Theoretical Study of the Catalytic Mechanism of the Cu-Only Superoxide Dismutase.

The catalytic mechanisms for the wild-type and the mutated Cu-only superoxide dismutase were studied using the hybrid density functional B3LYP and a quantum chemical cluster approach. Optimal protonation states of the active site were examined for each stage of the catalytic cycle. For both the reductive and the oxidative half-reactions, the arrival of the substrate was found to be accompanied by a charge-compensating H with exergonicities of -15.

Theoretical study of the mechanism of the manganese catalase KatB.

The mechanism of the HO disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger models of increasing sizes were employed with the help of the high-resolution X-ray structure. In the reaction pathway suggested for KatB using the Large chemical model, the O-O homolysis of the first substrate HO occurs through a μ-η:η coordination mode and requires a barrier of 10.

Geometric structures of Ge(n) (n=34-39) clusters.

The structures of Ge(n) (n=34-39) clusters were searched by a genetic algorithm using a tight-binding interatomic potential. First-principles calculations based on density functional theory were performed to further identify the lowest-energy structures. The calculated results show that Ge(n) (n=34-39) clusters favor prolate or Y-shaped three-arm structures consisting of two or three small stable clusters (Ge(6), Ge(7), Ge(9), or Ge(10)) linked by a Ge(6) or Ge(9) bulk unit.

Platelike structures of semiconductor clusters Ge(n) (n = 40-44).

The structures of Ge(n) (n=40-44) clusters were searched by genetic algorithm combined with a tight-binding method. First-principles calculations based on density functional theory were performed to further optimize the isomer structures. The calculated results show that Ge(n) (n=40-44) clusters favor platelike structures, consisted of four small magic clusters (Ge(9) or Ge(10)), and a Ge(4) core.

Structures and stabilities of Pb(n) (n

We have performed global structural optimizations for neutral lead clusters Pb(n) (n = 2-20) by using a genetic algorithm (GA) coupled with a tight-binding (TB) potential. The low-energy structures identified from a GA/TB search were further optimized at the DFT-PBE level. The calculated results show that the Pb(n) (14 < n View Article and Find Full Text PDF

Theoretical study on stabilities of multiple hydrogen bonded dimers.

A series of self-constituted multiple hydrogen bonded (MHB) complexes has been investigated systematically by density functional theory (PBE1PBE /6-31G**), the Morokuma energy decomposition method (HF/6-31G**) and MP2 (6-31G** and 6-311++G**) calculation. We have discovered that (i) for doubly hydrogen bonded (DHB) complexes, both the interaction energy and stability increase with the charge transfer energy; (ii) for quadruple hydrogen bonded (QHB) complexes, cooperativity is the most important factor determining stability of the complex: stronger cooperative energy correlates well with larger interaction energy and thus more stable complex and vice versa; (iii) correlation energy plays an important role in intermolecular interactions. The correlation energy, mainly consisting of dispersive energy, also exhibits cooperativity in MHB dimers: positive for M-aadd and generally negative for other complexes.

Bending effect on the stabilities of quadruple hydrogen bonding systems: theoretical study of a series of self-constituted quadruple hydrogen bonded complexes (C9H9N5O2)2.

A series of self-constituted quadruple hydrogen bonded (QHB) complexes (C9H9N5O2)2 has been designed and studied systematically using density functional theory (B3LYP/6-31G**) and the Morokuma energy decompose method (HF/6-31G**). Despite very similar structures of these systems, the interaction energies fluctuate significantly from 22.33 to 88.

Hydrogen bonded oligohydrazide foldamers and their recognition for saccharides.

This paper describes the synthesis and characterization of the first series of hydrogen bonding-driven hydrazide foldamers and their recognition for alkyl saccharides in chloroform. Oligomers 1, 2-4, 5, 6, and 7, which contain one, two, four, six, or twelve repeated dibenzoyl hydrazide residues, respectively, have been prepared. The rigid and planar conformations of 1 and 2 or 4 have been established with X-ray analysis and (1)H NMR spectroscopy, whereas the folding and helical conformations of 5-7 have been evidenced by the 1D and 2D (1)H NMR and IR spectroscopy and molecular mechanics calculations.

Solvophobically-driven oligo(ethylene glycol) helical foldamers. Synthesis, characterization, and complexation with ethane-1,2-diaminium.

Oligo(ethylene glycols) 1a-h, which are incorporated with one to eight 2,3-naphthylene units, respectively, have been synthesized and characterized. The conformational changes of the new oligomers have been investigated in chloroform-acetonitrile binary solvents by the UV-vis, (1)H NMR, and fluorescent spectroscopy. It has been revealed that the naphthalene units in hexamer 1f, heptamer 1g, and octamer 1h are driven by solvophobic interaction to stack in polar solvents.

Zipper-featured delta-peptide foldamers driven by donor--acceptor interaction. Design, synthesis, and characterization.

Donor-acceptor interaction between electron-rich 1,5-dioxynaphthalene (DAN) and electron-deficient pyromellitic diimide (PDI) has been utilized to induce the formation of a new kind of zipper-featured delta-peptide foldamers. Seven l-ornithine-based delta-peptides 1a-g, in which one to three DNA and PDI units are incorporated to the two ends of the peptide backbones, respectively, have been designed and prepared by the standard liquid-phase synthetic method. (1)H NMR, UV-vis, and fluorescent quenching studies reveal that all the delta-peptides adopt folding conformations in nonpolar chloroform and polar DMF as a result of intramolecular donor-acceptor interaction between the DAN and PDI units.

Hydrazide-based quadruply hydrogen-bonded heterodimers. Structure, assembling selectivity, and supramolecular substitution.

This paper describes the synthesis, self-assembly, and characterization of a new class of highly stable hydrazide-based quadruply hydrogen-bonded heterodimers. All of the hydrazide-derived heterodimers possess the complementary ADDA-DAAD hydrogen-bonding sequences. Hydrazide derivatives 1, which has two intramolecular S(6) RO.

First zipper-featured molecular duplexes driven by cooperative donor-acceptor interaction.

[structure: see text] The first class of zipper-shaped artificial duplexes, which are driven by multiple donor-acceptor interactions between electron-rich 1,5-dioxynaphthalene or 1,4-dioxybenzene and electron-deficient pyromellitic dimide units, have been studied in organic media by (1)H NMR, UV-vis, and vapor pressure osmometry. (1)H NMR binding investigations reveal substantial cooperativity of the donor-acceptor interaction in the duplexes.