The structure of the monobarium salt of glucose 6-phosphate heptahydrate

C6H11o9P2-.Ba2+.7H2o, M, = 521.5, is monoclinic, space group P21, a = 11.881 (4), b = 8.616 (5), c = 8.350 (4) A,B = 102.95 (3)0, Z = 2, U = 833.0 A 3, d m = 2.09, d c = 2.08 Mg m -3, F(000) = 516. Mo Ka (u = 0.034 mm -1) intensity data. R is 0.068 for 1603 reflections. Of the two endocyclic C-O bonds in the glucose ring, C(5)-O(5) [1.463 (23)] is longer than C(1)-O(5) [1.395 (23)A]. The pyranose sugar ring takes a 4C1 chair conformation. The Cremer-Pople puckering parameters are, 0 = 6.69 o, Q = 0.619 A and 0 = 263.7o. The conformation about the exocyclic C(5)-C(6) bond is gauche-gauche, in contrast to gauche-trans observed in the structure of glucose 1-phosphate. The phosphate ester bond, P-O(6), is 1.61 (1)A. It is similar in length to the 'high-energy' P~O bond in phosphoenolpyruvate. The Ba 2÷ ion is surrounded by nine O atoms within a distance of 2.95 A, of which seven are from water molecules. There is an intramolecular hydrogen bond between the sugar hydroxyl 0(4) and phosphate oxygen O(12).

Molecular and crystal structure of deoxyguanosine 5'-phosphate

RECENT crystallographic studies of the dinucleosides ApU (ref. 1) and GpC (ref. 2) have given experimental proof for the base pairing arrangement proposed by Watson and Crick for the DNA double helix3. Another striking feature of this structure relates to the torsional angle about the C5'-C4' bond in the phosphate−sugar backbone chain. In the Crick and Watson model4, this conformation is gauche−trans (GT). Crystal structures of 5'-nucleotides, dinucleosides and dinucleotides so far studied, however, have shown only the gauche−gauche (GG) conformation about this bond. The GG conformer is also the only one found in the refined models of the proposed structure of the double helical nucleic acids and polynucleotides5−7. The only nucleotide with a GT conformation is 6-azauridine-5'-phosphate8 which is not a normal monomer unit of nucleic acids. It is also reported that 5'-dGMP assumes preferentially GT conformation in solution9.

Structural Crystallography and Crystal Chemistry

Abstract is not available.

Effect of administration of clofibrate and clofenapate on kidney mitochondria of the rat

Abstract is not available.

A Framework for Detecting Glaucomatous Progression in the Optic Nerve Head of an Eye Using Proper Orthogonal Decomposition

Glaucoma is the second leading cause of blindness worldwide. Often, the optic nerve head (ONH) glaucomatous damage and ONH changes occur prior to visual field loss and are observable in vivo. Thus, digital image analysis is a promising choice for detecting the onset and/or progression of glaucoma. In this paper, we present a new framework for detecting glaucomatous changes in the ONH of an eye using the method of proper orthogonal decomposition (POD). A baseline topograph subspace was constructed for each eye to describe the structure of the ONH of the eye at a reference/baseline condition using POD. Any glaucomatous changes in the ONH of the eye present during a follow-up exam were estimated by comparing the follow-up ONH topography with its baseline topograph subspace representation. Image correspondence measures of L-1-norm and L-2-norm, correlation, and image Euclidean distance (IMED) were used to quantify the ONH changes. An ONH topographic library built from the Louisiana State University Experimental Glaucoma study was used to evaluate the performance of the proposed method. The area under the receiver operating characteristic curves (AUCs) was used to compare the diagnostic performance of the POD-induced parameters with the parameters of the topographic change analysis (TCA) method. The IMED and L-2-norm parameters in the POD framework provided the highest AUC of 0.94 at 10 degrees. field of imaging and 0.91 at 15 degrees. field of imaging compared to the TCA parameters with an AUC of 0.86 and 0.88, respectively. The proposed POD framework captures the instrument measurement variability and inherent structure variability and shows promise for improving our ability to detect glaucomatous change over time in glaucoma management.

Molecular structures of cytidine-5-diphosphate and cytidine-5-diphospho-choline, and their role in intermediary metabolism

The nucleotide coenzyme cytidine-5-diphospho-choline is highly folded. The CMP-5 parts of the molecules in the crystal structure are strongly linked by metal ligation and hydrogen bonds leaving the phosphoryl-choline residues relatively free. Cytidine-5-diphosphoric acid exists as a zwitterion with N31 protonated. The P−O bond lengths from the anhydride bridging oxygen in the pyrophosphate are significantly different.

An uncommon nucleotide conformation shown by molecular structure of deoxyuridine-5-phosphate and nucleic acid stereochemistry

CRYSTAL structure determinations of nucleic acid fragments have shown that several of the conformational features found in the monomeric building blocks are also manifested at the nucleic acid level. Stereochemical variations between thymine and uracil nucleotides are therefore of interest as they can provide a structural basis for some of the differences between the conformations of DNA and RNA. X-ray studies have so far not shown any major dissimilarities between these two nucleotide species although the sugar ring of deoxyribonucleotides is found to possess greater flexibility than that in ribonucleotides. We report here the molecular structure of deoxyuridine-5'-phosphate (dUMP-5') which is not a common monomer unit of DNAs as it is replaced by its 5-methyl analogue deoxythymidine-5'-phosphate (dTMP-5'). The investigation was undertaken to help determine whether or not this implied a fundamental difference between the geometries of these two molecules.

L-Tyrosyl-L-glutarnie Acid Monohydrate, C14H18N206.H20

Mr=328.32, triclinic, P1, a=5.801 (1), b=7.977(1), c=9.110(2)A, ~t=102.33 (1), fl= 97.92 (1), y= 109.82 (1) °, v= 377.2 (1) A 3 at 293 K, Z=I, D x=1.45, D m=1.45 g cm -3, 2(MoKs)= 0.7107 A, ~ = 0.74 cm -1, F(000) = 174.0. R = 0.046 for 990 unique observed [F o > 4O(Fo)] reflections. The crystal structure is stabilized by extensive hydrogen bonding involving all N and O atoms.

Iterative solution of a class of linear equations with application to reconstruction of three-dimensional object arrays

An iterative algorithm baaed on probabilistic estimation is described for obtaining the minimum-norm solution of a very large, consistent, linear system of equations AX = g where A is an (m times n) matrix with non-negative elements, x and g are respectively (n times 1) and (m times 1) vectors with positive components.

Invariant magneto-electric and piezomagnetic coefficients

Invariant magneto-electric coefficients and invariant piezomagnetic coefficients are obtained for all the magnetic crystal classes.

Neutron-diffraction study of structure and conformation of nucleotide uridine-5 phosphate (disodium salt)

Acta Crystallographica Section A: Foundations of Crystallography covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.

Structural studies of analgesics and their interactions. II. The crystal structure of a 1:1 complex between antipyrine and salicyclic acid (salipyrine)

The complex crystallizes in the space group P21/c with four formula units in a unit cell of dimensions a= 12.747, b= 7.416, c= 17.894 A and/3= 90.2 °. The structure has been solved by the symbolic addition procedure using three-dimensional photographic data and refined to an R value of 0.079 for 2019 observed reflexions. The pyramidal nature of the two hetero nitrogen atoms in the antipyrine molecule is inter:nediate between that observed in free antipyrine and in some of its metal complexes. The molecule is more polar than that in crystals of free antipyrine but less so compared with that in metal complexes. In the salicylic acid molecule, the hydroxyl group forms an internal hydrogen bond with one of the oxygen atoms in the carboxyl group. The association between the salicylic acid and the antipyrine molecules is achieved through an intermolecular hydrogen bond with the other carboxyl oxygen atom in the salicylic acid molecule as the proton donor and the carboxyl oxygen atom of the antipyrine molecule as the acceptor.

Photocytotoxic 3d-Metal Scorpionates with a 1,8-Naphthalimide Chromophore Showing Photoinduced DNA and Protein Cleavage Activity

Ternary 3d-metal complexes of formulation [M(Tp(Ph))(py-nap)](ClO4)(1-3), where M is Co(II) (1), Cu(II) (2), and Zn(II) (3); Tp(Ph) is anionic tris (3-phenylpyrazolyl)borate; and py-nap is a pyridyl ligand with a conjugated 1,8-naphthalimide moiety, have been prepared from the reaction of metal perchlorate with KTp(Ph) and py-nap in CH2Cl2. The complexes have been characterized from analytical and physicochemical data. The complexes are stable in solution as evidenced from the electrospray ionization mass spectrometry data. The complexes show good binding propensity with calf thymus (CT) DNA, giving binding constant (K-b) values of similar to 10(5) M-1 and a molecular ``light-switch'' effect that results in an enhancement of the emission intensity of the naphthalimide chromophore on binding to CT DNA. The complexes do not show any hydrolytic cleavage of DNA. They show poor chemical nuclease activity in the presence of 3-mercaptopropionic acid or hydrogen peroxide (H2O2). The Co(II) and Cu(II) complexes exhibit oxidative pUC19 DNA cleavage activity in UV-A light of 365 rim. The Zn(II) complex shows moderate DNA photocleavage activity at 365 nm. The Cu(II)complex 2 displays photoinduced DNA cleavage activity in red light of 647.1 nm and 676 rim and near-IR light of >750 rim. A mechanistic studyin UV-A and visible light suggests the involvement of the hydroxyl radical as the reactive species in the DNA photocleavage reactions. The complexes also show good bovine serum albumin (BSA) protein binding propensity, giving K-BSA values of similar to 10(5) M-1. Complexes 1 and 2 display significant photoinduced BSA cleavage activity in UV-A light. The Co(II) complex 1 shows a significant photocytotoxic effect in HeLa cervical cancer cells on exposure to UV-A light of 365 nm, giving an IC50 value of 32 mu M. The IC50 value for the py-nap ligand alone is 41.42 mu m in UV-A light. The IC50 value is >200 mu M in the dark, indicating poor dark toxicity of 1. The Cu(II) complex 2 exhibits moderate photocytotoxicity and significant dark toxicity, giving IC50 values of 18.6 mu m and 29.7 mu m in UV-A light and in the dark, respectively.

Structural studies of analgesics and their interactions. III. The crystal and molecular structure of amidopyrine

Amidopyrine (1-phenyl-2,3-dimethyl-4-dimethylaminopyrazolone), C13HzvN30, a dimethylamino derivative of antipyrine and an important analgesic and antipyretic agent, crystallizes in the triclinic space group P1 with four molecules in a unit cell of dimensions a= 7.458 (5), b = 10.744 (5), c= 17.486 (15)/~,, e=98.6 (2),/~= 85.6 (3), y= 108-6 (2) . The structure was solved by direct methods and refined to an R value of 0.055 for 3706 photographically observed reflexions. The dimensions of the two crystallographically independent molecules are very nearly the same. The pyrazolone moiety in the molecule has dimensions comparable to those in antipyrine. Unlike antipyrine, the molecular dimensions of amidopyrine in the free state (the present structure) are close to those found in some of its hydrogenbonded complexes. Thus it appears that the presence of the dimethylamino group makes the molecule more resistant to changes in its dimensions resulting from molecular association. An attempt has also been made to correlate the polar nature of the pyrazolone moiety and the hybridization state of the hetero nitrogen atoms in antipyrine, amidopyrine and their complexes.

Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2'-Monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P21 with a = 7.472(3)Å, b = 26.853(6) Å, c = 9.184(1)Å, b = 113.36(1)Å and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P31 and P3121 with a = 8.762(1)Å, c = 34.630(5)Å, Z= 6 and a = 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6522 and P21 with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (cCN = -156.4(2)°) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose O4' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose O4' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.