Photochemistry of the model phototropic system involving flavins and indoles. I. Fluorescence polarization and MO calculations of the direction of the electronic transition moments in flavins

Abstract— The fluorescence polarization spectra of riboflavin, lumiflavin, and alloxazine under different conditions have been obtained. It has been shown that the polarization spectrum of riboflavin is not affected significantly by media such as D₂O-glycerol (50: 50) and castor oil. Our data do not indicate the anomalous spectral shift of riboflavin in castor oil, in contrast to the previous finding described by Thomas. The electronic structures of lumiflavin and alloxazine are similar to that of riboflavin, as revealed by the fluorescence polarization measurements and the molecular orbital calculations. The Pariser-Parr-Pople semiempirical SCF ASMO CI computations have been performed to compare the calculated transition moments with the polarization data. The theory predicts an angle of 42° between the 450 and 365 nm transition oscillators, in reasonable agreement with the experimental angle of about 49°. It has been shown, from the comparison of the calculated and observed spectral quantities, that the pseudo-heteroatom model for treating methyl groups in the flavin molecule is not adequate. The group orbital and inductive approximations appear to be satisfactory. Finally, the implication of the present findings has been briefly discussed in connection with phototropism.     

POTENTIOMETRIC and LASER FLASH PHOTOLYSIS STUDIES OF THE pH DEPENDENCE OF HYDROGEN PEROXIDE PRODUCTION BY THE SEMICARBAZIDE/LUMIFLAVIN/OXYGEN PHOTOSYSTEM

The effect of pH on hydrogen peroxide photoproduction by the semicarbazide/lumiflavin/ oxygen system has been investigated by using the potentiometric and laser flash photolysis techniques. Kinetic analysis of (a) primary and secondary reactions involved in the photoreduction of lumiflavin and (b) lumiflavin reoxidation by oxygen have been carried out at varying pH values, drastic differences being observed in the pH dependence of both types of reactions. The reaction mechanism appears to proceed by semicarbazide-quenching (reductive type) of the light-excited lumiflavin in its triplet state followed, depending on pH, either by reoxidation of the so formed flavosemiquinone by molecular oxygen or by flavosemiquinone disproportionation into oxidized and fully reduced lumiflavin.     

DNA PHOTOLYASE FROM THE FUNGUS NEUROSPORA CRASSA. PURIFICATION, CHARACTERIZATION AND COMPARISON WITH OTHER PHOTOLYASES

Abstract A phr-gene from the filamentous fungus Neurosporu crassa was overexpressed in Escherichia coli cells, yielding a biologically active photolyase. After purification till apparent homogeneity, the 66 kDa protein was found to contain equimolar amounts of 5,1O-methenyltetrahydrofolic acid (MTHF) and FAD, classifying it as an MTHF-type photolyase. Compared to other MTHF photolyases the absorption maximum of Neurosporu photolyase is shifted from ca 380 nm to 391 nm (t = 34 800), while an additional shoulder is present at 465 nm. In dark-adapted enzyme the FAD chromophore is predominantly present in the oxidized form, in contrast with E. coli and Saccharomyces cerevisiue photolyase, which contain mainly semiquinone or fully reduced FAD, respectively. Preillumination or dithionite treatment converted oxidized FAD in Neurospora photolyase into the fully reduced form, with a concomitant shift of the absorption maximum from 391 to 396 nm and disappearance of the 465 nm shoulder. The action spectrum of photoreactivation coincides with the absorption spectrum of preilluminated (reduced) photolyase, extending the spectral region of MTHF-type photolyases from 380 till 396 nm. A quantum yield of 0.57 was obtained for the overall repair reaction. Comparison of spectral properties of FAD in Neurospora photolyase and the model compound lumiflavin points to an apolar microenvironment of photolyase-bound FAD. Neurosporu photolyase has distinct advantages over E. coli photolyase as it is more stable and contains a full complement of chromophores.     

Experimental detection and theoretical characterization of the H2-NHX van der Waals complex

The H2-NH(X) van der Waals complex has been examined using ab initio theory and detected via fluorescence excitation spectroscopy of the A(3)Pi-X(3)Sigma(-) transition. Electronic structure calculations show that the minimum energy geometry corresponds to collinear H2-NH(X), with a well depth of D(e)=116 cm(-1). The potential-energy surface supports a secondary minimum for a T-shaped geometry, where the H atom of NH points towards the middle of the H2 bond (C(2v) point group). For this geometry the well depth is 73 cm(-1). The laser excitation spectra for the complex show transitions to the H2+NH(A) dissociative continuum. The onset of the continuum establishes a binding energy of D(0)=32+/-2 cm(-1) for H2-NH(X). The fluorescence from bound levels of H2-NH(A) was not detected, most probably due to the rapid reactive decay [H2-NH(A)-->H+NH2]. The complex appears to be a promising candidate for studies of the photoinitiated H2+NH abstraction reaction under conditions were the reactants are prealigned by the van der Waals forces.     

Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase

Flavin adenine dinucleotide (FAD) is a common cofactor in redox proteins, and its reduction potentials are controlled by the protein environment. This regulation is mainly responsible for the versatile catalytic functions of flavoenzymes. In this article, we report computations of the reduction potentials of FAD in medium-chain acyl-CoA dehydrogenase (MCAD) and cholesterol oxidase (CHOX). In addition, the reduction potentials of lumiflavin in aqueous solution have also been computed. Using molecular dynamics and free-energy perturbation techniques, we obtained the free-energy changes for two-electron/two-proton as well as one-electron/one-proton addition steps. We employed a combined quantum mechanical and molecular mechanical (QM/MM) potential, in which the flavin ring was represented by the self-consistent-charge density functional tight-binding (SCC-DFTB) method, while the rest of the enzyme-solvent system was treated by classical force fields. The computed two-electron/two-proton reduction potentials for lumiflavin and the two enzyme-bound FADs are in reasonable agreement with experimental data. The calculations also yielded the pKa values for the one-electron reduced semiquinone (FH*) and the fully reduced hydroquinone (FH2) forms. The pKa of the FAD semiquinone in CHOX was found to be around 4, which is 4 units lower than that in the enzyme-free state and 2 units lower than that in MCAD; this supports the notion that oxidases have a greater ability than dehydrogenases to stabilize anionic semiquinones. In MCAD, the flavin ring interacts with four hydrophobic residues and has a significantly bent structure, even in the oxidized state. The present study shows that this bending of the flavin imparts a significant destabilization (approximately 5 kcal/mol) to the oxidized state. The reduction potential of lumiflavin was also computed using DFT (M06-L and B3LYP functionals with 6-31+G(d,p) basis set) with the SM6 continuum solvation model, and the results are in good agreement with results from explicit free-energy simulations, which supports the conclusion that the SCC-DFTB/MM computation is reasonably accurate for both 1e(-)/1H+ and 2e(-)/2H+ reduction processes. These results suggest that the first coupled electron-proton addition is stepwise for both the free and the two enzyme-bound flavins. In contrast, the second coupled electron-proton addition is also stepwise for the free flavin but is likely to be concerted when the flavin is bound to either the dehydrogenase or the oxidase enzyme.     

Hot hydrogen atom reactions moderated by H2 and He

Photolysis experiments were performed on the H2-CD4-NH3 and the He-CD4-NH3 systems. The photolysis (1849 angstoms) involved only NH3. Mixtures of H2:CD4:NH3 included all combinations of the ratios (200,400,800):(10,20,40):4. Two He:CD4:NH3 mixtures were examined where the ratios equalled the combinations 100:(10,20):4. Abstraction of a D from CD4 by the photolytically produced hot hydrogen from ammonia was monitored by mass spectrometric determination of HD. Both experiment and semiempirical hot-atom theory show that H2 is a very poor thermalizer of hot hydrogens with excess kinetic energy of about 2 eV. Applications of the hard-sphere collision model to the H2-CD4-NH3 system results in predicted ratios of net HD production to NH3 decomposition that were two orders of magnitude smaller than the experimental ratios. On the other hand, helium is found to be a very efficient thermalizer; here, the classical model yields reasonable agreement with experiments. Application of a semiempirical hot-atom program gave quantitative agreement with experiment for either system.     

An electrochemical investigation of the redox properties of lumiflavin in acidic media

The electrochemistry of lumiflavin in acidic media (1% to 40% sulfuric acid) has been investigated using cyclic voltammetry and bulk electrolysis in conjunction with UV—Vis absorption spectroscopy. The observed stabilization of flavin radicals in strongly acidic media has been explained on the basis of differences in medium effects on fully reduced flavin cations (FH⁺₄) as compared with protonated oxidized (FH⁺₂) and radical (FH^∓+₃) species. The equilibrium constant for the comproportionation reaction between protonated lumiflavin species (FH⁺₂ + FH⁺₄ → 2 FH^∓+₃) has been determined. Acid dissociation constants for FH⁺₂ and FH⁺₄ have also been evaluated. These data are used in conjunction with the pK_a reported for FH^∓+₃ to estimate the value of the comproportionation constant for the neutral lumiflavin species.     

Supramolecular cation assemblies of hydrogen-bonded (NH4+/NH2NH3+)(crown ether) in [Ni(dmit)2]-based molecular conductors and magnets

Hydrogen-bonded supramolecular cation assemblies of (NH4+/NH2-NH3+)(crown ether), where the crown ether is [12]crown-4, [15]crown-5, or [18]crown-6, were incorporated into electrically conducting [Ni(dmit)2] salts (dmit2- = 2-thioxo-1,3-dithiole-4,5-dithiolate). (NH4+)([12]crown-4)[Ni(dmit)2]3(CH3CN)2 had a pyramidal shape, while ionic channels were observed in (NH4+)(0.88)([15]crown-5)[Ni(dmit)(2)]2 and (NH4+)(0.70)([18]crown-6)[Ni(dmit)(2)]2. Both (NH4+)(0.88)([15]crown-5) and (NH4+)(0.70)([18]crown-6) contained regularly spaced [Ni(dmit)(2)] stacks formed by N-H.O hydrogen bonding between the oxygen atoms in crown ethers and the NH4+ ion. NH4+ occurred nonstoichiometrically; there were vacant ionic sites in the ionic channels. The ionic radius of NH4+ is larger than the cavity radius of [15]crown-5 and [18]crown-6. Therefore, NH4+ ions could not pass through the cavity and were distributed randomly in the ionic channels. The static disorder caused the conduction electrons to be randomly localized to the [Ni(dmit)2] stacks. Hydrazinium (NH2-NH3+) formed the supramolecular cations in (NH2-NH3+)([12]crown-4)2[Ni(dmit)2]4 and (NH2-NH3+)2([15]crown-5)3[Ni(dmit)2]6, possessing a sandwich and club-sandwich structure, respectively. To the best of our knowledge, these represent the first hydrazinium-crown ether assemblies to be identified in the solid. In the supramolecular cations, hydrogen bonding was detected between the ammonium or the amino protons of NH2-NH3+ and the oxygen atoms of crown ethers. The sandwich-type cations coexisted with the [Ni(dmit)2] dimer stacks. Although the assemblies were typically semiconducting, ferromagnetic interaction (Weiss temperature = +1 K) was detected in the case of (NH2-NH3+)2([15]crown-5)3[Ni(dmit)2]6. The (NH2-NH3+)0.8([18]crown-6)[Ni(dmit)2]2 and (NH4+)0.76([18]crown-6)[Ni(dmit)2]2 crystals were isomorphous. The large and flexible [18]crown-6 allowed for maintaining the same ionic channel structure through replacement of the NH4+ cation by NH2-NH3+.     

锗钼杂多酸单扫描极谱法测定枸杞中的微量锗

在ＰＨ８．９的氨性缓冲溶液中,锗钼杂多在示波极谱上,于－１．０５Ｖ（ｖｓ．ＳＣＥ）产生灵敏的吸附波。导数波高与锗 度在６．９＊１０＾－８－５．５＊１０＾－５ｍｏＬ范围内有好的线性关系,检出限为３．５＊１０＾－８ｍｏｌ／Ｌ。用本法测定了中药枸杞中的锗,得到满意的结果。     

Magnetic circular dichroism spectroscopy of antiferromagnetically coupled hetero-metallic rings [H2NR2][Cr7MF8(O2CCMe3)16

The optical and magnetic properties of the multi-metal rings [NH(2)R(2)][Cr(7)MF(8)(O(2)CCMe(3))(16)], where M = Cd(II), Mn(II) or Ni(II), have been studied using variable-field and variable-temperature magnetic circular dichroism (MCD) in the UV-visible spectra. Spectra of samples were recorded in a frozen organic matrix or cast in a polymethacrylate (PMMA) polymer film between 1.7 and 75 K. The spectra are characteristic of the Cr(III) ion (d(3)) in a rhombic field when M = Cd(II). In the case that M = Ni(II) additional optical transitions arise from the d(8) ion whereas for M = Mn(II) no additional transitions are observed. The influence of magnetic exchange is apparent from a change in the sign of the MCD signal between complexes in which the hetero-atom has a local spin moment greater, or less, than that of Cr(III), S = 3/2, namely, Mn(II), S = 5/2, and Ni(II), S = 1. The exchange coupling generates a manifold of thermally accessible electronic states that give rise to variations in MCD intensity as well as additional spectral features as the temperature is raised. Equations have been derived to relate the splittings observed in the optical spectrum to the single-ion ground state zero-field splittings of chromium(III). There is reasonable agreement between the sign and magnitude of the contribution to the cluster anisotropy from that of the single ion with values estimated from other techniques.     

The role of aromaticity in the planarity of lumiflavin

Ab initio MP2/6-31G(d,p) and density functional theory B3LYP/6-31G(d,p) calculations were performed to investigate the molecular structure of the active part of flavins in the oxidized and reduced forms, using lumiflavin as a model compound. The possible aromatic character of these systems was explored by using the following aromaticity indexes: nucleus-independent chemical shifts, the anisotropy of the magnetic susceptibility, the Bird index, and natural bond orbital analysis. To provide further insight, calculations on the 2+ charged species were also carried out. Both the MP2 and B3LYP computations predict a planar conformation for the oxidized form and a bent structure for the reduced form, in agreement with previous experience. For both the oxidized and reduced states, ring A is found to be the most aromatic, as expected. The calculations suggest that the folding in the reduced form is mainly a result of electronic preferences rather than steric hindrance.     

DFT studies on the favored and rare tautomers of neutral and redox cytosine

The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311+G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo –OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino- and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-beta3-hAla-NHMe and Ac-beta3-hAla-beta3-hPhe-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-beta3-hAla-NHMe (1) and Ac-beta3-hAla-beta3-hPhe-NHMe (2), have been explored under jet-cooled, isolated-molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl substituents (37,200-37,800 cm(-1)). UV-UV hole-burning spectroscopy was used to determine the ultraviolet spectral signatures of five conformational isomers of both 1 and 2. Transitions due to two conformers (labeled A and B) dominate the R2PI spectra of each molecule, while the other three are minor conformers (C-E) with transitions a factor of 3-5 smaller. Resonant ion-dip infrared spectroscopy was used to obtain single-conformation infrared spectra in the 3300-3700 cm(-1) region. The infrared spectra showed patterns of NH stretch transitions characteristic of the number and type of intramolecular H-bonds present in the beta-peptide backbone. For comparison with experiment, full optimizations of low-lying minima of both molecules were carried out at DFT B3LYP/6-31+G*, followed by single point MP2/6-31+G* and selected MP2/aug-cc-pVDZ calculations at the DFT optimized geometries. Calculated harmonic vibrational frequencies and infrared intensities for the amide NH stretch vibrations were used to determine the beta-peptide backbone structures for nine of the ten observed conformers. Conformers 1B, 1D, and 2A were assigned to double ring structures containing two C6 H-bonded rings (C6a/C6a), conformers 1A and 2B are C10 single H-bonded rings, conformers 1C and 2D are double ring structures composed of two C8 H-bonded rings (C8/C8), and conformers 1E and 2E are double ring/double acceptor structures in which two NH groups H-bond to the same C=O group, thereby weakening both H-bonds. Both 1E and 2E are tentatively assigned to C6/C8 double ring/double acceptor structures, although C8/C12 structures cannot be ruled out unequivocally. Finally, no firm conformational assignment has been made for conformer 2C whose unusual infrared spectrum contains one very strong H-bond with NH stretch frequency at 3309 cm(-1), a second H-bonded NH stretch fundamental of more typical value (3399 cm(-1)), and a third fundamental at 3440 cm(-1), below that typical of a branched-chain free NH. The single conformation spectra provide characteristic wavenumber ranges for the amide NH stretch fundamentals ascribed to C6 (3378-3415 cm(-1)), C8 (3339-3369 cm(-1)), and C10 (3381-3390 cm(-1)) H-bonded rings.     

Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

The structure and properties of flavins: Molecular orbital study based on totally optimized geometries. I. Molecular geometry investigations

Molecular orbital calculations (MINDO /3) using energy minimized molecular geometries were performed on oxidized and reduced lumiflavin and related methylated isoalloxazines, including cationic and anionic species. Close agreement with experimental geometry, photoelectron spectra, and NMR data supports the importance of optimized geometries for these molecular systems and provides the basis for interpretation of chemical and biological properties. Oxidized forms are shown to be most stable in the planar configuration but also highly flexible about the N(5)—N(10) axis; only 1 kcal/mol is required for a 10° bend. N(10) is generally out of the plane slightly; also, C(9)-methyl substitution introduces nonplanarity. The unsubstituted isoalloxazine is computed to be 0.76 kcal/mol (ΔH) less stable than its isomer, alloxazine. Calculations were also performed on enol as well as quinone-methide tautomeric forms. Reduced flavin geometry depends on methyl substitution pattern: N(10) substituted forms are bent with typical fold angles around 155°, whereas the unsubstituted reduced form is planar. Both oxidized and reduced forms are also flexible. Proton affinities were calculated for protonation and deprotonation of oxidized and reduced forms. Protonation of oxidized forms is favored at N(1) by 10–12 kcal/mol and produces somewhat nonplanar isoalloxazinium ions. In addition, ΔH for the two-electron reduction of lumiflavin is estimated to be ?19.7 kcal/mol. In this paper investigations of geometric aspects are presented along with introductory and background material. Orbital structure and electron distribution studies are presented in paper II.     

Infrared photodissociation spectroscopy of protonated ammonia cluster ions, NH4+(NH3)n (n=5-8), by using infrared free electron laser

Infrared photodissociation action spectra of protonated ammonia cluster ions, NH(4) (+)(NH(3))(n) (n=5-8), were measured in the range of 1020-1210 cm(-1) by using a tunable infrared free electron laser. Analyses by the density functional theory (DFT) show that the spectral features observed can be assigned to the nu(2) vibrational mode of the NH(3) molecules in NH(4) (+)(NH(3))(n). Size dependence of the spectra supports structural models obtained by the DFT calculations, in which the NH(4) (+) ion is solvated by the four nearest-neighbor NH(3) molecules. For NH(4) (+)(NH(3))(5), the spectrum between 1000 and 1700 cm(-1) was measured. The nu(4) bands of the NH(3) molecules and the NH(4) (+) ion were found in the range of 1420-1700 cm(-1).     

Vibrational delocalization in ammonia aerosol particles

The present contribution investigates shape effects and surface effects in the infrared spectra of pure (NH(3)) and mixed (NH(3)-CO(2) and NH(3)-NH(2)D-NHD(2)-ND(3)) ammonia particles with sizes between about 1 and 50 nm. The particles investigated have been generated in a collisional cooling cell as aerosols at temperatures between 20 and 80 K. The contribution reveals that only the combination with a microscopic model leads to a comprehensive understanding of the various features observed in the experimental infrared spectra. As one of the major results, the corresponding exciton model explains why pronounced shape effects observed for pure particles only play a minor role in the case of mixed particles.     

The reaction of tetrakis(dimethylamido)titanium with self-assembled alkyltrichlorosilane monolayers possessing -OH, -NH2, and -CH3 terminal groups

The reactions of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with alkyltrichlorosilane self-assembled monolayers (SAMs) terminated by -OH, -NH(2), and -CH(3) groups have been investigated with X-ray photoelectron spectroscopy (XPS). For comparison, a chemically oxidized Si surface, which serves as the starting point for formation of the SAMs, has also been investigated. In this work, we examined the kinetics of adsorption, the spatial extent, and stoichiometry of the reaction. Chemically oxidized Si has been found to be the most reactive surface examined here, followed by the -OH, -NH(2), and -CH(3) terminated SAMs, in that order. On all surfaces, the reaction of Ti[N(CH(3))(2)](4) was relatively facile, as evidenced by a rather weak dependence of the initial reaction probability on substrate temperature (T(s) = -50 to 110 degrees C), and adsorption could be described by first-order Langmuirian kinetics. The use of angle-resolved XPS demonstrated clearly that the anomalous reactivity of the -CH(3) terminated SAM could be attributed to reaction of Ti[N(CH(3))(2)](4) at the SAM/SiO(2) interface. Reaction on the -NH(2) terminated SAM proved to be the "cleanest", where essentially all of the reactivity could be associated with the terminal amine group. In this case, we found that approximately one Ti[N(CH(3))(2)](4) adsorbed per two SAM molecules. On all surfaces, there was significant loss of the N(CH(3))(2) ligand, particularly at high substrate temperatures, T(s) = 110 degrees C. These results show for the first time that it is possible to attach a transition metal coordination complex from the vapor phase to a surface with an appropriately functionalized self-assembled monolayer.     

On the influence of semirigid environments on proton transfer along molecular chains

The dynamics of proton transfer along ammonia chains (chemical composition N(x)H(+)(3x+1), x=2, 4, and 6) in a constraining environment is investigated by ab initio molecular dynamics simulations. A carbon nanotube of defined length and diameter is used as an idealized constraining environment such that the ammonia chain is forced to maintain its quasilinear geometry. It is found that, although the energetics of proton transport shows considerable energetic barriers, proton translocation along the wire is possible at finite temperature for all chain lengths studied. The proton transport involves rotational reorientation of the proton-carrying ammonia molecule. High level ab initio calculations (MP2/aug-cc-pVTZ) yield barriers for internal rotation of 9.1 kcal/mol for NH(4) (+)-NH(3) and 11.7 kcal/mol for OH(3) (+)-OH(2), respectively. The infrared spectrum calculated from the dipole-dipole autocorrelation function shows distinct spectral features in the regions (2000-3000 cm(-1)) where the NHN proton transfer mode is expected to absorb. Assigning moderate opposite total charges between 0.002 and 0.2e to the carbon atoms at the end caps of the nanotube leads to a considerable speedup of the proton transfer.     

Linkage isomerism in the binding of pentapeptide Ac-His(Ala)3His-NH2 to (ethylenediamine)palladium(II): effect of the binding mode on peptide conformation

The reaction of the pentapeptide Ac-His1-Ala2-Ala3-Ala4-His5-NH2 (AcHAAAHNH2) (1) with [Pd(en)(ONO2)2] (en = NH2CH2CH2NH2) in either DMF-d(7) or H2O:D2O (90%:10%) gave three linkage isomers of [Pd(en)(AcHAAAHNH2)](2+) (2), 2a, 2b, and 2c, which differ only in which pair of imidazole nitrogen atoms bind to Pd. In the most abundant isomer, 2a, Pd is bound by N1 from each of the two imidazole rings. In the minor isomers 2b and 2c, Pd is bound by N1(His1) and N3(His5) and by N3(His1) and N1(His5), respectively. The reactions of [Pd(en)(ONO2)2] with the N-methylated peptides Ac-(N3-MeHis)-Ala-Ala-Ala-(N3-MeHis)-NH2 (AcH*AAAH*NH2) (3), Ac-(N3-MeHis)-Ala-Ala-Ala-(N1-MeHis)-NH2 (AcH(*)AAAH(#)NH2) (4), and Ac-(N1-MeHis)-Ala-Ala-Ala-(N3-Me-His)-NH2 (AcH(#)AAAH(*)NH2) (5) each gave a single species [Pd(en)(peptide)](2+) in N,N-dimethylformamide (DMF) or aqueous solution, 7, 8, and 9, respectively, with Pd bound by the two nonmethylated imidazole nitrogen atoms in each case. These complexes were analogous to 2a, 2b, and 2c, respectively. Ac-(N1-MeHis)-Ala-Ala-Ala-(N1-MeHis)-NH2 (AcH(#)AAAH(#)NH2) (6) with [Pd(en)(ONO2)2] in DMF slowly gave a single product, [Pd(en)(AcH(#)AAAH(#)NH2)](2+) (10), in which Pd was bound by the N3 of each imidazole ring. The corresponding linkage isomer of 2 was not observed. Complex 10 was also the major product in aqueous solution, but other species were also present. All compounds were exhaustively characterized in solution by multinuclear 1D ((1)H , (13)C, and, with (15)N-labeled ethylenediamine, (15)N) and 2D (correlation spectroscopy, total correlation spectroscopy, transverse rotating-frame Overhauser effect spectroscopy (T-ROESY), heteronuclear multiple-bond correlation, and heteronuclear single quantum coherence) NMR spectra, circular dichroism (CD) spectra, electrospray mass spectroscopy, and reversed-phase high-performance liquid chromatography. ROESY spectra were used to calculate the structure of 2a, which contained a single turn of a peptide alpha helix in both DMF and water, the helix being better defined in DMF. The Pd(en)(2+) moiety was not used in structure calculations, but its location and coordination by one imidazole N1 from each histidine to form a 22-membered metallocycle were unambiguously established. Convergence of the structures was greatest when calculated with two hydrogen-bond constraints (Ala4 peptide NH...OC acetyl and His5 peptide NH...OC-His1) that were indicated by the low temperature dependence of these NH chemical shifts. Vicinal HN-CHalpha coupling constants and chemical shifts of alpha-H atoms were also consistent with a helical conformation. Similar long-range ROE correlations were observed for [Pd(en)(AcH(*)AAAH(*)NH2)](2+) (7), which displayed a CD spectrum in aqueous solution that suggested the presence of some helicity. Long-range ROE correlations were not observed for 8, 9, or 10, but a combination of NMR data and CD spectroscopy was interpreted in terms of the conformational behavior of the coordinated pentapeptide. Only for the linkage isomer [Pd(en)(AcH(*)AAAH(#)NH2)](2+) (8) was there evidence of a contribution from a helical conformation. The data for 8 were interpreted as interconversion between the helix and random coil conformations. Zn(2+) with peptides gave broad NMR peaks attributed to lability of this metal ion, while reactions of cis-[Pt(NH3)2(ONO2)2] were slow, giving a complex mixture of products rather than the macrochelate ring observed with Pd(en)(2+). In summary, these studies indicate that Pd(en)(2+) coordinates to histidine with similar preference for each of the two imidazole nitrogens, enabling the formation of up to four linkage isomers in its complexes with pentapeptides His-xxx-His. Only the N1-N1 linkage isomer that forms a 22-membered macrochelate ring is able to induce an alpha-helical peptide conformation, whereas the 20- and 21-membered rings of linkage isomers do not. This suggests that linkage isomeric mixtures may compromise histidine coordination to metal ions and reduce alpha-helicity.