Recurrence of carboxylic acid-pyridine supramolecular synthon in the crystal structures of some pyrazinecarboxylic acids.

X-ray crystal structures of pyrazinic acid 1 and isomeric methylpyrazine carboxylic acids 2-4 are analyzed to examine the occurrence of carboxylic acid-pyridine supramolecular synthon V in these heterocyclic acids. Synthon V, assembled by (carboxyl)O-H...N(pyridine) and (pyridine)C-H...O(carbonyl) hydrogen bonds, controls self-assembly in the crystal structures of pyridine and pyrazine monocarboxylic acids. The recurrence of acid-pyridine heterodimer V compared to the more common acid-acid homodimer I in the crystal structures of pyridine and pyrazine monocarboxylic acids is explained by energy computations in the RHF 6-31G* basis set. Both the O-H.N and the C-H...O hydrogen bonds in synthon V result from activated acidic donor and basic acceptor atoms in 1-4. Pyrazine 2,3- and 2,5-dicarboxylic acids 10 and 11 crystallize as dihydrates with a (carboxyl)O-H...O(water) hydrogen bond in synthon VII, a recurring pattern in the diacid structures. In summary, the carboxylic acid group forms an O-H...N hydrogen bond in pyrazine monocarboxylic acids and an O-H...O hydrogen bond in pyrazine dicarboxylic acids. This structural analysis correlates molecular features with supramolecular synthons in pyridine and pyrazine carboxylic acids for future crystal engineering strategies.     

S−H…O and O−H…O Hydrogen Bonds-Comparison of Dimers of Thiocarboxylic and Carboxylic Acids

ωB97-XD/aug-cc-pVTZ calculations were performed on dimers of selected thiocarboxylic acids and on analogous carboxylic acids. The sample of calculated thiocarboxylic acids is an extension of the Cambridge Structural Database search that contains only a few such structures. The Natural Bond Orbital (NBO) method, Symmetry-Adapted Perturbation Theory (SAPT) approach, Non-Covalent Interaction (NCI) method and Quantum Theory of Atoms in Molecules (QTAIM) were applied additionally to analyse interactions in dimers of thiocarboxylic and carboxylic acids. The insights into crystal structures as well as into results of calculations show that the formation of S−H…O hydrogen bonds between molecules of thiocarboxylic acids is steered by the same mechanisms as the formation of much stronger O−H…O hydrogen bonds in carboxylic acids. The intramolecular O−H…O and C−H…S hydrogen bonds occurring in few considered structures are also analysed.     

1,2,4,5‐Tetrazines vs. Carboxylic Acid Dimers: Molecular Chemistry vs. Supramolecular Chemistry

The structures of six new tetrazines have been determined and their molecular packing has been compared to the supermolecular architecture observed in related carboxylic acid dimers. In the tetrazines, covalent N? N bonds are considered to replace the intermolecular O? H???O hydrogen bonds of the carboxylic acids. In the systems investigated, it is apparent that, in the majority of cases, the covalent six‐membered ring of the tetrazine is an appropriate replacement for the carboxylic acid synthon. This apparent interplay between molecular and supramolecular units may have applications in the crystal engineering of new materials.     

Sarcosine-maleic acid (1:1) crystal: structure, 13C NMR and vibrational properties,protonation character

The crystal structure of sarcosine-maleic acid (1:1) complex has been determined by X-ray diffraction method at 293 K as monoclinic, space group C2/c, Z=8. The crystal unit consists of semi-maleate and sarcosinium ions with two strong hydrogen bonds: the intramolecular one in the maleic part of the complex and the intermolecular one between sarcosinium and semi-maleate carboxylic groups. Phase transitions in this crystal are excluded. Its structure is in accordance with FT-IR, FT-Raman and 13C NMR study. Properties of the titled crystal and a family of similar amino acid-maleic acid systems are compared and discussed. Special attention is paid for relations between different structural and spectroscopic parameters as well as for character of hydrogen bonds formed in these crystalline complexes.     

Synthesis and Structure of Manganese Coordinated Polymer with Regular X-shaped Cavity

A coordination polymer [Mn(IDA)2(H2o)47, (H2IDA=N-iminodiacetic acid) was synthesized and char-acterized by single crystal X-ray diffraction. The crystal belongs to the tetragonal system, the space group is P-421C with the crystal cell parameters a=0.81120(8) nm, b=0.81120(8)nm, c=0.96196(4)nm, V=0.6330(1)nm^3, Mr=355.17, R=0.0224, ωR=0.061. The four carboxylic oxygen atoms of the differentN-iminodiacetic acid ligands and two water molecules coordinate to the manganese atom. The manganeseatom is in an approximates octahedral coordination sphere. Each carboxylic acid ligand bridges two man-ganese atoms, forming two zig-zag supramolecular chains. The twisted chains construct a two-dimension lay-er structure with regularly arranged X-shaped window cavity. The three-dimension supramolecular networkis formed by coordination bonds and hydrogen bonds.     

Beta-alanine-oxalic acid (1:1) hemihydrate crystal: structure, 13C NMR and vibrational properties,protonation character

The crystal structure of beta-alanine-oxalic acid (1:1) hemihydrate complex has been reinvestigated by X-ray diffraction method at 293 K. Formation of monoclinic crystal system belonging to C2/c space group and consisting of semi-oxalate chains, diprotonated beta-alanine dimers and water molecules bonded to both these units is confirmed. New results are obtained for distances in the carboxylic groups and hydrogen bonds. These structural observations are used for protonation degree monitoring on the carboxylic oxygen atoms. They are in accordance with our vibrational study. The 13C NMR spectra provide insights into the solid structure of this complex, character of its hydrogen bonds and the beta-alanine protonation.     

Helical self-assembly of substituted benzoic acids: influence of weaker X...X and C-H...X interactions

The X-ray crystal packing analyses of the sterically encumbered halogen-substituted benzene carboxylic acids 1-4 reveal a novel and unprecedented crystal packing in that the association of the carboxyl groups through O-H...O bonds results in the generation of a helix along the 41-screw axis. Such an organization of the acids is shown convincingly to be a result of the close packing, which exploits the weaker X...X and C-H...X interactions in conjunction with the stronger O-H...O hydrogen bonds. In contrast, the chloro- and bromo-substituted durene carboxylic acids 6 and 7 exhibit a pattern that is akin to tape/ribbon involving the centrosymmetric-dimer motif and X...X short intermolecular interactions. The structural investigations demonstrate the ability of the weaker interactions in modifying the supposedly "robust" centrosymmetric-dimer motif of the carboxyl groups in a decisive manner.     

Crystal structure of ciprofloxacin hydrochloride 1.34-hydrate.

Ciprofloxacin belongs to a family of quinolone antibacterial agents. The crystal structure of ciprofloxacin hydrochloride 1,34-hydrate was determined. Most of the bond lengths and angles of the ciprofloxacin cation are very similar to those of ciprofloxacin hexahydrate, which appears in the zwitterionic form. The exceptions are the carbon-oxygen bond distances in the carboxylic group, since in the title compound this group is not deprotonated. Various inter- and intramolecular hydrogen bonds were found in the molecule and are described.     

Structural and magnetic modulation of a purely organic open framework by selective guest inclusion

Solvent inclusion/evacuation caused variations in the structural and magnetic characteristics of the purely organic porous magnet based on the tricarboxylic-substituted PTMTC radical. Whereas no inclusion is observed for nonpolar solvents, the exposure of crystals of the alpha-phase of PTMTC to vapors of polar organic solvents with hydrogen acceptor and/or donor functionalities, such as, ethanol, benzoic alcohol, n-decanol, THF, and DMSO results in the inclusion of these solvents in the highly polar tubular channels of the alpha-phase. The resulting inclusion compounds of formula PTMTC.x(guest) show several structural rearrangements, as confirmed by IR and XRPD (X-ray powder diffraction) measurements. The crystal transformations have been studied for a specific case: the PTMTC.EtOH adduct. The crystal structure reveals that included guest solvent molecules participate in the formation of new hydrogen bonds with the carboxylic groups of PTMTC radicals, inducing the disruption of several direct hydrogen bonds among these radicals. As expected, the interruption of direct hydrogen bonds between PTMTC radicals induces large transformations in the magnetic properties. From the ferromagnetic behavior of the alpha-phase, predominant antiferromagnetic interactions are observed for the inclusion adducts. Interestingly, both structural and magnetic changes are reversible after removal of guest solvent molecules.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

Syntheses and Crystal Structures of Four New Complexes [Mn(4,4''-bip)2(OH2)4](DBA)·4H2O and [M(OH2)(HDPA)2]·3H2O (M = Mn, Co, Ni)

Four new transition metal complexes, [Mn(4,4'-bip)2(OH2)4](DBA)·4H2O 1(4,4'-bip = 4,4'-bipyridine, H2DBA = benzene-1,3-dicarboxylic acid) and [M(OH2)(HDPA)2]·3H2O (M = Mn 2, M = Co 3, M = Ni 4,H2DPA = 2,6-pyridine-dicarboxylic acid), have been prepared from the reaction of transition metals and carboxylic acids, and characterized by X-ray and elemental analyses. For compound 1, the packing diagram shows that a three-dimensional network is formed via hydrogen bonds and strong π-π interactions. For compounds 2, 3 and 4,a double-helical chain is formed through hydrogen bonds. Moreover, a three-dimensional network is constructed from chains via complicated hydrogen bonds between crystal water molecules and oxygen atoms of HDPA-.     

Three-dimensional supramolecular architecture based on 4,4′-methylene-bis(benzenamine) and aromatic carboxylic acid guests: Synthons cooperation, robust motifs and structural diversity

The two-component solid forms involving 4,4??-methylene-bis(benzenamine) included both salts and co-crystals, while 4,4??-methylene-bis(benzenamine) crystallized exclusively as a salt, in agreement with the differences in the pK _a values. Many of the crystal structures displayed either the neutral or the ionic form of the carboxylic acid-amino heterosynthon, and the similarity in crystal structures between the neutral and the ionized molecules makes the visual distinction between a salt and co-crystal dependent on the experimental location of the acidic proton. A variety of supramolecular hydrogen bonded motifs involving interactions between the aza molecules and carboxylic acid groups are observed rather than just the O-H??N/O-H??O motif. The motifs are identical in all the two compounds analyzed showing the robustness of these supramolecular synthons. In all adducts, recognition between the constituents is established through either N-H??O and/or O-H??O/O-H??N pairwise hydrogen bonds. In all adducts, COOH functional groups available on 1 and 2 interact with the N-donor compounds. The COOH moieties in 1 forms only single N-H??O hydrogen bonds, whereas in 2, it forms pairwise O-H??N/N-H??O hydrogen bonds. The supramolecular architectures are elegant and simple, with stacking of networks in 2, but a rather complex network with a threefold interpenetration pattern was found in 1. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

Syntheses and Crystal Structures of Four New Complexes [Mn(4,4′-bip)_2(OH_2)_4](DBA)·4H_2O and [M(OH_2)(HDPA)_2]·3H_2O (M = Mn,Co,Ni)

1 INTRODUCTION During the past years, dicarboxylic acids have been widely used as one polydentate ligand invo- lved in various metal chelation reactions to form transition or rare earth metal complexes with inter- esting properties in material science[1] and biological systems[2]. For example, Kim Y and his coworkers focused on the synthesis of copper(II) complexes containing malonate and pyrazine ligands to study their magnetic property and electronic conducti- vity[3]. The importance o…     

Hydrogen-bond structure and dynamics at the interface between water and carboxylic acid-functionalized self-assembled monolayers

Molecular dynamics computer simulations are used to study hydrogen-bond structure and dynamics at the interface between water and carboxylic acid-functionalized self-assembled monolayers (CAFSAMs). Water-water, water-CAFSAM, and internal CAFSAM hydrogen bonds are examined. Roughly half of all adjacent carboxylic acid-terminated hydrocarbon chains are hydrogen-bonded to one another. This is consistent with experimental results reflecting two pKa values for CAFSAMs. Hydrogen-bond dynamics are expressed in terms of hydrogen-bond population autocorrelation functions and are found to be nonexponential. The water-water hydrogen-bond dynamics are slower at the interface than in the bulk, which is similar to what was found at the interface between water and weakly polar liquids such as nitrobenzene. The water-CAFSAM hydrogen bonds are found to be long-lived, on the order of tens of picoseconds. Internal CAFSAM chain-chain hydrogen bonds show almost no relaxation on the simulation time scale.     

Carboxylic acid functionalized ortho-linked oxacalix[2]benzene[2]pyrazine: synthesis, structure, hydrogen bond and metal directed self-assembly

Cyclooligomerization of 2,6-dichloropyrazine 4 and benzyl 2,3-dihydroxybenzoate 5 under microwave irradiation resulted in a racemic pair of ester functionalized ortho-linked oxacalix[2]benzene[2]pyrazine 6, which was further transformed to the corresponding racemic carboxylic acid functionalized ortho-linked oxacalix[2]benzene[2]pyrazine 3. Both enantiomers of 3 adopt 1,3-alternate conformations with their two carboxylic acid groups pointing to opposite directions in the solid state. Enantiomers of 3 form a step-like one-dimensional supramolecular polymer via intermolecular hydrogen bond interactions between the carboxylic acids for crystals obtained in methanol. No hydrogen bonds were formed between the carboxylic acids for crystals of 3 obtained in pyridine and aqueous guanidine solutions; instead, intermolecular hydrogen bonds between the carboxylic acid groups of 3 and pyridine, as well as guanidinium ions were formed. Under metal-mediated self-assembly conditions, the pyrazinyl nitrogen atoms in 3 interacted with transition metal ions, such as Ag(I), Cu(II) and Zn(II), and resulted in the formation of four new metal-containing supramolecular complexes. Metallomacrocycles 7, 8 and 9 were formed by reactions of 3 with Ag(I) or Cu(II) ions by bridging two ligands 3 in the equatorial region via M-N coordination bonds. A one-dimensional coordination polymer 10 was generated by reaction between ligand 3 and Zn(II) ions, and a cage-based structure is presented in 10 by bridging of the cyclophane units by Zn(2+) ions via Zn-N and Zn-O bonds.     

Insights into the Crystallisation Process from Anhydrous,Hydrated and Solvated Crystal Forms of Diatrizoic Acid

Diatrizoic acid (DTA), a clinically used X‐ray contrast agent, crystallises in two hydrated, three anhydrous and nine solvated solid forms, all of which have been characterised by X‐ray crystallography. Single‐crystal neutron structures of DTA dihydrate and monosodium DTA tetrahydrate have been determined. All of the solid‐state structures have been analysed using partial atomic charges and hardness algorithm (PACHA) calculations. Even though in general all DTA crystal forms reveal similar intermolecular interactions, the overall crystal packing differs considerably from form to form. The water of the dihydrate is encapsulated between a pair of host molecules, which calculations reveal to be an extraordinarily stable motif. DTA presents functionalities that enable hydrogen and halogen bonding, and whilst an extended hydrogen‐bonding network is realised in all crystal forms, halogen bonding is not present in the hydrated crystal forms. This is due to the formation of a hydrogen‐bonding network based on individual enclosed water squares, which is not amenable to the concomitant formation of halogen bonds. The main interaction in the solvates involves the carboxylic acid, which corroborates the hypothesis that this strong interaction is the last one to be broken during the crystal desolvation and nucleation process.     

原位漫反射新方法研究煤中氢键的分解动力学

采用一种新的原位漫反射红外技术研究了干燥脱灰褐煤中氢键的分解动力学,同时介绍并应用了一种防止高温下挥发分冷凝的原位漫反射红外实验方法。基于两条假设,当煤加热至560℃时,单一反应模型可以用于除OH－π键以外氢键分解动力学参数的求解。结果表明,煤中羧酸二聚体、OH－N 和SH－N三种氢键的分解动力学遵循二级反应;OH－OR₂,紧密结合的羟基四聚体和自缔合的羟基多聚体则遵循一级反应。计算所得的几种氢键分解活化能与文献中采用其他 方法所得结果基本一致。在所考察的六种氢键中,羧酸二聚体、OH－N 、SH－N和紧密结合的羟基四聚体的分解可以分为两个阶段（230℃~380℃和 380℃~500℃）,而OH－OR₂和自缔合的羟基多聚体的分解可以按照一段来处理。另外,通过比较自缔合的羟基多聚体的分解活化能和文献中的氢键键能,获得了其分解机理。
     

Density functional theoretical study of pKa of RCOOH (RH,CH3, and C2H5) using the combination of the extended clusters‐continuum model

The accurate pK_a determinations for three carboxylic acids have been investigated using the combination of the extended clusters‐continuum model at B3LYP/6‐31+g(d,p) and B3LYP/6‐311++g(d,p) levels. To take into account of the effect of the water combined with carboxylic acids in different positions, eleven molecular clusters were considered. Among these clusters, the one involving the carboxylic acid wrapped up with water molecules and saturated with hydrogen bonds (four hydrogen bonds around ? COOH) leads to the best B3LYP pK_a results compared to the experimental data. For those clusters saturated with hydrogen bonds, when n = 3 (the number of water molecules), the average absolute errors between the calculated pK_a results and experimental data of these three carboxylic acids were 0.19 (0.23) and 0.12 (0.22) pK_a at B3LYP/6‐31+g(d,p)//PCM (IEFPCM) and B3LYP/6‐311++g(d,p)//PCM (IEFPCM) levels, respectively; when n = 4, they are 0.53 (1.23) and 1.09 (1.03) pK_a, respectively. On the basis of the above results, the molecular cluster saturated with four hydrogen bonds formed by three waters and one carboxylic acid molecule was the chief existence in the carboxylic acid solution. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

X-Ray Diffraction Study on Manganese(II) Complexes with Thiophene-2-Carboxylate and Furan-3-Carboxylate Ligands

Abstract

Mn(II) cations in the crystals of trisaquobis(μ-thiophen-2-carboxylato-O,O′)(thiophen-2-carboxylato-O)manganese(II) monohydrate are bridged by oxygen atoms donated by bidentate carboxylic groups of two thiophen-2-carboxylate ligands. In addition, each Mn(II) ion is coordinated by an oxygen atom of a monodentate carboxylic group of this ligand and three oxygen atoms of water molecules. The coordination around the Mn(II) cation is octahedral. The bridging of the ligands results in molecular ribbons propagating in the c-direction of the crystal held together by C?H…O hydrogen bonds. The crystal structure of diaquobis(μ-furan-3-carboxylato-O,O′)di(μ-furan-3-carboxylato-O,O)(μ-aqua-O)manganese(II) consists of dinuclear structural units. In each molecule Mn(II) cations are O,O′ bridged by oxygen atoms of bidentate carboxylic groups of two furan-3-carboxylate ligands and have a water located between the Mn cations. The units are O,O′ bridged to Mn(II) ions located in adjacent units by bidentate oxygen atoms, forming molecular ribbons extending in the c-direction. Octahedral coordination around each Mn(II) ion is completed by two water molecules. The octahedra around two adjacent metal ions in the unit share a common apex - the bridging oxygen atom of the water molecule. The ribbons are held together by C?H…O hydrogen bonds between furan ring oxygen atoms and the carbon atoms of adjacent furan rings.     

The crystal and molecular structure of delta-9-tetrahydrocannabinolic acid b.

The crystal and molecular structure of the title compound C-22H-30O-4, has been determined by X-ray methods using 1106 reflections above background level collected by counter methods. The crystals are orthorhombic, space group P2-12-12-1 with cell dimensions a equals 16.514(2) A; b equals 14.324(2) A; c equals 8.744(1) A; there are four molecules per unit cell. The structure was refined to an R of 0.084 (weighted R-w equals 0.068). The cyclohexene and the pyran part of the molecule occurs in the half-chair conformation. The bond distances and angles, and a slight twist of the benzene ring, indicate considerable stains in the aromatic system. Both the phenolic and carboxylic group are significantly out of the plane through the aromatig ring. The angle between this plane and a plane through the cyclohexene ring is 37.7 degrees. The pentyl sidechain occurs in an extended gauche conformation, and the thermal parameters of this part of the molecule are very high. The molecules are held together by van der Waals forces in the c-directions, and hydrogen bonds (2.688 A) from phenolic to carboxylic groups in the a-b plane. There is a short ultra-molecular hydrogen bond (2.490 A) from the carboxylic group to the pyran oxygen.