Unusual structural features of a siloxane

Crystals of the R, S diastereoisomer of [Cp(CO)₂-FeSiCH₃F]₂O are monoclinic, space group P2₁/c (No. 14), with a = 846.0(3) [836.4(1)], b = 768.0(3) [757.1(1)], c = 1548.5(4) [1522.3(2)] pro, β = 97.34(3)° [97.47(3)°] at 300 K [120 K] with Z = 2. Even at 120 K the SiOSi fragment is found to be strictly linear due to crystallographically imposed symmetry. To explain the unusual electron distribution derived from the X-ray data collected, several types of possible disorders are discussed, none of which leads to a satisfying explanation. Retaining the C_i symmetry (linear SiOSi fragment in the final model) the important bond lengths are FeSi 226.7(1) [226.5(1)] pm, SiF 160.9(2) [161.8(2)] pm, SiO 160.3(1) [161.1(1)] pm, SiC 185.0(3) [185.6(3)] pm. The electronic features of this compound were probed via molecular orbital calculations of the extended Hückel type. It was found that the lone pairs on the siloxane oxygen were tipped away from cylindrical symmetry. The tipping was directed toward the fluorine substituents on the silicon atoms and away from the CpFe(CO)₂ units. A pertubational approach was utilized to rationalize this effect.     

Application of ab initio molecular-orbital calculations to the structural moieties of carbohydrates. Part VI

Ab initio RHF/4–31G molecular-orbital calculations have been conducted on methoxymethyl formate and methoxymethyl acetate as models for examining the anomeric effect and stereochemistry of 1-O-acetylglycopyranoses. The results indicate that, as with the methyl glycopyranosides, the α-⁴C₁(D) configurations are more stable than the β-⁴C₁(D), except that the energy difference is more dependent on the disposition about the glycosidic bond. The lowest-energy conformations occur with glycosidic torsion-angles of ?  180°, where the anomeric energy is about 4 kcal/mol. There is a secondary energy-minimum at ?  90°, for which the anomeric energy is less, about 2 kcal/mol. This orientation corresponds to the conformation most commonly observed in the crystal structures of peracetylated glycopyranoses. Small differences in the CO single-bond lengths, which are observed experimentally in both the α and β anomers, are reproduced by the theoretical calculations.     

The strucrure of trans-O-β-D-glucopyranosyl methyl acetoacetate,and the interpretation of its optical rotations

Crystal-structure determination of trans-O-β-D-glucopyranosyl methyl acetoacetate, C₁₁H₁₈O₈, m.p. 186°, confirmed the trans orientation deduced previously from physical properties. The conformation of the D-glucopyranosyl group is ⁴C₁, although the most symmetrical chair-conformer is actually ³C_o. The glycosidic link is sc, with a CO anomeric bond of 1.428 Å (142.8 pm), i.e. longer than is normal in methyl β-glycopyranosides. All of the hydrogen bonding is intermolecular. The unusual optical rotations in solution can be interpreted in terms of rotameric populations that are derived from the solid-state conformers and are stabilized by intramolecular or solvent hydrogen-bonding.     

31P n.m.r. studies of complexes of NADPH and NADP+ with Escherichia coli dihydrofolate reductase

We have measured the ³¹P n.m.r. spectra of NADP⁺ and NADPH in their binary complexes with Escherichia coli dihydrofolate reductase and in ternary complexes with the enzyme and folate or methotrexate. The ³¹P chemical shift of the 2′ phosphate group is the same in all complexes; its value indicates that it is binding in the dianionic state and its pH independence suggests that it is interacting strongly with cationic residue(s) on the enzyme. Similar behaviour has been noted previously for the complexes with the Lactobacillus casei enzyme although the ³¹P shift is somewhat different in this complex, possibly due to an interaction between the 2′ phosphate group and His 64 which is not conserved in the E. coli enzyme. For the coenzyme complexes with both enzymes ³¹POC₂¹H_2′ spin-spin interactions were detected (7.5–7.8 Hz) on the 2′ phosphate resonances, indicating a POC₂H_2′ dihedral angle of 30 or 330 : this is in good agreement with the value of 330° measured in crystallographic studies¹ (Matthews et al., 1978) on the L. casei enzyme. NADPH-MTX complex. The pyrophosphate resonances are shifted to different extents in the various complexes and there is evidence that there is more OPO bond angle distortion in the E. coli enzyme complexes than in those with the L. casei enzyme. The effects of ³¹POC₅¹H_5′ spin coupling were detected on one pyrophosphate resonance and indicate that the POC₅H_5′ torsion angle has changed by at least ～30° on binding to the E. coli enzyme: this is considerably less than the distortion (～50°) observed previously in the L. casei enzyme complex.     

Ab initio refinement of an orbital-centred force field for biomolecules: Orbital localisation and parameterisation of the COP(O2)OC fragment of nucleotides

Classical calculations of conformational potential surfaces, based on simple analytical functions of the interactions between atomic centres, continue to be of considerable importance. However, it has become apparent that not all interactions of importance can be included as interactions between positions which are effectively those of the nuclei. Thus, there has been recent interest in including lone pairs and special functions for interactions involving excited state orbitals. A particularly interesting test case is the COP(O₂)OC fragment of the nucleic acid backbone, which would seem to be the most flexible “hinge point” of polynucleotides when the classical type of calculation is carried out. In contrast, ab initio quantum mechanical calculations show the conformational space of this fragment to be much more restricted. The disagreement is such that it calls into doubt the validity of the bench-top modelling of nucleotide behaviour. In the following study, a variety of ab initio calculations are carried out to localise, in an objective manner, non-core orbitals. Coulombic interactions are introduced between these localised orbitals, with charge parameters optimised to reproduce the total ab initio potential surface. The results imply an interesting disgreement with other authors, concerning the importance of lone pair interactions in the nucleotide backbone, and the origins of this disagreement are analysed in some detail.     

Crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside. A pyranoside system close to a skew-boat conformation

The crystal structure of methyl 2,6-dichloro-2,6-dideoxy-3,4-O-isopropylidene-α-D-altropyranoside (1) has been determined by X-ray diffraction. The compound crystallizes in the orthorhombic system, space group P2₁2₁2₁, with unit-cell dimensions a  7.932, b  8.133, and c  20.447 Å. The structure was solved by the heavy-atom method and refined by the least-squares technique to an R value of 0.047 by using 736 intensities measured on a diffractometer. The pyranoside ring is close to a skew-boat conformation, with C-2 and C-5 being maximally displaced from the least-squares plane through the remaining four atoms. The H-1H-2 dihedral angle of  158° is in agreement with the J_1,2 value of 4.5 Hz. Thus the solid-state conformation appears to correspond with the conformation in solution. The dioxolane ring is in a twist form, with O-4 and, C-8 puckered on opposite sides of the plane of the other ring atoms. The pyranose-ring substituents are in equatorial and pseudoequatorial orientations. The hydrogen atoms at C-3 and C-4 are in a cis arrangement. The orientations of both the methoxyl group and the chloromethyl group with respect to the ring are gauche—trans. The exocyclic anomeric C-1O-1 bond-distance (1.39 Å) is the shortest CO bond in the structure. The intracyclic CO bonds are significantly different, C-1O-5 being less than C-5O-5.     

Comparative structural studies of the first row early transition metal(III) chloride tetrahydrofuran solvates

Two compounds of empirical formula MCl₃- (THF)₃, M = V and Cr, have been characterized by single crystal X-ray studies. The VCl₃(THF)₃ molecule, which has a mer octahedral stereochemistry, crystallizes in the monoclinic space group P2₁/c with a= 8.847(2),b= 12.861(5),c= 15.134(3) Å, β = 91.94(2)°, V = 1721(1) ų and Z = 4. The V-Ci(1) and V-CI(2) distances have a mean value of 2.330 [3] Å while V-CI(3) = 2.297(2) Å, The VO(1) and VO(2) distances have a mean value of 2.061[8] Å while V-O(3) = 2.102(3) Å cis ClVCl angles average 92.0[5]° and cis OVO angles average 86.2[2]° . The isostmctural complex, CrCl₃(THF)₃, has a crystal structure made up of discrete octahedral mer-CrCl₃(THF)₃ molecules with the following unit cell dimensions (space group P2₁/c): a = 8.715(1), b= 12.786(3), c = 15.122(3) Å, β = 92.15(1)°, V = 1684(1) ų and Z = 4. The CrCl(1) and CrCl(2) distances have a mean value of 2.310131 Å while CrCl(3) = 2.283(2) Å. The CrO(1) and CrO(2) distances have a mean value of 2.0101171 Å while CrO(3) = 2.077(4) Å. cis ClCrCl angles average 90.9[4]° and cis OCrO angles average 86.1 [2]°. The structures of these two octahedral complexes and those previously reported for ScCl₃(THF)₃ and TiCl₃(THF)₃ are compared and certain general trends are discussed.     

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.     

Preparation and crystal structure of bis(acetato)(trans-1,2-diaminocyclohexane)platinum(II)

The structure of the complex [Pt(trans-1,2-di- aminocyclohexane) (acetate)₂]·H₂O has been determined by X-ray diffraction. This racemic compound is orthorhombic, space group Aba2, a = 20.813(9), b = 7.926(5), c = 17.296(8) Å, Z = 8. The structure was refined on 1214 nonzero Cu Kα reflections to R = 0.028. The square planar environment of Pt includes the amino groups of the diamine in cis positions and oxygens from two monodentate acetates. The PtN and PtO distances average 2.00(3) and 2.02(3) Å, respectively. The bite of the diamine ligand imposes a NPtN angle of 85(1)°, whereas the small OPtO angle of 85(1)° probably results from packing effects. The average plane through the puckered cyclohexyl ring makes an angle of 19° with the PtN₂O₂ plane. The molecules are stacked by pairs along the b axis. The two molecules of each pair are 180° apart about the stacking axis, and form altogether four NH···O hydrogen bonds.     

6-Azauridine, a nucleoside with unusual ribose conformation. The molecular and crystal structure

The cytostatic analogue ribo-6-azauridine crystallizes in the orthorhombic space group P2₁2₁2₁ with eight molecules per unit cell of dimensions $\text{a = 20.230, b = 7.709, c = 12.863}\text{A}\text{?}$. A trial structure was obtained by direct methods. Least-squares refinement of co-ordinates and anisotropic thermal parameters based on 1998 reflections measured on a four-circle diffractometer led to a discrepancy index R = 4.0%. Like uridine, 6-azauridine has the anti conformation about the glycosidic bond and a C(3′)-endo sugar pucker. Unlike uridine, it exhibits a close approach of N(6) to C(2′) at only 2.814 and 2.844 Å in the two independent molecules, and a C(5′)(5′) bond that is gauche to C(4′)O(1′) but trans to C(4′)C(3′); this conformation about a C(4′)C(5′) bond has never been observed before for C(3′)-endo puckered riboses in the crystalline state. The crystal structure displays a pseudo-A face centering and very similar conformational parameters for the two independent molecules. Every OH and NH group in the structure serves as a proton donor in a hydrogen bond, including an unusual N(3)—H(3) … O(1′) link. Molecular orbital calculations by the extended Hückel method indicate that from uridine to 6-azauridine the net charge changes sign at ring positions 5 and 6 and disappears at 1.     

Synthesis of 4,5-dideoxy-4-C-[(R,S)-phenylphosphinyl]-d-ribo- and l-lyxo-furanose and their 1,2,3-triacetates

2,3-O-Isopropylidene-d-ribose diethyl dithioacetal, prepared from d-ribose, was converted in three steps into the corresponding dimethyl acetal, which was monotosylated at O-5, and the ester oxidized at C-4 with pyridinium chlorochromate; addition of methyl phenylphosphinate to the resulting pentos-4-ulose derivative then provided (4R,S)-4,5-anhydro-2,3-O-isopropylidene-4-C-[(R,S)-(methoxy)phenylphosphinyl]-d-erythro-pentose dimethyl acetal. Hydrogenation of this compound in the presence of Raney Ni, followed by reduction with SDMA, hydrolysis, and acetylation, yielded the title compounds (seven kinds), the structures of which were established on the basis of their 400-MHz, ¹H-n.m.r. and mass spectra. A general dependence of the ²J_PH and ³J_PH values on the OPCH and PCCH dihedral angles provided an effective method for the assignment of the configurations and conformations of these 4-deoxy-4-phosphinyl-pentofuranoses.     

Synthesis and structure of an oxidation product of hemiporphyrazinatoiron(II): Monoaquo-μ-oxo-bis(hemiporphyrazinato)iron(III). A linear μ-oxo dimer containing six- and five-coordinated iron atoms

The interaction between dioxygen and wer N-base solutions of Fe(II) hemiporphyrazine (Fehp) leads to the title compound, which is a high-spin antiferromagnetically coupled iron(III) complex. The crystal and molecular structure has been determined by X-rays. The unit cell is the tetragonal space group P4/ncc, with a=b=19.083(5) and c=23.509(5) Å. 2141 unique observed reflections were used in the analysis, and the final conventional R is 0.059. The structure consists of Fe(III)hp μ-oxo dimers having strictly linear FeOFe units and a nearly eclipsed internal configuration. This is the first observation of the formation of a mono-adduct in μ-oxo dimer via axial coordination of a H₂O molecule. The resulting asymmetric dimer, H₂OFeAhpOFeBhp contains a six-coordinated Fe atom (FeA) lying in the plane of the four Ns of the macrocycle. The second Fe atom (FeB) is five-coordinated and lies outside of the coordination plane by 0.45 Å. The FeO distances are: FeAO=1.782(7) Å and FeBO=1.739(7) Å. The axial coordination of the water (FeAO_w=2.210(9) Å) seems weak, probably due to the labilising trans influence of the μ-oxo ligand. The dimers are paired coaxially to form tetramers, which are in turn connected via a two- dimensional net of hydrogen bonds. The structural results are correlated with spectroscopic, thermogravimetric and magnetic properties.     

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.     

Synthesis,characterization and crystal structure of 2-dimethylacetal-4-chloro-6-formylphenol and aquabis(2-dimethylacetal-4-chloro-6-formylphenolato)dioxouranium(VI)

The ligand 2-dimethylacetal-4-chloro-6-formylphenol, H(ALAC), prepared by boiling 2,6-diformyl-4-chlorophenol, H(DIAL), in methanol, was reacted with uranyl acetate to obtain the complex [UO₂(ALAC)₂(H₂O)]. The ligand and the uranyl complex were characterized by X-ray crystallography, infrared, ¹H NMR and electronic spectroscopy. Thermogravimetric and mass spectrometry data are also reported. In acid media H(ALAC) transforms easily into H(DIAL). H(ALAC) is monoclinic, P2₁/n, with a=13.951(5), b=7.902(5), c=9.465(5) Å, β= 91.33(3)°. The structure was refined to R=3.9%, based on 1657 observed reflexions. [UO₂(ALAC)₂(H₂O)] is tetragonal, P4₃2₁2, with a=11.147(5) and c=19.150(4) Å. The structure was refined to R=4.0%, based on 2938 observed reflexions. Four ligand oxygens and one water molecule are equatorially bonded to the uranyl group in this compound. Uranium and water oxygen lie in special positions on a crystallographic twofold axis so that the two halves of this molecule are symmetrically related. Selected bond distances for [UO₂(ALAC)₂(H₂O)] are: UO (charged) 2.28(2) Å, UO (neutral) 2.45(2) Å, UO (uranyl) 1.77(2) Å, UO (water) 2.44(4) Å.     

Conformation of 2,3-diformylglycerol, a model compound of membrane phospholipids

The conformations of 2,3-diformylglycerol, a model compound of the diacylglycerol portion of phospholipids, were analyzed both by the classical potential function method and by the INDO molecular orbital method. The results suggest that in membranes, the conformation of the diacylglycerol portion of phospholipids is such that the two ester planes of the β- and γ-hydrocarbon chains stack in an antiparallel way with the dihedral angles β′{C(3)C(2)O(21)C(21)} ? 270° and γ₁{C(2)C(3)O(31)C(31)} ? 270°.     

The preparation and electrochemistry of cysteine-ester oxovanadium(IV) complexes

An improved synthesis of VO(CysOCH₃)₂, (CysOCH₃  the anion of cysteine methyl ester), is reported, as is an analogous preparation of VO(CysOCH₂CH₃)₂, (CysOCH₂CH₃  the anion of cysteine ethyl ester). These are the first two examples of isolated vanadium-cysteine compounds. The oxidation of VO(CysOCH₃)₂ in DMSO is a reversible one electron change at 0.24 V versus SCE followed by a rapid chemical reaction which produces a stable vanadium(V) species. This species is reduced back to the vanadium(IV) complex at −1.30 V. The electrochemistry of VO(Cys-OCH₂CH₃)₂ is nearly identical to that of the methyl ester compound.     

Synthesis and x-ray structure of a Hg(II) complex with adenine N(1)-oxide. A model for mercury binding to DNA

The synthesis and crystal structure of the adenine N(1)-oxide complex with mercury(II) chloride, (C₅H₅N₅O)HgCl₂ are reported. Crystals of the coordination compound belong to the monoclinic system, space group P2₁/n with the following primary crystallographic data: a = 6.685(1) Å, b = 11.798(2) Å, c = 10.155(1) Å, β = 100.22(1)°, V = 906.04 ų, Z = 4. The structure was elucidated by conventional Patterson and Fourier methods and refined by the full matrix least-squares technique on the basis of 1977 observed reflections to an R value of 0.074. The basic unit of the structure is a dimer, with a centre of symmetry, consisting of two HgCl₂ moieties and two adenine N(1)-oxide ligands. A polymeric structure results from the bridging interactions of chloride ions. Adenine N(1)-oxide acts as a bidentate bridging ligand, coordinating through N(7) and O(1). The coordination geometry around the mercury ion is a distorted square pyramid with N(7) and three chlorines (two of which are centro-symmetrically related) forming the square plane and O(1) occupying the axial position. Hg also interacts indirectly with N(6) through a Cl

HN hydrogen bond. Principal intracomplex geometrical parameters are as follows: HgN(7) = 2.61(1) Å, HgO(1) = 2.55(1) Å, HgCl(1) = 2.330(3) Å, HgCl(2) = 2.318(3) Å, HgCl(2′) = 3.347(3) Å. The cis angles range from 77.5° to 107.9° and the two trans angles are 155.5° and 163.1°. The centro-symmetrically related bases overlap partially and pack at a distance of 3.2 Å. The glide-related bases are linked by a hydrogen bond, N(9)H

O(1) and are inclined to one another by 109.7°. The results are compared with those derived from spectroscopic and other physicochemical studies on metal interaction with adenine N(1)-oxide. Based on the present structural observations and earlier experimental results a possible mechanism is proposed for mercury interaction with DNA.