An activated O --> N acyl transfer auxiliary: efficient amide-backbone substitution of hindered "difficult" peptides

Overcoming the phenomenon known as "difficult" synthetic sequences has been a major goal in solid-phase peptide synthesis for over 30 years. In this work the advantages of amide backbone-substitution in the solid-phase synthesis of "difficult" peptides are augmented by developing an activated N(alpha)()-acyl transfer auxiliary. Apart from disrupting troublesome intermolecular hydrogen-bonding networks, the primary function of the activated N(alpha)()-auxiliary was to facilitate clean and efficient acyl capture of large or beta-branched amino acids and improve acyl transfer yields to the secondary N(alpha)()-amine. We found o-hydroxyl-substituted nitrobenzyl (Hnb) groups were suitable N(alpha)()-auxiliaries for this purpose. The relative acyl transfer efficiency of the Hnb auxiliary was superior to the 2-hydroxy-4-methoxybenzyl (Hmb) auxiliary with protected amino acids of varying size. Significantly, this difference in efficiency was more pronounced between more sterically demanding amino acids. The Hnb auxiliary is readily incorporated at the N(alpha)()-amine during SPPS by reductive alkylation of its corresponding benzaldehyde derivative and conveniently removed by mild photolysis at 366 nm. The usefulness of the Hnb auxiliary for the improvement of coupling efficiencies in the chain-assembly of difficult peptides was demonstrated by the efficient Hnb-assisted Fmoc solid-phase synthesis of a known hindered difficult peptide sequence, STAT-91. This work suggests the Hnb auxiliary will significantly enhance our ability to synthesize difficult polypeptides and increases the applicability of amide-backbone substitution.     

Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of the carbonyl (C'), nitrogen (N), and amide proton (H(N)) nuclei of 64 distinct amide bonds in human ubiquitin have been determined in isotropic solution by a set of 14 complementary auto- and cross-correlated relaxation rates involving the CSA interactions of the nuclei of interest and several dipole-dipole (DD) interactions. The CSA parameters thus obtained depend to some degree on the models used for local motions. Three cases have been considered: restricted isotropic diffusion, three-dimensional Gaussian axial fluctuations (3D-GAF), and independent out-of-plane motions of the NH(N) vectors with respect to the peptide planes.     

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity ( = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.     

Polyoxometalate HIV-1 protease inhibitors. A new mode of protease inhibition.

Nb-containing polyoxometalates (POMs) of the Wells-Dawson class inhibit HIV-1 protease (HIV-1P) by a new mode based on kinetics, binding, and molecular modeling studies. Reaction of alpha(1)-K(9)Li[P(2)W(17)O(61)] or alpha(2)-K(10)[P(2)W(17)O(61)] with aqueous H(2)O(2) solutions of K(7)H[Nb(6)O(19)] followed by treatment with HCl and KCl and then crystallization affords the complexes alpha(1)-K(7)[P(2)W(17)(NbO(2))O(61)] (alpha(1)()1) and alpha(2)-K(7)[P(2)W(17)(NbO(2))O(61)] (alpha(2)()1) in 63 and 86% isolated yields, respectively. Thermolysis of the crude peroxoniobium compounds (72-96 h in refluxing H(2)O) prior to treatment with KCl converts the peroxoniobium compounds to the corresponding polyoxometalates (POMs), alpha(1)-K(7)[P(2)W(17)NbO(62)] (alpha(1)()2) and alpha(2)-K(7)[P(2)W(17)NbO(62)] (alpha(2)()2), in moderate yields (66 and 52%, respectively). The identity and high purity of all four compounds were confirmed by (31)P NMR and (183)W NMR. The acid-induced dimerization of the oxo complexes differentiates sterically between the cap (alpha(2)) site and the belt (alpha(1)) site in the Wells-Dawson structure (alpha(2)()2 dimerizes in high yield; alpha(1)()2 does not). All four POMs exhibit high activity in cell culture against HIV-1 (EC(50) values of 0.17-0.83 microM), are minimally toxic (IC(50) values of 50 to >100 microM), and selectively inhibit purified HIV-1 protease (HIV-1P) (IC(50) values for alpha(1)()1, alpha(2)()1, alpha(1)()2, and alpha(2)()2 of 2.0, 1.2, 1.5, and 1.8 microM, respectively). Thus, theoretical, binding, and kinetics studies of the POM/HIV-1P interaction(s) were conducted. Parameters for [P(2)W(17)NbO(62)](7)(-) were determined for the Kollman all-atom (KAA) force field in Sybyl 6.2. Charges for the POM were obtained from natural population analysis (NPA) at the HF/LANL2DZ level of theory. AutoDock 2.2 was used to explore possible binding locations for the POM with HIV-1P. These computational studies strongly suggest that the POMs function not by binding to the active site of HIV-1P, the mode of inhibition of all other HIV-1P protease inhibitors, but by binding to a cationic pocket on the "hinge" region of the flaps covering the active site (2 POMs and cationic pockets per active homodimer of HIV-1P). The kinetics and binding studies, conducted after the molecular modeling, are both in remarkable agreement with the modeling results: 2 POMs bind per HIV-1P homodimer with high affinities (K(i) = 1.1 +/- 0.5 and 4.1 +/- 1.8 nM in 0.1 and 1.0 M NaCl, respectively) and inhibition is noncompetitive (k(cat) but not K(m) is affected by the POM concentration).     

Synthesis and structures of aluminum and magnesium complexes of tetraimidophosphates and trisamidothiophosphates: EPR and DFT investigations of the persistent neutral radicals {Me2Al[(mu-NR)(mu-NtBu)P(mu-NtBu)2]Li(THF)2}(*) (R = SiMe3, tBu)

Reactions of (RNH)(3)PNSiMe(3) (3a, R = (t)()Bu; 3b, R = Cy) with trimethylaluminum result in the formation of {Me(2)Al(mu-N(t)Bu)(mu-NSiMe(3))P(NH(t)()Bu)(2)]} (4) and the dimeric trisimidometaphosphate {Me(2)Al[(mu-NCy)(mu-NSiMe(3))P(mu-NCy)(2)P(mu-NCy)(mu-NSiMe(3))]AlMe(2)} (5a), respectively. The reaction of SP(NH(t)Bu)(3) (2a) with 1 or 2 equiv of AlMe(3) yields {Me(2)Al[(mu-S)(mu-N(t)Bu)P(NH(t)()Bu)(2)]} (7) and {Me(2)Al[(mu-S)(mu-N(t)()Bu)P(mu-NH(t)Bu)(mu-N(t)Bu)]AlMe(2)} (8), respectively. Metalation of 4 with (n)()BuLi produces the heterobimetallic species {Me(2)Al[(mu-N(t)Bu)(mu-NSiMe(3))P(mu-NH(t)()Bu)(mu-N(t)()Bu)]Li(THF)(2)} (9a) and {[Me(2)Al][Li](2)[P(N(t)Bu)(3)(NSiMe(3))]} (10) sequentially; in THF solutions, solvation of 10 yields an ion pair containing a spirocyclic tetraimidophosphate monoanion. Similarly, the reaction of ((t)BuNH)(3)PN(t)()Bu with AlMe(3) followed by 2 equiv of (n)BuLi generates {Me(2)Al[(mu-N(t)Bu)(2)P(mu(2)-N(t)Bu)(2)(mu(2)-THF)[Li(THF)](2)} (11a). Stoichiometric oxidations of 10 and 11a with iodine yield the neutral spirocyclic radicals {Me(2)Al[(mu-NR)(mu-N(t)Bu)P(mu-N(t)Bu)(2)]Li(THF)(2)}(*) (13a, R = SiMe(3); 14a, R = (t)Bu), which have been characterized by electron paramagnetic resonance spectroscopy. Density functional theory calculations confirm the retention of the spirocyclic structure and indicate that the spin density in these radicals is concentrated on the nitrogen atoms of the PN(2)Li ring. When 3a or 3b is treated with 0.5 equiv of dibutylmagnesium, the complexes {Mg[(mu-N(t)()Bu)(mu-NH(t)()Bu)P(NH(t)Bu)(NSiMe(3))](2)} (15) and {Mg[(mu-NCy)(mu-NSiMe(3))P(NHCy)(2)](2)} (16) are obtained, respectively. The addition of 0.5 equiv of MgBu(2) to 2a results in the formation of {Mg[(mu-S)(mu-N(t)()Bu)P(NH(t)Bu)(2)](2)} (17), which produces the hexameric species {[MgOH][(mu-S)(mu-N(t)()Bu)P(NH(t)Bu)(2)]}(6) (18) upon hydrolysis. Compounds 4, 5a, 7-11a, and 15-17 have been characterized by multinuclear ((1)H, (13)C, and (31)P) NMR spectroscopy and, in the case of 5a, 9a.2THF, 11a, and 18, by X-ray crystallography.     

Hydrothermal synthesis,structures, and magnetic properties of three novel 5-aminoisophthalic acid ligand bridged transition metal cation polymers

Three novel 5-aminoisophthalic acid (AIP) bridged polymers [Co(C(8)NH(5)O(4))(H(2)O)](n)() (1), [Ni(C(8)NH(5)O(4))(H(2)O)(2)](n)() (2), and [Zn(C(8)NH(5)O(4))(H(2)O)](n)() (3) were synthesized by hydrothermal reactions and characterized by IR, Raman, elemental analysis, ESR, and magnetic measurements. X-ray single-crystal analyses were carried out for [Co(C(8)NH(5)O(4))(H(2)O)](n)() (1), which crystallizes in the triclinic system, space group P1 macro, with a = 6.477(1) A, b = 7.130(1) A, c = 9.826(2) A, alpha = 108.9(1) degrees, beta = 93.97(3) degrees, gamma = 98.82(3) degrees, and Z = 2; for [Ni(C(8)NH(5)O(4))(H(2)O)(2)](n)() (2), in the triclinic system, space group P1 macro, a = 6.425(1) A, b = 8.115(2) A, c = 10.146(2) A, alpha = 113.09(3)(o), beta = 99.64(3)(o), gamma = 98.90(3)(o), and Z = 2; and for [Zn(C(8)NH(5)O(4))(H(2)O)](n)() (3), in the monoclinic system, space group P2(1)/n, a = 9.044(1) A, b = 8.264(1) A, c = 11.646(1) A, beta = 100.77(1) degrees, and Z = 4. The single X-ray diffraction studies reveal that 1 consists of an infinite honeycomb layer formed by four crystallographically independent motifs packed alternatively together; 2 consists of an infinite neutral railroad-like linear polymer, and 3 consists of infinite layers of alternating four-coordinated Zn(II) cations and AIP ligands. Finally, they are all packed into beautiful three-dimensional frameworks through complicated hydrogen bonding. Antiferromagnetic and ferromagnetic behaviors were observed for 1 and 2 from the magnetic measurements.     

Predicting internal protein dynamics from structures using coupled networks of hindered rotators

Internal motions in proteins, such as oscillations of internuclear vectors u(N(i)H(i) (N)) of amide bonds about their equilibrium position, can be characterized by a local order parameter. This dynamic parameter can be determined experimentally by measuring the longitudinal and transverse relaxation rates of (15)N(i) nuclei by suitable NMR methods. In this paper, it is shown that local variations of order parameters S(ii) (2) can be predicted from the knowledge of the structure. To this effect, the diffusive motion of the internuclear vector u(N(i)H(i) (N)) is described in a potential that takes into account the deviations of the angles theta(ij) between u(N(i)H(i) (N)) and neighboring vectors u(N(j)H(j) (N)) from their average value and similarly of deviations of the angles subtended between u(N(i)H(i) (N)) and u(X(j)Y(j)), where X(j) and Y(j) are heavy atoms in the vicinity of the u(N(i)H(i) (N)) vector under investigation. It is shown how the concept of vicinity can be defined by a simple cutoff threshold, i.e., by neglecting vectors u(X(j)Y(j)) with distances d(N(i),X(j))>7.5 A. The local order parameters S(ii) (2) can be predicted from the structure using a limited set of coordinates of heavy atoms. The inclusion of a larger number of heavy atoms does not improve the predictions. Applications to calmodulin, calbindin, and interleukin 4 illustrate the success and limitations of the predictions.     

Group 5 imido complexes derived from diamido-pyridine ligands

Reaction of the vanadium(V) imide [V(NAr)Cl(3)(THF)] (Ar = 2,6-C(6)H(3)(i)()Pr(2)) with the diamino-pyridine derivative MeC(2-C(5)H(4)N)(CH(2)NHSiMe(2)(t)()Bu)(2) (abbreviated as H(2)N'(2)N(py)) gave modest yields of the vanadium(IV) species [V(NAr)(H(3)N'N' 'N(py))Cl(2)] (1 where H(3)N'N' 'N(py) = MeC(2- C(5)H(4)N)(CH(2)NH(2))(CH(2)NHSiMe(2)(t)()Bu) in which the original H(2)N'(2)N(py) has effectively lost SiMe(2)(t)()Bu (as ClSiMe(2)(t)()Bu) and gained an H atom. Better behaved reactions were found between the heavier Group 5 metal complexes [M(NR)Cl(3)(py)(2)] (M = Nb or Ta, R = (t)()Bu or Ar) and the dilithium salt Li(2)[N(2)N(py)] (where H(2)N(2)N(py) = MeC(2-C(5)H(4)N)(CH(2)NHSiMe(3))(2)), and these yielded the six-coordinate M(V) complexes [M(NR)Cl(N(2)N(py))(py)] (M = Nb, R = (t)()Bu 2; M = Ta, R = (t)()Bu 3 or Ar 4). The compounds 2-4 are fluxional in solution and undergo dynamic exchange processes via the corresponding five-coordinate homologues [M(NR)Cl(N(2)N(py))]. Activation parameters are reported for the complexes 2 and 3. In the case of 2, high vacuum tube sublimation afforded modest quantities of [Nb(N(t)()Bu)Cl(N(2)N(py))] (5). The X-ray crystal structures of the four compounds 1, 2, 3, and 4 are reported.     

Atmospheric pressure electrospray ionization mass spectra of glucose and 2-fluorodeoxyglucose for quantitative analysis of 2-fluorodeoxyglucose by high-performance liquid chromatography

2-Fluoro-2-deoxy-D-glucose (FDG) labeled by fluorine-18 is the most widely used radiopharmaceutical for positron emission tomography (PET). For high-performance liquid chromatography (HPLC)/MS assay and quality control, the mass spectra of FDG and glucose (Glc) in organic + water solutions were studied by flow injection analysis (FIA) and in a chromatographic eluate. In acetonitrile (MeCN) + 0.025% ammonium formate (NH(4)HCO(2)) solvent (80 : 20), electrospray ionisation (ESI) of glucose-FDG provides M.NH(4)(+) and 2M.Na(+) (M = Glc or FDG) as the most intense positive ions. Formation of the latter ions and also of M.MeCN.Na(+) and 2MeCN. Na(+) is typical of the presence of NaCl in the ESI inlet. The positive ions include heavier ions corresponding to the impurities separated by HPLC and also to the cross-ring fragmentation of complexes (2FDG. aMeCNX)L, where a = 0 or 1, L is either Na(+) or NH(4)(+) and X is a fragmented pyranose or anhydropyranose residue. The second most abundant Glc negative ion is m/z = 359 which was interpreted as (2GlcH(+))(). The negative-ion spectrum of FDG has dominating lines due to FDG.HCO(2)() ions at m/z 227 and also (2FDGH(+))() at m/z 363. The m/z 363 signal is suppressed in the presence of NaCl at a molar ratio of 4 : 1 to NH(4)HCO(2), while the ions at m/z 217 and 219, i.e. FDG.Cl(), become three times more intense than FDG.HCO(2)(). The latter ion appears to be most suitable as an analytical signal for chemical analysis of FDG at m/z 226 and 227. Limits of FDG quantitation (LOQ) of 19 ng and 21 ng were found for the 200(+) and 227() ion signals, respectively, and are wholly adequate for verification of total FDG content in radiopharmaceuticals.     

Temperature dependence of anisotropic protein backbone dynamics

The measurement of (15)N NMR spin relaxation, which reports the (15)N-(1)H vector reorientational dynamics, is a widely used experimental method to assess the motion of the protein backbone. Here, we investigate whether the (15)N-(1)H vector motions are representative of the overall backbone motions, by analyzing the temperature dependence of the (15)N-(1)H and (13)CO-(13)C(alpha) reorientational dynamics for the small proteins binase and ubiquitin. The latter dynamics were measured using NMR cross-correlated relaxation experiments. The data show that, on average, the (15)N-(1)H order parameters decrease only by 2.5% between 5 and 30 degrees C. In contrast, the (13)CO-(13)C(alpha) order parameters decrease by 10% over the same temperature trajectory. This strongly indicates that there are polypeptide-backbone motions activated at room temperature that are not sensed by the (15)N-(1)H vector. Our findings are at variance with the common crank-shaft model for protein backbone dynamics, which predicts the opposite behavior. This study suggests that investigation of the (15)N relaxation alone would lead to underestimation of the dynamics of the protein backbone and the entropy contained therein.     

Peptide bond formation mediated by 4,5-dimethoxy-2-mercaptobenzylamine after periodate oxidation of the N-terminal serine residue

[reaction in text] A thiol linker-attached peptide was prepared from a nonprotected peptide via an N(alpha)()-alpha-oxoacyl peptide. Selective oxidation of the N-terminal serine with sodium periodate gave the N(alpha)-glyoxyloyl peptide, reductive amination of which with 4,5-dimethoxy-2-(triphenylmethylthio)benzylamine gave an N(alpha)-4,5-dimethoxy-2-mercaptobenzyl glycyl peptide after removal of the trityl group. The N(alpha)-4,5-dimethoxy-2-mercaptobenzyl peptide can be condensed with a peptide thioester, and the linker is removable. This strategy provides a useful method for the synthesis of peptides using recombinant proteins.     

Bis-diazeniumdiolates of dialkyldiamines: enhanced nitric oxide loading of parent diamines

[reaction: see text] The synthesis and characterization of a series of symmetric bis-dialkyldiamine-based diazeniumdiolates, RN[N(O)NO(-)Na(+)](CH(2))(x)()N[N(O)NO(-)Na(+)]R', are reported. Preparation of corresponding intramolecular diazeniumdiolates of the form RN[N(O)NO](-)(CH(2))(x)()NH(2)(+)R' with alkyl groups > (CH(2))(4)CH(3) have been shown previously to lack stability. In contrast, sodium-stabilized bis-diazeniumdiolates of such lipophilic species can be readily formed when these same diamines are reacted with NO in basic media. The resulting compounds release 4 mol of NO per mole of original diamine. This approach enables the synthesis of more lipophilic NO donors than previously possible.     

Characterizing hydrogen bonding and proton transfer in 2:1 FH:NH3 and FH:collidine complexes through one- and two-bond spin-spin coupling constants across hydrogen bonds

Ab initio equation-of-motion coupled cluster singles and doubles calculations have been carried out on a variety of 2:1 FH:NH(3) complexes (F(b)H(b):F(a)H(a):NH(3)) to investigate the effects of structural changes on one- and two-bond spin-spin coupling constants across F(a)-H(a)-N and F(b)-H(b)-F(a) hydrogen bonds and to provide insight into experimentally measured coupling constants for 2:1 FH:collidine (2:1 FH:2,4,6-trimethylpyridine) complexes. Coupling constants have been computed for 2:1 FH:NH(3) equilibrium structures and proton-transferred perpendicular and open structures at 2:1 FH:NH(3), FH:pyridine, and FH:collidine geometries. (2h)J(Fa)(-)(N), (1)J(Fa)(-)(Ha), and (1h)J(Ha)(-)(N) exhibit expected dependencies on distances, angles, and the nature of the nitrogen base. In contrast, one- and two-bond coupling constants associated with the F(b)-H(b)-F(a) hydrogen bond, particularly (2h)J(F)()b(-)(F)()a, vary significantly depending on the F-F distance, the orientation of the hydrogen-bonded pair, and the nature of the complex (HF dimer versus the anion FHF(-)). The structure of the 2:1 FH:collidine complex proposed on the basis of experimentally measured coupling constants is supported by the computed coupling constants. This study of the structures of open proton-transferred 2:1 FH:NH(3), FH:pyridine, and FH:collidine complexes and the coupling constants computed for 2:1 FH:NH(3) complexes at these geometries provides insight into the role of the solvent in enhancing proton transfer across both N-H(a)-F(a) and F(b)-H(b)-F(a) hydrogen bonds.     

Influence of Sulfur Metalation on the Accessibility of the Ni(II/I) Couple in [N,N'-Bis(2-mercaptoethyl)-1,5-diazacyclooctanato]nickel(II): Insight into the Redox Properties of [NiFe]-Hydrogenase

A redox model study of [NiFe] hydrogenase has examined a series of five polymetallics based on the metalation of the dithiolate complex [1,5-bis(mercaptoethyl)-1,5-diazacyclooctane]Ni(II), Ni-1. Crystal structures of three polymetallics of the series have been reported earlier: [(Ni-1)(2)()Ni]Cl(2)(), [(Ni-1)(2)()FeCl(2)()](2)(), and [(Ni-1)(3)()(ZnCl)(2)()]Cl(2)(). Two are described here: [(Ni-1)(2)()Pd]Cl(2)().2H(2)()Ocrystallizes in the monoclinic system, space group P2(1)/c with cell constants a = 12.212(4) ?, b = 7.642(2) ?, c = 16.625(3) ?, beta = 107.69(2) degrees, V = 1443.230(0) ?(3), Z = 2, R = 0.051, and R(w) = 0.056. [(Ni-1)(2)()CoCl]PF(6)() crystallizes in the triclinic system, space group P&onemacr;, with cell constants a = 8.14(2) ?, b = 13.85(2) ?, c = 15.67(2) ?, alpha = 113.59(10) degrees, beta = 101.84(14) degrees, gamma = 94.0(2) degrees, V = 1561.620(0)?(3), Z = 2, R = 0.072, and R(w) = 0.077. In all Ni-1 serves as a bidentate metallothiolate ligand with a "hinge" angle in the range 105-118 degrees and Ni-M distances of 2.7- 3.7 ?. The most accessible redox event is shown by EPR and electrochemistry to reside in the N(2)S(2)Ni unit and is the Ni(II/I) couple. Charge neutralization of the thiolate sulfurs by metalation can (dependent on the interacting metal) stabilize the Ni(I) state as efficiently as methylation forming a thioether. The implication of these results for the heterometallic active site of [NiFe]-hydrogenase as structured from Desulfovibrio gigas (Volbeda, A., et al. Nature, 1995, 373, 580), the generality of the Ni(&mgr;-SR)(2)M hinge structure, and a possible explanation for the unusual redox potentials are discussed.     

Three-dimensional etching profiles and surface speciations (via attenuated total reflection-fourier transform infrared spectroscopy) of silicon nanowires in NH4F-buffered HF solutions: a double passivation model

A systematic study of the etching behavior, in terms of three-dimensional profiles, of one-dimensional (1-D) silicon nanowires (SiNWs) in NH(4)F-buffered hydrofluoric acid (BHF) solutions of varying concentrations and pH values and the surface speciations of the resulting etched SiNW surfaces, as characterized by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, is reported. It was found that SiNWs are stable only in relatively narrow pH ranges of the BHF solutions. The results are rationalized in terms of a "double passivation" model. When SiNWs are etched in BHF solutions with pH values of 1-3, the surfaces are passivated with hydrogen (inner layer) giving rise to surface moieties such as Si-H(x) species (x = 1-3); at high HF concentrations, the H-terminated Si surfaces are covered with a hydrogen bonding network of HF and related molecules (oligomers, etc.), providing an outer-layer passivation. When SiNWs are etched in BHF solutions with pH values of 11-14 (by adding a strong base such as NaOH), the surfaces are oxygen-terminated with surface moieties such as Si-(O(-))(x)() species (x = 1-3); at high NH(4)F concentrations, the negatively charged Si surfaces are stabilized by NH(4)(+) ions via ionic bonding, again providing outer-layer passivation. In BHF solutions with pH values of 3-11, the surface speciation, consisting of Si-(OH)(x)(O(-))(y) (x + y = 1-3) species, is unstable and etched away rapidly. The surface speciations of SiNWs etched in various BHF solutions were explored via ATR-FTIR spectroscopy. It was found that, while etching SiNWs with HF-rich BHF solutions with pH < 4 gave rise to Si-H(x)() surface species, no surface Si-H(x) species were observed with SiNWs etched in BHF solutions with pH >/= 4 (HF/NH(4)F /= 4 on the other. These two factors, among others, contribute to the rapid hydrolysis of the surface Si-H(x)() species (and the etching of the SiNWs), particularly in BHF solutions with low HF/NH(4)F ratios and high pH values (pH >/= 4).     

Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta

NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics have not been possible. Here, we present new experiments for the measurement of side chain dynamics in methyl-containing residues in unfolded protein states. The pulse schemes are similar to recently proposed methods for measuring deuterium spin relaxation rates in (13)CH(2)D methyl groups in folded proteins.(1) However, because resolution in (1)H-(13)C correlation maps of unfolded proteins is limiting, relaxation data are recorded as a series of (1)H-(15)N spectra. The methodology is illustrated with an application to the study of side chain dynamics in delta131delta, a large disordered fragment of staphylococcal nuclease containing residues 1-3 and 13-140 of the wide-type protein. A good correlation between the order parameters of the symmetry axes of the methyl groups and the backbone (1)H-(15)N bond vectors of the same residue is observed. Simulations establish that such a correlation is only possible if the unfolded state is comprised of an ensemble of structures which are not equiprobable. A motional model, which combines wobbling-in-a-cone and Gaussian axial fluctuations, is proposed to estimate chi(1) torsion angle fluctuations, sigma(chi)()1, of Val and Thr residues on the basis of the backbone and side chain order parameters. Values of sigma(chi)()1 are approximately 10 degrees larger than what has previously been observed in folded proteins. Of interest, the value of sigma(chi)()1 for Val 104 is considerably smaller than for other Val or Thr residues, suggesting that it may be part of a hydrophobic cluster. Notably large (15)N transverse relaxation rates are observed in this region. To our knowledge, this is the first time that side chain dynamics in an unfolded state have been studied in detail by NMR.     

A comprehensive analysis of multifield 15N relaxation parameters in proteins: determination of 15N chemical shift anisotropies.

This study deals with the exploitation of the three classical 15N relaxation parameters (the longitudinal relaxation rate, R1, the transverse relaxation rate, R2, and the 1H-15N cross-relaxation rate, sigmaNH) measured at several magnetic fields in uniformly 15N-labeled proteins. Spectral densities involved in R1, R2 and sigmaNH are analyzed according to the functional form A + B/(1 + omega(2) taus(2)), where taus is the correlation time associated with slow motions sensed by the NH vector at the level of the residue to which it belongs. The coefficient B provides a realistic view of the backbone dynamics, whereas A is associated with fast local motions. According to the "model free approach", B can be identified with 2tausS(2) where S is the generalized order parameter. The correlation time taus is determined from the field dependency of the relaxation parameters while A and B are determined through linear equations. This simple data processing is needed for obtaining realistic error bars based on a statistical approach. This proved to be the key point for validating an extended analysis aiming at the determination of nitrogen chemical shift anisotropy. The protein C12A-p8(MTCP1) has been chosen as a model for this study. It will be shown that all data (obtained at five magnetic field strengths corresponding to proton resonance of 400, 500, 600, 700, and 800 MHz) are very consistently fitted provided that a specific effective correlation time associated with slow motions is defined for each residue. This is assessed by small deviations between experimental and recalculated values, which, in all cases, remain within experimental uncertainty. This strategy makes needless elaborate approaches based on the combination of several slow motions or their possible anisotropy. Within the core of the protein taus fluctuates in a relatively narrow range (with a mean value of 6.15 ns and a root-mean-square deviation of 0.36 ns) while it is considerably reduced at the protein extremities (down to approximately 3 ns). To a certain extent, these fluctuations are correlated with the protein structure. A is not obtained with sufficient accuracy to be valuably discussed. Conversely, order parameters derived from B exhibit a significant correlation with the protein structure. Finally, the multi-field analysis of the evolution of longitudinal and transverse relaxation rates has been refined by allowing the 15N chemical shift anisotropy (csa) to vary residue by residue. Within uncertainties (derived here on a statistical basis) an almost constant value is obtained. This strongly indicates an absence of correlation between the experimental value of this parameter obtained for a given residue in the protein, the nature of this residue, and the possible involvement of this residue in a structured area of the protein.     

Controlled synthesis of ternary II-II'-VI nanoclusters and the effects of metal ion distribution on their spectral properties

The reaction of [(3,5-Me(2)-C(5)H(3)N)(2)Zn(ESiMe(3))(2)] (E = Se, Te) with cadmium(II) acetate in the presence of PhESiMe(3) and P(n)Pr(3) at low temperature leads to the formation of single crystals of the ternary nanoclusters [Zn(x)()Cd(10)(-)(x)()E(4)-(EPh)(12)(P(n)()Pr(3))(4)] [E = Se, x = 1.8 (2a), 2.6 (2b); Te, x = 1.8 (3a), 2.6 (3b)] in good yield. The clusters [Zn(3)Hg(7)Se(4)(SePh)(12)(P(n)()Pr(3))(4)] (4) and [Cd(3.7)Hg(6.3)Se(4)(SePh)(12)(P(n)()Pr(3))(4)] (5) can be accessed by similar reactions involving [(3,5-Me(2)-C(5)H(3)N)(2)Zn(SeSiMe(3))(2)] or [(N,N'-tmeda)Cd(SeSiMe(3))(2)] (1) and mercury(II) chloride. The metal silylchalcogenolate reagents are efficient delivery sources of {ME(2)} in cluster synthesis, and thus, the metal ion content of these clusters can be readily moderated by controlling the reaction stoichiometry. The reaction of cadmium acetate with [(3,5-Me(2)-C(5)H(3)N)(2)Zn(SSiMe(3))(2)], PhSSiMe(3), and P(n)()Pr(3) affords the larger nanocluster [Zn(2.3)Cd(14.7)S(4)(SPh)(26)(P(n)()Pr(3))(2)] (6). The incorporation of Zn(II) into {Cd(10)E} (E = Se, Te) and Zn(II) or Cd(II) into {Hg(10)Se} nanoclusters results in a significant blue shift in the energy of the first "excitonic" transition. Solid-state thermolysis of complexes 2 and 3 reveals that these clusters can be used as single-source precursors to bulk ternary Zn(x)Cd(1)(-)(x)E materials as well as larger intermediate clusters and that the metal ion ratio is retained during these reactions.     

Molecular Orbital Calculation and Spectroscopic Study of the Photochemical Generation of Bis(2,2'-bipyridine)rhodium(I) from Bis(2,2'-bipyridine)(oxalato)rhodium(III)

A planar complex, [Rh(bpy)(2)](+) (bpy = 2,2'-bipyridine), was obtained from [Rh(ox)(bpy)(2)](+) (ox = oxalato) by photoirradiation. A rate constant k for the photoreaction was evaluated as 1 x 10(8) s(-1) in simple first-order kinetics, whereas a ligand dissociation, a reorganization of the coordinated bpy, and a two-electron transfer were involved in the reaction. The process of the Rh(I) complex generation was investigated in terms of a discrete variational (DV)-Xalpha molecular orbital calculation on [Rh(ox)(HN=CHCH=NH)(2)](+) instead of [Rh(ox)(bpy)(2)](+). From the calculation, using the transition-state method, it was predicted that a transition of the ox pi orbital to the metal 4d(z)()2 orbital caused the ligand dissociation and the reorganization of the coordinated bpy occurred in the ox pi to Rh 4d(x)()2(-y)2 excited state stabilized by the ox elimination. Upon release of the ligand and a change from octahedral to square-planar geometry, the electron density on the metal increased and the Rh 4d orbital acquired a d(8) electronic configuration.     

Rovibrational molecular hamiltonian in mixed bond-angle and umbrella-like coordinates

A new exact quantum mechanical rovibrational Hamiltonian operator for molecules exhibiting large amplitude inversion and torsion motions is derived. The derivation is based on a division of a molecule into two parts: a frame and a top. The nuclei of the frame only are used to construct a molecular system of axes. The inversion motion of the frame is described in the umbrella-like coordinates, whereas the torsion motion of the top is described by the nonstandard torsion angle defined in terms of the nuclear vectors and one of the molecular axes. The internal coordinates chosen take into account the properties of the inversion and torsion motions. Vibrational s and rotational Omega vectors obtained for the introduced internal coordinates determine the rovibrational tensor G defined by simple scalar products of these vectors. The Jacobian of the transformation from the Cartesian to the internal coordinates considered and the G tensor specify the rovibrational Hamiltonian. As a result, the Hamiltonian for penta-atomic molecules like NH2OH with one inverter is presented and a complete set of the formulas necessary to write down the Hamiltonian of more complex molecules, like NH2NH2 with two inverters, is reported. The approach considered is essentially general and sufficiently simple, as demonstrated by derivation of a polyatomic molecule Hamiltonian in polyspherical coordinates, obtained by other methods with much greater efforts.