Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

Unambiguous evidence for the engagement of CF3 group in N-H center dot center dot center dot F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional H-1, F-19, and natural abundant N-15 NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF3 groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, F-19-F-19 NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

Dramatic Structural Changes Resulting from the Loss of a Crucial Hydrogen Bond in the Hinge Region Involved in C-Terminal Helix Swapping in SurE: A Survival Protein from Salmonella typhimurium

Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two beta strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 angstrom and 2.35 angstrom resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2- H234 NE2 hydrogen bond (2.89 angstrom in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.

Estimation of the 2.0(5) helix type i -> i hydrogen bond energy at Aib*-Oxa motif: an isodesmic approach

Bending at the valence angle N-C-alpha-C' (tau) is a known control feature for attenuating the stability of the rare intramolecular hydrogen bonded pseudo five-membered ring C-5 structures, the so called 2.0(5) helices, at Aib. The competitive 3(10)-helical structures still predominate over the C5 structures at Aib for most values of tau. However at Aib*, a mimic of Aib where the carbonyl 0 of Aib is replaced with an imidate N (in 5,6-dihydro-4H-1,3-oxazine = Oxa), in the peptidomimic Piv-Pro-Aib*-Oxa (1), the C(5)i structure is persistent in both crystals and in solution. Here we show that the i -> i hydrogen bond energy is a more determinant control for the relative stability of the C5 structure and estimate its value to be 18.5 +/- 0.7 kJ/mol at Aib* in 1, through the computational isodesmic reaction approach, using two independent sets of theoretical isodesmic reactions. (C) 2014 Elsevier Ltd. All rights reserved.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor (I) is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate (I) as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric 0-H. ``.0 bonds R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the 0-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total (I) as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization (D(R), used previously to determine bond lengths. (C) 2015 AIP Publishing LLC.

Intramolecular hydrogen bond: Can it be part of the basis set of valence internal coordinates in normal mode analysis?

It has been shown earlier1] that the relaxed force constants (RFCs) could be used as a measure of bond strength only when the bonds form a part of the complete valence internal coordinates (VIC) basis. However, if the bond is not a part of the complete VIC basis, its RFC is not necessarily a measure of bond strength. Sometimes, it is possible to have a complete VIC basis that does not contain the intramolecular hydrogen bond (IMHB) as part of the basis. This means the RFC of IMHB is not necessarily a measure of bond strength. However, we know that IMHB is a weak bond and hence its RFC has to be a measure of bond strength. We resolve this problem of IMHB not being part of the complete basis by postulating `equivalent' basis sets where IMHB is part of the basis at least in one of the equivalent sets of VIC. As long as a given IMHB appears in one of the equivalent complete VIC basis sets, its RFC could be used as a measure of bond strength parameter.

Pattern formation and spatial solitons in bistable liquid-crystal microcavities

We report on spatial pattern formation, and appearances of 'optical bullet holes' in single-mode microcavities that are filled with liquid-crystals, when pumped above the cavity resonance frequency. These phenomena only occur beyond the bistability threshold. ©2002 Optical Society of America.

Wavelength-tuneable liquid crystal lasers from the visible to the near-infrared

The study of band-edge lasing from dye-doped chiral nematic liquid crystals has thus far been largely restricted to visible wavelengths. In this paper, a wide range of commercially available laser dyes are examined for their suitability as infrared emitters within a chiral nematic host. Problems such as poor solubility and reduced quantum efficiencies are overcome, and successful band-edge lasing is demonstrated within the range of 735-850 nm, using the dyes LD800, HITC-P and DOTC-P. This paper also reports on progress towards widely tuneable liquid crystal lasers, capable of emission in the region 460- 850 nm. Key to this is the use of common pump source, capable of simultaneously exciting all of the dyes (both infrared and visible) that are present within the system. Towards this aim, we successfully demonstrate near-infrared lasing (800 nm) facilitated by Förster energy transfer between the visible dye DCM, and the infra-red dye LD800, enabling pump wavelengths anywhere between 420 and 532 nm to be used. These results demonstrate that small and low-cost tuneable visible to near-infrared laser sources are achievable, using a single common pump source. Such devices are envisaged to have wide-ranging applications including medical imaging (including optical coherence tomography), point-of-care optical medical diagnostics (such as flow cytometry), telecommunications, and optical signatures for security coatings. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Wavelength-tuneable liquid crystal lasers from the visible to the near-infrared

The study of band-edge lasing from dye-doped chiral nematic liquid crystals has thus far been largely restricted to visible wavelengths. In this paper, a wide range of commercially available laser dyes are examined for their suitability as infrared emitters within a chiral nematic host. Problems such as poor solubility and reduced quantum efficiencies are overcome, and successful band-edge lasing is demonstrated within the range of 735-850 nm, using the dyes LD800, HITC-P and DOTC-P. This paper also reports on progress towards widely tuneable liquid crystal lasers, capable of emission in the region 460- 850 nm. Key to this is the use of common pump source, capable of simultaneously exciting all of the dyes (both infrared and visible) that are present within the system. Towards this aim, we successfully demonstrate near-infrared lasing (800 nm) facilitated by Förster energy transfer between the visible dye DCM, and the infra-red dye LD800, enabling pump wavelengths anywhere between 420 and 532 nm to be used. These results demonstrate that small and low-cost tuneable visible to near-infrared laser sources are achievable, using a single common pump source. Such devices are envisaged to have wide-ranging applications including medical imaging (including optical coherence tomography), point-of-care optical medical diagnostics (such as flow cytometry), telecommunications, and optical signatures for security coatings. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Threshold reduction in strained-layer InGaAs/GaAs quantum well lasers by liquid phase epitaxy regrowth

When liquid phase epitaxy regrowth at 780 degrees C for 2 h is applied to the samples after molecular beam epitaxy, a decrease of the threshold current density in strained InGaAs/GaAs quantum well lasers by a factor of 3 to 4 is obtained. We suggest that this improvement is attributed to the reduction of nonradiative centers associated with deep levels at the three regions of the active region, the graded layer and the cladding layer. Indeed, a significant reduction of deep center densities has been observed by using minority and majority carrier injection deep level transient spectroscopy measurements. (C) 1998 Elsevier Science B.V. All rights reserved.

Gas-phase Ion-molecular Reactions of C-60 and C-70 with Acetone and Quantum Chemistry Study

Gas-phase ion-molecular reactions of C-60 and C-70 with the ion system of acetone have been studied in this paper. The ions of protoned and acetylized C-60 and C-70 were formed by the reactions of C-60 and C-70 with some ions which existed in the ion system when mass spectrometer worked on chemical ionization conditions. The reactivity of C-70 is greater than that of C-60. Results of quantum chemical calculation for the adduct ions showed a sigma bond between the acyl carbon atom and C-60 may be Formed. These results will provide some valuable informations on the condense-phase acetylization of C-60.

THE CLEAVAGE REACTION OF THE MO-MO TRIPLE BOND - THE CRYSTAL-STRUCTURES OF MOLYBDENUM COMPLEXES [CPMO(CO)(2)(C(5)H(4)NS)], [CPMO(CO)(2)(C(9)H(6)NS)]O=PPH(3) AND [CPMO(CO)(2)(S(2)CNME(2)]

The reactions of [Cp2Mo2(CO)4] (1) with 2,2'-dipyridyl disulphide (C5H4NS-)2, 8,8'-diquinolyl disulphide (C9H6NS-)2 and tetramethyl thiuram disulphide (Me2NC(S)S-)2 in toluene solution resulted in the cleavage of the Mo-Mo triple bond to yield molybdenum complexes [CpMo(CO)2(C5H4NS)] (2), [CpMo(CO)2(C9H6NS)] (3) and [CpMo(CO)2(S2CNMe2)] (4), respectively. The molecular structures of 2, 3 . O=PPh3 and 4 were determined by X-ray diffraction studies. Crystals of 2 are monoclinic, space group P2(1)/n, with Z = 4, in a unit cell of dimensions a = 6.448(1), b = 12.616(2), c = 14.772(2) angstrom, beta = 92.85(1)-degrees. The structure was refined to R = 0.028 and R(w) = 0.039 for 1357 observed reflections. Crystals of 3 . O=PPh3 are triclinic, space group P1BAR, with Z = 2, in a unit cell of dimensions a = 11.351(3), b = 13.409(3), c = 9.895(2) angstrom, alpha = 94.59(2), beta = 90.35(2), gamma = 78.07(2)-degrees. The structure was refined to R = 0.033 and R(w) = 0.037 for 3260 observed reflections. Crystals of 4 are monoclinic, space group P2(1)/a and Z = 4 with a = 12.468(5), b = 7.637(2), c = 13.135(4) angstrom, beta = 96.62(3). The structure was refined to R = 0.032 and R(w) = 0.042 for 1698 observed reflections. Each of complexes 2-4 contains a cyclopentadienyl ligand, a cis pair of carbonyls and a chelate ligand (S,N donor or S,S donor). All the compounds have distorted square-pyramid structures.