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1.  1,4-Dihydro­benzo[g]quinoxaline-2,3-dione 
The title compound, C12H8N2O2, was prepared by the reaction of the diethyl ester of naphthalene­bis­(oxamate) with tert-BuNH2. The mol­ecule is nearly planar, with an r.m.s. deviation of 0.017 Å from the plane through all 16 non-H atoms. In the crystal, a three-dimensional network is formed, composed of layers of mol­ecules along the b- and c-axis directions, due to the formation of inter­molecular N—H⋯O hydrogen bonds, as well as of chains along the a-axis direction due to parallel displaced sandwich-type π–π inter­actions with average distances between the inter­acting mol­ecules in the range 3.35–3.40 Å.
PMCID: PMC3589036  PMID: 23476272
2.  trans-Bis(ethyl­enediamine)­bis­{2-[N-(2-hy­droxy­eth­yl)oxamoyl­amino]­benzoato}nickel(II) 
The title mononuclear NiII complex, [Ni(C11H11N2O5)2(C2H8N2)2], is built up by inversion symmetry associated with the central Ni atom. The ethyl­enediamine ligands are non-planar. The r.m.s. deviation from the mean plane of the five-membered Ni–ethyl­amine chelate ring plane is 0.1945 Å. In the crystal structure, complex mol­ecules are linked to each other via N—H⋯O and O—-H⋯O hydrogen bonding through translation symmetry along the b and c axes, resulting in an extended supra­molecular network.
PMCID: PMC3007825  PMID: 21588538
3.  N-[2-(2-Chloro­phen­yl)-2-hydroxy­ethyl]propan-2-aminium hemioxalate 
The asymmetric unit of the title compound, C11H17ClNO+·0.5C2O4 2−, consists of one N-[2-(2-chloro­phen­yl)-2-hydroxy­ethyl]propan-2-ammonium cation and one-half of a centrosymmetric oxalate anion. In the cation, the C/C/N plane of the ethyl­ammonium group is almost perpendicular to the benzene ring, with a dihedral angle of 88.72 (17)°. In the crystal structure, the two components are connected by O—H⋯O and N—H⋯O hydrogen bonds, forming a supra­molecular tape along the a axis. Between the tapes, a C—H⋯O inter­action is observed.
PMCID: PMC2969379  PMID: 21582930
4.  4-[Bis(4-fluoro­phen­yl)meth­yl]-1-[(2E)-3-phenyl­prop-2-en-1-yl]piperazin-1-ium 3-carb­oxy­propano­ate 
In the title salt, C26H27F2N2 +·C4H5O4 −, the piperazine N atom bearing the vinylic substituent is protonated. The piperazine ring adopts a chair conformation. In ther crystal, the succinate monoanions are connected via short O—H⋯O hydrogen bonds between the carb­oxy­lic acid and carboxyl­ate groups into undulating chains extending along [001] and the flunarizinium monocations are attached to these chains via N+—H⋯O− hydrogen bonds. C—H⋯O inter­actions connect these chains into a three-dimensional network. The shortest centroid–centroid distance of 3.7256 (10) Å was found between one of the fluorinated benzene rings and the non-fluorinated phenyl ring in the neighbouring mol­ecule related by a glide plane.
PMCID: PMC3569791  PMID: 23424537
5.  Bis(tetra­ethyl­ammonium) bis­(hydrogen l-tartrate) l-tartaric acid monohydrate 
In the title compound, 2C8H20N+·2C4H5O6 −·C4H6O6·H2O, the presence of the two tetra­ethyl­ammonium cations is balanced by two hydrogen l-tartrate anions. Also present in the asymmetric unit are a mol­ecule of l-tartaric acid and a water mol­ecule. The various components are linked by O—H⋯O hydrogen bonds. In the crystal, two-dimensional networks are formed via O—H⋯O hydrogen bonds and C—H⋯O inter­actions involving the water mol­ecule, the hydrogen l-tartrate anions and the l-tartaric acid mol­ecules. These layers, which stack along [001], are separated by tetra­ethyl­ammonium cations. The latter are also involved in C—H⋯O inter­actions with the anions and the l-tartaric acid and water mol­ecules participating in the two-dimensional network.
PMCID: PMC3120442  PMID: 21754714
6.  Acridinium 3-carb­oxy­pyrazine-2-carboxyl­ate 
The title ion pair, C13H10N+·C6H3N2O4 −, contains a protonated acridine cation and a 3-carb­oxy­pyrazine-2-carboxyl­ate monoanion, which are linked together through O—H⋯O, N—H⋯O and weak C—H⋯O hydrogen bonds. These hydrogen bonds generate a C(10) chain graph-set motif. The crystal structure is further stabilized by extensive π–π stacking inter­actions between nearly parallel [dihedral angle = 1.21(2)°] acridine systems. The shortest distance between the centroids of the six-membered rings within the cations is 3.6315 (8) Å. In addition, C—H⋯π edge-to-face inter­actions are present.
PMCID: PMC3008091  PMID: 21588601
7.  (R)-Doxylaminium (R,R)-tartrate 
In the title compound (systematic name: (R)-dimeth­yl{2-[1-phenyl-1-(pyridin-2-yl)eth­oxy]eth­yl}aza­nium (R,R)-3-carb­oxy-2,3-dihy­droxy­propano­ate), C17H23N2O+·C4H5O6 −, the doxylaminium cation is protonated at the N atom. The tartrate monoanions are linked by short, almost linear O—H⋯O hydrogen bonds into chains extended along [100]. These chains are inter­linked by anion–pyridine O—H⋯N hydrogen bonds into a two-dimensional grid structure. WeakC—H⋯O inter­actions also play a role in the crystal packing. An intra­molecular hy­droxy–carboxyl­ate O—H⋯O hydrogen bond influences the conformation of the anion: the hydrogen-bonded fragment is almost planar, the maximum deviation from the mean plane being 0.059 (14) Å. In the cation, the aromatic rings are almost perpendicular [dihedral angle = 84.94 (8)°] and the conformation of the O—C—C—N chain is gauche(−), the dihedral angle is −76.6 (2)°. The absolute configuration was assigned on the basis of known chirality of the parent compound.
PMCID: PMC3344015  PMID: 22589924
8.  3,5-Bis(ethoxy­carbon­yl)-2,6-dimethyl-1,4-dihydro­pyridine-4-carboxylic acid 
The title mol­ecule, C14H19NO6, was synthesized by the reaction of glyoxylic acid, ethyl acetoacetate and NH4HCO3. In the crystal structure, the dihydro­pyridine ring adopts an asymmetric boat-type conformation with the C atom bearing the carboxyl group showing a signficantly larger deviation [0.325 (2) Å] from the base plane then the N atom [0.137 (2) Å]. One of the ethyl groups is disordered over two positions with occupancies of 0.741 (10) and 0.259 (10). The crystal is stabilized by strong inter­molecular hydrogen bonds. N—H⋯O inter­actions form infinite chains in the a direction. O—H⋯O hydrogen bonds form typical carboxylic acid dimers, which link the N—H⋯O chains into a ladder-type double chain.
PMCID: PMC2977273  PMID: 21583459
Journal of Bacteriology  1964;87(1):75-80.
Bojanowski, R. (University of Illinois, Urbana), Elizabeth Gaudy, R. C. Valentine, and R. S. Wolfe. Oxamic transcarbamylase of Streptococcus allantoicus. J. Bacteriol. 87:75–80. 1964.—An improved colorimetric assay for carbamyl oxamate, which allows the precise measurement of the activity of oxamic transcarbamylase, has been developed. Activity is maximum over the pH range from 8.3 to 8.7. A cation requirement is satisfied by 2.5 × 10−3m Mg++ or Mn++. The equilibrium constant for the phosphorolysis of carbamyl oxamic acid is 1.6, corresponding to a negative free energy change of −285 cal per mole.
PMCID: PMC276964  PMID: 14102876
10.  Di-μ-azido-κ4 N:N-bis­({2-[(3-amino-2,2-dimethyl­prop­yl)imino­meth­yl]-6-meth­oxy­phenolato-1κ3 N,N′,O 1}copper(II)) 
The complete mol­ecule of the title complex, [Cu2(C13H19N2O2)2(N3)2], is generated by the application of a centre of inversion. The central Cu2N2 core is a rhombus as the μ2-azide ligands bridge in an asymmetric fashion. Each CuII atom is also coordinated by a monoanionic tridentate Schiff base ligand via the anti­cipated oxide O, imine N and amine N atoms. The resulting N4O coordination geometry is based on a square pyramid. No specific inter­molecular inter­actions are noted in the crystal packing, but the amine H atoms form intra­molecular N—H⋯O(oxide)/N(azide) hydrogen bonds.
PMCID: PMC3393238  PMID: 22807806
11.  Bis(2,6-diamino-3,5-dibromo­pyridinium) hexa­bromidostannate(IV) 
The asymmetric unit of the title compound, (C5H6Br2N3)2[SnBr6], contains one cation and one half-anion in which the Sn atom is located on a crystallographic centre of inversion and is in a quasi-octa­hedral geometry. The crystal structure is assembled via hydrogen-bonding inter­actions of two kinds, N(pyridine/amine)—H⋯Br—Sn, along with C—Br⋯Br—Sn interactions [3.4925 (19) Å]. The cations are involved in π–π stacking, which adds an extra supra­molecularity as it presents a strong case of offset-face-to-face motifs [centroid–centroid distance = 3.577 (3) Å]. The inter­molecular hydrogen bonds, short Br⋯Br inter­actions and π–π stacking result in the formation of a three-dimensional supra­molecular architecture.
PMCID: PMC2977624  PMID: 21583810
12.  Bis(adamantan-1-aminium) hydrogen phosphate fumaric acid sesquisolvate 
The asymmetric unit of the title compound, 2C10H18N+·HPO4 2−·1.5C4H4O4, contains two adamantan-1-aminium cations, one hydrogen phosphate anion, and one and a half mol­ecules of fumaric acid, one of which exhibits crystallographic inversion symmetry. Each HPO4 2− anion is hydrogen bonded, via all of its O atoms, to four NH3 + groups of the adamantan-1-aminium cations, forming chains along [100]. These chains are, in turn, inter­connected via a set of O—H⋯O hydrogen bonds involving the fumaric acid solvent mol­ecules, forming layers parallel to (001). Weak C—H⋯O inter­actions lead to a consolidation of the three-dimensional set-up.
PMCID: PMC3414978  PMID: 22904965
13.  (Z)-1-(2-Chloro­phen­yl)-3-methyl-4-[2-(4-nitro­phen­yl)hydrazin-1-yl­idene]-1H-pyrazol-5(4H)-one 
There are two independent mol­ecules, A and B, in the asymmetric unit of the title compound, C16H12ClN5O3. The relative orientations of the chloro­phenyl ring with respect to the pyrazole ring in the two crystallographically independent mol­ecules are different, and their corresponding dihedral angles are −53.3 (2) and 114.09 (18)° in mol­ecules A and B, respectively. There are two strong intramolecular N—H⋯O hydrogen bonds, and two weak intramolecular C—H⋯O and C—H⋯Cl hydrogen bonds. The crystal packing is constructed by weak C—H⋯O and N—H⋯O inter­actions, and two π–π stacking inter­actions [centroid–centroid distances = 3.7894 (9) and 3.5719 (10) Å], forming a mol­ecular ladder along the a axis.
PMCID: PMC3414286  PMID: 22904819
14.  4,4′-Bipyridine–terephthalic acid (1/1) 
The asymmetric unit of the title compound, C10H8N2·C8H6O4, consists of one half-mol­ecule of each moiety, 4,4′-bipyridine (bpy) and terephthalic acid (bdc), both being located on crystallographic inversion centers. They are linked together via strong inter­molecular O—H⋯N hydrogen bonds, forming infinite chains propagating along [1-21]. The chains are further connected through C—H⋯O inter­actions giving sheets in (012). The sheets are linked via π–π inter­actions between the bpy rings and the bdc–bpy rings [centroid–centroid distances = 3.690 (2) and 3.869 (2) Å], resulting in the formation of a three-dimensional supra­molecular layer-like structure.
PMCID: PMC3379304  PMID: 22719502
15.  1,4-Bis(4-pyridylmeth­yl)piperazin-1-ium perchlorate fumaric acid hemisolvate 
In the title salt, C16H21N4 +·ClO4 −·0.5C4H4O4, fumaric acid mol­ecules, situated across crystallographic inversion centres, are O—H⋯N hydrogen bonded to two protonated 1,4-bis­(4-pyridylmeth­yl)piperazine cations, forming trimolecular units. These construct one-dimensional supra­molecular ribbons by N—H⋯N hydrogen bonding, and further aggregate via π–π inter­actions [shortest C⋯C contact = 3.640 (1) Å] and perchlorate-mediated C—H⋯O inter­actions.
PMCID: PMC2977376  PMID: 21583520
16.  The ygeW Encoded Protein from Escherichia coli is a Knotted Ancestral Catabolic Transcarbamylase 
Proteins  2011;79(7):2327-2334.
The allantoin degradation pathway in E. coli has long been thought to involve a putative novel oxamate transcarbamylase (OXTCase) that converts oxaluric acid to oxamate and carbamyl phosphate (CP), a substrate for carbamate kinase (CK). In the genome sequence of E. coli, the only gene that could encode a novel transcarbamylase is the ygeW gene. However, the recombinant protein has no transcarbamylase activity with oxamate, allantoin, or twenty five other related compounds as potential substrates. The crystal structures of this transcarbamylase with unknown function (UTCase) has been determined and refined at 2.0 Å resolution, providing structural insights into its possible function. Like N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-transcarbamylase, UTCase has a deep 31 trefoil knot close to the active site, in contrast to aspartate transcarbamylase and ornithine transcarbamylase which do not have a knot. A Blast search of completed genomes indicates that 52 species including one non-bacterial species, Trichomonas vaginalis G3, have the ygeW gene. Gene context analysis and the structure of UTCase suggest that it is probably an ancestral catabolic transcarbamylase.
PMCID: PMC3115391  PMID: 21557323
ygeW gene; transcarbamylase; purine degradation pathway; knotted protein
17.  5-Methyl­isoxazole-4-carboxylic acid 
In the title compound, C5H5NO3, the mol­ecule lies on a crystallographic mirror plane with one half-mol­ecule in the asymmetric unit. An intramolecular C—H⋯O inter­action is present. In the crystal, strong inter­molecular O—H⋯N hydrogen bonds result in the formation of a linear chain structure along [100], and there are also weak C—H⋯O hydrogen bonds between the chains which help to stabilize the crystal packing.
PMCID: PMC2971889  PMID: 21578861
18.  Hexaaqua­magnesium bis­(3-carb­oxy-4-hy­droxy­benzene­sulfonate) dihydrate 
In the crystal structure of the title compound, [Mg(H2O)6](C7H5O6S)2·2H2O, the octa­hedral complex cation lies on an inversion centre and is hydrogen bonded through the coordinated water molecules to the substituted benzene­sulfonate monoanions and the water mol­ecules of solvation. These inter­actions together with a carb­oxy­lic acid O—H⋯O(sulfonate) association give a three-dimensional structure.
PMCID: PMC3200685  PMID: 22065818
19.  3,6-Diaza­octane-1,8-diaminium diiodide 
The asymmetric unit of the title salt, C6H20N4 2+·2I−, comprises half a 3,6-diaza­octane-1,8-diaminium dication plus an I− anion. The dications are symmetrical and lie across crystallographic centres of inversion. In the crystal, the ions form a network involving mainly weak N—H⋯I inter­molecular inter­actions: two H atoms of the ammonium group form inter­actions with two I− anions and the H atom of the secondary amine forms a weak inter­action with a third I− cation. The third ammonium H atom is hydrogen bonded to a secondary amine of an adjacent cation. The backbone of the cation does not form a uniformly trans chain, but is ‘kinked’ [C—N—C—C torsion angle = 71.5 (2)°], probably to accommodate the direct hydrogen bond between the ammonium group and the secondary amine in an adjacent cation.
PMCID: PMC3414312  PMID: 22904845
20.  Tetra­quinolinium ditelluro(VI)octa­vanadate(V) octa­hydrate 
In the title compound, (C9H8N)4[Te2V8O28]·8H2O, the com­plete heteropolyanion is generated by a crystallographic inversion centre. One of the two quniolinium ions forms an N—H⋯Op (p = polyoxidometallate) hydrogen bond and the other an N—H⋯Ow (w = water) hydrogen bond. The water mol­ecules further link the components by O—H⋯Op and O—H⋯Ow hydrogen bonds. A number of C—H⋯O inter­actions and aromatic π–π stacking inter­actions [shortest centroid–centroid separation = 3.541 (7) Å] are also observed. Together, these generate a three-dimensional network.
PMCID: PMC3884254  PMID: 24454030
21.  The betainic form of (imidazol-2-yl)phenylphosphinic acid hydrate 
Single crystals of the title compound, (imidazolium-2-yl)phenyl­phosphinate monohydrate, C9H9N2O2·H2O, were ob­tained from methanol/water after deprotection and oxidation of bis­(1-diethoxy­methyl­imidazol-2-yl)phenyl­phosphane. In the structure, several N–H⋯O and P—O⋯H–O hydrogen bonds are found. π–π inter­actions between the protonated imidazolyl rings [centroid–centroid distance = 3.977 (2) Å] help to establish the crystal packing. The hydrate water mol­ecule builds hydrogen bridges to three mol­ecules of the phosphinic acid by the O and both H atoms.
PMCID: PMC2979513  PMID: 21579513
22.  4-Carbamoylpiperidinium 2-carb­oxy­benzoate–benzene-1,2-dicarb­oxy­lic acid (1/1) 
The asymmetric unit of the title salt adduct, C6H13N2O+·C8H5O4 −·C8H6O4, comprises one isonipecotamide cation, a hydrogen phthalate anion and a phthalic acid adduct mol­ecule. These form a two-dimensional hydrogen-bonded network through head-to-tail cation–anion–adduct mol­ecule inter­actions which include a cyclic heteromolecular amide–carboxyl­ate motif [graph set R 2 2(8)], conjoint cyclic R 2 2(6) and R 3 3(10) piperidinium N—H⋯Ocarbox­yl associations, as well as strong carboxyl O—H⋯Ocarbox­yl hydrogen bonds.
PMCID: PMC3052136  PMID: 21522329
23.  N-[2-(2-Chloro­phen­yl)-2-hydroxy­ethyl]propan-2-aminium nitrate 
In the title compound, C11H17ClNO+·NO3 −, the side chain of the ethyl­ammonium group is orientated approximately perpendicular to the benzene ring, the dihedral angle between the C/C/N plane of the ethyl­ammonium group and the benzene ring being 79.40 (18)°. In the crystal structure, inter­molecular O—H⋯O and N—H⋯O hydrogen bonds are observed between the cation and the anion.
PMCID: PMC2979831  PMID: 21579812
24.  Conformational heterogeneity within the Michaelis complex of lactate dehydrogenase† 
The journal of physical chemistry. B  2011;115(23):7670-7678.
A series of isotope edited IR measurements, both static as well as temperature jump relaxation spectroscopy, are performed on lactate dehydrogenase (LDH) to determine the ensemble of structures available to its Michaelis complex. There clearly has been a substantial reduction in the number of states available to the pyruvate substrate (as modeled by the substrate mimic, oxamate) and NADH when bound to protein compared to dissolved in solution, as determined by the bandwidths and positions of the critical C2=O band of bound substrate mimic and the C4-H stretch of NADH reduced nicotinamide group. Moreover, it is found that a strong ionic bond (characterized by a signature IR band discovered in this study) is formed between the carboxyl group of bound pyruvate with (presumably) Arg171, forming a strong ‘anchor’ within the protein matrix. However, conformational heterogeneity within the Michaelis complex is found that has an impact on both catalytic efficiency and thermodynamics of the enzyme.
PMCID: PMC3111758  PMID: 21568287
25.  3,4-Dihy­droxy­benzoic acid pyridine monosolvate 
The asymmetric unit of the title compound, C7H6O4·C5H5N, consists of one 3,4-dihy­droxy­benzoic acid and one pyridine mol­ecule, both located on general positions. The 3,4-dihy­droxy­benzoic acid mol­ecules are arranged in layers and are connected by inter­molecular O—H⋯O hydrogen bonding, forming channels along the a axis in which the pyridine mol­ecules are located. The pyridine and the acid mol­ecules are additionally linked by strong O—H⋯N hydrogen bonding and by weak π–π stacking inter­actions with centroid–centroid distances between the pyridine rings of 3.727 (2) Å.
PMCID: PMC3011498  PMID: 21589515

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