Noncovalent interactions between cytosine and SWCNT: curvature dependence of complexes via pi...pi stacking and cooperative CH...pi/NH...pi

Fragments of C24H12, adapted from a variety of armchair [(n,n), (n = 5, 7, and 8)] and zigzag [(m,0) (m = 8, 10, and 12)] single-walled carbon nanotube (SWCNT), are used to model corresponding SWCNTs with different diameters and electronic structures. The parallel binding mainly through pi...pi stacking interaction, as well as the perpendicular binding via cooperative NH...pi and CH...pi between cytosine and the fragments of SWCNT have been extensively investigated with a GGA type of DFT, PW91LYP/6-311++G(d,p). The eclipsed tangential (ET) conformation with respect to the six-membered ring of cytosine and the central ring of SWCNT fragments is less stable than the slipped tangential (ST) conformation for the given fragment; perpendicular conformations with NH2 and CH ends have higher negative binding energy than those with NH and CH ends. At PW91LYP/6-311++G(d,p) level, two tangential complexes are less bound than perpendicular complexes. However, as electron correlation is treated with MP2/6-311G(d,p) for PW91LYP/6-311++G(d,p) optimized complexes, it turns out there is an opposite trend that two tangential complexes become more stable than three perpendicular complexes. This result implies that electron correlation, a primary source to dispersion energy, has more significant contributions to the pi...pi stacking complexes than to the complexes via cooperative NH...pi and CH...pi interactions. In addition, it was found for the first time that binding energies for two tangential complexes become more negative with increasing nanotube diameter, while those for three perpendicular complexes have a weaker dependence on the curvature; i.e., binding energies are slightly less and less negative. The performance of a novel hybrid DFT, MPWB1K, was also discussed.     

Exploring the lower limit in hydrogen bonds: analysis of weak C-H...O and C-H...pi interactions in substituted coumarins from charge density analysis

Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H...O and C-H...pi interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-31G* method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H...O) and a van der Waals interaction (C-H...pi). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.     

Computational characterization and modeling of buckyball tweezers: density functional study of concave-convex pi...pi interactions

The geometries and binding energies of a recent buckyball tweezers (C(60)H(28)) and its supramolecular complexes are investigated using recently developed density functionals (M06-L and M06-2X) that include an accurate treatment of medium-range correlation energy. The pincer part of the tweezers, corannulene, has a strong attractive interaction with C(60). However, due to the entropy penalty, the calculated gas-phase free energy of association of the C(60)@corannulene supramolecule is positive 3.5 kcal mol(-1); and this entropy penalty explains why it is difficult to observe C(60)@corannulene supramolecule experimentally. By using a pi-extended tetrathiafulvalene (TTF), in particular 9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene (TTFAQ or C(20)H(10)S(4)), as the pincer part, we modeled a new buckyball tweezers. The geometries and binding energies of the new buckyball tweezers and its supramolecular complexes are also calculated. Due to fact that the attractive interaction between TTFAQ and C(60) is weaker than that between corannulene and C(60), the gas-phase binding free energy in the C(60)@C(60)H (32)S(8) supramolecular complex is smaller than that in the C(60)@C(60)H(28) supramolecule. We also discuss solvent effects.     

Comparison of C-H...pi and hydrophobic interactions in a beta-hairpin peptide: impact on stability and specificity

We have examined the impact of C-H...pi and hydrophobic interactions in the diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe, Trp, or Cha (cyclohexylalanine) with Lys or Nle (norleucine). NMR studies, including NOESY and chemical shift perturbation studies, of the Lys side chain indicates that Lys interacts in a specific geometry with Phe or Trp through the polarized C epsilon. In contrast, Nle does not interact in a specific manner with the diagonal aromatic residue. Thermal denaturation provides additional support that Lys and Nle interact in fundamentally different manners. Folding of the peptide with a diagonal Trp...Lys interaction was found to be enthalpically driven, whereas the peptide with a diagonal Trp...Nle interaction displayed cold denaturation, as did the control peptide with a diagonal Cha...Nle interaction, indicating different driving forces for interaction of Lys and Nle with Trp. These findings have significant implications for specificity in protein folding and de novo protein design.     

Evidence for a C-H...pi type weak interaction: 1 : 1 complex of styrene with acetylene studied by mass selective high-resolution UV spectroscopy and ab initio calculations

The 1 : 1 complex of styrene with acetylene has been studied by mass selective low- and high-resolution UV resonance-enhanced two-photon ionisation (R2PI) spectroscopy combined with genetic-algorithm-based computer-aided fit of the spectra with partial rotational resolution, and high level ab initio quantum chemistry calculations. Two stable conformeric geometries of the 1 : 1 complex of styrene and acetylene have been theoretically found: one with acetylene binding to styrene as a proton donor, and one with acetylene acting as a proton acceptor. From the analysis of the vibronic structure of the S1<-- S0 spectrum and the fit of the highly resolved spectrum of the 0 origin band of the complex it is shown that the favoured conformation is the one in which acetylene binds to the benzene ring of styrene through formation of a non-conventional hydrogen bond of C-H...pi type with no marked change of the transition moment orientation of styrene. The styrene moiety remains planar and the acetylene molecule is tilted by a small angle of 4 degrees relative to the C6 symmetry axis of the benzene ring, most likely due to the reduced symmetry of the benzene ring pi electrons rather than to a direct interaction with the vinyl group.     

Organometallic chemistry of azuliporphyrins: synthesis, spectroscopy, electrochemistry, and structural characterization of nickel(II), palladium(II), and platinum(II) complexes of azuliporphyrins

Four azuliporphyrins, two meso-unsubstituted and two meso-tetraaryl substituted, were investigated in the synthesis of novel organometallic compounds. The meso-unsubstituted or "etio" series azuliporphyrins 8 reacted with nickel(II) acetate, palladium(II) acetate, and platinum(II) chloride in DMF to give the corresponding chelates 14-16, where the metal cation lies within the macrocyclic cavity and binds to all three nitrogens and the internal carbon atom. The newly available meso-tetraarylazuliporphyrins 13 similarly afforded the corresponding nickel(II), palladium(II), and platinum(II) complexes, 17-19, respectively. The new organometallic complexes are stable nonpolar compounds and were fully characterized spectroscopically and by mass spectrometry. The UV-vis data indicate that these complexes, in common with the parent azuliporphyrin system 8, do not possess porphyrin-type aromaticity. However, electron donation from the azulene unit can give rise to dipolar resonance contributors that provide a degree of carbaporphyrin-type aromatic character. The platinum(II) azuliporphyrins 16 gave noteworthy proton NMR spectra where the meso-protons showed satellite peaks due to transannular coupling to platinum-195. The pyrrolic protons of the platinum(II) meso-tetraarylazuliporphyrin 19b also showed similar satellite peaks due to coupling from the platinum-195 isotope. The electrochemistry of free base tetraphenylazuliporphyrin 13a and the related nickel(II) and palladium(II) complexes was investigated using cyclic voltammetry, and these data indicate that metal coordination improves the reversibility of the ligand-based oxidations. Nickel(II) azuliporphyrin 14a and palladium(II) tetrakis(4-chlorophenyl)azuliporphyrin 18b were also structurally characterized by X-ray crystallography. The macrocyclic core of the palladium(II) complex 18b was significantly more planar than the nickel(II) derivative 14b, and this difference was attributed to the better size match between the azuliporphyrin cavity and the larger palladium(II) ion. The straightforward synthesis of metalloazuliporphyrins under mild conditions, and their interesting spectroscopic, electrochemical, and structural features, demonstrates that the azuliporphyrin system holds great promise as a platform for organometallic chemistry.     

Hydrogen-bonded self-assembly of pyridinium and anilinium bisphenols mediated by the hydrogen difluoride ion: towards control of C-H...pi (aromatic) interactions

The role of C-H...pi and C-H...O interactions in HF(2)(-)-assisted self-assembly of nitrogen-containing bisphenols are investigated. Unusual control on the end-face and edge-face geometries of aromatic C-H...pi interactions by a water molecule in the 4-[(4-hydroxy-3,5-dimethylphenyl)methyl]pyridinium difluoride lattice is observed. The bis(4-hydroxy-3,5-dimethylphenyl)(4-ammoniophenyl)methane.HF(2)(-) self-assembles through the formation of hydrogen-bonded cyclic hexamers.     

Inclusion compounds of tetrakis(4-nitrophenyl)methane: C-H...O networks, pseudopolymorphism, and structural transformations.

Tetrakis(4-nitrophenyl)methane is a new host material with considerable structural adaptability over a range of solvents. The crystal structures of 14 of these solvates have been determined and classified into three groups. The diamondoid group, wherein the host molecules form a 2-fold interpenetrated diamondoid network structure, is unprecedented in that network connections are made exclusively with weak C-H...O and pi...pi interactions. This group consists of the solvates of THF, dioxane, nitrobenzene, 4-bromoanisole, anisole, phenetole, p-xylene, and chlorobenzene. The rhombohedral group, which is characterized by specific host.guest interactions of the C-H...O and halogen...O2N type, consists of the solvates of CHCl3 and CHBr3 and somewhat surprisingly DMF, which shows an unusual 3-fold disorder mimicking in part the shape and size of the haloform molecules though not their orientation. The third group comprises solvent-rich solvates of the host with mesitylene, collidine, and o-xylene with quite different crystal structures. The THF solvate was found to lose solvent over limited temperature ranges transforming reversibly from the diamondoid structure to the rhombohedral structure. A mechanism for this process is outlined. Material from which solvent has been removed by heating was also found to resolvate upon soaking in appropriate solvents. In summary, the title compound forms a host network that is partially robust and in part flexible. It is possible that this fluxional nature of the host network derives from the weakness of the connecting interactions.     

Specific C-H...N intramolecular interaction in 1-vinyl-2-cyanoethylthiobenzimidazole with the formation of a nine-membered intramolecular ring,according to1H and13C NMR data

In the¹H NMR spectrum of 1-vinyl-2-cyanoethylthiobenzimidazole, an abnormal downfield shift has been found in the signal of the -hydrogen atom of the vinyl group, and also an increase in the corresponding direct¹³C-¹H spin-spin coupling constant, in comparison with other 2-substituted benzimidazoles. This indicates a specific C-H...N intramolecular interaction in this molecule between the -hydrogen atom and the cyano nitrogen atom, forming a nine-membered intramolecular ring.Translated from Translated from Izvestiya Akademii Nauk SSSR No. 10, pp. 2285–2288, October, 1991.     

Multiple C-H bond activation in group 3 chemistry: synthesis and structural characterization of an yttrium-aluminum-methine cluster

Complete donor-induced alkylaluminate cleavage of halfmetallocene complex Cp*Y(AlMe4)2, that is, treatment of Cp*Y(AlMe4)2 with 2 equiv of diethyl ether, produces [Cp*Y(mu2-Me)2]3 in high yield (95%). In contrast, the equimolar reaction of Cp*Y(AlMe4)2 with diethyl ether reproducibly formed complex [Cp*4Y4(mu2-CH3)2{(CH3)Al(mu2-CH3)2}4(mu4-CH)2] in low yield (10-30%) via a multiple C-H bond activation. The synthesis of the heterooctametallic yttrium-aluminum-methine cluster was also accomplished in moderate yield (47%) by the equimolar reaction of discrete Cp*Y(AlMe4)2 and [Cp*Y(mu2-Me)2]3 in the absence of any donor solvent and "free" AlMe3. This gives strong evidence that preformed heterometal-bridged Y-CH3-Al moieties are prone to multiple hydrogen abstraction in the presence of a highly basic reagent such as [Cp*Y(mu2-Me)2]3. The monocylopentadienyl complexes [Cp*Y(mu2-Me)2]3 and [Cp*4Y4(mu2-CH3)2{(CH3)Al(mu2-CH3)2}4(mu4-CH)2] were structurally characterized.     

Origin of the attraction in aliphatic C-H/pi interactions: infrared spectroscopic and theoretical characterization of gas-phase clusters of aromatics with methane

An attractive intermolecular interaction between an aliphatic C-H bond and a pi-electron system (C-H/pi interaction) was characterized on the basis of infrared spectroscopy and high level ab initio calculations. Infrared spectroscopy was applied to several isolated methane clusters with benzene, toluene, p-xylene, mesitylene, and naphthalene in the gas phase, and the spectral changes of the C-H stretch bands in the methane moiety upon the cluster formation were observed. In the theoretical approach, interaction energies of the clusters were evaluated by high-level ab initio calculations. The forbidden symmetric C-H stretch transition weakly appeared in the IR spectra of the clusters, and it confirmed the small deformation of the methane moiety from the T(d)() symmetry, which was predicted by the ab initio calculations. On the other hand, the degenerated asymmetric C-H stretch band showed complicated splitting, which is qualitatively interpreted by a hindered rotor model. Low-frequency shifts upon the cluster formation were seen in the symmetric C-H stretch frequency, though the magnitude of the shifts was extremely small and no clear correlation with the interaction energy was found. On the other hand, the size of the calculated interaction energy well correlates with the polarizability of aromatics. The S(1)-S(0) electronic transition of the aromatic moiety was also observed, and it showed low-frequency shifts upon cluster formation. These results support the dominance of the dispersion interaction over the electrostatic and charge-transfer terms in the aliphatic C-H/pi interaction.     

Concerted interaction between conjugated double bond CHs and multiple OHs in polyene macrolide antibiotic chainin: weak =C-H...O interactions responsible for intrinsic molecular assembly

The concerted interactions observed between five conjugated double bond CHs and four hydroxy Os in the crystal of chainin, a polyene macrolide antibiotic, clarified the existence of unprecedented, weak =C-H...O interactions, which is important for forming its intrinsic molecular assembly.     

Syntheses of aromatic substituted hydrazino-thiazole derivatives to clarify structural characterization and antioxidant activity between 3-arylsydnonyl and aryl substituted hydrazino-thiazoles

This work clarifies the structural characterization and antioxidant activity between aromatic and 3-arylsydnonyl substituted hydrazino-thiazoles by further synthesizing a series of aromatic ring-substituted hydrazino-thiazole derivatives 8a-h and 9a-h. Hydrazino-thiazole derivatives 8a-h and 9a-h were obtained by reacting aromatic or heterocyclic aromatic aldehyde thiosemicarbazones 7a-h with cyclization reagents ethyl 2-chloroacetoacetate (2a) and 2-bromoacetophenone (2b), respectively. The ORTEP drawings of compounds 8g, 8h and 9f provide strong evidence of the structure of aromatic thiazole derivatives 8a-h and 9a-h. Undoubtedly, the structure of compounds 3e-h and 4e-h synthesized by the reaction of 3-aryl-4-formylsydnone thiosemicarbazones 1e-h with cyclization reagents 2a and 2b in the previous work should have the thiazole moiety, and not the thiazoline moiety. Both the new thiazole derivatives 8a-h and 9a-h and the 3-arylsydnonyl-substituted derivatives 3e-h and 4e-h were investigated to determine their antioxidant activity by two tests that have been highly documented-the direct scavenging effect on a stable free 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and the inhibition of the 2,2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical. Results of this study demonstrate that not only the thiazole ring and the aryl ring has the contribution to the antioxidant activities, the sydnone ring of 3-arylsydnonyl moiety also has its considerable contribution.     

Preparation of the first examples of ansa-spiro substituted fluorophosphazenes and their structural studies: analysis of C-H...F-P weak interactions in substituted fluorophosphazenes

The reactions of fluorophosphazenes, endo ansa FcCH(2)P(S)(CH(2)O)(2)[P(F)N](2)(F(2)PN) (1) (Fc = ferrocenyl) and spiro [RCH(2)P(S)(CH(2)O)(2)PN](F(2)PN)(2) (R = Fc (2), C(6)H(5) (3)], with dilithiated diols have been explored. The study resulted in the formation of the first examples of ansa-spiro substituted fluorinated cyclophosphazenes as well as a bisansa substituted fluorophosphazene. The bisansa compound [1,3-[FcCH(2)P(S)(CH(2)O)(2)]][1,5-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (4) was found to be nongeminaly substituted with both the ansa rings in cis configuration, which is in stark contrast to the observations on cyclic chlorophosphazenes where geminal bisansa formation has been observed. The ansa-spiro compounds (5-7) underwent the ansa to spiro transformation leading to dispiro compounds in the presence of catalytic amounts of CsF at room temperature. Two of the ansa-spiro compounds, endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (5) and endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[FcCH(2)P(S)(CH(2)O)(2)]]N(3)P(3)F(2) (6), were structurally characterized, and the crystal structures indicate boat-chair conformation as well as crown conformation for the eight-membered ansa rings. Weak C-H.F-P interactions observed in the crystal structures of the ansa-spiro substituted fluorophosphazene derivatives have been analyzed and compared with C-H.F-P interactions of other fluorinated phosphazenes and thionyl phosphazenes.     

First systematic investigation of C-H...Cl hydrogen bonding using inorganic supramolecular synthons: lamellar, stitched stair-case, linked-ladder, and helical structures

Using a group of six neutral M(II)Cl(2)-containing coordination compounds as building blocks, the first systematic investigation of C-H...Cl hydrogen-bonding interactions was performed. Single-crystal X-ray structural analyses of four new compounds (pseudo-tetrahedral Co(II) and Zn(II); distorted trigonal bipyramidal Zn(II)) authenticate the metal coordination geometry. To provide a unified view of the presence of noncovalent interactions in this class of compounds, we have re-examined the packing diagram of two previously reported compounds (a distorted square-pyramidal Cu(II) complex and a trans-octahedral Co(II) complex). The organic ligands of our choice comprise bidentate/tridentate pyrazolylmethylpyridines and an unsymmetrical tridentate pyridylalkylamine. This systematic investigation has allowed us to demonstrate the existence of versatile C-H...Cl(2)M interactions and to report the successful application of such units as inorganic supramolecular synthons. Additional noncovalent interactions such as C-H...O and O-H...Cl hydrogen bonding and pi-pi stacking interactions have also been identified. Formation of novel supramolecular architectures has been revealed: 2D lamellar (p-cyclophane) and 3D lamellar, 3D "stitched staircase" (due to additional hydrogen-bonding interactions by water tetramers, with an average O-O bond length in the tetramer unit of 2.926 A, acting as "molecular clips" between staircases), 3D linked ladder, and single-stranded 1D helix.     

Ruthenium(III) mediated C-H activation of azonaphthol: Synthesis, structural characterization and transfer hydrogenation of ketones

Treatment of [RuCl₃(PPh₃)₃] with 1-(arylazo)naphthol ligands in benzene under reflux afford air-stable new organoruthenium(III) complexes with general composition [Ru(an-R)Cl(PPh₃)₂] (where, R = H, Cl, CH₃, OCH₃, OC₂H₅) in fairly good yield. The 1-(arylazo)naphtholate ligands behave as dianionic tridentate C, N, O donors and coordinates to ruthenium through phenolic oxygen, azo nitrogen and ortho carbon generate two five-membered chelate rings. The composition of the complexes have been established by analytical (elemental analysis and magnetic susceptibility measurement) and spectral (FT-IR, UV-Vis, EPR) methods. The complexes are paramagnetic (low-spin, d⁵) in nature and in dichloromethane solution show intense d-d transitions and ligand-to-metal charge transfer (LMCT) transitions in the visible region. The solution EPR spectrum of complex [Ru(an-CH₃)Cl(PPh₃)₂] (3) in dichloromethane at 77 K shows rhombic distortion around the ruthenium ion with three different ‘g’ values (g_x ≠ g_y ≠ g_z). The single crystal structure of the complex [Ru(an-OCH₃)Cl(PPh₃)₂] (4) has been characterised by X-ray crystallography, indicates the presence of a distorted octahedral geometry in these complexes. All the complexes exhibit one quasi-reversible oxidative response in the range 0.60-0.79 V (Ru^IV/Ru^III) and two quasi-reversible reductive responses (Ru^III/Ru^II; Ru^II/Ru^I) within the range −0.50 to −0.62 V and −0.93 to −0.98 V respectively. The formal potential of all the couples correlate linearly with the Hammett constant of the para substituent in arylazo fragment of the 1-(arylazo)naphtholate ligand. Further, the catalytic efficiency of one of the ruthenium complexes (4) was determined for the transfer hydrogenation of ketones with an excellent yield up to 99% in the presence of isopropanol/KOH.     

NMR and quantum chemical study on the OH...pi and CH...O interactions between trehalose and unsaturated fatty acids: implication for the mechanism of antioxidant function of trehalose

Trehalose is a disaccharide that attracts much attention as a stress protectant. In this study, we investigated the mechanism of the antioxidant function of trehalose. The spin-lattice relaxation times (T(1)) of (1)H and (13)C NMR spectra were measured to investigate the interaction between trehalose and unsaturated fatty acid (UFA). We selected several kinds of UFA that differ in the number of double bonds and in their configurations (cis or trans). Several other disaccharides (sucrose, maltose, neotrehalose, maltitol, and sorbitol) were also analyzed by NMR. The T(1) values for the (1)H and (13)C signals assigned to the olefin double bonds in UFA decrease with increasing concentration of trehalose and the changes reaches plateaus at integer ratios of trehalose to UFA. The characteristic T(1) change is observed only for the combination of trehalose and UFA with cis double bond(s). On the other hand, from the (13)C-T(1) measurements for trehalose, the T(1) values of the C-3 (C-3') and C-6' (C-6) are found to change remarkably by addition of UFA. (1)H[bond](1)H NOESY measurements provide direct evidence for complexation of trehalose with linoleic acid. These results indicate that one trehalose molecule stoichiometrically interacts with one cis-olefin double bond of UFA. Computer modeling study indicates that trehalose forms a stable complex with an olefin double bond through OH...pi and CH...O types of hydrogen bonding. Furthermore, a significant increase in the activation energy is found for hydrogen abstraction reaction from the methylene group located between the double bonds that are both interacting with the trehalose molecules. Therefore, trehalose has a significant depression effect on the oxidation of UFA through the weak interaction with the double bond(s). This is the first study to elucidate the antioxidant function of trehalose.     

Conformation of S-vinyl-N,N-diethyldithiocarbamate and C-H...S intramolecular interaction between atoms of olefinic hydrogen and sulfur of thiocarbonyl group according to1H and13C NMR data

According to¹H and¹³C NMR data, in S-vinyl-N,N-diethyldithiocarbamate, which exists primarily in the s-trans conformation with a syn-position of the thiocarbonyl and vinyl groups, a specific interaction C-H...S apparently takes place between the -hydrogen atoms of the vinyl group and the thiono sulfur.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 1978–1982, September, 1990.     

Intermolecular oxidative C-N bond formation under metal-free conditions: control of chemoselectivity between aryl sp2 and benzylic sp3 C-H bond imidation

A new synthetic approach toward intermolecular oxidative C-N bond formation of arenes has been developed under transition-metal-free conditions. Complete control of chemoselectivity between aryl sp(2) and benzylic sp(3) C-H bond imidation was achieved by the choice of nitrogen sources, representatively being phthalimide and dibenzenesulfonimide, respectively.