectroscopy

2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate and its precursors were synthesized and characterized by H-1- and F-19-NMR spectroscopic methods and X-ray crystallography. These compounds are building blocks for the syntheses of the surfactants containing polyperfluoromethylene spacer. The molecule has extended all-trans conformation with molecular symmetry (1) over bar (C-i). There is a reasonably strong C-H ... O interaction in the crystal and there are two F ... F intermolecular contact distances less than the sum of van der Waals radii. (C) 1999 Elsevier Science B.V. All rights reserved.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Spin State Selective Excitation of Single Quantum Transitions Using Multiple Quantum Spectroscopy- an Aid to Analyse Complex Proton NMR spectra of Oriented Molecules

NMR spectra of molecules oriented in liquid-crystalline matrix provide information on the structure and orientation of the molecules. Thermotropic liquid crystals used as an orienting media result in the spectra of spins that are generally strongly coupled. The number of allowed transitions increases rapidly with the increase in the number of interacting spins. Furthermore, the number of single quantum transitions required for analysis is highly redundant. In the present study, we have demonstrated that it is possible to separate the subspectra of a homonuclear dipolar coupled spin system on the basis of the spin states of the coupled heteronuclei by multiple quantum (MQ)−single quantum (SQ) correlation experiments. This significantly reduces the number of redundant transitions, thereby simplifying the analysis of the complex spectrum. The methodology has been demonstrated on the doubly 13C labeled acetonitrile aligned in the liquid-crystal matrix and has been applied to analyze the complex spectrum of an oriented six spin system.

Time-Resolved Resonance Raman Spectroscopy: Exploring Reactive Intermediates

The study of reaction mechanisms involves systematic investigations of the correlation between structure, reactivity, and time. The challenge is to be able to observe the chemical changes undergone by reactants as they change into products via one or several intermediates such as electronic excited states (singlet and triplet), radicals, radical ions, carbocations, carbanions, carbenes, nitrenes, nitrinium ions, etc. The vast array of intermediates and timescales means there is no single ``do-it-all'' technique. The simultaneous advances in contemporary time-resolved Raman spectroscopic techniques and computational methods have done much towards visualizing molecular fingerprint snapshots of the reactive intermediates in the microsecond to femtosecond time domain. Raman spectroscopy and its sensitive counterpart resonance Raman spectroscopy have been well proven as means for determining molecular structure, chemical bonding, reactivity, and dynamics of short-lived intermediates in solution phase and are advantageous in comparison to commonly used time-resolved absorption and emission spectroscopy. Today time-resolved Raman spectroscopy is a mature technique; its development owes much to the advent of pulsed tunable lasers, highly efficient spectrometers, and high speed, highly sensitive multichannel detectors able to collect a complete spectrum. This review article will provide a brief chronological development of the experimental setup and demonstrate how experimentalists have conquered numerous challenges to obtain background-free (removing fluorescence), intense, and highly spectrally resolved Raman spectra in the nanosecond to microsecond (ns-mu s) and picosecond (ps) time domains and, perhaps surprisingly, laid the foundations for new techniques such as spatially offset Raman spectroscopy.