An Accurate Barrier for the Hydrogen Exchange Reaction from Valence Bond Theory: Is this Theory Coming of Age?

One of the landmark achievements of quantum chemistry, specifically of MO-based methods that include electron correlation, was the precise calculation of the barrier for the hydrogen-exchange reaction (B. Liu, J. Chem. Phys. 1973, 58, 1925; P. Siegbahn, B. Liu, J. Chem. Phys. 1978, 68, 2457). This paper reports an accurate calculation of this barrier by two recently developed VB methods that use only the eight classical VB structures. To our knowledge, the present work is the first accurate ab initio VB barrier that matches an experimental value. Along with the accurate barrier, the VB method provides accurate bond energies and diabatic quantities that enable the barrier height to be analyzed by the VB state correlation diagram approach, VBSCD (S. Shaik, A. Shurki, Angew. Chem. 1999, 111, 616; Angew. Chem. Int. Ed. Engl. 1999, 38, 586). This is a proof of principal that VB theory with appropriate account of dynamic electron correlation can achieve quantitative accuracy of reaction barriers, and still retain a compact and interpretable wave function. A sample of S(N)2 barriers and dihalogen bonding energies, which are close to CCSD(T) and G2(+) values, show that the H(3) problem is not an isolated case, and while it is premature to conclude that VB theory has come of age, the occurrence of this event is clearly within sight.     

How critical is the use of commercially available enzymes for selenium speciation?

The aim of this work was to check whether commercially available enzymes are pure enough to be used for selenium speciation analysis and the contribution that impurities could make to Se determination in real samples. For this purpose, twelve commercially available enzymes with different origins and classifications (protease, amylase, cellulase, lipase) were analysed. After the dissolution of the enzyme in water, the Se species were separated by ion exchange chromatography, with inductively coupled plasma mass spectrometry used as the detection system. The results showed that the Se content was significant in several cases. The highest value was obtained for β-amylase from barley, 3100 ng Se per g of enzyme. Speciation analysis showed that Se-methionine, selenite, selenate and some unknown compounds were present in several enzymes. In general, the Se species identified represented a small fraction of the total Se. For instance, only 17% of the total Se was determined for β-amylase from barley. On the other hand, about 100% of the total Se was identified in protease from Streptomyces griseus. Upon comparing the results from different lots of the same enzyme, not all of them were found to be comparable. Thus, the presence of selenium species in commercially available enzymes could be due to the preparation procedure used for the enzyme; they could be present as degradation products. Therefore, when determining selenium species in samples with low Se contents, attention should be paid to enzyme purity in relation to selenium compounds when an enzyme is used for hydrolysis.     

How large is the conjugative stabilization of diynes?

The conjugation stabilization energies of dienes and diynes are considerably larger than estimates based on heat of hydrogenation differences between 1,3-butadiyne and 1-butyne as well as between 1,3-butadiene and 1-butene. Such comparisons do not take into account the counterbalancing hyperconjugative stabilization of the partially hydrogenated products by their ethyl groups. When alkyl hyperconjugation is considered, the conjugation stabilization of diynes ( approximately 9.3 kcal/mol) is found by two methods (involving isomerization of nonconjugated into conjugated isomers and heats of hydrogenation) to be larger than that of dienes ( approximately 8.2 kcal/mol).     

How possible is the detection of correlated mutations?

The remarkable conservation of protein structure, compared to that of sequences, suggests that, in the course of evolution, residue substitutions which tend to destabilise a particular structure must be compensated by other substitutions that confer greater stability on that structure. Given the compactness of proteins, spatially close residues are expected to undergo the compensatory process. Surprisingly, approaches designed to detect such correlated changes have led, until now, only to limited success in detecting pairs of residues adjacent in the three-dimensional structures. We have undertaken, by simulating the evolution of DNA sequences including sites mutating in a correlated manner, to analyse whether such poor results can be attributed to the detection methods or if this failure could result from a compensatory process more complex than that implicitly underlying the different approaches. Present results show that only methods taking into account the phylogenetic reconstruction can lead to correct detection. Received: 24 April 1998 / Accepted: 8 August 1998 / Published online: 11 November 1998     

How Does the Intrinsic Barrier of Intermolecular Proton Transfer Depend on Molecular Parameters?

The question in the title is of fundamental importance , because the intrinsic barrier ΔG_int^≠ is the key parameter connecting thermodynamics and kinetics. With a valence bond configuration mixing model for proton self-exchange (see picture), it is shown that ΔG_int^≠ is a linear function of I_v−E(σ_NH^*), where I_v is the ionization potential of the base and E(σ_NH^*) the energy of the antibonding orbital of the N−H bond in the conjugated acid. With para-substituted N,N′-dimethylanilines, this manifests itself by a linear relationship between ΔG_int^≠ and the Hammett parameter σ⁺.     

How is the CH/pi interaction important for molecular recognition?

Ab initio calculations illustrate that CH/pi attractions significantly contribute to host-guest complexation, but are not always a direct factor in molecular recognition.     

Effect of Ni Loading on the Catalytic Properties of Molybdenum Oxides for the Isomerization of Heptane

The catalytic properties of MoOx and incorporation Ni onto the MoOx for the isomerization of heptane have been investigated under atmospheric pressure at different conditions such as different flow rate of H2,different reaction temperature tec. Compared with MoOx, the Ni addition to the MoOx markedly improved the isomerization activity of heptane by improving the reducibility of MoO3 and activation of H2 in reaction.     

How accurate is the CASPT2 method?

This paper is a reply to a recent paper on the isomers of trisulfur oxides (Chem. Commun., 2005, 3712) where the accuracy of the CASPT2 method is called in question. We illustrate that their results are due to an inadequate choice of active orbitals. Some results for related O and S containing molecules are also presented to strengthen the argumentation. It is concluded that the CASPT2 method is accurate to at least 0.1 eV (2 kcal mol(-1)) for this type of systems.     

How stable is trans-cycloheptene?

There is a discrepancy between the observed and calculated stability of trans-cycloheptene (t-CHP). Generation of t-CHP has always led to its low-temperature (-40 degrees C) isomerization to cis-cycloheptene (c-CHP). However, force field and semiempirical calculations on the energy difference between the two isomers have suggested that t-CHP should be stable at room temperature. We performed a series of ab initio calculations, which predicted that the simple process of double bond rotation leading from t-CHP to c-CHP would have an activation barrier too high to permit isomerization below 100 degrees C (35 kcal/mol). The validity of our calculation method on this very strained system was supported by the agreement between the calculation and the dynamics of the ring flip of the unsymmetrical t-CHP ring and the observed NMR shifts and coupling constants for the system. This incompatibility between the experimental behavior of t-CHP and our calculations led to our reexamining the decay kinetics of t-CHP. We find that this decay is second order and represents an "interrupted" dimerization, where an initially formed 1,4-biradical rapidly changes its geometry and cleaves back to produce two c-CHP molecules. This mechanism was supported by calculations of the 1,4-biradical potential energy surface.     

How much is the accuracy of activation energy affected by ignoring thermal inertia?

This work estimates the magnitude of the effect of thermal inertia on the value of the activation energy determined from heat-flux differential scanning calorimetry (DSC) data. The estimates are obtained via analysis of the literature data on crystallization of copper and thermal degradation of isotactic polystyrene (iPS). The copper crystallization data have been obtained for very large masses (200 mg) and fast heating rates up to 80 K min⁻¹. The iPS degradation data have been collected on small masses (3 mg) and at the heating rates up to 20 K min⁻¹. For crystallization of copper, the Kissinger activation energy obtained from the DSC data corrected for thermal inertia is 34% larger than the value estimated from uncorrected data. This difference drops to 8% and becomes statistically insignificant when the fastest heating rate used is decreased to 10 K min⁻¹. For iPS degradation, the difference in the isoconversional activation energies estimated, respectively, from corrected and uncorrected DSC data is less than 3% and is not statistically significant. Overall, the effect of thermal inertia on the activation energy appears negligible provided that DSC measurements are conducted on smaller samples and at slower heating rates, that is, as advised by the International Confederation for Thermal Analysis and Calorimetry (ICTAC) recommendations. It is suggested that the difference in the activation energies should generally be within the typical 5-10% uncertainty as long as the product of the time constant and the maximum heating rate does not exceed 2-3 K.     

Where is the road to bio-water-saving for the globe?

The First International Conference on the Theory and Practices in Bio-water-saving (ICTPB) was held from May 21 to 25, 2006 in Beijing, China. This indicated that the work related to this hot topic on the globe has been paid more attention to. Most progress in this field has been presented from near 300 participating people worldwide, who were meeting together to discuss about the theory and practices of water-saving biology and how to serve global agricultural and ecological sustainable development. The work related to bio-water-saving has been involved in different scales and soil–plant root biointerfaces. On the basis of this background and in combination with the work from our laboratory and the center, we provided some ideas for global bio-water-saving in this paper, sharing the achievement in this field and advocating true bio-water-saving for the world and promoting the pace of global bio-water-saving.     

How Important is Parity Violation for Molecular and Biomolecular Chirality?

Parity violation leads to energy differences Δ_pvH =N_AΔ_pvE of enantiomers in the femtojoule to picojoule per mole range. Recently introduced methods of electroweak quantum chemistry predict such energy differences to be one to two orders of magnitude larger than previously accepted—but still very small. How can such small energies be measured and what are the consequences for our understanding of molecular chirality, biomolecular homochirality, and perhaps fundamental physics? The review gives some tentative answers to these questions. We discuss the current status of theory and some of the current experimental approaches.     

Similar,or dissimilar,that is the question. How different are methods for comparison of compounds similarity?

Comparison of compounds similarity is one of the main strategies of virtual screening protocols. Both similarity and dissimilarity concepts are of great importance during the search for new active compounds. Similarity is important due to the assumption that underlies the process of searching for new drug candidates: structurally similar compounds should induce similar biological response. On the other hand, we are also interested in dissimilarity, as we usually aim to find structurally novel ligands. In the study, we compared several approaches of evaluating compound similarity. Various representations and metrics were applied and we indicated the rate of variation of the results that can occur when shifting from one strategy to another. We compared both general similarity of datasets using different approaches, as well as examined the changes in the set of nearest neighbors when changing one compound representation into another, and the influence of representation/metric settings on the clustering outcome. We hope that the study will be of great help during the preparation of virtual screening experiments, stressing the need for careful selection of the way, the compound similarity is assessed. The differences in the results that can be obtained via the application of particular strategy can significantly influence the outcome of comparison studies; therefore, its settings should be carefully selected beforerunning the comparison.     

How important is the back reaction of electrons via the substrate in dye-sensitized nanocrystalline solar cells?

The role of the conducting glass substrate (fluorine-doped tin oxide, FTO) in the back reaction of electrons with tri-iodide ions in dye-sensitized nanocrystalline solar cells (DSCs) has been investigated using thin-layer electrochemical cells that are analogues of the DSCs. The rate of back reaction is dependent on the type of FTO and the thermal treatment. The results show that this back-reaction route cannot be neglected in DSCs, particularly at lower light intensities, where it is the dominant route for the back transfer of electrons to tri-iodide. This conclusion is confirmed by measurements of the intensity dependence of the photovoltages of DSCs with and without blocking layers. It follows that blocking layers should be used to prevent the back reaction in mechanistic studies in which the light intensity is varied over a wide range. Conclusions based on studies of the intensity dependence of the parameters of DSCs such as photovoltage and electron lifetime in cells without blocking layers, must be critically re-examined.     

What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?

Site‐selective isotopic labeling of amide carbonyls offers a nonperturbative means to introduce a localized infrared probe into proteins. Although this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric fields (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α‐helix is determined to be approximately 1.4 cm^?1/(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, by using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant.     

How easy are the syntheses of allenes?

Allenes have proven themselves to be valuable building blocks toward complex molecular targets, revealing novel applications in natural product synthesis, pharmaceutical chemistry and materials science. The ongoing interest in allene chemistry results in a variety of new methodologies and pathways for the synthesis of allenes. This feature article highlights some of the recent important developments on the synthesis of allenes and the applications on the synthesis of allenic natural products and allenic-based optoelectronic materials.