Solvation properties of N-substituted cis and trans amides are not identical: significant enthalpy and entropy changes are revealed by the use of variable temperature 1H NMR in aqueous and chloroform solutions and ab initio calculations

The cis/trans conformational equilibrium of N-methyl formamide (NMF) and the sterically hindered tert-butylformamide (TBF) was investigated by the use of variable temperature gradient 1H NMR in aqueous solution and in the low dielectric constant and solvation ability solvent CDCl3 and various levels of first principles calculations. The trans isomer of NMF in aqueous solution is enthalpically favored relative to the cis (deltaH(o) = -5.79 +/- 0.18 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = -0.23 +/- 0.17 kJ mol(-1)) playing a minor role. The experimental value of the enthalpy difference strongly decreases (deltaH(o) = -1.72 +/- 0.06 kJ mol(-1)), and the contribution of entropy at 298 K (298 x deltaS(o) = -1.87 +/- 0.06 kJ mol(-1)) increases in the case of the sterically hindered tert-butylformamide. The trans isomer of NMF in CDCl3 solution is enthalpically favored relative to the cis (deltaH(o) = -3.71 +/- 0.17 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = 1.02 +/- 0.19 kJ mol(-1)) playing a minor role. In the sterically hindered tert-butylformamide, the trans isomer is enthalpically disfavored (deltaH(o) = 1.60 +/- 0.09 kJ mol(-1)) but is entropically favored (298 x deltaS(o) = 1.71 +/- 0.10 kJ mol(-1)). The results are compared with literature data of model peptides. It is concluded that, in amide bonds at 298 K and in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side chains, the free energy difference of the cis/trans isomers and both the enthalpy and entropy contributions are strongly dependent on the N-alkyl substitution and the solvent. The significant decreasing enthalpic benefit of the trans isomer in CDCl3 compared to that in H2O, in the case of NMF and TBF, is partially offset by an adverse entropy contribution. This is in agreement with the general phenomenon of enthalpy versus entropy compensation. B3LY/6-311++G** and MP2/6-311++G** quantum chemical calculations confirm the stability orders of isomers and the deltaG decrease in going from water to CHCl3 as solvent. However, the absolute calculated values, especially for TBF, deviate significantly from the experimental values. Consideration of the solvent effects via the PCM approach on NMF x H2O and TBF x H2O supermolecules improves the agreement with the experimental results for TBF isomers, but not for NMF.     

Development of adaptive modeling techniques for non-linear hysteretic systems

Adaptive estimation procedures have gained significant attention by the research community to perform real-time identification of non-linear hysteretic structural systems under arbitrary dynamic excitations. Such techniques promise to provide real-time, robust tracking of system response as well as the ability to track time variation within the system being modeled. An overview of some of the authors’ previous work in this area is presented, along with a discussion of some of the emerging issues being tackled with regard to this class of problems. The trade-offs between parametric-based modeling and non-parametric modeling of non-linear hysteretic dynamic system behavior are discussed. Particular attention is given to (1) the effects of over- and under-parameterization on parameter convergence and system output tracking performance, (2) identifiability in multi-degree-of-freedom structural systems, (3) trade-offs in setting user-defined parameters for adaptive laws, and (4) the effects of noise on measurement integration. Both simulation and experimental results indicating the performance of the parametric and non-parametric methods are presented and their implications are discussed in the context of adaptive structures and structural health monitoring.     

Quantitative analysis of energy transfer between fluorescent proteins in CFP-GBP-YFP and its response to Ca2+

This article reports the full characterisation of the optical properties of a biosynthesised protein consisting of fused cyan fluorescent protein, glucose binding protein and yellow fluorescent protein. The cyan and yellow fluorescent proteins act as donors and acceptors for intramolecular fluorescence resonance energy transfer. Absorption, fluorescence, excitation and fluorescence decays of the compound protein were measured and compared with those of free fluorescent proteins. Signatures of energy transfer were identified in the spectral intensities and fluorescence decays. A model describing the fluorescence properties including energy transfer in terms of rate equations is presented and all relevant parameters are extracted from the measurements. The compound protein changes conformation on binding with calcium ions. This is reflected in a change of energy transfer efficiency between the fluorescent proteins. We track the conformational change and the kinetics of the calcium binding reaction from fluorescence intensity and decay measurements and interpret the results in light of the rate equation model. This visualisation of change in protein conformation has the potential to serve as an analytical tool in the study of protein structure changes in real time, in the development of biosensor proteins and in characterizing protein-drug interactions.     

Monitoring conformational changes in protein complexes using chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: the effect of calcium binding on the calmodulin-melittin complex

Calmodulin is an EF hand calcium binding protein. Its binding affinities to various protein/peptide targets often depend on the conformational changes induced by the binding of calcium. One such target is melittin, which binds tightly to calmodulin in the presence of calcium, and inhibits its function. Chemical cross-linking combined with Fourier transform ion cyclotron resonance mass spectrometry has been employed to investigate the coordination of calmodulin and melittin in the complex at different concentrations of calcium. This methodology can be used to monitor structural changes of proteins induced by ligand binding, and study the effects these changes have on non- covalent interactions between proteins. Cross-linking results indicate that the binding place of the first melittin in the calcium free calmodulin form is the same as in the calcium loaded calmodulin/melittin complex.     

Direct simulation of two‐dimensional turbulent flow over a surface‐mounted obstacle

Two‐dimensional turbulent flow over a surface‐mounted obstacle is studied as a numerical experiment that takes place in a wind tunnel. The transient Navier–Stokes equations are solved directly with Galerkin finite elements. The Reynolds number defined with respect to the height of the wind tunnel is 12 518. Instantaneous streamline patterns are shown that give a complete picture of the flow phenomena. Energy and enstrophy spectra yield the dual cascade of two‐dimensional turbulence and the ?1 power law decay of enstrophy. Mean values of velocities and root mean square fluctuations are compared with the available experimental results. Other statistical characteristics of turbulence such as Eulerian autocorrelation coefficients, longitudinal and lateral coefficients are also computed. Finally, oscillation diagrams of computed velocity fluctuations yield the chaotic behaviour of turbulence. Copyright © 2007 John Wiley & Sons, Ltd.     

Computer-aided analysis of flow past a surface-mounted obstacle

The incompressible, laminar, isothermal flow of a Newtonian fluid at steady state past a surface-mounted obstacle (flow over a step) is studied in a two-dimensional numerical experiment using the Galerkin finite element method. The dimensionless Navier–Stokes equations are solved in the whole range of the laminar flow regime. The numerical predictions are compared with available experimental data. The emphasis in the discussion of the results is on the presentation of the streamlines for various Reynolds numbers, the pressure distribution over and downstream of the step, the shear stress distribution along the surface of the step and the length of the recirculation region as a function of the Reynolds number. This analysis may be used in numerous applications from agricultural to civil, mechanical and chemical engineering. © 1997 John Wiley & Sons, Ltd.     

Examination of the Spatial Distribution of Dyes and Polymers in Thin Films by Two-Photon Microscopy

Summary.  Two-photon absorption induced fluorescence microscopy was used as a tool for the examination of the spatial distribution of a thin dye film. The two-photon absorption induced fluorescence signal is essentially the same as that produced by excitation with a single photon of equivalent energy. When femtosecond pulses are focused into a sample there is an intrinsic spatial selectivity of the two-photon emission signal, since it is dependent upon the square of the light intensity. This has tremendous implications in fluorescence microscopy. Since two-photon absorption is confined in a small region at the focal waist of an objective lens, photodamage and photobleaching of the sample are significantly reduced. In addition, the two-photon signal has inherent z-axis spatial resolution, which facilitates the construction of 3-D images. In the present work an application of this technique to a thin film of a dye is presented. The method can generally be applied to thin films made from photonic polymers. Received June 23, 2000. Accepted (revised) July 31, 2000     

1H NMR determination of hypericin and pseudohypericin in complex natural mixtures by the use of strongly deshielded OH groups

The ¹H NMR spectra of the commercially available compounds hypericin and its derivative pseudohypericin in CD₃OH solutions indicate significantly deshielded signals in the region of 14-15 ppm. These resonances are attributed to the peri hydroxyl protons OH(6), OH(8) and OH(1), OH(13) of hypericins which participate in a strong six-membered ring intramolecular hydrogen bond with CO(7) and CO(14), respectively, and therefore, they are strongly deshielded. In the present work, we demonstrate that one-dimensional ¹H NMR spectra of hypericin and pseudohypericin, in Hypericum perforatum extracts show important differences in the chemical shifts of the hydroxyl groups with excellent resolution in the region of 14-15 ppm. The facile identification and quantification of hypericin and its derivative compound pseudohypericin was achieved, without prior HPLC separation, for two H. perforatum extracts from Greek cultivars and two commercial extracts: a dietary supplement, and an antidepressant medicine. The results were compared with those obtained from UV-vis and LC/MS measurements.     

A new method for the determination of free L-carnitine in serum samples based on high field single quantum coherence filtering 1H-NMR spectroscopy

The rapid and accurate determination of specific metabolites present in biofluids is a very demanding task which is essential in both medicine and chemistry. l-carnitine (3-hydroxy-4-N-trimethylammonium butyrate) is an important metabolite which participates in a series of biological paths and therefore its determination is of diagnostic importance. A single quantum coherence filtering ¹H NMR methodology was used for the accurate and rapid determination of l-carnitine in human serum samples. The methodology is based on spectral simplification, and specifically on the distinction of the N-methyl proton signal of l-carnitine that is greatly overlapped in the ¹H-NMR spectrum of serum. The quantitative results provided by the proposed method are in excellent agreement with those obtained by the enzymatic method, which is widely used. The proposed method is rapid (~20 min of experimental time), selective, sensitive, and has good analytical characteristics (accuracy, reproducibility). Selected protein precipitation methods were also investigated and sample pretreatment with EtOH is suggested.