Activation of C--H... Halogen (Cl, Br, and I) hydrogen bonds at the organic/inorganic interface in fluorinated tetrathiafulvalenes salts

The electrocrystallization of fluorinated bis(2,2'-difluoropropylenedithio)tetrathiafulvalene (1) in the presence of linear (ICl2-, IBr2-, I2Br-) or cluster ([Mo6Cl14]2-) anions affords 1:1 and 2:1 cation radical salts such as [1][ICl2] and [1]2[Mo6Cl14].(CH3CN)2. In both salts, the 1*+ radical ion adopts a boat conformation and envelops the anion through C-H...Hal(anion) (Hal(anion) = Cl, Br, I) hydrogen bonds. This demonstrates the activating role of the neighboring electron-withdrawing CF2 moieties in the stabilization of bi- or trimolecular neutral entities. With smaller linear anions, fluorine segregation controls the solid-state associations of the bimolecular [1]*+[X] entities, and gives rise to layered materials with a limited overlap interaction between the open-shell organic cations and magnetic spin chain behavior. With the larger [Mo6Cl14]2 ions, a strong overlap interaction between radical cations gives rise to diamagnetic [1]2(2+) dimers, which alternate with the cluster anions to form hybrid organic/inorganic ...[1]2(2+)[Mo6Cl14]2... chains. This behavior is also observed in [2]2(2+)[Mo6Cl14]2-.(CH2Cl2)2, in which compound 2 is the unsymmetrically substituted (ethylenedithio)(2,2'-difluoropropylenedithio)tetrathiafulvalene. On the other hand, the unsymmetrically substituted 2,2'-difluoropropylenedithiotetrathiafulvalene (3) affords a mixed-valence 4:1 salt with [Mo6Cl14]2, which is formulated as [3]4[Mo6Cl14].(CH3CN)2. This semiconducting salt is characterized by the coexistence of both the fluorine/fluorine segregation (with solvent inclusion) and the organic/inorganic segregation (with delocalized overlap interactions). Both Csp2-H...Cl and Csp3-H...Cl hydrogen bonds facilitate the stabilization of the organic/inorganic interface and the presence of conducting organic slabs.     

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.     

Theoretical study on cation-anion interaction and vibrational spectra of 1-allyl-3-methylimidazolium-based ionic liquids

In order to deepen the understanding of the cation-anion interaction in ionic liquids, the structures of cation, anions, and cation-anion ion-pairs of 1-allyl-3-methylimidazolium-based ionic liquids are optimized using density functional theory (DFT), and their most stable geometries are discussed. The structural parameters, hydrogen bonds and interaction energies of 1-allyl-3-methylimidazolium dicyanamide ([Amim]DCA), 1-allyl-3-methylimidazolium chloride ([Amim]Cl), 1-allyl-3-methylimidazolium formate ([Amim]FmO) and 1-allyl-3-methylimidazolium acetate ([Amim]AcO) ion pairs are studied. The vibrational frequencies of [Amim]DCA and [Amim]Cl have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes.     

Crystal Structures of Fluoride and Chloride Complexes of Tris[（2-benzimidazolyl）methyl]amine

The crystal structures of fluoride and chloride complexes of tris[（2-benzimidazolyl）methyl]amine 1 were characterized by X-ray crystallography. 1 adopts （73 symmetrical geometry and cone-like conformation so as to allow its three NHs to associate with the anions through hydrogen bonds. Despite the different sizes of the anions, the two crystals are unexpectedly isostructural. The binding ability of the anions of 1 in solution was also studied by using of UV-vis spectroscopy.     

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2(1)/c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H...O and N-H...O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-Hcdots, three dots, centeredpi type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.     

Synthesis and characterization of triphenylphosphine adducts of ferrocene-based palladacycles and their performance in the Suzuki and Sonogashira reactions with bromo- and chloroarenes

A new triphenylphosphine adduct of cyclopalladated ferrocenylpyridazine containing a chloride anion, 2a, has been synthesized from the reaction of the chloride-bridged palladacyclic dimer 1a with triphenylphosphine. The corresponding adducts 3a,b containing iodide anion have been readily prepared through anion exchange reactions of 2a,b with NaI in acetone. These complexes were characterized by elemental analysis, IR and 1H-NMR. Additionally, their crystal structures have been determined by X-ray diffraction and intermolecular C-H···X (Cl, Br, I) bonds were found in the crystals. The use of these palladacycles as catalysts for the Suzuki and Sonogashira reactions was examined. The complexes 2a,b exhibited higher catalytic activity than the corresponding 3a,b in the Suzuki reaction. However, the order of activity of adducts with varying halogen anions is 3a~3b > 2a~>2b in the Sonogashira reaction.     

Conformational preferences of the aglycon moiety in models and analogs of GlcNAc-Asn linkage: crystal structures and ab initio quantum chemical calculations of N-(beta-D-glycopyranosyl)haloacetamides

The biological addition of oligosaccharide structures to asparagine residues of N-glycoproteins influences the properties and bioactivities of these macromolecules. The linkage region constituents, 2-acetamino-2-deoxy-beta-D-glucopyranose monosaccharide (GlcNAc) and L-asparagine amino acid (Asn), are conserved in the N-glycoproteins of all eukaryotes. In order to gain information about the structure and dynamics of glycosylated proteins, two chloroacetamido sugars, Glc betaNAcNHCOCH2Cl and Man betaNHCOCH2Cl, have been synthesized, and their crystal structures have been solved. Structural comparison with a series of other models and analogs gives insight about the influence of the N-acetyl group at position C2 on the conformation of the glycan-peptide linkage at C1. Interestingly, this N-acetyl group also influences the packing and network of hydrogen bonds with involvement in weak hydrogen bonds C-H...X that are of biological importance. DFT ab initio calculations performed on a series of models and analogs also confirm that the GlcNAc derivatives present different preferred conformation about the N-CO-CH2-X (chi2) torsion angle of the glycan-peptide linkage, when compared to other monosaccharide derivatives. The energy profiles that have been obtained will be useful for parametrization of molecular mechanics force-field. The conjunction of crystallographic and computational chemistry studies provides arguments for the structural effect of the N-acetyl group at C2 in establishing an extended conformation that presents the oligosaccharide away from the protein surface.     

Ab initio molecular dynamics of liquid 1,3-dimethylimidazolium chloride

Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.     

Characterizing the properties of the N7,N9-dimethylguaninium chloride ion pairs: prospecting for the design of a novel ionic liquid

The structures, infrared spectra, and electronic properties of the N7,N9-dimethylguaninium chloride have been studied. The interaction of one cation with one to four Cl anions and one Cl anion with two cations were investigated. Fifteen stable conformers are obtained. It is found that there are four acidic regions in the vicinity of the guaninium cations. In these regions, the cation could H-bond with one to three Cl anions but no more than three nearest anions. One Cl anion could H-bond with two cations. Additionally, evidence of a Cl...pi interaction between the anion and cation is observed. Among these structures, one cation interaction with two anions and two cations interaction with one anion have the larger interaction energies than the other series. Natural bond orbital analyses and molecular orbitals reveal that the charge transfer from anion(s) to the cation(s) occurs mainly through either the Cllp --> sigma C-H, Cllp --> sigma N-H, or Cllp --> pi C8-N7 interactions. The interaction between Cl and sigma (C/N-H) or pi C-N produces a small bond order. This indicates that the Cl...H (Cl...pi) interaction exhibits a weak covalent character and suggests a strong ionic H-bond (Cl...pi bond). What's more, formation of Cl...H/Cl...pi bond decreases the bond order of the associated C/N-H bond or C8-N7 bond. In addition, examination of vibrational spectrum of each conformer explains the origin of H-bonding character.     

N,N′-二[3-氯-5S-(l-孟氧基)-2(5H)-4-呋喃酮基]-1,4-丁二胺的合成及晶体结构(英文)

合成了N,N′-二[3-氯-5S-(l-孟氧基)-2(5H)-4-呋喃酮基]-1,4-丁二胺,并通过IR,1H NMR,MS和X射线单晶衍射对其进行了表征.X射线单晶衍射结果表明:标题化合物的不对称结构单元中包含一个平面的呋喃酮环和一个椅式的环己烷环,四个手性中心.标题化合物通过N—H…O分子间氢键作用实现空间堆积.     

超分子化合物[UO2Cl4][phenH]2的合成、晶体结构、荧光性质及[UO2Cl4][phenH]2/PVA薄膜的发光性能

水热条件下合成了一种含铀的超分子化合物[UO2Cl4][phenH]2(phen=1,10-邻菲罗啉),进行了X射线单晶衍射、红外光谱、紫外光谱和荧光光谱分析。 晶体结构分析表明,该化合物由2个[phenH]+阳离子和1个阴离子[UO2Cl4]2-组成。 红外光谱和X射线单晶衍射表明,标题化合物的三维框架是由N-H…Cl、C-H…Cl和C-H…O弱氢键相互作用所构建。 中心U原子是六配位,有4个Cl原子和2个O原子。 此外,没参与配位的phen利用氢键和π…π堆积与[UO2Cl4]2-相互作用。 含U原子的阴离子是一种扭曲八面体结构。 利用溶胶-凝胶法合成了化合物的PVA薄膜。 标题化合物和薄膜均有较强的荧光性。CCDC:713149     

Unclassical hydrogen bonds of C-H?O and C-H?Cl in the crystals of 1,4-diaryl Hantzsch esters

Three novel N1-substituted derivatives of Hantzsch ester were synthesized and the molecular structures were studied by using X-ray crystallography. Two types of unclassical hydrogen bonds C-H?O and C-H?Cl were presented in the crystals. The formation of such a hydrogen bond is dependent on the nature of the substituent at C23.     

C-H...N and C-H...S hydrogen bonds--influence of hybridization on their strength

Simple complexes connected through C-H...S and C-H...N interactions are investigated: CH4...NH3, C2H4...NH3, C2H2...NH3, CH4...SH2, C2H4...SH2, and C2H2...SH2. Ab initio and DFT calculations are performed (SCF, MP2, B3LYP) using different basis sets up to the MP2/aug-cc-pVQZ//MP2/aug-cc-pVDZ level of approximation. The Bader theory is applied since MP2/6-311++G(d,p) wave functions are used to find and to characterize bond critical points in terms of electron densities and their Laplacians. The influence of hybridization on the properties of C-H...S and C-H...N systems is also studied showing that the strength of such interactions increases in the following order: C(sp3)-H...Y, C(sp2)-H...Y, C(sp)-H...Y, where Y = S, N--it is in line with the previous findings on C-H...O hydrogen bonds. The results also show that CH4...SH2 and C2H4...SH2 complexes should be rather classified as van der Waals interactions and not as hydrogen bonds. The frequency associated with the C-H stretch of C(sp3)-H...S is blue-shifted.     

One-dimensional metal-organic framework with unprecedented heptanuclear copper units

The reaction of copper(II) sulfate, copper(II) chloride, 3,5-diacetylamino-1,2,4-triazole, and 3-acetylamino-5-amino-1,2,4-triazole in water yields green, plate-shaped crystals of [[{Cu3(mu3-OH(1/2))L(H2O)2Cl}2{mu-Cu(H2O)2Cl2}].12H2O]n (1), where L is a new triazole-derived macrocyclic ligand. The structure of 1 consists of heptanuclear (H)OCuII(3)-CuII-CuII(3)O(H) entities linked in pairs through symmetric mu3-O...H...O-mu3 hydrogen bonds to form a double-stranded one-dimensional network. A significant overall antiferromagnetic behavior has been observed for 1.     

Resorcarenes in the boat conformation as building blocks for hydrogen-bonded assemblies including two ammonium cations

Crystal structures are reported for various co-crystals of rccc-resorcarenes with triethylammonium chloride. Usually, two molecules of a C2v-symmetric tetraester 2 in the boat conformation are linked through four hydrogen-bonded chloride anions to give dimeric assemblies. Two of the chloride anions may be replaced by four hydrogen-bonded ethanol molecules in an otherwise similar structure. These assemblies, which consist of six or eight components, posses voluminous, negatively charged chambers in which two triethylammionium cations, 3+, are included as guests by strong electrostatic and hydrogen-bonding interactions. The host-guest N-H...Cl hydrogen bonds were clearly detected at 173 K. These are the first examples of hydrogen-bonded, solid-state capsules trapping two ions of the same charge in close proximity. In the 1:2 complex with 3+ Cl-, the molecule of the parent resorcarene 1 also adopts a boat conformation whose cavity is considerably extended by four hydrogen-bonded chloride anions. The pocket formed in this way again includes two 3+ ions as a result of electrostatic and hydrogen bonding host-guest interactions. All these structures show that the boat conformers of resorcarenes can be used as a novel motif for the construction of hydrogen-bonded assemblies capable of molecular inclusion and encapsulation.     

Ion pair formation in water. association constants of bolaform, bisquaternary ammonium, electrolytes by chemical trapping

The first and second association constants, K1 and K2, for ion pair formation in aqueous 0.02-3.5 M solutions of bis(trimethyl)-alpha,omega-alkanediammonium halides with variable spacer lengths, 1-n-1 2X (n = 2-4, X = Cl, Br) and bolaform salts and for tetramethylammonium halides (TMAX, X = Cl, Br), K(TMAX), were determined by the chemical trapping method. Values for K(TMAX) are small, K(TMABr) = 0.83 M(-1) and K(TMACl) = 0.29 M(-1), in agreement with literature values. For the bolaform salts, K1 depends on spacer length and counterion type, ranges from 0.4 to 17 M(-1), is 2-10 times larger than K2, is larger for Br- than Cl-, and decreases by a factor of approximately 3 for Cl- and approximately 10 for Br- as n increases from 2 to 4. K2, for the formation of bolaform dihalide pair, is essentially the same as that for ion pair formation in TMAX solutions, i.e., K2 approximately K(TMAX). Values of K1 and K(TMABr) obtained from changes in 79Br line widths are in good agreement with those obtained by chemical trapping. The results are consistent with a thermodynamic model in which the ion association depends on the balance of the ion specific hydration free energies of cations and anions and their ion specific and hydration interactions in ion pairs. Spacer length dependent ion pairing by bolaform electrolytes, which are analogues of the headgroups and counterions of gemini amphiphiles, suggests a new model for the spacer length dependent sphere-to-rod transitions of gemini micelles. Neutral, but polar, headgroup-counterion pairs have a lower demand for hydration that free headgroups and counterions, and headgroup-counterion pair formation releases interfacial water into the bulk aqueous phase, permitting tighter amphiphile packing in rodlike micelles.     

Synthesis, crystal structure and luminescence properties of one inorganic-organic hybrid compound [FTMA]2[Co(NCS)4] (FTMA = ferrocenylmethyltrimethylammonium cation)

A new inorganic-organic hybrid compound [FTMA](2)[Co(NCS)(4)] (FTMA = ferrocenylmethyltrimethylammonium cation) has been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Co(II) atom has a distorted tetrahedral environment with four N atoms of four NCS(-) anions. In the solid state there are C-H?π interactions between adjacent ferrocenyl cations, which generate one-dimensional (1-D) supramolecular chain, and C-H?S hydrogen bonds between [FTMA](+) cations and cobalt thiocyanate anions. The title compound shows strong purple fluorescence emission in the solid state at room temperature.     

Crystal Structure,Vibrational Studies,Optical Properties and TG-DTA Investigations of a New Chlorocadmate Templated by 1-Methylimidazolium

Chemical preparation, X-ray single crystal diffraction, thermal analysis, electrochemical measurements, IR, Raman and UV spectroscopic investigations of a novel organic-inorganic hybrid material(C₄H₇N₂)CdCl₃(H₂O)(1) were described. 1-Methylimidazolium aquapentachlorocadmate(II) crystallized in the monoclinic system with P2₁/n space group. Its structure provided a new interesting example of infinite inorganic layers of [CdCl₃(H₂O)]_n^n- centered by (-101) planes. The [CdCl5(H₂O)]-anions were interconnected by O-H···Cl hydrogen bonds. Acidic protons of the chloride group were transferred to the organic molecule, giving the singly-protonated cations. The ability of ions to form a spontaneous three-dimensional structure through O-H···Cl and N-H···Cl hydrogen bonds was fully utilized. These hydrogen bonds induced notable vibrational effects. IR and Raman spectra were reported and discussed on the basis of group theoretical analysis and on quantum chemical density theory(DFT) calculation. The molecular HOMO-LUMO compositions and their respective energy gaps were also drawn to explain the activity of our compound. The role of the intermolecular interaction in this crystal was analyzed. The optical study was also investigated by UV-Vis absorption spectrum. Thermal analysis reveals the hydrous character of the compound. Cyclic voltammetry was studied to evaluate the spectral and structural changes accompanying electron transfer.     

A spiral-like chain from a hydrogen-bonded cyclic dichloride containing a water dimer in a quaternary diammonium dichloride trihydrate

The reaction of benzyl chloride with tetramethylethylenediamine (tmen) results in the formation of the quaternary diammonium dichloride trihydrate (dbtmen)Cl₂·3H₂O 1 (dbtmen is N,N′-dibenzyl-N,N,N′,N′-tetramethylethylenediammonium) in good yields. 1 crystallises in the monoclinic P2₁/c space group and its structure consists of N,N′-dibenzyl-N,N,N′,N′-tetramethylethylenediammonium dication, two chloride anions and three crystal water molecules all of which are located in general positions. The organic dication is H-bonded to the chloride anions and the crystal waters with the help of intra-and intermolecular C-H···Cl and C-H···O interactions, while the chloride anions are linked to the crystal waters via O-H···Cl interactions. One of the crystal waters is linked through an intermolecular O-H···O bond with another water resulting in the formation of a water dimer. The O-H···Cl and O-H···O interactions between the chloride anions and water molecules lead to the formation of a five-membered {O₃Cl₂} cyclic dichloride containing a water dimer. The five-membered rings are linked into a chain with the aid of a O-H···Cl interaction. The organic cations are organised in zigzag fashion on either side of the chain and are further linked to the anionic water chain via weak C-H···O and C-H···Cl interactions, leading to the supramolecular organisation of the rings into a spiral-like of chain. Dedicated to Prof. Sabyasachi Sarkar on the occasion of his 60^th birthday     

Structure and matrix isolation infrared spectrum of formyl fluoride dimer: blue-shift of the C-H stretching frequency

Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the dimer with two C-H...O hydrogen bonds. This observation includes the HCOF dimer to the class of hydrogen bonded complexes showing blue shift in their vibrational energies.