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Chemical Systems (chemical + system)
Selected AbstractsA phase-space method for arbitrary bimolecular gas-phase reactions: Theoretical descriptionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2001A. Gross Abstract A theoretical model for the calculation of rate constants for arbitrary bimolecular gas-phase reactions was developed. The method is based on the phase-space statistical method developed by Light and co-workers 1,6. In the present article this method is extended to arbitrary molecular systems. The new method requires knowledge of the molecular properties in the reaction and products channels of the chemical system. The properties are the vibrational frequencies, moments of inertia, and potential energy for the interacting species in their ground state equilibrium configuration. Furthermore, we have to calculate either the energy barrier or the long-range potential for the chemical system (if the reaction channel does not have an energy barrier). The usefulness of the method is that it can be applied to all bimolecular reactions, trimolecular reactions, and even reactions of higher orders. Therefore, it can be applied to cases where rate constants of complex chemical reactions are required, but reliable laboratory measurements or other means to estimate rate parameters are not yet possible. Even if spectroscopic data are not available for the reactants and products, it is possible to use electronic structure theory to calculate the required data. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Discrete thermodynamics of chemical equilibria and classical limit in thermodynamic simulationISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2007Boris Zilbergleyt This article sets forth comprehensive basic concepts of the discrete thermodynamics of chemical equilibrium as balance between internal and external thermodynamic forces. Conditions of chemical equilibrium in the open chemical system are obtained in the form of a logistic map, containing only one new parameter that defines the chemical system's resistance to external impact and its deviation from thermodynamic equilibrium. Solutions to the basic map are bifurcation diagrams that have quite traditional shape but the diagram areas feature specific meanings for chemical systems and constitute the system's domain of states. The article is focused on two such areas: the area of "true" thermodynamic equilibrium and the area of open chemical equilibrium. The border between them represents the classical limit, a transition point between the classical and newly formulated equilibrium conditions. This limit also separates regions of the system ideality, typical for isolated classical systems, and non-ideality due to the limitations imposed on the open system from outside. Numerical examples illustrating the difference between results of classical and discrete thermodynamic simulation methods are presented. The article offers an analytical formula to find the classical limit, compares analytical results with these obtained by simulation, and shows the classical limit dependence upon the chemical reaction stoichiometry and robustness. [source] A comparison of modern data analysis methods for X-ray and neutron specular reflectivity dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2007A. Van Der Lee Data analysis methods for specular X-ray or neutron reflectivity are compared. The methods that have been developed over the years can be classified into different types. The so-called classical methods are based on Parrat's or Abelès' formalism and rely on minimization using more or less evolved Levenberg,Marquardt or simplex routines. A second class uses the same formalism, but optimization is carried out using simulated annealing or genetic algorithms. A third class uses alternative expressions for the reflectivity, such as the Born approximation or distorted Born approximation. This makes it easier to invert the specular data directly, coupled or not with classical least-squares or iterative methods using over-relaxation or charge-flipping techniques. A fourth class uses mathematical methods founded in scattering theory to determine the phase of the scattered waves, but has to be coupled in certain cases with (magnetic) reference layers. The strengths and weaknesses of a number of these methods are evaluated using simulated and experimental data. It is shown that genetic algorithms are by far superior to traditional and advanced least-squares methods, but that they fail when the layers are less well defined. In the latter case, the methods from the third or fourth class are the better choice, because they permit at least a first estimate of the density profile to be obtained that can be refined using the classical methods of the first class. It is also shown that different analysis programs may calculate different reflectivities for a similar chemical system. One reason for this is that the representation of the layers is either described by chemical composition or by scattering length or electronic densities, between which the conversion of the absorptive part is not straightforward. A second important reason is that routines that describe the convolution with the instrumental resolution function are not identical. [source] Modified evolving window factor analysis for process monitoringJOURNAL OF CHEMOMETRICS, Issue 9 2004S. Kamaledin Setarehdan Abstract Reaction process monitoring and control are usually involved with direct measurement or indirect model-based prediction of concentration profiles of the constituents of interest in a chemical reaction at regular time intervals. These approaches are expensive, time-consuming and sometimes impossible. On the other hand, application of so-called ,calibration-free' techniques such as EFA and EWFA to spectral data usually provides important information regarding the structural variations in the chemical system without identification of the chemical components responsible for the variations. In this paper a novel spectral data pre-processing algorithm is presented which helps EWFA to extract the concentration trends of the components of interest within the reaction. The proposed algorithm uses the pure spectrum of the component of interest to develop a so-called ,weighting filter' which is applied to the input spectral information before EWFA. The algorithm was applied to a real Raman spectral data set obtained from a pre-treatment distillation column used for removing unwanted heavy/cyclic hydrocarbons from naphtha in an oil company. Comparison of the concentration trends resulting from the proposed algorithm with those obtained using conventional PLS1 models shows that the new calibration-free and on-line algorithm outperforms the calibration models obtained by difficult and expensive laboratory work. Copyright © 2005 John Wiley & Sons, Ltd. [source] Fast fragments: The development of a parallel effective fragment potential methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2004Heather M. Netzloff Abstract The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1926,1935, 2004 [source] Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2003Maurizio Cossi Abstract The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 669,681, 2003 [source] A method for calculating effective bulk composition modification due to crystal fractionation in garnet-bearing schist: implications for isopleth thermobarometryJOURNAL OF METAMORPHIC GEOLOGY, Issue 6 2004T. P. Evans Abstract Quantitative P,T path determination in metamorphic rocks is commonly based on the variation in composition of growth-zoned garnet. However, some component of growth zoning in garnet is necessarily the result of an effective bulk composition change within the rock that has been generated by crystal fractionation of components into the core of garnet. Therefore, any quantitative calculation of the P,T regime of garnet growth should be completed using an accurate assessment of the composition of the chemical system from which garnet is growing. Consequently, a method for calculating the extent of crystal fractionation that provides a means of estimating the composition of the unfractionated rock at any stage during garnet growth is developed. The method presented here applies a Rayleigh fractionation model based on measured Mn content of garnet to generate composition v. modal proportion curves for garnet, and uses those curves to estimate the vectors of crystal fractionation. The technique is tested by calculating the precision of the equilibrium between three garnet compositional variables within the chemical system determined to be appropriate for each of a series of microprobe analyses from garnet. Application of the fractionation calculations in conjunction with the P,T estimates based on intersecting compositional isopleths provides a means of calculating P,T conditions of garnet growth that is based on individual point-analyses on a garnet grain. Such spatially precise and easily obtainable P,T data allow for detailed parallel studies of the microstructural, the P,T, and the chemical evolution of metamorphosed pelites. This method provides a means of studying the dynamics of orogenic systems at a resolution that was previously unattainable. [source] Addressing chemical diversity by employing the energy landscape conceptACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2010Martin Jansen Exploring the structural diversity of a chemical system rests on three pillars. First, there is the global exploration of its energy landscape that allows one to predict which crystalline modifications can exist in a chemical system at a given temperature and pressure. Next, there is the development of new synthesis methods in solid-state chemistry, which require only very low activation energies such that even metastable modifications corresponding, for example, to minima on the landscape surrounded by low barriers can be realized. Finally, there is the theoretical design of optimal synthesis routes, again based on the study of the system's energy landscape. In this paper the energy landscape approach to the prediction of stable and metastable compounds as a function of temperature and pressure is presented, with a particular focus on possible phase transitions. Furthermore, several examples are presented, where such predicted compounds were subsequently successfully synthesized, often employing a newly developed synthesis method, low-temperature atom-beam deposition. [source] Predicting solid compounds via global exploration of the energy landscape of solids on the ab initio level without recourse to experimental informationPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2010J. Christian Schön Abstract Predicting which crystalline modifications can exist in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this might introduce some bias favoring certain types of chemical bonding and entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, it is necessary to employ ab initio energy functions during the global optimization phase of the structure prediction. In this paper, we review the current state of the field of structure prediction on the ab initio level. [source] Evaluation of an Entropy-Based Combustion Model using Stochastic ReactorsCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 7 2008J. Leicher Abstract The entropy transport concept (ETC) presented in this paper is a novel approach to describe reaction systems such that the dynamic behavior of a chemical system can be reproduced with a minimum in independent parameters. It is shown that, for adiabatic conditions, the mixture fraction and the reaction entropy are sufficient to describe combustion processes without significant loss of information. Entropy is used as a measure of the reaction progress in this context. In order to evaluate the applicability of the ETC for combustion modeling in turbulent systems, the entropy transport concept was implemented into a stochastic reactor model. For several test cases, the results of this ETC-based reactor were compared with a reactor that directly integrates the species transport equations. [source] Influence of Growth Temperature and Carrier Flux on the Structure and Transport Properties of Highly Oriented CrO2 on Al2O3 (0001),CHEMICAL VAPOR DEPOSITION, Issue 10 2007M. Sousa Abstract In this work we report on the structure and magnetic and electrical transport properties of CrO2 films deposited onto (0001) sapphire by atmospheric pressure (AP)CVD from a CrO3 precursor. Films are grown within a broad range of deposition temperatures, from 320 to 410,°C, and oxygen carrier gas flow rates of 50,500,sccm, showing that it is viable to grow highly oriented a -axis CrO2 films at temperatures as low as 330,°C i.e., 60,70,°C lower than is reported in published data for the same chemical system. Depending on the experimental conditions, growth kinetic regimes dominated either by surface reaction or by mass-transport mechanisms are identified. The growth of a Cr2O3 interfacial layer as an intrinsic feature of the deposition process is studied and discussed. Films synthesized at 330,°C keep the same high quality magnetic and transport properties as those deposited at higher temperatures. [source] Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and BacteriaFEMS MICROBIOLOGY REVIEWS, Issue 2 2001Jan P. Amend Abstract Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe2+, H2S, S, S2O32,, S4O62,, sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe3+, CO2, CO, NO3,, NO2,, NO, N2O, SO42,, SO32,, S2O32,, and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (,Gr°) as a function of temperature to 200°C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of ,Gr° for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (,G°) at temperatures to 200°C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of ,Gr° for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25°C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H,O, H,O,N, H,O,S, H,O,N,S, H,O,Cinorganic, H,O,C, H,O,N,C, H,O,S,C, H,O,N,S,Camino acids, H,O,S,C,metals/minerals, and H,O,P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (,Gr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems. [source] Discrete thermodynamics of chemical equilibria and classical limit in thermodynamic simulationISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2007Boris Zilbergleyt This article sets forth comprehensive basic concepts of the discrete thermodynamics of chemical equilibrium as balance between internal and external thermodynamic forces. Conditions of chemical equilibrium in the open chemical system are obtained in the form of a logistic map, containing only one new parameter that defines the chemical system's resistance to external impact and its deviation from thermodynamic equilibrium. Solutions to the basic map are bifurcation diagrams that have quite traditional shape but the diagram areas feature specific meanings for chemical systems and constitute the system's domain of states. The article is focused on two such areas: the area of "true" thermodynamic equilibrium and the area of open chemical equilibrium. The border between them represents the classical limit, a transition point between the classical and newly formulated equilibrium conditions. This limit also separates regions of the system ideality, typical for isolated classical systems, and non-ideality due to the limitations imposed on the open system from outside. Numerical examples illustrating the difference between results of classical and discrete thermodynamic simulation methods are presented. The article offers an analytical formula to find the classical limit, compares analytical results with these obtained by simulation, and shows the classical limit dependence upon the chemical reaction stoichiometry and robustness. [source] Analysis of video images from a gas,liquid transfer experiment: a comparison of PCA and PARAFAC for multivariate image analysisJOURNAL OF CHEMOMETRICS, Issue 7 2003Stephen P. Gurden Abstract The use of chemical imaging is a developing area which has potential benefits for chemical systems where spatial distribution is important. Examples include processes in which homogeneity is critical, such as polymerizations, pharmaceutical powder blending and surface catalysis, and dynamic processes such as the study of diffusion rates or the transport of environmental pollutants. Whilst single images can be used to determine chemical distribution patterns at a given point in time, dynamic processes can be studied using a sequence of images measured at regular time intervals, i.e. a movie. Multivariate modeling of image data can help to provide insight into the important chemical factors present. However, many issues of how best to apply these models remain unclear, especially when the data arrays involved have four or five different dimensions (height, width, wavelength, time, experiment number, etc.). In this paper we describe the analysis of video images recorded during an experiment to investigate the uptake of CO2 across a free air,water interface. The use of PCA and PARAFAC for the analysis of both single images and movies is described and some differences and similarities are highlighted. Some other image transformation techniques, such as chemical mapping and histograms, are found to be useful both for pretreatment of the raw data and for dimensionality reduction of the data arrays prior to further modeling. Copyright © 2003 John Wiley & Sons, Ltd. [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] Refining the P,T records of UHT crustal metamorphismJOURNAL OF METAMORPHIC GEOLOGY, Issue 2 2008S. L. HARLEY Abstract Ultra-high-temperature (UHT) metamorphism occurs when the continental crust is subjected to temperatures of greater than 900 °C at depths of 20,40 km. UHT metamorphism provides evidence that major tectonic processes may operate under thermal conditions more extreme than those generally produced in numerical models of orogenesis. Evidence for UHT metamorphism is recorded in mineral assemblages formed in magnesian pelites, supported by high-temperature indicators including mesoperthitic feldspar, aluminous orthopyroxene and high Zr contents in rutile. Recent theoretical, experimental and thermodynamic data set constraints on metamorphic phase equilibria in FMAS, KFMASH and more complex chemical systems have greatly improved quantification of the P,T conditions and paths of UHT metamorphic belts. However, despite these advances key issues that remain to be addressed include improving experimental constraints on the thermodynamic properties of sapphirine, quantifying the effects of oxidation state on sapphirine, orthopyroxene and spinel stabilities and quantifying the effects of H2O,CO2 in cordierite on phase equilibria and reaction texture analysis. These areas of uncertainty mean that UHT mineral assemblages must still be examined using theoretical and semi-quantitative approaches, such as P(,T),, sections, and conventional thermobarometry in concert with calculated phase equilibrium methods. In the cases of UHT terranes that preserve microtextural and mineral assemblage evidence for steep or ,near-isothermal' decompression P,T paths, the presence of H2O and CO2 in cordierite is critical to estimates of the P,T path slopes, the pressures at which reaction textures have formed and the impact of fluid infiltration. Many UHT terranes have evolved from peak P,T conditions of 8,11 kbar and 900,1030 °C to lower pressure conditions of 8 to 6 kbar whilst still at temperature in the range of 950 to 800 °C. These decompressional P,T paths, with characteristic dP/dT gradients of ,25 ± 10 bar °C,1, are similar in broad shape to those generated in deep-crustal channel flow models for the later stages of orogenic collapse, but lie at significantly higher temperatures for any specified pressure. This thermal gap presents a key challenge in the tectonic modelling of UHT metamorphism, with implications for the evolution of the crust, sub-crustal lithosphere and asthenospheric mantle during the development of hot orogens. [source] Calculated phase equilibria in K2O-FeO-MgO-Al2O3 -SiO2 -H2O for silica-undersaturated sapphirine-bearing mineral assemblagesJOURNAL OF METAMORPHIC GEOLOGY, Issue 4 2005D. E. KELSEY Abstract Silica-undersaturated, sapphirine-bearing granulites occur in a large number of localities worldwide. Such rocks have historically been under-utilized for estimating P,T evolution histories because of limited experimental work, and a consequent poor understanding of the topology and P,T location of silica-undersaturated mineral equilibria. Here, a calculated P,T projection for sapphirine-bearing, silica-undersaturated metapelitic rock compositions is constructed using THERMOCALC for the FeO-MgO-Al2O3 -SiO2 (FMAS) and KFMASH (+K2O + H2O) chemical systems, allowing quantitative analysis of silica-undersaturated mineral assemblages. This study builds on that for KFMASH sapphirine + quartz equilibria [Kelsey et al. (2004) Journal of Metamorphic Geology, vol. 22, pp. 559,578]. FMAS equilibria are significantly displaced in P,T space from silicate melt-bearing KFMASH equilibria. The large number of univariant silica-undersaturated KFMASH equilibria result in a P,T projection that is topologically more complex than could be established on the basis of experiments and/or natural assemblages. Coexisting sapphirine and silicate melt (with or without corundum) occur down to c. 900 °C in KFMASH, some 100 °C lower than in silica-saturated compositions, and from pressures of c.,1 to ,12 kbar. Mineral compositions and composition ranges for the calculated phases are consistent with natural examples. Bulk silica has a significant effect on the stability of sapphirine-bearing assemblages at a given P,T, resulting in a wide variety of possible granulite facies assemblages in silica-undersaturated metapelites. Calculated pseudosections are able to reproduce many naturally occurring silica-undersaturated assemblages, either within a single assemblage field or as the product of a P,T trajectory crossing several fields. With an understanding of the importance of bulk composition on sapphirine stability and textural development, silica-undersaturated assemblages may be utilized in a quantitative manner in the detailed metamorphic investigation of high-grade terranes. [source] Separation techniques for the analysis of artists' acrylic emulsion paintsJOURNAL OF SEPARATION SCIENCE, JSS, Issue 4 2004Dominique Scalarone Abstract Emulsion paints are complex chemical systems. The main problems in their characterization are related to the similarities in polymer composition and to the presence of many different types of additives. Thus high resolution separations, sensitivity, and response specificity are required to identify simultaneously the polymer matrix and the minor components. Especially surfactants and pigments are thought to affect significantly the properties of the paint layers during ageing and their identification is the first step in evaluating the behaviour of these products in working conditions. Representative samples of acrylic emulsion paints for artists have been investigated by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) and size exclusion chromatography-Fourier transform infrared spectroscopy (SEC-FTIR), and the results have been compared. All the analysed samples were bound in ethyl acrylate-methyl methacrylate, poly(EA-co-MMA), or n -butyl acrylate-methyl methacrylate, poly(nBA-co-MMA), copolymers. Two types of nonionic surfactants, ethoxylated fatty alcohols and alkylaryl polyethoxylates, commonly used as emulsifiers and dispersive agents have been identified, together with a number of organic pigments. [source] Probing interactions by means of pulsed field gradient nuclear magnetic resonance spectroscopy,MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2008Sara Cozzolino Abstract Molecular self-diffusion coefficients (D) of species in solution are related to size and shape and can be used for studying association phenomena. Pulsed field gradient nuclear magnetic resonance (PFG-NMR) spectroscopy has been revealed to be a powerful analytical tool for D measurement in different research fields. The present work briefly illustrates the use of PFG-NMR for assessing the existence of interactions in very different chemical systems: organic and organometallic compounds, colloidal materials and biological aggregates. The application of PFG-NMR is remarkable for understanding the role of anions in homogenous transition metal catalysis and for assessing the aggregation behaviour of biopolymers in material science. Copyright © 2008 John Wiley & Sons, Ltd. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 8-9 20108-9/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 6-7 20107/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 5 20105/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 4 20104/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 3 20103/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Cover Picture: (Mol. Inf.MOLECULAR INFORMATICS, Issue 1-2 20101-2/2010) Molecular Informatics publishes research that will deepen our understanding about information storage and processing on the molecular level, signaling and regulation of biological and chemical systems including cellular systems and macromolecular assemblies, modeling of molecular interactions and networks, and the design of molecular modulators that exhibit desired biochemical and pharmacological effects. Various aspects of this transdisciplinary scientific area are depicted on the cover: Cells with their nuclei and membranes (image courtesy of Dr. A. Schreiner and E. Resch), models of receptor-ligand interactions, and an artistic representation of "biological information" as multiple bit-codes presented on a right-handed helix. [source] Tuning the Reaction Site for Enzyme-Free Primer-Extension Reactions through Small Molecule SubstituentsCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2006Jan A. Rojas Stütz Dr. Abstract The replication of genetic information relies on the template-directed extension of DNA primers catalyzed by polymerases. The active sites of polymerases accept four different substrates and ensure fidelity and processivity for each of them. Because of the pivotal role of catalyzed primer extension for life, it is important to better understand this reaction on a molecular level. Here we present results from primer-extension reactions performed with chemical systems that show high reactivity in the absence of polymerases. Small molecular caps linked to the 5,-terminus of templates are shown to enhance the rate and selectivity of primer extension driven by 2-methylimidazolides as activated monomers for any of the four different templating bases (A, C, G, and T). The most consistent effect is provided by a stilbene carboxamide residue, rather than larger aromatic or aliphatic substituents. Up to 20-fold rate enhancements were achieved for the reactions at the terminus of the template. The preference for a medium size cap can be explained by competing interactions with both the oligonucleotides and the incoming deoxynucleotide. The data also show that there is no particularly intractable problem in combining promiscuity with fidelity. Exploratory experiments involving a longer template and a downstream-binding strand with a 5,-cap show up to 38-fold rate acceleration over the same reaction templated by a single overhanging nucleotide. [source] Toward Safe Genetically Modified Organisms through the Chemical Diversification of Nucleic AcidsCHEMISTRY & BIODIVERSITY, Issue 6 2009Piet Herdewijn Abstract It is argued that genetic proliferation should be rationally extended so as to enable the propagation in vivo of additional types of nucleic acids (XNA for ,xeno-nucleic acids'), whose chemical backbone motifs would differ from deoxyribose and ribose, and whose polymerization would not interfere with DNA and RNA biosynthesis. Because XNA building blocks do not occur in nature, they would have to be synthesized and supplied to cells which would be equipped with an appropriate enzymatic machinery for polymerizing them. The invasion of plants and animals with XNA replicons can be envisioned in the long run, but it is in microorganisms, and more specifically in bacteria, that the feasibility of such chemical systems and the establishment of genetic enclaves separated from DNA and RNA is more likely to take place. The introduction of expanded coding through additional or alternative pairing will be facilitated by the propagation of replicons based on alternative backbone motifs and leaving groups, as enabled by XNA polymerases purposefully evolved to this end. [source] Entropy production in chiral symmetry breaking transitions,CHIRALITY, Issue 3-4 2008Dilip Kondepudi Abstract It is now well known that nonequilibrium chemical systems may reach conditions that spontaneously generate chiral asymmetry. One can find a host of model reactions that exhibit such behavior in the literature. Among these, models based on one originally devised by Frank have been studied extensively. Though the kinetic aspects of such model reactions have been discussed in great detail, the behavior of entropy in such systems is rarely discussed. In this article, the rate of entropy production per unit volume, ,, in a modified Frank model is discussed. It is shown that the slope of , changes at the point at which the asymmetric states appear, behavior similar to that observed in second-order phase transitions. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] | |||||||||||||||||||||||||