Crystal structure of hexakis(2,6-di-O-methyl)-alpha-cyclodextrin-acetonitrile dihydrate: a channel formed by methyl groups harbors a chain of five partially occupied water sites

Hexakis(2,6-di-O-methyl)-alpha-cyclodextrin (DIMEA) crystallizes from 1:1 water-acetonitrile as DIMEA-acetonetril-dihydrate in the orthorhombic space group P2(1)2(1)2(1), unit cell dimensions a = 14.2775(5), b = 15.7312(5), c = 31.1494(11) A. Refinement of the structure against 5540 X-ray diffraction data converged at an R factor of 0.083. The macrocycle exhibits a 'round' conformation and is stabilized by intramolecular, interglucose O-3-H(n)...O-2(n + 1) and C-6-H(n)...O-5(n + 1) hydrogen bonds. Acetonitrile is included in the central cavity of DIMEA and held in position by C-5-H...N interactions. The two water molecules in the asymmetric units are distributed over six sites. One is fully occupied due to hydrogen bonding to O-3 groups of two symmetry-related DIMEA molecules, whereas the five remaining sites show occupancies between 0.15 and 0.25. These sites are in hydrogen bonding contact with O...O distances between 2.59 and 3.50 A and are located in infinite, hydrophobic channels parallel to the alpha-axis, which are coated with methyl groups of symmetry-related DIMEA.     

The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues

The crystal structure of an alternating RNA octamer, r(guauaca)dC (RNA bases are in lower case while the only DNA base is in upper case), with two 3' overhang residues one of them a terminal deoxycytosine and the other a ribose adenine, has been determined at 2.2 A resolution. The refined structure has an Rwork 18.6% and Rfree 26.8%. There are two independent duplexes (molecules I and II) in the asymmetric unit cell, a = 24.95, b = 45.25 and c = 73.67 A, with space group P2(1)2(1)2(1). Instead of forming a blunt end duplex with two a+.c mispairs and six Watson-Crick base-pairs, the strands in the duplex slide towards the 3' direction forming a two-base overhang (radC) and a six Watson-Crick base-paired duplex. The duplexes are bent (molecule I, 20 degrees; molecule II, 25 degrees) and stack head-to-head to form a right-handed superhelix. The overhang residues are looped out and the penultimate adenines of the two residues at the top end (A15) are anti and at the bottom (A7) end are syn. The syn adenine bases form minor groove A*(G.C) base triples with C8-H...N2 hydrogen bonds. The anti adenine in molecule II also forms a triple and a different C2-H...N3 hydrogen bond, while the other anti adenine in molecule I does not, it stacks on the looped out overhang base dC. The 3' terminal deoxycytosines form two stacked hemiprotonated trans d(C.C)+ base-pairs and the pseudo dyad related molecules form four consecutive deoxyribose and ribose zipper hydrogen bonds in the minor groove.     

Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H(A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H-N3(T), present in A-T base pair is also investigated.      

Absolute configuration of Rp-uridine 3'',5''-cyclic phosphorothioate.

Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined to R = 5.1%. The configuration of the thiophosphate group is Rp; conformational parameters are: glycosyl torsion angle anti, -151.9(5) degrees, sugar pucker C(3')-endo with P = 27.3 degrees, vmax = 45.5 degrees, six-membered cycle in chair form. The bond distances in the non-esterified P-S and P-O suggest that the negative charge is distributed between the groups. As illustrated in this and other studies, P-O has a much higher affinity for hydrogen bonds than P-S, indicated here by interactions with triethyl-ammonium N-H and O(2')-H as donors. One additional hydrogen bond N(3)-H---0(4) ties the bases which form a ribbon-like structure. 0(2) and S are not engaged in hydrogen bonds. The triethylammonium ion is two-fold disordered.     

C-H ... O hydrogen bonding in solutions of methylated nucleic acid base analogs as revealed by NMR

Formation and thermodynamic characteristics of C-H ... O hydrogen bonding of methylated uracils and caffeine have been studied by nmr along two lines. 1. The concentration and temperature dependencies of the PMR spectra of 1,3-dimethyluracil (m2 1,3Ura), 1,3-dimethylthymine (m2 1,3Thy), and 1,3,6-trimethyluracil (m3 1,3,6Ura) in chloroform at high concentrations of base analogs indicated the self-association of m2 1,3Ura and m2 1,3Thy via C(6)H ... O hydrogen bonding and the competitive formation of C-H ... O bonds between carbonyl oxygens and chloroform. The intermolecular interaction energy and the arrangement of molecules in the local minima of various m2 1,3Ura dimers were calculated by the method of atom-atom potentials. The deepest minimum for the m2 1,3Ura coplanar dimer corresponds to a C(6)-H ... O hydrogen-bond formation. 2. At low concentration of m2 1,3Ura and caffeine in CCl4, C(6)-H ... O bonding for m2 1,3Ura and C(8)-H ... O bonding for caffeine with oxygens of dimethyl sulfoxide (DMSO) and acetone were observed. The association constants of these complexes were obtained at different temperatures. The enthalpies delta H, of the m2 1,3Ura-DMSO, m2 1,3Ura-accetone, caffeine-DMSO, and caffeine-acetone complexes were -2 +/- 0.1 kcal/mol. The calculations showed that the deepest minimum of the caffeine-acetone coplanar complex corresponds to C(8)-H ... O bonding with energy of -3.5 kcal/mol and that of the m2 1,3Ura-acetone complexes corresponds to C(6)-H ... O bonding with energy of -3.4 kcal/mol. The approximate correction for the solvent effect provides good agreement of the experimental data with the calculations.     

Conformational preferences of hypermodified nucleoside lysidine (k2C) occurring at "wobble" position in anticodon loop of tRNA(Ile)

Conformational preferences of hypermodified nucleoside, 4-amino-2-(N(6)-lysino)-1-(beta-D-ribofuranosyl) pyrimidinium (Lysidine or 2-lysyl cytidine), usually designated as k(2)C, have been investigated theoretically by the quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The zwitterionic, non-zwitterionic, neutral, and tautomeric forms have been studied. Automated geometry optimization using molecular mechanics force field (MMFF), semi-empirical quantum chemical PM3, and ab initio molecular orbital Hartree-Fock SCF quantum mechanical calculations have also been made to compare the salient features. The predicted most stable conformations of zwitterionic, non-zwitterionic, neutral, and tautomeric form are such that in each of these molecules the orientation of lysidine moiety (R) is trans to the N(1) of cytidine. The preferred base orientation is anti (chi = 3 degrees ) and the lysine substituent folds back toward the ribose ring. This results in hydrogen bonding between the carboxyl oxygen O(12a) of lysine moiety and the 2'-hydroxyl group of ribose sugar. In all these four forms of lysidine O(12a)...H-C(9) and O(12b)...H-N(11) interactions provide stability to respective stable conformers. Watson-Crick base pairing of lysidine with A is feasible only with the tautomeric form of usual anti oriented lysidine. This can help in recognition of AUA codon besides in avoiding misrecognition of AUG.     

Crystal structure of beta-cyclodextrin-benzoic acid inclusion complex

The inclusion complex of beta-cyclodextrin (beta-CD) with benzoic acid (BA) has been characterized crystallographically. Two beta-CDs cocrystallize with two BAs, 0.7 ethanol and 20.65 water molecules [2(C(6)H(10)O(5))(7).2(C(7)H(6)O(2)).0.7(C(2)H(6)O).20.65H(2)O] in the triclinic space group P1 with unit cell constants: a=15.210(1), b=15.678(1), c=15.687(1) A, alpha=89.13(1), beta=74.64(1), gamma=76.40(1) degrees. The anisotropic refinement of 1840 atomic parameters against 16,201 X-ray diffraction data converged at R=0.078. In the crystal lattice, beta-CD forms dimers stabilized by direct O-2(m)_1/O-3(m)_1...O-2(n)_2/O-3(n)_2 hydrogen bonds (intradimer) and by indirect O-6(m)_1...,O-6(n)_2 hydrogen bonds with one or two bridging water molecules joined in between (interdimer). These dimers are stacked like coins in a roll constructing endless channels where the guest molecules are included. The BA molecules protrude with their COOH groups at the beta-CD O-6-sides and are maintained in positions by hydrogen bonding to the surrounding O-6-H groups and water molecules. Water molecules (20.65) are distributed over 30 positions in the interstices between beta-CD molecules, except the water sites W-1, W-2 that are located in the channel of the beta-CD dimer. Water site W-2 is hydrogen bonded to the disordered ethanol molecule (occupancy 0.7).     

A new crystal form of beta-cyclodextrin-ethanol inclusion complex: channel-type structure without long guest molecules

A new crystal form of beta-cyclodextrin (beta-CD)[bond]ethanol[bond]dodecahydrate inclusion complex [(C(6)H(10)O(5))(7).0.3C(2)H(5)OH.12H(2)O] belongs to monoclinic space group C2 (form II) with unit cell constants a=19.292(1), b=24.691(1), c=15.884(1) A, beta=109.35(1) degrees. The beta-CD macrocycle is more circular than that of the complex in space group P2(1) [form I: J. Am. Chem. Soc. 113 (1991) 5676]. In form II, a disordered ethanol molecule (occupancy 0.3) is placed in the upper part of beta-CD cavity (above the O-4 plane) and is sustained by hydrogen bonding to water site W-2. In form I, an ethanol molecule located below the O-4-plane is well ordered because it hydrogen bonds to surrounding O-3[bond]H, O-6[bond]H groups of the symmetry-related beta-CD molecules. In the crystal lattice of form I, beta-CD macrocycles are stacked in a typical herringbone cage structure. By contrast, the packing structure of form II is a head-to-head channel that is stabilized at both O-2/O-3 and O-6 sides of each beta-CD by direct O(CD)...O(CD) and indirect O(CD)...O(W)...(O(W))...O(CD) hydrogen bonds. The 12 water molecules are disordered in 18 positions both inside the channel-like cavity of beta-CD dimer (W-1[bond]W-6) and in the interstices between the beta-CD macrocycles (W-7[bond]W-18). The latter forms a cluster that is hydrogen bonded together and to the neighboring beta-CD O[bond]H groups.     

Discrimination in resolving systems. VI. Comparison of the diastereomers of deoxyephedrinium and ephedrinium 4'-fluoromandelates

(-)-(R)-Deoxyephedrine forms poorly discriminating diastereomeric salts with 4'-fluoromandelic acid from 95% ethanol. Both less-soluble (L) (S)-4'-fluoromandelate and more-soluble (M) (R)-4'-fluoromandelate phases are monoclinic and unsolvated. Their solubility ratio (M/L) in 95% ethanol is only 1.2, which correlates with the similarity and small differences in their respective heats of fusion and fusion temperatures. The (R)-deoxyephedrinium and the related (1R;2S)-ephedrinium 4'-fluoromandelate systems show L-salts with higher ion-pair volumes and lower densities than their M-salts. (R)-Deoxyephedrinium salts have higher volumes than the comparable (1R;2S)-ephedrinium salts even though the resolving base (R)-deoxyephedrine lacks the benzylic hydroxy. In the solids, bilayered structures segregate polar and nonpolar molecular regions. The principle interionic interactions are hydrogen bonds between protonated secondary ammonium ions and carboxylates forming infinite chains with a six-atom repeating unit H-N(+)-H...O-C(-)-O [C(2)(2)(6)]. These are buttressed by mandelate hydroxy to carboxylate hydrogen bonds. Differing interactions between phenyl and 4'-fluorophenyl rings in the nonpolar layers of the salts correlate with the density and stability inversion.     

Crystal form III of beta-cyclodextrin-ethanol inclusion complex: layer-type structure with dimeric motif

The crystal form III of the beta-cyclodextrin (beta-CD)-ethanol inclusion complex [2(C(6)H(10)O(5))(7).1.5C(2)H(5)OH.19H(2)O] belongs to the triclinic space group P1 with unit cell constants: a=15.430(1), b=15.455(1), c=17.996(1)A, alpha=99.30(1) degrees , beta=113.18(1) degrees , gamma=103.04(1) degrees . beta-CD forms dimers comprising two identical monomers that adopt a 'round' conformation stabilized by intramolecular, interglucose O-3(n)cdots, three dots, centeredO-2(n+1) hydrogen bonds. The two beta-CD monomers of form III are isostructural to that of form I in the monoclinic space group P2(1) [Steiner, T.; Mason, S. A.; Saenger, W. J. Am. Chem. Soc.1991, 113, 5676-5687], but exhibit a striking difference from that of form II in the monoclinic space group C2 [Aree, T.; Chaichit, N. Carbohydr. Res.2003, 338, 1581-1589]. The small guest EtOH molecule orients differently in the large beta-CD cavity. In form III, two disordered EtOH molecules are embedded in the beta-CD-dimer cavity. A half occupied EtOH molecule (#1) is located above the O-4 plane of beta-CD #1, whereas another doubly disordered EtOH molecule (#2, #3) is situated at about the middle of the beta-CD-dimer cavity. The three EtOH sites are maintained in positions by making van der Waals contacts to each other and to the surrounding water sites and beta-CD O-3-H group. The EtOH molecules disordered (occupancy 0.3) above the beta-CD O-4 plane in form I and fully occupied beneath the O-4 plane in form II are strongly held in positions by hydrogen bonding with the surrounding water site and beta-CD O-6-H, O-3-H groups. Occurrence of the beta-CD dimer as a structural motif of channel-type packing (form II) and layer-type packing (form III) is attributed to the higher tendency for self aggregation under the moderate acidic conditions. At weak acidic conditions, beta-CD prefers a herringbone mode (form I).     

Linkage and pyranosyl ring twisting in cyclodextrins

Acylated beta-cyclodextrins (beta-CDs) were studied to gain perspective on maltose octapropanoate, the crystal structure of which was reported in the preceding paper in this issue. Acylated beta-CDs are distorted so we looked at other CDs and gained increased understanding of distortion in CDs and possibly, shapes in starch. Classic CDs have six to eight glucose residues in a doughnut shape that is stabilized by a ring of inter-residue O3,,,O2' hydrogen bonds. On a phi,psi energy map for a maltose analog that does not form hydrogen bonds, classic CD linkages have higher energies than structures that are stabilized by the exo-anomeric effect. In distorted beta-CDs, which lack hydrogen bonding, some linkages attain low-energies from the exo-anomeric effect and acyl stacking. Those linkages result in left-handed helical geometry so other linkages are forced by the CD macrocycle to have counter-balancing right-handed character. Permethylated gamma-CDs have two 'flipping' linkages as do some larger native CDs. Flipping linkages allow two left-handed segments to join into a macrocycle, thus avoiding the higher-energy, right-handed forms. Some glucose rings in derivatized beta-CDs have substantial positive twists of the pseudo torsion angle O1-C1...C4-O4, adding right-handed character to balance the left-handed linkages. In substituted gamma-CD, all residues have negative twists, giving extra left-handed character to the short, pseudo-helical segments. In non-macrocyclic molecules the twists ranged from -14 degrees to +2 degrees , averaging -6.1 degrees. In these beta- and gamma-CDs, the twists ranged from -22 degrees to +16 degrees for (4)C(1) rings, and the (O)S(2) ring in acetylated beta-CD has a twist of +34 degrees . Glucose residues in other CDs were less twisted.     

Molecular recognition motifs in cytidinium and 2'-deoxycytidinium salts with composite anions.

In the crystal structures of N3-protonated cytidinium and 2'-deoxycytidinium salts with composite XYn anions capable of accepting hydrogen bonds through their Y atoms, the dominating motif of cytosinium...anion interactions consists of a pair of hydrogen bonds donated from the N3+ -H protonation site and from the exoamino N4-H41 group cis to N3, and accepted by two Y centers of one anion. This multipoint recognition pattern is stable and robust and thus can be classified as a supramolecular synthon. In a broader group of N3-protonated, N1-substituted cytosinium salts with composite anions it occurs with 70% frequency. The C5 side of the cytosine ring mimics the N3+ -H type synthon and shows a propensity to form an analogous motif in which a C5-H5...Y hydrogen bond replaces the strong N3+ -H...Y interaction. Since the C-H...Y bond is much weaker, the secondary motif shows higher deformability and is less frequent (44%).     

Insights into the nature of the hydrogen bonding of *Tyr272 in apo-galactose oxidase

The synthesis and structure of an o-methylthio-phenol-imidazole, 2-(2'-(4'-tert-butyl-6'-methylsulfanyl)-hydroxyphenyl))-4,5-diphenyl-imidazole ((MeS)LH), is reported; X-ray crystallographic studies have shown that (MeS)LH involves an O-H...N(+) hydrogen bond between the phenol and an imidazole nitrogen. (MeS)LH undergoes a reversible, one-electron, oxidation to form the radical cation [(MeS)LH](*)(+) the EPR spectrum of which is remarkably similar to that of (*)Tyr(272) in Cu-free, oxidized, apo-GO. Density Functional Theory calculations, have shown that the proton-transferred (R-O(*)...H-N(+)) form of [(MeS)LH](*)(+) has a spin density distribution--with a substantial delocalization of the unpaired electron spin density onto the ortho sulfur atom--and EPR properties that are in good agreement with those of (*)Tyr(272) in Cu-free, oxidized, apo-GO whereas the non-proton-transferred (R-O(*)(+)-H...N) form does not. The results reported herein are a further demonstration of the influence of hydrogen bonding on the nature and properties of phenoxyl radicals and strongly suggest that the phenoxyl oxygen of (*)Tyr(272) in Cu-free, oxidized, apo-GO is involved in a O(*)...H-O/N hydrogen bond.     

Crystal structure and aqueous solubility of ammonium D-glucarate

Ammonium D-glucarate, NH(4)(C(6)H(9)O(8)) [ammonium D-saccharate, NH(4)-SAC], has been synthesized, and its crystal structure solved by single-crystal X-ray diffraction methods. NH(4)-SAC crystallizes in the monoclinic space group P2(1) (#4) with cell parameters a = 4.8350(4) Angstroms, b = 11.0477(8) Angstroms, c = 16.7268(12) Angstroms, beta = 90.973(1) degrees, V = 894.34(12) Angstroms(3), Z = 3. The structure was refined by full-matrix least-squares on F(2) yielding final R-values (all data) R1 = 0.0353 and R(w)2 = 0.0870. The structure consists of alternating (NH(4))(+) and (C(6)H(11)O(6))(-) layers parallel to the bc plane. An extended network of N-H...O(SAC) and O(SAC)-H...O(SAC) hydrogen bonds provide the 3-D connectivity. The aqueous solubility (S(w)) has been shown to be pH independent at ambient conditions within the range 4.5 < pH < 10 with S(w) = 2.19 M/L, whose value is about a factor of two lower than that of the ammonium isosaccharate analogue.     

Molecular and crystal structures of N-arylglycopyranosylamines formed by reaction between sulfanilamide and D-ribose, D-arabinose and D-mannose

The X-ray crystal structures of three monosaccharide derivatives prepared by the reaction of sulfanilamide with D-ribose, D-arabinose, and D-mannose have been determined. The derivatives are N-(p-sulfamoylphenyl)-alpha-D-ribopyranosylamine (1), N-(p-sulfamoylphenyl)-alpha-D-arabinopyranosylamine (2), and N-(p-sulfamoylphenyl)-beta-D-mannopyranosylamine monohydrate (3). The monosaccharide ring of 1 and 2 has the 1C4 conformation, stabilized in 1 by an intramolecular hydrogen bond from 0-2 to 0-4. Compound 3 has the 4C1 conformation at the monosaccharide ring and the gt conformation at the C-6-O-6 side chain. Occupancy of the water molecule in the crystal of 3 actually examined was 22%. The degree of interaction between sulfamoyl groups and monosaccharide moieties varies from structure to structure. The packing arrangement of 2 involves hydrogen bonding between sulfamoyl groups and monosaccharide hydroxyl groups, but interactions of this type are fewer in 1, and in 3 the hydrogen bonds are either strictly between monosaccharide hydroxyl groups or strictly between sulfamoyl groups. Pairs of hydrogen bonds (two-point contacts) link neighboring molecules in all three structures, between screw-axially related molecules in 1 and 2 and between translationally related molecules in 3. The contact in 3 defined by the O-3-H...O-5 and O-6-H...O-4 hydrogen bonds is found in several other N-aryl-beta-D-mannopyranosylamine crystal structures and is apparently an especially favorable mode of intermolecular interaction in these compounds.     

Crystal structure of beta-cyclodextrin-dimethylsulfoxide inclusion complex

beta-Cyclodextrin (beta-CD) crystallizes from 27% DMSO-water as beta-CD.0.5DMSO.7.35H(2)O in the monoclinic space group P2(1) with unit cell constants: a=15.155(1), b=10.285(1), c=20.906(1) A, beta=109.86(1) degrees. Anisotropic refinement of 888 atomic parameters against 9,127 X-ray diffraction data converged at an R-factor of 0.055. The beta-CD macrocycle adopts a 'round' conformation stabilized by intramolecular, interglucose O-3(n) triplebond O-2(n+1) hydrogen bonds. In the beta-CD cavity, DMSO, water sites W-1, W-3 (occupancies 0.5, 0.25, 0.75) are not located concurrently with the water site W-2 because the interatomic distances to W-2 are too short (1.56-1.75 A). DMSO is placed in the beta-CD cavity such that its S-atom is shifted from the O-4 plane center to the beta-CD O-6-side ca. 0.9 A and the C-S bond which is inclined 13.6 degrees to the beta-CD molecular axis. It is maintained in position by hydrogen bonding to water site W-3 and the O-31-H group. 7.35 water molecules are extensively disordered in 13 positions both inside (W-1-W-4) and outside (W-5-W-13) the beta-CD cavity. They act as hydrogen bonding mediators contributing significantly to the stability of the crystal structure.     

Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: crystal structure of hepta- and octapeptides containing alpha-aminoisobutyric acid

The crystal structures of two helical peptides Boc-Val-Ala-Leu-Aib-Val-ala-Leu-OMe (VALU-7) and Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe (VALU-8) have been determined to a resolution of 1.0 and 0.9 A, respectively. Both the seven and eight residue peptides crystallize with two conformers per asymmetric unit. The VALU-8 conformers are completely helical and differ only at the C-terminus by a sign reversal of the phi, psi angles of the last residue. One of the VALU-7 conformers occurs as a normal alpha-helix, whereas in the other, the N(7)--O(3) alpha-type hydrogen bond is ruptured by the entry of a water molecule (W) into the helix, which in turn makes hydrogen bonds N(7)...W = 2.97 A and W...O(3) = 2.77 A. The other side of the water molecule is surrounded by a hydrophobic pocket. These two conformers give a static representation of a step in a possible helix unwinding or folding process. In the VALU-8 crystal the helices aggregate in a parallel mode, whereas the aggregation is anti-parallel in the VALU-7 crystal. The crystal parameters are VALU-7, P2(1), a = 10.203 (3) A, b = 19.744 (6) A, c = 22.561 (6) A, beta = 96.76 degrees, Z = 4, C38H69N7O10.0.5H2O, R = 6.65% for 3674 reflections observed greater than 3 sigma (F); and VALU-8, P2(1), a = 10.593 (4) A, b = 27.57 (6) A, c = 17.745 (5) A, beta = 95.76 (3) degrees, Z = 4, C42H76N8O11.0.25 CH3OH, R = 6.63% for 4701 reflections observed greater than 3 sigma (F).     

Pulse sequences for detection of NH2···N hydrogen bonds in sheared G⋅A mismatches via remote, non-exchangeable protons

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.     

Study on temperature-dependent changes in hydrogen bonds in cellulose Ibeta by infrared spectroscopy with perturbation-correlation moving-window two-dimensional correlation spectroscopy

Infrared (IR) spectra were measured for cellulose Ibeta prepared from the mantle of Halocynthia roretzi over a temperature range of 30-260 degrees C to explore the temperature-dependent changes in hydrogen bonds (H-bonds) in the crystal. Structural changes at the phase transition temperature of 220 degrees C are elucidated at the functional group level by perturbation-correlation moving-window two-dimensional (PCMW2D) correlation spectroscopy. The PCMW2D correlation spectra show that the intensities of bands arising from O3-H3...O5 and O2-H2...O6 intrachain H-bonds dramatically decrease at 220 degrees C, whereas the intensity changes of bands due to interchain H-bonds are not observed adequately. These results suggest that the phase transition is induced by the dissociation of the O3-H3...O5 and O2-H2...O6 intrachain H-bonds. However, the interchain H-bonds are not so much responsible for the transition directly.     

Molecular and crystal structures of Aib-containing oligopeptides Boc-Leu4-Aib-Leu4-OBzl and Boc-(Leu4-Aib)2-OBzl.

Sample peptides Boc-Leu4-Aib-Leu4-OBzl and Boc-(Leu4-Aib)2-OBzl, were crystallized by the solvent-evaporation method. Both crystals are monoclinic, with space group of P2(1) and Z = 2. The cell parameters are a = 16.580 (7), b = 21.105 (7), c = 11.583 (4) A, and beta = 104.90 (3) degrees (Boc-Leu4-Aib-Leu4-OBzl), and a = 15.247 (9), b = 19.04 (1), c = 16.311 (9) A, and beta = 117.10 (1) degrees [Boc-(Leu4-Aib)2-OBzl]. Crystal structures were solved by the direct method and refined to R values of 0.096 (the former peptide) and 0.112 (the latter). Peptide backbones fold into a right-handed alpha-helix, except for the C-terminal Aib residue in Boc-(Leu4-Aib)2-OBzl. Both peptide molecules are stabilized by six (the former) or seven (the latter) intramolecular (5----1) hydrogen bonds, and arranged in the head-to-tail fashion, which makes an infinite column. In this column, one (the former) or two (the latter) intermolecular hydrogen bonds link the neighboring molecules. In the case of Boc-Leu4-Aib-Leu4-OBzl, the solvent molecule N,N-dimethylformamide was found in the difference Fourier map. There was a hydrogen bond between peptide and solvent molecule. Along the lateral direction, only hydrophobic contacts were observed between adjacent peptide molecules.