Periodic ab initio approach for the cooperative effect of CH/pi interaction in crystals: relative energy of CH/pi and hydrogen-bonding interactions

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.     

CH/pi interactions in DNA and proteins. A theoretical study

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.     

Assessment of weak intermolecular interactions across QM/MM noncovalent boundaries

An assessment of a number of quantum mechanical/molecular mechanical (QM/MM) combinations was performed for weak intermolecular interactions across noncovalent QM/MM 'boundaries'. The popular S22 data set, comprising of a number of weak hydrogen-bonded, dispersion-bound and complexes with mixed interactions was used for the assessment. A range of QM methods was combined with a number of popular MM force fields. The single-point interaction energies, at reference geometries, are presented as deviations to accurate CCSD(T)/CBS reference values. This investigation employed both additive and subtractive QM/MM schemes. The density functional has only a negligible effect; the choice of basis set was also negligible in terms of accuracy. The importance of selecting the most appropriate MM force field for accurately describing interactions at the noncovalent 'boundary' region has a dramatic effect on the accuracy.     

Electron delocalization mediates the metal-dependent capacity for CH/pi interactions of acetylacetonato chelates

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.     

Saturated hydrocarbon-benzene complexes: theoretical study of cooperative CH/pi interactions

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.     

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.     

A single CH/pi weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein

Importance of the CH/pi interaction on the structure and function of the photoactive yellow protein (PYP) was substantiated. Focusing on the phenyl ring of Phe6 adjacent to the alkyl chain of Lys123, the mutants for these amino acid residues were characterized. The results demonstrated that the mutants lacking the pi-electron at position 6 or the alkyl chain at position 123 show substantial malfunction. This is a clear example that single CH/pi weak interaction plays a crucial role in the normal action of the protein.     

CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field

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.     

Eugenol and safrole as starting materials for the synthesis of 3-alkyl muconic acid mono and dimethyl esters and 4,4-dialkyl butenolides

Compounds $\text{1b-e}$ and $\text{2b-d}$ prepared from eugenol ($\text{1a}$) and safrole ($\text{2a}$) respectively were submitted to ozonation in methanol at 0°C. The 3-alkyl muconic acid dimethyl esters $\text{4b-e}$ were produced from $\text{1b-e}$ (～ 45%), while starting from $\text{2b-d}$ the 3-alkyl muconic acid monomethyl esters $\text{6b-d}$ were obtained regiospecifically (～ 75%). These latter compounds were transformed (～ 85%) into the 4,4-dialkyl butenolides $\text{7b-d}$.     

Self-assembly of nanotubes and ordered mesostructures using weak interactions

Two simple organic compounds, 5-nitroisophthalic acid (npa) and 4,4′-bipyridine (bpy), were used as building blocks for supramolecular self-assembly by hydrothermal synthesis. SEM, TEM, and XRD were used to analyse the multi-step assembly process in which npa and bpy assembled into nanotubes (or nanobelts) of about 30–100 nm in diameter and several millimetres in length and microtubes (or microbelts). The tubes then further assembled to form complex ordered structures, such as pom-pom-shaped and flower-like mesostructures.     

Gels from a semifluorinated n-alkane in fluorinated solvents as a probe for intermolecular interactions

Diblock semifluorinated n-alkanes can form aggregates and gels in fluorinated solvents. We have investigated the thermal behavior of binary mixtures comprising F(CF₂)₈(CH₂)₁₆H and fluorinated solvents. The solvents were perfluorohexane, perfluoroheptane, perfluorooctane, perfluorooctyl bromide, perfluorodecalin, and perfluorotributylamine. The phase diagrams were used to calculate the activity coefficients of the two components and the main excess thermodynamic functions. The solubility and self-assembly behavior of F₈H₁₆ in the fluorinated solvents are related to the different solute–solvent dispersion interactions that depend on the polarizabilities and ionization potentials of the interacting species, and on the structural properties of the solvent.     

Crystal structures of mucochloric and mucobromic acids: pseudosymmetry,polymorphism, and intermolecular interactions

Russian Chemical Bulletin - The crystal structure of the known triclinic modification of mucochloric acid (MCA) was refined significantly, as well as its earlier unknown orthorhombic modification...     

Cooperation of multiple CH...pi interactions to stabilize polymers in aromatic nanochannels as indicated by 2D solid state NMR

Advanced 2D solid state NMR techniques reveal weak intermolecular interactions that cooperatively sustain nanostructures of high molecular mass aliphatic polymers entrapped as guests in channels formed by an aromatic host.     

First example of N-heterocyclic carbenes as catalysts for living polymerization: organocatalytic ring-opening polymerization of cyclic esters

A novel metal-free, organocatalytic approach to living polymerization is presented. N-heterocyclic carbenes were employed as nucleophilic catalysts for the ring-opening polymerization (ROP) of cyclic ester monomers. The catalysts is used in combination with an initiator, such as an alcohol, which generates an alpha-end group bearing the ester from the initiating alcohol upon ring-opening and a hydroxyl functional omega-chain end that propagates the chain. This class of catalyst proved to be more reactive than tertiary amine and phosphine nucleophiles, producing narrowly dispersed polymers of predictable molecular weights at room temperature in 1-2 h. Catalysis with respect to both initiating alcohol and monomer was observed. Control of the alpha and omega end-groups was demonstrated with a pyrene-labeled initiator, allowing the preparation of well-defined macromolecular architectures. Analogous to the ROP of cyclic esters using biocatalysts, the polymeriztion pathway using the N-heterocyclic carbenes is believed to ensue through a monomer-activated mechanism.     

Free-radical polymerization of vinyl esters using fluoroalcohols as solvents: Effect of monomer structure on stereochemistry

Free-radical polymerization of vinyl esters including vinyl propionate (VPr), vinyl isobutylate (ViBu), vinyl 2,2-dimethylbutylate (VDMB), vinyl 2,2-dimethylvalerate (VDMV), vinyl 2,2-bis(trifluoromethyl)propionate (VF6Pi), and vinyl benzoate (VBz) was carried out using fluoroalcohols as solvents, and the tacticity of the obtained polymers was determined by NMR analysis of the produced poly(vinyl alcohol) (PVA). The polymerization of VPr, ViBu, VDMB, and VDMV, which are bulkier than VAc, in fluoroalcohols afforded polymers rich in heterotacticity (up to mr = 61%) similar to that of vinyl pivalate (VPi) whereas VAc is known to give a syndiotactic polymer under the reaction conditions used here. The polymerization of VF6Pi, which is the bulkiest among the monomers used in this study, gave a polymer rich in syndiotacticity in bulk and in fluoroalcohols regardless of the structure of the solvents. On the other hand, the polymerization of VBz in fluoroalcohols gave polymers with a higher isotacticity (up to mm = 33%) than bulk polymerization. Thus the monomer structure strongly affected the stereochemistry of the free-radical polymerization of vinyl esters in fluoroalcohols. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2677–2683, 1999     

Ethylene polymerization using crosslinked polystyrene as support for zirconocene dichloride/methylaluminoxane

In this paper we report on a zirconocene dichloride/methylaluminoxane catalyst system supported on a crosslinked polystyrene in order to provide ethylene polymerization catalysts for gas phase or slurry processes. Our novel approach uses the Diels‐Alder reaction of cyclopentadiene functions as the final, cross‐linking synthetic step. This provides polymer supported zirconocene catalysts with a homogeneous distribution of active sites. The catalysts were shown to be highly active and to form spherical beads as proven by scanning electron microscopy.     

The influence of intermolecular interactions on polymerization—2. Polymers of 1-naphthyl methacrylate and 2-naphthyl methacrylate obtained by radical polymerization

1-Naphthyl methacrylate and 2-naphthyl methacrylate were polymerized with azoisobutyronitrile in n-hexane, cyclohexane and benzene in the absence and in the presence of tetracyanoethylene. Products were transformed into poly(methyl methacrylate) by hydrolysis and methylation; tacticities were then determined by proton NMR.     

Magnitude of CH/O interactions between carbohydrate and water

The interaction energy potentials for six orientations of the fucose–water complex were calculated for evaluating the magnitude of the CH/O interactions in the complex. The calculations show that the C–H bonds of the nonpolar surface of fucose prefer to have contact with the oxygen atom of the water. The substantial attraction exists between the C–H bonds of fucose and water. The interaction energy calculated for the fucose–water complex at the MP2/aug-cc-pVTZ level is −2.55 kcal/mol. The CH/O interactions in the fucose–water complex are significantly larger than those in the cyclohexane–water complex (−1.13 kcal/mol), which shows that the oxygen atoms of fucose enhance the CH/O interactions. The electrostatic and dispersion interactions are responsible for the attraction in the CH/O interactions in the fucose–water complex, while the electrostatic contributions to the attraction in the CH/O interactions in the cyclohexane–water complex is small. The DFT-SAPT calculations also show that the electrostatic interactions are responsible for the larger attraction in the fucose–water complex. These results suggest that the nature of the CH/O interactions between carbohydrate and water is significantly different from that of the CH/O interactions between saturated hydrocarbon and water.