Molecular Mechanics: The Cross-conjugated Carbonyl Group in Heterocyclic Compounds. 2. Parameterisation (MM2) of the Adjacent C-O and C-N Bonds

The definition, in a previous paper, of a new type of carbon atom (type 44) in the MM2 force field, i.e. when it is cross-conjugated, implies the reparameterisation of the bonds adjacent to the carbonyl bond. By means of a statistical study based on data issued from the Cambridge Structural Data System, we propose here new σ dipole moments and new stretching parameters for the C(44)-O(41) and C(44)-N(40) bonds included in heterocyclic compounds. These stretching parameters, which are π-bond-order dependent, are quite satisfactory (mean of unsigned deviations: 0.023Å) within limited π-bond-order ranges: 0.25 to 0.32 for the C-O bond, 0.37 to 0.53, for the C-N bond. As for the C(44)=O(7) bond the parameters are generally inappropriate for compounds in which both atoms connected to the type 44 carbon are heteroatoms. The maximum deviation from the experimental bond length, for both bond types can reach ±0.03Å. Here also, part of the dispersion of the results could be attributed to the variation of the effective dielectric constant D from one crystal to another.     

Molecular Mechanics: The Cross-conjugated Carbonyl Group in Heterocyclic Compounds. 1. Parameterisation (MM2) of the >C=O Bond

A new type of carbon atom has been included in the MM2 force field when it is part of a carbonyl group cross-conjugated in a heterocyclic molecule. This carbon atom is fully included in the π system calculation. New stretching parameters for the C=O bond have been estimated by a statistical process from X-ray molecular structures recorded in the Cambridge Structural Database System. The proposed parameters have been found appropriate for compounds in which the atoms adjacent to the carbonyl are a carbon and a heteroatom i.e. mainly for the α-pyrone ring and the conjugated "lactams". They are inappropriate for carbonates and oxazo-ones but should be valid for quinones provided that they are not involved in a charge transfer complex. The mean unsigned deviation for 111 bond lengths (89 cyclic molecules) is 0.01Å but the maximum deviation can reach ± 0.03Å. Part of the observed dispersion could be the result of the variation of the effective dielectric constant D from one crystal to another.     

Molecular Mechanics: The Conjugate Nitro Group Parameters in the MM2 Force Field

The conjugated nitro group has been included in the π system calculation within the MM2 force field. New parameters have been estimated by a statistical process from X-ray molecular structures recorded in the C.S.D.S. Comparison of the corresponding results with those given by the MM2(91) force field parameters show a clear improvement for dihedral and bond angles. For N-O and C-N bond lengths a slight global improvement is also observed. A closer examination of the results for the latter bond shows that sometimes MM2(91) gives better results for six membered ring nitro compounds. By contrast the parameters proposed here are more adapted to five membered ring derivatives. The derived linear relations permit the study of molecules over a wider range of π indices. The introduction of a correction factor to the calculated molecular π dipole moment in conjunction with a necessary reestimation of some σ-bond dipole moments also leads to improved total molecular dipole moments.     

Molecular Mechanics: The Conjugate Nitro Group Parameters in the MM2 Force Field

The conjugated nitro group has been included in the π system calculation within the MM2 force field. New parameters have been estimated by a statistical process from X-ray molecular structures recorded in the C.S.D.S. Comparison of the corresponding results with those given by the MM2(91) force field parameters show a clear improvement for dihedral and bond angles. For N-O and C-N bond lengths a slight global improvement is also observed. A closer examination of the results for the latter bond shows that sometimes MM2(91) gives better results for six membered ring nitro compounds. By contrast the parameters proposed here are more adapted to five membered ring derivatives. The derived linear relations permit the study of molecules over a wider range of π indices. The introduction of a correction factor to the calculated molecular π dipole moment in conjunction with a necessary reestimation of some σ-bond dipole moments also leads to improved total molecular dipole moments.     

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.     

Structural studies of the O6meG.C interaction in the d(C-G-C-G-A-A-T-T-C-O6meG-C-G) duplex

One- and two-dimensional nuclear magnetic resonance (NMR) experiments have been undertaken to investigate the conformation of the d(C1-G2-C3-G4-A5-A6-T7-T8-C9-O6meG10-C11-G12) self-complementary dodecanucleotide (henceforth called O6meG.C 12-mer), which contains C3.O6meG10 interactions in the interior of the helix. We observe intact base pairs at G2.C11 and G4.C9 on either side of the modification site at low temperature though these base pairs are kinetically destabilized in the O6meG.C 12-mer duplex compared to the G.C 12-mer duplex. One-dimensional nuclear Overhauser effects (NOEs) on the exchangeable imino protons demonstrate that the C3 and O6meG10 bases are stacked into the helix and act as spacers between the flanking G2.C11 and G4.C9 base pairs. The nonexchangeable base and H1', H2', H2', H3', and H4' protons have been completely assigned in the O6meG.C 12-mer duplex at 25 degrees C by two-dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) experiments. The observed NOEs and their directionality demonstrate that the O6meG.C 12-mer is a right-handed helix in which the O6meG10 and C3 bases maintain their anti conformation about the glycosidic bond at the modification site. The NOEs between the H8 of O6meG10 and the sugar protons of O6meG10 and adjacent C9 exhibit an altered pattern indicative of a small conformational change from a regular duplex in the C9-O6meG10 step of the O6meG.C 12-mer duplex. We propose a pairing scheme for the C3.O6meG10 interaction at the modification site. Three phosphorus resonances are shifted to low field of the normal spectral dispersion in the O6meG.C 12-mer phosphorus spectrum at low temperature, indicative of an altered phosphodiester backbone at the modification site. These NMR results are compared with the corresponding parameters in the G.C 12-mer, which contains Watson-Crick base pairs at the same position in the helix.     

High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods.

We have compared hydrogen bond lengths on enzymes derived with high precision (< or = +/- 0.05 A) from both the proton chemical shifts (delta) and the fractionation factors (phi) of the proton involved with those obtained from protein X-ray crystallography. Hydrogen bond distances derived from proton chemical shifts were obtained from a correlation of 59 O--H....O hydrogen bond lengths, measured by small molecule high-resolution X-ray crystallography, with chemical shifts determined by solid-state nuclear magnetic resonance (NMR) in the same crystals (McDermott A, Ridenour CF, Encyclopedia of NMR, Sussex, U.K.: Wiley, 1996:3820-3825). Hydrogen bond distances were independently obtained from fractionation factors that yield distances between the two proton wells in quartic double minimum potential functions (Kreevoy MM, Liang TM, J Am Chem Soc, 1980;102:3315-3322). The high-precision hydrogen bond distances derived from their corresponding NMR-measured proton chemical shifts and fractionation factors agree well with each other and with those reported in protein X-ray structures within the larger errors (+/-0.2-0.8 A) in distances obtained by protein X-ray crystallography. The increased precision in measurements of hydrogen bond lengths by NMR has provided insight into the contributions of short, strong hydrogen bonds to catalysis for several enzymatic reactions.     

The contribution of C alpha-H...O hydrogen bonds to membrane protein stability depends on the position of the amide

Structural analyses of membrane proteins reveal a large number of C(alpha)-H...O contacts between transmembrane helices, presumed to be hydrogen bonds. Recent experiments produced conflicting results for the contribution of such hydrogen bonds to membrane protein stability. An FTIR study estimated an energy of -0.88 kcal/mol for the G79-C(alpha)-H...I76-O hydrogen bond in glycophorin A, whereas a mutagenesis study showed that the A51-C(alpha)-H...T24-O(gamma) hydrogen bond does not stabilize bacteriorhodopsin. Here, we reconcile these results using molecular mechanics calculations and an implicit membrane model (IMM1). With explicit hydrogen atoms, the potential energy of the G79-C(alpha)-H...I76-O interaction in GpA ranges from -0.54 to -0.9 kcal/mol and its contribution to stability (effective energy) from -0.49 to -0.83 kcal/mol, depending on the structural model used. The average values of these quantities in GpA-like motifs are similar. In bR, the corresponding numbers for the A51-C(alpha)-H...T24-O(gamma) interaction are +0.15 and +0.32 kcal/mol. The difference results from the different arrangement of the interacting groups and specifically the position of the acceptor with respect to the C(alpha) and N atoms. This conclusion likely applies to soluble proteins as well.     

H atom positions and nuclear magnetic resonance chemical shifts of short H bonds in photoactive yellow protein

Recent neutron diffraction studies on photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore-ionized p-coumaric acid (pCA) is a low-barrier H bond (LBHB) mainly because the H atom position was assigned at the midpoint of the O(Glu46)-O(pCA) bond. However, the (1)H nuclear magnetic resonance (NMR) chemical shift (δ(H)) was 15.2 ppm, which is lower than the values of 17-19 ppm for typical LBHBs. We evaluated the dependence of δ(H) on an H atom position in the O(Glu46)-O(pCA) bond in the PYP ground state by using a quantum mechanical/molecular mechanical (QM/MM) approach. The calculated chemical shift unambiguously suggested that a δ(H) of 15.2 ppm for the O(Glu46)-O(pCA) bond in NMR studies should correspond to the QM/MM geometry (δ(H) = 14.5 ppm), where the H atom belongs to the Glu moiety, rather than the neutron diffraction geometry (δ(H) = 19.7 ppm), where the H atom is near the midpoint of the donor and acceptor atoms.     

Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations

(Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H2O.     

Pressure dependence on electronic structures,charge distribution and bond orders of solid nitromethane using nonlocal DFT functional

The electronic properties of solid nitromethane are studied using nonlocal exchange-correlation functional (optPBE–vdW) under hydrostatic compression up to 40?GPa. We found that the optPBE–vdW functional can reproduce well the crystalline structures compared with the experiments, and an isomorphic phase transition has been verified by their P–V curve. Bader’s charge analysis shows the electron flows from CH₃ group to NO₂ group with the pressure. Moreover, the calculated bond orders show that the pressure only strengthens the intermolecular C–N bond and intermolecular C–H···O hydrogen bonds though it shortens all bond lengths. Furthermore, the electronic structure and its pressure dependence have also been discussed in detail.     

Variability in the backbone conformation of cyclic pentapeptides. Crystal structure of cyclic(Gly-L-Pro-D-Phe-Gly-L-Ala)

All the peptide bonds in cyclic(Gly-L-Pro-D-Phe-Gly-L-Ala) are in the trans conformation; however, the peptide bond C'5-N1 is twisted by 19 degrees from planarity (omega 5 = -161 degrees). A Type II beta-turn encompasses the L-Pro-D-Phe residues. Carbonyl oxygens O2, O4 and O5 are directed to the same side of the average plane through the backbone ring and they form hydrogen bonds with N3, N5 and N1, respectively, in adjacent molecules in a stacked column where the adjacent molecules are related by one translational unit. The conformation of the backbone is different from that established in other molecules with the DLDDL chirality sequence. The P21 cell contains two molecules of C21H26N5O5 with a = 4.836(2) A, b = 18.346(8) A, c = 12.464(5) A and beta = 100.05(4) degrees. The R factor for 1382 data with [F0[ greater than 1 sigma is 7.0%.     

Topography of cyclodextrin inclusion complexes : Part II. The iodine-cyclohexa-amylose tetrahydrate complex; its molecular geometry and cage-type crystal structure

Iodine-cyclohexa-amylose tetrahydrate [(C₆H₁₀O₅)₆ ·I₂·d4H₂O] crystallizes in the orthorhombic space-group P2₁2₁2₁, a  14.240 Å, b  36.014 Å, c  9.558 Å. The structure was solved by heavy-atom techniques and refined by least-squares methods to a conventional discrepancy index R  0.148 for the 2872 observed data. The six d-glucose residues are in the C1 chair conformation; the conformational angles vary in magnitude from 45 to 66°, the angles O(5)-C(5)-C(6)-O(6) are close to · 70°, and the six O(4) atoms are almost coplanar (r.m. s. displacement 0.13 Å). Only four of the six O(2) ?O(3) intramolecular hydrogen bonds have formed, which renders the molecule less symmetrical and more conical-shaped than in the previously determined α-cyclodextrin-potassium acetate complex. The iodine molecule is coaxial with the cyclohexa-amylose molecule. The I-I distance is a conventional 2.677 Å. Close interactions between the iodine atoms and the host molecule comprise carbon atoms C(5) and C(6) and oxygen atoms O(4), with interatomic distances all equal to or greater than van der Waals contacts. Intermolecular, almost-linear, short contacts O ? I-I?O with I?O distances of 3.22 and 3.07 Å indicate attractive interaction.The molecules are arranged in herring-bone “cage-type” fashion, with the four water molecules as space-filling mediators; the structure is held together by an intricate network of hydrogen bonds.     

Formate dehydrogenase molybdenum and tungsten sites--observation by EXAFS of structural differences

Preliminary EXAFS data has been collected on the molybdenum (K-edge) in C. pasteurianum formate dehydrogenase and the tungsten (LIII-edge) in C. thermoaceticum formate dehydrogenase. In the presence of dithionite, the tungsten enzyme was devoid of W = O bonds, and exhibited average W-(O, N) and W-S bond lengths of 2.13 +/- 0.03 A and 2.39 +/- 0.03 A, respectively. In sharp contrast, the C. pasteurianum molybdenum site has three Mo = O bonds with an average bond length of 1.74 +/- 0.03 A. It is also the first molybdenum enzyme found lacking Mo-S bonds, and does not appear to be redox active in the presence of formate or dithionite. Model compounds WO2(8-hydroxyquinoline)2 = WO2(ox)2, and WO2(8 mercaptoquinoline)2 = WO2(tox)2, were also examined. Respective predicted bond lengths for WO2(ox)2 and WO2(tox)2 were W = O of 1.71, 1.73 A; W-N of 2.31, 2.29 A; W-O or W-S of 1.92 or 2.40 A, with estimated uncertainties of +/- 0.03 A.     

Actin, troponin C, Alzheimer amyloid precursor protein and pro-interleukin 1 beta as substrates of the protease from human immunodeficiency virus

We show here for the first time that actin, troponin C, Alzheimer amyloid precursor protein (AAP), and pro-interleukin 1 beta (pro-IL-1 beta), are substrates of the protease encoded by the human immunodeficiency virus (HIV) type-1. As has been seen in other non-viral protein substrates of the HIV protease, the presence of Glu residues in the P2' position appears to play an important role in substrate recognition. Three of the four bonds cleaved in actin, two of the three in troponin C, and all of the bonds hydrolyzed in AAP and pro-IL-1 beta have a P2' Glu residue. In fact, Glu residues are accommodated in all positions from P4 to P4' surrounding the scissile bond in substrates of the HIV proteases, and as many as 4 adjacent Glu residues were seen in one of the bonds cleaved in AAP. This study of non-viral protein substrates has also revealed unexpected amino acids such as Gly, Arg, and Glu in the scissile bond itself rather than the more conventional hydrophobic amino acids. The HIV-2 protease hydrolyzed actin in a manner similar to that of the HIV-1 enzyme, but its cleavage of troponin C was distinct in that it split a bond adjacent to a triplet of Glu residues in P2, P3, and P4 that was refractory to the HIV-1 enzyme. Documentation of cleavage sites in the several important cellular proteins noted above has extended our understanding of the features in a substrate that are recognized by these multi sub-site proteases of retroviral maturation. Moreover, the present work adds to an accumulating body of evidence which demonstrates that these enzymes can damage crucial structural and regulatory cellular proteins if ever their activity is expressed outside the viral particle itself.     

Differential Stability of the Triple Helix of (Pro-Pro-Gly)10 in H2O and D2O: Thermodynamic and Structural Explanations

Abstract

(Pro-Pro-Gly)₁₀ [(PPG₁₀)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5°C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D₂O to an H₂O solution of (PPG)₁₀, with the melting temperature reaching 40°C in pure D₂O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalphy of unfolding in D₂O vs. H₂O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)₁₀ that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H₂O or D₂O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D₂O resulted in a significant lowering of the potential energy of hydrated (PPG)₁₀. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG₁₀) energy, plus the water-(PPG₁₀) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D₂O vs. H₂O. This result indicates that the geometry of the carbonyl-D₂O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H₂O.     

Wobble dG X dT pairing in right-handed DNA: solution conformation of the d(C-G-T-G-A-A-T-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra

We report below on features of the three-dimensional structure of the d(C-G-T-G-A-A-T-T-C-G-C-G) self-complementary duplex (designated 12-mer GT) containing symmetrical G X T mismatches in the interior of the helix. The majority of the base and sugar protons in the 12-mer GT duplex were assigned by two-dimensional nuclear Overhauser effect (NOESY) spectra in H2O and D2O solution. A set of 92 short (less than 4.5-A) proton-proton distances defined by lower and upper bounds for one symmetrical half of the 12-mer GT duplex were estimated from NOESY data sets recorded as a function of mixing time. These experimental distances combined with nucleotide bond length parameters were embedded into Cartesian space; several trial structures were refined to minimize bond geometry and van der Waals and chirality error. Confidence in this approach is based on the similarity of the refined structures for the solution conformation of the 12-mer GT duplex. The G and T bases pair through two imino-carbonyl hydrogen bonds, and stacking is maintained between the G X T wobble pair and adjacent Watson-Crick G X C pairs. The experimental distance information is restricted to base and sugar protons, and hence structural features such as base pair overlap, glycosidic torsion angles, and sugar pucker are well-defined by this combination of NMR and distance geometry methods. By contrast, we are unable to define the torsion angles about the bonds C3'-O3'-P-O5'-C5'-C4' in the backbone of the nucleic acid.     

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.     

Solvated helical backbones: x-ray diffraction study of Boc-Ala-Leu-Aib-Ala-Leu-Aib-OMe.H2O

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc-Aib-(Ala-Leu-Aib)3-OMe. The backbone of the title compound assumes an approximate 3(10)-helical form with three 4----1 hydrogen bonds. In the place of a fourth 4----1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) ... W(1) (2.95 A) and W(1) ... O(1) (2.81 A). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) ... O(4) (2.91 A). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P2(1)2(1)2(1) with a = 12.024(4) A, b = 15.714(6) A, c = 21.411(7) A, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9.H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities greater than 3 sigma(F) and the resolution is 0.90 A.