Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Luminescent platinum(II) dimers with a cyclometallating aryldiamine ligand

Triflate salts of three (Pt(pip2NCN))2(mu-L)2+ (pip2NCNH = 1,3-bis(piperidylmethyl)benzene) dimers bridged by a series of nitrogen-donor ligands (L = pyrazine (pyz), 1,2-bis(4-pyridyl)ethane (bpa), trans-1,2-bis(4-pyridyl)ethylene (bpe)) are reported. These complexes have been fully characterized by 1H NMR spectroscopy and elemental analysis. The X-ray crystal structures of [(Pt(pip2NCN))2(mu-pyz)](CF3SO3)2 and [(Pt(pip2NCN))2(mu-bpe)](CF3SO3)2 x 2CH2Cl2 are reported. [(Pt(pip2NCN))2(mu-pyz)](CF3SO3)2: triclinic, P, a = 12.5240(5) A, b = 14.1570(6) A, c = 14.2928(6) A, alpha = 106.458(1) degrees , beta = 92.527(1) degrees , gamma = 106.880(1) degrees , V = 2303.46(17) A(3), Z = 2. [(Pt(pip2NCN))2(mu-bpe)](CF3SO3)2 x 2CH2Cl2: monoclinic, P21/c, a = 10.1288(6) A, b = 16.3346(9) A, c = 17.4764(10) A, beta = 90.882(2) degrees , V = 2891.1(3) A3, Z = 2. These structures and solution measurements provide evidence for the strong trans-directing properties of the pip2NCN- ligand. The electronic structures of these complexes and those of the 4,4'-bipyridine (bpy) dimer, (Pt(pip2NCN))2(mu-bpy)2+, also have been investigated by UV-visible absorption and emission spectroscopies, as well as cyclic voltammetry. The accumulated data indicate that variations in the bridging ligands provide remarkable control over the electronic structures and photophysics of these complexes. Notably, the bpa dimer exhibits a broad, low-energy emission from a metal-centered 3LF excited state, whereas the bpe and bpy dimers exhibit structured emission from a lowest pyridyl-centered 3(pi-pi*) excited state. In contrast, the pyz dimer exhibits remarkably intense yellow emission tentatively assigned to a triplet metal-to-ligand charge-transfer excited state.     

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.     

Chemical and structural implications of 1',2'- versus 2',4'- conformational constraints in the sugar moiety of modified thymine nucleosides

In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1',2'-azetidine- and 1',2'-oxetane-fused thymidines, as well as their 2',4'-fused thymine (T) counterparts such as LNA-T, 2'-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1',2'-fused or a tricyclic 2',4'-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37 degrees +/- 27 degrees , phi(m) = 25 degrees +/- 18 degrees ) of the 1',2'-fused systems, and (ii) pure North type (P = 19 degrees +/- 8 degrees , phi(m) = 48 degrees +/- 4 degrees ) for the 2',4'-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1',2'- or 2',4'-linked modification. The comparison of pK(a)s of the 1-thyminyl aglycon as well as that of endocyclic sugar-nitrogen obtained by theoretical and experimental measurements showed that the nature of the sugar conformational constraints steer the physicochemical property (pK(a)) of the constituent 1-thyminyl moiety, which in turn can play a part in tuning the strength of hydrogen bonding in the basepairing.     

Sterically hindered and robust pnictogen ligands derived from carboranes: synthesis and X-ray structure determination of tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))phosphine, tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))arsine and chloro(tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))phosphine)gold(I)

Sterically hindered phosphine and arsine ligands derived from ortho-carborane were synthesized and characterized by X-ray crystallography. Tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))phosphine, 2 (crystal data, hexagonal, space group P6(3), a = b = 12.251(3) A, c = 11.514(4) A, alpha = beta = 90 degrees, gamma = 120 degrees, V = 1496.6(7) A(3), Z = 2, R(1) = 0.0568) and tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))arsine, 3 (crystal data, hexagonal, space group P6(3), a = b = 12.330(3) A, c = 11.474(4) A, alpha = beta = 90 degrees, gamma = 120 degrees, V = 1510.7(7) A(3), Z = 2, R(1) = 0.0930) were prepared in 82% and 68% yield, respectively. The phosphine ligand is resistant to air-oxidation but was converted to corresponding oxide when heated with hydrogen peroxide. The tertiary carboranyl phosphine reacted with (Tht)AuCl to yield chloro(tris(1'-methyl(1,2-dicarba-closo-dodecaboran-1-yl))phosphine)gold(I), 4 (crystal data, monoclinic, space group P2(1)/c, a = 19.101(4) A, b = 12.167(2) A, c = 13.846(3) A, alpha = gamma = 90 degrees, beta = 91.13(3) degrees, V = 3217.2(11) A(3), Z = 4, R(1) = 0.0396) in 82% yield. From the X-ray structure of the gold complex, the cone angle of the phosphine was determined to be 213(2) degrees, which is among the largest values reported to date.     

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method

An automatic procedure is proposed for reconstruction of a protein backbone from its C(alpha)-trace; it is based on optimization of a simplified energy function of a peptide backbone, given its alpha-carbon trace. The energy is expressed as a sum of the energies of interaction between backbone peptide groups that are not neighbors in the sequence, the energies of local interactions within all amino acid residues, and a harmonic penalty function accounting for the conservation of standard bond angles. The energy of peptide group interactions is calculated using the assumption that each peptide group acts as a point dipole. For local interaction energy, use is made of a two-dimensional Fourier series expansion of the energies of model terminally blocked amino acid residues, calculated with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field in the angles lambda((1)) and lambda((2)) defining the rotation of peptide groups adjacent to a C(alpha) carbon atom about the corresponding C(alpha) em leader C(alpha) virtual-bond axes. To explore all possible rotations of peptide groups within a fixed C(alpha)-trace, a Monte Carlo search is carried out. The initial lambda angles are calculated by aligning the dipoles of the peptide groups that are close in space, subject to the condition of favorable local interactions. After the Monte Carlo search is accomplished with the simplified energy function, the energy of the structure is minimized with the ECEPP/3 force field, with imposition of distance constraints corresponding to the initial C(alpha)-trace geometry. The procedure was tested on model alpha-helices and beta-sheets, as well as on the crystal structure of the immunoglobulin binding protein (PDB code: 1IGD, an alpha/beta protein). In all cases, complete backbone geometry was reconstructed with a root-mean-square (rms) deviation of 0.5 A from the all-atom target structure.     

Hydrothermal synthesis and structure determination from powder data of new three-dimensional titanium(IV) diphosphonates Ti(O(3)P-(CH(2))(n)-PO(3)) or MIL-25(n) (n = 2, 3)

Ti(O(3)P-(CH(2))(n)-PO(3)) or MIL-25(n) (n = 2, 3) were prepared under hydrothermal conditions (4 days, 463 K, autogenous pressure). Their structures were determined ab initio from X-ray diffraction powder data. MIL-25(2) is triclinic (space group P-1 (no. 2)), with a = 5.033(1), b = 5.092(1), c = 6.859(1) A, alpha = 95.860(1) degrees, beta = 99.994(1) degrees, gamma = 118.217(1) degrees, and Z = 2. MIL-25(3) exhibits an orthorhombic symmetry (space group Cm2m (no. 38)), with a = 5.230(1), b = 8.451(1), c = 17.400(2) A, and Z = 4. Their three-dimensional structures are built up from TiO(6) titanium(IV) octahedra linked together via diphosphonate groups. This leads to pillared structures whose inorganic sheets are closely related to those of the alphaTiP titanium phosphate structure.     

A Nearly Linear Single Hydroxo Bridge. Synthesis, Structure, and Magnetic Susceptibility of (&mgr;-Hydroxo)bis((tetraphenylporphinato)manganese(III)) Perchlorate

The synthesis, X-ray structure, and magnetic susceptibility characterization of a hydroxo-bridged complex, (&mgr;-hydroxo)bis((tetraphenylporphinato)manganese(III)) perchlorate, {[Mn-(TPP)](2)(OH)}ClO(4), are described. The complex is readily prepared by a controlled hydrolysis of monomeric diaquo(tetraphenylporphinato)manganese(III) perchlorate. Interestingly, the bridging hydroxo complex appears to be more stable than the putative &mgr;-oxo complex in halocarbon solvents. The X-ray structure determination shows a complex in which two five-coordinate manganese(III) ions are bridged by a single hydroxo ligand with an average Mn-O distance of 2.026(1) ? and a Mn-O(H)-Mn bridge angle of 160.4(8) degrees. The two porphyrin planes are nearly coplanar, and the two metal ions are separated by 3.993 ?. The average Mn-N(P) distance is 2.008(7) ?. The two manganese ions are displaced by 0.19 and 0.20 ? from their respective 24-atom mean planes. Both of the two porphyrin rings are moderately S(4) ruffled and have a near-staggered orientation (the N-Mn-Mn'-N' dihedral angle is 29.9 degrees ). The four inter-ring pairs of meso-phenyl groups of the binuclear cation are extremely crowded, with a nearly perpendicular orientation for each pair. The solid-state magnetic susceptibility was measured over the temperature range 2-300 K. The observed behavior is typical of an exchange-coupled binuclear complex. The data were fit to the total spin Hamiltonian (H(tot) = H(1) + H(2) - 2J&Svector;(1).&Svector;(2)) of a zero-field-split, high-spin d(4)-d(4) dimer in its actual crystallographic geometry, using numerical techniques. The hydroxide bridge supports a relatively strong antiferromagnetic coupling (2J = -74.0 cm(-1)) between two zero-field-split (D = -10.8 cm(-1)) manganese(III) ions. Crystal data: a = 16.807(7) ?, b = 17.061(6) ?, c = 17.191(5) ?, alpha = 85.64(3) degrees, beta = 79.75(3) degrees, gamma = 61.95(2) degrees, triclinic, space group P&onemacr;, V = 4281(3) ?(3), Z = 2, R(1) = 0.0707 for 14 802 observed data based on F(o) >/= 4.0sigma(F(o)), R(2w) = 0.2007 for 21 696 total unique data, least-squares refinement on F(2) using all data.     

Structure and dynamics of neutral beta-H agostic nickel alkyls: a combined experimental and theoretical study

Addition of BF(3).OEt(2) to ethereal solutions of the Ni(II) beta-diketiminates [Me(2)NN]Ni(R)(2,4-lutidine) (R = Et (1), Pr (2)) allows the isolation of the neutral beta-H agostic monoalkyls [Me(2)NN]Ni(R) (R = Et (3), Pr (4)). X-ray studies of primary alkyls 3 and 4a reveal acute Ni-C(alpha)-C(beta) angles with short Ni-C(beta) distances, indicating structures along the beta-H elimination pathway. Positional disorder of the alkyl group in the X-ray structure of 4 corresponds to partial (22%) occupancy by the secondary alkyl [Me(2)NN]Ni(CHMe(2)) (4b). Variable-temperature NMR spectra of 3 and 4 reveal fluxional behavior that result from beta-H elimination, in-plane rotation of the beta-CH(3) group, and a tetrahedral triplet structure for 3 that were investigated by density functional theory calculations at the Becke3LYP/6-31G level of theory without simplifications on the beta-diketiminate ancillary ligand. Calculations support low temperature NMR studies that identify the linear beta-H agostic propyl isomer 4a as the ground state with the branched beta-H agostic isomer 4b slightly higher in energy. NMR studies and calculations show that the beta-agostic 3 reluctantly coordinates ethene and that 3 is the ground state for this ethylene oligomerization catalyst. The thermodynamic isotope effect K(H)/K(D) = 1.3(2) measured for the loss of 2,4-lutidine from 1 to form beta-agostic 3 was also examined by DFT calculations.     

Syntheses, crystal structures, magnetic properties, and EPR spectra of tetranuclear copper(II) complexes featuring pairs of "roof-shaped" Cu2X2 dimers with hydroxide, methoxide, and azide bridges

Hydroxo- and methoxo-bridged tetranuclear copper(II) complexes of the tetramacrocyclic ligand 1,2,4,5-tetrakis(1,4,7-triazacyclonon-1-ylmethyl)benzene (Ldur), have been prepared from [Cu4Ldur(H2O)8](ClO4)8.9H2O (1). Addition of base to an aqueous solution of 1 gave [Cu4Ldur(mu2-OH)4](ClO4)4 (2). Diffusion of MeOH into a DMF solution of 2 produces [Cu4Ldur(mu2-OMe)4](ClO4)4.HClO4.2/3MeOH (3), a complex which hydrolyzes on exposure to moisture regenerating 2. The structurally related azido-bridged complex, [Cu4Ldur(mu2-N3)4](PF6)4.4H2O.6CH3CN (4), was produced by reaction of Ldur with 4 molar equiv of Cu(OAc)2.H2O and NaN3 in the presence of excess KPF6. Compounds 2-4 crystallize in the triclinic space group P1 (No. 2) with a = 10.248(1) A, b = 12.130(2) A, c = 14.353(2) A, alpha = 82.23(1) degrees, beta = 80.79(1) degrees, gamma = 65.71(1) degrees, and Z = 1 for 2, a = 10.2985(4) A, b = 12.1182(4) A, c = 13.9705(3) A, alpha = 89.978(2) degrees, beta = 82.038(2) degrees, gamma = 65.095(2) degrees, and Z = 1 for 3, and a = 12.059(2) A, b = 12.554(2) A, c = 14.051(2) A, alpha = 91.85(1) degrees, beta = 98.22(1) degrees, gamma = 105.62(1) degrees, and Z = 1 for 4. The complexes feature pairs of isolated dibridged copper(II) dimers with "roof-shaped" Cu2(mu2-X)2 cores (X = OH-, OMe-, N3-), as indicated by the dihedral angle between the two CuX2 planes (159 degrees for 2, 161 degrees for 3, and 153 degrees for 4). This leads to Cu.Cu distances of 2.940(4) A for 2, 2.962(1) A for 3, and 3.006(5) A for 4. Variable-temperature magnetic susceptibility measurements indicate weak antiferromagnetic coupling (J = -27 cm(-1)) for the hydroxo-bridged copper(II) centers in 2 and very strong antiferromagnetic coupling (J = -269 cm(-1)) for the methoxo-bridged copper(II) centers in 3. Pairs of copper(II) centers in 4 display the strongest ferromagnetic interaction (J = 94 cm(-1)) reported thus far for bis(mu2-1,1-azido)-bridged dicopper units. Spectral measurements on a neat powdered sample of 4 at 33.9 GHz or 90 Ghz confirm the spin-triplet ground state for the azido-bridged copper(II) pairs.     

Synthesis, structure, and multi-NMR studies of (Me4N)[A(M(SC(O)Ph)3)2] (A = Na, M = Hg; A = K, M = Cd or Hg)

The compounds (Me4N)[A(M(SC(O)Ph)3)2] (A = K, M = Cd (2); A = Na, M = Hg (3); and A = K, M = Hg (4)) were synthesized by reacting the appropriate metal chloride with A+PhC(O)S- and Me4NCl in the ratios 1:3:1 and 2:6:1. The structures of these compounds were determined by single-crystal X-ray diffraction methods. All the compounds are isomorphous, isostructural, and crystallized in the space group P1 with Z = 1. Single-crystal data for 2: a = 106670(2) A, b = 111522(2) A, c = 119294(2) A, alpha = 71782(1) degrees, beta = 85208(1) degrees, gamma = 69418(1) degrees, V = 126140(4) A3, Dcalc = 1528 g cm-3. Single-crystal data for 3: a = 10840(2) A, b = 10946(4) A, c = 12006(3) A, alpha = 7218(2) degrees, beta = 8675(2) degrees, gamma = 6743(2) degrees, V = 12493(6) A3, Dcalc = 1756 g cm-3. Single-crystal data for 4: a = 104780(1) A, b = 112563(2) A, c = 119827(2) A, alpha = 71574(1) degrees, beta = 85084(1) degrees, gamma = 70705(1) degrees, V = 126523(3) A3, Dcalc = 1755 g cm-3. In the [A(M(SC(O)Ph)3)2]- anions, each M(II) atom is bonded to three thiobenzoate ligands through sulfur atoms, giving a trigonal planar MS3 geometry. The carbonyl oxygen atoms from the two [M(SC(O)Ph)3]- anions are bonded to the alkali metal atom, providing an octahedral environment. Solution metal NMR studies showed the concentration-dependent dissociation of the alkali metal ions in the trinuclear anions.     

Comparative molecular dynamics studies of wild-type and oxidized forms of full-length Alzheimer amyloid beta-peptides Abeta(1-40) and Abeta(1-42)

In this study, all-atom 50 ns molecular dynamics simulations are performed on the full-length amyloid beta (Abeta) monomers (WT-Abeta(1-40) and WT-Abeta(1-42)) and their oxidized forms (Met35(O)-Abeta(1-40) and Met35(O)-Abeta(1-42)) in aqueous solution. The effects of the oxidation state of Met35 and the presence of dipeptide (Ile41-Ala42) on the secondary structures of the three distinct regions (the central hydrophobic core region 17-21 (LVFFA), the loop 23-28 (DVGSNK), and the second hydrophobic domain 29-35 (GAIIGLM)) of all monomers have been analyzed in detail, and results are compared with the available experimental information. Our simulations indicate that the WT-Abeta(1-40) monomer adopts an overall beta-hairpin-like structure, which is promoted by the turn region (24-27). This turn region is stabilized through salt-bridge formation between the Asp23 and Lys28 residues. In contrast, the overall structure of the oxidized (Met35(O)-Abeta(1-40)) monomer can be divided into three well-defined bend regions separated by coil segments. These structural differences may be critical for the measured decrease in the rate of aggregation of Met35(O)-Abeta(1-40) peptide. In the WT-Abeta(1-42) monomer, in comparison to the WT-Abeta(1-40), the Asp23-Lys28 salt bridge is absent, and consequently, the turn in the middle (24-27) region has a smaller curvature. The observed difference in the aggregation rates of these two peptides may be related to the opening of the turn (24-27) stabilized by the Asp23-Lys28 salt bridge. For WT-Abeta(1-42), in the absence of this salt bridge, the unfolding and aggregation events may be more favorable than for WT-Abeta(1-40).     

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.     

Synthesis, pH-dependent structural characterization, and solution behavior of aqueous aluminum and gallium citrate complexes

Reactions of Al(III) and Ga(III) with citric acid in aqueous solutions, yielded the complexes (NH(4))(5)[M(C(6)H(4)O(7))(2)].2H(2)O (M(III) = Al (1), Ga (2)) at alkaline pH, and the complexes (Cat)(4)[M(C(6)H(5)O(7))(C(6)H(4)O(7))].nH(2)O (M(III) = Al (3), Ga (4), Cat. = NH(4)(+), n = 3; M(III) = Al (5), Ga (6), Cat. = K(+), n = 4) at acidic pH. All compounds were characterized by spectroscopic (FT-IR, (1)H, (13)C, and (27)Al NMR, (13)C-MAS NMR) and X-ray techniques. Complex 1 crystallizes in space group P1, with a = 9.638(5) A, b = 9.715(5) A, c = 7.237(4) A, alpha = 90.96(1) degrees, beta = 105.72(1) degrees, gamma = 119.74(1) degrees, V = 557.1(3) A(3), and Z = 1. Complex 2 crystallizes in space group P1, with a = 9.659(6) A, b = 9.762(7) A, c = 7.258(5) A, alpha = 90.95(2) degrees, beta = 105.86(2) degrees, gamma = 119.28(1) degrees, V = 564.9(7) A(3), and Z = 1. Complex 3 crystallizes in space group I2/a, with a = 19.347(3) A, b = 9.857(1) A, c = 23.412(4) A, beta = 100.549(5) degrees, V = 4389(1) A(3), and Z = 8. Complex 4 crystallizes in space group I2/a, with a = 19.275(1) A, b = 9.9697(6) A, c = 23.476(1) A, beta = 100.694(2) degrees, V = 4432.8(5) A(3), and Z = 8. Complex 5 crystallizes in space group P1, with a = 7.316(1) A, b = 9.454(2) A, c = 9.569(2) A, alpha = 64.218(4) degrees, beta = 69.872(3) degrees, gamma = 69.985(4) degrees, V = 544.9(2) A(3), and Z = 1. Complex 6 crystallizes in space group P1, with a = 7.3242(2) A, b = 9.4363(5) A, c = 9.6435(5) A, alpha = 63.751(2) degrees, beta = 70.091(2) degrees, gamma = 69.941(2) degrees, V = 547.22(4) A(3), and Z = 1. The crystal structures of 1-6 reveal mononuclear octahedral complexes of Al(III) (or Ga(III)) bound to two citrates. Solution NMR, on both 4- and 5- species, reveals rapid intramolecular exchange of the bound and unbound terminal carboxylates. Upon dissolution in water, the complexes, through a complicated reaction cascade, transform to oligonuclear 1:1 species that, in agreement with previous studies, represent the thermodynamically stable state in solution. The data provide, for the first time, structural details of low MW, mononuclear complexes of Al(III) (or Ga(III)) with citrate that are dictated, among other factors, by pH. The properties of 1-6 may provide clues relevant to their biological association with humans.     

Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (alpha, phi, psi) and (beta, phi, psi), whereas for three-bond linkages, there are 54 possible regions that can be defined by (alpha, phi, psi, omega) and (beta, phi, psi, omega). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.     

Syntheses and characterization of anti-inflammatory dinuclear and mononuclear zinc indomethacin complexes. Crystal structures of [Zn2(indomethacin)4(L)2] (L = N,N-dimethylacetamide, pyridine, 1-methyl-2-pyrrolidinone) and [Zn(indomethacin)2(L1)2] (L1 = ethanol, methanol)

The syntheses and spectral and structural characterizations of Zn(II) indomethacin [1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indole-3-acetic acid = IndoH] complexes, as different solvent adducts, have been studied. The complexes are unusual in that both monomeric and dimeric complexes are formed and that this is the first example of the same carboxylato ligand binding via both carboxylate oxygen atoms in monomeric and dimeric Zn(II) complexes. The crystal structures of Zn-Indo complexes with N,N-dimethylacetamide (DMA), pyridine (Py), 1-methyl-2-pyrrolidinone (NMP), EtOH, and MeOH as solvent ligands, [Zn2(Indo)4(DMA)2].2DMA, 1, [Zn2(Indo)4(Py)2].2H2O, 2b, [Zn2(Indo)4(NMP)2], 3, cis-[Zn(Indo)2(EtOH)2], 4, and cis-[Zn(Indo)2(MeOH)2], 5, were determined. Complexes 1, 2b, and 3 crystallize in the triclinic space group P1 (No. 2): a = 13.628(2) A, b = 17.462(2) A, c = 11.078(1) A, alpha = 99.49(1) degrees, beta = 108.13(1) degrees, gamma = 110.10(1) degrees for 1; a = 13.347(3) A, b = 16.499(5) A, c = 10.857(1) A, alpha = 99.48(2) degrees, beta = 108.25(2) degrees, gamma = 106.24(2) degrees for 2; a = 14.143(3) A, b = 14.521(2) A, c = 11.558(2) A, alpha = 109.07(1) degrees, beta = 90.80(2) degrees, gamma = 116.40(1) degrees for 3. The three complexes exhibit dinuclear paddle-wheel structures with a Zn...Zn distance of 2.9686(6) A, Zn-ORCOO distances of 2.035(2)-2.060(2) A, and a Zn-ODMA distance of 1.989(2) A in 1, a Zn...Zn distance of 2.969(1) A, Zn-ORCOO distances of 2.020(3)-2.049(3) A, and a Zn-NPy distance of 2.036(3) A in 2, and a Zn...Zn distance of 2.934(1) A, Zn-ORCOO distances of 2.009(3)-2.051(3) A, and a Zn-ONMP distance of 1.986(3) A in 3. In these cases, the zinc ions are offset along the z direction such that the L-Zn...Zn-L moiety is nonlinear, unlike the Cu analogues. Each Zn has a square-pyramidal geometry bridged by four carboxylato ligands in the basal plane with the solvent ligands containing an O- or N-donor atom at the apex. Complexes 4 and 5 are isostructural, with space group C2/c (No. 15). For 4, a = 30.080(2) A, b = 5.3638(6) A, c = 24.739(2) A, beta = 90.342(7) degrees, and for 5, a = 29.419(2) A, b = 5.320(2) A, c = 24.461(2) A, beta = 90.840(4) degrees. The Zn resides on a 2-fold axis and the complexes have a distorted cis octahedral structure with Zn-ORCOO bond lengths of 2.183(3) and 2.169(3) A, a Zn-OEtOH bond length of 2.015(3) A in 4, Zn-ORCOO bond lengths of 2.195(2) and 2.151(2) A, and a Zn-OMeOH bond length of 2.022(3) A in 5.     

Dithiacrown Ether Substituted Porphyrazines: Synthesis, Single-Crystal Structure, and Control of Aggregation in Solution by Complexation of Transition-Metal Ions

The synthesis of novel magnesium, copper, and metal-free porphyrazines, peripherally substituted with dithia-7-crown-2 (MPz(7)), dithia-15-crown-5 (MPz(15)), and dithia-18-crown-6 (MPz(18)) macrocycles is reported. These compounds are prepared starting from dicyanoethylene containing crown ethers 3, 2(1), and 2(2), respectively, which contain sulfur as well as oxygen heteroatoms. The "crowned" porphyrazines bind silver(I) and mercury(II) perchlorates. UV/vis spectroscopy and electron paramagnetic resonance measurements reveal that addition of the transition-metal ions leads to dimerization of the porphyrazine complexes. In the case of the dithia-18-crown-6-substituted porphyrazines, the dimers break up to form monomeric 6:1 guest-host complexes when more than 2 equiv of the metal ion is added. The single-crystal structures of the crown ether 2(2) and the porphyrazine MgPz(18) are presented. Compound C(14)H(20)N(2)O(4)S(2) (2(2)) crystallizes in the monoclinic space group P2(1)/c with a = 10.9310(13) ?, b = 19.383(3) ?, c = 8.6976(14) ?, beta = 108.898(11) degrees, V = 1743.5(5) ?(3), and Z = 4. The structure refinement converged to R = 0.0366 and R(w) = 0.0504. Compound C(56)H(82)MgN(8)O(17)S(8) (MgPz(18)) crystallizes in the triclinic space group P&onemacr; with a = 9.584(3) ?, b = 17.672(2) ?, c = 19.620(4) ?, alpha = 84.904(14) degrees, beta = 85.21(2) degrees, gamma = 89.29(2) degrees, V = 3298.4(13) ?(3), and Z = 2. The structure refinement converged to R1 = 0.0839 and wR2 = 0.2196. The electrical properties of H(2)Pz(18) have been studied by complex impedance spectroscopy. The bulk electrical conductivity of this compound is approximately 1 order of magnitude higher than that of the corresponding 18-crown-6 phthalocyanine.     

Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin

High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D (13)C-(13)C correlation spectroscopy under magic angle spinning conditions. High-resolution (13)C spectra have been acquired from hydrated microcrystals of site-directed (13)C-enriched ubiquitin. Inter-residue carbon-carbon distance constraints defining the global protein structure have been evaluated from 'dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.     

Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation

The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.