Inverse design and synthesis of acac-coumarin anchors for robust TiO2 sensitization

An inverse design methodology suitable to assist the synthesis and optimization of molecular sensitizers for dye-sensitized solar cells is introduced. The method searches for molecular adsorbates with suitable photoabsorption properties through continuous optimization of "alchemical" structures in the vicinity of a reference molecular framework. The approach is illustrated as applied to the design and optimization of linker chromophores for TiO(2) sensitization, using the recently developed phenyl-acetylacetonate (i.e., phenyl-acac) anchor [McNamara et al. J. Am. Chem. Soc.2008, 130, 14329-14338] as a reference framework. A novel anchor (3-acac-pyran-2-one) is found to be a local optimum, with improved sensitization properties when compared to phenyl-acac. Its molecular structure is related to known coumarin dyes that could be used as lead chromophore anchors for practical applications in dye-sensitized solar cells. Synthesis and spectroscopic characterization confirms that the linker provides robust attachment to TiO(2), even in aqueous conditions, yielding improved sensitization to solar light and ultrafast interfacial electron injection. The findings are particularly relevant to the design of sensitizers for dye-sensitized solar cells because of the wide variety of structures that are possible but they should be equally useful for other applications such as ligand design for homogeneous catalysis.     

Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

A method of structure-based ligand design – DycoBlock – has been proposed and tested by Liu et al.[1]. It was further improved by Zhu et al. and applied to design new selective inhibitors of cyclooxygenase 2 [2]. In the current work, we present a new methodology – F-DycoBlock that allows for the incorporation of receptor flexibility. During the designing procedure, both the receptor and molecular building blocks are subjected to the multiple-copy stochastic molecular dynamics (MCSMD) simulation [1], while the protein moves in the mean field of all copies. It is tested for two enzymes studied previously – cyclooxygenase 2 (COX-2) and human immunodeficiency type 1 (HIV-1) protease. To identify the applicability of F-DycoBlock, the binding protein structure was used as starting point to explore the conformational space around the bound state. This method can be easily extended to accommodate the flexibility in different degree. Four types of treatment of the receptor flexibility – all-atom restrained, backbone restrained, intramolecular hydrogen-bond restrained and active-site flexible – were tested with or without the grid approximation. Two inhibitors, SC-558 for COX-2 and L700417 for HIV-1 protease, are used in this testing study for comparison with previous results. The accuracy of recovery, binding energy, solvent accessible surface area (SASA) and positional root-mean-square (RMS) deviation are used as criteria. The results indicate that F-DycoBlock is a robust methodology for flexible drug design. It is particularly notable that the protein flexibility has been perfectly associated with each stage of drug design – search for the binding sites, dynamic assembly and optimization of candidate compounds. When all protein atoms were restrained, F-DycoBlock yielded higher accuracy of recovery than DycoBlock (100%). If backbone atoms were restrained, the same ratio of accuracy was achieved. Moreover, with the intramolecular hydrogen bonds restrained, reasonable conformational changes were observed for HIV-1 protease during the long-time MCSMD simulation and L700417 was reassembled at the active site. It makes it possible to study the receptor motion in the binding process.     

A quasiclassical trajectory study of the time-delayed forward scattering in the hydrogen exchange reaction

The time-delayed forward scattering mechanism recently identified by Althorpe et al. [Nature (London) 416, 67 (2002)] for the H+D(2)(v=0,j=0)-->HD(v(')=3,j(')=0)+D reaction was analyzed by using quasiclassical trajectory (QCT) methodology. The QCT results were found to match the quantum wavepacket snapshots of Althorpe et al., albeit without the quantum scattering effects. Trajectories were analyzed on the fly to investigate the dynamics of the atoms during the reaction. The dominant reaction mechanism progresses from hard collinear impacts, leading to direct recoil, toward glancing impacts. The increased time required for forward scattered trajectories is due to the rotation of the transient HDD complex. Forward scattered trajectories display symmetric stretch vibrations of the transient HDD complex, a signature of the presence of a resonance, or a quantum bottleneck state.     

Hybrid process scheme for the synthesis of ethyl lactate: conceptual design and analysis

Hybrid processes have received increased attention in the field of chemical and biochemical engineering because of their ability to overcome certain obstacles related to thermodynamics of the separation task to be carried out. Usually, in a hybrid process two processes are coupled; either reaction with separation or two different separation processes. In the design of such hybrid systems, the performance of each constituent element has to be taken into account, while their optimisation must account for their interdependency. In this paper, the methodology presented by Mitkowski et al. (2009a) is applied to design and analyse a hybrid process scheme for the synthesis of ethyl lactate. Generated hybrid process schemes have been validated through computer-aided simulations.     

Computational design of enzymes

The de novo design of enzymes with activities not found in natural biocatalysts is a major challenge for molecular biology. Sophisticated computational methods have recently led to impressive progress in this exciting and rapidly evolving field (R?thlisberger et al., 2008; Jiang et al., 2008).     

Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach

Breen et al. (Electrophoresis 2000; 21: 2243) proposed a method for finding monoisotopic peptide peaks in mass spectra based on an approximation of the distribution of different isotopic variants of a peptide by a Poisson distribution. They developed the method using all protein sequences from the SWISS-PROT database. We investigate the suitability of this method to predict the isotopic distribution in an environment which enriches for peptides carrying sulphur. More specifically, we focus on mass spectra obtained by a COmbined FRActional DIagonal Chromatography (COFRADIC) approach, developed by Gevaert et al. (Nature Biotechnology 2003; 21: 566), targeting a specific subset of peptides, in this case the N-terminal peptides. One can therefore ask whether the original results of Breen et al. apply to spectra generated by the particular COFRADIC method. We investigate whether the proposed approximation holds for N-terminal peptides. We also evaluate whether ignoring sulphur atoms while developing the approximation, as proposed by Breen et al., does not increase the risk of missing monoisotopic peaks corresponding to sulphur-containing peptides. Finally, we check the sensitivity of the quality of the approximation to optimization criteria used in the development process. The results are not simply restricted to a COFRADIC setting but are also applicable more generally, for any method which enriches for sulphur-containing peptides.     

Resonance light scattering and derived techniques in analytical chemistry: past, present, and future

From 1993 to 1995, with a conventional fluorescence spectrophotometer (CFS) (convenient) and working in a synchronous scan model (easy-to-use), Pasternack et al. proposed the resonance light-scattering (RLS) technique, to efficiently characterize self-assemblies or self-aggregations of chromophores with good electronic coupling. Incident wavelengths were specially considered within their absorption envelopes (rather unorthodox), and their amplified signals were observed (good sensitivity and selectivity). Due to these absorbing benefits, RLS technique, as a novel readout method, commenced on its exciting analytical tours soon after Liu et al. and especially Li et al., separately, set out their corresponding pioneering investigations from 1995 to 1997. From then on, it has received an increasing attention by analysts, as a consequence exhibiting more and more fascinating analytical applications. Moreover, various attractive RLS-derived techniques have been developed successively to improve it or to enlarge its possibilities. Later on, Liu et al. and Li et al., Tabak et al., Yguerabide et al., Huang et al., Lakowicz et al. and Fernández Band et al. have made their outstanding contributions. In this review, we concentrate on major achievements of RLS in analytical chemistry for over a decade, involving the developments and analytical applications of RLS derived techniques treated as an impacting progress of RLS technique in analytical chemistry. Finally, an indication of future directions of RLS technique in analytical chemistry is provided.     

A mass spectrometric study of Al(2)O(3)-SiO(2) melts using a Knudsen cell

The thermodynamic activities of SiO(2) in Al(2)O(3)-SiO(2) liquid slags were measured by the high-temperature Knudsen cell mass spectromeric method in the present work. The measurements were carried out in the temperature range 1863-2169 K. Tungsten crucibles were used to hold the slags. The system was calibrated using a CaF(2) standard. The mass spectra obtained for pure SiO(2) were in agreement with earlier data. The activities of silica, measured in the present work at 2150 K, show a slight negative deviation at very low alumina mole fractions which changed to a positive deviation at higher alumina contents. The activity values are in reasonable agreement with the assessment carried out by Hillert et al. The results were analysed on the basis of a slag model developed earlier at KTH, Stockholm. The present results are found to be compatible with the phase diagram proposed by Klug et al.     

Modeling the electrophoresis of peptides and proteins: improvements in the "bead method" to include ion relaxation and "finite size effects"

A bead model methodology developed in our lab (Xin et al. J. Phys. Chem. B 2006, 110, 1038) and applicable to modeling the free solution electrophoretic mobility of peptides and proteins is generalized in two significant ways. First, an approximate account is taken of the relaxation effect, which makes the methodology applicable to more highly charged peptides and proteins than was previously possible. Second, a more accurate account is taken of the finite size of the beads making up the model structure. This improvement makes the method applicable at higher salt concentrations and/or to models consisting of larger sized subunits. The relaxation effect is accounted for by correcting "unrelaxed" mobilities on the basis of model size and average electrostatic surface, or zeta potential. Correction factors are estimated using those of spheres with the same hydrodynamic radius and zeta potential as the model structure. The correction factors of spheres are readily determined. The more general methodology is first applied to two sets of peptides (74 different peptides total) varying in size from 2 to 42 amino acids. The sets also cover a wide range of net charges. It is shown that accounting for finite bead size results in a small change in model mobilities under the conditions of the experiments (35 mM monovalent salt). The correction for ion relaxation, however, can be significant for highly charged peptides and improves agreement between model and experimental mobilities. Our correction procedure is also tested by examining the electrophoretic mobility of a particular protein "charge ladder" (Carbeck et al. J. Am. Chem. Soc. 1999, 121, 10,671), where the protein charge is varied over a wide range yet the conformation remains essentially constant. In summary, the effects of ion relaxation can be significant if the absolute electrophoretic mobility of a peptide exceeds approximately 0.20 cm2/(kV s).     

Semi-empirical models for auger electron energy calculations

Three approaches to the semi-empirical calculation of Auger electron energies developed by Shirley et al., Larkins and Hoogewijs et al. respectively are critically discussed using a common notation.     

DNA sequence design based on template strategy

In DNA based computation and DNA nanotechnology, the design of proper DNA sequences has turned out to be an elementary problem. This paper takes a further look at the template strategy proposed in work by Frutos, A. G. et al. (Nucleic Acids Res. 1997, 25, 4748-4757). The H-measure proposed by Garzon et al. (Proceedings of the Second Annual Genetic Programming Conference, 1997; pp 472-487) is combined in this strategy to optimize the template and map sets obtained. Finally we describe a constructing method that can still produce more sequences by the results obtained in this paper.     

Using electrophoretic mobility and bead modeling to characterize the charge and secondary structure of peptides

Using a modeling methodology developed in our laboratory previously, the free solution electrophoretic mobilities of several peptides are examined to see what they can tell us about: (i) the pK(a)s of specific side groups, and (ii) possible secondary structure. Modeling is first applied to mobility versus pH data of several small peptides (Messana, I. et al., J. Chromatogr. B 1997, 699, 149) where the only adjustable parameter associated with the charge state of the peptide is the pK(a )of the C-terminal. In addition to examining this parameter, the question of possible secondary structure is addressed. For two of the peptides considered, GGNA and GGQA, it is possible to account for the observed mobilities using "random" models with little restriction on the allowed range of Phi-Psi angles. For GGRA and RPPGF, "compact" models (possibly involving an I-turn) must be used to match modeling mobilities with experiment. Finally, three more complicated peptides ranging in size from 15 to 20 amino acids are also examined and characterized (Sitaram, B. R. et al., J. Chromatogr. A 1999, 857, 263). Here also, we find evidence of I-turns or some other "compact" structure in two of the three peptides examined.     

Do benzodiazepines mimic reverse-turn structures?

The role of benzodiazepine derivatives (BZD) as a privileged scaffold that mimics beta-turn structures (Ripka et al. (1993) Tetrahedron 49:3593-3608) in peptide/protein recognition was reexamined in detail. Stable BZD ring conformers were determined with MM3, and experimental reverse-turn structures were extracted from the basis set of protein crystal structures previously defined by Ripka et al. Ideal beta-turns were also modeled and similarly compared with BZD conformers. Huge numbers of conformers were generated by systematically scanning the torsional degrees of freedom for BZDs, as well as those of ideal beta-turns for comparison. Using these structures, conformers of BZDs were fit to experimental structures as suggested by Ripka et al., or modeled classical beta-turn conformers, and the root-mean-square deviation (RMSD) values were calculated for each pairwise comparison. Pairs of conformers with the smallest RMSD values for overlap of the four alpha-beta side-chain orientations were selected. All overlaps of BZD conformers with experimental beta-turns yielded one or more comparisons where the least RMSD was significantly small, 0.48-0.86 angstroms, as previously suggested. Utilizing a different methodology, the overall conclusion that benzodiazepines could serve as reverse-turn mimetics of Ripka et al. is justified. The least RMSD values for the overlap of BZDs and modeled classical beta-turns were also less than 1 angstrom. When comparing BZDs with experimental or classical beta-turns, the set of experimental beta-turns selected by Ripka et al. fit the BZD scaffolds better than modeled classical beta-turns; however, all the experimental beta-turns did not fit a particular BZD scaffold better. A single BZD ring conformation, and/or chiral orientation, can mimic some, but not all, of the experimental beta-turn structures. BZD has two central ring conformations and one chiral center that explains why the four variations of the BZD scaffold can mimic all types of beta-turn structure examined. It was found, moreover, that the BZD scaffold also mimics each of the nine clusters of experimental orientations of side chains of reverse turns in the Protein Data Bank, when the new classification scheme for the four side-chain directions (the relative orientations of alpha-beta vectors of residues i through i+3) was considered (Tran et al. (2005) J Comput-Aided Mol Des 19:551-566).     

Statistical thermodynamics models for polyatomic adsorbates: application to adsorption of n-paraffins in 5A zeolite

Experimental adsorption isotherms of five n-paraffins (ethane, propane, butane, pentane, and hexane) in 5A zeolite were described by means of a statistical thermodynamics model for linear adsorbates (MLA) developed by Ramirez-Pastor et al. (1999) and compared with the well-known multisite Langmuir model (MSL) of Nitta et al. (1984). The experimental data, obtained by different authors in a wide range of temperatures and pressures, were correlated by using an algorithm of multiple fitting. Two main conclusions were drawn from the analysis of experimental data: (i) for small molecules (ethane, propane), MLA is the more accurate model, validating the hypothesis of the linear rigid character of the adsorbate and reinforcing previous results obtained from the analysis of computational experiments developed for dimers and linear trimers; (ii) for large molecules (n-butane, n-pentane, n-hexane), the better performance of the MSL model suggests that the admolecules adsorb in a nonlinear structure. The isosteric heat of adsorption dependence on the number of carbons obtained from our study, ranging between 23.84 kJ/mol for ethane and 59.26 kJ/mol for hexane, showed a very good agreement with previous results reported in the literature, confirming the consistency of our analysis.     

含o-Me2N-C6H4-C(CH3)(CH3)-基团的茂铬催化剂的合成及催化乙烯聚合研究

High-density polyethylene (PE) was developed in the 1950s by Hogan et al[1] using a Cr2O3/SiO2 catalyst and by the Union Carbide Corporation[2,3] using a Cp2Cr catalyst. Chromium catalysts have played a key role in the early development of heterogeneous catalysts for the alkene polymerization.     

Artificial neural network modeling of peptide mobility and peptide mapping in capillary zone electrophoresis

Recently, we have developed an artificial neural network model, which was able to predict accurately the electrophoretic mobilities of relatively small peptides. To examine the robustness of this methodology, a 3-3-1 back-propagation artificial neural network (BP-ANN) model was developed using the same inputs as the previous model, which were the Offord's charge over mass term (Q/M(2/3)), corrected steric substituent constant (E(s,c)) and molar refractivity (MR). The data set consisted of 102 peptides with a larger range of size than that of our earlier report - up to 42 amino acid residues as compared to 13 amino acids in the initial study - that also included highly charged and hydrophobic peptides. The entire data set was obtained from the published result by Janini and co-workers. The results of this model are compared with those obtained using multiple linear regressions (MLR) model developed in this work and the multi-variable model released by Janini et al. Better predictive ability of the BP-ANN model over the MLR indicates the non-linear characteristics of the electrophoretic mobility of peptides. The present model exhibits better robustness than the MLR models in predicting CZE mobilities of a diverse data set at different experimental conditions. To explore the utility of the ANN model in simulation of the CZE peptide maps, the profiles for the endoproteinase digests of melittin, glucagon and horse cytochrome C is studied in the present work.     

Electrooxidation of Azulene Compounds

Azulenoid, a parent structure of bicyclo[5,3,0] decapentaene with 10 π-electrons, is a class of the fused bicyclic compounds, non-benzenoid hydrocarbons. It is essentially used for the dye materials, the medical treatment of inflammation and hypertension and the development of liquid crystals. More recently, azulopquinones have been found to exhibit a significant antitumor activity. In the early organic electrochemical studies, azulene was first known the oxidation potential, 0.91 V vs SCE in acetic acid. The reversible and irreversible reduction potential,-1.6 V and -2.6 V vs Ag/AgCl in liquid methyl amine and dimethyl amine, respectively, were measured by Heinze et al in 1989 using cyclovoltammetric method. The conducting polymers were successfully developed from azulene and 4,6,8-trimethylazulene via electropolymeriztion by Waltman et al in 1986. Recently in 1993, Shono et al revealed that azulene was easily reduced to 5,5'-biazulene or consequently to react with alkyl halides producing 1,1'-dialkyl-5,5'-biazulene.     

Theoretical studies of some nonbenzenoid hydrocarbons—IV : Pleiadiene and related compounds

Pleiadiene and other similar compounds have been studied by the semi-empirical SCFMO method of Pariser, Parr and Pople using the core resonance integral value developed by Lo and Whitehead, Dewar et al. and Yamaguchi et al. It has been found that π^*←π transitions predicted by the methods of Lo and Whiteheadand Dewar et al. suitable for the prediction of ground state properties are also in good agreement with experimental results where available and comparable to those predicted by the method of Yamaguchi et al. developed for the prediction of spectral transitions. The resonance stabilization of the molecules 3,4.5,7,8 and 9 have also been studied. It is found that ethylinic linkage across the naphthalene moity in pleiadiene increases the resonance energy of the final compound, in contrast to our previous observation, i.e. ethylinic linkage across the naphthalene moiety reduces the resonance energy of the final compound.     

Coordinated design of cofactor and active site structures in development of new protein catalysts

New methods for the synthesis of artificial metalloenzymes are important for the construction of novel biocatalysts and biomaterials. Recently, we reported new methodology for the synthesis of artificial metalloenzymes by reconstituting apo-myoglobin with metal complexes (Ohashi, M. et al., Angew Chem., Int. Ed. 2003, 42, 1005-1008). However, it has been difficult to improve their reactivity, since their crystal structures were not available. In this article, we report the crystal structures of M(III)(Schiff base).apo-A71GMbs (M = Cr and Mn). The structures suggest that the position of the metal complex in apo-Mb is regulated by (i) noncovalent interaction between the ligand and surrounding peptides and (ii) the ligation of the metal ion to proximal histidine (His93). In addition, it is proposed that specific interactions of Ile107 with 3- and 3'-substituent groups on the salen ligand control the location of the Schiff base ligand in the active site. On the basis of these results, we have successfully controlled the enantioselectivity in the sulfoxidation of thioanisole by changing the size of substituents at the 3 and 3' positions. This is the first example of an enantioselective enzymatic reaction regulated by the design of metal complex in the protein active site.