Theoretical Study of the Quadrupolarity of Carbodiimide

Solventless supramolecular chemistry via vapor diffusion of volatile small molecules upon a new trinuclear silver(I)-nitrated pyrazolate macrometallocyclic solid: an experimental/theoretical investigation of the dipole/quadrupole chemisorption phenomena

A comparative study on the tendency of a new trinuclear silver(I) pyrazolate, namely, [N,N-(3,5-dinitropyrazolate)Ag]3 (1), and a similar compound known previously, [N,N-[3,5-bis(trifluoromethyl)pyrazolate]Ag]3 (2), to adsorb small volatile molecules was performed. It was found that 1 has a remarkable tendency to form adducts, at room temperature and atmospheric pressure, with acetone, acetylacetone, ammonia, pyridine, acetonitrile, triethylamine, dimethyl sulfide, and tetrahydrothiophene, while carbon monoxide, tetrahydrofuran, alcohols, and diethyl ether were not adsorbed. On the contrary, 2 did not undergo adsorption of any of the aforementioned volatile molecules. Adducts of 1 were characterized by elemental analysis, IR, thermogravimetric analysis (TGA), Brunauer-Emmett-Teller (BET) surface area, and diffusion NMR measurements. The crystal structures of 1·2CH3CN and compound 3, derived from an attempt to crystallize the adduct of 1 with ammonia, were determined by single-crystal X-ray diffractometric studies. The former shows a sandwich structure with a 1:2 stoichiometric [Ag3]/[CH3CN] ratio in which one acetonitrile molecule points above and the other below the centroid of the Ag3N6 metallocycle. Compound 3 formed via rearrangement of the ammonia adduct to yield an anionic trinuclear silver(I) derivative with an additional bridging 3,5-dinitropyrazolate and having [Ag(NH3)2](+) as the counterion, [Ag(NH3)2][N,N-(3,5-dinitropyrazolate)4Ag3]. Irreversible sorption and/or decomposition upon vapor exposure are desirable advantages toward toxic gas filtration applications, including ammonia inhalation. TGA confirms the analytical data for all of the samples, showing weight loss for each adsorbed molecule at temperatures significantly higher than the corresponding boiling temperature, which suggests a chemical-bonding nature for adsorption as opposed to physisorption. BET surface measurements of the "naked" compound 1 excluded physical adsorption in its porous cavities. Density functional theory simulation results are also consistent with the chemisorption model, explain the experimental adsorption selectivity for 1, and attribute the lack of similar adsorption by 2 to significantly less polarizable electrostatic potential and also to strong argentophilic bonding whose energy is even higher than the quadrupole-dipole adduct bond energy upon proper selection of the density functional.

Electronic structures and spin topologies of gamma-picoliniumyl radicals. A study of the homolysis of N-methyl-gamma-picolinium and of benzo-, dibenzo-, and naphthoannulated analogs

Radicals resulting from one-electron reduction of (N-methylpyridinium-4-yl) methyl esters have been reported to yield (N-methylpyridinium-4-yl) methyl radical, or N-methyl-gamma-picoliniumyl for short, by heterolytic cleavage of carboxylate. This new reaction could provide the foundation for a new structural class of bioreductively activated, hypoxia-selective antitumor agents. N-methyl-gamma-picoliniumyl radicals are likely to damage DNA by way of H-abstraction and it is of paramount significance to assess their H-abstraction capabilities. In this context, the benzylic C-H homolyses were studied of toluene (T), gamma-picoline (P, 4-methylpyridine), and N-methyl-gamma-picolinium (1c, 1,4-dimethylpyridinium). With a view to providing capacity for DNA intercalation the properties also were examined of the annulated derivatives 2c (1,4-dimethylquinolinium), 3c (9,10-dimethylacridinium), and 4c (1,4-dimethylbenzo[g]quinolinium). The benzylic C-H homolyses were studied with density functional theory (DFT), perturbation theory (up to MP4SDTQ), and configuration interaction methods (QCISD(T), CCSD(T)). Although there are many similarities between the results obtained here with DFT and CI theory, a number of significant differences occur and these are shown to be caused by methodological differences in the spin density distributions of the radicals. The quality of the wave functions is established by demonstration of internal consistencies and with reference to a number of observable quantities. The analysis of spin polarization emphasizes the need for a clear distinction between "electron delocalization" and "spin delocalization" in annulated radicals. Aside from their relevance for the rational design of new antitumor drugs, the conceptional insights presented here also will inform the understanding of ferromagnetic materials, of spin-based signaling processes, and of spin topologies in metalloenzymes.

Effect of Hexafluorobenzene on the Photophysics of Pyrene

Absorption and fluorescence spectroscopy studies reveal the formation of a weak complex between pyrene and C(6)F(6) even in very dilute systems. The complex affects the photophysics of pyrene and reveals a combination of static and dynamic-quenching phenomena in both polar and nonpolar solvents. The results are supported by computational studies that shed light on the structure of the complex and the interactions involved and suggest that ground and excited-state interactions are of comparable magnitude; the association is believed to be driven by quadrupolar interactions. Understanding these interactions in solution is important for applications that aim at controlling the regio- or stereoselectivity of organic reactions.

Use of fourier transform infrared spectroscopy to follow the heterocumulene aided thermal dehydration of phthalic and naphthalic acids

Fourier transform infrared (FT-IR) spectroscopy has been successfully employed to follow the formation of phthalic anhydride and 1,8-naphthalic anhydride on heating their corresponding acids. The effects of three heterocumulenes, cyanamide, dicyandiamide, and sodium cyanate, on the temperature of formation of the anhydrides were also investigated using this method. It was found that the carbodiimides cyanamide and dicyandiamide dramatically lowered the temperature at which thermal dehydration of the acid led to anhydride formation. It was noted that cyanamide had a stronger catalytic effect than dicyandiamide, presumably due to the electron-withdrawing effect of the amidine group. Sodium cyanate was also found to promote the thermal dehydration of the acids to form the corresponding anhydrides. Under more severe conditions, phthalic acid anhydride formed is seen to react further, leading to the formation of phthalimide. The discrepancy between the products obtained with cyanamide and sodium cyanate leads to the conclusion that, unlike earlier claims, imide formation is not due to the reaction of the anhydride with the urea formed but with sodium cyanate itself. However, only the phthalic anhydride five-membered ring system is sufficiently reactive towards the CNO- nucleophile to form the imide; the six-membered 1,8-naphthalic anhydride system does not react in this way.

Chemical carcinogens in non-enzymatic cytosine deamination: 3-isocyanatoacrylonitrile

Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed of the 3-isocyanatoacrylonitriles (Z,s-cis)-10, (E,s-cis)-11, (Z,s-trans)-12, and (E,s-trans)-13. The electronic structures of 7 and 10-13 have been analyzed and a rationale is provided for the thermodynamic preference for (Z,s-cis)-10. It is shown that s-cis/s-trans-interconversion occurs via C-N rotation-inversion paths with barriers below 3 kcal mol(-1). The proton affinities of 3-isocyanatoacrylonitrile 10 and water are nearly identical and, thus, 3-isocyanatoacrylonitriles can and should be formed in aqueous media from 7 along with 3-aminoacrylonitriles 9. The results highlight the relevance of the chemistry of 3-isocyanatoacrylonitriles for the understanding of the chemical toxicology of nitrosation of the nucleobase cytosine.

Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation

Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazole and Nitrosative Guanine Deamination. A Theoretical Study of Geometries, Electronic Structures, and N-Protonation

The 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole 1 (R = H), its N1-derivatives 2 (R = Me) and 3 (R = MOM) and their cyano-N (4, 6, 8) and imino-N protonated (5, 7, 9) derivatives were studied with RHF, B3LYP, and MP2 theory. Solvation effects were estimated with the isodensity polarized continuum model (IPCM) at the MP2 level using the dielectric constant of water. Carbodiimide 10, cyanamide 12, N-cyanomethyleneimine 13, and its protonated derivatives 14 and 15 were considered for comparison as well. Adequate theoretical treatment requires the inclusion of dispersion because of the presence of intramolecular van der Waals, charge-dipole, and dipole-dipole (including H-bonding) interactions. All conformers were considered for the MOM-substituted systems, and direct consequences on the preferred site of protonation were found. The vicinal push (oxomethylene)-pull (cyanoimino) pattern of the 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazoles results in the electronic structure of aromatic imidazoles with 4-acylium and 5-cyanoamido groups. The gas-phase proton affinities of 1-3 are over 30 kcal/mol higher than that for N-cyanomethyleneimine 13, and this result provides compelling evidence in support of the zwitterionic character of 1-3. Protonation enhances the push-pull interaction; the OC charge is increased from about one-half in 1-3 to about two-thirds in the protonated systems. In the gas phase, cyano-N protonation is generally preferred but imino-N protonation can compete if the R-group contains a suitable heteroatom (hydrogen-bond acceptor, Lewis base). In polar solution, however, imino-N protonation is generally preferred. Solvation has a marked consequence on the propensity for protonation. Whereas protonation is fast and exergonic in the gas phase, it is endergonic in the polar condensed phase. It is an immediate consequence of this result that the direct observation of the cations 8 and 9 should be possible in the gas phase only.