The structure and antiviral activity of ribavirin analogs. I. Molecular and crystal structure of 1-(2-hydroxyethoxymethyl)-1,2,4-triazole-5-carboxamide

The crystal and molecular structures of the antiviral compound 1-(2-hydroxyethoxymethyl)-1,2,4-triazole-5-carboxamide has been determined by the X-ray diffraction method. The space group is P2i/c, unit cell parameters a = 4,381, b = 18,679, c = 10,776 A, beta = 107,40 degrees, Z = 4. The structure was solved by the direct method and refined by a full-matrix least-squares procedure to R = 4.9%. Two planar groups of atoms can be distinguished in the molecule. The first group involves the atoms of triazole ring, C6, and C1', the second one contains C5, C6, O6 and N6 atoms. The angle between these planes is 5.6 degrees. The carboxyamide group is rotated by 180 degrees in comparison with this group in ribavirin. That is why the intramolecular hydrogen bond C1'-H1'. 1...O6 can form. Torsion angle O5'-C5'-C4'-O4' is 73.9 degrees and it corresponds to gauche-rotamer. The conformation about O4'-C4' bond is trans. The C1'-C4' bond is approximately perpendicular to the aglycone.     

DFT studies of the disaccharide, alpha-maltose: relaxed isopotential maps

The disaccharide, alpha-maltose, forms the molecular basis for the analysis of the structure of starch, and determining the conformational energy landscape as the molecule oscillates around the glycosidic bonds is of importance. Thus, it is of interest to determine, using density functionals and a medium size basis set, a relaxed isopotential contour map plotted as a function of the phi(H) and psi(H) dihedral angles. The technical aspects include the method of choosing the starting conformations, the choice of scanning step size, the method of constraining the specific dihedral angles, and the fitting of data to obtain well defined contour maps. Maps were calculated at the B3LYP/6-31+G( *) level of theory in 5 degrees intervals around the (phi(H),psi(H))=(0 degrees ,0 degrees ) position, out to approximately +/-30 degrees or greater, for gg-gg'-c, gg-gg'-r, gt-gt'-c, gt-gt'-r, tg-tg'-c, and tg-tg'-r conformers, as well as one-split gg(c)-gg'(r) conformer. The results show that the preferred conformation of alpha-maltose in vacuo depends strongly upon the hydroxyl group orientations ('c'/'r'), but the energy landscape moving away from the minimum-energy position is generally shallow and transitions between conformational positions can occur without the addition of significant energy. Mapped deviations of selected parameters such as the dipole moment; the C1-O1-C4', H1-C1-O1, and H4'-C4'-O1 bond angles; and deviations in hydroxymethyl rotamers, O5-C5-C6-O6, O5'-C5'-C6'-O6', C5-C6-O6-H, and C5'-C6'-O6'-H', are presented. These allow visualization of the structural and energetic changes that occur upon rotation about the glycosidic bonds. Interactions across the bridge are visualized by deviations in H(O2)...O3', H(O3')...O2, and H1...H4' distances and the H(O2)-O2-C2-C1 and H'(O3')-O3'-C3'-C4' hydroxyl dihedral angles.     

The structure and antiviral activity of ribavirin analogs. III. Molecular and crystal structure of 1-(2-hydroxyethoxymethyl)-1,2,4-triazole-carboxamide

The crystal and molecular structure of a ribavirin acyclic analogue, 1-(2-hydroxyethoxymethyl)-1,2,4-triazole-3-carboxamide, has been determined by X-ray diffraction method. The space group is P1, unit cell parameters: a = 5,237, b = 6,960, c = 11,483 A, alpha = 93,89, beta = 97,43, gamma = 94,26 degrees; Z = 2. The structure was solved by the direct method and refined by least-squares procedure to R = 3.7%. Two molecular conformers statistically coexist in the unit cell, differing in the hydroxyethoxymethyl group conformation. Trans-conformation about O4'-C4' bond and gauche about C4'-C5' bond are observed in both molecules. C1'-O4' bond is approximately perpendicular to the aglicon.     

The structure and antiviral activity of ribavirin analogs. II. Molecular and crystal structure of 1-(1,5-dihydroxy-3-oxapent-2-yl)-1,2,4-triazole-5-carboxamide

X-ray structure of the title compound, an antiviral agent moderately active towards Herpes simplex virus type 1, has been determined. The space group is P2i/n, unit cell parameters: a = 10,119, b = 7,529, c = 13,585 A, beta = 107,82 degrees, Z = 4. The structure was solved by the direct method and refined by least-squares procedure to R = 2.9%. The gauche-conformation about C4'-C5' bond and trans-conformation about O4'-C4' bond are realized in the molecule. The carboxyamide group at the C5 atom of triazol cycle provides a steric opportunity for the intramolecular hydrogen bond C1'-H1'...O6 formation.     

Structural analysis of 2',3'-dideoxyinosine, 2',3'-dideoxyadenosine, 2',3'-dideoxyguanosine and 2',3'-dideoxycytidine by 500-MHz 1H-NMR spectroscopy and ab-initio molecular orbital calculations.

Solution structure of anti-AIDS drug, 2',3'-dideoxyinosine (ddI) has been assessed by NMR spectroscopy and pseudorotational analysis in conjunction with its analogues: 2',3'-dideoxyadenosine (ddA), 2',3'-dideoxyguanosine (ddG) and 2',3'-dideoxycytidine (ddC). The absence of 3'-hydroxyl groups in these compounds has prompted us to establish the relationship between proton-proton and corresponding endocyclic torsion angles in the 2',3'-dideoxyribofuranose moiety on the basis of five available crystal structures of 2',3'-dideoxynucleosides. A subsequent pseudorotational analysis on ddI (1), ddA (2), ddG (3) and ddC (4) shows that the twist C2'exo-C3'-endo forms of sugar are overwhelmingly preferred (75-80%) over the C2'-endo envelope forms. The phase angles (P) for North and South conformers with the corresponding puckering amplitude (psi m) for ddI (1), ddA (2) and ddG (3) are as follows: PN = 0.1 degrees, PS = 161 degrees and psi m = 34.1 degrees for ddI (1); PN = 1.4 degrees, PS = 160 degrees and psi m = 34.2 degrees for ddA (2) and PN = 2.4 degrees, PS = 163 degrees and psi m = 33.6 degrees for ddG (3). The predominant North conformer of ddC (4) is intermediate between twist C2'-exo-C3'-endo and C3'-endo envelope (P = 10.9 degrees) with a psi m of 34.7 degrees. Note that these preponderant North-sugar structures (approx. 75-80%) found in the solution studies of ddI (1), ddA (2), dG (3) and ddC (4) are not reflected in the X-ray crystal structures of 2',3'-dideoxyadenosine and 2',3'-dideoxycytidine. The constituent sugar residues in both of these crystal structures denosine and 2',3'-dideoxycytidine. The constituent sugar residues in both of these crystal structures are found to be in the South-type geometry (ddA crystalizes in C3'-exo envelope form, while ddC adopts the form intermediate between the C3'-exo envelope and C3'-endo-C4'-exo twist form). This means that X-ray structures of ddA (2) and ddC (4) only represent the minor conformer of the overall pseudorotamer population in solution. An assumption that the structure of the pentofuranose sugar (i.e. P and psi m) participating in conformational equilibrium described by the two-state model remains unchanged at different temperatures has been experimentally validated by assessing five unknown pseudorotational parameters with eight unique observables (3J1'2', 3J1'2", 3J2'3', 3J2'3", 3J2"3', 3J2"3", 3J3'4' and 3J3"4') for 2',3'-dideoxynucleosides.(ABSTRACT TRUNCATED AT 400 WORDS)     

Crystal structure and conformation of 5-fluorouridine: conformational preferences for 5-fluorinated pyranosides

Crystals of 5-fluorouridine (5FUrd) have unit cell dimensions a = 7.716(1), b = 5.861(2), c = 13.041(1)A, alpha = gamma = 90 degrees, beta = 96.70 degrees (1), space group P2(1), Z = 2, rho obs = 1.56 gm/c.c and rho calc = 1574 gm/c.c The crystal structure was determined with diffractometric data and refined to a final reliability index of 0.042 for the observed 2205 reflections (I > or = 3sigma). The nucleoside has the anti conformation [chi = 53.1(4) degrees] with the furanose ring in the favorite C2'-endo conformation. The conformation across the sugar exocyclic bond is g+, with values of 49.1(4) and -69.3(4) degrees for phi(theta c) and phi (infinity) respectively. The pseudorotational amplitude tau(m) is 34.5 (2) with a phase angle of 171.6(4) degrees. The crystal structure is stabilized by a network of N-H...O and O-H...O involving the N3 of the uracil base and the sugar 03' and 02' as donors and the 02 and 04 of the uracil base and 03' oxygen as acceptors respectively. Fluorine is neither involved in the hydrogen bonding nor in the stacking interactions. Our studies of several 5-fluorinated nucleosides show the following preferred conformational features: 1) the most favored anti conformation for the nucleoside [chi varies from -20 to + 60 degrees] 2) an inverse correlation between the glycosyl bond distance and the chi angle 3) a wide variation of conformations of the sugar ranging froni C2'-endo through C3'-endo to C4'-exo 4) the preferred g+ across the exocyclic C4'-C5' bond and 5) no role for the fluorine atom in the hydrogen bonding or base stacking interactions.     

Bis-ketol nucleoside triesters as prodrugs of the antiviral nucleoside triphosphate analogues of 3'-deoxythymidine and 3'-deoxy-2',3'-didehydrothymidine

Derivatives of 3'-deoxythymidine (ddT) and 3'-deoxy-2',3'-didehydrothymidine (d4T) were prepared in which the 5'-hydroxyl group of the nucleoside was esterified to a bis-ketol phosphate. The resulting phosphate triesters are postulated to be prodrugs of the corresponding 5'-mononucleotides, which are formed intracellularly by the hydrolysis of the two ketol ester groups. The triesters were tested for anti-HIV activity with the result that those derived from ddT showed enhanced antiviral activity when compared to the parent nucleoside.     

Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)hypoxanthine.

The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and their structures were solved by direct methods. Least-squares refinement produced final R-factors of 0.027 for the 2'-F-dd-araA structure and of 0.044 for the 2'-F-dd-aral structure, respectively. The latter structure contains a two-fold disordered conformation of the sugar moiety. All three conformers (one for 2'-F-dd-araA and two for 2'-F-dd-aral) adopt an anti chi CN glycosyl torsion angle. The sugar in the 2'-F-dd-araA structure has a C2'-endo pucker conformation, whereas the sugar in the 2'-F-dd-aral structure has a mixture of C2'-endo and C3'-endo pucker conformations. When the sugar adopts the C2'-endo conformation, the torsion angle about the C4'-C5' bond is in a transgauche+ conformation. In contrast, when the sugar adopts the C3'-endo conformation, the torsion angle about the C4'-C5' bond is in a gauche(+)-gauche- conformation. The C2'-F bond distance is 1.406(3) A, similar to that found in other aliphatic C-F bonds. The results suggest that the 2'-fluoro-2',3'-dideoxyarabinosyl nucleosides do not have a strong preference for either C2'-endo or C3'-endo sugar pucker.     

Design of peptides: synthesis, crystal structure, molecular conformation, and conformational calculations of N-Boc-L-Phe-Dehydro-Ala-OCH3.

It is noteworthy that the dehydro-Ala residue adopts an extended conformation that is different than those observed in dehydro-Phe, dehydro-Leu, and dehydro-Abu. The peptide N-Boc-L-Phe-dehydro-Ala-OCH3 (C18H24N2O5) was synthesized by the usual workup procedure and finally by converting N-Boc-L-Phe-L-Ser-OCH3 to N-Boc-L-Phe-dehydro-Ala- OCH3. It was crystallized from its solution in a methanol-water mixture at room temperature. The crystals belong to the monoclonic space group P2(1), with a = 9.577(1) A, b = 5.195(3) A, c = 19.563(3) A, beta = 94.67(5) degrees, V = 970.1(6) A3, Z = 2, dm = 1.201(5) Mg m-3, dc = 1.197(5) Mg m-3. The structure was determined using direct method procedures. It was refined by a full-matrix least-squares procedure to an R value of 0.048 for 1370 observed reflections. The C2 alpha-C2 beta distance is 1.327(8) A, while the bond angles N2-C2 alpha-C2' and C1'-N2-C2 alpha are 109.8(5) degrees and 127.8(5) degrees, respectively. The backbone adopts a nonspecific conformation with dehydro-Ala in a fully extended conformation with the following torsion angles: theta 1 = 175.2(4) degrees, omega 0 = 170.2(4) degrees, phi 1 = 135.8(5) degrees, psi 1 = -22.6(6) degrees, omega 1 = 168.5(5) degrees, phi 2 = -170.3(5) degrees, psi 2T = -178.6(5) degrees, theta T = 178.4(7) degrees. The rigid planar and trans conformation of dehydro-Ala forces Phe to adopt a strained conformation. The Boc group has a trans-trans conformation.(ABSTRACT TRUNCATED AT 250 WORDS)     

1H-NMR studies on nucleotide binding to the sarcoplasmic reticulum Ca2+ ATPase. Determination of the conformations of bound nucleotides by the measurement of proton-proton transferred nuclear Overhauser enhancements

The glycosidic bond torsion angles and the conformations of the ribose of Mg2+ATP, Mg2+ADP and Mg2+AdoPP[NH]P (magnesium adenosine 5'-[beta, gamma-imido]triphosphate) bound to Ca2+ATPase, both native and modified with fluorescein isothiocyanate (FITC), in intact sarcoplasmic reticulum have been determined by the measurement of proton-proton transferred nuclear Overhauser enhancements by 1H-NMR spectroscopy. This method shows clearly the existence of a low-affinity ATP binding site after modification of the high-affinity site with FITC. For all three nucleotides bound to both the high-affinity (catalytic) site and the low-affinity site, we find that the conformation about the glycosidic bond is anti, the conformation of the ribose 3'-endo of the N type and the conformation about the ribose C4'-C5' bond either gauche-trans or trans-gauche. The values for the glycosidic bond torsion angles chi (O4'-C1'-N9-C4) for Mg2+ATP, Mg2+ADP and Mg2+AdoPP[NH]P bound to the low-affinity site of FITC-modified Ca2+ATPase are approximately equal to 270 degrees, approximately equal to 260 degrees and approximately equal to 240 degrees respectively. In the case of the nucleotides bound to the high-affinity (catalytic) site of native Ca2+ATPase, chi lies in the range 240-280 degrees.     

X-ray crystal structure of galabiose, O-alpha-D-galactopyranosyl-(1---4)-D-galactopyranose

O-alpha-D-Galactopyranosyl-(1---4)-D-galactopyranose, C12H22O11, Mr = 342.30, crystallises in the orthorhombic space group P2(1)2(1)2(1), and has alpha = 5.826(1), b = 13.904(3), c = 17.772(4) A, Z = 4, and Dx = 1.579 g.cm-3. Intensity data were collected with a CAD4 diffractometer. The structure was solved by direct methods and refined to R = 0.063 and Rw = 0.084 for 2758 independent reflections. The glycosidic linkage is of the type 1-axial-4-axial with torsion angles phi O-5' (O-5'-C-1'-O-1'-C-4) = 98.1(2) degrees, psi C-3 (C-3-C-4-O-1'-C-1') = -81.9(3) degrees, phi H (H-1'-C-1'-O-1'-C-4) = -18 degrees, and psi H (H-4-C-4-O-1'-C-1') = 35 degrees. The conformation is stabilised by an O-3 . . . O-5' intramolecular hydrogen-bond with length 2.787(3) A and O-3-H . . . O-5' = 162 degrees. The glycosidic linkage causes a folding of the molecule with an angle of 117 degrees between the least-square planes through the pyranosidic rings. The crystal investigated contained 56(1)% of alpha- and 44(1)% of beta-galabiose as well as approximately 70% of the gauche-trans and approximately 30% of the trans-gauche conformers about the exocyclic C-5'-C-6' and C-5-C-6 bonds. The crystal packing is governed by hydrogen bonding that engages all oxygen atoms except the intramolecular acceptor O-5' and the glycosidic O-1' oxygen atoms.     

Synthesis, crystal structure, and molecular conformation of N-Ac-dehydro-Phe-L-Val-L-Val-OCH3.

The peptide N-Ac-dehydro-Phe-L-Val-L-Val-OCH3 (C22H31N3O5) was synthesized by the usual workup procedure and finally by coupling the N-Ac-dehydro-Phe-L-Val-OH to valine methyl ester. It was crystallized from its solution in acetonitrile-water mixture at 4 degrees C. The crystals belong to the space group P1 with a = 8.900(3) A, b = 11.135(2) A, c = 12.918(2) A, alpha = 90.36(1) degrees, beta = 110.14(3) 14(3) degrees, V = 1207.7(6) A, 3Z = 2, dm = 1.156(5) Mgm-3, dc = 1.148(5) Mgm-3. The structure was determined by direct methods using SHELXS86. The structure was refined by full-matrix least-squares procedure to an R value of 0.077 for 3916 observed reflections. The molecular dimensions and conformations of the two crystallographically independent molecules are in good agreement. In the dehydro residues, the average C alpha-C beta distance is 1.31(2) A whereas the bond angle C alpha-C beta-C gamma is 132(1) degrees. The average backbone torsion angles are omega 0 = 169(1) degrees, phi 1 = -40(1) degree, psi 1 = -50(1) degree, omega 1 = -177(1) degree, phi 2 = 54(1) degree, psi 2 = 46(1) degree, omega 2 = -174(1) degree, phi 3 = 103(1) degree, psi T3 = -139(1) degree, and theta T3 = -176(1) degree. The acetyl group is in the trans conformation, while the backbone adopts a right-handed and left-handed helical conformation alternatingly.(ABSTRACT TRUNCATED AT 250 WORDS)     

Synthesis, crystal structure, and molecular conformation of N-Boc-L-Phe-dehydro-Leu-L-Val-OCH3

The peptide N-Boc-L-Phe-dehydro-Leu-L-Val-OCH3 was synthesized by the usual workup procedure and finally by coupling the N-Boc-L-Phe-dehydro-Leu-OH to valine methyl ester. It was crystallized from its solution in methanol-water mixture at 4 degrees C. The crystals belong to the triclinic space group P1 with a = 5.972(5) A, b = 9.455(6) A, c = 13.101(6) A, alpha = 103.00(4) degrees, beta = 97.14(5) degrees, gamma = 102.86(5) degrees, V = 690.8(8) A, Z = 1, dm = 1.179(5) Mg m-3 and dc = 1.177(5) Mg m-3. The structure was determined by direct methods using SHELXS86. It was refined by block-diagonal least-squares procedure to an R value of 0.060 for 1674 observed reflections. The C alpha 2-C beta 2 distance of 1.323(9) A in dehydro-Leu is an appropriate double bond length. The bond angle C alpha-C beta-C gamma in the dehydro-Leu residue is 129.4(8) degrees. The peptide backbone torsion angles are theta 1 = -168.6(6) degrees, omega 0 = 170.0(6) degrees, phi 1 = -44.5(9) degrees, psi 1 = 134.5(6) degrees, omega 1 = 177.3(6) degrees, phi 2 = 54.5(9) degrees, psi 2 = 31.1(10) degrees, omega 2 = 171.7(6) degrees, phi 3 = 51.9(8) degrees, psi T3 = 139.0(6) degrees, theta T = -175.7(6) degrees. These values show that the backbone adopts a beta-turn II conformation. As a result of beta-turn, an intramolecular hydrogen bond is formed between the oxygen of the ith residue and NH of the (i + 3)th residue at a distance of 3.134(6) A.(ABSTRACT TRUNCATED AT 250 WORDS)     

Crystal structure and molecular conformation of the peptide N-Boc-L-Gly-dehydro-Phe-NHCH3

The peptide N-Boc-L-Gly-dehydro-Phe-NHCH3 was synthesized by the combination of N-Boc-L-Gly-dehydro-Phe azlactone and methylamine. The peptide crystallizes in orthorhombic space group P2(1)2(1)2(1) with a = 5.679(2) A, b = 16.423(9) A, c = 19.198(10) A, V = 1791(2) A3, Z = 4, dm = 1.212(5) Mg m-3, dc = 1.237(1) Mg m-3. The structure was determined by direct methods using SHELXS 86. The structure was refined by full-matrix least squares procedure to an R value of 0.049 for 1509 observed reflections. The molecular dimensions are, in general, in good agreement with the standard values. The bond angle C alpha-C beta-C gamma in the dehydro-Phe residue is 133.6(5) degrees. The peptide backbone torsion angles are theta 1 = -171.4(4) degrees, omega 0 = 178.2(4) degrees, phi 1 = -57.2(6) degrees, psi 1 = 141.2(4) degrees, omega 1 = -174.4(4) degrees, phi 2 = 71.5(6) degrees, psi 2 = 7.2(6) degrees, and omega 2 = -179.8(5) degrees. These values show that the backbone adopts the beta-bend type II conformation. The Boc group has a trans-trans conformation. The side-chain torsion angles in dehydro-Phe are chi 2 = 1.6(9) degrees, chi 2(2, 1) = 0.5(9) degrees, and chi 2(2, 2) = 179.8(6) degrees. The plane of C2 alpha-C2 beta-C2 gamma is rotated with respect to the plane of the phenyl ring at 0.5(6) degrees, which indicates that the atoms of the side chain of the dehydro-Phe residue are essentially coplanar.(ABSTRACT TRUNCATED AT 250 WORDS)     

Crystal structure of tert.-butyloxycarbonyl-L-prolyl-D-alanyl-D-alanyl-N-methylamide. Dimeric beta-sheet formation.

The crystal structure of the tripeptide t-Boc-L-Pro-D-Ala-D-Ala-NHCH3, monohydrate, (C17H30N4O5.H2O, molecular weight = 404.44) has been determined by single crystal X-ray diffraction. The crystals are monoclinic, space group P2(1), a = 9.2585(4), b = 9.3541(5), c = 12.4529(4)A, beta = 96.449(3) degrees, Z = 2. The peptide units are in the trans and the tBoc-Pro bond in the cis orientation. The first and third peptide units show significant deviations from planarity (delta omega = 5.2 degrees and delta omega = 3.7 degrees, respectively). The backbone torsion angles are: phi 1 = -60 degrees, psi 1 = 143.3 degrees, omega 1 = -174.8 degrees, phi 2 = 148.4 degrees, psi 2 = -143.1 degrees, omega 2 = -179.7 degrees, phi 3 = 151.4 degrees, psi 3 = -151.9 degrees, omega 3 = -176.3 degrees. The pyrrolidine ring of the proline residue adopts the C2-C gamma conformation. The molecular packing gives rise to an antiparallel beta-sheet structure formed of dimeric repeating units of the peptide. The surface of the dimeric beta-sheet is hydrophobic. Water molecules are found systematically at the edges of the sheets interacting with the urethane oxygen and terminal amino groups. Surface catalysis of an L-Ala to D-Ala epimerization process by water molecules adsorbed on to an incipient beta-sheet is suggested as a mechanism whereby crystals of the title peptide were obtained from a solution of tBoc-Pro-D-Ala-Ala-NHCH3.     

Crystal structure and conformation of 8-(2-hydroxyethylamino) and 8-(pyrrolidin-1-yl) adenosines

In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 2(1); a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) A, beta = 92.261(1) degrees, V = 707.10(3) A3, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2')-endo conformation and gauche-gauche form across C(4')-C(5') bond. The molecular structure is stabilized by intramolecular hydrogen bond of N-HO type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) A, beta = 103.254(2), V = 1524.4(2) degrees A3, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2')-endo conformation and gauche -gauche form across C(4')- C(5') bond. The molecular structure is stabilized by intramolecular hydrogen bond of O-HN type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.     

Conformation and hydrogen bonding of N-formylmethionyl peptides. Parallel beta-sheet in the crystal structure of N-formyl-L-methionyl-L-valine

Crystals of N-formyl-L-methionyl-L-valine (C11H20N2O)4S, M.W. = 276.3) are orthorhombic, space group )2(1)2(1)2(1) with cell constants at 294K of a = 4.851 (1), b = 14.925 (1), c = 19.745 (3) A, V = 1429.8 (1) A3, Z = 4 and observed (Dm) and calculated (Dx) of 1.49 and 1.488 g x cm-3, respectively. The crystal structure was solved using automatic diffractometer data (1260 reflections larger than or equal to 3 sigma) and refined to a final R-value of 0.035. This structure contains a short (2.626 (3) A) intermolecular hydrogen bond between the carboxyl OH and the N-acyl oxygen, a feature common to most N-acylamino acids and N-acylpeptides. The peptide is nearly planar (omega = 174.6 (5)); the values of psi 1, phi 2, psi 1T and psi 2T are, respectively, 131.8 (4) degrees, -139.9 (5) degrees, -39.3 (4) degrees and 142.1 (4) degrees. The methionine side chain is not zig-zag transplanar; the side chain torsion angles are: chi 1(1) = -60.0 (4) degrees, chi 2(1) = 176.0 (4) degrees and chi 3(1) = 71.8 (4) degrees. The two C gamma's for valine have psi 1-values of -64.4 (5) degrees and 173.7 (5) degrees. The formation of the parallel rather than antiparallel beta-sheet structure, the participation of the N-formyl group in the parallel beta-sheet and the use of C-H ... O hydrogen bonds to stabilize the beta-sheet are novel features found in this structure.     

Crystal and molecular structure of methyl O-alpha-D-manno-pyranosyl-(1----2)-alpha-D-mannopyranoside

The crystal and molecular structure of a synthetic mannosyl disaccharide, methyl O-alpha-D-mannopyranosyl-(1----2)-alpha-D-mannopyranoside, has been determined from X-ray diffractometer data by direct methods by use of the Multan programs. The crystals are monoclinic, space group P2 with unit cell dimensions, a 8.086(1), b 9.775(1), c 9.975(2) A, beta 104.58(1) degrees, Z 2, and Dm 1.54 g/cm3. The structure was refined to an R-value of 0.033 for 1359 reflections measured with CuK alpha radiation. The mannopyranose units have the chair conformations 4C(D) with C-5' and C-2' deviating from the best plane through the other four atoms of the ring by -0.68 and +0.53 A in the nonreducing group, and C-3 and O-5 deviating from the mean plane through the other four atoms by +0.57 and -0.66 A, respectively, in the "potentially" reducing residue. The ring-to-ring conformation can be described as (phi, psi) = (-64.5, 105.5 degrees). The conformation across the C-5--C-6 bond is gauche-gauche in both the sugars. The crystal structure is stabilized by a network of intermolecular O-H...O hydrogen bonds.