Browsing by Author "Machinek, R."

The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG[(BrU)-U-5]T-3' provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A T) T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.

Fast and efficient intramolecular charge transfer (ICT) and dual fluorescence is observed with the planarized aminobenzonitrile 1-tert-butyl-6-cyano-1,2,3,4-tetrahydroquinoline (NTC6) in a series of solvents from n-hexane to acetonitrile and methanol. Such a reaction does not take place for the related molecules with 1-isopropyl (NIC6) and 1-methyl (NMC6) groups, nor with the 1-alkyl-5-cyanoindolines with methyl (NMC5), isopropyl (NIC5), or tert-butyl (NTC5) substituents. For these molecules, a single fluorescence band from a locally excited (LE) state is found. The charge transfer reaction of NTC6 is favored by its relatively small energy gap AE(S-1,S-2), in accordance with the PICT model for ICT in aminobenzonitriles. For the ICT state of NTC6, a dipole moment of around 19 D is obtained from solvatochromic measurements, similar mu(a)(ICT) = 17 D of 4-(dimethylamino)benzonitrile (DMABN). For NMC5, NIC5, NTC5, NMC6, and NIC6, a dipole moment of around 10 D is determined by solvatochromic analysis, the same as that of the LE state of DMABN. For NTC6 in diethyl ether at -70 degreesC, the forward ICT rate constant (1.3 x 10(11) s(-1)) is much smaller than that of the back reaction (5.9 x 10(9) s(-1)), showing that the equilibrium is on the ICT side. The results presented here make clear that ICT can very well take place with a planarized molecule such as NTC6, when DeltaE(S-1,S-2) is sufficiently small, indicating that a perpendicular twist of the amino group relative to the rest of the molecule is not necessary for reaching an ICT state with a large dipole moment. The six-membered

Measurements of one-bond carbon-carbon coupling constants, (1)J(C, C), were performed for two series of compounds, alkyl-substituted cyclopropenes and cyclopropanes. The experimental data were complemented by a set of DFT-calculated J couplings for the parent cyclopropene (1), its methyl and silyl derivatives and, additionally, for 1-methylcyclobutene (3), 1-methylcyclopentene (4) and 1-methylcyclohexene (5) and good agreement was observed between the experimental and the calculated data; all the trends are perfectly maintained, including a dramatic decrease in the couplings across endocyclic single bonds in cyclopropene and its derivatives, and a significant decrease in the corresponding couplings in cyclobutene. Using the data obtained, the s characters of the carbon hybrid orbitals involved in the formation of the cyclopropene were calculated. The results clearly show that the ring closure and the related strain exerted upon the cyclopropene molecule only slightly disturb the electron structure of the double bond. The s character of the corresponding carbon orbital is 0.314 in cyclopropene vs the theoretical value of 0.333 in ethene. This is at variance with the endo- and exocyclic single bonds, where the s characters of the orbitals forming the endocyclic single bonds are much smaller than those of the bonds in the open-chain compounds, i.e. 0.229 (C-1 and/or C-2) and 0.166 (C-3). The s values calculated for the exocyclic CH bonds are 0.334 for C-3 and 0.456 for C-1 and/or C-2. Copyright (C) 2002 John Wiley Sons, Ltd.

The five 2,3,5,6-tetrafluoro-4-aminobenzonitriles XABN4F with a dimethyl-amino (DMABN4F), diethyl-amino (DEABN4F), azetidinyl (AZABN4F), methyl-amino (MABN4F) or amino (ABN4F) group undergo ultrafast intramolecular charge transfer (ICT) at room temperature, in the polar solvent acetonitrile (MeCN) as well as in the nonpolar n-hexane. ICT also takes place with the corresponding non-fluorinated aminobenzonitriles DMABN, DEABN and AZABN in MeCN, whereas for these molecules in n-hexane only minor (DMABN, DEABN) or no (AZABN) ICT fluorescence is detected. For the secondary (MABN) and primary (ABN) amines, on ICT reaction does not occur, which makes ABN4F the first electron donor/acceptor molecule with an NH2 group for which ICT is observed, The ICT state of the XABN4Fs has a dipole moment of around 14 D, clearly smaller than that of DMABN (77 D). This difference is attributed to the electron withdrawing from the CN group to the phenyl ring, exerted by the four F-substituents. The reaction from the initially prepared locally excited (LE) to the ICT state in n-hexane proceeds in the sub-picosecond time range: 0.35 ps (DMABN4F), 0.29 ps (DEABN4F) and 0.13 ps (AZABN4F), as determined from femtosecond transient absorption measurements. In the highly polar solvent MeCN, an ICT reaction time of around 90 Is is observed for all five XABN4Fs, irrespective nature of their amino group. This shows that with these molecules in MeCN the ICT reaction rate is limited by the solvent dielectric relaxation time of MeCN, for which a value of around 90 Is has been reported. It is therefore concluded that, during this ultrashort ICT reaction, a large-amplitude motion such as a full 90 degrees twist of the amino group is unlikely to occur in the XABN4Fs. The ICT state of the XABN4Fs is strongly quenched via internal conversion (IC), with a lifetime tau(0)' (ICT) down to 3 ps, possibly by a reaction passing through a conical intersection made accessible due to a deformation of the phenyl group by out-of-plane motions induced by vibronic coupling between low-lying pi sigma and pi pi states in the XABN4Fs.