Vibrational spectroscopy and DFT calculations of di-amino acid cyclic peptides. Part I: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(t-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C-2 and C-1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cydo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cydo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

Vibrational spectroscopic studies of the structure of di-amino acid peptides. Part II: cyclo(L-Asp-L-Asp) in the solid state and in aqueous solution

Solid-state protonated and N,O-deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di-amino acid peptide cyclo(L-Asp-L-Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3-LYP/cc-pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L-Asp-L-Asp), assuming C-2 symmetry, predicts a boat conformation for the DKP ring with both the two L-aspartyl side chains being folded slightly above the ring. The C=O stretching vibrations have been assigned for the side-chain carboxylic acid group (e.g. at 1693 and 1670 cm(-1) in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm(-1) in the Raman spectrum). The presence of two bands for the carboxylic acid C=O stretching modes in the solid-state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm(-1) in the solid-state Raman spectrum, which is in agreement with results for cyclic di-amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C-alpha atom is increased, the amide II band wavenumber decreases to below 1500 cm(-1); this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm(-1)), which indicates that this band has a smaller N-H bending contribution than the trans amide II vibrational band observed for linear peptides.

IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ~ 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring.

Preparation of o/w emulsions stabilized by solid particles and their characterization by oscillatory rheology

The purpose of this investigation was to examine the preparation and characterisation of hexane-in-water emulsions stabilised by clay particles. These emulsions, called Pickering emulsions, are characterised by the adsorption of solid particles at the oil/water (o/w) interface. The development of an elastic film at the o/w interface following the adsorption of colloidal particles helps to promote emulsion stability. Three different solid materials were used: silica sand, kaolin, and bentonite. Particles were added to the liquid mixtures in the range of 0.5–10 g dm−3. Emulsions were prepared using o/w ratios of 0.1, 0.2, 0.3, and 0.4. The effect of sodium chloride, on the stability of the prepared emulsions, was assessed in the range of 0–0.5 mol dm−3. In addition the use of a cationic surfactant hexadecyl-trimethylammonium bromide (CTAB) as an aid to improving emulsion stability was assessed in the concentration range of 0–0.05% (w/v). Characterisation of emulsion stability was realised through measurements of rheological properties including non-Newtonian viscosity, the elastic modulus, G', the loss modulus, G", and complex modulus, G*. The stability of the emulsions was evaluated immediately after preparation and 4 weeks later. Using the stability criteria, that for highly stable emulsions: G' > G" and both G' and G" are independent of frequency (varpi) it was concluded that highly stable emulsions could be prepared using a bentonite concentration of 2% (or more); an o/w ratio greater than 0.2; a CTAB concentration of 0.01%; and a salt concentration of 0.05 M or less—though salt was required.

Breast milk levels of zinc and omega-6 polyunsaturated fatty acids and growth of healthy Chinese infants

AIM: To examine the concentrations of zinc and omega-6 polyunsaturated fatty acids (omega-6 PUFAs) in breast milk, the impact of zinc on omega-6 PUFA metabolism, and the growth rate of infants. METHODS: Forty-one mother-term infant pairs from a rural area of northern Beijing, China, who were 1 month (n = 18, group I) and 3 months (n = 23, group II) old and exclusively breastfed, were studied. The dietary records and the concentrations of zinc and omega-6 PUFAs in the milk of lactating women and the increase in weight and length of their infants during 1 and 3 postnatal months were analysed. RESULTS: The dietary intakes of mothers in the two groups were the same, i.e. high in carbohydrate and low in fat, protein and energy. The maternal zinc intake was 7.5mg/d and thus reached only 34.6% of the current Recommended Nutrient Intake (RNI). The levels of zinc and arachidonic acid (AA, C20:4 omega-6) in the milk of group I were significantly higher than those in group II. Furthermore, significant positive correlations were found between the concentrations of zinc and AA in the breast milk and between the level of milk AA and weight gain. CONCLUSION: Zinc may be a co-factor and essential for essential fatty acids (EFA) metabolism. Thus suboptimal zinc intake may cause EFA imbalance. Further studies of Chinese rural mother-infant pairs are necessary to determine whether zinc supplementation should be recommended when lactation exceeds 3 months.

Polyunsaturated fatty acids in the pathogenesis and treatment of multiple sclerosis

Epidemiological, biochemical, animal model and clinical trial data described in this overview strongly suggest that polyunsaturated fatty acids, particularly n-6 fatty acids, have a role in the pathogenesis and treatment of multiple sclerosis (MS). Data presented provides further evidence for a disturbance in n-6 fatty acid metabolism in MS. Disturbance of n-6 fatty acid metabolism and dysregulation of cytokines are shown to be linked and a "proof of concept clinical trial" further supports such a hypothesis. In a randomised double-blind, placebo controlled trial of a high dose and low dose selected GLA (18:3n-6)-rich oil and placebo control, the high dose had a marked clinical effect in relapsing-remitting MS, significantly decreasing the relapse rate and the progression of disease. Laboratory findings paralleled clinical changes in the placebo group in that production of mononuclear cell pro-inflammatory cytokines (TNF-alpha, IL-1 beta) was increased and anti-inflammatory TGF-beta markedly decreased with loss of membrane n-6 fatty acids linoleic (18:2n-6) and arachidonic acids (20:4n-6). In contrast there were no such changes in the high dose group. The improvement in disability (Expanded Disability Status Scale) in the high dose suggests there maybe a beneficial effect on neuronal lipids and neural function in MS. Thus disturbed n-6 fatty acid metabolism in MS gives rise to loss of membrane long chain n-6 fatty acids and loss of the anti-inflammatory regulatory cytokine TGF-beta, particularly during the relapse phase, as well as loss of these important neural fatty acids for CNS structure and function and consequent long term neurological deficit in MS.

On the coupling of Navier–Stokes and linearised Euler equations for aeroacoustic simulation

Aerodynamic generation of sound is governed by the Navier–Stokes equations while acoustic propagation in a non-uniform medium is effectively described by the linearised Euler equations. Different numerical schemes are required for the efficient solution of these two sets of equations, and therefore, coupling techniques become an essential issue. Two types of one-way coupling between the flow solver and the acoustic solver are discussed: (a) for aerodynamic sound generated at solid surfaces, and (b) in the free stream. Test results indicate how the coupling achieves the necessary accuracy so that Computational Fluid Dynamics codes can be used in aeroacoustic simulations.

Computational modelling of bubbles, droplets and particles in metals reduction and refining

The CFD modelling of metals reduction processes particularly always seems to involve the interaction of liquid metals, a gas (often air) top space, liquid droplets in the top space and injection of both solid particles and gaseous bubbles into the bath. These phases all interact and exhange mass, momentum and energy. Often it is the extent to which these multi-phase phemomena can be effectively captured within the CFD model which determines whether or not a tool of genuine use to the target industry sector can constructed. In this paper we discuss these issues in the context of two problems - one involving the injection of sparging gases into a steel continuous caster and the other based on the development of a novel process for aluminium electrolysis.

Assessing the scalability of multiphysics tools for modeling solidification and melting processes on parallel clusters

A comprehensive solution of solidification/melting processes requires the simultaneous representation of free surface fluid flow, heat transfer, phase change, nonlinear solid mechanics and, possibly, electromagnetics together with their interactions, in what is now known as multiphysics simulation. Such simulations are computationally intensive and the implementation of solution strategies for multiphysics calculations must embed their effective parallelization. For some years, together with our collaborators, we have been involved in the development of numerical software tools for multiphysics modeling on parallel cluster systems. This research has involved a combination of algorithmic procedures, parallel strategies and tools, plus the design of a computational modeling software environment and its deployment in a range of real world applications. One output from this research is the three-dimensional parallel multiphysics code, PHYSICA. In this paper we report on an assessment of its parallel scalability on a range of increasingly complex models drawn from actual industrial problems, on three contemporary parallel cluster systems.

Computational modelling of bubbles, droplets and particles in metals reduction and refining

A multi-phase framework is typically required for the CFD modelling of metals reduction processes. Such processes typically involve the interaction of liquid metals, a gas (often air) top space, liquid droplets in the top space and injection of both solid particles and gaseous bubbles into the bath. The exchange of mass, momentum and energy between the phases is fundamental to these processes. Multi-phase algorithms are complex and can be unreliable in terms of either or both convergence behaviour or in the extent to which the physics is captured. In this contribution, we discuss these multi-phase flow issues and describe an example of each of the main “single phase” approaches to modelling this class of problems (i.e., Eulerian–Lagrangian and Eulerian–Eulerian). Their utility is illustrated in the context of two problems – one involving the injection of sparging gases into a steel continuous slab caster and the other based on the development of a novel process for aluminium electrolysis. In the steel caster, the coupling of the Lagrangian tracking of the gas phase with the continuum enables the simulation of the transient motion of the metal–flux interface. The model of the electrolysis process employs a novel method for the calculation of slip velocities of oxygen bubbles, resulting from the dissolution of alumina, which allows the efficiency of the process to be predicted.

Rheological characterisation of solder pastes and isotropic conductive adhesives used for flip-chip assembly

Solder pastes and isotropic conductive adhesives (ICAs) are widely used as a principal bonding medium in the electronic industry. This study investigates the rheological behaviour of the pastes (solder paste and isotropic conductive adhesives) used for flip-chip assembly. Oscillatory stress sweep test are performed to evaluate solid characteristic and cohesiveness of the lead-free solder pastes and isotropic conductive adhesive paste materials. The results show that the G' (storage modulus) is higher than G '' (loss modulus) for the pastes material indicating a solid like behaviour. It result shows that the linear visco-elastic region for the pastes lies in a very small stress range, below 10 Pa. in addition, the stress at which the value of storage modulus is equal to that of loss modulus can be used as an indicator of the paste cohesiveness. The measured cross-over stress at G'=G '' shows that the solder paste has higher stress at G'=G '' compared to conductive adhesives. Creep-recovery test method is used to study the slump behaviour in the paste materials. The conductive adhesive paste shows a good recovery when compared to the solder pastes. (C) 2008 Elsevier B.V. All rights reserved.

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di-amino acid peptide cyclo(L-Glu-L-Glu)

Cyclo(L-Glu-L-Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P21 and form 2 is in space group C2. Raman scattering and FT-IR spectroscopic studies have been conducted for the N,O-protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid-state and aqueous solution samples have also been recorded. The different hydrogen-bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N&bond;H and C&dbond;O stretching character. DFT (B3-LYP/cc-pVDZ) calculations of the isolated cyclo(L-Glu-L-Glu) molecule predict that the minimum energy structure, assuming C2 symmetry, has a boat conformation for the diketopiperazine ring with the two L-Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X-ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.

Spectroscopic studies of oligomers containing 2,5-trans furanoid sugar amino acids

Sugar amino acids and their oligomers, known as carbopeptoids, are commonly studied as foldamers. However, study of their conformational preference is often challenging when the adopted conformations are extended and/or disordered. This study is the first to explore the disordered nature of such carbopeptoids by utilizing a family of 2,5-trans carbopeptoids. An array of spectroscopic techniques has been used to investigate the conformational preference of these carbopeptoids. However, using this data alone it has not been possible to assign conformational preference as an ordered extended conformation or as a disordered family of closely related conformations. Computational methods need to be employed to achieve reliable interpretation of the spectroscopic data. Chirality, 2008. © 2008 Wiley-Liss, Inc.

Co-acquisition of hyperpolarised 13C and 15N NMR spectra

Recent developments in dynamic nuclear polarisation now allow significant enhancements to be generated in the cryo solid state and transferred to the liquid state for detection at high resolution. We demonstrate that the Ardenkjaer-Larsen method can be extended by taking advantage of the properties of the trityl radicals used. It is possible to hyperpolarise 13C and 15N simultaneously in the solid state, and to maintain these hyperpolarisations through rapid dissolution into the liquid state. We demonstrate the almost simultaneous measurement of hyperpolarised 13C and hyperpolarised 15N NMR spectra. The prospects for further improvement of the method using contemporary technology are also discussed.