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Simon Parsons

Publications and source records attributed to Simon Parsons.

At least 55 records · Page 3Linked to original sources

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↗

1,1,1-Tris(hydroxymethyl)propane in manganese carboxylate chemistry: synthesis, structure and magnetic properties of a mixed-valence [MnIII4MnII4] cluster featuring the novel [MnIII4MnII4(mu3-OR)6(mu2-OR)8]6+ core.

The reaction between MnBr(2).4H(2)O with H(3)tmp (1,1,1-tris(hydroxymethyl)propane) in MeCN in the presence of Na(O(2)CCMe(3)) and NBu(4)Br produces the complex [Mn(8)(O(2)CCMe(3))(2)(tmp)(2)(Htmp)(4)Br(4)(H(2)O)(2)].2MeCN (1.2MeCN) in good yield. The centrosymmetric octanuclear molecule consists of four Mn(III) and four Mn(II) ions assembled together by fourteen alkoxo bridges to give a [Mn(III)(4)Mn(II)(4)(mu(3)-OR)(6)(mu(2)-OR)(8)](6+) rod-like core in which the metal centres are arranged in a planar zigzag fashion. Peripheral ligation is provided by a combination of bridging pivalate ions, terminal bromides and water molecules. Dc magnetic susceptibility measurements reveal the presence of dominant antiferromagnetic interactions leading to a spin ground state of S = 0. A rationalization of this result is attempted by structural comparison with previously reported tetranuclear manganese complexes containing the [Mn(III)(2)Mn(II)(2)(mu(3)-OR)(2)(mu(2)-OR)(4)] core in which the magnetic interactions are ferromagnetic.

Bromides↗

Contrasting chemistry of cis- and trans-platinum(II) diamine anticancer compounds: hydrolysis studies of picoline complexes.

cis-[PtCl2(NH3)(2-picoline)] (AMD473) is currently on clinical trials as an anticancer drug. The trans isomer, AMD443 (1), is also cytotoxic in a variety of cancer cell lines. The X-ray crystal structure of the trans isomer (1) shows that the pyridine ring is tilted by 69 degrees with respect to the platinum square-plane in contrast to the cis isomer in which it is almost perpendicular (103 degrees ). In the 3-picoline (2) and 4-picoline (3) trans isomers, the ring is tilted by 58 degrees /60 degrees (2 molecules/unit cell) and by 56 degrees , respectively. Hydrolysis may be an important step in the intracellular activation and anticancer mechanism of action of these complexes. The first hydrolysis step is relatively fast even at 277 K, with rate constants (determined by 1H,15N NMR) of k1 = 2.6 x 10(-5) s(-1), 12.7 x 10(-5) s(-1), and 5.2 x 10(-5) s(-1) (I = 0.1 M) for formation of the monoaqua complexes of 1-3, respectively. Although the hydrolysis of 3 is slower than 2, it is hydrolyzed to a greater extent. No formation of the diaqua complex was observed for any of the three complexes at 277 K, and it accounts for <3% of the platinum species at 310 K. In general the extent of hydrolysis of the trans complexes is much less than for their cis analogues. The pK(a) values for the monoaqua adducts of 1-3 were determined to be 5.55, 5.35, and 5.39, respectively, suggesting that they would exist largely as the monohydroxo complex at physiological pH. The pKa values for the diaqua adducts were determined to be 4.03 and 7.01 for 1, 3.97 and 6.78 for 2, and 3.94 and 6.88 for 3, the first pK(a) being >1 unit lower than for related cis complexes.

Animals↗

Decomposition of monochlorogallane, [H2GaCl]n, and adducts with amine and phosphine bases: formation of cationic gallane derivatives.

Thermal decomposition of monochlorogallane, [H2GaCl]n, at ambient temperatures results in the formation of subvalent gallium species. To Ga[HGaCl3], previously reported, has now been added a second mixed-valence solid, Ga4[HGaCl3]2[Ga2Cl6] (1), the crystal structure of which at 150 K shows a number of unusual features. Adducts of monochlorogallane, most readily prepared from the hydrochloride of the base and LiGaH4 in appropriate proportions, include not only the 1:1 molecular complex Me3P.GaH2Cl (2), but also 2:1 amine complexes which prove to be cationic gallane derivatives, [H2Ga(NH2R)2]+Cl-, where R = tBu (3a) or sBu (3b). All three of these complexes have been characterized crystallographically at 150 K.

Journal Article↗

Synthesis and structural characterisation of primary amine adducts of gallane, RH2N.GaH3, and of their decomposition products, [RHNGaH2]n(R = Me, n= 3; R =tBu, n= 2).

Primary amine-gallane adducts, RH(2)N.GaH(3)[R = Me (1) and (t)Bu (2)], have been isolated for the first time from the reaction of [RNH(3)]Cl with LiGaH(4) in Et(2)O solution at ca. 273 K and characterised by their vibrational and (1)H NMR spectra. The structures of single crystals, grown at low temperatures and determined by X-ray diffraction, reveal pseudo-polymeric arrays of RH(2)N.GaH(3) molecules with Ga-N distances of 2.0424(18) and 2.058(5)A for 1 and 2, respectively. The adducts decompose at or near ambient temperatures with the elimination of H(2) and formation of the corresponding monoalkylamido derivative [RHNGaH(2)](n). The crystal structures of these at 150 K consist of either [MeHNGaH(2)](3) molecules with a "skew-boat" conformation for the cyclic Ga(3)N(3) skeleton (3) or [(t)BuHNGaH(2)](2) molecules with a four-membered Ga(2)N(2) core (4), with Ga-N distances averaging 1.986(8) and 1.991(3)A for 3 and 4, respectively. The crystalline solids 1, 3 and 4 feature intermolecular N-H...H-Ga interactions with H...H distances estimated to fall in the range 2.1-2.3 A. The significance of these is discussed.

Journal Article↗

A temporal constraint structure for extracting temporal information from clinical narrative.

INTRODUCTION: Time is an essential element in medical data and knowledge which is intrinsically connected with medical reasoning tasks. Many temporal reasoning mechanisms use constraint-based approaches. Our previous research demonstrates that electronic discharge summaries can be modeled as a simple temporal problem (STP). OBJECTIVE: To categorize temporal expressions in clinical narrative text and to propose and evaluate a temporal constraint structure designed to model this temporal information and to support the implementation of higher-level temporal reasoning. METHODS: A corpus of 200 random discharge summaries across 18 years was applied in a grounded approach to construct a representation structure. Then, a subset of 100 discharge summaries was used to tally the frequency of each identified time category and the percentage of temporal expressions modeled by the structure. Fifty random expressions were used to assess inter-coder agreement. RESULTS: Six main categories of temporal expressions were identified. The constructed temporal constraint structure models time over which an event occurs by constraining its starting time and ending time. It includes a set of fields for the endpoint(s) of an event, anchor information, qualitative and metric temporal relations, and vagueness. In 100 discharge summaries, 1961 of 2022 (97%) identified temporal expressions were effectively modeled using the temporal constraint structure. Inter-coder evaluation of 50 expressions yielded exact match in 90%, partial match with trivial differences in 8%, partial match with large differences in 2%, and total mismatch in 0%. CONCLUSION: The proposed temporal constraint structure embodies a sufficient and successful implementation method to encode the diversity of temporal information in discharge summaries. Placing data within the structure provides a foundational representation upon which further reasoning, including the addition of domain knowledge and other post-processing to implement an STP, can be accomplished.

Database Management Systems↗

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↗

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↗

G-G base-pairing in nucleobase adducts of the anticancer drug cis-[PtCl2(NH3)(2-picoline)] and its trans isomer.

cis-[PtCl2(NH3)(2-picoline)] (AMD473) is a sterically-hindered anticancer complex with a profile of chemical and biological activity that differs significantly from that of cisplatin. Adducts of AMD473 with neutral 9-ethylguanine (9-EtGH) and anionic (N1-deprotonated) 9-ethylguanine (9-EtG) as perchlorate and nitrate salts, and also a nitrate salt of the trans isomer (AMD443), were prepared and their structures determined by X-ray crystallography: cis-[Pt(NH3)(2-pic)(9-EtGH)2](ClO4)2 (1).2H(2)OMe(2)CO, cis-[Pt(NH3)(2-pic)(9-EtGH)2](NO3)2 (2).2H2O, cis-[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (3),3.5 H2O, trans-[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (4).8H2O. In all cases, platinum coordination is through N7 of neutral (1, 2) and anionic (3, 4) guanine. In each complex, the guanine bases are arranged in the head-to-tail conformation. In complex 1, there is an infinite array of six-molecule cycles, based on both hydrogen bonding and pi-pi stacking of the 2-picoline and guanine rings. Platinum(II) coordinated at N7 acidifies the N1 proton of neutral 9-ethylguanine (pKa = 9.57) to give pKa1 = 8.40 and pKa2 = 8.75 for complex 2, and pKa1 = 7.77 and pKa2 = 9.00 for complex 4. In complexes 3 and 4, three intermolecular hydrogen bonds are formed between neutral and deprotonated guanine ligands involving O6, N1 and N2 sites. Unusually, both of the platinated guanine bases of complexes 3 and 4 participate in this triple G triple bond G hydrogen bonding. This is the first report of X-ray crystal structures of nucleobase adducts of the promising anticancer drug AMD473.

Antineoplastic Agents↗

Studies of an enneanuclear manganese single-molecule magnet.

The reaction of [Mn(3)O(O(2)CMe)(6)(py)(3)] with the tripodal ligand H(3)thme (1,1,1-tris(hydroxymethyl)ethane) affords the enneanuclear complex [Mn(9)O(7)(O(2)CCH(3))(11)(thme)(py)(3)(H(2)O)(2)] 1.1MeCN.1Et(2)O. The metallic skeleton of complex 1 comprises a series of 10 edge-sharing triangles that describes part of an idealized icosahedron. Variable temperature direct current (dc) magnetic susceptibility data collected in the 1.8-300 K temperature range and in fields up to 5.5 T were fitted to give a spin ground state of S = (17)/(2) with an axial zero-field splitting parameter D = -0.29 cm(-)(1). Ac susceptibility studies indicate frequency-dependent out-of-phase signals below 4 K and an effective barrier for the relaxation of the magnetization of U(eff) = 27 K. Magnetic measurements of single crystals of 1 at low temperature show time- and temperature-dependent hysteresis loops which contain steps at regular intervals of field. Inelastic neutron scattering (INS) studies on complex 1 confirm the S = (17)/(2) ground state and analysis of the INS transitions within the zero-field split ground state leads to determination of the axial anisotropy, D = -0.249 cm(-)(1), and the crystal field parameter, B(4)(0) = 7(4) x 10(-)(6) cm(-)(1). Frequency domain magnetic resonance spectroscopy (FDMRS) determined the same parameters as D = -0.247 cm(-)(1) and B(4)(0) = 4.6 x 10(-)(6) cm(-)(1). DFT calculations are fully consistent with the experimental findings of two Mn(II) and four Mn(III) ions "spin up" and three Mn(IV) ions "spin down" resulting in the S = (17)/(2) spin ground state of the molecule, with D = -0.23 cm(-)(1) and U = 26.2 K.

Journal Article↗

1,1,3,3-Tetramethylguanidine-gallane, (Me2N)2CN(H).GaH3: an unusually strongly bound gallane adduct.

The novel adduct 1,1,3,3-tetramethylguanidine-gallane, (Me2N)2CN(H).GaH3, has been prepared by the reaction of [(Me2N)2CNH2]+Cl- with LiGaH4 in Et2O solution. Its spectroscopic properties indicate a monomeric species with an unusually strong coordinate link between the imido function and GaH3, an inference confirmed by the crystal structure at 150 K which also reveals significant secondary interactions through non-classical N-H...H-Ga bridges. Despite the intrinsic strength of the Ga-N bond, however, vaporisation at ca. 310 K occurs with partial dissociation, and decomposition via more than one pathway proceeds at temperatures >330-350 K to give a variety of products, including the free base, Me2NH, H2, and a novel gallium-nitrogen compound composed of a Ga4N4 cubane-like core bridged on three edges by -N{C(NMe2)2}GaH2- units.

Journal Article↗

Protein recognition of macrocycles: binding of anti-HIV metallocyclams to lysozyme.

The macrocyclic antiviral drug xylyl-bicyclam blocks entry of HIV into cells by targeting the CXCR4 coreceptor, a seven-helix transmembrane G-protein-coupled receptor. Its affinity for CXCR4 is enhanced by binding to Cu2+, Ni2+, or Zn2+. Metallocyclams have a rich configurational chemistry and proteins may bind selectively to specific metallocyclam configurations. Our studies of lysozyme reveal structural details of protein-metallocyclam interactions that are important for receptor recognition. Solution NMR studies show that Cu-cyclam interacts with specific tryptophan residues of lysozyme (Trp-62, Trp-63, and Trp-123). Two major binding sites for both Cu-cyclam and Cu2-xylyl-bicyclam were detected by x-ray crystallography. In the first site, Cu2+ in one cyclam ring of Cu2-xylyl-bicyclam adopts a trans configuration and is coordinated to a carboxylate oxygen of Asp-101, whereas for Cu-cyclam two ring NH groups form H bonds to the carboxylate oxygens of Asp-101, stabilizing an unusual cis (folded) cyclam configuration. For both complexes in this site, a cyclam ring is sandwiched between the indole side chains of two tryptophan residues (Trp-62 and Trp-63). In the second site, a trans cyclam ring is stacked on Trp-123 and H bonded to the backbone carbonyl of Gly-117. We show that there is a pocket in a model of the human CXCR4 coreceptor in which trans and cis configurations of metallobicyclam can bind by direct metal coordination to carboxylate side chains, cyclam-NH...carboxylate H bonding, together with hydrophobic interactions with tryptophan residues. These studies provide a structural basis for the design of macrocycles that bind stereospecifically to G-coupled and other protein receptors.

Animals↗