Novel matrix invariants for characterization of changes of proteomics maps

Previous studies on mathematical characterization of proteomics maps by sets of map invariants were based on the construction of a set of distance-related matrices obtained by matrix multiplication of a single matrix by itself. Here we consider an alternative characterization of proteomics maps based on a set of matrices characterizing local features of an embedded zigzag curve over the map. It is shown that novel invariants can well characterize proteomics maps. Advantages of the novel approach are discussed.     

Magnetic Modulation in Heteroallene and Heterocumulene Based tert-butyl Nitroxide Diradicals: Spin Delocalization and Conformation Play Crucial Roles

We have theoretically investigated the magnetic properties of heteroallene (>C=C=X−) and heterocumulene (>C=C=C=X−) based tert-butyl nitroxide diradicals (X is P/As). Calculation of magnetic exchange coupling constant (J) shows ferromagnetic interaction in heteroallene based diradicals. Whereas, in heterocumulene based diradicals, tuning of J value from antiferro- to ferro-magnetic state is observed from Z- to E- isomer. Delocalization of spin density from radical site to the coupler (in planar arrangement) is observed in spin distribution analysis which is also advocated by molecular orbital analysis. The typical feature of tert-butyl nitroxide radical creates spin delocalization along with spin polarization within the coupler. The J values of all the diradicals strongly depend on the dihedral angle between radical center and coupler. Magneto-structural correlation shows that the change in dihedral angle tunes the magnetic property for both the Z- and E- isomers of heterocumulenes depending on the spin accumulation on two nearby magnetic centers. The extent of spin delocalization and conformation of spin centers on the molecular axis are important for the different J values observed in our designed systems.     

Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)

A combined theoretical and experimental approach has been employed to characterize the hydrido-cobaloxime [HCo(dmgH)(2)(PnBu(3))] compound. This complex was originally investigated by Schrauzer et al. [Schrauzer et al., J. Am. Chem. Soc. 1971, 93,1505] and has since been referred to as a key, stable analogue of the hydride intermediate involved in hydrogen evolution catalyzed by cobaloxime compounds [Artero, V. et al. Angew. Chem., Int. Ed. 2011, 50, 7238-7266]. We employed quantum chemical calculations, using density functional theory and correlated RI-SCS-MP2 methods, to characterize the structural and electronic properties of the compound and observed important differences between the calculated (1)H NMR spectrum and that reported in the original study by Schrauzer and Holland. To calibrate the theoretical model, the stable hydrido tetraamine cobalt(III) complex [HCo(tmen)(2)(OH(2))](2+) (tmen = 2,3-dimethyl-butane-2,3-diamine) [Rahman, A. F. M. M. et al. Chem. Commun. 2003, 2748-2749] was subjected to a similar analysis, and, in this case, the calculated results agreed well with those obtained experimentally. As a follow-up to the computational work, the title hydrido-cobaloxime compound was synthesized and recharacterized experimentally, together with the Co(I) derivative, giving results that were in agreement with the theoretical predictions.     

Modulated Binary–Ternary Dual Semiconductor Heterostructures

A generic modular synthetic strategy for the fabrication of a series of binary‐ternary group II‐VI and group I‐III‐VI coupled semiconductor nano‐heterostructures is reported. Using Ag₂Se nanocrystals first as a catalyst and then as sacrificial seeds, four dual semiconductor heterostructures were designed with similar shapes: CdSe‐AgInSe₂, CdSe‐AgGaSe₂, ZnSe‐AgInSe₂, and ZnSe‐AgGaSe₂. Among these, dispersive type‐II heterostructures are further explored for photocatalytic hydrogen evolution from water and these are observed to be superior catalysts than the binary or ternary semi‐conductors. Details of the chemistry of this modular synthesis have been studied and the photophysical processes involved in catalysis are investigated.     

Structure, interactions, and antibacterial activities of MSI-594 derived mutant peptide MSI-594F5A in lipopolysaccharide micelles: role of the helical hairpin conformation in outer-membrane permeabilization

Lipopolysaccharide (LPS) provides a well-organized permeability barrier at the outer membrane of Gram-negative bacteria. Host defense cationic antimicrobial peptides (AMPs) need to disrupt the outer membrane before gaining access to the inner cytoplasmic membrane or intracellular targets. Several AMPs are largely inactive against Gram-negative pathogens due to the restricted permeation through the LPS layer of the outer membrane. MSI-594 (GIGKFLKKAKKGIGAVLKVLTTG) is a highly active AMP with a broad-spectrum of activities against bacteria, fungi, and virus. In the context of LPS, MSI-594 assumes a hairpin helical structure dictated by packing interactions between two helical segments. Residue Phe5 of MSI-594 has been found to be engaged in important interhelical interactions. In order to understand plausible structural and functional inter-relationship of the helical hairpin structure of MSI-594 with outer membrane permeabilization, a mutant peptide, termed MSI-594F5A, containing a replacement of Phe5 with Ala has been prepared. We have compared antibacterial activities, outer and inner membrane permeabilizations, LPS binding affinity, perturbation of LPS micelles structures by MSI-594 and MSI-594F5A peptides. Our results demonstrated that the MSI-594F5A has lower activities against Gram-negative bacteria, due to limited permeabilization through the LPS layer, however, retains Gram-positive activity, akin to MSI-594. The atomic-resolution structure of MSI-594F5A has been determined in LPS micelles by NMR spectroscopy showing an amphipathic curved helix without any packing interactions. The 3D structures, interactions, and activities of MSI-594 and its mutant MSI-594F5A in LPS provide important mechanistic insights toward the requirements of LPS specific conformations and outer membrane permeabilization by broad-spectrum antimicrobial peptides.     

High‐spin behavior of molecular crystals and extended π systems

The qualitative rules for the existence of high‐spin ground states in extended systems and molecular crystals are examined here on a firmer theoretical footing. Extended systems have been categorized into three groups, namely, type I, type II, and type III, depending on the type of bonding interactions. The general form of the spin Hamiltonian operators have been written down. The active spaces have been restricted to the minimum size for each of these three types of spin systems. The zeroth‐order state vectors and the Hartree–Fock ground‐state energies have been identified for unit species of each type. The extended system Hamiltonian operators are further truncated in such a way that only the nearest‐neighbor interactions are retained. Expressions have been derived for the energy gap from a molecular orbital approach. The relatively small effects of electron correlation on the energy gaps have been estimated for the type I systems, which belong to the systems of solid‐state physics. In particular, it has been shown that for the type I systems the singlet–triplet gap, and hence the ferromagnetic coupling constant, primarily depends upon the difference of one‐electron kinetic energies and not on the two‐electron exchange integrals. This result agrees with the concept of kinetic exchange that was introduced in the context of a resonating valence‐bond formalism. Type II systems are exemplified by extended systems that can be prepared from conjugated molecules while organic molecular crystals form examples of type III species. For these systems, however, the Coulomb exchange interaction has been shown to dominate the energy gap. A quick review of the Heisenberg spin Hamiltonian for the H₂ molecule is sufficient to point out that the sign of the calculated ferromagnetic coupling constant depends on the method of calculation, the nature of the basis set, and the bond length. This is amply supported by ab initio calculations on this species. Numerical data have also been obtained from computations on m‐phenylene‐coupled nitroxy radicals and stacks of α‐nitronyl nitroxide, but these calculations have been based on a semiempirical quantum chemical methodology (INDO) since some of the species involved are exceedingly large. Computed energy gaps are in good agreement with experimental and other theoretical (AM1, PM3) results. Nevertheless, for the dimer, trimer, tetramer, and pentamer of the type II specimen, the important π orbitals are far from being degenerate. The quantitative results clearly deviate from the criterion of degeneracy that was suggested from qualitative theories for the existence of a high‐spin ground state. Therefore, the criteria for the existence of high spins have been reformulated in terms of the monomer orbitals. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 308–324, 2000