Enabling Directional Sequence-Control via Step-Growth Polymerization of Heterofunctionalized Precision Macromonomers.

The synthesis of periodic copolymers with a regularly recurring sequence in one direction along the polymeric backbone is presented, applying a step-growth polymerization of heterofunctionalized precision macromonomers derived from solid phase synthesis (SPS) via photoinduced thiol-ene coupling (TEC). Heterofunctional macromonomers with monomer sequence-control of the AB type present a terminal alkene and a terminal thiol group carrying a photolabile protecting group to avoid uncontrolled polymerization by self-initiation. As protecting group, 3,4-methylenebisoxy-6-nitrobenzyl is attached onto the thiol via its bromide derivative directly on solid support. The protected heterofunctionalized macromonomer is polymerized in a two-step procedure, first cleaving the photolabile group and subsequent polymerization of the macromonomer via TEC, giving a high molecular weight polymer with M ¯ n of 23.8 kDa corresponding to a X ¯ n of 10 with one directional sequence-control due to their consistent head-to-tail linkage.

Thiophene Syntheses by Ring Forming Multicomponent Reactions.

Thiophenes occur as important building blocks in natural products, pharmaceutical active compounds, and in materials for electronic and opto-electronic devices. Therefore, there is a considerable demand for efficient synthetic strategies for producing these compounds. This review focuses on ring-forming multicomponent reactions for synthesizing thiophenes and their derivatives.

On the photophysics of 1,6-diphenyl-1,3,5-hexatriene isomers and rotamers.

Herein, the low-lying electronic states of various isomers and rotamers of 1,6-diphenyl-1,3,5-hexatriene (DPH) are studied by a combination of density functional theory and multireference configuration interaction. Starting from the all-trans nuclear arrangement, trans-cis isomerization pathways in the electronic ground state and in the first excited triplet state were determined. Further, spin-orbit coupling calculations were carried out at selected points where singlet-triplet energy gaps are small. The calculations reveal that the primarily excited, optically bright 1(1)B(u) state undergoes a curve crossing with the optically dark multiconfigurational 2(1)A(g) state upon geometry relaxation in the excited state. The strong vibronic coupling of the two singlets in the neighborhood of the conical intersection provides a conclusive explanation for the experimentally observed fast equilibration of the states and the appearance of delayed fluorescence. With regard to the trans-cis isomerization of the central CC bond, the perpendicular conformation is found to represent a maximum on the energy profile not only of the electronic ground state, but also of the low-lying excited states. The lack of a strong driving force along the torsional coordinate explains the low tendency of DPH for isomerization. Finally, the results of our spin-orbit coupling calculations suggest that the intramolecular formation of DPH molecules in the T(1)(1(3)B(u)) state proceeds from the 1(1)B(u) state and involves intermediately the T(2)(1(3)A(g)) state.

Fourier transform infrared spectroscopy of 2'-deoxycytidine aggregates in CDCl3 solutions.

We investigated the self-aggregation of 2'-deoxy-3',5'-bis(tert-butyldimethylsilyl)-cytidine dC(TBDMS)(2) in CDCl(3) solutions by Fourier transform infrared (FT-IR) spectroscopy and report the formation of larger aggregates than dimers in this solvent for the first time. The hydrogen bonding patterns in these complexes, which occur with increasing concentration may serve as a model for DNA super-structures such as triplexes. From the IR spectra, wavelength dependent absolute extinction coefficients of the monomer, dimer as well as a contribution from larger clusters which are supposedly trimers are deduced on the basis of a simple deconvolution method. Our results are supported by RI-B3LYP/TZVP calculations within the conductorlike screening model framework, to account for solvent effects in the ab initio calculations.

Thermodynamic aspects of solubility process of some sulfonamides.

The thermodynamic aspects of solubility process of sulfonamides with the general structures C(6)H(5)-SO(2)NH-C(6)H(4)-R (R=4-NO(2); 4-Cl) and 4-NH(2)-C(6)H(4)-SO(2)NH-C(6)H(4)-R (R=4-NO(2); 4-CN; 4-Cl; 4-OMe; 4-C(2)H(5)) in water, phosphate buffer with pH 7.4 and n-octanol (as phases modeling various drug delivery pathways) were studied using the isothermal saturated method.

The α,5-dicarboxy-2-nitrobenzyl caging group, a tool for biophysical applications with improved hydrophilicity: synthesis, photochemical properties and biological characterization.

Earlier we reported on the synthesis of α,4-dicarboxy-2-nitrobenyzl caged compounds (Schaper, K. et al. [2002] Eur. J. Org. Chem., 1037-1046). These compounds have the advantage of an increased hydrophilicity compared with the well-established α-carboxy-2-nitrobenzyl caged compounds; however, the release of the active compound becomes slower due to the introduction of the additional carboxy group. Based upon theoretical calculations we predicted that the release would become faster when the additional carboxy group is moved to the 5-position. Here we describe the synthesis and the photochemical and biological characterization of an α,5-dicarboxy-2-nitrobenyzl caged compound. The high hydrophilicity of the new caging group is maintained due to the fact that the additional carboxy moiety is preserved, while the release of the active species from the new derivative is even faster than for the reference, an α-CNB caged compound.

Diphenylhexatrienes as photoprotective agents for ultrasensitive fluorescence detection.

Given the particular importance of dye photostability for single-molecule investigations, fluorescence fluctuation spectroscopy, and laser-scanning microscopy, refined strategies were explored for enhancing the fluorescence signal by selectively quenching the first excited triplet state of the laser dye Rhodamine 123 (Rh123). The strategy is to quench the T(1) state by Dexter triplet energy transfer, while undesired quenching of the singlet state via Forster or Dexter singlet energy transfer and the generation of free radicals through electron transfer should be avoided. Diphenylhexatrienes (DPHs) were tested in ethanol for their beneficial effects as a novel class of photoprotective agents using fluorescence correlation spectroscopy. A library of DPHs with electron-donating (dimethlyamino) and withdrawing substituents (e.g., trifluormethyl) was synthesized to optimize the electronic properties. Quantum chemical calculations, optical spectroscopy, and cyclic voltammetry were used to determine the electronic properties. The computed T(1) emission energy of Rh123 and the T(1) excitation energies of all DPHs allow for exergonic triplet energy transfer to the quencher. The parent compound quenches the T(1) state of Rh123 nearly diffusion controlled (4.9 x 10(9) M(-1) s(-1)). All electron-deficient DPHs significantly increase (3x) the fluorescence rate of Rh123 by reducing the triplet state population and by avoiding the formation of other long-lived dark radical states. The quenching constants are reduced by more than a factor of 2, if substituents with increasing size or electronegativity are introduced. The beneficial effect of triplet quenching of substituted DPHs is governed by a delicate interplay of steric, electronic, and intermolecular Coulombic effects.

Biolabeling with 2,4-dichlorophenoxyacetic acid derivatives: the 2,4-D tag.

Many bioanalytic and diagnostic procedures rely on labels with which the molecule of interest can be tracked in or discriminated from accompanying like substances. Herein, we describe a new labeling and detection system based on derivatives of 2,4-dichlorophenoxyacetic acid (2,4-D) and anti-2,4-D antibodies. The 2,4-D system is highly sensitive with a K(D) of 7 x 10(-11) M for the hapten-antibody pair, can be used on a large variety of biomolecules such as proteins, peptides, carbohydrates, and nucleic acids, is not hampered by endogenous backgrounds because 2,4-D is a xenobiotic, and is robust because 2,4-D is a very stable compound that withstands the conditions of most reactions usually performed on biomolecules. With this unique blend of properties, the 2,4-D system compares favorably with its rivals digoxigenin (DIG)/anti-DIG and biotin/(strept)avidin and provides an interesting and powerful tool in biomolecular labeling.

Theoretical investigation of the excited states of 2-nitrobenzyl and 4,5-methylendioxy-2-nitrobenzyl caging groups.

The photochemistry of caged compounds of the o-nitrobenzyl type has been investigated thoroughly in the past. However, even recently new side reactions have been discovered. Earlier, we reported [Bley, F., K. Schaper, and H. Görner (2008), Photochem. Photobiol.84 162-171] that we found long-lived triplet states which do not lead to product formation for the bathochromic absorbing compounds with 4,5-methylendioxy-2-nitrobenzyl caging group. Here, we report on theoretical studies which explain the special behavior of these compounds. These studies reveal that the bathochromic shift of absorption for these compounds compared with o-nitrobenzyl compounds themselves is not due to a shift in energy of the involved states, but due to a substantial change of oscillator strength of the respective transitions. The lack of reactivity of the triplet state of 4,5-methylendioxy-2-nitrobenzyl compounds can be attributed to state switching. In the triplet manifold the lowest state is a nonreactive charge transfer state, while the lowest state in the singlet manifold is a reactive local excitation in the nitro-group. From these results we conclude that it will be most likely not possible to create derivatives of caged compounds based on the o-nitrobenzyl caging group which have absorption which is shifted even more strongly to longer wavelengths.

Thermodynamic and structural aspects of sulfonamide crystals and solutions.

The crystal structures of three sulfonamides with the general structure 4-NH(2)-C(6)H(4)-SO(2)NH-C(6)H(4/3)-R (R = 4-Et; 4-OMe; 5-Cl-2-Me) have been determined by X-ray diffraction. On the basis of our previous data and the results obtained a comparative analysis of crystal properties was performed: molecular conformational states, packing architecture, and hydrogen bond networks using graph set notations. The thermodynamic aspects of the sulfonamide sublimation process have been studied by investigating the temperature dependence of vapor pressure using the transpiration method. A regression equation was derived describing the correlation between sublimation entropy terms and crystal density data calculated from X-ray diffraction results. Also correlations between sublimation Gibbs energies and melting points, on the one hand, and between sublimation enthalpies and fusion enthalpies at 298 K, on the other hand, were found. These dependencies give the opportunity to predict sublimation thermodynamic parameters by simple thermo-physical experiments (fusion characteristics). Solubility processes of the compounds in water, n-hexane, and n-octanol (as phases modeling various drug delivery pathways and different types of membranes) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of sulfonamide solvation were evaluated. For compounds with similar structures processes of transfer from one solvent to another one were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight that the contribution of these terms is different for different molecules (entropy- or enthalpy-determined). Thus, in contrast to interpretation of only the Gibbs energy of transfer, being extensively used for pharmaceuticals in the form of the partition coefficient (log P), the analysis of thermodynamic functions of the transfer process provides additional mechanistic information. This may be important for further evaluation of the physiological distribution of drug molecules and may provide a better understanding of biopharmaceutical properties of drugs.

NMR-spectroscopic investigation of o-nitrosobenzoic acid.

The synthesis of o-nitrosobenzoic acid 2 has been known for more than 100 years, and the photochemical preparation from o-nitrobenzaldehyde 1 became a textbook example for [1,5]-hydrogen shifts. However, neither the (1)H-NMR spectra nor the (13)C--{(1)H}-NMR of this compound have been reported so far. This fact can most likely be attributed to the monomer-dimer equilibrium of the nitrosobenzoic acid, which leads to rather complex, concentration-dependent NMR spectra. In this paper, we report a thorough investigation of these spectra. In the (13)C-{(1)H}-NMR spectra, all 21 lines could be assigned to the monomeric form, the E-dimer, and the Z-dimer.

Structural assignment of adenine aggregates in CDCl3.

We reinvestigated the self-association of 9-substituted adenine derivatives in CDCl3 solutions and present the infrared spectra of 9-ethyladenine and N-methyl-9-ethyladenine and its aggregates in the spectral regions between 1500 and 1800 cm(-1) and between 2700 and 3600 cm(-1). Wavelength dependent absolute extinction coefficients of the monomer and dimers are presented on the basis of a simple deconvolution method. Comparison of the deconvoluted dimer spectra with quantum chemical calculations allows for a structural assignment of the two dimer structures that coexist in 9-ethyladenine/CDCl3 solutions. In contrast, the dimer spectrum of N-methyl-9-ethyladenine is dominated by a single isomer.

Photoprocesses of molecules with 2-nitrobenzyl protecting groups and caged organic acids.

The 308 nm photoinduced formation of the nitroso product and the intermediacy of the aci-nitro form(s) were studied for a series of 2-nitrobenzyl alkyl and aryl esters (1a-4e) and bis-(nitrophenyl)methyl acetates (5a-6b) by time-resolved UV-vis spectroscopy. A triplet state appears as major transient, when 2-nitrobenzyl derivatives 1 are substituted by 4,5-dimethoxy (2) and 4,5-methylenedioxy (3/4) groups. This triplet of charge transfer character is, however, not part of the route via the aci-nitro into the 2-nitroso form. The activation energy and preexponential factor of the longest lifetime component (tau(aci)), i.e. the major part of the aci-nitro decay, were determined. The carboxylic acids as leaving groups have rather small effects on tau(aci). An additional nitrated phenyl ring in alpha-position (5) leads generally to shorter tau(aci) value. Otherwise, the photogeneration of nitroso products is similar. The quantum yield (Phi(d)) varies only moderately with structure, the yield of the aci-nitro form and Phi(d) are correlated and little affected by solvent properties.

Sulfonamides as a subject to study molecular interactions in crystals and solutions: sublimation, solubility, solvation, distribution and crystal structure.

Crystal structures of 4-amino-N-(4-chlorophenyl)-benzene-sulfonamide (IV), 4-amino-N-(2,3-dichlorophenyl)-benzene-sulfonamide (V), 4-amino-N-(3,4-dichlorophenyl)-benzene-sulfonamide (VI) and 4-amino-N-(2,5-dichlorophenyl)-benzene-sulfonamide (VII) were solved by X-ray diffraction method. Temperature dependencies of saturated vapour pressure and thermodynamic functions of sublimation process were calculated (IV: delta Gsub298=74.0 kJ mol(-1), delta Hsub298=134.1+/-1.2 kJ mol(-1), delta Ssub298=202+/-3 J mol(-1)K(-1); V: delta Gsub298=61.7 kJ mol(-1), delta Hsub298=141.1+/-0.7 kJ mol(-1), delta Ssub298=266+/-2 J mol(-1)K(-1); VI: delta Gsub298=85.8 kJ mol(-1), delta Hsub298=167.5+/-3.6 kJ mol(-1), delta Ssub298=274+/-8 J mol(-1)K(-1); VII: delta Gsub298=75.7 kJ mol(-1), delta Hsub298=155.4+/-1.6 kJ mol(-1), delta Ssub298=268+/-4 J mol(-1)K(-1)). Thermochemical parameters of fusion and evaporation processes for the compounds were obtained. Temperature dependencies of the solubility in water, n-octanol were measured. The thermodynamic functions of solubility and solvation processes were deduced. The transfer processes of the molecules from water to n-octanol were analysed by diagram method and main driven forces were established.

Studying thermodynamic aspects of sublimation, solubility and solvation processes and crystal structure analysis of some sulfonamides.

Crystal structures of N-(2-chlorophenyl)-benzene-sulfonamide (I), N-(2,3-dichlorophenyl)-benzene-sulfonamide (II), N-(4-chlorophenyl)-benzene-sulfonamide (III) were solved by X-ray diffraction method. Temperature dependencies of saturated vapor pressure and thermodynamic functions of sublimation process were calculated (I: DeltaG(sub)(298)=50.4kJmol(-1); DeltaH(sub)(298)=114+/-1kJmol(-1); DeltaS(sub)(298)=213+/-3Jmol(-1)K(-1); II: DeltaG(sub)(298)=54.1kJmol(-1); DeltaH(sub)(298)=124.9+/-1.6kJmol(-1); DeltaS(sub)(298)=237+/-5Jmol(-1)K(-1); III: DeltaG(sub)(298)=49.9kJmol(-1); DeltaH(sub)(298)=98.6+/-1.9kJmol(-1); DeltaS(sub)(298)=163+/-5Jmol(-1)K(-1)). Thermochemical parameters of fusion process for the compounds were obtained. Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in water, n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and non-specific solvation terms were distinguished using the transfer from the "inert"n-hexane to the other solvents. The transfer processes of the molecules from water to n-octanol were analyzed and main driven forces were established.

CDK1-inhibitory activity of paullones depends on electronic properties of 9-substituents.

Multiple linear regression analysis was employed in an effort to establish a quantitative structure-activity relationship model for the CDK1-inhibitory activity of a series of 9-substituted paullones. While the electronic properties of the 9-substituents proved to be of high relevance for CDK1 inhibition, both lipophilic and a steric parameters could not be included in a meaningful equation for the calculation of biological properties. The equation solely based on the electronic parameter was successfully used for the prediction of the CDK1-inhibitory activity of a small test set comprising novel paullones with sulfur-containing 9-substituents. Among these new derivatives, 2-methoxy-9-methylsulfonylpaullone proved to be superior to the standard alsterpaullone with respect to CDK1 inhibition.

Folate-synthesizing enzyme system as target for development of inhibitors and inhibitor combinations against Candida albicans-synthesis and biological activity of new 2,4-diaminopyrimidines and 4'-substituted 4-aminodiphenyl sulfones.

The paper describes the design, synthesis, and testing of inhibitors of folate-synthesizing enzymes and of whole cell cultures of Candida albicans. The target enzymes used were dihydropteroic acid synthase (SYN) and dihydrofolate reductase (DHFR). Several series of new 2,4-diaminopyrimidines were synthesized and tested as inhibitors of DHFR and compared with their activity against DHFR derived from mycobacteria and Escherichia coli. To test for selectivity, also rat DHFR was used. A series of substituted 4-aminodiphenyl sulfones was tested for inhibitory activity against SYN and the I(50) values compared to those obtained previously against Plasmodium berghei- and E. coli-derived SYN. Surprisingly, QSAR equations show very similar structural dependencies. To find an explanation for the large difference in the I(50) values observed for enzyme inhibition (SYN, DHFR) and for inhibition of cell cultures of Candida, mutant strains with overexpressed efflux pumps and strains in which such pumps are deleted were included in the study and the MICs compared. Efflux pumps were responsible for the low activity of some of the tested derivatives, others showed no increase in activity after pumps were knocked out. In this case it may be speculated that these derivatives are not able to enter the cells.

Tertiary structure of bacterial murein: the scaffold model.

Although the chemical structure and physical properties of peptidoglycan have been elucidated for some time, the precise three-dimensional organization of murein has remained elusive. Earlier published computer simulations of the bacterial murein architecture modeled peptidoglycan strands in either a regular (D. Pink, J. Moeller, B. Quinn, M. Jericho, and T. Beveridge, J. Bacteriol. 182: 5925-5930, 2000) or an irregular (A. Koch, J. Theor. Biol. 204: 533-541, 2000) parallel orientation with respect to the plasma membrane. However, after integrating published experimental data on glycan chain length distribution and the degree of peptide side chain cross-linking into this computer simulation, we now report that the proposed planar network of murein appears largely dysfunctional. In contrast, a scaffold model of murein architecture, which assumes that glycan strands extend perpendicularly to the plasma membrane, was found to accommodate published experimental evidence and yield a viable stress-bearing matrix. Moreover, this model is in accordance with the well-established principle of murein assembly in vivo, i.e., sequential attachment of strands to the preexisting structure. For the first time, the phenomenon of division plane alternation in dividing bacteria can be reconciled with a computer model of the molecular architecture of murein.