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Research discusses the effect of proline puckering on the stability of the collagen triple helix by quantum mechanical and molecular mechanical analysis of the (proline-proline-glycine)(sub)n polypeptides. Results indicate that inclusion of interresidue interactions do not lead to significant stabilization of the peptides .

The importance of local (intraresidue) effects in determining the stability of the collagen triple helix has been investigated with special reference to the role played by hydroxyproline. The dipeptide analogues of L-proline (ProDA), 4(R)-hydroxy-L-proline (HypDA), and 4(R)-fluoro-L-proline (FlpDA) have been studied by means of quantum mechanical initio calculations, taking into account solvent effects by the polarizable continuum model (PCM).

The orientational order parameters and conformational behavior of five relatively large rodlike molecules, biphenyl, trans-stilbene, 1,3-diphenyl-butadiene, 1,3,5-diphenyl-hexatriene, and 1,3,5,7-diphenyl-octatetraene, dissolved in the thermotropic liquid crystal ZLI-1167, have been studied using an integrated approach combining 13C NMR measurements and quantum mechanical computations of carbon chemical shift tensors. Besides biphenyl, the phenyl moiety of all structures has been found to have a high rotational mobility in the temperature range of the present experiments. The rank-two order parameter in the nematic phase is found to increase steadily from the shortest to the longest term of the series at any temperature within the nematic range. The molecular biaxiality order parameter is found to be small and essentially constant with temperature, giving further support to the common assumption of effective uniaxiality for these probes [ABSTRACT FROM AUTHOR]

High-level ab initio g and A tensor components have been calculated for PD-tempone and tempo-palmitate (TP) radical spin probes dissolved in n-pentyl and n-hexyl cyanobiphenyl liquid crystals. Solvent effects have been included in the proposed approach by means of the polarizable continuum model, allowing for solvent anisotropy. An in-depth analysis of the electronic structure of probes was performed to choose a suitable model for TP and make the calculations more accessible. Computed magnetic tensor components have been compared with corresponding values measured in the rigid limit. The quality of the results suggests the use of quantum-mechanical data to determine the order parameter of the nematic from experimental electron-spin resonance measurements. [ABSTRACT FROM AUTHOR]

The development of a stochastic model for the interpretation of the emission fluorescence of 4-(N,N-dimethylamino)benzonitrile (DMABN) in polar environment is reported. The model allows to estimate the emission fluorescence by numerically solving the diffusion/sink/source equation for the stationary population of excited state.

A combined theoretical and experimental procedure to evaluate the order parameters of solutes in liquid crystals is developed. The ordering properties of an anisotropic liquid crystal can be studied by recording (super 13)C NMR spectra at different temperatures for a number of rigid solutes.

We discuss an interpretation of the emission signal of a class of dimethylaminobenzonitrile (DMABN) derivatives, based on a stochastic model approach. This study is prompted by the interest in building relatively simple theoretical tools for understanding the static and dynamic properties of metal chelation-controlled fluorescent molecular systems with internal flexibility and solvation effects, which can be used as fluorescent sensors of metal ions. We proceed by extending a stochastic modeling approach, previously used for DMABN, in which internal degrees of freedom are coupled to an effective solvent relaxation variable. The model is based on an integrated approach that combines stochastic methods and QM calculations. The static and dynamic properties of the molecule are obtained by a combination of a continuum treatment and a detailed solute dynamics. Simple computational approximations lead to a semianalytical treatment of the resulting equations, which reproduce correctly the static spectra at room temperature of 4-(1-aza-4,7,10-trioxacyclododecyl) benzonitrile (DMABN-Crown4) and 4-(1-aza-4,7,10,13-tetraoxacyclododecyl) benzonitrile (DMABN-Crown5) in solvents with different polarity. A qualitative analysis of the dynamic spectra of the DMABN-Crown4 is also presented. A discussion is finally provided on how combined quantum and classical methods can be used to define a general robust and reliable computational approach for predicting fluorescence properties of organic molecules in solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod-like molecules in spherical or rod-like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1096–1105, 2005 [ABSTRACT FROM AUTHOR]

Examines the importance of vicinal and long-range interresidue effects in determining collagen stability. Elucidation of collagen structure; Conformational behavior of the collagen triple helix; Influence of the proline puckering on the stability of helix.

A symmetric squaraine and its related non-symmetric structure are shown to have comparable efficiencies in DSCs, but with undoubtedly advantages in the low cost and easiness of synthesis for the symmetrical structure., (This journal is © The Royal Society of Chemistry 2012)

Mesoporous silica nanoparticles are being explored as versatile tools for various biomedical and biotechnological applications including disease diagnosis, drug delivery, and intracellular imaging. In this paper, the synthesis and characterization of a fluorescent hybrid mesoporous silica nanomaterial, which is noncytotoxic and shows great potential for "in-cell" bioimaging applications, will be described. The hybrid mesoporous material has been obtained by confining highly fluorescent organic dyes, belonging to the indocyanine family, within the channels of mesoporous MCM-41. To explore the dispersion of the dye inside the mesoporous channels and the formation of dye aggregates, several hybrid samples with increasing dye/MCM-41 loading (up to 100 mg/g) were prepared. A uniform distribution of monomeric 1,1'-diethyl-3,3,3',3'-tetramethylindocarbocyanine iodide has been achieved at low dye loading (1 mg/g), as evidenced by photoluminescence spectra and lifetime, while a progressive formation of J-aggregates is induced by an increase in the dye loading. To elucidate the properties of the dye immobilized in mesoporous MCM-41, a detailed physical chemical characterization by structural (X-ray diffraction), volumetric and optical (Fourier transform infrared, diffuse-reflectance UV-vis and photoluminescence) techniques has been performed. By ultrasonication of the bulk material, nanoparticles of 2-20 nm diameter were obtained. Biocompatibility, endocytic uptake, and intracellular compartmentalization of such fluorescent nanoparticles were investigated in mammalian cultured cells.

The orientational order parameters and conformational behavior of five relatively large rodlike molecules, biphenyl, trans-stilbene, 1,3-diphenyl-butadiene, 1,3,5-diphenyl-hexatriene, and 1,3,5,7-diphenyl-octatetraene, dissolved in the thermotropic liquid crystal ZLI-1167, have been studied using an integrated approach combining (13)C NMR measurements and quantum mechanical computations of carbon chemical shift tensors. Besides biphenyl, the phenyl moiety of all structures has been found to have a high rotational mobility in the temperature range of the present experiments. The rank-two order parameter in the nematic phase is found to increase steadily from the shortest to the longest term of the series at any temperature within the nematic range. The molecular biaxiality order parameter is found to be small and essentially constant with temperature, giving further support to the common assumption of effective uniaxiality for these probes.

The ordering properties of an anisotropic liquid crystal can be studied by recording 13C NMR spectra at different temperatures for a number of rigid solutes. The traditional difficulty in analyzing 13C data comes from the scarcity of experimental information about the carbon shielding tensors and from their limited transferability among different solutes. We show that these obstacles can be overcome by computing high-level ab initio shielding tensors, also including the solvent effects by the polarizable continuum model. The reliability of this combined approach is carefully verified, and the order parameters of several solutes are obtained by reanalyzing previously published spectra. The quality of the results is shown to be comparable to deuterium NMR without the need of isotopic substitution.

The conceptual and numerical problems involved in the computation of reliable NMR chemical shifts for molecules in condensed phases are analyzed with reference to a number of case studies ranging from aromatic compounds in low-polarity solvents to carbonyl and amidic models in aqueous solution and to large polypeptides. The results show that an integrated tool including the most recent density functionals, mixed discrete-continuum solvent models, hybrid QM/MM approaches and, when needed, averaging from molecular dynamics simulations are becoming an invaluable complement to experimental results., (Copyright 2004 John Wiley & Sons, Ltd.)