Purification and structural properties of the precursors of the globin messenger RNAs

X-ray diffraction data have been obtained from sodium and calcium salts of a proteoglycan rich in chondroitin 4-sulfate isolated from the Swarm rat chondrosarcoma. When sodium is the only countercation associated with the proteoglycan, the oriented polysaccharide chains adopt a 3-fold helical conformation in the solid state and pack in a trigonal unit cell with dimensions a = b = 1.45 nm and c = 2.88 nm. Addition of small amounts of calcium or full conversion of the polyanion from a sodium to a calcium salt form results in a conformational transition to a somewhat more extended 2-fold structure.For the calcium salt X-ray intensity data were used to refine the polysaccharide conformation and packing arrangement in the unit cell. Two antiparallel chains were found to crystallize in an orthorhombic unit cell with space group P22₁2₁ and dimensions a = 0.745 nm, b = 1.781 nm and c = 1.964 nm. The individual helix axes intersect the base plane of the unit cell at (x_f = 0, y_f = 0) and ($\text{x}{}_{\mathrm{f}}\text{= 0, y}{}_{\mathrm{f}}\text{=}\text{1}\text{2}$), and the polyanions are crystallographically equivalent, being related by the symmetry of the space group.The conformation of chondroitin 4-sulfate is stabilized intramolecularly by O.3 … O.5 hydrogen bonds across the β(1 → 4) linkage as well as by OSO^?₃ … Ca²⁺ … ^?OOC co-ordination across the β(1 → 3) linkage. Within the lattice adjacent parallel chains interact through COO^? … Ca²⁺ … ^?OOC bridges, and each calcium co-ordination shell is completed with an additional five water molecules to form a distorted, square antiprism. These water molecules are hydrogen-bonded to neighboring polyanions, and all intermolecular interactions involve water bridges or calcium ion co-ordination.On the basis of the refined packing model and the known structural features of the proteoglycan, models are considered for proteoglycan organization in connective tissue. Consideration of the conformational directing influence and relative abundance of calcium in the intercellular matrix suggest that the secondary structure of chondroitin 4-sulfate in vivo is likely to be similar to the conformation described in this study.     

X-ray fibre diffraction study of conformational changes in hyaluronate induced in the presence of sodium,potassium and calcium cations

Hyaluronate purified from all cations by ion exchange chromatography was introduced to the cations sodium, potassium and calcium in a controlled way. The conformations formed in the presence of these ions were studied as a function of ionic strength, hydrogen ion activity, humidity and temperature using X-ray fibre diffraction. In sodium hyaluronate above pH 4.0 a contracted helix is found which approximates to a four-fold helix with an axial rise per disaccharide of 0.84 nm. There is no requirement for water molecules in the unit cell as the Na⁺ can be coordinate by the hyaluronate chains alone. On crystallizing hyaluronate below pH 4.0 an extended 2-fold helix with an axial rise per disaccharide of 0.98 nm is formed. In the presence of potassium above pH 4.0 a conformation similar, but not identical, to that of sodium was found where the helix backbone is again four-fold with an axial rise per disaccharide h=0.90 nm. To maintain the coordination of the potassium ion, four water molecule/disaccharide are required and on removal of these the conformation is destabilized going to a new helix where n = 4 and h = 0.97 nm. Below pH 4.0 the conformation is a contracted 4-fold helix with h = 0.82 nm. In this structure two antiparallel chains intertwine to form a double helix. The packing of the double helical units is stabilized by water molecules, the unit cell requiring 8 water molecules/disaccharide. Formation of the calcium hyaluronate complex above pH 3.5 yields a three-fold helix with h = 0.95 nm. The requirement for water in the unit cell to maintain full crystallinity is high, at 9 water molecules/disaccharide; however, on removal of this water, though the crystallinity is disrupted, the conformation remains constant. The acid form of calcium-hyaluronate yields an equivalent conformation to that of sodium under the same condition, i.e. a helix with n = 2, h = 0.98 nm. The presence of small quantities of calcium in what are otherwise potassium or sodium solutions of hyaluronate yield the 3-fold conformation for hyaluronate. Thus calcium has an important role to play in deciding the dominating conformation present in hyaluronate. The variety of conformations yielded by the different cations indicates a subtle interaction between hyaluronate and its environment, in which the balance between the cations will control to some degree the interactions between hyaluronate chains and thus affect the mechanical properties of the matrix which they form. The conformations of individual chains are all stabilized in varying degrees by intra-chain hydrogen bonds.     

Isolation of bacteriophage MX4, a generalized transducing phage for Myxococcus xanthus.

The structure of α-chitin has been determined by X-ray diffraction, based on the intensity data from deproteinized lobster tendon. Least-squares refinement shows that adjacent chains have alternating sense (i.e. are antiparallel). In addition, there is a statistical distribution of side-chain orientations, such that all the hydroxyl groups form hydrogen bonds. The unit cell is orthorhombic with dimensions a = 0.474 ± 0.001 nm, b = 1.886 ± 0.002 nm and c = 1.032 ± 0.002 nm (fiber axis); the space group is P2₁2₁2₁ and the cell contains disaccharide sections of the two chains passing through the center and corner of the ab projection. The chains form hydrogen-bonded sheets linked by CO…HN bonds approximately parallel to the a axis, and each chain has an O-3′H…O.5 intramolecular hydrogen bond, similar to that in cellulose. Adjacent chains along the ab diagonal have different conformations for the CH₂OH groups: on one chain these groups form O.6H…O.6′ intermolecular hydrogen bonds to the CH₂OH group on the adjacent chain along the ab diagonal. The latter group is oriented to form an intramolecular O.6′H…O.7 bond to the carboxyl oxygen on the next residue. The results indicate that a statistical mixture of CH₂OH orientations is present, equivalent to half oxygens on each residue, each forming inter- and intramolecular hydrogen bonds. As a result the structure contains two types of amide groups, which differ in their hydrogen bonding, and account for the splitting of the amide I band in the infrared spectrum. The Inability of this chitin polymorph to swell on soaking in water is explained by the extensive intermolecular hydrogen bonding.     

Hyaluronic acid: The role of divalent cations in conformation and packing

X-ray diffraction data typical of helical structures have been obtained from strontium and calcium salts of hyaluronic acid. The data indicate three disaccharides in each helix repeat with an average pitch of 2.84 nm and therefore suggest a conformational similarity with other highly extended hyaluronate polymorphs, the packing of which in crystalline arrays is influenced both by the particular cation involved and by the extent of hydration.Intensity data from a high humidity calcium salt were used in a detailed structure refinement. Six chains were found to pack in a trigonal unit cell with symmetry P3₂12 and dimensions a = b = 2.093 nm, c = 2.830 nm. The polyanion conformation is stabilized by O(3)_AO(5)_B and O(4)_BO(5)_A hydrogen bonds across the (1 → 4) and (1 → 3) linkages, respectively. Both crystallographic and steric considerations imply a non-equivalence of the three disaccharide residues in each helix turn.Adjacent antiparallel chains are tied together through COO^?Ca²⁺^?OOC bridges while the co-ordination of each Ca²⁺ ion is completed by three pairs of dyadically related water molecules. These water molecules are also extensively hydrogen-bonded to the polyanions. Sensitivity of the a and b unit cell dimensions to the ambient relative humidity further supports the conclusion that water of hydration surrounds the polyanions.Consideration of isolation and purification procedures together with elemental analysis for a large number of hyaluronate samples demonstrates the importance of divalent cations, even in small quantities, in inducing extended 3-fold helical conformations. If interactions between chain segments have a role in determining the properties of hyaluronate-containing tissues and fluids then it is likely, because of the abundant calcium which is also present, that any polymer secondary structures usually will be similar to the conformer described in this study.     

Structural components of alginic acid. II. The crystalline structure of poly-alpha-L-guluronic acid. Results of x-ray diffraction and polarized infrared studies

A structural investigation of the marine algal polysaccharide poly-α-L -guluronic acid is described. The molecular chains consist of 1 → 4 diaxially linked L -guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra-molecular O(2)H … O(6)D hydrogen-bond. The X-ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 Å, b (fiber axis) = 8.7 Å, c = 10.7 Å. A structure corresponding to the space group P2₁2₁2₁ is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.     

Hyaluronic acid: a double-helical structure in the presence of potassium at low pH and found also with the cations ammonium, rubidium and caesium.

An anti-parallel double-helical structure is proposed for hyaluronic acid in the presence of the cations K ⁺, NH⁺₄, Rb⁺ and Cs⁺. In particular the crystalline phase containing potassium ions, and in a defined pH range, has been determined and refined against the X-ray diffraction amplitudes. The reflections in the diffraction pattern index on a tetragonal unit cell (a = b = 1.714 nm, c (fibre axis) = 3.28 nm) with observed systematic absences of the form h + k + l = 2n for general hkl reflections and l = 4n (where n is an integer) for 001 reflections. Two double-helical molecules pass through the unit cell at positions ($\text{1}\text{4}\text{,}\text{1}\text{4}\text{, 0}$) and ($\text{3}\text{4}\text{,}\text{3}\text{4}\text{, 0}$) as defined by space group I4₁22. Each chain forms a contracted (axial advance per disaccharide repeat of 0.82 nm) 4-fold left-handed helix which intertwines with a neighbouring chain of opposite polarity about a common axis. Features of the structure are the positioning of the carboxyl group toward the core of the double helix and the presence of hydrophobic and hydrophilic pockets between adjacent double helices. The state of protonation of the hyaluronate molecule is discussed in the light of the infrared evidence. Common physicochemical features of these four cations which promote this particular doublehelical conformation for hyaluronate are considered.     

Structure of the single-stranded polyribonucleotide poly(2'-O-methylcytidylic acid)

X-ray diffraction studies have been made on oriented polycrystalline fibres of poly(2′-O-methylcytidylic acid). A form observed at 66% relative humidity has orthorhombic (P2₁2₁2₁) symmetry and unit cell dimensions a = 1.58 nm, b = 2.16 nm, c = 1.89 nm (fibre repeat). In this form the molecules are singlestranded, 6-fold (6₁) helices with a conformation very similar to that observed for polycytidylic acid. Evidently methylation at O-2′ does not necessarily cause a change in the pucker of the sugar ring. Nor are the intermolecular hydroxyl-hydroxyl hydrogen bonds observed in the polycytidylic acid rhombohedral crystal structure necessary to maintain the 6-fold helical symmetry. However, they may be necessary to maintain the symmetry at very high relative humidities where the polycytidylic acid structure is conserved but poly(2′-O-methylcytidylic acid) undergoes a transition to a form in which the rotation per residue is reduced from 60 ° to a value near 50 °.     

f-Element/crown ether complexes. 26. Crystallization of two hydrated forms of hydrogen bonded complexes of NdCl3·nH2O and 15-crown-5. Crystal structures of [Nd(OH2)9]Cl3·15-crown-5·H2O and [NdCl2(OH2)6]Cl·15-crown-5

When slowly evaporated, the reaction of NdCl₃· nH₂O with 15-crown-5 in a 3:1 mixture of acetonitrile:methanol produces two crystalline hydrates. The decahydrate, [Nd(OH₂)₉]Cl₃·15-crown-5·H₂O, is orthorhombic, P2₁2₁2₁, with (at −150 °C) a = 10.571(4), b = 15.220(7), c = 15.686(7) Å, and D_calc = 1.71 g cm⁻³ for Z = 4. These crystals are stable to the moisture in air. Each Nd is nine-coordinate with tricapped trigonal prismatic geometry. The nine coordinated water molecules are hydrogen bonded to two symmetry related crown ethers, all three chloride ions, and the tenth water molecule. The crown has a total of six hydrogen bonds, four on one side (two to a single oxygen atom) and two on the other. This ether exhibits conformational disorder. The hexahydrate, [NdCl₂(OH₂)₆]Cl·15-crown-5 is deliquescent, dissolving in air and recrystallizing as [NdCl₂(OH₂)₆]Cl. Crystals of this complex are monoclinic, P2₁/n, with (at 20 °C) a = 9.821(3), b = 16.978(9), c = 12.849(8) Å, β = 94.06(5)°, and D_calc = 1.80 g cm⁻³ for Z = 4. The Nd atom exists in a distorted dodecahedral geometry with one chlorine in an A site and one in a B site. The coordinated chlorine atoms accept hydrogen bonds producing polymeric zigzag hydrogen bonded chains along c. The third noncoordinated chloride ion accepts four hydrogen bonds, three from one formula unit and one from a second formula unit related by a unit translation along a. The crown ethers accept five hydrogen bonds, two on one side, and three on the other, thus separating the zigzag chains along b.     

Proton translocation in hydrogen bonds with large proton polarizability formed between a Schiff base and phenols

OH…N ? O^?…H⁺N hydrogen bonds formed between N-all-transretinylidene butylamine (Schiff base) and phenols (1:1) are studied by IR spectroscopy. It is shown that both proton limiting structures of these hydrogen bonds have the same weight with Δ pK_a (50%) = (pK_a protonated Schiff base minus pK_a phenol) = 5.5. With the largely symmetrical systems, continua demonstrate that these hydrogen bonds show great proton polarizability. In the Schiff base + tyrosine system in a non-polar solvent the residence time of the proton at the tyrosine residue is much larger than that at the Schiff base. In CH₂CCl₂ these hydrogen bonds show, however, still proton polarizability, i.e., the position of the proton transfer equilibrium OH…N ? O^?…H⁺N is shifted to and fro as function of the nature of the environment of this hydrogen bond. Consequences regarding bacteriorhodopsin are discussed.     

Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids

A survey has been made, by using computer methods, of the types of helices which polypeptide chains can form, taking into account steric requirements and intramolecular hydrogen-bonding interactions. The influence on these two requirements, of small variations in the bond angles of the peptide residues, or of small changes in the overall dimensions of the helix (pitch and residues per turn), have been assessed for the special case of the α-helix. Criteria for the formation of acceptable hydrogen bonds have also been applied to helices of other types, viz., the 3, γ^?, ω^?, and π-helices. It was shown that the N? H … O and H … O? C angles in hydrogen bonds are sensitive to changes in either the NC^αC′ bond angle or in the rotational angles about the N? C^α and C^α? C′ bonds. However, the variants of the α-helix observed experimentally in myoglobin can all be constructed without distortion of the hydrogen bonds. For α-helices, the steric and hydrogen bonding requirements are more easily fulfilled with an NC^αC′ bond angle of 111°, rather than 109.5°. The decreased stability observed for the left-handed α-helix relative to the right-handed one for L -amino acids is due essentially only to interactions of the C^β atom of the side chains with atoms in adjacent peptide units in the backbone, and interactions with atoms in adjacent turns of the helical backbone are not significantly different in the two helices. Restrictions in the freedom of rotation of bulky side chains may have significant kinetic effects during the formation of the α-helix from the “random coil” state.     

Hydration effect on proton transfer in melamine−cyanuric acid complex

Self-assembly of melamine-cyanuric acid (MC) leads to urinary tract calculi and renal failure. The hydration effects on molecular geometry, the IR spectra, the frontier molecular orbital, the energy barrier of proton transfer (PT), as well as the stability of MC were explored by density functional theory (DFT) calculations. The intramolecular PT breaks the big π-conjugated ring of melamine or converts the p-π conjugation (:N-C'=O) to π-π conjugation (O=C-N=C') of cyanuric acid. The intermolecular PT varies the coupling between melamine and cyanuric acid from pure hydrogen bonds (N_a…HN_d and NH…O) to the cooperation of cation…anion electrostatic interaction (N_aH⁺…N_d ^-) and two NH…O hydrogen bonds. Distinct IR spectra shifts occur for N_a…HN_d stretching mode upon PT, i.e., blue-shift upon intramolecular PT and red-shift upon intermolecular PT. It is expected that the PT would inhibit the generation of rosette-like structure or one-dimensional tape conformer for the MC complexes. Hydration obviously effects the local geometric structure around the water binding site, as well as the IR spectra of NH…O and N…HN hydrogen bonds. Hydration decreases the intramolecular PT barrier from ~45 kcal mol^-1 in anhydrous complex to ~11.5 kcal mol^-1 in trihydrated clusters. While, the hydration effects on intermolecular PT barrier is slight. The relative stability of MC varies slightly by hydration due to the strong hydrogen bond interaction between melamine and cyanuric acid fragments.

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Graphical Abstract Hydration effect on proton transfer in melamine?cyanuric acid complex

     

Double coned inverse sandwich complexes [M-(η4-C4H4)-M′] of Gr-IA and Gr-IIA Metals: theoretical study of electronic of structure and second hyperpolarizability

Molecular interaction between dioxane and methanol involves certain polar and nonpolar bonding to form a one to one complex. Interatomic distances between hydrogen and oxygen within 3 Å have been considered as hydrogen bonding. Optimizations of the structures of dioxane-methanol complexes were carried out considering any spatial orientation of a methanol molecule around a chair/boat/twisted-boat conformation of dioxane. From 45 different orientations of dioxane and water, 23 different structures with different local minima were obtained and the structural characteristics like interatomic distances, bond angles, dihedral angles, dipole moment of each complex were discussed. The most stable structure, i.e., with minimum heat of formation is found to have a chair form dioxane, one O-H…O, and two C-H…O hydrogen bonds. In general, the O-H…O hydrogen bonds have an average distance of 1.8 Å while C-H…O bonds have 2.6 Å. The binding energy of the dioxane-methanol complex is found to be a linear function of number of O-H…O and C-H…O bonds, and hydrogen bond length. Graphical Abstract

Sixteen orientations of methanol around dioxane converge to six local minima including the global minima with one H-O…H and two C-H…O hydrogen bonds.     

Crystal Structure of 2′-Deoxycytidine Hemidihydrogenphosphate Reveals C+·C Base Pairs and Tight,Hydrogen-Bonded (H2PO4 −)∞ Columns (1)

Abstract

2′-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6₂ with α=25.839(3), c = 12.529(1) Å. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2′-deoxycytidine dimers and two H₂PO₄ ^? anions. The C⁺·C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3)…N(3) bonds being 2.850(7) and 2.884(5) Å. The conformations of the four nucleosides fall in the same category (sugar puckers 2·-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H₂PO₄ ^? anions are located on twofold axes and form two types of tight columns with P…P separations about 4.18 Å The neighboring units along a column are linked via two very short O…H…O hydrogen bonds (O…O about 2.49 Å) leading to effective equalization of the P-O bonds. The base pairs of the two dC⁺·dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through 0(5′)…O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H…O-P and 0(3′)-H…O-P] to the phosphate groups.     

Real space refinement of neutron diffraction data from sperm whale carbonmonoxymyoglobin

Neutron diffraction data from crystals of sperm whale carbonmonoxymyoglobin have been refined by the real space refinement technique. Estimates of the neutron occupancies at the end of the refinement show that the mean for each atom type (including hydrogen and deuterium) is close to the expected value and has a standard deviation from the mean of about 5%. Mean neutron occupancies of main-chain atoms involved in deuterium bonds versus those not involved in deuterium bonds demonstrate that the hydrogen/deuterium exchange of the latter group is higher. The oxygen and deuterium co-ordinates for 40 water molecules have been determined: 27 of these water molecules were involved in bridges between protein atoms, and nine were involved in deuterium bonds with main-chain atoms. The deuterium-bond angles in helical regions show significant deviations from linearity. The mean ND … O angle was 154(3) °² and the mean CO … D angle was 145(3) °.     

The crystallochemistry of tetracyanocomplexes. The crystal and molecular structures of tris(1,2-diaminoethane)zinc(II) tetracyanoniccolate(II) monohydrate and tris(1,2-diaminoethane)zinc(II) tetracyanoniccolate(II)

C₁₀H₂₆N₁₀ONiZn, tris(1,2-diaminoethane) zinc(II) tetrakis(cyano)niccolate(II) monohydrate (I), orthorhombic, Pbca, a = 1.1680(4), b = 1.5844(3), c = 1.9981(6) nm, Z = 8 d(meas) = 1.54, d(calc) = 1.53 g cm^?3. C₁₀H₂₄N₁₀NiZn, tris(1,2-diaminoethane) zinc(II) terakis(cyano)niccolate(II), (II), monoclinic, P2₁/n, a = 0.7957(2), b = 1.5170(5), c = 1.4932(4) nm, β = 96.41(2)°, Z = 4, d(meas) = 1.49, d(calc) = 1.51 g cm^?3. Both the structures (I) and (II) have been solved by the heavy atom method and refined by full-matrix least-squares to R(I) = 0.086 for 1890 independent reflections and R(II) = 0.058 for 1689 independent reflections, respectively. In the case of (II) the superlattice structure problem was solved. The crystal structure of (I) consists of [Zn(en)₃]²⁺ cations, [Ni(CN)₄]^2? anions and water molecules. Two of the cyano groups in trans positions are bonded to water molecules by hydrogen bonds, the distances CN?O being 0.289 and 0.291 nm, respectively. The crystal structure of (II) is constituted by [Zn(en)₃]²⁺ cations and [Ni(CN)₄]^2? anions.     

Structure of a cellulose II-hydrazine complex

The structure of a crystalline cellulose II-hydrazine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose-solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x-ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked-atom least-squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen-bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an N? H…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.     

Crystal and molecular structure of V-anhydrous amylose

The conformation and crystalline packing of V-anhydrous amylose has been investigated by a combination of linked atom model building and X-ray diffraction analysis. The unit cell, the P2₁2₁2₁ space group, the left-handed sixfold helical conformation with all O(6) in gt rotational positions, and the intrahelical O(2)---O(3) and O(2)---O(6) hydrogen bonds are substantially in agreement with previous studies. A new model for packing of the chains in the unit cell and the presence of crystallographic water is proposed. Packing appears to be stabilized by corner-to-center chain O(2)---O(2) hydrogen bonds. The nature of the transition from the amylose–DMSO complex to V_a-amylose was considered and it is shown that the transition involves translation of the amylose chains parallel to the a and b unit cell axes with only slight changes in the orientation of the helix. No significant conformational changes result from the transition.     

Proton polarizability and proton transfer in histidine-phosphate hydrogen bonds as a function of cations present: ir investigations

(L -His)_n- dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ? O^?…H⁺N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li⁺ to the K⁺ system. In the K⁺?system, His-P_i-P_i chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ? O^?…H^?N equilibria are determined from ir bands. With the Li⁺ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na⁺ system (41%), and amounts to only 32% with the K⁺ system. With the increasing degree of hydration the removal of the degeneracy of ν_as?PO^2?₃ vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ? O^?…H⁺N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.     

The crystal structure of 2-deoxy-β-d-arabino-hexopyranose at −150°

2-Deoxy-β-d-arabino-hexopyranose, C₆H₁₂O₅, is orthorhombic, P2₁2₁2₁, with cell dimensions at ?150° [20°], a = 6.484(2) [6.510(3)], b = 10.364(2) [10.427(4)], c = 11.134(3) [11.153(5)] Å, V = 748.2 [757.1] ų, Z = 4, D_x = 1.457 [1.440], and D_m = [1.455] g.cm^?3. The intensities of 1269 reflections were measured by using MoKα radiation. The structure was solved by direct methods, and refined by full-matrix least-squares, with anisotropic, thermal parameters for the carbon and oxygen atoms, and isotropic parameters for the hydrogen atoms. The pyranose has the ⁴C₁(d) conformation, with puckering parameters Q = 0.563 Å, θ = 3.9°, and ? = 350.3°. The departure from ideality is very small, and less than that in β-d-glucopyranose, Q = 0.584 Å and θ = 6.9°. The β-glycosidic, CO bond is short, 1.383(4) Å, and the OCOH torsion angle is ?87°, consistent with the anomeric effect. The hydrogen-bonding scheme consists of infinite chains, with side chains terminating at a ring-oxygen atom.     

Conformations and interactions of pectins: I. X-ray diffraction analyses of sodium pectate in neutral and acidified forms

X-ray diffraction patterns of uniaxially oriented, polycrystalline fibers of neutral sodium pectate can be indexed on the basis of an orthogonal unit cell with dimensions a = 0.84 nm, b = 1.43 nm, c (fiber axis) = 1.34 nm, which contains trisaccharide fragments of two polygalacturonic chains of opposite sense. The polysaccharide chains have 3₁ screw symmetry but are arranged in a lattice that has space group symmetry P2₁ (unique axis b). There are three sodium ions in each crystal asymmetric unit. They are all octahedrally co-ordinated to oxygen atoms of the galacturonan chains or of water molecules. Every oxygen atom is involved also in at least one hydrogen bond. Sodium pectate can be partially converted to pectic acid whose polysaccharide chains preserve the 3₁ pectate conformation, are packed in an orthogonal unit cell also with P2₁ symmetry but with quite different dimensions a = 0.99 nm, b (unique 2₁ axis) = 1.23 nm, c (fiber axis) = 1.33 nm. In this lattice, the polygalacturonic acid chains form corrugated sheets in which alternate molecules have opposite sense and are extensively hydrogen-bonded through their carboxyl groups.