How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order Ω(-3∕2) for reaction systems which do not obey detailed balance and at least accurate to order Ω(-2) for systems obeying detailed balance, where Ω is the characteristic size of the system. Hence, the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order Ω(-1∕2) and variance estimates accurate to order Ω(-3∕2). This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.     

Closed and endoreversible chemical oscillation

Based on a simple nonideal chemical reaction model, the closed system with reversible nonideal reactions and illumination is shown to be able to exhibit sustained oscillation. The essential points in the occurrence of such oscillations are the nonideality of reacting media, which gives rise to multiple chemical equilibria, and the energy flow through illumination and heat conduction, which gives rise to spontaneous transitions repeatedly between the multiple equilibrium states. During the oscillation, reacting media undergo only reversible chemical transformation and all irreversibilities are restricted to the coupling of the system to external world. This oscillation provides an example of the so-called endoreversible machine and a possible way to convert radiation energy of the light directly into mechanical energy.     

The hierarchical structure of chemical engineering

Around the turn of the present century,scholars began to recognize chemical engineering as a com-plex system,and have been searching for a convenient point of entry for refreshing its knowledge base.From our study of the dynamic structures of dispersed particles in fluidization and the resultingmulti-scale method,we have been attempting to extend our findings to structures prevailing in othermultiphase systems as well as in the burgeoning industries producing functional materials.Chemicalengineering itself is hierarchically structured.Besides structures based on space and time,such hier-archy could be built from ChE history scaled according to science content,or from ChE operation ac-cording to the expenditure of manpower and capital investment.     

Mining a chemical database for fragment co-occurrence: discovery of "chemical clichés"

Nowadays millions of different compounds are known, their structures stored in electronic databases. Analysis of these data could yield valuable insights into the laws of chemistry and the habits of chemists. We have therefore explored the public database of the National Cancer Institute (>250,000 compounds) by pattern searching. We split the molecules of this database into fragments to find out which fragments exist, how frequent they are, and whether the occurrence of one fragment in a molecule is related to the occurrence of another, nonoverlapping fragment. It turns out that some fragments and combinations of fragments are so frequent that they can be called "chemical clichés". We believe that the fragment data can give insight into the chemical space explored so far by synthesis. The lists of fragments and their (co-)occurrences can help create novel chemical compounds by (i) systematically listing the most popular and therefore most easily used substituents and ring systems for synthesizing new compounds, (ii) being an easily accessible repository for rarer fragments suitable for lead compound optimization, and (iii) pointing out some of the yet unexplored parts of chemical space.     

Valence bond theoretical study for chemical reactivity

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O−• chemical ionization of carbonyl compounds

The negative ion chemical ionization mass spectra of twentyeight C₄ to C₇ carbonyl compounds were recorded using the oxide radical anion O^?? as reagent ion. As noted earlier, the reactions occurring include H⁺ abstraction, H ₂ ^+? abstraction, H? atom displacement, and alkyl radical displacement. In addition, the [M?2H]^? ions fragment further by alkyl radical elimination. The relative importance of these reactions depends strongly on molecular structure, with the result that isomer distinction frequently is possible. Where this is not possible, as for isomeric aldehydes, the collisional charge inversion mass spectra of common product ions provides isomer distinction. The H ₂ ^+? abstraction reaction is shown to involve abstraction not only of two hydrogens from the same α-carbon but also, in part, abstraction of one hydrogen from each α-carbon.     

How different are two chemical structures?

We extend the scope of a recent method for superimposing two molecules ( J. Chem. Phys. 2009, 131, 124126-1-124126-10 ) to include the identification of chiral structures. This methodology is tested by applying it to several organic molecules and water clusters that were subjected to geometry optimization. The accuracy of four simpler, non-superimposing approaches is then analyzed by comparing pairs of structures for argon and water clusters. The structures considered in this work were obtained by a Markovian walk in the coordinate space. First, a random geometry is generated, and then, the iterative application of a mutation operator ensures the creation of increasingly dissimilar structures. The discriminating power of the non-superimposing approaches is tested by comparing the corresponding dissimilarity measures with the root-mean-square distance obtained from the superimposing method. Finally, we showcase the application of those methods to characterize the diversity of solutions in global geometry optimization by evolutionary algorithms.     

Does chemical cross-linking with NHS esters reflect the chemical equilibrium of protein-protein noncovalent interactions in solution?

Chemical cross-linking in combination with mass spectrometry has emerged as a powerful tool to study noncovalent protein complexes. Nevertheless, there are still many questions to answer. Does the amount of detected cross-linked complex correlate with the amount of protein complex in solution? In which concentration and affinity range is specific cross-linking possible? To answer these questions, we performed systematic cross-linking studies with two complexes, using the N-hydroxysuccinimidyl ester disuccinimidyl suberate (DSS): (1) NCoA-1 and mutants of the interacting peptide STAT6Y, covering a K_D range of 30 nM to >25 μM, and (2) α-thrombin and basic pancreatic trypsin inhibitor (BPTI), a system that shows a buffer-dependent K_D value between 100 and 320 μM. Samples were analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For NCoA-1· STAT6Y, a good correlation between the amount of cross-linked species and the calculated fraction of complex present in solution was observed. Thus, chemical cross-linking in combination with MALDI-MS can be used to rank binding affinities. For the mid-affinity range up to about K_D ≈ 25 μM, experiments with a nonbinding peptide and studies of the concentration dependence showed that only specific complexes undergo cross-linking with DSS. To study in which affinity range specific cross-linking can be applied, the weak α-thrombin · BPTI complex was investigated. We found that the detected complex is a nonspecifically cross-linked species. Consequently, based on the experimental approach used in this study, chemical cross-linking is not suitable for studying low-affinity complexes with K_D ? 25 μM.     

Quantum chemical investigation on solvation of Ginkgolides

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Accurate thermochemistry from quantum chemical calculations?

The answer to the title question is definitely “yes” – at least for fairly small molecules. Computational procedures, namely the Weizmann (Wn) and Gaussian-3 (G3) family of methods, the complete basis set extrapolation scheme (CBS-x), the “high accuracy extrapolated ab initio thermochemistry” (HEAT) as well as the “correlation consistent composite approach” (ccCA), aimed at energies with chemical accuracy or even better (sub kJ?mol^?1) are described and several applications illustrating the level of accuracy that can be achieved are presented.     

An electrochemical microRNAs biosensor with the signal amplification of alkaline phosphatase and electrochemical–chemical–chemical redox cycling

MicroRNAs (MiRNAs) have been regarded as clinically important biomarkers and drug discovery targets. In this work, we reported a simple and ultrasensitive electrochemical method for miRNAs detection based on single enzyme amplification and electrochemical–chemical–chemical (ECC) redox cycling. Specifically, upon contact with the target miRNAs, the hairpin structure of biotinylated DNA immobilized on gold electrode was destroyed and the biotin group in DNA was forced away from the electrode surface, allowing for the coupling of streptavidin-conjugated alkaline phosphatase (SA-ALP). Then, ascorbic acid (AA, the enzymatic product of ALP) triggered the ECC redox cycling with ferrocene methanol (FcM) and tris(2-carboxyethyl)phosphine (TCEP) as the redox mediator and the chemical reducing reagent, respectively. The method was more sensitive than that with horseradish peroxidase (HRP) or glucose oxidase (GOx) triggered recycling since one ALP molecule captured by one target miRNA molecule promoted the production of thousands of AA. Analytical merits (e.g., detection limit, dynamic range, specificity, regeneration and reproducibility) were evaluated. The feasibility of the method for analysis of miRNA-21 in human serum has also been demonstrated.     

A novel chemical route to SiO_2 nanowires

A white substance was got by directly heating TiSi powder on Ti foil, under Ar+O2 atmosphere. ED, EDX, SEM and HRTEM studies reveal that the white substance consists of amorphous SiO2nanowires of smooth surface and uniform diameter (40-90 nm). X-ray-induced luminescent emission experiment shows that two broad peaks are at 430 and 570 nm. A one-dimensional growth mechanism, on the basis of the one-dimensional thermal flow during nanowire formation, is discussed.     

The fifth chemical revolution: 1973–1999

A new chronology is introduced to address the history of chemistry, with educational purposes, particularly for the end of the twentieth century and here identified as the fifth chemical revolution. Each revolution are considered in terms of the Kuhnian notion of ‘exemplar,’ rather than ‘paradigm.’ This approach enables the incorporation of instruments, as well as concepts and the rise of new subdisciplines into the revolutionary process and provides a more adequate representation of such periods of development and consolidation. The fifth revolution developed from 1973 to 1999 and is characterized by a deep transformation in the very heart of chemistry. That is to say, the size and type of objects (substances), the way in which they must be done and the time in which they are transformed. In one way or another, chemistry’ limits had been set out.     

Do we fully understand what controls chemical selectivity?

Reaction rates and product selectivity of kinetically controlled reactions are not always sufficiently described by standard RRKM or TST theory. Reactions taking place on potential energy surfaces featuring a valley ridge inflection point belong to this class of reactions. Though various research groups could show that reaction path bifurcations are far from being an exception in organic reactions the underlying principles that govern product distributions of those bifurcating reaction pathways are yet not fully understood. This Perspective has the intention to provide an overview of how far our understanding and the development of the theoretical foundation have progressed.     

Is there a future for sequential chemical extraction?

Since their introduction in the late 1970s, sequential extraction procedures have experienced a rapid increase in use. They are now applied for a large number of potentially toxic elements in a wide range of sample types. This review uses evidence from the literature to consider the usefulness and limitations of sequential extraction and thereby to assess its future role in environmental chemical analysis. It is not the intention to provide a comprehensive survey of all applications of sequential extractions or to consider the merits and disadvantages of individual schemes. These aspects have been covered adequately in other, recent reviews. This review focuses in particular on various key issues surrounding sequential extractions such as nomenclature, methodologies, presentation of data and interpretation of data, and discusses typical applications from the recent literature for which sequential extraction can provide useful and meaningful information. Also covered are emerging developments such as accelerated procedures using ultrasound- or microwave energy-assisted extractions, dynamic extractions, the use of chemometrics, the combination of sequential extraction with isotope analysis, and the extension of the approach to non-traditional analytes such as arsenic, mercury, selenium and radionuclides.