Quantum mechanical/molecular mechanical study on the mechanisms of compound I formation in the catalytic cycle of chloroperoxidase: an overview on heme enzymes

The formation of Compound I (Cpd I), the active species of the enzyme chloroperoxidase (CPO), was studied using QM/MM calculation. Starting from the substrate complex with hydrogen peroxide, FeIII-HOOH, we examined two alternative mechanisms on the three lowest spin-state surfaces. The calculations showed that the preferred pathway involves heterolytic O-O cleavage that proceeds via the iron hydroperoxide species, i.e., Compound 0 (Cpd 0), on the doublet-state surface. This process is effectively concerted, with a barrier of 12.4 kcal/mol, and is catalyzed by protonation of the distal OH group of Cpd 0. By comparison, the path that involves a direct O-O cleavage from FeIII-HOOH is less favored. A proton coupled electron transfer (PCET) feature was found to play an important role in the mechanism nascent from Cpd 0. Initially, the O-O cleavage progresses in a homolytic sense, but as soon as the proton is transferred to the distal OH, it triggers an electron transfer from the heme-oxo moiety to form water and Cpd I. This study enables us to generalize the mechanisms of O-O activation, elucidated so far by QM/MM calculations, for other heme enzymes, e.g., cytochrome P450cam, horseradish peroxidase (HRP), nitric oxide synthase (NOS), and heme oxygenase (HO). Much like for CPO, in the cases of P450 and HRP, the PCET lowers the barrier below the purely homolytic cleavage alternative (in our case, the homolytic mechanism is calculated directly from FeIII-HOOH). By contrast, the absence of PCET in HO, along with the robust water cluster, prefers a homolytic cleavage mechanism.     

Photochemical monoalkylation of propanedinitrile by electron-rich alkenes

The synthesis of monoalkylated propanedinitriles was achieved upon photoirradiation of MeCN/H(2)O solutions containing propanedinitrile (1; malononitrile) and electron-rich alkenes in the presence of lithium carbonate and a catalytic amount of 9-cyanophenanthrene or redox-type photosensitizers (electron-mediating photosensitizers), through regioselective anti-Markovnikov photochemical polar addition of 1 into electron-rich alkenes. With 2,5-dimethyl-2,4-hexadiene (2g) as an electron-rich alkene, propanedinitrile-incorporated dimer 4g was obtained.     

Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides

It is known that Huntington's disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms. Here, we perform molecular dynamics calculations on the stability of the structure based on the β-helix structure suggested by Perutz et al. (2002) [Perutz, M.F., Finch, J.T., Berriman, J., Lesk, A., 2002. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA 99, 5591]. We ensure that perfect hydrogen bonds are present between main chains of the β-helix based on the previous studies, and perform simulations of stretches with 20, 25, 30, 37 and 40 glutamine residues (20Q, 25Q, 30Q, 37Q and 40Q) for the Perutz models with 18.5 and 20 residues per turn (one coil). Our results indicate that the structure becomes more stable with the increase of repeated number of Q, and there is a critical Q number of around 30, above which the structure of the Perutz model is kept stable. In contrast to previous studies, we started molecular dynamics simulations from conformations in which the hydrogen bonds are firmly formed between stacked main chains. This has rendered the initial β-helix structures of polyQ much more stable for longer time, as compared to those proposed previously. Model calculations for the initial structures of polyQ dimer and tetramer have also been carried out to study a possible mechanism for aggregation.     

Correlation between dynamic heterogeneity and medium-range order in two-dimensional glass-forming liquids

A glassy state of matter results if crystallization is avoided upon cooling or increasing density. However, the physical factors controlling the ease of vitrification and nature of the glass transition remain elusive. Using numerical simulations of polydisperse hard disks, we find a direct relation between medium-range crystalline ordering and the slow dynamics which characterizes the glass transition. This suggests an intriguing scenario that the strength of frustration controls both the ease of vitrification and nature of the glass transition. Vitrification may be a process of hidden crystalline ordering under frustration, at least in our system.     

Control of the liquid-liquid transition in a molecular liquid by spatial confinement

Generally, phase transitions are seriously affected by spatial confinement. This effect is important for its own sake, but also for applications to nanotechnology. Here we report the first systematic experimental study on confinement effects on a liquid-liquid transition of a molecular liquid. We found that one liquid can be transformed into another purely by spatial confinement. This indicates that the liquid state cannot be specified by the temperature and pressure alone, but it is also affected by its size in a discontinuous manner: the phase of a liquid in a narrow space can, in principle, be different from that in the bulk. This finding would deepen our basic understanding of the liquid state.     

NR transfer reactivity of azo-compound I of P450. How does the nitrogen substituent tune the reactivity of the species toward C-H and C=C activation?

We studied electronic structures and reactivity patterns of azo-compound I species (RN-Cpd I) by comparison to O-Cpd I of, e.g., cytochrome P450. The study shows that the RN-Cpd I species are capable of C=C aziridination and C-H amidation, in a two-state mechanism similar to that of O-Cpd I. However, unlike O-Cpd I, here the nitrogen substituent (R) exerts a major impact on structure and reactivity. Thus, it is demonstrated that Fe=NR bonds of RN-Cpd I will generally be substantially longer than Fe=O bonds; electron-withdrawing R groups will generate a very long Fe=N bond, whereas electron-releasing R groups should have the opposite effect and hence a shorter Fe=N bond. The R substituent controls also the reactivity of RN-Cpd I toward C=C and C-H bonds by exerting steric and electronic effects. Our analysis shows that an electron-releasing substituent will lower the barriers for both bond activation reactions, since the electronic factor makes the reactions highly exothermic, while an electron-withdrawing one should raise both barriers. The steric bulk of the substituent is predicted to inhibit more strongly the aziridination reactions. It is predicted that electron-releasing substituents with small bulk will create powerful aziridination reagents, whereas electron-withdrawing substituents like MeSO(2) will prefer C-H bond activation with preference that increases with steric bulk. Finally, the study predicts (i) that the reactions of RN-Cpd I will be less stereospecific than those of O-Cpd I and (ii) that aziridination will be more stereoselective than amidation.     

Chemical and Genetic Study of Ligularia anoleuca and L. veitchiana in Yunnan and Sichuan Provinces of China

Chemical and genetic study of Ligularia anoleuca and L. veitchiana, which belong to section Ligularia, series Speciosae, was carried out. From L. anoleuca samples, collected in Yunnan and Sichuan Provinces of China, a new compound, furanoeremophil‐1(10)‐en‐6α‐ol, was isolated together with known 6β‐{[2‐(hydroxymethyl)prop‐2‐enoyl]oxy}furanoeremophil‐1(10)‐ene and 1β,10β‐epoxy‐6β‐{[2‐(hydroxymethyl)prop‐2‐enoyl]oxy}furanoeremophilane. From L. veitchiana samples, collected in Yunnan Province, euparin, 2‐isopropenyl‐5,6‐dimethoxybenzofuran, and 6‐hydroxy‐3β‐methoxytrementone were isolated. DNA Sequencing of the internal transcribed spacers of the ribosomal RNA gene showed that the two species are not particularly close despite morphological similarities, in agreement with the chemical results.     

Growth and characterization of Fe nanostructures on GaN

We have investigated the growth of Fe nanostructures on GaN(0 0 0 1) substrates at room temperature using reflection high-energy electron diffraction (RHEED), scanning tunneling microscopy (STM), and superconducting quantum interference device magnetometer. Initially, a ring RHEED pattern appears, indicating the growth of polycrystalline α-Fe. At around 0.5 nm deposition, the surface displays a transmission pattern from α-Fe films with the epitaxial relationship of Fe(1 1 0)//GaN(0 0 0 1) and Fe[1 −1 1]//GaN[1 1 −2 0] (Kurdjumov-Sachs (KS) orientational relationship). Further deposition to 1 nm results in the appearance of a new spot pattern together with the pattern from domains with the KS orientation relationship. The newly observed pattern shows that Fe layers are formed with the epitaxial relationship of Fe(1 1 0)//GaN(0 0 0 1) and Fe[0 0 1]//GaN[1 1 −2 0] (Nishiyama-Wasserman (NW) orientational relationship). From STM images for Fe layers with the KS and NW orientational relationships, it can be seen that Fe layers with the KS relationship consist of round-shaped Fe nanodots with below 7 nm in average diameter. These nanodots coalesce to form nanodots elongating along the Fe[1 0 0] direction, and they have the KS orientational relationship. Elongated Fe nanodots with the NW relationship show ferromagnetism while round-shaped Fe nanodots with the KS relationship show super-paramagnetic behavior. We will discuss their magnetic properties in connection with the change in crystalline configurations of nanodots.