The influence of intramolecular hydrogen bonding on the structure and E ↔ Z photoisomerization of urocanic acid derivatives

The molecular structures and E ? Z photoisomerization reactions of methyl urocanate and several urocanamides were investigated. All of the Z isomers possess intramolecular hydrogen bonds. The intramolecular hydrogen bonds may influence the efficiency of photoisomerization but do not totally inhibit its occurrence. The relative energies of the electronic absorption of the E and Z isomers depends on the mode of hydrogen bonding and are accurately predicted in the case of methyl urocanate using INDO/S-CI calculations. The solvent dependence of the absorption spectra of methyl urocanate can be related to the effects of inter- and intramolecular hydrogen bonding.     

Measuring salty samples without adducts with MALDI MS

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been used for the discovery of hundreds of novel cell to cell signaling peptides. Beyond its advantages of sensitivity and minimal sample preparation requirements, MALDI MS is attractive for biological analyses as high quality mass spectra may be obtained directly from specific locations within prepared tissue sections. However, due to the large quantity of salts present in physiological tissues, these mass spectra often contain many adducts of cationic salts such as sodium and potassium, in addition to the molecular ion [M + H]⁺. To reduce the presence of cation adducts in MALDI mass spectra obtained directly from tissues, we present a methodology that uses a slow condensation procedure to enable the formation of distinct regions of matrix/analyte crystals and cation (salt) crystals. Secondary ion mass spectrometric imaging suggests that the salts and MALDI matrix undergo a mutually exclusive crystallization process that results in the separation of the salts and matrix in the sample.     

Substituent,solvent and steric effects on the electrochemical reduction of aziridinium salts

The polarographic behavior of a series of N,N-dimethyl-2-arylaziridinium fluorosulfonates was investigated as another example of ring-opening reactions of this important class of compounds. Half-wave potentials showed that in water reduction was facilitated by electron-donating groups. This unusual result was explained in terms of electron transfer to an aminocarbonium ion-like species. In methylene chloride, however, two one-electron waves were observed, with the first showing a normal substituent effect (? = 0.17 ± 0.03 V). This result indicated direct electron transfer to the aziridinium ion itself to form a radical species which was detected by cyclic voltammetry. Reasons for the change in mechanism are presented, and E_1/2 values for selected aziridinium salts illustrate the importance of steric effects on the reduction process.     

Ruthenium(III) triazacyclononane dithiocarbamate,pyridinecarboxylate, or aminocarboxylate complexes as scavengers of nitric oxide

The preparation of a series of [Ru(III)(tacn)(eta(2)-dtc)(eta(1)-dtc)][PF(6)] (tacn = 1,4,7-triazacyclononane; dtc = dimethyldithiocarbamate, diethyldithiocarbamate, pyrrolidinedithiocarbamate, l-prolinedithiocarbamate, l-prolinemethyl ester dithiocarbamate, l-N-methylisoleucinedithiocarbamate) complexes, 5-11, is described. Complex 5 reacts with NO to form the ruthenium nitrosyl complex 12. A series of [Ru(III)(tacn)(pyc)Cl][PF(6)] (pyc = 2-pyridinecarboxylic acid, 2,4- and 2,6-pyridinecarboxylic acid) complexes, 14-16, were prepared along with [Ru(III)(tacn)(mida)][PF(6)] (mida = N-methyliminodiacetic acid), 13, and [Ru(III)(Hnota)Cl], 17, (Hnota = 1-acetic acid-4,7-bismethylcarboxylate-1,4,7-triazacyclononane). Complexes 5-17 were evaluated for use as NO scavengers in an in vitro assay using RAW264 murine macrophage cells. [Ru(III)(tacn)(eta(2)-dtc)(eta(1)-dtc)][PF(6)] complexes 5-11 are very efficient NO scavengers in this assay.     

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.     

Designs,Codes and Crypts—A Puzzle Altogether

In this paper we present an algebraic specificationof a puzzle commercially available on the toy market which isclosely related to the area of designs, codes and cryptography.The purpose of this article is to show the different ways ofapproaching the problem of solving this puzzle. An algebraicapproach for finding a solution is given. The seemingly unknowncombinatorial type of this puzzle and the lack of a general theoreticalbackground have stimulated the set-up of this paper to be presentedin this volume.     

Global search for minimum energy (H2O)n clusters, n = 3-5

The Gaussian-3 (G3) model chemistry method has been used to calculate the relative deltaG(o) values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3-5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20,736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.     

Tunable DNA photocleavage by an acridine-imidazole conjugate

We report the synthesis and characterization of photonucleases N,N'-bis[2-[bis(1H-imidazol-4-ylmethyl)amino]ethyl]-3,6-acridinediamine (7) and N-[2-[bis(1H-imidazol-4-ylmethyl)amino]ethyl]-3,6-acridinediamine (10), consisting of a central 3,6-acridinediamine chromophore attached to 4 and 2 metal-coordinating imidazole rings, respectively. In DNA reactions employing 16 metal salts, photocleavage of pUC19 plasmid is markedly enhanced when compound 7 is irradiated in the presence of either Hg(II), Fe(III), Cd(II), Zn(II), V(V), or Pb(II) (low-intensity visible light, pH 7.0, 22 degrees C, 8-50 microM 7). We also show that DNA photocleavage by 7 can be modulated by modifying buffer type and pH. Evidence of metal complex formation is provided by EDTA experiments and by NMR and electrospray ionization mass spectral data. Sodium azide, sodium benzoate, superoxide dismutase, and catalase indicate the involvement of type I and II photochemical processes in the metal-assisted DNA photocleavage reactions. Thermal melting studies show that compound 7 increases the Tm of calf thymus DNA by 10 +/- 1 degrees C at pH 7.0 and that the Tm is further increased upon the addition of either Hg(II), Cd(II), Zn(II), or Pb(II). In the case of Fe(III) and V(V), a colorimetric assay demonstrates that compound 7 sensitizes one electron photoreduction of these metals to Fe(II) and V(IV), likely accelerating the production of type I reactive oxygen species. Our data collectively indicate that buffer, pH, Hg(II), Fe(III), Cd(II), Zn(II), V(V), Pb(II), and light can be used to "tune" DNA cleavage by compound 7 under physiologically relevant conditions. The 3,6-acridinediamine acridine orange has demonstrated great promise for use as a photosensitizer in photodynamic therapy. In view of the distribution of iron in living cells, compound 7 and other metal-binding acridine-based photonucleases should be expected to demonstrate excellent photodynamic action in vivo.     

Ramanujan complexes of type<Emphasis Type="Italic">Ã</Emphasis><Subscript><Emphasis Type="Italic">d</Emphasis></Subscript>

We define and construct Ramanujan complexes. These are simplicial complexes which are higher dimensional analogues of Ramanujan graphs (constructed in [LPS]). They are obtained as quotients of the buildings of typeà _d?1 associated with PGL _d (F) whereF is a local field of positive characteristic.     

A New Class of Designs Which Protect against Quantum Jumps

We present the theory and construction of a new class of designs, which we call SEEDs (spontaneous emission error designs), arising in the study of decay processes of certain quantum systems used in the newly emerging field of quantum computing. We show that there is a simple and surprising connection between subspaces of the system Hilbert space, stable against these quantum jumps and the incidence matrices of SEEDs.