Density functional theory studies of interactions of ruthenium-arene complexes with base pair steps

Density functional theory (DFT) calculations have been performed to determine the strength and geometry of intermolecular interactions of "piano-stool" ruthenium arene complexes, which show potential as anticancer treatments. Model complexes with methane and benzene indicate that the coordinated arene has C-H···π acceptor ability similar to that of free benzene, whereas this arene acts as a much stronger C-H donor or partner in π-stacking than free benzene. The source of these enhanced interactions is identified as a combination of electrostatic and dispersion effects. Complexes of Ru-arene complexes with base-pair step fragments of DNA, in which the arene has the potential to act as an intercalator, have also been investigated. Binding energies are found to be sensitive to the size and nature of the arene, with larger and more flexible arenes having stronger binding. π-stacking and C-H···π interactions between arene and DNA bases and hydrogen bonds from coordinated N-H to DNA oxygen atoms, as well as covalent Ru-N bonding, contribute to the overall binding. The effect of complexation on DNA structure is also examined, with larger rise and more negative slide values than canonical B-DNA observed in all cases.     

The art of stacking: structural folding and self-assembly of branched π-conjugation assisted by O-H···O and C-H···F hydrogen bonds

An intimate interplay of O-H···O/C-H···F hydrogen bonds and π-π stacking interactions allows a phenyleneethynylene-based dendritic molecule to fold and self-assemble into two distinctively different molecular crystals as pseudopolymorphs.     

Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions

The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.     

The structure, properties, and nature of HArF-benzene complex: redshift and blueshift of Ar-H stretch frequency and rare gas atomic number dependence of hydrogen bonds

Ab initio calculations have been performed for the complexes of benzene with HArF, HKrF, and HXeF. The computed results indicate that the complexes of benzene-HArF exist in different conformations and among them those with π-hydrogen bonds are the more stable than those with C-H···F hydrogen bonds. Interestingly, the Ar-H stretching frequency is redshifted in the more stable isomer and blueshifted in the less stable form. The Ng (Ng=Ar, Kr, and Xe) atomic number dependence of the Ng-H···π and C-H···F hydrogen bonds has been explored. The result indicates that the strength of Ng-H···π and C-H···F hydrogen bonds is weakened with the increase of Ng atomic number. Natural bond orbital analysis has been performed to understand the interaction nature, frequency shift of H-Ng stretch, and dependence of Ng-H···π and C-H···F hydrogen bonds on the Ng atomic number.     

Characteristics of X-H···π interactions: ab initio and QTAIM studies

The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.     

Luminescence enhancement and tuning via multiple cooperative supramolecular interactions in an ion-paired multinuclear complex

[(3,5-(CF(3))(2)Pz)(AgL)(2)](+)[Ag(5)(3,5-(CF(3))(2)Pz)(6)(CH(3)CN)](-) (L = 2-(N,N-diethylanilino-4-yl)-4,6-bis(3,5-dimethylpyrazol-1-yl)-1,3,5-triazine) shows bright and tunable emissions influenced by its supramolecular structure. Columnar stacks are assembled via cooperative interactions that include Ag(I)···Ag(I) argentophilic bonding, π···π stacking and Ag(I)···π interactions.     

Communication: Competition between π···π interaction and halogen bond in solution: a combined 13C NMR and density functional theory study

Competition between π···π interaction and halogen bond in solution has been investigated by using carbon nuclear magnetic resonance spectroscopy ((13)C NMR) combined with density functional theory calculation. Both experimental and theoretical results clearly show that there are no C-Cl···π or C-Br···π halogen bonds and only the π···π interactions exist in the binary liquid mixtures of C(6)D(6) with C(6)F(5)Cl and C(6)F(5)Br, respectively. The case is totally different for the binary liquid mixtures of C(6)D(6) with C(6)F(5)I in which the C-I···π halogen bonds not the π···π interactions are present. The important role of entropy in the competition between π···π interaction and halogen bond in solution was also discussed.     

Microwave spectroscopic and theoretical studies on the phenylacetylene···H2O complex: C-H···O and O-H···π hydrogen bonds as equal partners

Rotational spectra of five isotopologues of the title complex, C(6)H(5)CCH···H(2)O, C(6)H(5)CCH···HOD, C(6)H(5)CCH···D(2)O, C(6)H(5)CCH···H(2)(18)O and C(6)H(5)CCD···H(2)O, were measured and analyzed. The parent isotopologue is an asymmetric top with κ = -0.73. The complex is effectively planar (ab inertial plane) and both 'a' and 'b' dipole transitions have been observed but no c dipole transition could be seen. All the transitions of the parent complex are split into two resulting from an internal motion interchanging the two H atoms in H(2)O. This is confirmed by the absence of such doubling for the C(6)H(5)CCH···HOD complex and a significant reduction in the splitting for the D(2)O analog. The rotational spectra, unambiguously, reveal a structure in which H(2)O has both O-H···π (π cloud of acetylene moiety) and C-H···O (ortho C-H group of phenylacetylene) interactions. This is in agreement with the structure deduced by IR-UV double resonance studies (Singh et al., J. Phys. Chem. A, 2008, 112, 3360) and also with the global minimum predicted by advanced electronic structure theory calculations (Sedlack et al., J. Phys. Chem. A, 2009, 113, 6620). Atoms in Molecule (AIM) theoretical analysis of the complex reveals the presence of both O-H···π and C-H···O hydrogen bonds. More interestingly, based on the electron densities at the bond critical points, this analysis suggests that both these interactions are equally strong. Moreover, the presence of both these interactions leads to significant deviation from linearity of both hydrogen bonds.     

Syntheses, Crystal Structures and Fluorescence Properties of Two Triazolyl Derivatives with Biphenyl Links

Two novel triazolyl derivatives with biphenyl links, namely 4,4-bis（1,2,4-triazol-1-ylmethyl）biphenylene 1 and 4,4-bis（3,5-dimethyl-1,2,4-triazol-1-ylmethyl）biphenylene 2, have been synthesized and structurally characterized by single-crystal X-ray diffraction. Compounds 1·H2O·HCl and 2·2H2O·2HCl crystallize in the monoclinic system with space group C2/c and P21/c, respectively. The dihedral angles of the two phenyl rings are 30.26（6）° in 1·H2O·HCl, while co-planar （0.00（7）°） in 2·2H2O·2HCl. In 1·H2O·HCl, the N-H…O hydrogen bonds link 1 to form chain-like structures which are further connected by O-H…Cl, C-H…Cl, C-H…O and π-π supramolecular interactions. The hydrogen bonds of O-H…Cl in 2·2H2O·2HCl provide distinguishing P/M helical chains along the b axis, and these chains are further connected by N-H…O hydrogen bonds to generate a 2D structure. Compounds 1 and 2 in methanol solution show much stronger emission bands at 319 nm than biphenyl at 316 nm under excitation at 260 nm.     

Novel C-H···C contacts involving 3,5-dimethylpyrazole ligands in a tetracoordinate Co(II) complex

A violet-blue cobalt(II) complex [Co(4-nbz)(2)(DMP)(2)] (1), where 4-nbz = 4-nitrobenzoate and DMP = 3,5-dimethylpyrazole, has been prepared at room temperature. Crystallographic studies on 1·0.5H(2)O reveal that the molecules of 1 are linked by a variety of non-covalent bonds including a novel type of C-H···C contact forming, with assistance from N-H···O, C-H···O and C-H···π interactions, an intricate 3-D supramolecular network. Theoretical calculations suggest that the observed C-H···C interactions are energetically quite significant.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

Spectral studies of copper(II) complexes of tridentate acylhydrazone ligands with heterocyclic compounds as coligands: X-ray crystal structure of one acylhydrazone copper(II) complex

Six copper(II) complexes of 2-hydroxy-4-methoxybenzaldehyde nicotinoylhydrazone (H2hmbn), 2-hydroxy-4-methoxyacetophenone nicotinoylhydrazone (H2hman), 2-hydroxy-4-methoxybenzaldehyde benzoylhydrazone (H2hmbb) and 2-hydroxy-4-methoxyacetophenone benzoylhydrazone (H2hmab) have been synthesized. The complexes viz. [Cu(hmbn)](2)·2H(2)O (1), [Cu(hman)](2) (2), [Cu(hmbb)](2)·2H(2)O (3), [Cu(hmbb)phen]·1(1/2)H2O (4), [Cu(hmbb)(bipy)·H2O] (5) and [Cu(hmab)phen] (6) were characterized by different physicochemical techniques. The crystal structure of [Cu(hman)phen] is obtained and it has a distorted square pyramidal geometry with π-π stacking interactions and significant C-H π interactions.     

Synthesis and Structure of 1.5Zn（phen）3·L·3NO3 Supramolecule （phen = o-Phenanthroline,L = 4-Aminoacetophenone Thiosemicarbazone）

A supramolecular framework, 1.5Zn（phen）3·L·3NO3 （C63H48Zn1.5N16O9S）, has been synthesized. The ligand L was synthesized by the condensation of p-aminoacetophenone with thiosemicarbazide. The crystal belongs to the monoclinic system, space group C2/c, with a = 31.005（2）, b = 15.114（2）, c = 24.887（3） A, β = 94.260（2）° Z = 8, V = 11630（2）A^3 Dc = 1.489 g/cm^3, Mr = 1303.29,λ（MoKa） = 0.71069 A,μ= 0.735 mm^-1, F（000） = 5368, Rint = 0.0699, R= 0.0505 and wR= 0.0707. Two independent Zn atoms are both coordinated by six N atoms from three phen ligands. π-π and C-H…π interactions among the L ligands and Zn（phen）3 cations, π-π and C-H...π interactions among the Zn（phen）3 cations and N-H...O hydrogen bonds among the L ligands and nitrate anions connect the whole structure into a 3-D supramolecular framework.     

Host-guest supramolecular interactions in the coordination compounds of 4,4'-azobis(pyridine) with MnX2 (X = NCS–, NCNCN–, and PF6(–)): structural analyses and theoretical study

Three new Mn(II) coordination compounds {[Mn(NCNCN)(2)(azpy)]·0.5azpy}(n) (1), {[Mn(NCS)(2)(azpy)(CH(3)OH)(2)]·azpy}(n) (2), and [Mn(azpy)(2)(H(2)O)(4)][Mn(azpy)(H(2)O)(5)]·4PF(6)·H(2)O·5.5azpy (3) (where azpy = 4,4'-azobis(pyridine)) have been synthesized by self-assembly of the primary ligands, dicyanamide, thiocyanate, and hexafluorophosphate, respectively, together with azpy as the secondary spacer. All three complexes were characterized by elemental analyses, IR spectroscopy, thermal analyses, and single crystal X-ray crystallography. The structural analyses reveal that complex 1 forms a two-dimensional (2D) grid sheet motif. These sheets assemble to form a microporous framework that incorporates coordination-free azpy by host-guest π···π and C-H···N hydrogen bonding interactions. Complex 2 features azpy bridged one-dimensional (1D) chains of centrosymmetric [Mn(NCS)(2)(CH (3)OH)(2)] units which form a 2D porous sheet via a CH(3)···π supramolecular interaction. A guest azpy molecule is incorporated within the pores by strong H-bonding interactions. Complex 3 affords a 0-D motif with two monomeric Mn(II) units in the asymmetric unit. There exist π···π, anion···π, and strong hydrogen bonding interactions between the azpy, water, and the anions. Density functional theory (DFT) calculations, at the M06/6-31+G* level of theory, are used to characterize a great variety of interactions that explicitly show the importance of host-guest supramolecular interactions for the stabilization of coordination compounds and creation of the fascinating three-dimensional (3D) architecture of the title compounds.     

Tetrathiafulvalene-triazine-dipyridylamines as multifunctional ligands for electroactive complexes: synthesis, structures, and theoretical study

The electroactive ligands (2,4-bis-tetrathiafulvalene[6-(dipyridin-2'-ylamino)]-1,3,5-triazine) TTF(2)-tz-dpa (1) and (2-tetrathiafulvalene[4,6-bis-(dipyridin-2'-ylamino)]-1,3,5-triazine) TTF-tz-dpa(2) (2) have been synthesized by palladium cross-coupling catalysis, and the single crystal X-ray structure for 1 was determined. In the solid state the TTF and triazine units are practically coplanar and short intermolecular S···S contacts are established. Two neutral and one tetracationic Zn(II) complexes, formulated as (TTF(2)-tz-dpa)ZnCl(2) (3), [ZnCl(2)(TTF-tz-dpa(2))Zn(H(2)O)Cl(2)] (4), and {[(H(2)O)(2)Zn(TTF-tz-dpa(2))](ClO(4))(2)}(2) (5) have been crystallized and analyzed by single crystal X-ray analysis. A peculiar feature is the evidence for anion-π interactions, as shown by the short Cl···triazine and O(perchlorate)···triazine distances of 3.52 and 3.00 ?, respectively. A complex set of intermolecular π···π, S···S, and hydrogen bonding interactions sustain the supramolecular organizations of the complexes in the solid state. Electronic absorption spectra provide evidence for the intramolecular charge transfer from TTF to triazine, also supported by time-dependent density functional theory (TD DFT) calculations.     

双核银配合物[Ag2(μ-(4-MeC6H4O)2PS2)2(Phen)2]的光谱性质和晶体结构

合成了双核银配合物[Ag2(μ-(4-MeC6H4O)2PS2)2(Phen)2](phen为1,10-邻菲咯啉),用元素分析、红外光谱、紫外-可见光谱和热重分析进行了表征,并用X-射线衍射法测定了晶体结构。该晶体属于正交晶系,Pbca空间群,晶胞参数为:a=1.2035(2)nm,b=1.638 3(3)nm,c=2.517 1(5)nm,V=4.963 1(17)nm 3,Dc=1.599 g.m-3,Z=4,F(000)=2 416,μ(Mo Kα)=1.072 mm-1,S=1.066,(Δ/σ)max=0.001,R1=0.037 6,wR2=0.088 8(I>2σ(I))。晶体结构研究表明每个Ag原子与不同配体(4-MeC6H4O)2PS2-的2个S原子和1个phen配体的2个N原子配位形成了具有椅式构型的八元环Ag2S4P2,Ag原子为畸变四面体AgS2N2构型,配合物通过phen的π-π堆积形成了一维结构,分子间的弱氢键C-H…O和C-H…π作用使分子进一步形成了三维网络结构。     

Synthesis of 1,3,5-alternate azacalix[3]pyridine[3]pyrimidine and its complexation with fullerenes via multiple π/π and CH/π interactions

Azacalix[3]pyridine[3]pyrimidine was synthesized efficiently by means of a [3+3] fragment coupling approach. Adopting a preorganized symmetric 1,3,5-alternate conformation, the macrocycle formed complexes with fullerenes through the multiple intramolecular π/π and CH/π interactions.     

Observation of a double C-H···π interaction in the CH2ClF···HCCH weakly bound complex

The structure of the CH(2)ClF···HCCH dimer has been determined using both chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy. The complex has C(s) symmetry and contains both a double C-H···π interaction, in which one π-bond acts as acceptor to two hydrogen atoms from the CH(2)ClF donor, and a weak C-H···Cl interaction, with acetylene as the donor. Analysis of the rotational spectra of four isotopologues (CH(2)(35)ClF···H(12)C(12)CH, CH(2)(37)ClF···H(12)C(12)CH, CH(2)(35)ClF···H(13)C(13)CH, and CH(2)(37)ClF-H(13)C(13)CH) has led to a structure with C-H···π distances of 3.236(6) ? and a C-H···Cl distance of 3.207(22) ?, in good agreement with ab initio calculations at the MP2/6-311++G(2d,2p) level. Both weak contacts are longer than those observed in similar complexes containing a single C-H···π interaction that lies in the C(s) plane; however, this appears to be the first double C-H···π contact to be studied by microwave spectroscopy, so there is little data for direct comparison. The rotational and chlorine nuclear quadrupole coupling constants for the most abundant isotopologue are: A = 5262.899(14) MHz, B = 1546.8074(10) MHz, C = 1205.4349(7) MHz, χ(aa) = 28.497(5) MHz, χ(bb) = -65.618(13) MHz, and χ(cc) = 37.121(8) MHz.     

Novel neutral guest recognition and interpenetrated complex formation from pillar[5]arenes

Simple alkyl-substituted pillar[5]arenes can form stable interpenetrated complexes with neutral bis(imidazole) guests utilizing multiple C-H···O(N) hydrogen bond and C-H···π interactions.     

Unprecedented π···π interaction between an aromatic ring and a pseudo-aromatic ring formed through intramolecular H-bonding in a bidentate Schiff base ligand: crystal structure and DFT calculations

A combination of a single crystal X-ray diffraction study and density functional theory calculations has been applied to a bidentate Schiff base compound to elucidate different cooperative non-covalent interactions involved in the stabilization of the keto form over the enol one in the solid state. The single crystal X-ray structure reveals a remarkable supramolecular assembly of the keto form through a cyclic hydrogen bonded dimeric motif. The most interesting feature in the supramolecular assembly is the formation of a 'dimer of dimer' motif by π···π, CH···π and N···O/O···O interactions in which the π···π interaction involving the aromatic phenyl ring and the intramolecularly hydrogen bonded pseudo-aromatic ring of the keto form lying just above or below the phenyl ring of the other dimer seems to be unprecedented. The optimized geometry of the hydrogen bonded dimeric motif of the keto form of the organic molecule has been obtained by DFT calculations and agrees very well with that found within the crystalline state. The X-ray crystallographic geometry of the 'dimer of dimer' has also been computed, which shows that in the HOMO, the π electrons are localized in the phenyl rings away from each other, while in the LUMO, there is a strong π-π interaction between the phenyl ring of one dimer with the pseudo-aromatic ring of another dimer with an energy estimated to be 7.95 kJ mol(-1). Therefore, on HOMO → LUMO excitation there is localization of π electrons in the central part of the complex moiety which plays a stabilizing role of the dimer of dimer motif in the solid state.