Graph-set Analysis Research Articles

Pseudopolymorphism of N-acetyl-L-phenylalanine methyl ester

The structures of two pseudopolymorphs of N-acetyl-L-phenylalanine methyl ester, L-AcFOMe, were determined at both 293 (2) and 150 (2) K. At room temperature, the orthorhombic phase C(12)H(15)NO(3) (I), with space group P2(1)2(1)2(1), converts into the tetragonal phase C(12)H(15)NO(3).0.5H(2)O (II), with space group P4(1)2(1)2, in the presence of water. In the structures of both pseudopolymorphs, alternating layers of hydrophilic and hydrophobic intermolecular interaction can be distinguished. In the hydrophilic layers the structures are stabilized by moderate hydrogen bonds of the type N-H...O for the anhydrous L-AcFOMe and of types N-H...O and O-H...O for the hemihydrate. Weak C-H...pi interactions are observed within the hydrophobic layers: for (I) they are of type III [Malone et al. (1997). J. Chem. Soc. Faraday Trans. 93, 3429-3436], whereas typical type I edge-to-face interactions are present for (II). The differences between the hydrogen-bonding networks of (I) and (II) are discussed in terms of graph-set analysis.

Nitrogen-Rich Tetrazolium Azotetrazolate Salts: A New Family of Insensitive Energetic Materials

The metathesis reaction of sodium azotetrazolate with tetrazolium iodides 5and 6 at reflux in water yielded dihydrated species in both instances (1 and 3, respectively). However, when silver azotetrazolate (Ag2ZT) was used instead of the sodium salt in dry methanol, the anhydrous compounds 2 and 4 formed. An alternative synthesis for 2 and 4 that avoids handling highly sensitive Ag2ZT is introduced. All materials were fully characterized by means of elemental analysis, mass spectrometry (MS), and vibrational (IR, Raman) and NMR (1H, 13C) spectroscopy. Additionally, the crystal structures of the new compounds were determined (1, monoclinic, P21/c; 2–4, triclinic,P1̅). A discussion of the hydrogen bonding by means of graph-set analysis is provided. The thermal behaviors of 1–4 and their constant volume energies of combustion were assessed by DSC and bomb calorimetry measurements, respectively. Their sensitivity to shock, friction, and electrostatic discharge was measured by submitting the compounds to standard tests. The detonation pressures and velocities were calculated from the energies of formation using the EXPLO5 code (1, P = 20.2 GPa, D = 7820 m s−1; 2, P = 20.0 GPa, D = 7803 m s−1; 3, P = 22.4 GPa, D = 8090 m s−1; and 4, P = 21.1 GPa, D = 7977 m s−1. Lastly, the decomposition products were both calculated and experimentally determined.

Hydrogen bonding in diaquatetrakis(urea-κO)MIIdinitrates, withM= Ni and Co

The isomorphous title compounds, [Ni{(NH(2))(2)CO}(4)(H(2)O)(2)](NO(3))(2) and [Co{(NH(2))(2)CO}(4)(H(2)O)(2)](NO(3))(2), feature discrete centrosymmetric cations in octahedral coordinations, formed by four urea molecules linked via their O atoms to the central ion in equatorial positions and two water molecules in trans positions. The complexes are packed in a pseudo-hexagonal manner separated by the nitrate counter-ions. All H atoms are involved in moderate hydrogen bonds of four types: N-H...O=C, N-H...O-N, O-H...O-N and N-H...O-H. Graph-set analysis was applied to distinguish the hydrogen-bond patterns at unitary and higher level graph sets.

Non-Bonded Intermolecular Interactions and Crystal Stability of trans-1,4-Cyclohexanedicarboxylic Acid, 1,4-dibromo

Molecular geometry, crystal packing and thermal stability of trans-1,4-cyclohexanedicarboxylic acid, 1,4-dibromo (I) are examined, in order to analyse the relative influence of the different intermolecular interactions at play. From a comparison with the corresponding properties of trans1,4-cyclohexanedicarboxylic acid (II), some insights on the results of the competition between Br and carboxylic groups are obtained. In the crystalline state, the molecules of both compounds present chair centrosymmetric geometry and build infinite chains through ring hydrogen bonds involving the carboxylic groups. These groups are axial in I and equatorial in II, giving rise to different assembly of the chains. In both compounds there is in general good agreement between the in-crystal geometry and the B3LYP/LanL2DZ optimized geometry of the corresponding isolated molecule. The only significant differences are related to the carboxylic groups. The intermolecular contacts in I have been rationalized on the basis of a graph set analysis. A molecular dynamics based method has been used to analyse the temperature dependence of the mean life time of the different kinds of hydrogen bonds characterized in I. It has been found that the O–H⋅ < eqid2 > ⋅O and C–H⋅ < eqid3 > ⋅O(carbonyl) interactions are the main source of thermal stability. The melting point of I determined within this approach agrees very well with the experimental value.

α-Lactose monohydrate: a redetermination at 150 K

The structure of the monohydrate of α-4-(β-d-galactopyran­osido)-d-glucopyran­ose, more commonly known as α-lactose monohydrate, C12H22O11·H2O, has been previously studied by single-crystal diffraction at ca 296 K [Beevers & Hansen (1971). Acta Cryst. B27, 1323–1325; Fries et al. (1971). Acta Cryst. B27, 994–1005; Noordik et al. (1984). Z. Kristallogr. 168, 59–65]. This redetermination at low temperature [150 (2) K] shows improved precision of geometry. Graph-set analysis of the hydrogen-bonding motifs is presented for the first time.

Derivatives of 1,5-Diamino-1H-tetrazole: A New Family of Energetic Heterocyclic-Based Salts

1,5-Diamino-1H-tetrazole (2, DAT) can easily be protonated by reaction with strong mineral acids, yielding the poorly investigated 1,5-diaminotetrazolium nitrate (2a) and perchlorate (2b). A new synthesis for 2 is introduced that avoids lead azide as a hazardous byproduct. The reaction of 1,5-diamino-1H-tetrazole with iodomethane (7a) followed by the metathesis of the iodide (7a) with silver nitrate (7b), silver dinitramide (7c), or silver azide (7d) leads to a new family of heterocyclic-based salts. In all cases, stable salts were obtained and fully characterized by vibrational (IR, Raman) spectroscopy, multinuclear NMR spectroscopy, mass spectrometry, elemental analysis, X-ray structure determination, and initial safety testing (impact and friction sensitivity). Most of the salts exhibit good thermal stabilities, and both the perchlorate (2b) and the dinitramide (7c) have melting points well below 100 degrees C, yet high decomposition onsets, defining them as new (7c), highly energetic ionic liquids. Preliminary sensitivity testing of the crystalline compounds indicates rather low impact sensitivities for all compounds, the highest being that of the perchlorate (2b) and the dinitramide (7c) with a value of 7 J. In contrast, the friction sensitivities of the perchlorate (2b, 60 N) and the dinitramide (7c, 24 N) are relatively high. The enthalpies of combustion (Delta(c)H degrees ) of 7b-d were determined experimentally using oxygen bomb calorimetry: Delta(c)H degrees (7b) = -2456 cal g(-)(1), Delta(c)H degrees (7c) = -2135 cal g(-)(1), and Delta(c)H degrees (7d) = -3594 cal g(-)(1). The standard enthalpies of formation (Delta(f)H degrees ) of 7b-d were obtained on the basis of quantum chemical computations using the G2 (G3) method: Delta(f)H degrees (7b) = 41.7 (41.2) kcal mol(-)(1), Delta(f)H degrees (7c) = 92.1 (91.1) kcal mol(-)(1), and Delta(f)H degrees (7d) = 161.6 (161.5) kcal mol(-)(1). The detonation velocities (D) and detonation pressures (P) of 2b and 7b-d were calculated using the empirical equations of Kamlet and Jacobs: D(2b) = 8383 m s(-)(1), P(2b) = 32.2 GPa; D(7b) = 7682 m s(-)(1), P(7b) = 23.4 GPa; D(7c) = 8827 m s(-)(1), P(7c) = 33.6 GPa; and D(7d) = 7405 m s(-)(1), P(7d) = 20.8 GPa. For all compounds, a structure determination by single-crystal X-ray diffraction was performed. 2a and 2b crystallize in the monoclinic space groups C2/c and P2(1)/n, respectively. The salts of 7 crystallize in the orthorhombic space groups Pna2(1) (7a, 7d) and Fdd2 (7b). The hydrogen-bonded ring motifs are discussed in the formalism of graph-set analysis of hydrogen-bond patterns and compared in the case of 2a, 2b, and 7b.

Hydrogen bond directed supramolecular arrays utilising hemimellitic acid: Solvent inclusion clathrates

Hemimellitic acid (benzene-1,2,3-tricarboxylic acid) has received surprisingly little attention in the field of crystal engineering, despite it possessing three carboxylic acid groups. Here we utilise this robust functionality in the creation of hydrogen bonding arrays within which solvent molecules (methanol, ethanol, 1-propanol, 2-propanol, 2-methylpropan-2-ol, acetonitrile and acetone) are enclosed. The nature of the solvent of crystallisation (and hence inclusion) allows the hydrogen bonding networks to adopt various architectures including the common brick-wall and herringbone arrangements. The supramolecular hydrogen bonding motifs within the arrays are identified using Etter's graph set analysis.

Structure characterization of molecular complexes for non-linear optical materials I. X-ray analysis and AM1 calculations of 1 : 1 complexes of 8-hydroxiquinoline (1) and isonicotinamide (2) with 2,4,6-trinitrophenol

Abstract C6H2N3O7 –·C9H8NO+ (1), Mr = 374.27, P21/c, a = 8.2606(9), b = 9.2574(9), c = 19.906(2) Å, β = 91.441(8)°, Z = 4, R 1 = 0.0405. C6H2N3O7 –·C6H7N2O+, (2), Mr = 351.24, P21/n, a = 14.3064(6), b = 7.4451(7), c = 14.7209(7) Å, β = 116.626(3)°, Z = 4, R 1 = 0.0385. The packing units in both compounds consist of hydrogen bonded cation-anion pairs. The basic first and second-level graph set analysis are given. The (hyper)polarizabilities have been calculated for the crystallographic and optimized molecules, by the semi-empirical quantum method AM1.

A Whole Output Strategy for Polymorph Screening: Combining Crystal Structure Prediction, Graph Set Analysis, and Targeted Crystallization Experiments in the Case of Diflunisal

This paper describes the combined application of crystal structure prediction and targeted experimental crystallization to diflunisal, a fluorinated, aromatic carboxylic acid. Graph set analysis has been used to analyze and classify the structural predictions, and crystallization solvents have been selected to promote the formation of crystals containing the most commonly predicted hydrogen-bonding motifs. Accordingly, four new crystal structures of this material were solved, two solvates and two new polymorphs. This example further highlights both the insight offered by crystal structure prediction software and the limitations of current solution crystallization strategies.

Crystal structure of iminodiacetic acid monomethyl ester monohydrate, C5H9NO4 · H2O

C5H11NO5, monoclinic, P12i/cl (No. 14), a = 5.212 Â, b= 16.881 Â,c= 10.116 Â,/?= 119.09°, V= 777.8 Â, Ζ = 4, R#(F) = 0.058, wRrefiF) = 0.180, Τ = 293 Κ. Source of material A mixture of iminodiacetic acid (16.8 g, 0.13 mol), thionyl chloride (30.9 g, 0.26 mol) and methanol (85 ml) was placed in a 250 ml round bottoned flask fitted with a reflux condenser and a silica guard tube. The mixture was stirred and heated under reflux for 4 hours. The solution was then washed with water/dichloromethane and the organic layer dried with anhydrous Na2SC>4, evaporated under reduced pressure and left to crystallise from dichloromethane/n-hexane. The (methoxycarbonylmethylamino)-acetic acid was obtained with 15% yield. Melting point: 411 Κ 413 Κ. Ft-IR (cm; group): (1643; C=0 ketone form), (3503; Ν—H). Experimental details The structure was solved by direct methods. The hydrogen atoms of the main residue were placed at calculated positions and refined as riding using the SHELXL-97 defaults [1], The crystal structure contains one water molecule disordered over three positions, sum of the their freely refined occupancies is 1.00(3). The isotropic temperature factors of the three water O atoms were constrained to be equal, the water Η atoms could not be located. Discussion Iminodiacetic acid and its derivatives are important compounds in coordination chemistry. The presence of two close carboxylic groups makes this molecule and its derivatives excellent ion coordination agents. This property has been fully exploited in the preparation of modified polymers and resins for ion capture, both for analytical [2-4] or industrial uses [5,6]. In medical related sciences, iminodiacetic acid derivatives are used as solid phase supports for peptide synthesis [7] and as base for chemical libraries in combinatory chemistry [8]. Iminodiacetic acid is also of great importance in organic chemistry, namely on the synthesis of maleimides [9] and 3,4 di-substituted pyrroles [10] by Friedman method. Following the preparation of the manganese complex of -octaphenyl-porphyrin for our studies of metalloporphyrin-based oxidation of hydrocarbons [11], we synthesised several iminodiacetic derivatives as pyrrole precursors, amongst them, the title compound. The conformation of the zwitterion is close to that found in the second polymorph form of iminodiacetic acid, IMDA2 [12]. The C4 atom is gauche to C1 when the ion is viewed along Ν—C3 and with C3 trans to C2 when viewed along Ν—C1. The formal negative charge is spread over the carboxylate group 03-C4-04 (C—O distances are: d(C4—03) = 1.250(2) Â, d(C4—04) = 1.243(3) Â). The bond distances of the carboxylic acid group indicate one double bond (d(C2=02) = 1.196(3) Â) and one single bond (d(C2—Ol) = 1.326(3) Â). The substituted half of the iminodiacetic acid molecule is approximated planar with Cl, C2, 01,02, C5 lying in a plane (rms deviation from L.S. plane 0.02 A), the nitrogen atom is 0.186(3) Â away from that plane. The zwitterions are bonded together by hydrogen bonds forming layers. The nitrogen atom donates its two hydrogen atoms to the oxygen atoms of the carboxylate groups of neighbouring molecules (N-Hl —03': 2.670(3) Â, 176.2°, 1: x+l, -y-1/2, z+1/2; N-H2-04: 2.986(3) A, 139.0°, ii: x+l.y, z). Using graph-set analysis [13] one recognise at the unitary level, chains of degree 5 running along the [ 100] and [201] directions. In the second polymorph form of iminodiacetic acid, one of the N-H—O bonds also forms a chain of degree 5 while the other displays only discrete patterns [13]. Table 1. Data collection and handling. Crystal: colourless prism, size 0.08 χ 0.10 χ 0.42 mm Wavelength: Cu Ka radiation (1.54180 Â) ft11.06 cm Diffractometer, scan mode: Enraf-Nonius Mach 3, ω/2θ 20max: 144.88° Admeasured, JVfAWjunique: 3178, 1550 Criterion for lobs, Nfhktfe: Jobs > 2 af/obs), 1346 N(param)Knaai: 105 Programs: SHELXS-97 [14], SHELXL-97 [1], PLATON [15], ORTEPn [16] * Correspondence author (e-mail: manuela@pollux.fis.uc.pt)

Conformational flexibility and hydrogen‐bonding patterns of the neotame molecule in its various solid forms

The conformational flexibility and the molecular packing patterns of the neotame molecule in its various crystal forms, including neotame monohydrate, methanol solvate, ethanol solvate, benzene solvate, and anhydrate polymorph G, are analyzed in this work. The Cerius2,™ molecular modeling program with the Dreiding 2.21 force field was employed to calculate the most stable conformations of neotame molecules in the gaseous state and to analyze the conformations of the neotame molecule in its various crystal forms. Using graph set analysis, the hydrogen bond patterns of these crystal forms were compared. The neotame molecule takes different conformations in its crystal forms and in the free gaseous state. Cerius2,™ found 10 conformers with lower conformational energies than those in the actual crystal structures, which represent an energetic compromise. The relatively large differences between the energies of the conformers indicate the necessity for rewriting or customizing the force field for neotame. The hydrogen bonding patterns of the neotame methanol and ethanol solvates are identical, but different from those of the other three forms, which also differ from each other. The neotame molecule in its various crystal forms takes different conformations that differ from those in the gaseous state because of the influence of crystal packing. The intramolecular ring, S(5), is present in all the crystal forms. The following hydrogen bonding patterns occur in some of the crystal forms: diad, D; intramolecular rings, S(6) and S(7); chains, C(5) and C(6); and an intermolecular ring, R22(12). © 2002 Wiley‐Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 91:2047–2056, 2002

A Model for Resonance-Assisted Hydrogen Bonding in Crystals and Its Graph Set Analysis

Resonance-assisted hydrogen bonding is treated by the simple quantum-mechanical model of a particle on a ring with different effective masses in the hydrogen bond and in the conjugated segment attached to its ends. The model is applied to an intramolecular hydrogen bond and extended to a hydrogen-bonded dimer and rings of arbitrary size up to an infinite chain of molecules, thus covering the main patterns of bonding identified by graph-set analysis. Analysis of intramolecular hydrogen bonding yields an electron effective mass in the hydrogen bond segment of about 34 electron masses. Conjugation always lowers the energy, but the lowering per molecule decreases with increasing ring size, that for the chain being one-third of that for the intramolecular hydrogen bond. This result rationalizes a predominance of intramolecular hydrogen bonds and dimer rings, given that geometrical factors also affect bonding.

Disappearing and reappearing polymorphs. The benzocaine:picric acid system.

The low-melting polymorphic modification of the 1:1 complex of benzocaine (BC) and picric acid (PA) had earlier been reported to be an example of a "disappearing polymorph". The BC:PA system has been reinvestigated by thermomicroscopy, calorimetry, solid-state NMR, and X-ray crystallography. The phase diagram has been derived, and robust procedures for the crystallization of the two 1:1 complexes, a hydrate of the 1:1 complex, and a 2:1 complex have been devised. The structures of all four phases have been determined and compared using graph set analysis to characterize the hydrogen-bonding patterns. It is shown that the thorough microscopic investigation of the thermal behavior, combined with calorimetric methods, can lead to the development of strategies to crystallize metastable polymorphic forms which may be difficult to obtain once their stable congeners have been obtained.

Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database.

The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of -psi approximately varphi approximately 105 degrees allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH(2) spacers, this conformation leads to a parallel ladder with rings of equal size. If varphi approaches -60 degrees and psi 180 degrees, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH(2) spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks.

Graph-set analysis of hydrogen-bond patterns: some mathematical concepts. Erratum.

Owing to a serious printing error, this article [Grell et al. (1999). Acta Cryst. B55, 1030-1043] was printed incorrectly. Pages 1029-1044 have thus been reprinted and included as a loose insert with this issue of the journal.

Graph-set analysis of hydrogen-bond patterns: some mathematical concepts.

To provide a foundation for further theoretical and software development of the application of graph sets to patterns of hydrogen bonding and other intermolecular interactions a number of mathematical concepts and tools are defined, developed and demonstrated. Following a review of the basic definitions and uses of graph sets, the directional properties of hydrogen bonds are now included in the treatment. The concepts of a constructor graph and covalent distance matrix have been developed to aid in the generation of a qualitative descriptor for the straightforward, consistent and ultimately automatic (with appropriate software) definition of patterns. An additional mathematical tool, the arrowed T-labeling, has been developed to deal with situations in which pattern-forming moieties are located on crystallographic special positions. To demonstrate the utility and various features of these concepts they are applied in detail to two particular structures, polymorphic iminodiacetic acid [N-(carboxymethyl)glycine] and trans-tetraamminedinitrocobalt(III) acetate. To facilitate the application and use of graph sets many of these developments have already been incorporated into the software of the Cambridge Structural Database, as described in the accompanying paper.

The supramolecular architecture of 4-aminoacetophenone (1-(4-fluorophenyl)ethylidene)hydrazone hydrate. Double T-contacts and extremely low-density water layers in a mixed azine

The crystal structure of unsymmetrical azine 4-aminoacetophenone (1-(4-fluorophenyl)ethylidene)hydrazone hydrate, 1·H2O, was determined. Comparison to the X-ray structures of the symmetrical 4-fluoro- and 4-aminoacetophenone azines, 2 and 3, respectively, reinforces the view of the azine bridge as a conjugation stopper. The focus of the analysis lies with the supramolecular architecture. The structure demonstrates azines as double T-contact synthons and suggests that novel L-type arene-arene contacts also might play a significant role in the supramolecular architecture. The absence of inter-water hydrogen bonding in an extremely low-density water layer is one of the surprising and unique features of the solid-state structure of the title compound. The water layers connect azine layers through a hydrogen bonded network which is described by graph set analysis.Key words: arene-arene interaction, hydrogen bonding, graph set analysis, azine, supramolecular synthon, low density water monolayer.

Hydrogen bonding in two isomorphous bis-guanidinium salts: tetrachlorozincate(II) and tetrabromozincate(II)

The crystal structures of bis-guanidinium tetrachlorozincate(II) and bis-guanidinium tetrabromozincate(II) have been determined by X-rays. Both crystal structures are highly isomorphous; the descriptors of the isomorphism phenomenon are discussed and applied to the present case. The zinc ions are tetrahedrally coordinated. An extensive network of hydrogen bonds determine crystal packing. In each structure, two symmetrically independent cations exhibit quite different hydrogen bond patterns. These patterns are described and discussed in terms of graph set analysis.

5,7-Dichlorokynurenic Acid Hydrate, an Antagonist for the Glycine Binding Site on the NMDA Receptor

The structure of 5,7-dichlorokynurenic acid hydrate (IUPAC name: 5,7-dichloro-4-oxo-1,4-dihydro-2-quinolinecarboxylic acid hydrate), C10H5Cl2NO3.H2O, has been determined by X-ray analysis. The molecule exists as a keto tautomer. All hydrogen-bond donors and acceptors take part in the hydrogen-bonding network which connects molecules into a three-dimensional array. Graph set analysis shows that there are both rings and chains in the network; however, there are no carboxylic acid dimers. The O—H portion of the carboxylic acid group is in a trans orientation with respect to the N—H group of the bicyclic ring system; the plane of the carboxylic group makes an angle of 7.6 (2)° with the plane of heterocyclic ring.

ChemInform Abstract: Pattern in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals

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