Structural characterization of backbone-expanded helices in hybrid peptides: (αγ) n and (αβ) n sequences with unconstrained β and γ homologues of L-Val

Learning your αβγ's: The diversity of hydrogen-bonding patterns in backbone-expanded hybrid helices is shown by crystal-structure determination of several oligomeric peptides (see scheme; C=gray; H=white; O=red; N=blue). C 12 helices were observed in the αγ peptide series for n=2-8. In comparison, the αα peptide and αβ peptide sequences show C 10 and mixed C 14/C 15 helices, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular probe dynamics reveals suppression of ice-like regions in strongly confined supercooled water

The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448-11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed.

Synthesis and supramolecular assembly of the bifunctional borinic acid 1,2-fcB(OH)](2)

Treatment of the chloro-substituted diboradiferrocene derivative 1 with Me3SiOMe and subsequent hydrolysis resulted in formation of the novel organometallic bis(borinic acid) derivative 3. The assembly of 3 into supramolecular structures via hydrogen bonding and reversible covalent boron-oxygen bond formation was explored. Upon crystallization from acetone or THF one-dimensional chains form in which molecules of 3 alternately serve as hydrogen bond donors and acceptors. The additional OH hydrogens that are not involved in hydrogen bonding within the polymeric chains undergo hydrogen bonding to the solvent molecules. Removal of the solvent was achieved at moderate temperature under high vacuum. While the polymeric chains remain intact, in the absence of the solvent as a hydrogen bond acceptor, short contacts to the Cp rings of neighboring polymer strands lead to a network-like structure. At higher temperatures, further dehydration occurs with formation of B-O-B linkages as confirmed by MALDI-TOF mass spectrometry. Oligomers with up to 15 repeating units (30 ferrocenes) were detected.

Thermal degradation kinetics of thermoresponsive poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers prepared via RAFT polymerization

Reversible addition-fragmentation chain transfer polymerization at 70 A degrees C in N,N-dimethylformamide was used to prepare poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide) copolymers in various compositions to afford well-defined polymers with pre-determined molecular weight, narrow molecular weight distribution, and precise chain end structure. The copolymer compositions were determined by H-1 NMR spectroscopy. The reactivity ratios of N-isopropylacrylamide (NIPAM) and N,N-dimethylacrylamide (DMA) were calculated as r (NIPAM) = 0.838 and r (DMA) = 1.105, respectively, by the extended Kelen-Tudos method at high conversions. The lower critical solution temperature of PNIPAM can be altered by changing the DMA content in the copolymer chain. Differential scanning calorimetry and thermogravimetric analysis at different heating rates were carried out on these copolymers to understand the nature of thermal degradation and to determine its kinetics. Different kinetic models were applied to estimate various parameters like the activation energy, the order, and the frequency factor. These studies are important to understand the solid state polymer degradation of N-alkyl substituted polymers, which show great potential in the preparation of miscible polymer blends due to their ability to interact through hydrogen bonding.

Synthesis, structural analysis and solvatochromic behaviour of 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile mesogen

In this communication, we report the synthesis and characterisation of a new luminescent liquid crystalline material, 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile (3). We have confirmed its structure by Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy, elemental analysis and X-ray single crystal diffraction studies. The newly synthesised compound crystallises in a monoclinic system with the space group C2/c and its cell parameters are found to be a?=?25.181(4) angstrom, b?=?15.651(4)angstrom, c?=?12.703(19) angstrom, V?=?4880.4 (16) angstrom, Z?=?8. The results indicate that the presence of weak CH center dot center dot center dot O and CH center dot center dot center dot N hydrogen bonding as short-range intermolecular interactions are responsible for the formation of its crystal assembly. The measured torsion angle shows the existence of a distorted structure for the molecule wherein 4-butoxyphenylene ring substituent at the fourth position of the central pyridine ring forms a torsion angle chiC(4), C(3), C(10), C(19)] of 40.55 degrees. Its liquid crystalline behaviour was investigated with the aid of polarised optical microscopy and differential scanning calorimetry. The study reveals that the compound displays a broad nematic phase in the range of 78112 degrees C. Further, solution phase optical studies indicate that it is a blue light emitter in different non-polar and polar organic solvents at a concentration of 10-5M.

From Molecular to Supramolecular: An Exploration into the Modes of Self-assembly in Conformationally Locked Polycyclitols

This brief account highlights the notable findings of our investigation into the supramolecular chemistry of conformationally locked polycyclitols in the solid state. The study was aimed at analyzing the crystal packing and unraveling the modalities of non-covalent interactions (particularly, intramolecular vis-a-vis intermolecular OH center dot center dot center dot O hydrogen bonds) in polyols. The know-how obtained thereof, was successfully utilized to engineer self-assemblies of designer polycyclitols, having hydrogen bond donors and acceptors fettered onto a trans-decalin scaffold. The results seek to draw particular attention to the intrinsic attribute of this rigid carbocyclic framework to lock functional groups into spatially invariant positions and bring potential intramolecular hydrogen bonding partners into favorable interaction geometry to engender predictability in the self-assembly patterns.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Electron rich supramolecular polymers as fluorescent sensors for nitroaromatics

Three pi-electron rich fluorescent supramolecular polymers (1-3) have been synthesized incorporating 2-methyl-3-butyn-2-ol groups in reasonable yield by employing Sonagashira coupling. They were characterized by multinuclear NMR (H-1, C-13), ESI-MS and single crystal X-ray diffraction analyses 1 = 1( 2-methyl-3-butyn-2-ol) pyrene; 2 = 9,10-bis(2-methyl-3-butyn-2-ol) anthracene; 3 = 1,3,6,8-tetrakis(2methyl- 3-butyn-2-ol) pyrene]. Single crystal structures of 1-3 indicated that the incorporation of hydroxy (-OH) groups on the peripheral of the fluorophores helps them to self-associate into an infinite supramolecular polymeric network via intermolecular hydrogen bonding interactions between the adjacent discrete fluorophore units. All these compounds showed fluorescence characteristics in chloroform solution due to the extended pi-conjugation and were used as selective fluorescent sensors for the detection of electron deficient nitroaromatics. The changes in photophysical properties of fluorophores (1-3) upon complex formation with electron deficient nitroaromatic explosives were studied in chloroform solution by using fluorescence spectroscopy. All these fluorophores showed the largest quenching response with moderate selectivity for nitroaromatics over various other electron deficient/ rich aromatic compounds tested (Chart 1). Analysis of the fluorescence titration profile of 9,10-bis(2-methyl-3butyn- 2-ol) anthracene fluorophore (2) with 1,3,5-trinitrotoluene/ 2,4-dinitrotoluene provided evidence that this particular fluorophore detects nitroaromatics in the nanomolar range 2.0 ppb for TNT, 13.7 ppb for DNT]. Moreover, sharp visual color change was observed upon mixing nitroaromatic (DNT) with fluorophores (1-3) both in solution as well as in solid phase. Furthermore, the vapor-phase sensing study of thin film of fluorophores (1-3) showed efficient quenching responses for DNT and this sensing process is reproducible. Selective fluorescence quenching response including a sharp visual color change for nitroaromatics make these tested fluorophores (1-3) as potential sensors for nitroaromatic compounds with a detection limit of ppb level.

Diaminotriazine substituted diphenyl ether: reversible structural transformation and solvent dependent solid state fluorescence

The effect of molecular shape and position of hydrogen bonding functionality in the solid state structural self-assembly was investigated using diaminotriazine substituted diphenyl ether based positional isomers (1-5). The molecular shape was modulated by changing diaminotriazine position that produced channel supramolecular structures in 1, 3 and 5. There exists a direct correlation between the molecular shape and three dimensional structures; more linear molecules resulted in close-packing whereas molecules with a labyrinthine topology formed a channel structure. Supramolecular aspects pertaining to the influence of solvent of crystallization in structure formation and reversible structural transformation in solid state were also explored. 1-5 exhibited tunable solid state fluorescence (lambda(max) = 437-496 nm) depending on the diaminotriazine substitutional position and 3 showed solvent-dependent solid state fluorescence. The present study describes the generation of a supramolecular channel structure with functional properties such as tunable fluorescence by varying the position of hydrogen bond functionality and solvent of crystallization.

Chemical unfolding of chicken villin headpiece in aqueous dimethyl sulfoxide solution: cosolvent concentration dependence, pathway, and microscopic mechanism

Unfolding of a protein often proceeds through partial unfolded intermediate states (PUIS). PUIS have been detected in several experimental and simulation studies. However, complete analyses of transitions between different PUIS and the unfolding trajectory are sparse. To understand such dynamical processes, we study chemical unfolding of a small protein, chicken villin head piece (HP-36), in aqueous dimethyl sulfoxide (DMSO) solution. We carry out molecular dynamics simulations at various solution compositions under ambient conditions. In each concentration, the initial step of unfolding involves separation of two adjacent native contacts, between phenyl alanine residues (11-18 and 7-18). This first step induces, under appropriate conditions, subsequent separation among other hydrophobic contacts, signifying a high degree of cooperativity in the unfolding process. The observed sequence of structural changes in HP-36 on increasing DMSO concentration and the observed sequence of PUIS, are in approximate agreement with earlier simulation results (in pure water) and experimental observations on unfolding of HP-36. Peculiar to water-DMSO mixture, an intervening structural transformation (around 15% of DMSO) in the binary mixture solvent retards the progression of unfolding as composition is increased. This is reflected in a remarkable nonmonotonic composition dependence of RMSD, radius of gyration and the fraction of native contacts. At 30% mole fraction of DMSO, we find the extended randomly coiled structure of the unfolded protein. The molecular mechanism of DMSO induced unfolding process is attributed to the initial preferential solvation of the hydrophobic side chain atoms through the methyl groups of DMSO, followed by the hydrogen bonding of the oxygen atom of DMSO to the exposed backbone NH groups of HP-36.

Relation Between the Diffusivity, Viscosity, and Ionic Radius of LiCl in Water, Methanol, and Ethylene Glycol: A Molecular Dynamics Simulation

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several; structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent solvent interaction is important in EG while solute solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes we show that there is a relation between the void and neck radius on e one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (lambda(0)) of TMA(+), while in water in EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in lambda(0) as a function ionic radius is seen for Br- in water EG but for the larger ClO4- ion in methanol. The relation between the void and neck distribution and the variation in lambda(0) with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Induction of Supramolecular Chirality in the Self-Assemblies of Lipophilic Pyrimidine Derivatives by Choice of the Amino Acid-Based Chiral Spacer

A new family of supramolecular organogelators, based on chiral amino acid derivatives of 2,4,6-trichloro-pyrimidine-5-carbaldehyde, has been synthesized. L-alanine was incorporated as a spacer between the pyrimidine core and long hydrocarbon tails to compare the effect of chirality and hydrogen bonding to that of the achiral analogue. The role of aromatic moiety on the chiral spacer was also investigated by introducing L-phenyl alanine moieties. The presence of intermolecular hydrogen-bonding leading to the chiral self-assembly was probed by concentration-dependent FTIR and UV/Vis spectroscopies, in addition to circular dichroism (CD) studies. Temperature and concentration-dependent CD spectroscopy ascribed to the formation of -sheet-type H-bonded networks. The morphology and the arrangements of the molecules in the freeze-dried gels were examined by scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction (XRD) techniques. Calculation of the length of each molecular system by energy minimization in its extended conformation and comparison with the small-angle XRD pattern reveals that this class of gelator molecules adopts a lamellar organization. Polarized optical microscopy (POM) and differential scanning calorimetry (DSC) indicate that the solid state phase behavior of these molecules is totally dependent on the choice of their amino acid spacers. Structure-induced aggregation properties based on the H-bonding motifs and the packing of the molecule in three dimensions leading to gelation was elucidated by rheological studies. However, viscoelasticity was shown to depend only marginally on the H-bonding interactions; rather it depends on the packing of the gelators to a greater extent.

Enhancing Surface Coverage and Growth in Layer-by-Layer Assembly of Protein Nanoparticles

Thin films of bovine serum albumin (BSA) nanoparticles are fabricated via layer-by-layer assembly. The surface of BSA nanoparticles have two oppositely acting functional groups on the surface: amine (NH2) and carboxylate (COO-). The protonation and deprotonation of these functional groups at different pH vary the charge density on the particle surface, and entirely different growth can be observed by varying the nature of the complementary polymer and the pH of the particles. The complementary polymers used in this study are poly(dimethyldiallylammonium chloride) (PDDAC) and poly(acrylic acid) (PAA). The assembly of BSA nanoparticles based on electrostatic interaction with PDDAC suffers from the poor loading of the nanoparticles. The assembly with PAA aided by a hydrogen bonding interaction shows tremendous improvement in the growth of the assembly over PDDAC. Moreover, the pH of the BSA nanoparticles was observed to affect the loading of nanoparticles in the LbL assembly with PAA significantly.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed using CRYSTAL09 with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N-N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C-H center dot center dot center dot N, C-H center dot center dot center dot O and N-H center dot center dot center dot N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Effect of Substrate Temperature on the Microstructure Variation in Sputter-deposited Hydrogenated Amorphous Silicon Thinfilms

Vacancy, void incorporation and Si-H-x configuration in hydrogenated amorphous silicon (a-Si:H) thin films was studied. Films were grown by Direct Current (DC), pulsed DC and Radio Frequency (RF) magnetron sputtering. Fourier Transform Infrared (FTIR) spectroscopic analysis has been carried out on the films and found that, the a-Si: H films grown by DC magnetron sputtering are of good quality compared to pulsed DC and RF deposited films. The effect of Substrate temperature (T-S) on the total hydrogen concentration (C-H), configuration of hydrogen bonding, density (decided by the vacancy and void incorporation) and the microstructure factor (R*) was studied. T-S is found to be an active parameter in affecting the above said properties of the films. The films contain both vacancies and voids. At low hydrogen dilutions the films are vacancy dominated and at high hydrogen dilutions they are void dominated. It is found that T-S favors monohydride (Si-H) bonding at the cost of dihydride (Si-H-2) bonding. This dividing line is at C-H=14 at.% H for DC sputter deposited films. The microstructure structure factor R* is found to be zero for as deposited DC films at T-S=773K. The threshold C-H for void dominated region is found to be C-H=23 at.% H for RF, C-H=18 at.% H for PDC and C-H similar to 14 at.%H for DC sputter deposited films.