Droplet Epitaxy of InN Quantum Dots on Si(111) by RF Plasma-Assisted Molecular Beam Epitaxy

InN quantum dots (QDs) were fabricated on Si(111) substrate by droplet epitaxy using an RF plasma-assisted MBE system. Variation of the growth parameters, such as growth temperature and deposition time, allowed us to control the characteristic size and density of the QDs. As the growth temperature was increased from 100 C to 300 degrees C, an enlargement of QD size and a drop in dot density were observed, which was led by the limitation of surface diffusion of adatoms with the limited thermal energy. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to assess the QDs size and density. The chemical bonding configurations of InN QDs were examined by X-ray photo-electron spectroscopy (XPS). Fourier transform infrared (FTIR) spectrum of the deposited InN QDs shows the presence of In-N bond. Temperature-dependent photoluminescence (PL) measurements showed that the emission peak energies of the InN QDs are sensitive to temperature and show a strong peak emission at 0.79 eV.

Conformations of synthetic alamethicin fragments. Evidence for 310 helical folding from 270-MHz hydrogen-1 nuclear magnetic resonance and circular dichroism studies

IH NMR studies at 270 MHz on the synthetic alamethicin fragments Z-Aib-Pro-Aib-Ala-Aib-Ala-OMe (1-6), Boc-Gln-Aib-Val-Aib-Gly-Leu-Aib-OMe (7-1 3), Boc-Leu-Aib-Pro-Val-Aib-OMe (1 2-16), and Boc-Gly-Leu- Aib-Pro-Val-Aib-OMe (1 1-16) have been carried out in CDC13 and (CD3)2S0. The intramolecularly hydrogen bonded amide hydrogens in these peptides have been delineated by using solvent titration experiments and temperature coefficientsof NH chemical shifts in (CD3)+30. All the peptides adopt highly folded structures, characterized by intramolecular 4 - 1 hydrogen bonds. The 1-6 fragment adopts a 310 helical conformation with four hydrogen bonds, in agreement with earlier studies (Rao, Ch. P., Nagaraj, R., Rao, C. N. R., & Balaram, P. (1980) Biochemistry 19, 425-4311. The 7-13

An infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptides

The ir-spectra in the N-H stretching region of Piv-Pro-NHMe and Boc-Pro-NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the N-H stretching bands, it has been shown that the characteristic N-H stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm-'. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the N-H stretching bands. The band around 3335 cm-* need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc-Leu-NHMe, which undergoes only intermolecular hydrogen bonding We have shown that 2-Aib-Aib-OMe and Z-Aib- Ala-OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.

N-H center dot center dot center dot F hydrogen bonds in fluorinated benzanilides: NMR and DFT study

Using F-19 and H-1-NMR (with N-14 decoupling) spectroscopic techniques together with density functional theoretical (DFT) calculations, we have investigated weak molecular interactions in isomeric fluorinated benzanilides. Simultaneous presence of through space nuclear spin-spin couplings ((1h)J(N-H center dot center dot center dot F)) of diverse strengths and feeble structural fluctuations are detected as a function of site specific substitution of fluorine atoms within the basic identical molecular framework. The transfer of hydrogen bonding interaction energies through space is established by perturbing their strengths and monitoring the effect on NMR parameters. Multiple quantum (MQ) excitation, up to the highest possible MQ orders of coupled protons, is utilized as a tool for accurate H-1 assignments. Results of NMR studies and DFT calculations are compared with the relevant structural parameters taken from single crystal X-ray diffraction studies.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Crystal and molecular structure of l-valyl-l-lysine hydrochloride

l-Valyl-l-lysine hydrochloride, C11N3O3H23 HCl, rystallizes in the monoclinic space group P2, with a = 5.438(5), b = 14.188(5), c = 9.521(5) Å, β= 95.38(2)° and Z = 2. The crystal structure, solved by direct methods, refined to R = 0.036, using full matrix least-squares method. The peptide exists in a zwitterionic form, with the N atom of the lysine side-chain protonated. The two γ-carbons of the valine side-chain have positional disorder, giving rise to two conformations, χ111= -67.3 and 65.9°, one of which (65.9°) is sterically less favourable and has been found to be less popular amongst residues branching at β-C. The lysine side-chain has the geometry of g− tgt, not seen in crystal structures of the dipeptides reported so far. Interestingly, χ32 (63.6°) of lysine side-chain has a gauche+ conformation unlike in most of the other tructures, where it is trans. The neighbouring peptide molecules are hydrogen bonded in a head-to-tail fashion, a rather uncommon interaction in lysine peptide structures. The structure shows considerable similarity with that of l-Lys-l-Val HO in conformational angles and H-bond interactions [4].

Crystal and molecular structure of sym-homospermidine monohydrate

Sym-homospermidine, [formula; see text] is a naturally occurring rare-polyamine found in relatively large concentration in sandal leaves. As part of our studies on structure and interactions of polyamines, ym-homospermidine was purified from sandal leaves and its structure was determined by single crystal X-ray diffraction technique. The phosphate salt of the molecule crystallized in the triclinic space group P1- with a = 8.246(1)A, b = 8.775(1)A, c = 15.531(2)A, alpha = 74.20(1) degrees, beta = 88.36(1) degrees and gamma = 65.41(1) degrees. The structure was determined by direct methods and refined to a final R factor of 5.4% for 2087 reflections with magnitude of F(obs) greater than 5 sigma [F(obs)]. The amine exists in its most favourable all trans conformation. For each amine molecule three phosphate groups exist in the crystal structure, suggesting that two of the oxygens of each phosphate group are protonated. There is also a single water molecule in the asymmetric unit in contrast to that of spermidine phosphate which has 3 water molecules. These differences probably reflect the hydrogen bonding properties of mono-ionic and di-ionic phosphate groups. The structure is predominantly stabilized by a network of hydrogen bonds.

C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

The serendipitous observation of a C–Hcdots, three dots, centeredO hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).

Probing the role of the C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val- (D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all L analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed a-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-(HO)-O-... hydrogen bond between residue 4 (CH)-H-alpha and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C-alpha atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt at conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-(HO)-O-... hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

Reactivity Of Pph3 Toward Ruiiruiiicl(O2car)4 - Syntheses, Molecular-Structures, And Spectroscopic And Electrochemical Properties Of Ruiiruiii(Oh2)Cl(Mecn)(O2car)4(Pph3)2 And Ruii2(Oh2)(Mecn)2(O2car)4(Pph3)2

By the reaction of Ru2Cl(O2CAr)4 (1) and PPh3 in MeCN-H2O the diruthenium(II,III) and diruthenium(II) compounds of the type Ru2(OH2)Cl(MeCN)(O2CAr)4(PPh3)2 (2) and Ru2(OH2)(MeCN)2(O2CAr)4(PPh3)2 (3) were prepared and characterized by analytical, spectral, and electrochemical data (Ar is an aryl group, C6H4-p-X; X = H, OMe, Me, Cl, NO2). The molecular structure of Ru2(OH2)Cl(MeCN)(O2CC6H4-p-OMe)4(PPh3)2 was determined by X-ray crystallography. Crystal data are as follows: triclinic, P1BAR, a = 13.538 (5) angstrom, b = 15.650 (4) angstrom, c = 18.287 (7) angstrom, alpha = 101.39 (3)-degrees, beta = 105.99 (4)-degrees, gamma = 97.94 (3)-degrees, V = 3574 angstrom 3, Z = 2. The molecule is asymmetric, and the two ruthenium centers are clearly distinguishable. The Ru(III)-Ru(II), Ru(III)-(mu-OH2), and Ru(II)-(mu-OH2) distances and the Ru-(mu-OH2)-Ru angle in [{Ru(III)Cl(eta-1-O2CC6H4-p-OMe)(PPh3)}(mu-OH2)(mu-O2CC6H4-p-OMe)2{Ru(II)(MeCN)(eta-1-O2CC6H4-p-OMe)(PPh3)}] are 3.604 (1), 2.127 (8), and 2.141 (10) angstrom and 115.2 (5)-degrees, respectively. The compounds are paramagnetic and exhibit axial EPR spectra in the polycrystalline form. An intervalence transfer (IT) transition is observed in the range 900-960 nm in chloroform in these class II type trapped mixed-valence species 2. Compound 2 displays metal-centered one-electron reduction and oxidation processes near -0.4 and +0.6 V (vs SCE), respectively in CH2Cl2-TBAP. Compound 2 is unstable in solution phase and disproportionates to (mu-aquo)diruthenium(II) and (mu-oxo)diruthenium(III) complexes. The mechanistic aspects of the core conversion are discussed. The molecular structure of a diruthenium(II) compound, Ru2(OH2)(MeCN)2(O2CC6H4-p-NO2)4(PPh3)2.1.5CH2Cl2, was obtained by X-ray crystallography. The compound crystallizes in the space group P2(1)/c with a = 23.472 (6) angstrom, b = 14.303 (3) angstrom, c = 23.256 (7) angstrom, beta = 101.69 (2)-degrees, V = 7645 angstrom 3, and Z = 4. The Ru(II)-Ru(II) and two Ru(II)-(mu-OH2) distances and the Ru(II)-(mu-OH2)-Ru(II) angle in [{(PPh3)-(MeCN)(eta-1-O2CC6H4-p-NO2)Ru}2(mu-OH2)(mu-O2CC6H4-p-NO2)2] are 3.712 (1), 2.173 (9), and 2.162 (9) angstrom and 117.8 (4)-degrees, respectively. In both diruthenium(II,III) and diruthenium(II) compounds, each metal center has three facial ligands of varying pi-acidity and the aquo bridges are strongly hydrogen bonded with the eta-1-carboxylato facial ligands. The diruthenium(II) compounds are diamagnetic and exhibit characteristic H-1 NMR spectra in CDCl3. These compounds display two metal-centered one-electron oxidations near +0.3 and +1.0 V (vs SCE) in CH2Cl2-TBAP. The overall reaction between 1 and PPh3 in MeCN-H2O through the intermediacy of 2 is of the disproportionation type. The significant role of facial as well as bridging ligands in stabilizing the core structures is observed from electrochemical studies.

Structure of valinomycin by molecular dynamics studies

Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.

Ruthenium-Oxygen Coordination-Driven Self-Assembly of a Ru-8(II) Incomplete Prism: Synthesis, Structure, and Shape-Selective Molecular Recognition Study

Coordination-driven self-assembly of 1,3,5-benzenetricarboxylate (tma; 1) and oxalato-bridged p-cymeneruthenium(II) building block Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (2) affords an unusual octanuclear incomplete prism Ru-8(eta(6)-p-cymene)(8)(tma)(2)(mu-eta(4)-C2O4)(2)(OMe)(4)](O3SCF3)( 2) (3), which exhibits a remarkable shape-selective binding affinity for neutral phenolic compounds via hydrogen-bonding interactions (p-cymene = p-(PrC6H4Me)-Pr-i). Such a binding was confirmed by single-crystal X-ray diffraction analysis using 1,3,5-trihydroxybenzene as an analyte.

Stereochemical studies on cyclic peptides. Part XI. Conformation of cyclic pentapeptides having intramolecular 3 leads to 1 hydrogen bonds.

Conformational analysis of cyclic pentapeptides having two intra-ring 3 leads to 1 hydrogen bonds has been carried out. It is found that the structure can easily be formed with trans planar peptide units without causing significant angular strain at the alpha-carbon atoms. Four different types of conformations designated Types I--IV are possible for the backbone structure. Details of these four types of conformations and also the accommodating possibility of these types for allglycyl and all-alanyl residues are presented. Three of the four types have relatively low energies for glycyl residues whereas the other one has a slightly higher energy. When alanyl residues are introduced at the five alpha-carbon atoms, the types that are energetically favourable depend upon the sequence of isomers. Energy calculations have also been carried out for the combinations of glycyl, L- and D-alanyl residues. The theoretical results are compared with available experimental observations both from solution and solid state studies.