'KINFITSIM'--a software to fit kinetic data to a user selected mechanism.

A new software package, 'KINFITSIM', for fitting and simulating kinetic data is presented. The main goals of the KINFITSIM package are to obtain the best-fit parameters-rate constants, amplitudes and others-to a user specified chemical mechanism, plots of the calculated and experimental absorbance versus time, and a report to the user with the results. The KINFITSIM package can be used in either chemical research or for educational purposes.

A laser flash photolysis and quantum chemical study of the fluorinated derivatives of singlet phenylnitrene.

Laser flash photolysis (LFP, Nd:YAG laser, 35 ps, 266 nm, 10 mJ or KrF excimer laser, 10 ns, 249 nm, 50 mJ) of 2-fluoro, 4-fluoro, 3,5-difluoro, 2,6-difluoro, and 2,3,4,5,6-pentafluorophenyl azides produces the corresponding singlet nitrenes. The singlet nitrenes were detected by transient absorption spectroscopy, and their spectra are characterized by sharp absorption bands with maxima in the range of 300-365 nm. The kinetics of their decay were analyzed as a function of temperature to yield observed decay rate constants, k(OBS). The observed rate constant in inert solvents is the sum of k(R) + k(ISC) where k(R) is the absolute rate constant of rearrangement of singlet nitrene to an azirine and k(ISC) is the absolute rate constant of nitrene intersystem crossing (ISC). Values of k(R) and k(ISC) were deduced after assuming that k(ISC) is independent of temperature. Barriers to cyclization of 4-fluoro-, 3,5-difluoro-, 2-fluoro-, 2,6-difluoro-, and 2,3,4,5,6-pentafluorophenylnitrene in inert solvents are 5.3 +/- 0.3, 5.5 +/- 0.3, 6.7 +/- 0.3, 8.0 +/- 1.5, and 8.8 +/- 0.4 kcal/mol, respectively. The barrier to cyclization of parent singlet phenylnitrene is 5.6 +/- 0.3 kcal/mol. All of these values are in good quantitative agreement with CASPT2 calculations of the relative barrier heights for the conversion of fluoro-substituted singlet aryl nitrenes to benzazirines (Karney, W. L. and Borden, W. T. J. Am. Chem. Soc. 1997, 119, 3347). A single ortho-fluorine substituent exerts a small but significant bystander effect on remote cyclization that is not steric in origin. The influence of two ortho-fluorine substituents on the cyclization is pronounced. In the case of the singlet 2-fluorophenylnitrene system, evidence is presented that the benzazirine is an intermediate and that the corresponding singlet nitrene and benzazirine interconvert. Ab initio calculations at different levels of theory on a series of benzazirines, their isomeric ketenimines, and the transition states converting the benzazirines to ketenimines were performed. The computational results are in good qualitative and quantitative agreement with the experimental findings.

Carbomethoxychlorocarbene: spectroscopy, theory, chemistry and kinetics.

Photolysis (254 nm) of methyl 8-chloro-3a,7a-methanoindan-8-carboxylate (5) in argon at 14 K produces carbomethoxychlorocarbene (6) as a persistent species. The IR and UV-vis spectra of the carbene were recorded and analyzed with the aid of density functional calculations (B3-LYP/6-31G). The IR spectrum of 6 is consistent with the carbene having a nonplanar singlet ground state, in agreement with the G3(MP2)//B3-LYP calculations of Scott and Radom (accompanying paper). Irradiation (300 nm) of 5 in solution produces indane in 97% yield. In cyclohexane, carbene 6 is trapped by insertion into a CH bond, whereas in 2,3-dimethylbutene it adds to the double bond to form a cyclopropane. Laser flash photolysis of 5 (308 nm, 17 ns, XeCl excimer) produces carbene 6 which reacts with pyridine to form an ylide (lambda(max) = 440 nm). It was possible to resolve the growth of the ylide in Freon-113 (CF(2)ClCFCl(2)) to measure the lifetime (tau = 114 ns, ambient temperature) of the carbene and the absolute rate constant of its reaction with pyridine (k(pyr) = 2 x 10(9) M(-)(1) s(-)(1)). A plot of log(1/tau) versus 1/T in CF(2)ClCFCl(2) is linear with Arrhenius parameters E(a) = 10.9 +/- 0.8 kJ/mol and A = 10(9.1)(+/-)(0.2) s(-)(1). In perfluorohexane, a less reactive solvent than Freon-113, E(a) = 23.4 +/- 1.7 kJ/mol, A = 10(10.6)(+/-)(0.) s(-)(1), and tau = 354 ns at 293 K. It is argued that the activation barrier to carbene disappearance in perfluorohexane represents the lower limit to the barrier to Wolff rearrangement of the carbene.

Singlet-triplet splittings and barriers to Wolff rearrangement for carbonyl carbenes.

High-level ab initio calculations at the G3(MP2)//B3-LYP level have been used to study carbomethoxychlorocarbene and related halogenocarbenes and carbonyl carbenes. Initial calculations at the more accurate W1' level on the subset CH(2), HCCl, HCF, CCl(2), and CF(2) provide support for the reliability of G3(MP2)//B3-LYP for this type of problem. The W1' calculations also suggest that the experimental S-T splitting is slightly underestimated for HCCl and CF(2) and substantially underestimated for CCl(2), in keeping with other recent high-level studies. Whereas the parent carbonyl carbenes, namely formylcarbene, carbohydroxycarbene, and carbomethoxycarbene, are all predicted to have triplet ground states, their chloro and fluoro derivatives are predicted to have singlet ground states. In particular, carbomethoxychlorocarbene is predicted to have a singlet ground state, with the singlet-triplet splitting estimated as -16.0 kJ mol(-)(1). The barriers to Wolff rearrangement of the singlet carbonyl carbenes generally (but not always) correlate with the exothermicity accompanying the production of ketenes. In the case of the parent carbonyl carbenes, for which the rearrangement reaction is most exothermic, the barriers lie between about 10 and 30 kJ mol(-)(1), whereas for the less exothermic rearrangements of the chloro- and fluoro-substituted carbonyl carbenes, the Wolff rearrangement barriers increase significantly to between 58 and 75 kJ mol(-)(1). The calculated barrier for carbomethoxychlorocarbene is 58.2 kJ mol(-)(1).

The interplay of theory and experiment in the study of phenylnitrene.

The intra- and intermolecular chemistry of phenylnitrene (PhN), its singlet-triplet energy separation, and its electronic spectra are interpreted with the aid of ab initio molecular orbital theory. The key to understanding singlet PhN is the recognition that this species has an open-shell electronic structure, in contrast to the related species, phenylcarbene, which has a closed-shell electronic structure. The thermodynamics of nitrenes, benzazirines, dehydroazepines, aminyl radicals, and their hydrocarbon analogues are also discussed.

Photochemical and photophysical studies of 3-amino-6-iodoacridine and the inactivation of lambda phage.

The photochemistry and photophysics of 3-amino-6-iodoacridine (Acr-I) was studied. Photolysis (350 nm) of Acr-I (free base) generates products consistent with a free radical intermediate in methanol, benzene and carbon tetrachloride. The Acr-I hydrochloride is shown to bind to calf thymus DNA and to the self-complementary dinucleotide cytidylyl-(3'-5')-guanosine (CpG) miniduplex in a manner similar to that of proflavine (Acr-NH2), a known DNA intercalator. The Acr-I is shown to more efficiently nick supercoiled plasmid DNA pBR322 upon 350 nm or 420 nm photolysis than Acr-NH2. The efficiency of Acr-I-sensitized DNA nicking is not oxygen dependent. Photolysis of the Acr-I/(CpG)2 complex leads to cleavage of the dinucleotide and to cytidine base release by selective damage to a specific ribose moiety. Dinucleotide cleavage occurs equally well in the presence or absence of oxygen, thereby eliminating a singlet oxygen- or peroxyl radical-mediated process. Photolysis of Acr-I in the presence of a mononucleotide (GMP) or a non-self-complementary dinucleotide (uridylyl-[3'-5']-cytidine-UpC) does not lead to fragmentation and base release. Similarly, photolysis of the Acr-NH2/(CpG)2 complex does not lead to fragmentation and base release. The data indicate that photolysis of an iodinated intercalator bound to CpG or plasmid DNA generates an intercalated aryl radical and that the reactive intermediate initiates a sequence of reactions that efficiently nick nucleic acids. The inactivation of lambda phage sensitized by Acr-I with UV (350 nm) light is oxygen independent but with visible (420 nm) light is strongly oxygen dependent. The Acr-I fluoresces more intensely when excited at 446 than at 376 nm. Thus, UV photolysis may lead to C-I bond homolysis and free radical formation, a process that is not energetically feasible with visible light. The results demonstrate the difficulty of extrapolating model studies involving simple molecules and DNA to understanding the mechanism of viral inactivation with a particular sensitizer.

Exploratory photochemistry of 5-azido-8-alkoxy-substituted psoralens free and bound to DNA.

5-Azido-8-alkoxy psoralens were synthesized. Laser flash photolysis (LFP: XeF, 351 nm, 55 mJ, 17 ns) of the azides in acetonitrile or benzene solution produces the triplet nitrene and a small amount of ketenimine. Laser flash photolysis of the azides in methanol or aqueous solution cleanly produces the triplet nitrene. In aqueous solution containing highly polymerized calf thymus DNA, LFP produces a mixture of triplet nitrene and ketenimine corresponding to photolysis of free and bound psoralen, respectively. The two transients decay slowly but at different rates. Assignment of the transient spectra were secured by matrix EPR and UV-visible spectroscopy. The triplet nitrene lifetime is the same in buffer and in the presence and absence of calf thymus DNA. The results explain why psoralen azides are unable to efficiently nick plasmid DNA pBR322 upon UV activation.

Selective inactivation of viruses in the presence of human platelets: UV sensitization with psoralen derivatives.

Inactivation of viruses in blood products requires that the method employed display selectivity in its action for viral elements while not affecting the biological entity of interest. Several methods have been developed for the treatment of human plasma or products derived from human plasma. An effective technique for the treatment of the cellular components of blood has been lacking, in part due to the inability to develop agents capable of selectively targeting viral agents in the milieu of cellular material. In this paper, we examine the behavior of a group of viral sensitizers designed to be added to cellular samples and be activated upon exposure to UVA light. Upon activation, these agents are capable of disrupting nucleic acids of the virus in a manner that renders them inactive for proliferation. The selectivity observed in this inactivation is determined by the chemical structure of the sensitizer, which can be varied to increase viral killing capacity while diminishing collateral damage to cellular and protein constituents.

Synthesis and binding of new polyfluorinated aryl azides to alpha-chymotrypsin. New reagents for photoaffinity labeling.

The preparation of several new, water-soluble, polyfluorinated aryl azide reagents for use in photoaffinity labeling studies is described. The ability of some of these reagents and their nonfluorinated controls to noncovalently bind to alpha-chrymotrypsin is reported. It is found that polyfluorination does not interfere with ligand binding.

Dramatic improvements in viral inactivation with brominated psoralens, naphthalenes and anthracenes.

Amino or polyamino derivatives of naphthalene (N-H), anthracene (A-H) and 8-alkoxypsoralen (PSR-H) were prepared along with their monobrominated analogs (N-Br, A-Br and PSR-Br). The ammonium salts of these compounds are all water soluble and bind strongly to calf thymus DNA and to lambda phage, a double-helical DNA, protein-coated virus. Binding of the sensitizer to DNA occurs, presumably by a mixture of hydrophobic, intercalative and electrostatic interactions. Relative binding constants to calf thymus DNA and to lambda phage were measured by the ethidium bromide fluorescence quenching assay. In general the brominated analogs bind more tightly to calf thymus DNA and to the virus than to the nonhalogenated analogs. It is demonstrated that the brominated aromatics are much more effective at inactivating lambda phage upon photoactivation (lambda approximately 310 or 350 nm) than are their nonbrominated analogs. At identical sensitizer concentrations (by weight) and light flux N-Br, A-Br, and PSR-Br produce 5-6 more logs of viral inactivation than their nonbrominated counterparts (N-H, A-H and PSR-H, respectively). The bromine effect may originate from light-induced electron transfer and subsequent cleavage of the C-Br bond of the sensitizer radical anion bonds to form aryl radicals. Singlet oxygen cannot be responsible for the viral inactivation because the brominated sensitizers are equally effective in the presence and absence of oxygen. Dithiothreitol does not protect lambda phage from light-induced inactivation by the brominated sensitizer thereby demonstrating that the photogenerated reactive intermediates responsible for the effect are complexed to the virus and are not generated free in solution.

A laser flash photolysis study of di-, tri- and tetrafluorinated phenylnitrenes; implications for photoaffinity labeling.

Several fluorinated aryl azides (2,6 and 2,4-difluorophenyl azide, 2,4,6-triflurorophenyl azide, and methyl 4-azido-2,3,5,6-tetrafluorobenzoate) were studied by laser flash photolysis techniques. In each case, the azides from singlet nitrenes which can be intercepted with pyridine to form ylides. This allowed determination of the rate constant for ring expansion of the singlet nitrene to the dehydroazepine and measurement of the absolute rate constants for reaction of the singlet nitrenes with typical quenchers.

Exploratory photochemistry of fluorinated aryl azides. Implications for the design of photoaffinity labeling reagents.

A series of fluorinated aryl azides and fluorinated azidobenzoates were studied by laser flash photolysis techniques. Using the pyridine ylide probe method it was possible to determine whether a singlet nitrene or ring-expanded ketenimine ylide is the trappable intermediate that is generated at ambient temperature. It was determined that two fluorine substituents, ortho and ortho' substituted relative to the azide group, are required to retard ring expansion and allow bimolecular capture of the singlet nitrene. LFP of ortho, ortho' difluorinated aryl azides in methanol produces the ground triplet state of the nitrene. The results are consistent with chemical analysis of reaction mixtures. The implications of this data for the design of photoaffinity labeling reagents are discussed.

Inactivation of lambda phage with 658 nm light using a DNA binding porphyrin sensitizer.

Exposure of lambda phage to 658 nm light in the presence of 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21H,23H-porphine, tetra-p-tosylate leads to complete (greater than 7 logs) inactivation as measured by the plaque assay. The sensitizer without light and 658 nm photolysis of lambda phage in the absence of sensitizer do not lead to a measurable decrease in viral inactivity. Viral inactivation is not dependent upon the presence of oxygen.

The photochemistry of iodo, methyl and thiomethyl substituted aryl azides in toluene solution and frozen polycrystals.

The photolysis of para-methyl and para-thiomethylphenylazide at 77 K produces the corresponding triplet nitrenes which can be detected by electron paramagnetic resonance (EPR) spectroscopy. Photolysis of these azides in frozen toluene at 77 K leads to insertion of the nitrene into a benzylic C-H bond of the matrix in modest yields. Photolysis of iodinated aryl azides under these conditions does not produce triplet nitrenes that can be detected by EPR spectroscopy. In contrast to the para-methyl and para-thiomethyl substituted phenyl nitrenes, photo-induced coupling of iodo-substituted phenyl nitrenes to toluene proceeds in very poor yield.