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Large Molecules (large + molecule)
Selected AbstractsBackbone-Only Protein Solution Structures with a Combination of Classical and Paramagnetism-Based Constraints: A Method that Can Be Scaled to Large MoleculesCHEMPHYSCHEM, Issue 6 2004Renato Barbieri Dr. Abstract Herein, it is shown that a medium-resolution solution structure of a protein can be obtained with the sole assignment of the protein backbone and backbone-related constraints if a derivative with a firmly bound paramagnetic metal is available. The proof-of-concept is provided on calbindin D9k, a calcium binding protein in which one of the two calcium ions can be selectively substituted by a paramagnetic lanthanide ion. The constraints used are HN (and H,) nuclear Overhauser effects (NOEs), hydrogen bonds, dihedral angle constraints from chemical shifts, and the following paramagnetism-based constraints: 1) pseudocontact shifts, acquired by substituting one (or more) lanthanide(s) in the C-terminal calcium binding site; 2) NHN residual dipolar couplings due to self-orientation induced by the paramagnetic lanthanide(s); 3) cross-correlations between the Curie and internuclear dipole,dipole interactions; and 4) paramagnetism-induced relaxation rate enhancements. An upper distance limit for internuclear distances between any two backbone atoms was also given according to the molecular weight of the protein. For this purpose, the paramagnetism-based constraints were collectively implemented in the program CYANA for solution structure determinations, similarly to what was previously done for the program DYANA. The method is intrinsically suitable for large molecular weight proteins. [source] Large molecules in space?ASTRONOMY & GEOPHYSICS, Issue 6 2003David Williams First page of article [source] Effect of gamma-ray irradiation on the physicochemical properties of flour and starch granule structure for wheatINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 4 2009Jun Wang Summary Effect of gamma irradiation on the physicochemical properties of flour and starch granule structure of wheat was compared to non-irradiated wheat. The moisture content of wet gluten and titratable acidity of wheat flour were significantly affected by gamma irradiation. This treatment also destroyed the starch granules of wheat grain and their breakage augmented as the dose of gamma irradiation increased, apparently resulting in the increase of small starch granules. Probably, these results were due to the disruption of large molecule, such as proteins, lipids and starch. The irradiated wheat flour for RVA pasting properties (flour viscosity) was also evaluated. Besides the difference in RVA profile, starch pasting curves showed a considerable decrease for six main parameters as gamma irradiation dose at different velocity increased. [source] Singlet states open the way to longer time-scales in the measurement of diffusion by NMR spectroscopyCONCEPTS IN MAGNETIC RESONANCE, Issue 1 2008Simone Cavadini Abstract Nuclear magnetic resonance is a powerful nonintrusive technique for measuring diffusion coefficients through the use of pulsed field gradients. The main limitation to the application range of this method is imposed by the relaxation time constants of the magnetization. The recently introduced singlet-state spectroscopy affords obtaining relaxation time constants for pairs of coupled spins which can be longer by more than an order of magnitude than the spin-lattice relaxation time constants. We review in this paper the advantages that are offered by these long relaxation time constants for diffusion measurements. Using experiments that combine singlet-state and diffusion spectroscopy, slower diffusion constants can be determined. The coupling of the two methods constitutes an alternative to the use of special probes equipped with strong gradients for the study of large molecules that diffuse slowly in solution. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part A 32A: 68,78, 2008. [source] Allergic contact dermatitis to copolymers in cosmetics , case report and review of the literatureCONTACT DERMATITIS, Issue 5 2006Sarah Quartier Copolymers or heteropolymers are large molecules with high molecular weights (>1000 D). They have been underestimated for a long time as to their sensitizing capacities. Allergic contact dermatitis to 6 copolymers in cosmetics and 1 in a medical dressing has been described; however, the nature of the hapten is still unknown. We report a case of allergic contact dermatitis to polyvinylpyrrolidone (PVP)/hexadecene copolymer in a purple-colored lipstick and review the literature on allergic contact dermatitis to 7 copolymers: PVP/hexadecene, PVP/eicosene, PVP/1-triacontene, methoxy polyethyleneglycol (PEG)-22/dodecyl glycols, methoxy PEG-17/dodecyl glycols, phthalic anhydride/trimellitic anhydride/glycols, and polyvinyl methyl/maleic acid anhydride. [source] Platelet activating factor (PAF) increases plasma protein extravasation and induces lowering of interstitial fluid pressure (Pif) in rat skinACTA PHYSIOLOGICA, Issue 1 2005V. V. Iversen Abstract Aim:, To investigate the ability of the microdialysis technique to measure capillary selectivity of different sized plasma proteins induced by local administration of platelet activating factor (PAF). Methods:, We used hollow plasmapheresis fibres with 3 cm membrane (cut off 3000 kDa) placed on the back of anaesthetized rats. Results:, Platelet activating factor (50 ,g mL,1) administered locally via the fibre, increased extravasation of radiolabelled 125I-HSA from plasma to the microdialysis fibre by approximately 900% compared both to baseline and the control fibre within 70 min (n = 6, P < 0.05). The extravasation in the control fibre did not change over time. HPLC measurement of plasma proteins in the microdialysis perfusate also demonstrated decreased capillary selectivity for proteins in the diameter range of 73 Å, 56 Å and 39 Å after local administration of PAF (n = 6, P < 0.05). PAF also significantly lowered interstitial fluid (Pif) pressure after subcutaneous administration (50 ,g mL,1). Mean arterial pressure (MAP) after intravenous injection of PAF (0.4 ,g kg,1) fell instantly by about 50 mmHg, and stabilized at 50 mmHg after 15 min (n = 6). MAP was unaltered when PAF was given through the microdialysis fibre (n = 4). Both total tissue water (TTW) and extravasation of albumin, measured as the plasma-to-tissue clearance (E-alb) showed a significant increase after PAF (n = 7, P < 0.05). Conclusions:, The present study demonstrates that PAF induces plasma protein extravasation and decrease capillary selectivity of different sized plasma proteins. It also increases transcapillary fluid flux, and lowers Pif, indicating a role for PAF in the interstitium for generation of transcapillary transport of water and large molecules followed by formation of oedema. [source] Cover Picture: Electrophoresis 4'09ELECTROPHORESIS, Issue 4 2009Article first published online: 26 FEB 200 Issue no. 4 is a special issue on "CEC and EKC" containing 20 papers including 2 Fast Track papers. The first Fast Track paper deals with high-resolution computer simulations of EKC while the second Fast Track paper reports the use of camera cell phone to detect the gold nanoparticle-labeled immunoassay results on microfluidic chip. The remaining 18 papers of this special issue are distributed into four parts. Part I is on monolithic capillaries for CEC and has five papers demonstrating the continuous efforts in developing novel monolithic stationary phases. Part II, which assembles six contributions, is on various aspects of MEKC separations of a wide range of compounds in the presence of different types of micelles. On-line concentration cum EKC/CEC is the subject of Part III that has five contributions demonstrating signal enhancement for various small and large molecules. This issue concludes with Part IV on enantioseparations by chiral EKC and CEC. [source] Deposition of Functionalized Cr7Ni Molecular Rings on Graphite from the Liquid PhaseADVANCED FUNCTIONAL MATERIALS, Issue 10 2010Alberto Ghirri Abstract Graphite is a clean substrate and its nanostructures hold great potential for applications. Anchoring large molecules on graphite represents a challenge for several reasons that essentially rise from the planar bonds of the packed honeycomb structure of carbon. Here, a systematic investigation by AFM and XPS on different derivatives of molecular Cr7Ni rings deposited on highly oriented pyrolytic graphite (HOPG) is reported. Cr7Ni is emerging as a prototipical example of molecular antiferromagnet on which quantum phenomena and coherence have been demonstrated. For the deposition of Cr7Ni on HOPG, two strategies are adopted: 1) Cr7Ni rings are functionalized with extended alkyl/benzene terminations and 2) a self-assembled monolayer of alkyl chains with sulfonate terminations is deposited and then a cationic Cr7Ni derivative is used. In both cases the electronic bond with the carbon surface is soft, but the two-step procedure is efficient, albeit indirect, in sticking molecular Cr7Ni on HOPG. These strategies can be easily extended to deposit other complex molecular aggregates on graphite from the liquid phase. [source] Drug,Membrane Interaction on Immobilized Liposome Chromatography Compared to Immobilized Artificial Membrane (IAM), Liposome/Water, and Octan-1-ol/Water SystemsHELVETICA CHIMICA ACTA, Issue 2 2010Xiangli Liu Abstract The objective of this study was to investigate drug,membrane interaction by immobilized liposome chromatography (ILC; expressed as lipophilicity index log,Ks) and the comparison with lipophilicity indices obtained by liposome/H2O, octan-1-ol/H2O, and immobilized artificial membrane (IAM) systems. A set of structurally diverse monofunctional compounds and drugs (nonsteroidal anti-inflammatory drugs and , -blockers) were selected in this study. This set of solutes consists of basic or acidic functionalities which are positively or negatively charged at physiological pH,7.4. No correlation was found between log,Ks from ILC and lipophilicity indices from any of the other membrane model systems for the whole set of compounds. For structurally related compounds, significant correlations could be established between log,Ks from ILC and lipophilicity indices from IAM chromatography and octan-1-ol/H2O. However, ILC and liposome/H2O systems only yield parallel partitioning information for structurally related large molecules. For hydrophilic compounds, the balance between electrostatic and hydrophobic interactions dominating drug partitioning is different in these two systems. [source] Effect of packing density of hollow fibers on solute removal performances of dialyzersHEMODIALYSIS INTERNATIONAL, Issue 2009Akihiro C. YAMASHITA Abstract Solute removal performances of dialyzers are dependent not only on the solute permeabilities of the membrane but also on the module design. We have investigated how the packing density of hollow fiber (PDF) affects the solute removal performances. A series of 4 polyester polymer alloy membrane test dialyzers were assembled with varying PDFs of 29.6%, 35.3%, 44.1%, and 53.1%. Clearances (CL) were measured in vitro for creatinine (MW113), vitamin B12 (MW1355), and chymotrypsin (MW25300) with various QB=100 to 400 and QD=350 to 650 mL/min in the absence of net ultrafiltration. When QB was ,300 mL/min, no significant changes were found in creatinine CL with the increase of PDF up to 35.3%. A slightly greater increase was found in CL when QB=400 mL/min. Clearances for vitamin B12, however, increased with the increase of PDF in the range of 29.6% to 35.3%. The effects of PDF on CL were greater with larger QB. More importantly, an abrupt increase of CL was found when PDF was increased from 44.1% to 53.1%. According to a rigorous mathematical model, this may be caused by the internal filtration, which is reverse ultrafiltration occurring in a dialyzer at any given time. No significant increase was found in chymotrypsin CL when the PDF was ,35.3%, which suggested that CL for large molecules was strongly dependent on the solute permeability rather than the conditions of flow patterns. A very steep increase was also found in CL for chymotrypsin when the PDF was >44.1%, which was also considered to be due to the internal filtration. Packing density of hollow fiber can be optimized in terms of solute removal performances when the target solute and therapeutic conditions are specified. [source] Polarized basis sets for accurate calculations of static and dynamic electric properties of moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2010Angelika Baranowska Abstract We report on the development and testing of large polarized basis sets (LPolX, where X is the element symbol) for accurate calculations of linear and nonlinear electric properties of molecules. The method used to generate LPolX sets is based on our studies of the analytic dependence of Gaussian functions on external time-independent and time-dependent electric fields. At variance with the earlier investigations of small, highly compact (ZPolX) basis sets for moderately accurate calculations of electric properties of large molecules, the present goal is to obtain basis sets that are nearly saturated with respect to the selected class of electric properties and can be used for accurate studies of interaction-induced properties. This saturation makes the LPolX sets also useful in calculations of optical properties for chiral molecules. In this article, the LPolX sets are generated for X = H, C, N, O, and F, and examined in calculations of linear and nonlinear electric properties of four standard test systems: HF, N2, CO, and HCN. The study of the performance of LPolX basis sets has been carried out at different levels of approximation ranging from the SCF HF method to highly correlated CCSD(T) approach. The results obtained in this study compare favorably with accurate reference data and show a high level of saturation of LPolX basis sets with respect to the polarization effect due to external electric fields. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Selected excitation for CAS-SDCI calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2007Benoît Bories Abstract A new selected-configuration interaction method is proposed, based on the use of local orbitals. A corresponding code has been written, which is devoted to CI calculations of rather large systems (about 50,100 carbon-like atoms). Taking advantage of the locality, and then of the fact that interactions vanish when the distance is large, the dimension of the CI space is largely reduced. The determinants that would be created by long range excitations are expected to have a small weight in the wave function and are therefore eliminated. This selected excitation CI space is particularly suited for large molecules. It is tested on large polyene chains and on a transition metal complex. For large enough systems, the CPU time saving is important and, what is more noticeable, calculations that were impossible to perform without selection are feasible in this approach. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 632,643, 2007 [source] Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2007Ross C. Walker Abstract The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 478,490, 2007 [source] A new parallel algorithm of MP2 energy calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2006Kazuya Ishimura Abstract A new parallel algorithm has been developed for second-order Møller,Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2,16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C47H51NO14) and luciferin (C11H8N2O3S2), the former with the 6-31G* and 6-311G** basis sets (1032 and 1484 basis functions, 164 correlated orbitals), and the latter with the aug-cc-pVDZ and aug-cc-pVTZ basis sets (530 and 1198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C130H10 (1970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 407,413, 2006 [source] Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2003K. Babu Abstract The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree,Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N3) scaling order within HF theory to an n·O(N,3) one, where n is the number of fragments and N,, the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 484,495, 2003 [source] Activation of large lons in FT-ICR mass spectrometryMASS SPECTROMETRY REVIEWS, Issue 2 2005Julia Laskin Abstract The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has enabled the extension of mass spectrometric methods to large molecules and molecular complexes. This both greatly extends the applications of mass spectrometry and makes the activation and dissociation of complex ions an integral part of these applications. This review emphasizes the most promising methods for activation and dissociation of complex ions and presents this discussion in the context of general knowledge of reaction kinetics and dynamics largely established for small ions. We then introduce the characteristic differences associated with the higher number of internal degrees of freedom and high density of states associated with molecular complexity. This is reflected primarily in the kinetics of unimolecular dissociation of complex ions, particularly their slow decay and the higher energy content required to induce decomposition,the kinetic shift (KS). The longer trapping time of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) significantly reduces the KS, which presents several advantages over other methods for the investigation of dissociation of complex molecules. After discussing general principles of reaction dynamics related to collisional activation of ions, we describe conventional ways to achieve single- and multiple-collision activation in FT-ICR MS. Sustained off-resonance irradiation (SORI),the simplest and most robust means of introducing the multiple collision activation process,is discussed in greatest detail. Details of implementation of this technique, required control of experimental parameters, limitations, and examples of very successful application of SORI-CID are described. The advantages of high mass resolving power and the ability to carry out several stages of mass selection and activation intrinsic to FT-ICR MS are demonstrated in several examples. Photodissociation of ions from small molecules can be effected using IR or UV/vis lasers and generally requires tuning lasers to specific wavelengths and/or utilizing high flux, multiphoton excitation to match energy levels in the ion. Photodissociation of complex ions is much easier to accomplish from the basic physics perspective. The quasi-continuum of vibrational states at room temperature makes it very easy to pump relatively large amounts of energy into complex ions and infrared multiphoton dissociation (IRMPD) is a powerful technique for characterizing large ions, particularly biologically relevant molecules. Since both SORI-CID and IRMPD are slow activation methods they have many common characteristics. They are also distinctly different because SORI-CID is intrinsically selective (only ions that have a cyclotron frequency close to the frequency of the excitation field are excited), whereas IRMPD is not (all ions that reside on the optical path of the laser are excited). There are advantages and disadvantages to each technique and in many applications they complement each other. In contrast with these slow activation methods, the less widely appreciated activation method of surface induced dissociation (SID) appears to offer unique advantages because excitation in SID occurs on a sub-picosecond time scale, instantaneously relative to the observation time of any mass spectrometer. Internal energy deposition is quite efficient and readily adjusted by altering the kinetic energy of the impacting ion. The shattering transition,instantaneous decomposition of the ion on the surface,observed at high collision energies enables access to dissociation channels that are not accessible using SORI-CID or IRMPD. Finally, we discuss some approaches for tailoring the surface to achieve particular aims in SID. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:135,167, 2005 [source] A New Group Contribution Method based on Equation of State Parameters to Evaluate the Critical Properties of Simple and Complex MoleculesTHE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2006José O. Valderrama Abstract A new group contribution method to evaluate the critical properties (temperature, pressure and volume) is presented and applied to estimate the critical properties of biomolecules. Similar to other group contribution methods, the one proposed here divides the molecule into conveniently defined groups and evaluates the properties as the sum of the different contributions according to a specified model equation for each of the properties. The proposed method consists of a one-step calculation that uses simple model equations and does not require additional data besides the knowledge of the structure of the molecule, except for isomers. For these substances the normal boiling temperature, the molecular mass and the number of atoms in the molecule are used to distinguish among isomers. The method is applicable to high molecular weight compounds, as most biomolecules and large molecules present in natural products. On présente une nouvelle méthode de contribution de groupe pour évaluer les propriétés critiques (température, pression et volume) de biomolécules. Comme dans le cas d'autres méthodes de contribution de groupe, celle qu'on présente ici divise la molécule en groupes définis de manière pratique et évalue les propriétés comme la somme des différentes contributions selon une équation de modèle spécifique pour chacune des propriétés. La méthode proposée consiste en un calcul en une étape qui utilise des équations de modèle simple et, excepté pour les isomères, ne requiert pas de données supplémentaires hormis la structure de la molécule. Pour ces substances, on utilise la température d'ébullition normale, la masse moléculaire et le nombre d'atomes dans la molécule pour distinguer entre les isomères. La méthode est applicable à des composés de poids moléculaire élevé, comme la plupart des biomolécules et des molécules larges présentes dans les produits naturels. [source] A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large moleculesACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2004Virginie Pichon-Pesme The differences between two databases describing the polypeptide main chain in terms of charge-density parameters, directly usable in protein structure refinements, are discussed. These databases contain averaged multipole populations of peptide pseudo-atoms obtained from refinement against theoretical simulated data and against high-resolution experimental data on small peptide or amino acid molecules. The main discrepancy becomes apparent when electrostatic properties are calculated. [source] On a fast calculation of structure factors at a subatomic resolutionACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2004P. V. Afonine In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9,Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high-quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small-molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re-examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362,367; Ten Eyck (1977). Acta Cryst. A33, 486,492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct-formulae calculations. The impact of the different parameters on the computer efficiency of structure-factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested. [source] Continuum molecular electrostatics, salt effects, and counterion binding,A review of the Poisson,Boltzmann theory and its modificationsBIOPOLYMERS, Issue 2 2008Grochowski Abstract This work is a review of the Poisson,Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding. The PB model is one of the mesoscopic theories that describes the electrostatic potential and equilibrium distribution of mobile ions around molecules in solution. It serves as a tool to characterize electrostatic properties of molecules, counterion association, electrostatic contributions to solvation, and molecular binding free energies. We focus on general formulations which can be applied to large molecules of arbitrary shape in all-atomic representation, including highly charged biomolecules such as nucleic acids. These molecules present a challenge for theoretical description, because the conventional PB model may become insufficient in those cases. We discuss the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT, simple empirical extensions to this model accounting for finite size of ions, the modified PB theory including ionic correlations and fluctuations, the cell model, and supplementary methods allowing to incorporate site-bound ions in the PB calculations. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 93,113, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Control of Drug Release through the In Situ Assembly of Stimuli-Responsive Ordered Mesoporous Silica with Magnetic ParticlesCHEMPHYSCHEM, Issue 17 2007Shenmin Zhu Dr. Abstract A site-selective controlled delivery system for controlled drug release is fabricated through the in situ assembly of stimuli-responsive ordered SBA-15 and magnetic particles. This approach is based on the formation of ordered mesoporous silica with magnetic particles formed from Fe(CO)5 via the surfactant-template sol-gel method and control of transport through polymerization of N-isopropyl acrylamide inside the pores. Hydrophobic Fe(CO)5 acts as a swelling agent as well as being the source of the magnetic particles. The obtained system demonstrates a high pore diameter (7.1 nm) and pore volume (0.41 cm3,g,1), which improves drug storage for relatively large molecules. Controlled drug release through the porous network is demonstrated by measuring the uptake and release of ibuprofen (IBU). The delivery system displays a high IBU storage capacity of 71.5 wt,%, which is almost twice as large as the highest value based on SBA-15 ever reported. In vitro testing of IBU loading and release exhibits a pronounced transition at around 32,°C, indicating a typical thermosensitive controlled release. [source] Determining Molecular Structures and Conformations Directly from Electron Diffraction using a Genetic AlgorithmCHEMPHYSCHEM, Issue 2 2006Scott Habershon Dr. Abstract A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all- trans retinal and p -coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data. [source] Calculation of conformational energies and optical rotation of the most simple chiral alkane,CHIRALITY, Issue 9 2008Stefan Grimme Abstract Quantum chemical calculations have been performed to investigate the conformer distribution of 4-ethyl-4-methyloctane and its optical rotation. With the reference methods MP2 and SCS-MP2, the energies of seven conformers are found within a range of about 1.5 kcal mol,1. It is demonstrated that the relative energies cannot be reliably predicted with conventional GGA or hybrid density functionals, Hartree-Fock, semiempirical AM1, and classical force field (MM3) calculations. An empirical dispersion correction to GGA (PBE-D), hybrid (B3LYP-D), or double hybrid (B2PLYP-D) functionals corrects these errors and results in very good agreement with the reference energies. Optical rotations have been calculated for all seven conformers at the TDDFT(BHLYP/aTZV2P) level. The computed macroscopic rotation is derived from a classical Boltzmann average. The result (1.9,3.2 deg dm,1 (g/mL),1) is very close to the experimental value of 0.2 deg dm,1 (g/mL),1 for the (R)-enantiomer and has the right sign. Because six conformers are significantly populated at room temperature and the rotations of individual conformers differ in sign and magnitude, the calculated average rotation is rather sensitive to the conformer population used. From the electronic structure point of view, this example emphasizes the effect of long-range dispersion effects for the evaluation of population averaged quantities in large molecules. Computations based on free enthalpies are in worse agreement with experiment that is attributed to artefacts of the harmonic approximation used to compute the vibrational entropy terms. Chirality, 2008. © 2008 Wiley-Liss, Inc. 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