Strongly regular graphs from reducible cyclic codes

Journal of Algebraic Combinatorics - Let p be a prime number. Reducible cyclic codes of rank 2 over $$\mathbb {Z}_{p^m}$$ are shown to have exactly two Hamming weights in some cases. Their weight...     

Comparison of the AIM delocalization index and the Mayer and fuzzy atom bond orders

In this paper the behavior of three well-known electron-sharing indexes, namely, the AIM delocalization index and the Mayer and fuzzy atom bond orders are studied at the Hartree-Fock level. A large number of five-membered ring molecules, containing several types of bonding, constitute the training set chosen for such purpose. A detailed analysis of the results obtained shows that the three indexes studied exhibit strong correlations, especially for homonuclear bonds. The correlation is somewhat poorer but still significant for polar bonds. In this case, the bond orders obtained with the Mayer and fuzzy atom approaches are normally closer to the formally predicted bond orders than those given by the AIM delocalization indexes, which are usually smaller than those expected from chemical intuition. In some particular cases, the use of diffuse functions in the calculation of Mayer bond orders leads to unrealistic results. In particular, noticeable trends are found for C-C bonds, encouraging the substitution of the delocalization index by the cheaper fuzzy atom or even the Mayer bond orders in the calculation of aromaticity indexes based on the delocalization index such as the para-delocalization index and the aromatic fluctuation index.     

Laser excited S2 → S1 and S1 → S0 emission spectra and the S2 → Sn absorption spectrum of azulene in solution

We present the S₁ → S₀ fluorescence spectrum, between 740 and 940 nm, of azulene solutions (10^?3 M in methanol) excited with a Q-switched ruby laser. The nitrogen-laser excited S₂ → S₁ fluorescence spectrum, between 700 and 930 nm, is also reported. The transient S₁ → S_n spectrum between 500 and 650 nm was studied, using synchronous nitrogen laser and dye laser excitation. The S₅ (¹B₁(3)) state of azulene was found to be located at 45500 cm^?1 and the cross section σ₂₅ of the transient absorption S₂ → S₅ is estimated to be 3 × 10^?18 cm²/molecule.     

Mechanism of 1,3-migration in allylperoxyl radicals: computational evidence for the formation of a loosely bound radical-dioxygen complex

The three pathways postulated for 1,3-migration of the peroxyl group in the allylperoxyl radical (1a), a key reaction involved in the spontaneous autoxidation of unsaturated lipids of biological importance, have been investigated by means of quantum mechanical electronic structure calculations. According to the barrier heights calculated from RCCSD(T)/6-311+G(3df,2p) energies with optimized molecular geometries and harmonic vibrational frequencies determined at the UMP2/6-311+G(3df,2p) level, the allylperoxyl rearrangement proceeds by fragmentation of 1a through a transition structure (TS1) with a calculated DeltaH++(298 K) of 21.7 kcal/mol to give an allyl radical-triplet dioxygen loosely bound complex (CX). In a subsequent step, the triplet dioxygen moiety of CX recombines at either end of the allyl radical moiety to convert the complex to the rearranged peroxyl radical (1a') or to revert to the starting peroxyl radical 1a. CX shows an electron charge transfer of 0.026 e in the direction allyl --> O(2). The dominant attractive interactions holding in association the allyl radical-triplet dioxygen pair in CX are due chiefly to dispersion forces. The DeltaH(298 K) for dissociation of CX in its isolated partners, allyl radical and triplet dioxygen, is predicted to be at least 1 kcal/mol. The formation of CX prevents the diffusion of its partners and maintains the stereocontrol along the fragmentation-recombination processes. The concerted 1,3-migration in allylperoxyl radical is predicted to take place through a five-membered ring peroxide transition structure (TS2) showing two long C-O bonds. The DeltaH++(298 K) calculated for this pathway is less favorable than the fragmentation-recombination pathway by 1.9 kcal/mol. The cyclization of 1a to give a dioxolanyl radical intermediate (2a) is found to proceed through a five-membered ring transition structure (TS3) with a calculated DeltaH++(298 K) of 33.9 kcal/mol. Thus, the sequence of ring closure 1a --> 2a and ring opening 2a --> 1a' is unlikely to play any significant role in allylperoxyl rearrangement 1a --> 1a'. In the three pathways investigated, the energy of the transition structure is predicted to be somewhat lower in either heptane or aqueous solution than in the gas phase. Although the energy lowering calculated for TS1 is smaller than the calculated for TS2 and TS3, it is very unlikely that the solvent effects may reverse the predicted preference of the fragmentation-recombination pathway over the concerted and stepwise ring closure-ring opening mechanisms.     

STRUCTURE-ACTIVITY RELATIONSHIP OF PORPHINES FOR PHOTOINACTIVATION OF BACTERIA

Abstract— The antibacterial photodynamic effects of uncharged ( o -tetrahydroxyphenyl porphine [THPP], m -THPP and p -THPP), cationic (5,10,15,20-tetra[4- N -methylpyridyllporphine [TMPyP]) and anionic (5,10,15,20-tetra[4-sulfonatophenyl porphine] [TPPS₄]) porphines on Staphylococcus aureus and Escherichia coli bacteria inactivation were examined. The results show that uncharged porphines provoked antibacterial photodynamic activity on S. aureus, and also on E. coli in the presence of the membrane-disorganizing peptide polymixin B nonapeptide (PMNP). The TMPyP compound was highly photoactive toward gram-positive bacteria but only marginally effective on gram-negative cells, whereas TPPS₄ showed no activity on either gram-positive or gram-negative bacteria. The photoactivity of TMPyP is due to the electrostatic attraction between the positively charged sensitizer molecule and the negatively charged membrane of the gram-positive target cells. For TPPS₄, the inactivity toward gram-positive bacteria is due to electrostatic repulsion between the charged sensitizer molecule and the cell membrane. For gram-negative bacteria, the inactivity is conceivably due to preferential (electrostatic) binding to the positively charged PMNP, which is an adjuvant for membrane disorganization, but has no effect on cell viability. For hydrophobic sensitizers, the photoactivity depends on the state of aggregation. The extent of deaggregation of the different THPP isomers was determined by fluorescence measurements of bound sensitizers and could be positively correlated with their photoinactivation capacity. We conclude that the structure-activity relationships of these porphines are affected by their net charge and by aggregation.     

Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si)

To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S(N)2@C) and at silicon in chlorosilane (S(N)2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl(-), CH(3)Cl] reactant complex, the [Cl-CH(3)-Cl](-) transition state and the stable [Cl-SiH(3)-Cl](-) transition complex is -10.42, +2.52, and -27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triple-zeta quality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S(N)2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP).     

Reactions between germylenes (silylenes) and phosphaalkenes: an experimental and theoretical study. Preparation of the first representative of germaphosphacyclopropanes

Reactions of a number of germylenes and dimethylsilylene with a phosphaalkene, 2,2-bis(trimethylsilyl)-1-phenyl-1-phosphaethene (1), were studied. The reaction of short-lived dimethylgermylene with 1 produced a phosphagermirane 3 (the first representative of a new class of heterocyclic compounds). Compound 3 was characterized in solution by ¹H, ¹³C, ³¹P, and ²⁹Si NMR spectroscopy. Subsequent reaction of 3 with dimethylgermylene results in 2,2,3,3-tetramethyl-4,4-bis(trimethylsilyl)-1-phenyl-2,3-digerma-1-phosphacyclobutane 4, which has not been reported so far. In order to rationalize different reactivities of germylenes towards alkenes and phosphaalkenes, the addition products of GeH₂ to ethylene and phosphaethene (HP=CH₂) were studied using the G2 computational scheme and DFT PBE technique. The adducts of GeMe₂ (GeCl₂) with HP=CH₂ and of GeMe₂ with PhP=C(SiH₃)₂ were also calculated by the DFT PBE method. According to calculations, the exothermicity, DE, of cycloaddition of GeH₂ and GeMe₂ to the phosphaalkenes HP=CH₂ and PhP=C(SiH₃)₂ (43.5—39.7 kcal mol^–1) is nearly twice as high as the exothermicity of cycloaddition of these germylenes to ethylene. In addition to the minimum corresponding to the three-membered cycle, a number of minima corresponding to quite stable donor-acceptor complexes in which the Ge atom is coordinated by the lone electron pair of the P atom in the phosphaalkene molecule were located on the potential energy surface of the germylene—phosphaalkene system. The complexation energy of the complex of GeH₂ (GeMe₂) with phosphaethene is 25.0 (16.9) kcal mol^–1. For GeCl₂, the exothermicity of cycloaddition to HP=CH₂ decreases to 7.6 kcal mol^–1 and the complexation energy decreases to 8.2 kcal mol^–1.