Biomedical subjects
Publications and source records attributed to Matthew S Platz.
A photosensitive precursor (1) to phenylsulfanylcarbene 2 has been synthesized. Laser flash photolysis (308 nm) of 1 and chemical trapping studies of 2 are reported. [structure: see text]
Ar matrix photolysis of 1- and 2-naphthyl azides 3 and 4 at 313 nm initially affords the singlet naphthyl nitrenes, (1)()1 and (1)()2. Relaxation to the corresponding lower energy, persistent triplet nitrenes (3)()1 and (3)()2 competes with cyclization to the azirines 15 and 18, which can also be formed photochemically from the triplet nitrenes. On prolonged irradiation, the azirines can be converted to the seven-membered cyclic ketenimines 10 and 13, respectively, as described earlier by Dunkin and Thomson. However, instead of the o-quinoid ketenimines 16 and 19, which are the expected primary ring-opening products of azirines 15 and 18, respectively, we observed their novel bond-shift isomers 17 and 20, which may be formally regarded as cyclic nitrile ylides. The existence of such ylidic heterocumulenes has been predicted previously, but this work provides the first experimental observation of such species. The factors which are responsible for the special stability of the ylidic species 17 and 20 are discussed.
Carbomethoxyfluorocarbene was studied in solution by laser flash photolysis with UV-vis and infrared detection. In contrast to expectations, carbomethoxyfluorocarbene is more reactive than carbomethoxychlorocarbene. [structure: see text]
Phenyl azide, 2,6-diethylphenyl azide, 2,6-diisopropylphenyl azide, and 2,4,6-tri-tert-butylphenyl azide were studied by laser flash photolysis (LFP) methods. LFP (266 nm) of the azides in glassy 3-methylpentane at 77 K produces the transient UV-vis absorption spectra of the corresponding singlet nitrenes. At 77 K, the singlet nitrenes relax to the corresponding triplet nitrenes. The triplet nitrenes are persistent at 77 K and their spectra were recorded. The rate constants of singlet to triplet intersystem crossing were determined at this temperature. LFP of 2,4,6-tri-tert-butyl phenyl azide in pentane at ambient temperature again produces a singlet nitrene, which is too short-lived to detect by nanosecond spectroscopy under these conditions. Unlike the other azides, the first detectable intermediate produced upon LFP of 2,4,6-tri-tert-butyl phenyl azide at ambient temperature is the benzazirine (285 nm) which has a lifetime of 62 ns controlled by ring opening to a didehydroazepine. The results are interpreted with the aid of Density Functional Theoretical and Molecular Orbital Calculations.
[reaction: see text] Laser flash photolysis (LFP, 266 nm) of carboethoxyazide produces a mixture of the ethoxycarbonyl radical (lambda(max) = 333 nm, tau = 0.4 micros, CF(2)ClCFCl(2), ambient temperature) and triplet carboethoxynitrene (lambda(max) = 400 nm, tau = 1.5 micros, CF(2)ClCFCl(2), ambient temperature). The carbon-centered radical is selectively scavenged by oxygen allowing sole observation of the triplet nitrene. We deduce that the singlet nitrene has a lifetime between 2 and 10 ns in CF(2)ClCFCl(2) at ambient temperature.
Arylazide mediated photocrosslinking has been widely used to obtain structural constraints in biological systems, even though the reactive species generated upon photolysis in aqueous solution have not been well characterized. We establish a mechanistic framework for formation of adducts between photoactivated 3-hydroxyphenyl azide and RNA. Tethered to an internal site in an RNA duplex via a 2'-amido linkage, photolysis of the aryl azide yields a cross-strand cross-link. Analysis of the ability of reagents with diagnostic reactivities to intercept formation of this cross-strand cross-link supports the assignment that the photoactivated intermediate is the ketenimine or a ketenimine-derived ring expansion product. Neither the initially produced singlet nitrene nor the subsequently formed triplet nitrene contribute to cross-link formation. Argon matrix and time-resolved solution experiments show that photolysis of free 3-hydroxyphenyl azide releases (in <or=20 ns) either a ketenimine or azepinone intermediate that reacts with nucleophiles. Adenosine, uridine, and guanosine monophosphate nucleotides have approximately equivalent abilities to quench the cross-strand cross-link, indicating that the photoactivated intermediate reacts broadly with functional groups in RNA. The reactive intermediate forms an adduct with adenosine monophosphate when tethered to both an RNA duplex or unstructured single strand; thus, cross-link formation is independent of the local RNA environment. The lifetime of the reactive intermediate generated upon photolysis of free 3-hydroxyphenyl azide in 50 mM Hepes diamine buffer is found to be 60-160 micros or significantly shorter than large scale RNA folding events. RNA-tethered 3-hydroxyphenyl azide cross-linking in aqueous buffer can thus be used with confidence to map structural neighbors, including most dynamic interactions, in RNA.
The photochemistry of ortho-biphenyl azide (1a) has been studied by laser flash photolysis (LFP), with UV-vis and IR detection of the transient intermediates formed. LFP (266 nm) of 1a in glassy 3-methylpentane at 77 K releases singlet ortho-biphenylnitrene (1b) (lambda(max) = 410 nm, tau = 59 +/- 6 ns), which under these conditions decays cleanly to the lower energy triplet state. In fluid solution at 298 K, 1b rapidly (tau < 10 ns) partitions between formation of isocarbazole (4) (lambda(max) = 430 nm, tau = 70 ns) and benzazirine (1e) (lambda(max) = 305 nm, tau = 12 ns). Isocarbazole 4 undergoes a 1,5-hydrogen shift, with k(H)/k(D) = 3.4 at 298 K to form carbazole 9 and smaller amounts of two other isocarbazoles (7 and 8). Benzazirine 1e ring-opens reversibly to azacycloheptatetraene (1f), which serves as a reservoir for singlet nitrene 1b. Azacycloheptatetraene 1f ultimately forms carbazole 9 on the millisecond time scale by the pathway 1f --> 1e --> 1b --> 4 --> 9. The energies of the transient intermediates and of the transition structures connecting them were successfully predicted by CASPT2/6-31G calculations. The electronic and vibrational spectra of the intermediates, computed by density functional theory, support the assignment of the transient spectra, observed in the formation of 9 from 1a.
The structures of halogen atom-benzene complexes were investigated by modern DFT and ab initio computational methods. The spectroscopic properties of the complexes are also predicted and are in good agreement with experiment where such data have been reported. The fluorine atom-benzene complex is predicted to be a sigma complex due to the strength of a C-F bond. The chlorine atom-benzene complex is predicted to have an eta(1) pi complex structure, which is only slightly more favorable (1.1 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than a sigma complex but is significantly more stable (4.4 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than the eta(6) pi complex. The bromine and iodine benzene complexes are also predicted to prefer an eta(1) pi complex structure.
[reaction: see text] The time-resolved infrared (TRIR) spectra of chlorophenylcarbene (CPC) and fluorophenylcarbene (FPC) were recorded in heptane at ambient temperature. The C[bond]C and C[bond]F vibrational frequencies involving the carbene carbon were obtained in heptane, benzene, and acetonitrile and in heptane containing 0.1M tetrahydrofuran or benzene. It is concluded that carbene-solvent interactions of CPC and FPC are quite weak.
As a model for riboflavin, lumiflavin was investigated using density functional theory methods (B3LYP/6-31G* and B3LYP/6-31+G**) with regard to the proposed cascade of intermediates formed after excitation to the triplet state, followed by electron-transfer, proton-transfer, and radical[bond]radical coupling reactions. The excited triplet state of the flavin is predicted to be 42 kcal/mol higher in energy than the singlet ground state, and the pi radical anion lies 45.1 kcal/mol lower in energy than the ground-state flavin and a free electron in the gas phase. The former value compares to a solution-phase triplet energy of 49.8 kcal/mol of riboflavin. For the radical anion, the thermodynamically favored position to accept a proton on the flavin ring system is at N(5). A natural population analysis also provided spin density information for the radicals and insight into the origin of the relative stabilities of the six different calculated hydroflavin radicals. The resulting 5H-LF* radical can then undergo radical[bond]radical coupling reactions, with the most thermodynamically stable adduct being formed at C(4'). Vibrational spectra were also calculated for the transient species. Experimental time-resolved infrared spectroscopic data obtained using riboflavin tetraacetate are in excellent agreement with the calculated spectra for the triplet flavin, the radical anion, and the most stable hydroflavin radical.
The absorption and fluorescence spectra of 3-aminobenzo-1,2,4-triazine di-N-oxide (tirapazamine) have been recorded and exhibit a dependence on solvent that correlates with the Dimroth ET30 parameter. Time-dependent density functional theory calculations reveal that the transition of tirapazamine in the visible region is pi-->pi* in nature. The fluorescence lifetime is 98+/-2 ps in water. The fluorescence quantum yield is approximately 0.002 in water. The fluorescence of tirapazamine is efficiently quenched by electron donors via an electron-transfer process. Linear Stern-Volmer fluorescence quenching plots are observed with sodium azide, potassium thiocyanate, guanosine monophosphate and tryptophan (Trp) methyl ester hydrochloride. Guanosine monophosphate, tyrosine (Tyr) methyl ester hydrochloride and Trp methyl ester hydrochloride appear to quench the fluorescence at a rate greater than diffusion control implying that these substrates complex with tirapazamine in its ground state. This complexation was detected by absorption spectroscopy.
Methylene blue (MB), riboflavin (RB) and psoralen sensitizers (4' aminomethyl-4,5',8-trimethylpsoralen [AMT] and derivatives) are under study as sensitizers of viral inactivation of blood products such as plasma proteins, platelets and red cells, all of which lack genomic nucleic acid. To predict where these sensitizers accumulate in viruses and in cells, their relative affinities for calf thymus DNA, neutral and negatively charged phospholipids and albumin were determined by dialysis. MB has a strong affinity for nucleic acid and negatively charged phospholipid, but little affinity for albumin or neutral phospholipid. RB has modest affinity for nucleic acid and little affinity for albumin or either phospholipid. AMT has substantial affinity for nucleic acid, neutral and negatively charged phospholipids and albumin. Neither AMT nor RB binds to poly G, although MB has some affinity for this polymer. Evidence of association of RB with guanosine monophosphate, adenosine monophosphate and tryptophan methylester hydrochloride in PBS buffer in the presence and absence of formamide was obtained from nonlinear Stern-Volmer plots and shifts in the ground state absorption spectrum of RB.
We are developing a technology based on the combined application of riboflavin (RB) and light for inactivating pathogens in blood products while retaining the biological functions of the treated cells and proteins. Virus and bacteria reduction measured by tissue culture infectivity or colony formation with UV light alone and in combination with RB yield equivalent results. The effects of RB as a sensitizing agent on DNA in white cells, bacteria and viruses in combination with UV light exposure have been evaluated. UV-mediated DNA degradation in Jurkat T cells and leukocytes in plasma as measured by the FlowTACS assay was significantly increased in the presence of RB. Agarose gel electrophoretic analysis of DNA in Escherichia coli and leukocytes in plasma demonstrated enhanced DNA degradation in the presence of RB. UV light in combination with RB prevented the reactivation of lambda phage compared with samples irradiated in the absence of RB. UV-mediated oxidative damage in calf thymus DNA was also enhanced in the presence of RB. These observations clearly demonstrate that the presence of RB and UV light selectively enhances damage to the guanine bases in DNA. These data also suggest that the type and extent of damage to DNA for virus in the presence of RB and light make it less likely to be repaired by normal repair pathways available in host cells.