苯分子与Si6O18H12和Al6O24H30团簇模型相互作用的理论研究

粘土矿已经被广泛用来去除有机物,修复和净化被石油碳氢化合物污染的土壤和地下水. 我们选择高岭石作为研究对象,构造了Si₆O₁₈H₁₂和Al₆O₂₄H₃₀两个团簇模型分别代表高岭石的硅氧层表面和铝氧层表面,在MP2/6-31G(d,p)//B3LYP/6-31G(d,p)的理论水平上系统地研究了气态下苯分子和高岭石团簇模型的相互作用. 并进一步分析了苯分子和高岭石表面相互作用的各种气态性质,比如：优化的几何构型、结构参数、吸附能、自然键轨道电荷分布、振动频率变化、静电势、电子密度性质(次级氢键的电子密度和拉普拉斯算符值)和电子密度差分等. 优化的几何构型表明苯分子吸附在高岭石表面的本质可能是次级氢键的形成. 其他性质的结果进一步验证了次级氢键的存在,并指出苯更倾向于吸附在高岭石的铝氧层表面,且苯环和铝氧层表面形成近似90°的夹角.     

Electronic and topological properties of interactions between imidazolium-based ionic liquids and thiophenic compounds: a theoretical investigation

To deepen the understanding the interactions of thiophenic compounds in ionic liquids, we have performed a systemic study on the electronic structures, and topological properties of interactions between N-ethyl-N-ethylimidazolium diethyl phosphate ([EEIM][DEP]) ionic liquid and 3-methylthiophene (3-MT), benzothiophene (BT), or dibenzothiophene (DBT) using density functional theory. From NBO atomic charges and electrostatic potential analyses, most of the positive charge is located on C2–H2 in the [EEIM] cation, and the negative charge is focused on oxygen atoms in [DEP] anion, implying oxygen atoms in [DEP] should easily attack C2–H2 in [EEIM]. The electrostatic interaction between anion and cation may be dominant for the formation of the [EEIM]–[DEP] ion pair. The large stabilizing effect is due to the strong orbital interactions between the antibonding orbital of proton donor σ*(C2–H2) in [EEIM] cation and the lone pairs of proton acceptor LP(O) in [DEP] anion. A common feature of [EEIM][DEP], [EEIM][DEP]-3-MT/BT/DBT complexes is the presence of hydrogen bonds between [EEIM] cation and [DEP] anion. This work has also given the interacting mechanism of 3-MT, BT, and DBT adsorption on [EEIM][DEP] ionic liquid. Both [EEIM] cation and [DEP] anion are shown to play important roles in interactions between 3-MT, BT, DBT and [EEIM][DEP], which has been corroborated by NBO and AIM analyses. The π···π, π···C–H and hydrogen bonding interactions occur between [EEIM][DEP] and 3-MT, BT, DBT. The strength of sulfur involved interactions between 3-MT, BT, DBT and [EEIM][DEP] follows the order of 3-MT > BT > DBT. The order of interaction energies between [EEIM][DEP] and 3-MT, BT, DBT is 3-MT < BT < DBT, in agreement with the order of extractive selectivity from fuel oils (DBT > BT > 3-MT) in terms of sulfur partition coefficients.     

Different supramolecular interactions mediated by Br atoms in the crystal structures of three anisole derivatives

Three anisole building blocks featuring bis(hydroxymethyl) or bis(bromomethyl) pendants have been analyzed with regard to their molecular structures and packing behaviour. The compounds are ethyl 3,5‐bis(hydroxymethyl)‐4‐methoxybenzoate, C₁₂H₁₆O₅, (I), [5‐bromo‐3‐(hydroxymethyl)‐2‐methoxyphenyl]methanol [or 4‐bromo‐2,6‐bis(hydroxymethyl)anisole], C₉H₁₁BrO₃, (II), and 5‐bromo‐1,3‐bis(bromomethyl)‐2‐methoxybenzene [or 4‐bromo‐2,6‐bis(bromomethyl)anisole], C₉H₉Br₃O, (III). A typical supramolecular pattern involved C—H…π interactions generating molecular stacks, while π–π interactions were only observed in the absence of bromine, indicating a striking influence on the distances between adjacent aromatic moieties. When comparing bis(hydroxymethyl) compound (II) with bis(bromomethyl) compound (III), we found that the strong O—H…O hydrogen bonds in a zigzag arrangement in the first are replaced by C—H…Br interactions in the second without a change in the general packing.     

Synthesis,crystal structure and study of the crystal packing in the complex bis(4‐aminopyridine‐κN1)dichloridocobalt(II)

Despite the large number of reported crystalline structures of coordination complexes bearing pyridines as ligands, the relevance of π–π interactions among these hereroaromatic systems in the stabilization of their supramolecular structures and properties is not very well documented in the recent literature. The title compound, [CoCl₂(C₅H₆N₂)₂], was obtained as bright‐blue crystals suitable for single‐crystal X‐ray diffraction analysis from the reaction of 4‐aminopyridine with cobalt(II) chloride in ethanol. The new complex was fully characterized by a variety of spectroscopic techniques and single‐crystal X‐ray diffraction. The crystal structure showed a tetrahedral complex stabilized mainly by bidimensional motifs constructed by π–π interactions with large horizontal displacements between the 4‐aminopyridine units, and N—H…Cl hydrogen bonds. Other short contacts, such as C—H…Cl interactions, complete the three‐dimensional arrangement. The supramolecular investigation was extended by statistical studies using the Cambridge Structural Database and a Hirshfeld surface analysis.     

Different supramolecular architectures mediated by different weak interactions in the crystals of three N‐aryl‐2,5‐dimethoxybenzenesulfonamides

The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N‐aryl‐2,5‐dimethoxybenzenesulfonamides, namely N‐(2,3‐dichlorophenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (I), N‐(2,4‐dichlorophenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (II), and N‐(2,4‐dimethylphenyl)‐2,5‐dimethoxybenzenesulfonamide, C₁₆H₁₉NO₄S, (III), are described. The asymmetric unit of (I) consists of two symmetry‐independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C—H…O interactions in (I), N—H…Cl and C—H…O interactions in (II), and C—H…O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C—H…O, C—H…Cl, C—H…π(aryl), π(aryl)–π(aryl) and Cl…Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The d _norm and shape‐index surfaces of (I)–(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H…H contacts, followed by H…O/O…H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N—H…O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N—H…O hydrogen bonds form either C (4) chain motifs or R ₂²(8) rings. Further comparison reveals that the characteristics of the N—H…O hydrogen‐bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the benzenesulfonyl ring, with the nature and position of the substituents on the aniline ring exerting little effect. On the other hand, the crystal structures of (I)–(III) display several weak interactions other than the common N—H…O hydrogen bonds, resulting in supramolecular architectures varying from one‐ to three‐dimensional depending on the nature and position of the substituents on the aniline ring.     

Synthesis,crystal structure and studies on the interaction with albumin of a new silver(I) complex based on 2‐(4‐nitrobenzenesulfonamido)benzoic acid

In the present work, the two‐dimensional (2D) polymer poly[[μ₄‐2‐(4‐nitrobenzenesulfonamido)benzoato‐κ⁴O¹:O¹:O^1′:N⁶]silver(I)] (AgL), [Ag(C₁₃H₉N₂O₆S)]_n, was obtained from 2‐(4‐nitrobenzenesulfonamido)benzoic acid (HL), C₁₃H₁₀N₂O₆S. FT–IR, ¹H and ¹³C{¹H} NMR spectroscopic analyses were used to characterize both compounds. The crystal structures of HL and AgL were determined by single‐crystal X‐ray diffraction. In the structure of HL, O—H…O hydrogen bonds between neighbouring molecules result in the formation of dimers, while the silver(I) complex shows polymerization associated with the O atoms of three distinct deprotonated ligands (L^?). Thus, the structure of the Ag complex can be considered as a coordination polymer consisting of a one‐dimensional linear chain, constructed by carboxylate bridging groups, running parallel to the b axis. Neighbouring polymeric chains are further bridged by Ag—C monohapto contacts, resulting in a 2D framework. Fingerprint analysis of the Hirshfeld surfaces show that O…H/H…O hydrogen bonds are responsible for the most significant contacts in the crystal packing of HL and AgL, followed by the H…H and O…C/C…O interactions. The Ag…Ag, Ag…O/O…Ag and Ag…C/C…Ag interactions in the Hirshfeld surface represent 12.1% of the total interactions in the crystal packing. Studies of the interactions of the compounds with human serum albumin (HSA) indicated that both HL and AgL interact with HSA.     

Syntheses,supramolecular networks and Hirshfeld surface and thermal analyses of two new cadmium chloride coordination polymers with an N,O‐chelating ligand

Two new coordination polymers, namely poly[[(3‐aminopyrazin‐4‐ium‐2‐carboxylate‐κ²N¹,O)di‐μ‐chlorido‐cadmium(II)] monohydrate], {[CdCl₂(C₅H₅N₃O₂)]·H₂O}_n, (1), and poly[2‐amino‐3‐carboxypyrazin‐1‐ium [(3‐aminopyrazine‐2‐carboxylato‐κ²N¹,O)di‐μ‐chlorido‐cadmium(II)] monohydrate], {(C₅H₆N₃O₂)[Cd(C₅H₄N₃O₂)Cl₂]·H₂O}_n, (2), have been synthesized from the reaction of cadmium(II) chloride and 3‐aminopyrazine‐2‐carboxylic acid (Hapca) under mild conditions in acidic media. The two coordination polymers have been characterized by single‐crystal X‐ray diffraction and show chloride‐bridged zigzag chains with octahedrally coordinated metal ions, where Hapca acts as a bidentate ligand via the π‐conjugated N atom and a carboxylate O atom. The chains are further interconnected via noncovalent interactions into three‐dimensional supramolecular networks. The dominant H…O and H…Cl interactions for both compounds were quantified using Hirshfeld surface analysis. The thermal stability and topological analysis of the two‐dimensional networks of (1) and (2) are also discussed.     

Adsorption behaviour of a CdII–triazole MOF for butan‐2‐one in a single‐crystal‐to‐single‐crystal (SCSC) fashion: the role of hydrogen bonding and C—H…π interactions

The adsorption behaviour of the Cd^II–MOF {[Cd(L)₂(ClO₄)₂]·H₂O ( 1 ), where L is 4‐amino‐3,5‐bis[3‐(pyridin‐4‐yl)phenyl]‐1,2,4‐triazole, for butan‐2‐one was investigated in a single‐crystal‐to‐single‐crystal (SCSC) fashion. A new host–guest system that encapsulated butan‐2‐one molecules, namely poly[[bis{μ₃‐4‐amino‐3,5‐bis[3‐(pyridin‐4‐yl)phenyl]‐1,2,4‐triazole}cadmium(II)] bis(perchlorate) butanone sesquisolvate], {[Cd(C₂₄H₁₈N₆)₂](ClO₄)₂·1.5C₄H₈O}_n, denoted C₄H₈O@Cd‐MOF ( 2 ), was obtained via an SCSC transformation. MOF 2 crystallizes in the tetragonal space group P4₃2₁2. The specific binding sites for butan‐2‐one in the host were determined by single‐crystal X‐ray diffraction studies. N—H…O and C—H…O hydrogen‐bonding interactions and C—H…π interactions between the framework, ClO₄^? anions and guest molecules co‐operatively bind 1.5 butan‐2‐one molecules within the channels. The adsorption behaviour was further evidenced by ¹H NMR, IR, TGA and powder X‐ray diffraction experiments, which are consistent with the single‐crystal X‐ray analysis. A ¹H NMR experiment demonstrates that the supramolecular interactions between the framework, ClO₄^? anions and guest molecules in MOF 2 lead to a high butan‐2‐one uptake in the channel.     

Violuric acid monohydrate: a second polymorph with more extensive hydrogen bonding

Crystals of a second polymorph of violuric acid monohydrate [systematic name: pyrimidine‐2,4,5,6(1H,3H)‐tetrone monohydrate], C₄H₃N₃O₄·H₂O, have higher density and a more extensive hydrogen‐bonding arrangement than the previously reported polymorph. Violuric acid and water molecules form essentially planar hydrogen‐bonded sheets, which are stacked in an offset …ABCABC… repeat pattern involving no ring‐stacking interactions.     

The different modes of chiral [1,2,3]triazolo[5,1‐b][1,3,4]thiadiazines: crystal packing,conformation investigation and cellular activity

The crystal structures of four new chiral [1,2,3]triazolo[5,1‐b][1,3,4]thiadiazines are described, namely, ethyl 5′‐benzoyl‐5′H,7′H‐spiro[cyclohexane‐1,6′‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine]‐3′‐carboxylate, C₁₉H₂₂N₄O₃S, ethyl 5′‐(4‐methoxybenzoyl)‐5′H,7′H‐spiro[cyclohexane‐1,6′‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine]‐3′‐carboxylate, C₂₀H₂₄N₄O₄S, ethyl 6,6‐dimethyl‐5‐(4‐methylbenzoyl)‐6,7‐dihydro‐5H‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine‐3‐carboxylate, C₁₇H₂₀N₄O₃S, and ethyl 5‐benzoyl‐6‐(4‐methoxyphenyl)‐6,7‐dihydro‐5H‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine‐3‐carboxylate, C₂₁H₂₀N₄O₄S. The crystallographic data and cell activities of these four compounds and of the structures of three previously reported similar compounds, namely, ethyl 5′‐(4‐methylbenzoyl)‐5′H,7′H‐spiro[cyclopentane‐1,6′‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine]‐3′‐carboxylate, C₁₉H₂₂N₄O₃S, ethyl 5′‐(4‐methoxybenzoyl)‐5′H,7′H‐spiro[cyclopentane‐1,6′‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine]‐3′‐carboxylate, C₁₉H₂₂N₄O₄S, and ethyl 6‐methyl‐5‐(4‐methylbenzoyl)‐6‐phenyl‐6,7‐dihydro‐5H‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine‐3‐carboxylate, C₂₂H₂₂N₄O₃S, are contrasted and compared. For both crystallization and an MTT assay, racemic mixtures of the corresponding [1,2,3]triazolo[5,1‐b][1,3,4]thiadiazines were used. The main manner of molecular packing in these compounds is the organization of either enantiomeric pairs or dimers. In both cases, the formation of two three‐centre hydrogen bonds can be detected resulting from intramolecular N—H…O and intermolecular N—H…O or N—H…N interactions. Molecules of different enantiomeric forms can also form chains through N—H…O hydrogen bonds or form layers between which only weak hydrophobic contacts exist. Unlike other [1,2,3]triazolo[5,1‐b][1,3,4]thiadiazines, ethyl 5′‐benzoyl‐5′H,7′H‐spiro[cyclohexane‐1,6′‐[1,2,3]triazolo[5,1‐b][1,3,4]thiadiazine]‐3′‐carboxylate contains molecules of only the (R)‐enantiomer; moreover, the N—H group does not participate in any significant intermolecular interactions. Molecular mechanics methods (force field OPLS3e) and the DFT B3LYP/6‐31G+(d,p) method show that the compound forming enantiomeric pairs via weak N—H…N hydrogen bonds is subject to greater distortion of the geometry under the influence of the intermolecular interactions in the crystal. For intramolecular N—H…O and S…O interactions, an analysis of the noncovalent interactions (NCIs) was carried out. The cellular activities of the compounds were tested by evaluating their antiproliferative effect against two normal human cell lines and two cancer cell lines in terms of half‐maximum inhibitory concentration (IC₅₀). Some derivatives have been found to be very effective in inhibiting the growth of Hela cells at nanomolar and submicromolar concentrations with minimal cytotoxicity in relation to normal cells.     

Hypervalent organoselenium compounds stabilized by intramolecular coordination: synthesis and crystal structures

Two novel hypervalent selenium(IV) compounds stabilized by intramolecular interactions, namely 6‐phenyl‐6,7‐dihydro‐5H‐2,3‐dioxa‐2aλ⁴‐selenacyclopenta[hi]indene, C₁₄H₁₂O₂Se, 14 , and 5‐phenyl‐5,6‐dihydro‐4H‐benzo[c][1,2]oxaselenole‐7‐carbaldehyde, C₁₄H₁₂OSe₂, 15 , have been synthesized by the reaction of 2‐chloro‐1‐formyl‐3‐(hydroxymethylene)cyclohexene with in‐situ‐generated disodium diselenide (Na₂Se₂). The title compounds were characterized by FT–IR spectroscopy, ESI–MS, and single‐crystal X‐ray diffraction studies. For 14 , there is whole‐molecule disorder, with occupancies of 0.605 (10) and 0.395 (10), a double bond between C and Se, and the five‐membered selenopentalene rings are coplanar. The packing is stabilized by π–π stacking interactions involving one of the five‐membered Se/C/C/C/O rings [centroid–centroid (Cg…Cg) distance = 3.6472 (18) Å and slippage = 1.361 Å], as well as C—H…π interactions involving a C—H group and the phenyl ring. In addition, there are bifurcated C—H…Se,O interactions which link the molecules into ribbons in the c direction. For 15 , the C—Se bond lengths are longer than those of 14 . The two five‐membered rings are coplanar. There are no π–π or C—H…π interactions; however, molecules are linked by C—H…O interactions into centrosymmetric dimers, with graph‐set notation R₂²(16).     

Supramolecular architectures in CoII and CuII complexes with thiophene‐2‐carboxylate and 2‐amino‐4,6‐dimethoxypyrimidine ligands

The coordination chemistry of mixed‐ligand complexes continues to be an active area of research since these compounds have a wide range of applications. Many coordination polymers and metal–organic framworks are emerging as novel functional materials. Aminopyrimidine and its derivatives are flexible ligands with versatile binding and coordination modes which have been proven to be useful in the construction of organic–inorganic hybrid materials and coordination polymers. Thiophenecarboxylic acid, its derivatives and their complexes exhibit pharmacological properties. Cobalt(II) and copper(II) complexes of thiophenecarboxylate have many biological applications, for example, as antifungal and antitumor agents. Two new cobalt(II) and copper(II) complexes incorporating thiophene‐2‐carboxylate (2‐TPC) and 2‐amino‐4,6‐dimethoxypyrimidine (OMP) ligands have been synthesized and characterized by X‐ray diffraction studies, namely (2‐amino‐4,6‐dimethoxypyrimidine‐κN)aquachlorido(thiophene‐2‐carboxylato‐κO)cobalt(II) monohydrate, [Co(C₅H₃O₂S)Cl(C₆H₉N₃O₂)(H₂O)]·H₂O, (I), and catena‐poly[copper(II)‐tetrakis(μ‐thiophene‐2‐carboxylato‐κ²O:O′)‐copper(II)‐(μ‐2‐amino‐4,6‐dimethoxypyrimidine‐κ²N¹:N³)], [Cu₂(C₅H₃O₂S)₄(C₆H₉N₃O₂)]_n, (II). In (I), the Co^II ion has a distorted tetrahedral coordination environment involving one O atom from a monodentate 2‐TPC ligand, one N atom from an OMP ligand, one chloride ligand and one O atom of a water molecule. An additional water molecule is present in the asymmetric unit. The amino group of the coordinated OMP molecule and the coordinated carboxylate O atom of the 2‐TPC ligand form an interligand N—H…O hydrogen bond, generating an S(6) ring motif. The pyrimidine molecules also form a base pair [R₂²(8) motif] via a pair of N—H…N hydrogen bonds. These interactions, together with O—H…O and O—H…Cl hydrogen bonds and π–π stacking interactions, generate a three‐dimensional supramolecular architecture. The one‐dimensional coordination polymer (II) contains the classical paddle‐wheel [Cu₂(CH₃COO)₄(H₂O)₂] unit, where each carboxylate group of four 2‐TPC ligands bridges two square‐pyramidally coordinated Cu^II ions and the apically coordinated OMP ligands bridge the dinuclear copper units. Each dinuclear copper unit has a crystallographic inversion centre, whereas the bridging OMP ligand has crystallographic twofold symmetry. The one‐dimensional polymeric chains self‐assemble via N—H…O, π–π and C—H…π interactions, generating a three‐dimensional supramolecular architecture.     

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5‐fluorocytosine

Three new metal(II)–cytosine (Cy)/5‐fluorocytosine (5FC) complexes, namely bis(4‐amino‐1,2‐dihydropyrimidin‐2‐one‐κN³)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI₂(C₄H₅N₃O)₂], ( I ), bis(4‐amino‐1,2‐dihydropyrimidin‐2‐one‐κN³)bis(nitrato‐κ²O,O′)cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO₃)₂(C₄H₅N₃O)₂], ( II ), and (6‐amino‐5‐fluoro‐1,2‐dihydropyrimidin‐2‐one‐κN³)aquadibromidozinc(II)–6‐amino‐5‐fluoro‐1,2‐dihydropyrimidin‐2‐one (1/1) or (6‐amino‐5‐fluorocytosine)aquadibromidozinc(II)–4‐amino‐5‐fluorocytosine (1/1), [ZnBr₂(C₄H₅FN₃O)(H₂O)]·C₄H₅FN₃O, ( III ), have been synthesized and characterized by single‐crystal X‐ray diffraction. In complex ( I ), the Cd^II ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr₂(C₄H₅N₃O)₂] [Muthiah et al. (2001). Acta Cryst. E 57 , m558–m560]. In compound ( II ), each of the two cytosine molecules coordinates to the Cd^II ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N—H…O hydrogen bond involving two cytosine molecules is also present. In compound ( III ), one zinc‐coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The Zn^II atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)—H tautomer of 5FC mimics N(3)‐protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R₂²(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a‐axis direction, forming the rungs of a ladder motif, whereas Zn—Br bonds and N—H…Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O—H…O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound ( III ), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N—H…O, N—H…N, O—H…O, N—H…I and N—H…Br hydrogen bonds, and stacking interactions.     

Twist‐chair conformation of the tetraoxepane ring remains unchanged in tetraoxaspirododecane diamines

A detailed structural analysis has been performed for N,N′‐bis(4‐chlorophenyl)‐7,8,11,12‐tetraoxaspiro[5.6]dodecane‐9,10‐diamine, C₂₀H₂₂Cl₂N₂O₄, (I), N,N′‐bis(2‐fluorophenyl)‐7,8,11,12‐tetraoxaspiro[5.6]dodecane‐9,10‐diamine, C₂₀H₂₂F₂N₂O₄, (II), and N,N′‐bis(4‐fluorophenyl)‐7,8,11,12‐tetraoxaspiro[5.6]dodecane‐9,10‐diamine, C₂₀H₂₂F₂N₂O₄, (III). The seven‐membered ring with two peroxide groups adopts a twist‐chair conformation in all three compounds. The lengths of the C—N and O—O bonds are slightly shorter than the average statistical values found in the literature for azepanes and 1,2,4,5‐tetraoxepanes. The geometry analysis of compounds (I)–(III), the topological analysis of the electron density at the (3, ?1) bond critical points within Bader's quantum theory of `Atoms in molecules' (QTAIM) and NBO (natural bond orbital) analysis at the B3LYP/6‐31G(d,2p) level of theory showed that there are n_O→σ*(C—O), n_N→σ*(C—O) and n_O→σ*(C—N) stereoelectronic effects. The molecules of compounds (I) and (III) are packed in the crystals as zigzag chains due to strong N—H…O and C—H…O hydrogen‐bond interactions, whereas the molecules of compound (II) form chains in the crystals bound by N—H…O, C—H…π and C—H…O contacts. All these data show that halogen atoms and their positions have a minimal effect on the geometric parameters, stereoelectronic effects and crystal packing of compounds (I)–(III), so that the twist‐chair conformation of the tetraoxepane ring remains unchanged.     

Semiempirical studies on the interactions of dialkyldi(aquo)tin cations, [R2Sn(H2O)2]2+, with selected nucleotides

Semiempirical calculations have been carried out on the interactions of [R₂Sn(H₂O)₂]²⁺, [R = H(CH₂)_n: n = 1–8], mainly with five nucleotides, 5′‐adenosine monophosphate (5′‐AMP), but also with guanosine 5′‐monophosphate (5′‐GMP), cytidine 5′‐monophosphate (5′‐CMP), uridine‐5′‐monophosphate (5′‐UMP) and inosine 5′‐monophosphate (5′‐IMP). The preferred sites of interaction were calculated to be the ribose O2 and O3 hydroxyl oxygens and/or the phosphate oxygens, with the nitrogen sites in the bases the least attractive to the tin compounds. This is in general agreement with experimental findings. Structures of the 1:1 coordination complexes vary from distorted tetrahedral, to distorted trigonal pyramidal to distorted octahedral geometries. Copyright © 2007 John Wiley & Sons, Ltd.     

Lithium and sodium yttrium ortho­silicate oxy­apatite,LiY9(SiO4)6O2 and NaY9(SiO4)6O2, at both 100 K and near room temperature

Lithium yttrium orthosilicate oxyapatite [lithium nonayttrium hexakis­(silicate) dioxide], LiY₉(SiO₄)₆O₂, crystallizes in the centrosymmetric space group P6₃/m at both 295 and 100 K. The structure closely resembles those of fluorine apatite and sodium yttrium orthosilicate oxyapatite [sodium nonayttrium hexakis­(silicate) dioxide], NaY₉(SiO₄)₆O₂, which was also investigated, at 270 and 100 K, in this study. There are two different crystallographic sites for the Y³⁺ ion, which are coordinated by seven and nine O atoms. One‐fourth of the nine‐coordinated site is occupied by Li or Na atoms, thus maintaining charge balance. The Si atom occupies a tetrahedral site. The two compounds show no symmetry change between room temperature and 100 K, and the alterations in structural parameters are small.     

Two single‐enantiomer amidophosphoesters: a database study on the chirality of (O)2P(O)(N)‐based structures

The crystal structures of two single‐enantiomer amidophosphoesters with an (O)₂P(O)(N) skeleton, i.e. diphenyl [(R)‐(+)‐α‐methylbenzylamido]phosphate, (I), and diphenyl [(S)‐(?)‐α‐methylbenzylamido]phosphate, (II), both C₂₀H₂₀NO₃P, are reported. In both structures, chiral one‐dimensional hydrogen‐bonded architectures, along [010], are mediated by N—H…OP interactions. The statistically identical assemblies include the noncentrosymmetric graph‐set motif C(4) and the compounds crystallize in the chiral space group P2₁. As a result of synergistic co‐operation from C—H…O interactions, a two‐dimensional superstructure is built including a noncentrosymmetric R₄⁴(22) hydrogen‐bonded motif. A Cambridge Structural Database survey was performed on (O)₂P(O)(N)‐based structures in order to review the frequency of space groups observed in this family of compounds; the hydrogen‐bond motifs in structures with chiral space groups and the types of groups inducing chirality are discussed. The ^2,3J_X–P (X = H or C) coupling constants from the NMR spectra of (I) and (II) have been studied. In each compound, the two diastereotopic C₆H₅O groups are different, which is reflected in the different chemical shifts and some coupling constants.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.     

Effect of the position of a methoxy substituent on the antimicrobial activity and crystal structures of 4‐methyl‐1,6‐diphenylpyrimidine‐2(1H)‐selenone derivatives

Derivatives of pyrimidine‐2(1H)‐selenone are a group of compounds with very strong antimicrobial activity. In order to study the effect of the position of the methoxy substituent on biological activity, molecular geometry and intermolecular interactions in the crystal, three derivatives were prepared and evaluated with respect to their antimicrobial activities, and their crystal structures were determined by X‐ray diffraction. The investigated compounds, namely, 1‐(X‐methoxyphenyl)‐4‐methyl‐6‐phenylpyrimidine‐2(1H)‐selenones (X = 2, 3 and 4 for 1 , 2 and 3 , respectively), C₁₈H₁₆N₂OSe, showed very strong activity against selected strains of Gram‐positive bacteria and fungi. Two compounds, 1 and 2 , crystallize in the monoclinic space group P2₁/c, while 3 crystallizes in the space group P2₁/n; 1 has two molecules in the asymmetric unit and the other two ( 2 and 3 ) have one molecule. The geometries of the investigated compounds differ slightly in the mutual orientations of the aromatic and pyrimidineselenone rings. The O atom in 1 stabilizes the conformation of the molecules via intramolecular C—H…O hydrogen bonding. The packing of molecules is determined by weak C—H…N and C—H…Se intermolecular interactions and additionally in 1 and 2 by C—H…O intermolecular interactions. The introduction of the methoxy substituent results in greater selectivity of the investigated compounds.     

Two cadmium(II) fluorous coordination compounds tuned by different bipyridines

Fluorine is the most electronegative element and can be used as an excellent hydrogen‐bond acceptor. Fluorous coordination compounds exhibit several advantageous properties, such as enhanced high thermal and oxidative stability, low polarity, weak intermolecular interactions and a small surface tension compared to hydrocarbons. C—H…F—C interactions, although weak, play a significant role in regulating the arrangement of the organic molecules in the crystalline state and stabilizing the secondary structure. Two cadmium(II) fluorous coordination compounds formed from 2,2′‐bipyridine, 4,4′‐bipyridine and pentafluorobenzoate ligands, namely catena‐poly[[aqua(2,2′‐bipyridine‐κ²N ,N ′)(2,3,4,5,6‐pentafluorobenzoato‐κO )cadmium(II)]‐μ‐2,3,4,5,6‐pentafluorobenzoato‐κ²O :O ′], [Cd(C₇F₅O₂)₂(C₁₀H₈N₂)(H₂O)]_n , (1), and catena‐poly[[diaquabis(2,3,4,5,6‐pentafluorobenzoato‐κO )cadmium(II)]‐μ‐4,4′‐bipyridine‐κ²N :N ′], [Cd(C₇F₅O₂)₂(C₁₀H₈N₂)(H₂O)₂]_n , (2), have been synthesized solvothermally and structurally characterized. Compound (1) shows a one‐dimensional chain structure composed of Cd—O coordination bonds and is stabilized by π–π stacking and O—H…O hydrogen‐bond interactions. Compound (2) displays a one‐dimensional linear chain structure formed by Cd—N coordination interactions involving the 4,4′‐bipyridine ligand. Adjacent one‐dimensional chains are extended into two‐dimensional sheets by O—H…O hydrogen bonds between the coordinated water molecules and adjacent carboxylate groups. Moreover, the chains are further linked by C—H…F—C interactions to afford a three‐dimensional network. In both structures, hydrogen bonding involving the coordinated water molecules is a primary driving force in the formation of the supramolecular structures.