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2.
Acta Crystallogr B ; 54 ( Pt 6): 912-20, 1998 Dec 01.
Article in English | MEDLINE | ID: mdl-9880899

ABSTRACT

The crystal structure of 2-pyridone has been redetermined from high-resolution X-ray data collected at 123 K. The molecule is in the lactam form. Bond lengths (corrected for rigid-body libration) and angles have been determined with s.u.'s of 0.001 A and 0.1 degree, respectively. The hydrogen-bonded cyclic dimers which occur in the vapor and in solution are absent in the crystal where molecules are linked by N-H...O hydrogen bonds to form puckered chains. There also appears to be a weaker C-H...O interaction (H...O, 2.57 A) and weak C-H...pi or van der Waals interactions occurring on both sides of the pyridone ring. Following a refinement of the structure assuming Stewart's rigid pseudo-atom model, the electronic charge density distribution in the crystal and its Laplacian have been calculated for atoms at rest. The total electrostatic potential has been mapped for an isolated molecule and the molecular dipole moment has been determined [8.8 (19) D; 1D approximately = 3.33564 x 10(-30) C m]. Critical points in the electron density have been located for the bonds within the molecule and for the molecular interactions cited above. For the C-H...pi interactions, only the spherical components of the valence density for the pyridone ring atoms contribute effectively at the critical points. Hence, these may be better described as van der Waals interactions.


Subject(s)
Pyridones/chemistry , Static Electricity , Hydrogen Bonding , X-Ray Diffraction
3.
Acta Crystallogr B ; 53 ( Pt 5): 787-94, 1997 Oct 01.
Article in English | MEDLINE | ID: mdl-9351188

ABSTRACT

Spermine phosphate hexahydrate crystallizes in space group P2(1)/a with unit-cell dimensions a = 7.931 (1), b = 23.158 (5), c = 6.856 (2) A, and beta = 113.44 (2) degrees at 125 K with unit-cell contents [(C10H30N4)2(4+)(HPO4)4(2-).12H2O]. The packing of spermines and monohydrogen phosphates in this crystal structure has features which may be relevant to the binding of spermine to DNA. Another important structural feature is the presence of channels containing water that is hydrogen bonded as in ice-Ih with disordered protons. The channels occur between sheets of spermine long chains and are also bordered by hydrogen-bonded monohydrogen phosphate chains. The hydrogen-bonding scheme of these water chains proposed on the basis of an earlier X-ray study is now confirmed. Nuclear positions, anisotropic mean-square (m.s.) displacements, an overall scale factor and two extinction parameters (rho and g) were refined using full-matrix least-squares giving values of R(F0(2)) = 0.09, Rw(F0(2)) = 0.11 and S = 1.02. Thermal vibrational analysis revealed that the backbone of the spermine cation can be described as a single rigid segment with a substantial libration of 27 deg2 around the spermine molecular long axis.


Subject(s)
Spermine/chemistry , Crystallization , Crystallography, X-Ray , Molecular Structure , Neutrons , Temperature , Thermodynamics
4.
Med Sci Law ; 37(3): 215-27, 1997 Jul.
Article in English | MEDLINE | ID: mdl-9264228

ABSTRACT

The purpose of this paper is to examine issues of regulation of the market for, and use of, blood and blood products. The situation has changed since the discovery of the Human Immune Deficiency Virus (HIV), the presumed cause of AIDS, because it was recognized that some haemophiliacs were infected with HIV from transfused blood and blood products before 1985. When the danger was realized in that year, regulations were introduced internationally to prevent this, but meanwhile some haemophiliacs developed AIDS. In several countries, governments have accepted responsibility, without liability, for possible transmission of infection, and paid compensation to victims. In France three health service officials have been convicted of fraud and criminal negligence. In March 1997 a trial began in Japan of three drugs company executives accused of promoting the sale of HIV-contaminated blood products. Since then there has been a class action in the USA resulting in awards. Further issues have arisen with regard to the outcome and treatment of asymptomatic infection with HIV. The implications for public safety, and for medical and legal practice, are far reaching and reveal a need for more effective monitoring of the existing procedure for supply and clinical use of blood and blood products.


Subject(s)
Acquired Immunodeficiency Syndrome/prevention & control , Blood Transfusion/legislation & jurisprudence , Blood Transfusion/standards , Acquired Immunodeficiency Syndrome/etiology , Blood-Borne Pathogens , Europe , Female , Hemophilia A/therapy , Human Rights/legislation & jurisprudence , Humans , Male , Social Responsibility , Transfusion Reaction , United Kingdom , United States
5.
Health Care Anal ; 5(1): 31-40; discussion 40-1, 1997 Mar.
Article in English | MEDLINE | ID: mdl-10166048

ABSTRACT

In the UK, over 70% of AIDS, including new cases, is located in a few Districts in central London where the distribution of previously occurring and new cases is essentially confined to the original risk groups of homosexual/bisexual men, drug addicts of both sexes, and some of their sexual partners and consorts. But control policy is still based on the assumption that HIV has already spread from persons in these risk groups into the general population, and that it will spread hereafter at an increased rate because of heterosexual transmission to cause a widespread epidemic of AIDS. The basis and implications of this policy were investigated in the South East region adjacent to London. Analysis of demographic and epidemiological data shows that, with one exception, there is very little extension of AIDS from affected Districts in London to the surrounding region or even to the suburban fringe. Where AIDS is prevalent, as in this exception, the distribution follows the same, original pattern which relates essentially to risks arising from life-styles. There is no significant association between the prevalence or spread of AIDS and conventional markers of deprivation, economic and social disadvantage. Allocations of personnel, services and expenditure, assessed from returns required under the AIDS Control Act of 1987 and official registration data, continue to follow the original policy assumptions. They are therefore unrelated to the numbers of existing and new cases, disproportionate and unrealistic. Claims that this widespread excess of effort is justified by the fact that AIDS has not spread to the general population are falsified by the continuation of cases almost exclusively in risk groups. There is nothing in the data required under the Act or in registrations in this main locus of AIDS in the UK to suggest any change in this or to justify continuation of current expenditure and redundant activities. There is no evidence in these data that ethnic variations in the resident populations of Districts are associated with variations in the prevalence of AIDS. However, the larger figures available in some of the national data do indicate a disproportionate increase in some minority ethnic groups. Further detail about risks factors in these groups are required and, meanwhile, effort and expenditure should be re-orientated toward treatment, contact tracing and other public health measures for more effective containment of the continuing spread of AIDS in all the high risk groups.


Subject(s)
Acquired Immunodeficiency Syndrome/epidemiology , Acquired Immunodeficiency Syndrome/economics , Acquired Immunodeficiency Syndrome/transmission , Communicable Disease Control/economics , Communicable Disease Control/organization & administration , Demography , England/epidemiology , Ethnicity/statistics & numerical data , HIV Seroprevalence , Health Policy , Humans , Incidence , London/epidemiology , Male , Risk Factors , Socioeconomic Factors , Urban Population
6.
Acta Crystallogr B ; 52 ( Pt 2): 357-68, 1996 Apr 01.
Article in English | MEDLINE | ID: mdl-8624243

ABSTRACT

The crystal structures of piperazinium hexanoate-h11, 1/2C4H12N2(2+).C6H11O2-, and piperazinium hexanoate-d11, 1/2C4H12N2(2+).C6D11O2-, have been determined from neutron diffraction data collected at 15 K. Nuclear anisotropic displacement parameters have been analyzed to obtain the internal molecular displacements of the H and D nuclei, given by (u(obs)2)-(u(ext)2) where (u(ext)2) is the contribution assuming all H/D to be carried rigidly on the vibrating molecular framework consisting of the heavier nuclei. In both crystal structures the cation ring is well fitted by the rigid-body model and the anion chain by a model with two rigid segments. In the piperazinium cations the corresponding protons in the two structures have about the same internal vibrational directions and magnitudes except for the two N--H protons, perhaps owing to differences in N--H...O hydrogen bonding. The internal vibrations of corresponding H/D in the h11 and d11 anions have approximately the same vibrational directions. The internal mean-square displacements of the H nuclei are systematically greater than the values of the corresponding D nuclei by an average factor 1.7(3). For both anions, normal-mode analyses have been carried out using the force fields derived from ab initio quantum-mechanical calculations with HF/3-21G and HF/6-31G** basis sets. The values of the resultant H/D internal displacements for C--H(D) bond stretching and methylene out-of-plane vibrations are in good agreement with experiment. However, with either basis set, theory predicts methylene in-plane mean-square displacements significantly greater than the experimental values.


Subject(s)
Caproates/chemistry , Piperazines/chemistry , Chemical Phenomena , Chemistry, Physical , Deuterium , Hydrogen Bonding , Models, Chemical , Molecular Structure , Piperazine , Thermodynamics
7.
Acta Crystallogr B ; 51 ( Pt 6): 1081-96, 1995 Dec 01.
Article in English | MEDLINE | ID: mdl-8554725

ABSTRACT

The charge-density distribution in the crystal structure of the nucleoside beta-cytidine at 123 K has been determined from X-ray diffraction data (Ag K alpha, lambda = 0.5608 A) using all 7233 reflections with sin theta/lambda < or = 1.14 A-1. Maps of electrostatic potential for the cytosine base in cytidine are similar to those derived from previous charge-density studies of cytosine monohydrate and 1-beta-D-arabinosyl-cytosine, after taking chemical differences into account. These results were obtained from pseudoatom multipole refinements including kappa as a variable to describe the expansion or contraction of the spherical valence shell for each atom type. A new structure refinement of this type has also been carried out for cytosine monohydrate. A survey of kappa values for hydrogen indicates that this is a variable which is not well determined experimentally. Variations in kappa H are relayed into the population parameters obtained for other pseudoatoms and can have a small but significant effect on molecular properties, such as the dipole moment. Assuming an average theoretical value of kappa H = 1.24, the molecular dipole moments calculated from the monopole and dipole pseudoatom population parameters are 17 (4) and 8.2 (15) Debye for cytidine nucleoside and cytosine in the monohydrate, respectively. Systems of atomic point charges are presented for cytidine, cytosine and water. These are generally satisfactory in reproducing the experimentally determined molecular electrostatic potentials and dipole moments.


Subject(s)
Cytidine/chemistry , Cytosine/chemistry , Chemical Phenomena , Chemistry, Physical , Crystallization , Crystallography, X-Ray , Electrochemistry , Models, Molecular
8.
Acta Crystallogr A ; 51 ( Pt 4): 489-97, 1995 Jul 01.
Article in English | MEDLINE | ID: mdl-7632379

ABSTRACT

Neutron diffraction data have been collected for hexamethylenetetramine (HMT) at 15, 50, 80, 120, 160 and 200K using a single crystal (mass 8.1 mg). The structure refinement at each temperature included two extinction parameters and third-order thermal parameters for the H nuclei. Extinction effects are very severe with extinction factors as small as 0.2Fkin2 for three reflections (800, 110 and 440). Application of the Sabine extinction theory indicates that the crystal domain size decreases from 115 microns at 200 K to 85 microns at 15 K. The half-width in the mosaic spread (7" of arc) is almost independent of temperature. An extinction model without phase correlations between mosaic blocks gives a slightly better fit to the diffraction data. The nuclear mean square thermal displacements have been analysed assuming no coupling between the external (rigid body) and internal vibrations. This gives mean square displacements for rigid-body vibration in which zero-point vibrational effects are apparent. The methylene H nuclei have internal vibrations approximately independent of temperature. At 200 K, the H nuclear vibrations have a small anharmonic component, but at temperatures below 160 K this becomes insignificant in terms of the experimental error.


Subject(s)
Methenamine/chemistry , Crystallization , Neutrons , Temperature
9.
J Lipid Res ; 36(2): 332-42, 1995 Feb.
Article in English | MEDLINE | ID: mdl-7751821

ABSTRACT

The crystal structure of piperazinium oleate ([C4H12N2]2+.2[C18H34O2]-) has been determined from X-ray diffraction data at -150 degrees C in order to study the oleate chain conformation and molecular packing. Differential scanning calorimetry shows three reversible crystalline state phase transitions (54.5, -34.8, and -54.8 degrees C) in the range from the melting point (84.8 degrees C) to -160 degrees C. The cell constants for a flash-frozen crystal at -150 degrees C are a = 5.630(2), b = 14.900(2), c = 24.825(4) A, alpha = 88.77(2), beta = 88.12(2), gamma = 80.38(2) degrees; Z = 2, space group P1; Dc = 1.05 g cm-3, m.p. = 84.8 degrees C. The cell constants are similar at room temperature except for a doubling of b at -150 degrees C. The crystal structure at -150 degrees C has been refined to R(F2) = 0.116 for 8410 independent reflections. There are two independent oleate anions (A and B), both having an overall extended conformation except for kinks that are different at the cis olefin group. The oleate A chain is ordered while the oleate B chain is disordered in two regions. Because of different torsion angles at bonds adjacent to the double bond, the B-chain olefin group adopts two configurations, one of which is predominant. From the olefin group to the terminal methyl group, the B-chain adopts one of two all-trans configurations with equal probability. It cannot be determined whether the two kinds of disorder are correlated. Taking into account the centrosymmetrically related oleate chains, the crystal structure contains at least six and possibly eight extended chain conformers with different kinks at the olefin group. Third and fourth order displacement parameters have been determined for the partially resolved atomic sites in the oleate B chain and these have been used to map probability density functions for the disordered atoms. The piperazinium cations are in a chair conformation. Each is hydrogen bonded to four oleate anions, forming an infinite ribbon parallel to (025). These ribbons are stacked upon each other to form a monolayer 24.8 A thick parallel to (001).


Subject(s)
Oleic Acids/chemistry , Piperazines/chemistry , Calorimetry , Crystallization , Molecular Structure , Piperazine , Temperature
10.
Acta Crystallogr B ; 50 ( Pt 6): 695-703, 1994 Dec 01.
Article in English | MEDLINE | ID: mdl-7840917

ABSTRACT

Neutron diffraction data for suberic acid [HOOC(CH2)6COOH] were collected at 18.4, 75 and 123 K using a twinned crystal. The neutron data reduction included derivation of a complete set of corrected intensities, as if from a single crystal. This was followed by full-matrix structure refinement in the usual way. The molecule has an almost fully extended conformation with the hydrocarbon chains packed in an orthorhombic mode. Molecules form infinite hydrogen-bonded chains with crystallographic inversion centers occuring at the center and at the ends of each molecule. We suggest that at the twin boundary the hydrogen bonding is different, involving only the hydroxyl groups as both donors and acceptors. Accurate bond lengths have been obtained with corrections for thermal vibration (harmonic for C--C, C--O; harmonic and anharmonic for C--H). Values at the three temperatures agree well in terms of their e.s.d.'s (0.001 A for C--C and C--O and 0.005 A for C--H). Similar agreement is obtained for the corrected bond angles (e.s.d.'s 0.1 degrees for C--C--C, 0.2 degrees for H--C--H). For the methylene groups, the observed m.s. displacement parameters at each temperature are significantly greater at the middle of the molecule than at the ends. This indicates that the molecular backbone is vibrating internally. The thermal vibrations of the molecule have been analysed in terms of a simple segmented body model.


Subject(s)
Caprylates , Dicarboxylic Acids/chemistry , Cold Temperature , Crystallography , Molecular Structure , Neutrons
11.
Acta Crystallogr B ; 50 ( Pt 6): 737-41, 1994 Dec 01.
Article in English | MEDLINE | ID: mdl-7840918

ABSTRACT

The charge-density distribution has been determined from 333 independent X-ray reflections with sin theta/lambda < 1.47 A-1, which were collected with Ag K alpha radiation. As found in a recent refinement using room-temperature data, full-matrix least squares refinement with a multipole model gives rise to an almost complete correlation between certain octapole deformation terms. This is the worst case example of a problem which will always arise to some degree when applying the multipole model in a noncentrosymmetric space group. In this example, the correlation arises between terms which are predominant for describing the bonding density between atoms of the molecule, thereby causing the deformation charge density to have little meaning. However, the total molecular electrostatic potential and the molecular octapole moment are reliably obtained.


Subject(s)
Methenamine/chemistry , Cold Temperature , Electrochemistry , Molecular Structure , X-Ray Diffraction
12.
J Lipid Res ; 35(11): 2069-82, 1994 Nov.
Article in English | MEDLINE | ID: mdl-7868985

ABSTRACT

Cholesteryl butanoate has a complex crystal structure that differs from those of the three main structure type for cholesteryl esters. It contains four molecules (C31H52O2) unrelated by crystal symmetry. The molecules are packed in almost planar sheets and have molecular long axes nearly parallel. However, the molecules have different orientations about their long axes and furthermore, in a given sheet, one of the independent molecules is antiparallel to the other three. Viewed down the molecular long axes, each molecule has six nearest neighbors, but the detailed environment is different for the four independent molecules. Thus the molecular arrangement has features that are characteristic of the short-range order present in the cholesteric mesophase. The monotropic transformation from the crystalline to the cholesteric phase occurs at 98 degrees C. The crystal structure has been accurately determined using 12,146 independent X-ray reflections having sin theta/lambda < 0.63 A-1. All hydrogen atoms were located from a difference Fourier and were included in a refinement that gave R(F2) = 0.064. The C-C bond lengths have sigma = 0.003 A and C-C-C bond angles have sigma = 0.2 degrees. Conformations for the steroid ring system are similar but there are differences in the C17 side chains and the butanoate chains of the four independent molecules. Analysis of atomic m.s. displacement tensors using a segmented-body model indicates that there are internal librations involving both the C17 and butanoate chains in all molecules.


Subject(s)
Cholesterol Esters/chemistry , Crystallography, X-Ray , Fatty Acids/chemistry , Crystallization , Fourier Analysis , Models, Molecular , Molecular Conformation , Molecular Structure
13.
Chem Phys Lipids ; 71(2): 219-28, 1994 May 23.
Article in English | MEDLINE | ID: mdl-8076404

ABSTRACT

At 123 K, the crystal structure of 1,2-dipalmitoyl-sn-glycerol (C35H68O5, M(r) = 568.9) is monoclinic with space group P2(1), a = 5.480(1), b = 7.301(1), c = 43.145(7) A, beta = 92.91(1) degrees, V = 1724 A3, Dc = 1.0960 g cm-3 and Z = 2. Integrated X-ray intensities for 3574 independent reflections were measured with Ni-filtered Cu-K alpha radiation (lambda = 1.5418 A, mu = 0.56 mm-1), and these were all used in a full-matrix least-squares refinement which gave R(F2) = 0.142. Bond lengths and angles have e.s.d.s less than 0.01 A and 0.1 degrees for non-hydrogen atoms. Comparison with a previously reported study of the room temperature structure shows a very similar orthorhombic mode of chain packing but significant conformational differences in the polar headgroup. These changes may occur in conjunction with small changes in enthalpy (less than 1 kJ/mol) observed at 202, 193 and 136 K and with a discontinuity in the unit cell volume observed in the range 200-190 K. Analysis of the atomic mean square displacements at 123 K indicates the presence of internal torsional vibrations in the headgroup region that involve the carbonyl and hydroxyl O-atoms.


Subject(s)
Crystallography, X-Ray , Diglycerides/chemistry , Cold Temperature , Molecular Conformation , Molecular Structure , Temperature , Terminology as Topic , Thermodynamics
14.
Biophys J ; 65(3): 998-1005, 1993 Sep.
Article in English | MEDLINE | ID: mdl-8241415

ABSTRACT

Given the electronic charge parameters obtained from a diffraction study of the charge density distribution in a crystal, a mathematical procedure is presented for deriving the electrostatic potential. The procedure allows the mapping of electrostatic potential for a molecule or group of molecules removed from the crystal structure but with each molecule retaining the effects of polarization owing to the original crystal environment. The method is applied for the neurotransmitter gamma-aminobutyric acid. The potential for a gamma-aminobutyric acid molecule is analyzed in terms of a simple model that is suitable for rapid computations concerned with Coulombic molecular interactions. Outside the molecular envelope at 1.2 A from the atomic nuclei, the total potential is well represented by a sum of spherical atom contributions with V(r) = (q/r) + exp(-beta r2). The most important aspherical component in the potential is the dipole contribution from the hydrogen atoms. This can be represented as V(r, phi) = (0.162 cos phi)/(r2 + 0.615). Here, V is in e/A, r is the distance from each nucleus in A, q is the experimentally determined net atomic charge in electron units, and phi is the angle between r and the bond X-H. We obtain beta = 1.47, 1.66, 1.83 A-2 for C, N, and O respectively. For H, no term in beta is needed.


Subject(s)
gamma-Aminobutyric Acid/chemistry , Biophysical Phenomena , Biophysics , Crystallography, X-Ray , Electrochemistry , Models, Chemical , Molecular Structure
15.
Acta Crystallogr A ; 49 ( Pt 5): 685-92, 1993 Sep 01.
Article in English | MEDLINE | ID: mdl-8217024

ABSTRACT

New refinements of the crystal structure of hexamethylenetetramine (HMT, C6H12N4) have been carried out using previously reported neutron and X-ray diffraction data collected at 298 K. A new feature in the structure model is the inclusion of third-order Gram-Charlier coefficients for the description of the anharmonic C-H bond stretching, which is found to be significant. The charge-density distribution is analyzed in terms of the pseudoatom model of Stewart [Acta Cryst. (1976). A32, 565-574]. Our experimental determination of the molecular octapole moment gives = +1.0 (3)/e/ A3. The refinement involving HMT provides a worst-case example of a general deficiency in the application of the multipole model to noncentrosymmetric structures. Strong least-squares correlations occur involving the electron population parameters of all atoms for certain of the multipole terms, namely those odd-order terms that are invariant under the symmetry operations of the space group.


Subject(s)
Methenamine/chemistry , Crystallography, X-Ray , Electrons , Fourier Analysis , Hot Temperature , Molecular Structure , Neutrons
16.
Acta Crystallogr A ; 49 ( Pt 1): 10-22, 1993 Jan 01.
Article in English | MEDLINE | ID: mdl-8442928

ABSTRACT

For molecular crystals, a procedure is proposed for interpreting experimentally determined atomic mean square anisotropic displacement parameters (ADPs) in terms of the overall molecular vibration together with internal vibrations with the assumption that the molecule consists of a set of linked rigid segments. The internal librations (molecular torsional or bending modes) are described using the variable internal coordinates of the segmented body. In paper I of this two-part report, it is assumed as a zero-order approximation that the internal vibrations about the linkage axes between pairs of segments are uncorrelated with each other and with the overall molecular rigid-body vibrations. As a first-order approximation, the possibility that each internal vibration can be correlated with the external vibrations is also considered. An important feature of this approach is that the internal librations are required to give zero contribution to the overall momentum of the molecule at all times, so the internal coordinates must be orthogonal to the external ones. Also, each of the internal librations involves the motion of all atoms in the molecule. The resulting internal vibrational parameters are invariant to the choice of reference segment. With this procedure, the experimental ADPs obtained from crystal structure determinations involving six small molecules (sym-trinitrobenzene, adenosine, tetra-cyanoquinodimethane, benzamide, alpha-cyanoacetic acid hydrazide and N-acetyl-L-tryptophan methylamide) have been analyzed. As a consequence, vibrational corrections to the bond lengths and angles of the molecule are calculated as well as the frequencies and force constants (with e.s.d.'s) for each internal torsional or bending vibration. Compared with other models used for describing internal vibrations, there are differences in how the total ADP is partitioned between the internal and overall molecular vibrations.


Subject(s)
Molecular Structure , Thermodynamics , Adenosine/chemistry , Benzamides/chemistry , Chemical Phenomena , Chemistry, Physical , Hydrazines/chemistry , Nitriles/chemistry , Trinitrobenzenes/chemistry , Tryptophan/analogs & derivatives , Tryptophan/chemistry , X-Ray Diffraction
17.
Biopolymers ; 32(9): 1141-54, 1992 Sep.
Article in English | MEDLINE | ID: mdl-1420983

ABSTRACT

The charge density distribution in the crystal structure of ammonium dimethylphosphate at 123 K has been determined from x-ray diffraction data (MoK alpha) using 8437 reflections with sin theta/lambda less than 1.33 A-1 [NH4+.(CH3)2PO4-, M(r) = 143.08, monoclinic, P2(1)/c, a = 10.007(1), b = 6.926(1), c = 9.599(2) A, beta = 105.40(1) degrees, V = 641.4(3) A3, Z = 4, F000 = 304, Dx = 1.4815 g.cm-3, mu = 3.726 cm-1]. Least-squares structure refinement assuming Stewart's rigid pseudoatom model (variables including Slater-type radial exponents and electron populations for multipole terms extending to octapoles for C, N, O, and P, and dipoles for H) gave R(F2) = 0.039 for all reflections. The dimethylphosphate anion is in the gauche-gauche conformation and has approximate twofold symmetry. One phosphoryl O atom forms three hydrogen bonds and the other forms one. Neither of the ester O atoms is hydrogen bonded. For the dimethylphosphate anion isolated from the crystal structure, a map of the electrostatic potential obtained using the pseudoatom charge parameters shows that the phosphoryl O atoms are considerably more electronegative than the ester O atoms. The electrostatic potential distribution obtained in this way has been fitted by least squares to a system of atom-centered point charges. The potential calculated from these point charges agrees with the experimental result. It also agrees reasonably well with potentials obtained from three other systems of point charges that are widely used as part of the semiempirical force field for molecular mechanics and molecular dynamics calculations involving nucleic acids.


Subject(s)
Organophosphates/chemistry , Quaternary Ammonium Compounds/chemistry , Electric Conductivity , Fourier Analysis , Models, Molecular , Molecular Conformation , X-Ray Diffraction
18.
Acta Crystallogr B ; 48 ( Pt 2): 217-27, 1992 Apr 01.
Article in English | MEDLINE | ID: mdl-1515111

ABSTRACT

1-Methyluracil (1-methyl-2,4-dioxopyrimidine), C5H6-N2O2, M(r) = 126.12, orthorhombic, Ibam, a = 13.188 (6), b = 13.175 (5), c = 6.214 (3) A, V = 1079.7 (8) A3, Z = 8, Dx = 1.552 g cm-3, lambda (Mo K alpha) = 0.7107 A, mu = 1.317 cm-1, F(000) = 528, T = 123 K, R(F2) = 0.068 for 2996 reflections with sin theta/lambda less than 1.08 A-1. The electronic charge-density distribution has been analyzed in terms of Stewart's rigid pseudoatom model, using restricted Slater radial functions and angular multipole terms extending to octapoles for C, N and O, and quadrupoles for H pseudoatoms. Three different structure refinements have been carried out based on two X-ray diffraction data sets from different crystals collected at temperatures differing by about 20 K. The molecular dipole moment is 6.4 (27) D. Maps of the electrostatic potential for a molecule isolated from the crystal show that atoms O2 and O4 confer overall electro-negativity on one side of the molecule while the CH groups and the C1 methyl group confer electropositivity on the other. For the centrosymmetric hydrogen-bonded dimer (N3-H3...O4'; H...O distances 1.77 A) the electrostatic potential shows electropositive bridges between the molecules. These features are lacking for the C-H...O interactions (distances H6...O2, 2.37; H11...O4, 2.34 A). The electron density and its Laplacian have been determined at the intramolecular bond-critical points and also for the intermolecular H...O interactions. Values for the former are characteristic of covalent bonds. Values of the electron density and Laplacian for the C-H...O interactions are very small and have little or no significance in terms of their e.s.d.'s. The electrostatic energy of interaction for the N-H...O hydrogen-bonded dimer is -10 (12) kJ mol-1. The attractive electrostatic energy increases to -67 (33) kJ mol-1 for a centrosymmetric planar tetramer in which the C-H...O interactions are also formed.


Subject(s)
Uracil/analogs & derivatives , Calorimetry , Electrochemistry , Molecular Conformation , Uracil/chemistry , X-Ray Diffraction
19.
Acta Crystallogr C ; 48 ( Pt 1): 19-22, 1992 Jan 15.
Article in English | MEDLINE | ID: mdl-1605928

ABSTRACT

2Na+.CH3O4P2-.6H2O, Mr = 264.09, monoclinic, Pc, a = 7.277 (1), b = 6.298 (2), c = 11.477 (4) A, beta = 92.44 degrees, V = 525.5 A3, Z = 2, Dx = 1.669 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 35.26 cm-1, F(000) = 276, T = 298 K, R = 0.028 for 781 independent reflections. Three P-O bond lengths are the same (1.513 A) within experimental error, with the ester P-O bond length significantly longer [1.626 (3) A]. The Na ions are octahedrally coordinated by water O atoms and have no direct interaction with the phosphate O atoms. Water molecules form three hydrogen bonds with each phosphate O atom, except the ester O atom which at most forms one weak interaction.


Subject(s)
Organophosphates/chemistry , X-Ray Diffraction , Crystallization , Models, Chemical , Molecular Conformation , Oxygen/chemistry , Sodium/chemistry , Water/chemistry
20.
Acta Crystallogr B ; 47 ( Pt 6): 968-75, 1991 Dec 01.
Article in English | MEDLINE | ID: mdl-1772632

ABSTRACT

(I) Piperazinium n-tetradecanoate (myristate), C4H12N2(2+).2C14H27O2-, Mr = 542.85, m.p. = 368.9 K, triclinic, P1, a = 5.681 (1), b = 7.454 (1), c = 20.676 (3) A, alpha = 84.59 (1), beta = 86.37 (1), gamma = 81.73 (1) degrees, V = 861.5 A3, Z = 1, T = 296 K, Dm = 1.05, Dx = 1.05 g cm-3, F(000) = 304, Mo K alpha, lambda = 0.7107 A, mu = 0.723 cm-1, R = 0.062 for 2198 independent reflections with I greater than sigma (I). (II) Piperazinium n-hexadecanoate (palmitate), C4H12N2(2+).2C16H31O2-, Mr = 598.95, m.p. = 370.2 K, triclinic, P1, a = 5.678 (1), b = 7.472 (1), c = 22.916 (3) A, alpha = 84.64 (1), beta = 89.82 (1), gamma = 81.32 (1) degrees, V = 956.8 A3, Z = 1, T = 296 K, Dm = 1.04, Dx = 1.04 g cm-3, F(000) = 336, Mo K alpha, lambda = 0.7107 A, mu = 0.708 cm-1, R = 0.052 for 1931 independent reflections with I greater than sigma (I). These crystal structures, together with the previously reported n-decanoate and n-dodecanoate (laurate) salts, form an isostructural series. The piperazinium cations, which have a crystallographic centre of symmetry, are in the chair conformation. Each cation forms a salt bridge to four different anions with N ... O distances ranging from 2.67 to 2.70 A. The alkanoate chains are bent with torsion angles of 78.6 degrees (I) and 79.7 degrees (II) at the C3-C4 bond. The longer sections of the alkanoate chains are close-packed together in an antiparallel array.(ABSTRACT TRUNCATED AT 250 WORDS)


Subject(s)
Fatty Acids/chemistry , Myristic Acids/chemistry , Palmitic Acids/chemistry , Piperazines/chemistry , Fourier Analysis , Hot Temperature , Myristic Acid , Palmitic Acid , Piperazine , X-Ray Diffraction
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