Simulation of Adsorbate-Induced Surface Reconstruction

Abstract

Adsorbed atomic monolayers of atoms such as carbon and nitrogen can cause substantial reconstructions of a nickel {001} surface. In this simulation we combine an atomic-orbital-based calculation of electronic structure with an empirical pair-wise repulsive potential to model the covalent part of the total energy. For 0.5 monolayer coverage by the adsorbate, the surface metal layer relaxes into a p(2 × 2) structure, with transverse displacements of about 0.4 Å. At the same time these displaced surface nickel atoms ride up above second layer nickels, with a vertical displcement of about 0.4 Å. The covalent contribution to the relaxation energy comes out at about 2.0 eV per carbon atom and 1.4eV per nitrogen atom, of which the reconstruction contributes about 0.3eV.     

Synthesis and theoretical analysis of the structures and bonding in five new neutral square planar bis[2,4-di(aryl)-1,3,5-triazapentadienato]nickel(II) complexes

Solvothermal reactions in methanol of nickel acetate tetrahydrate, Ni(OAc)₂ · 4H₂O, with benzonitrile derivatives NC(C₆H₄)X, where X is one of the electron withdrawing substituents -CN, -NO₂, or -CF₃, located at the m- or p-positions relative to -CN, yield complexes of the general formula Ni{HNC(R)-NC(R)-NH}₂. More specifically, 3-nitrobenzonitrile, 4-nitrobenzonitrile, 1,3-dicyanobenzene, 1,4-dicyanobenzene, and ααα-trifluoro-p-toluonitrile are found to react with Ni(OAc)₂ · 4H₂O to yield Ni{HNC(R)-NC(R)-NH}₂, where R = 3-(NO₂)C₆H₄, 4-(NO₂)C₆H₄, 3-(CN)C₆H₄, 4-(CN)C₆H₄, or 4-(CF₃)C₆H₄, respectively. Analogous reactions of nitriles lacking electron withdrawing groups do not occur under similar conditions. Solid-state structures have been determined for the complexes with p-NO₂, p-CN, and p-CF₃ substituents on the phenyl rings. In addition, we describe density functional theory (DFT) and natural bonding orbital theory (NBO) studies on a simplified analog of these compounds, aimed at understanding their molecular bonding. It is shown that the new compounds for which solid-state structures have been determined are model examples of coordination compounds containing robust ω-bonds.     

On the role of the axial ligand in heme-based catalysis of the peroxidase and P450 type

 The present commentary focusses on the role of the axial ligand in peroxidase- and P450-type catalysis. Based on molecular orbital calculations and the experimental evidence available, it is argued that the ligand of a heme-containing enzyme may be a factor in setting the relative chance, although not the intrinsic capability, of the enzyme to catalyse a specific type of heme-based reaction chemistry. The ligand can do so by influencing the electrophilicity, i.e. the redox potential of the high-valency iron-oxo complex, and also by influencing the energy barrier for a reaction pathway through delocalization of valence electrons along the axial ligands, thereby, in the case of a cysteinate but not a histidine axial ligand, stabilizing oxygen transfer pathways. Received and accepted: 7 May 1996     

Ultra-low dose radiotherapy in the management of low-grade orbital lymphomas

BackgroundUltra-low dose radiotherapy (ULDRT) (2 × 2 Gy) has been used for symptomatic control of low-grade lymphomas with surprising local control rates, suggesting that these entities could respond to lower doses. These are particularly desirable for the treatment of orbital sites and some publications refer to high rates of complete responses. In this paper, we present our experience with the use of ULDRT for indolent orbital lymphomas.Materials and methodsElectronic files and treatment plans of patients treated with ULDRT for low-grade orbital lymphoma were retrospectively reviewed. Oncological outcomes and toxicities were collected and described for each patient.ResultsSeven patients (median age of 75 years) with 8 lesions (3 follicular, 2 MALT, 1 marginal and 1 low-grade non-Hodgkin lymphoma) were considered for analysis. The majority had stage IE disease and one patient had bilateral disease. Six tumors were detected on imaging (median size of 20 mm). Involved orbital sites were periocular, conjunctival and palpebral; there was one case of intraocular (choroid) and one case of lacrimal gland involvement. One patient received consolidative rituximab after RT. The median follow-up time was 22 months. Two patients had partial response, one of them with persistent minimal choroidal disease and the other with partial response on CT. Five (71%) patients had clinical (n = 2) or radiologic (n = 3) complete response on treated sites. Reported late toxicities were minimal and included dry eye and pruritus.ConclusionIn our experience, ULDRT achieved a local control rate of 100% and complete response rate of 71% with minimal toxicity.     

Kinetics and pathway of biodegradation of dibutyl phthalate by Pleurotus ostreatus

Dibutyl phthalate (DBP) is a plasticizer, whose presence in the environment as a pollutant has attained a great deal of attention due to its reported association with endocrine system disturbances on animals. Growth parameters, glucose uptake, percentage of removal efficiency (%E) of DBP, biodegradation constant of DBP (k) and half-life of DBP biodegradation (t_1/2) were evaluated for Pleurotus ostreatus grown on media containing glucose and different concentrations of DBP (0, 500 and 1000 mg l^?1). P. ostreatus degraded 99.6 % and 94 % of 500 and 1000 mg of DBP l^?1 after 312 h and 504 h, respectively. The k was 0.0155 h^?1 and 0.0043 h^?1 for 500 and 1000 mg of DBP l^?1, respectively. t_1/2 was 44.7 h and 161 h for 500 and 1000 mg of DBP l^?1, respectively. Intermediate compounds of biodegraded DBP were identified by GC-MS and a DBP biodegradation pathway was proposed using quantum chemical calculation. DBP might be metabolized to benzene and acetyl acetate, the first would be oxidated to muconic acid and the latter would enter into the Krebs cycle. P. ostreatus has the ability to degrade DBP and utilizes it as source of carbon and energy.     

Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity

Mutations in human coagulation factor IX cause an X-linked bleeding disorder Hemophilia B, which can be classified as severe, moderately severe and mild based on the plasma levels of factor IX among affected individuals with respect to normal factor IX activity assayed in the patients' plasma (<1%, 2-5%, 6-30%, respectively). Recently, we identified hemophilia B to be a disease with mutations showing clinical variation and speculated that this phenotypic heterogeneity might be a replacement-specific property. Here, we have analyzed the differences in sequence and structural properties among identical mutations with varying phenotypes (IMVPs) by comparing with mutations with uniform phenotypes (MUPs), with recurring reports in Haemophilia B mutation database. Classification of mutations into IMVPs and MUPs has been done based on rigorous systematic evaluation of the clotting activity each mutation is associated with. IMVPs (n = 51) occur in less conserved mutant sites with more tolerated substitutions compared to MUPs (n = 100). A preponderance of CpG site mutations and Arg as the mutated residue in IMVPs compared to Cys in MUPs was observed. Hence, a CpG site substitution at less conserved Arg site might have an increased propensity of expressing variable phenotypes. The changes in intrinsic properties associated with the mutation are less drastic for IMVPs than for MUPs, though no significant differences were observed in structural properties. Based on this study and available literature we speculate that modifier genes at other loci, epigenetic interactions and environment may serve individually or cumulatively to bring about the clinical variation implicating hemophilia B to be deviation from classical Mendelian disorder with complete penetrance. We demonstrate that phenotypic heterogeneity appears to be site-specific also owing to the lesser conservation of the mutant site.     

Carbocations in the synthesis of prostaglandins by the cyclooxygenase of pgh synthase? a radical departure!

Evidence already available is used to demonstrate that although prostaglandin G/H synthase hydroxylates arachidonic acid through radical intermediates, it effects cyclizations through a carbocation center at C-10. This is produced following migration of H to the initial radical at C-13 and a 1epsilon oxidation. Under orbital symmetry control, the cyclizations can give only the ring size and trans stereochemistry actually observed. After cyclization, the H-shift reverses to take the sequence back into current radical theory for hydroxylation at C-15. Thus 10,10-difluoroarachidonic acid cannot be cyclized, although it can be hydroxylated. Acetylation of Ser516 in the isoform synthase-2 is considered to oppose carbocation formation and/or H-migration and so prevent cyclizations while permitting hydroxylations; the associated inversion of chirality at C-15 can then readily be accommodated without the change in conformation required by other schemes. Suicide inhibition occurs when carbocations form stable bonds upon (thermal) contact with adjacent heteroatoms, etc. Because the cyclooxygenase and peroxidase functions operate simultaneously through the same heme, phenol acts as reducing cosubstrate for the cyclooxygenase, thus enabling it to promote PGG2 production and protect the enzyme from oxidative destruction.     

Probing the ground state of the purple mixed valence CuA center in nitrous oxide reductase: a CW ENDOR (X-band) study of the 65Cu, 15N-histidine labeled enzyme and interpretation of hyperfine couplings by molecular orbital calculations

 CW ENDOR (X-band) spectra for the purple mixed-valence [Cu(1.5+)...Cu(1.5+)], S = 1/2, Cu_A site in nitrous oxide reductase were obtained after insertion of ⁶⁵Cu or both ⁶⁵Cu and ¹⁵N-histidine. The ¹⁴N/¹⁵N isotopic substitution allowed for an unambiguous deconvolution of proton and nitrogen hyperfine couplings in the spectra. A single nitrogen coupling with a value of 12.9 ± 0.4 MHz for ¹⁴N was detected. Its anisotropy was characteristic for imidazole bound to copper. A spin density of 3–5% was estimated for the nitrogen donors to Cu_A, indicating that the ground state is ²B_3u. Proton hyperfine structure was detected from four C_β protons of coordinating cysteine residues. Their isotropic and anisotropic parts were deconvoluted by spectral simulation. From the anisotropic couplings a spin density of 16–24% was estimated for each of the cysteine thiolate donors of Cu_A. The [N_HisCu(RS)₂CuN_His]⁺ core structure of Cu_A in nitrous oxide reductase from Pseudomonas stutzeri is predicted to be similar to the crystallographically determined Cu_A* structure (Wilmanns M, Lappalainen P, Kelly M, Sauer-Eriksson E, Saraste M (1995) Proc Natl Acad Sci USA 92 : 11955–11959), but distinct from the Cu_A structure of Paracoccus denitrificans cytochrome c oxidase (Iwata S, Ostermeier C, Ludwig B, Michel H (1995) Nature 376 : 660–669). The angular dependence of the isotropic couplings as a function of the electronic ground state was calculated by the INDO/S method. The Mulliken atomic-spin populations calculated by a gradient-corrected density functional method and the semiempirical INDO/S method were compared with experimentally derived spin populations, and good agreement between theory and experiment was found for both calculations. The ground state of Cu_A is best represented by the resonance structures of the form [Cu^IS^–S^–Cu^II↔ Cu^IS^•S^–Cu^I↔ Cu^IS^–S^•Cu^I↔ Cu^IIS^–S^–Cu^I]. It is proposed that the Cu 4s,p as well as sulfur 3d orbitals play a role in the stabilization of this novel type of cluster. Received: 17 September 1997 / Accepted: 28 October 1997     

Reduced basal and novelty-induced levels of activity-regulated cytoskeleton associated protein (Arc) and c-Fos mRNA in the cerebral cortex and hippocampus of APPswe/PS1ΔE9 transgenic mice

Activity-regulated cytoskeletal-associated protein (Arc) and c-Fos are immediate early gene (IEG) products induced by novelty in the hippocampus and involved in the consolidation of synaptic plasticity and long-term memory. We investigated whether induction of arc and c-fos after exposure to a novel open field environment was compromised in different neocortical areas and the hippocampal formation in APP/PS1ΔE9 transgenic mice characterized by pronounced accumulation and deposition of beta amyloid (Aβ). Notably, the basal level of Arc and c-fos mRNA in the neocortex was significantly lower in APP/PS1ΔE9 compared to wild-type mice. Novelty exposure induced an increase in Arc and c-Fos mRNA in the medial prefrontal cortex (mPFC), parietal cortex, and hippocampal formation in both APP/PS1ΔE9 transgenic and wild-type mice. However, novelty-induced IEG expression did not reach the same levels in APP/PS1ΔE9 as in the wild-type mice. In contrast, synaptophysin levels did not differ between mutant and wild type mice, suggesting that the observed effect was not due to a general decrease in the number of presynapses. These data suggest a reduction in basal and novelty-induced neuronal activity in a transgenic mouse model of Alzheimer’s disease, which is most pronounced in cortical regions, indicating that a decreased functional response in IEG expression could be partly responsible for the cognitive deficits observed in patients with Alzheimer’s disease.     

New binuclear model compounds for the study of the 4f-4f exchange interaction

Two new homobinuclear 4f-4f complexes, [Ln^III(L)₃]₂, (Ln=Pr 1; Gd 2) have been synthesized (L⁻=2,6-diformyl-4-methylphenolato). The crystallographic investigation of 1 reveals centrosymmetric binuclear entities with the metallic centers connected by two of the anionic ligands. The praseodymium ions are bridged by the phenoxo oxygen atoms. One carbonyl group of a bridging molecule is coordinated to one Pr(III) ion, while the other one is coordinated to the second Pr(III) ion. The other four L⁻ ions act as terminal chelated ligands, through the phenoxo oxygen atom and one carbonyl group. The distance between the Pr(III) ions within the binuclear entity is 4.0711(4) Å. The supramolecular solid-state architecture is sustained by a system of π-π interactions. The cryomagnetic study of 2 reveals a very weak antiferromagnetic interaction between the Gd(III) ions (J=−0.053 cm⁻¹, ).