PubMed Health⌕ Search

Biomedical subjects

David R Allan

Publications and source records attributed to David R Allan.

15 recordsLinked to original sources
PubMed2006

Exploration of the high-pressure behaviour of polycyclic aromatic hydrocarbons: naphthalene, phenanthrene and pyrene.

The structural response of three members of the family of polycyclic aromatic hydrocarbons (PAHs) to high-pressure recrystallization from dichloromethane solutions is presented. Recrystallization of naphthalene in the 0.2-0.6 GPa pressure range does not result in the formation of a new polymorph. Furthermore, direct compression of a single crystal to 2.1 GPa does not result in a phase transition. A density decrease of 18.2% over the 0.0-2.1 GPa pressure range is observed and the principal effect of pressure is to ;tighten' the herringbone structural motif and decrease the size of void regions. A new polymorph of pyrene, form III, has been crystallized at 0.3 and at 0.5 GPa. Structural investigation of this new polymorph by means of topological analysis and comparison of Hirshfeld surfaces and fingerprint plots shows that intermolecular interactions are substantially different from those found in the ambient-pressure structures, and do not fit a previously established packing model for PAHs. Similar discrepancies are found for the high-pressure polymorph of phenanthrene, which is here re-investigated in greater detail. The structures of these high-pressure polymorphs are dominated by pi...pi stacking with a limited contribution from C-H...pi (peripheral) interactions. It is perhaps not surprising that high-pressure polymorphs deviate from a model that has been devised for ambient-pressure structures, and this may be a direct consequence of the ability of pressure to modify and combine intermolecular interactions in ways that are not usually found at ambient pressure. This is achieved by modifying the relative orientations of molecules and by encouraging the formation of denser structures in which molecules pack together more efficiently.

Journal Article↗
PubMed2006

Combined magnetic and single-crystal X-ray structural study of the linear chain antiferromagnet [(CH3)4N][MnCl3] under varying pressure.

The magnetic susceptibility and single-crystal X-ray structure of the one-dimensional Heisenberg antiferromagnetic chain tetramethylammonium manganese trichloride (TMMC) have been studied under pressure as a facile route to develop structure-property relationships. The X-ray structure of TMMC was determined at 0, 2.1, 3.8, 6.8, 12.2, and 17.0 kbar using diamond-anvil cell techniques and synchrotron radiation. The space group is confirmed to be P6(3)/m up to 17 kbar, and structural refinement shows that the Mn-Mn separations between and along the chains change by about 3.4 and 2.5%, respectively, over 17 kbar. A structural transition from hexagonal to monoclinic symmetry possibly occurs at 17 kbar, associated with a loss of crystal quality. Variable-temperature magnetic susceptibility data were taken at 0, 0.3, 1.5, 2.9, 4.0, 5.2, and 6.5 kbar and show that the intrachain coupling constant changes from -6.85 to -7.81 K over this range. The interchain coupling constant of -0.54 K can also be extracted from the Fisher model modified for interacting chains. The pressure-temperature diagram shows the slope of the intrachain antiferromagnetic coupling with pressure, DeltaT(IAF)/DeltaP, changes from 0.5 to 1.6 K/kbar at 2 kbar where the structure changes from P2(1)/a to P2(1)/m. Comparison of the magnetic and structural data are consistent with the power-law relationship developed by Bloch where J proportional, variant r-n, r = Mn...Mn separation and n approximately 10.

Journal Article↗
PubMed2006

Hexamer formation in tertiary butyl alcohol (2-methyl-2-propanol, C4H10O).

The crystal structure of phase II of tertiary butyl alcohol (2-methyl-2-propanol, C(4)H(10)O) has been solved using a combination of single-crystal X-ray diffraction techniques and ab initio density functional calculations. This trigonal P3 phase, which is stable at both low temperature and high pressure, and the triclinic P1 phase (phase IV) have very similar enthalpies, the calculations revealing only a 3.859 kJ mol(-1) enthalpy difference at ambient pressure, despite the substantial change of the intermolecular bonding motif from helical catemer to hexamer with an increase in pressure or reduction in temperature. The hexamers in the trigonal phase adopt a chair conformation. There are two unique hexamers: at low temperature these are centred at (0, 0, 1/2) and (2/3, 1/3, 0.961 (13)), and at high pressure the centres are (0, 0, 1/2) and (2/3, 1/3, 0.958 (14)). A slight flattening of the hexamers is observed at high pressure and the calculations confirm that phase II becomes more stable relative to phase IV on pressure increase.

Journal Article↗
PubMed2006

High-pressure polymorphism in L-cysteine: the crystal structures of L-cysteine-III and L-cysteine-IV.

The crystal structure of the orthorhombic phase of L-cysteine (hereafter L-cysteine-I) consists of chains of molecules linked via NH...O hydrogen bonds. The chains are linked into a layer by other NH...O hydrogen bonds, forming R4(4)(16) ring motifs. The layers are linked by further NH...O and disordered SH...S/SH...O interactions. The main effects of compression to 1.8 GPa are to contract voids in the middle of the R4(4)(16) rings and to reduce S...S distances from 3.8457 (10) to 3.450 (4) angstroms. The latter is at the lower limit for S...S distances and we suggest that strain about the S atom is responsible for the formation of a new phase of L-cysteine, L-cysteine-III, above 1.8 GPa. The phase transition is accompanied by a change in the NCCS torsion angle from ca 60 to ca -60 degrees and small positional displacements, but with no major changes in the orientations of the molecules. The structure of L-cysteine-III contains similar R-type ring motifs to L-cysteine-I, but there are no S...S contacts within 3.6 angstroms. L-Cysteine-III was found to be stable to at least 4.2 GPa. On decompression to 1.7 GPa, another single-crystal to single-crystal phase transition formed another previously uncharacterized phase, L-cysteine-IV. This phase is not observed on increasing pressure. The structure consists of two crystallographically independent cysteine molecules in the same conformations as those found in L-cysteine-I and L-cysteine-III. The structure separates into zones with are alternately phase I-like and phase III-like. L-Cysteine-IV can therefore be thought of as an unusual example of an intermediate phase. Further decompression to ambient pressure generates L-cysteine-I.

Anisotropy↗
PubMed2006

Effect of pressure on the crystal structure of alpha-glycylglycine to 4.7 GPa; application of Hirshfeld surfaces to analyse contacts on increasing pressure.

The crystal structure of alpha-glycylglycine (alpha-GLYGLY) has been determined at room temperature at pressures between 1.4 and 4.7 GPa. The structure can be considered to consist of layers. The arrangement of molecules within each layer resembles the antiparallel beta-sheet motif observed in proteins, except that in alpha-GLYGLY the motif is constructed through NH...O hydrogen bonds rather than covalent amide links. Compression of alpha-GLYGLY proceeds via the reduction in void sizes. Voids close in such a way as to decrease the distances of stabilizing interactions such as hydrogen bonds and dipolar contacts. The largest reductions in interaction distances tend to occur for those contacts which are longest at ambient pressure. These longer interactions are formed between the beta-sheet-like layers, and the largest component of the strain tensor lies in the same direction. The N...O distance in one NH...O hydrogen bond measures 2.624 (9) angstroms at 4.7 GPa. This is very short for this kind of interaction and the crystal begins to break up above 5.4 GPa, presumably as the result of a phase transition. The changes that occur have been analysed using Hirshfeld surfaces. Changes in the appearance of these surfaces enable rapid assessment of the structural changes that occur on compression.

Anisotropy↗
PubMed2005

Pressure-induced polymorphism in cyclopropylamine.

The crystal structure of cyclopropylamine at 1.2 GPa has been determined by X-ray diffraction methods. The structure of this phase is orthorhombic, space group Pbca and the unit-cell dimensions are a = 5.0741 (10), b = 9.7594 (10) and c = 13.305 (2) A. Only one of the two H atoms of the amino group actively participates in the formation of the hydrogen-bonded chains, C(2) in graph-set notation, which lie parallel to the crystallographic a axis. Additionally, the topology of the crystal packing is studied using both Voronoi-Dirichlet polyhedra and Hirshfeld surface analyses for the low-temperature and the high-pressure structures of cyclopropylamine and the results are compared.

Journal Article↗
PubMed2005

The effect of pressure on the crystal structure of hexagonal L-cystine.

The crystal structure of hexagonal L-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa. The structure of this phase consists of molecules in their zwitterionic form, and crystallizes in the hexagonal space group P6(1)22. The structure consists of hydrogen-bonded layers which are strongly reminiscent of those seen in alpha-glycine, and consist of R_4;4(16) hydrogen-bonded ring motifs. These layers are connected on one side by the disulfide bridges within the cystine molecules, and on the other by NH...O hydrogen bonds to other glycine-like layers. The most compressible unit-cell dimension, and the direction of greatest strain in the structure, is along the c-axis, and application of pressure pushes the layers closer together. The compression occurs approximately equally in the regions of the interlayer hydrogen bonds and the disulfide bridges; in the latter, changes in the C-S-S-C torsion angles allow the cystine molecules to act like springs. The effects of pressure can be interpreted in terms of closing-up of voids in the structure, and this leads to (i) a lessening of the N-C-C-O and C-S-S-C torsional angles, (ii) shortening of the N-H...O hydrogen bonds by 0.10-0.60 A and (iii) a further shortening of an already short S...S contact from 3.444 (4) A to 3.264 (4) A.

Crystallization↗
PubMed2005

The low-temperature and high-pressure crystal structures of cyclobutanol (C4H7OH).

The low-temperature and high-pressure crystal structures of cyclobutanol (C4H7OH) have been determined using single-crystal X-ray diffraction techniques. At temperatures below 220 K, cyclobutanol crystallizes in the Aba2 space group (Z' = 2) and its crystal structure is composed of pseudo-threefold hydrogen-bonded molecular catemers [assigned as C_2;2(4) in graph-set notation], which lie parallel to the crystallographic a axis. At a pressure of 1.3 GPa, the crystal symmetry changes to Pna2(1) (Z' = 1) and the molecular catemers [expressed as C2 in graph-set notation] adopt a pseudo-twofold arrangement. This structural behaviour is in agreement with our previous observations for phenol and its halogenated derivatives 2-chlorophenol and 4-fluorophenol, where pressure was found to favour a molecular packing more closely associated with small alkyl groups rather than that of relatively bulky alkyl groups. In addition, an examination of the molecular coordination environment in the low-temperature and high-pressure structures of cyclobutanol reveals that the change in structure on application of pressure appears to be driven by the molecules assuming a packing arrangement which more closely resembles that adopted in hard-sphere structures.

Journal Article↗
PubMed2005

Structures of the monofluoro- and monochlorophenols at low temperature and high pressure.

2-Fluorophenol, 3-fluorophenol and 3-chlorophenol were recrystallized from frozen solids at 260, 263 and 283 K. All compounds were also crystallized by the application of high pressure (0.36, 0.12 and 0.10 GPa). While 3-fluorophenol and 3-chlorophenol yielded the same phases under both conditions, different polymorphs were obtained for 2-fluorophenol. 4-Chlorophenol was crystallized both from the melt and from benzene to yield two different ambient-pressure polymorphs; crystallization from the melt at 0.02 GPa yielded the same phase as from benzene at ambient pressure. 3-Fluorophenol is unusual in forming a hydrogen-bonded chain along a 2(1) screw axis. Such behaviour is usually only observed for small alcohols, but here it appears to be stabilized by intermolecular C-H...F hydrogen-bond formation. 3-Chlorophenol is a more typical large alcohol and emulates a fourfold screw axis with two independent molecules positioned about a 2(1) axis, although there are significant distortions from this ideal geometry. The two phases of 4-chlorophenol consist of chains or rings connected by C-Cl...H interactions. The low-temperature and high-pressure polymorphs of 2-fluorophenol consist of chains of molecules connected through OH...OH hydrogen bonds; while inter-chain C-H...F interactions are significant at high pressure, there are none in the low-temperature form.

Chlorophenols↗
PubMed2005

Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa.

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the -CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) A and an O...O...O angle of 148.5 (2) degrees ; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7) degrees . Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) A at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) A. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCalphaCO torsion angle from -178.1 (2) degrees at 4.8 GPa to -156.3 (10) degrees at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

Crystallography↗
PubMed2002

The formation of paracetamol (acetaminophen) adducts with hydrogen-bond acceptors.

The crystal structures of five hemiadducts of paracetamol with 1,4-dioxane, N-methylmorpholine, morpholine, N,N-dimethylpiperazine and piperazine and a related 1:1 adduct of paracetamol with 4,4'-bipyridine are described. All structures are characterized by the formation of chains of paracetamol molecules, which are linked via either OHtriplebondO=C interactions [C(9) chains in graph-set notation] or NHtriplebondO=C interactions [C(4) chains], depending on the presence or absence of substituent groups on the guest molecule. In all cases except for the morpholine and bipyridine adducts these chains are connected by hydrogen-bond interactions with the guest molecules, which reside on crystallographic inversion centres. In the bipyridine adduct this linkage also involves a pi-stacking interaction; in the morpholine adduct it is formed between the OH groups of two opposed paracetamol molecules. Most adducts (that with 4,4'-bipyridine is an exception) decompose on heating to give monoclinic paracetamol. This is the first systematic study of a series of co-crystals containing paracetamol.

Acetaminophen↗
PubMed2002

Pressure-induced polymorphism in phenol.

The high-pressure crystal structure of phenol (C(6)H(5)OH), including the positions of the H atoms, has been determined using a combination of single-crystal X-ray diffraction techniques and ab initio density-functional calculations. It is found that at a pressure of 0.16 GPa, which is just sufficient to cause crystallization of a sample held at a temperature just above its ambient-pressure melting point (313 K), a previously unobserved monoclinic structure with P2(1) symmetry is formed. The structure is characterized by the formation of hydrogen-bonded molecular chains, and the molecules within each chain adopt a coplanar arrangement so that they are ordered in an alternating 1-1-1 sequence. Although the crystal structure of the ambient-pressure P112(1) phase is also characterized by the formation of molecular chains, the molecules adopt an approximate threefold arrangement. A series of ab initio calculations indicates that the rearrangement of the molecules from helical to coplanar results in an energy difference of only 0.162 eV molecule(-1) (15.6 kJ mole(-1)) at 0.16 GPa. The calculations also indicate that there is a slight increase in the dipole moment of the molecules, but, as the high-pressure phase has longer hydrogen-bond distances, it is found that, on average, the hydrogen bonds in the ambient-pressure phase are stronger.

Journal Article↗
PubMed2002

Preparation and crystal structure of a trihydrate of paracetamol.

This work reports the preparation and crystal structure of a trihydrate of paracetamol. Crystals were grown by slow cooling of an aqueous solution of paracetamol to 0 degrees C. Single-crystal X-ray diffraction shows that the trihydrate crystallizes in the orthorhombic crystal system, space group Pbca, Z = 8, a = 7.3324(16), b = 12.590(3), c = 22.636(6) A, V = 2089.7(9) A(3). The crystals of the trihydrate dehydrate rapidly at 20 degrees C to give anhydrous paracetamol as its monoclinic form.

Acetaminophen↗