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1.
The bonding property of the CH/pi interaction in organic crystals has been investigated by the means of a periodic ab initio method. The energy of the CH(sp(2))/pi interaction in crystals, estimated with periodic RHF/6-21G*, showed a reasonable attractive CH(sp(2))/pi interaction owing to a cooperative effect, whereas the results calculated with RHF/cc-pVDZ indicate a negligibly small or repulsive interaction. The relative contribution of the CH(sp(2))/pi interaction to the column packing energy was found to be roughly half of the energy of a conventional hydrogen bond. The calculation of the charge distributions on the aromatic rings participating in the CH(sp(2))/pi interaction in crystals revealed that the atoms were more ionic than those in the gas phase. These theoretical calculations suggest a hydrogen-bonding characteristic for the CH(sp(2))/pi interaction in crystals, which does not occur in solution nor gas phase. We present computational evidence of the existence of the cooperative effect of CH(sp(2))/pi interaction in crystals. 相似文献
2.
Tárkányi G Király P Varga S Vakulya B Soós T 《Chemistry (Weinheim an der Bergstrasse, Germany)》2008,14(20):6078-6086
The impact of cooperativity between intermolecular interactions is demonstrated by the molecular self-recognition properties of highly enantioselective epi-cinchona bifunctional thiourea organocatalysts. Low-temperature NMR experiments in inert solvents have revealed two sets of nonequivalent resonances in equal population for thiourea-modified members of the epi-quinine and epi-quinidine families. In solution, the predominance of an asymmetric (C1) dimeric self-assembly with noteworthy structural motifs became evident: simultaneous intra- and intermolecular thiourea hydrogen bonding and a CH/pi interaction were observed. Both the stereochemical and the diverse conformational features of the system favor the observed quinoline T-shaped aromatic pi-pi stacking interaction. The structure findings are supported by quantitative proton-proton distance data that were available from NOE buildup curves. The 3D structure of the dimeric assembly has been modeled in agreement with the H-H distance restraints. Owing to the geometrical preference associated with the dimerization process, the self-assembled bifunctional system is interpreted as a charge-transfer complex with the potential for catalyst self-activation. 相似文献
3.
Enantiopure 2-naphthylglycolic acid (NGA) and cis-1-aminobenz[f]indan-2-ol (ABI) were rationally designed as new resolving agents on the model of mandelic acid (MA) and cis-1-aminoindan-2-ol (AI), respectively. As expected, NGA and ABI showed superior chiral recognition ability to racemates, compared with MA and AI. In order to clarify any factors governing the chiral recognition abilities of NGA and ABI, the crystal structures of their less- and more-soluble diastereomeric salts were determined by X-ray crystallographic analyses and revealed that CH/pi interactions play an intrinsic role in chiral recognitions. A theoretical investigation was also performed with the periodic ab initio method by using the X-ray crystal structures of the less-soluble salt crystals with AI and ABI to find the unique properties of CH/pi interaction in the crystalline state, which largely contributed to the stabilization of the crystals. 相似文献
4.
Kojima T Miyazaki S Hayashi K Shimazaki Y Tani F Naruta Y Matsuda Y 《Chemistry (Weinheim an der Bergstrasse, Germany)》2004,10(24):6402-6410
A Ru(II) complex with a hydrophobic cavity formed from two 1-naphthoylamide groups was prepared. Its reactions with beta-diketones gave beta-diketonato complexes in which hydrophobic pi-pi or CH/pi interactions were confirmed by NMR spectroscopy and X-ray crystallography. In the case of the asymmetric beta-diketone benzoylacetone, an isomer with a CH/pi interaction was afforded as the sole product owing to thermodynamic control. The reaction was found to involve a novel intramolecular rearrangement from the phenyl-included isomer to the methyl-included one without rupture of Ru-beta-diketonato coordination bonds (activation energy 52 kJ mol(-1)). This indicates that CH/pi interactions can be more favored thermodynamically than pi-pi interactions in a suitable hydrophobic environment. 相似文献
5.
Recently reported high-level ab initio calculations and gas phase spectroscopic measurements show that the nature of CH/pi interactions is considerably different from conventional hydrogen bonds, although the CH/pi interactions were often regarded as the weakest class of hydrogen bonds. The major source of attraction in the CH/pi interaction is the dispersion interaction and the electrostatic contribution is small, while the electrostatic interaction is mainly responsible for the attraction in the conventional hydrogen bonds. The nature of the "typical" CH/pi interactions is similar to that of van der Waals interactions, if some exceptional "activated" CH/pi interactions of highly acidic C-H bonds are excluded. Shifts of C-H vibrational frequencies and electronic spectra also support the similarity. The hydrogen bond is important in controlling structures of molecular assemblies, since the hydrogen bond is sufficiently strong and directional due to the large electrostatic contribution. On the other hand, the directionality of the "typical" CH/pi interaction is very weak. Although the "typical" CH/pi interaction is often regarded as an important interaction in controlling the structures of molecular assemblies as in the cases of conventional hydrogen bonds, the importance of the "typical" CH/pi interactions is questionable. 相似文献
6.
Tsuzuki S Honda K Uchimaru T Mikami M Fujii A 《The journal of physical chemistry. A》2006,110(33):10163-10168
The CCSD(T) level interaction energies of CH/pi complexes at the basis set limit were estimated. The estimated interaction energies of the benzene complexes with CH(4), CH(3)CH(3), CH(2)CH(2), CHCH, CH(3)NH(2), CH(3)OH, CH(3)OCH(3), CH(3)F, CH(3)Cl, CH(3)ClNH(2), CH(3)ClOH, CH(2)Cl(2), CH(2)FCl, CH(2)F(2), CHCl(3), and CH(3)F(3) are -1.45, -1.82, -2.06, -2.83, -1.94, -1.98, -2.06, -2.31, -2.99, -3.57, -3.71, -4.54, -3.88, -3.22, -5.64, and -4.18 kcal/mol, respectively. Dispersion is the major source of attraction, even if substituents are attached to the carbon atom of the C-H bond. The dispersion interaction between benzene and chlorine atoms, which is not the CH/pi interaction, is the cause of the very large interaction energy of the CHCl(3) complex. Activated CH/pi interaction (acetylene and substituted methanes with two or three electron-withdrawing groups) is not very weak. The nature of the activated CH/pi interaction may be similar to the hydrogen bond. On the other hand, the nature of other typical (nonactivated) CH/pi interactions is completely different from that of the hydrogen bond. The typical CH/pi interaction is significantly weaker than the hydrogen bond. Dispersion interaction is mainly responsible for the attraction in the CH/pi interaction, whereas electrostatic interaction is the major source of attraction in the hydrogen bond. The orientation dependence of the interaction energy of the typical CH/pi interaction energy is very small, whereas the hydrogen bond has strong directionality. The weak directionality suggests that the hydrogen atom of the interacting C-H bond is not essential for the attraction and that the typical CH/pi interaction does not play critical roles in determining the molecular orientation in molecular assemblies. 相似文献
7.
Manimaran B Lai LJ Thanasekaran P Wu JY Liao RT Tseng TW Liu YH Lee GH Peng SM Lu KL 《Inorganic chemistry》2006,45(20):8070-8077
Alkoxy- and thiolato-bridged Re(I) molecular rectangles [{(CO)3Re(mu-ER)2Re(CO)3}2(mu-bpy)2] (ER = SC4H9, 1a; SC8H17, 1b; OC4H9, 2a; OC12H25, 2b; bpy = 4,4'-bipyridine) exhibit strong interactions with several planar aromatic molecules. The nature of their binding was studied by spectral techniques and verified by X-ray diffraction analysis. Standard absorption and fluorescence titrations showed that a relatively strong 1:1 interaction occurs between aromatic guests such as pyrene and these rectangles. The results of a single-crystal X-ray diffraction analysis show that the recognition of 1 with a pyrene molecule is mainly due to CH...pi interactions and the face of the guest pyrene is located over the edges of the bpy linkers of 1. This is a fairly novel example of an interaction that is rarely designed into a host-guest pair. Furthermore, the interaction of 1 with Ag+ results in the self-organization of supramolecular arrays, as revealed by solid-state data. 相似文献
8.
Bautista-Ibañez L Ramírez-Gualito K Quiroz-García B Rojas-Aguilar A Cuevas G 《The Journal of organic chemistry》2008,73(3):849-857
Can a benzene molecule differentiate between two isomeric carbohydrates? It is generally accepted that two factors govern molecular recognition: complementarity and preorganization. Preorganization requires the presence of cavities for positioning the host's groups of complementary nature to those of the guest. This study shows that, in fact, groups should be complementary to recognize each other (for the case presented here, it is controlled by the CH/pi interaction) but preorganization is not essential. Since weak interactions have their origin in dispersion forces, they also have impact on the enthalpic term of the free energy, so it was considered that their participation can be demonstrated by measuring the energy involved. For recognition to happen, two conditions must be satisfied: specificity and associated stabilizing energy. In this study we evaluated the heat of dissolution of different carbohydrates such as methyl 2,3,4,6-tetra-O-methyl-alpha-d-mannopyranoside and methyl 2,3,4,6-tetra-O-methyl-beta-d-galactopyranoside using different aromatic solvents. The solvation enthalpies in benzene were -78.8 +/- 3.9 and -88.7 +/- 5.5 kJ mol(-1) for each carbohydrate, respectively; and these values yielded a CH/pi energy of interaction of 9.9 kJ mol(-1). In addition, NMR studies of the effect of the addition of benzene to chloroform solutions of the two carbohydrates showed that benzene specifically interacts with the hydrogen atoms of the pyranose ring at positions 3, 4, and 5 located on the alpha face of the methyl-beta-galactoside, so it is, in fact, able to recognize it. Thus, the interactions between carbohydrates and the aromatic residues of proteins occur in the absence of the confinement generated by the protein structure. By experimentally measuring the energy associated with this interaction and comparing it to theoretical calculations, it was also possible to unequivocally determine the existence of CH/pi interactions between carbohydrates and proteins. 相似文献
9.
The accurate CH/pi interaction energy of the benzene-methane model system was experimentally and theoretically determined. In the experiment, mass analyzed threshold ionization spectroscopy was applied to the benzene-methane cluster in the gas phase, prepared in a supersonic molecular beam. The binding energy in the neutral ground state of the cluster, which is regarded as the CH/pi interaction energy for this model system, was evaluated from the dissociation threshold measurements of the cluster cation. The experimentally determined binding energy (D(0)) was 1.03-1.13 kcal/mol. The interaction energy of the model system was calculated by ab initio molecular orbital methods. The estimated CCSD(T) interaction energy at the basis set limit (D(e)) was -1.43 kcal/mol. The calculated binding energy (D(0)) after the vibrational zero-point energy correction (1.13 kcal/mol) agrees well with the experimental value. The effects of basis set and electron correlation correction procedure on the calculated CH/pi interaction energy were evaluated. Accuracy of the calculated interaction energies by DFT methods using BLYP, B3LYP, PW91 and PBE functionals was also discussed. 相似文献
10.
Tsuzuki S Honda K Fujii A Uchimaru T Mikami M 《Physical chemistry chemical physics : PCCP》2008,10(19):2860-2865
Geometries and interaction energies for methane clusters with naphthalene and pyrene were studied. Estimated CCSD(T) interaction energies for the clusters at the basis set limit were -1.92 and -2.50 kcal mol(-1), respectively. Dispersion is mainly responsible for the attraction. Electrostatic interaction is very small. Although the benzene-methane cluster prefers a monodentate structure, in which a C-H bond of the methane points toward the benzene, the methane clusters with the polycyclic aromatic hydrocarbons do not prefer monodentate structures. In the benzene-methane cluster, the weak electrostatic interaction stabilizes the monodentate structure. On the other hand the dispersion interaction controls the orientation of methane in the naphthalene and pyrene clusters. The dispersion interactions in these clusters are significantly larger than those in the benzene-methane cluster. The methane prefers the orientation which is suitable for stabilization by dispersion. Hydrogen atoms of the methane locate above the centers of hexagonal rings of the polycyclic aromatic hydrocarbons in the stable structures. The structures have a small steric repulsion and this positions them only a short distance from the aromatic plane. The large dispersion contribution to the attraction shows that interactions between carbon atoms are mainly responsible for the attraction, and that hydrogen atoms are not important for the attraction. This shows that the interactions between the methane and polycyclic aromatic hydrocarbons are not pi-hydrogen bonds. 相似文献
11.
Fujii A Shibasaki K Kazama T Itaya R Mikami N Tsuzuki S 《Physical chemistry chemical physics : PCCP》2008,10(19):2836-2843
The CH/pi interaction energies between benzene and halomethanes (CH(2)Cl(2) and CHCl(3)) were accurately determined. Two-color ionization spectroscopy was applied to the benzene-CH(2)Cl(2) and -CHCl(3) clusters, and the binding energies in the neutral ground state, i.e. the CH/pi interaction energies in these model cluster systems, were precisely evaluated on the basis of the dissociation threshold measurements of the clusters in the cationic state and the ionization potential value of the bare molecule. The experimentally determined interaction energies were 3.8 +/- 0.2 and 5.2 +/- 0.2 kcal mol(-1) for benzene-CH(2)Cl(2) and -CHCl(3) respectively, and the remarkable enhancement of the CH/pi interaction energy with chlorine-substitution was quantitatively confirmed. The experimental interaction energies were well reproduced by the high-level ab initio calculations. The theoretical calculations clarified the unique nature of the activation of the CH/pi interaction by the chlorine-substitution. 相似文献
12.
A systematic study of the CH/pi interactions of methane with the purine and pyrimidine bases of nucleic acids and with the lateral chains of the four natural aromatic amino acids has been carried out for the first time. The MPWB1K/6-31+G(d,p) method has shown to be adequate for the study of these weak interactions in which dispersion forces play a main role. It has been shown that two different kinds of clusters exist, depending on whether one or two CH bonds point to the aromatic system. The latter one, which we have called bifurcated, is usually more stable. With regard to aromatic amino acids, our calculations agree with experimental data in the fact that tryptophan leads to the strongest interaction, while hystidine leads to the weakest one. In the case of nucleic acid bases, the differences in binding energies are not large. This is specially true for thymine and uracil, showing that these two bases have a similar acceptor character in CH/pi interactions. 相似文献
13.
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. 相似文献
14.
High-level ab initio calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug(d,p)-6-311G(d,p) level were employed to investigate the cooperative CH/pi effects between the pi face of benzene and several modeled saturated hydrocarbons, propane, isobutane, cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclopentane, cyclooctane, and bicyclo[2.2.2]octane. In all cases, multiple C-H groups (2-4) are found to interact with the pi face of benzene, with one C-H group pointing close to the center of the benzene ring. The geometries of these complexes are governed predominantly by electrostatic interaction between the interacting systems. The calculated interaction energies (10-14 kJ mol(-1)) are 2-3 times larger than that of the prototypical methane-benzene complex. The trends of geometries, interaction energies, binding properties, as well as electron-density topological properties were analyzed. The calculated interaction energies correlate well with the polarizabilities of the hydrocarbons. AIM analysis confirms the hydrogen-bonded nature of the CH/pi interactions. Significant changes in proton chemical shift and stretching frequency (blue shift) are predicted for the ring C-H bond in these complexes. 相似文献
15.
Seiji Tsuzuki Kazumasa Honda Tadafumi Uchimaru Masuhiro Mikami Kazutoshi Tanabe 《Journal of the American Chemical Society》2002,124(1):104-112
A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction. 相似文献
16.
Roy S Sarkar B Bubrin D Niemeyer M Zális S Lahiri GK Kaim W 《Journal of the American Chemical Society》2008,130(46):15230-15231
The heterodinuclear compound [(PhenQ)Cu(dppf)](BF4), PhenQ = 9,10-phenanthrenequinone and dppf = 1,1'-bis(diphenylphosphino)ferrocene, was identified structurally and spectroscopically (NMR, IR, UV-vis) as a copper(I) complex of a completely unreduced ortho-quinone. Crystallographic and DFT calculation results suggest that this stabilization of a hitherto elusive arrangement is partially owed to intramolecular pi/pi interactions phenyl/PhenQ. Intermolecular PhenQ/PhenQ pi stacking is also observed in the crystal. According to DFT calculations, the pi interactions are responsible for the considerably distorted coordination geometry at CuI with one short and one longer Cu-O and Cu-P bond, respectively, and with bond angles at copper ranging from 99 degrees to 133 degrees. Electrochemical reduction proceeds reversibly at low temperatures to yield an EPR spectroscopically characterized semiquinone-copper(I) species. 相似文献
17.
CH/pi interactions between the coordinated acetylacetonato ligand and phenyl rings were analyzed in the crystal structures from the Cambridge Structural Database and by quantum chemical calculations. The acetylacetonato ligand may engage in two types of interactions: it can be hydrogen atom donor or acceptor. The analysis of crystal structures and calculations show that interactions with the acetylacetonato ligand acting as hydrogen atom donor depend on the metal in an acetylacetonato chelate ring; the chelate rings with soft metals make stronger interactions. The same trend was not observed in the interactions where the acetylacetonato chelate ring acts as the hydrogen atom acceptor. 相似文献
18.
Bates DM Anderson JA Oloyede P Tschumper GS 《Physical chemistry chemical physics : PCCP》2008,10(19):2775-2779
Dimers composed of benzene (Bz), 1,3,5-triazine (Tz), cyanogen (Cy) and diacetylene (Di) are used to examine the effects of heterogeneity at the molecular level and at the cluster level on pi...pi stacking energies. The MP2 complete basis set (CBS) limits for the interaction energies (E(int)) of these model systems were determined with extrapolation techniques designed for correlation consistent basis sets. CCSD(T) calculations were used to correct for higher-order correlation effects (deltaE(CCSD)(T)(MP2)) which were as large as +2.81 kcal mol(-1). The introduction of nitrogen atoms into the parallel-slipped dimers of the aforementioned molecules causes significant changes to E(int). The CCSD(T)/CBS E(int) for Di-Cy is -2.47 kcal mol(-1) which is substantially larger than either Cy-Cy (-1.69 kcal mol(-1)) or Di-Di (-1.42 kcal mol(-1)). Similarly, the heteroaromatic Bz-Tz dimer has an E(int) of -3.75 kcal mol(-1) which is much larger than either Tz-Tz (-3.03 kcal mol(-1)) or Bz-Bz (-2.78 kcal mol(-1)). Symmetry-adapted perturbation theory calculations reveal a correlation between the electrostatic component of E(int) and the large increase in the interaction energy for the mixed dimers. However, all components (exchange, induction, dispersion) must be considered to rationalize the observed trend. Another significant conclusion of this work is that basis-set superposition error has a negligible impact on the popular deltaE(CCSD)(T)(MP2) correction, which indicates that counterpoise corrections are not necessary when computing higher-order correlation effects on E(int). Spin-component-scaled MP2 (SCS-MP2 and SCSN-MP2) calculations with a correlation-consistent triple-zeta basis set reproduce the trends in the interaction energies despite overestimating the CCSD(T)/CBS E(int) of Bz-Tz by 20-30%. 相似文献
19.
Yang W Jones LM Isley L Ye Y Lee HW Wilkins A Liu ZR Hellinga HW Malchow R Ghazi M Yang JJ 《Journal of the American Chemical Society》2003,125(20):6165-6171
Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability. 相似文献
20.
High-level ab initio calculations have been carried out to study weak CH/pi interactions and as a check of the CHARMM force field for aromatic amino acids. Comparisons with published data indicate that the MP2/cc-pVTZ level of theory is suitable for calculations of CH/pi interaction, including the T-shape benzene dimer. This level of theory was, therefore, applied to investigate CH/pi interactions between ethene or cis-2-butene and benzene in a variety of orientations. In addition, complexes between ethene and a series of model compounds (toluene, methylindole and p-cresol) representing the aromatic amino acids were studied motivated by the presence of CH/pi interactions in biological systems. Ab initio binding energies were compared to the binding energies obtained with the CHARMM22 force field. In the majority of orientations, CHARMM22 reproduces the preferred binding modes, with excellent agreement for the benzene dimer. Small discrepancies found in the calculations involving methylindole along with a survey of published thermodynamic data for the aromatic amino acids prompted additional optimization of the tryptophan force field. Partial atomic charges, Lennard-Jones parameters, and force constants were improved to obtain better intra- and intermolecular properties, with significant improvements obtained in the reproduction of experimental heats of sublimation for indole and free energies of aqueous solvation for methylindole. 相似文献