Slipped Parallel Structure Research Articles

Complex Formation of Ag+ and Li+ with Host Molecules Modeled on Intercalation of Graphite.

Pi-stacked and box-shaped host molecules with xanthene as the basis and pyrene as the π-plane were synthesized to verify cation-π interactions between graphene and metal cations. Since crystal structure analysis was not available, DFT calculations were performed to determine the optimized structure, and the π-planes were found to have a slipped parallel structure, with average distances of 456.2-581.0 pm for the stacked compound and 463.4-471.4 pm for the box-shaped compound. Li+ and Ag+ were chosen as acceptors for complexation with metal ions, and their interactions with the π-plane were clarified by NMR titration. Clearly, the interaction with metal ions increased when pyrene π-planes were stacked rather than the pyrene itself. In the stacked compound, the association constants of Ag+ and Li+ were similar; however, in the box-shaped host molecule, only Ag+ had moderate coordination ability, but the interaction with Li+ was very weak, comparable to the interaction with pyrene. As a result, intercalation is more likely to occur in stacked host compound 1, which has some degree of freedom in the pyrene rings, than in the box-shaped compound.

Rotational spectroscopic studies of the tetrel bonded CH3CN-CO2 complex

The rotational spectra of the weakly bound acetonitrile-carbon dioxide complex have been recorded using a pulsed-nozzle Fourier transform microwave spectrometer. In a supersonic expansion using helium as the carrier gas, the two lowest energy conformers were observed. A T-shaped structure where the nitrogen end of CH3CN donates electron density to the C center of CO2, and a slipped-parallel structure where the CO2 and CH3CN are aligned such that the linear heavy atom backbones are parallel. Spectra were also recorded for the CD3CN∙∙∙CO2 and the CH313CN∙∙∙CO2 isotopologues which help to confirm the structures observed. The spectra show hyperfine splitting due to nitrogen quadrupole coupling which could be resolved. The CH3CN∙∙∙CO2 complex offers the possibility to study the tetrel bond involving the three C atoms of the system. The observed T-shaped structure is bound by a N∙∙∙C carbon/tetrel bond. The Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses are used to identify the non-covalent interactions present in this complex and investigate different types of tetrel bonds.

High-level ab initio studies of NO(X2Π)–O2(X3Σg−) van der Waals complexes in quartet states

ABSTRACTGeometry optimisations were performed on nine different structures of NO(X2Π)–O2(X3Σg−) van der Waals complexes in their quartet states, using the explicitly correlated RCCSD(T)-F12b method with basis sets up to the cc-pVQZ-F12 level. For the most stable configurations, counterpoise-corrected optimisations as well as extrapolations to the complete basis set (CBS) were performed. The X structure in the 4A′ state was found to be most stable, with a CBS binding energy of −157 cm−1. The slipped tilted structures with N closer to O2 (Slipt-N), as well as the slipped parallel structure with O of NO closer to O2 (Slipp-O) in 4A″ states have binding energies of about −130 cm−1. C2v and linear complexes are less stable. According to calculated harmonic frequencies, the X isomer is bound. Isotropic hyperfine coupling constants of the complex are compared with those of the monomers.

The structure of the O2-N2O complex.

We have investigated the lowest energy structures and interaction energies of the oxygen nitrous oxide complex (O2-N2O) using explicitly correlated coupled cluster theory. We find that the intermolecular potential energy surface of O2-N2O is very flat, with two minima of comparable energy separated by a low energy first order saddle point. Our results are able to conclusively distinguish between the two sets of experimental geometric parameters for O2-N2O that were previously determined from rotationally resolved infrared spectra. The global minimum structure of O2-N2O is therefore found to be planar with a distorted slipped parallel structure. Finally, we show that the very flat potential energy surface of O2-N2O is problematic when evaluating vibrational frequencies with a numerical Hessian and that consideration should be given as to whether results might change if the step-size is varied.

Molecular design of boronic acid-functionalized squarylium cyanine dyes for multiple discriminant analysis of sialic acid in biological samples: selectivity toward monosaccharides controlled by different alkyl side chain lengths.

We designed a new series of boronic acid-functionalized squarylium cyanine dyes (SQ-BA) with different lengths of alkyl chain residues, suitable for multiple discriminant analysis (MDA) of sialic acid (Neu5Ac) in biological samples. The SQ-BA dyes form aggregates based on hydrophobic interactions, which result in quenched fluorescence in aqueous solutions. When the boronic acid binds with saccharides, the fluorescence intensity increases as a result of dissociation to the emissive monomeric complex. We inferred that different dye aggregate structures (H-aggregates and J-aggregates) were induced depending on the alkyl chain length, so that monosaccharides would be recognized in different ways (especially, multipoint interaction with J-aggregates). A distinctive emission enhancement of SQ-BA dyes with shorter-alkyl-chains in the presence of Neu5Ac was observed (2.4-fold fluorescence enhancement; with formation constant 10(1.7) M(-1)), with no such enhancement for SQ-BA dyes with longer-alkyl-chain. In addition, various enhancement factors for other monosaccharides were observed depending on the alkyl chain length. Detailed thermodynamic and NMR studies of the SQ-BA complexes revealed the unique recognition mechanism: the dye aggregate with a shorter-alkyl-chain causes the slipped parallel structure and forms a stable 2:1 complex with Neu5Ac, as distinct from longer-alkyl-chain dyes, which form a 1:1 monomeric complex. MDA using the four SQ-BA dyes was performed for human urine samples, resulting in the successful discrimination between normal and abnormal Neu5Ac levels characteristic of disease. Thus, we successfully controlled various responses to similar monosaccharides with a novel approach that chemically modified not the boronic acid moiety itself but the length of the alkyl chain residue attached to the dye in order to generate specificity.

Spectroscopy of dimers, trimers and larger clusters of linear molecules

Rotationally resolved spectra of van der Waals clusters provide the most direct, precise and unambiguous experimental probe of intermolecular potential energy surfaces, particularly in the lower energy range of attractive forces. The spectroscopy of such weakly bound complexes is reviewed with a focus on those containing only the following five small linear molecules: N2O, CO2, OCS, CS2 and C2H2. Even with this limitation, there are over 30 such complexes for which high-resolution spectroscopic results are now available in the microwave, millimetre wave and infrared regions. Dimers formed from these five species tend to be planar with slipped parallel structures, though there are some exceptions. Trimers tend to be barrel-shaped, that is, non-planar with approximately parallel monomers. Larger clusters are almost invariably non-planar and sometimes highly symmetric. Three significant themes emerge here. First, the possibility of determining low-frequency intermolecular vibrational modes by means of mid-infrared combination bands. Second, the increasing number of complexes for which more than one structural form, or isomer, is observed. And finally, the growing amenability of even ‘large’ clusters (say, tetramers and larger) to spectroscopic study. All three factors help to probe potential energy surfaces more completely in regions away from the global minimum.

Theoretical studies of the CO2–N2O van der Waals complex: Ab initio potential energy surface, intermolecular vibrations, and rotational transition frequencies

Theoretical studies of the potential energy surface and bound states were performed for the CO(2)-N(2)O van der Waals complex. A four-dimensional intermolecular potential energy surface (PES) was constructed from 11,466 ab initio data points which were calculated at the coupled-cluster single double (triple) level with aug-cc-pVTZ basis set supplemented with bond functions. Three co-planar local minima were found on this surface. They correspond to two equivalent isomers with a slipped parallel structure in which the O atom in N(2)O is near the C atom in CO(2) and a T-shaped isomer in which the terminal N atom in N(2)O is closest to the C atom in CO(2). The two slipped parallel isomers are energetically more stable than the T-shaped isomer by 178 cm(-1). Four fundamental vibrational excited states for the slipped parallel isomers and two fundamental vibrational excited states (torsion and disrotation) for the T-shaped isomer were assigned via bound states calculations based on this PES. The theoretical vibrational frequencies are in good agreement with the available experimental values for the slipped parallel isomers. Rotational excitations (J = 0-6) for the ground vibrational state of the slipped parallel structure were calculated and the accuracy of the PES in the vicinity of minima is validated by the good agreement between the theoretical and experimental transition frequencies and spectroscopic parameters.

Explicit correlation and basis set superposition error: The structure and energy of carbon dioxide dimer

We have investigated the slipped parallel and t-shaped structures of carbon dioxide dimer [(CO(2))(2)] using both conventional and explicitly correlated coupled cluster methods, inclusive and exclusive of counterpoise (CP) correction. We have determined the geometry of both structures with conventional coupled cluster singles doubles and perturbative triples theory [CCSD(T)] and explicitly correlated cluster singles doubles and perturbative triples theory [CCSD(T)-F12b] at the complete basis set (CBS) limits using custom optimization routines. Consistent with previous investigations, we find that the slipped parallel structure corresponds to the global minimum and is 1.09 kJ mol(-1) lower in energy. For a given cardinal number, the optimized geometries and interaction energies of (CO(2))(2) obtained with the explicitly correlated CCSD(T)-F12b method are closer to the CBS limit than the corresponding conventional CCSD(T) results. Furthermore, the magnitude of basis set superposition error (BSSE) in the CCSD(T)-F12b optimized geometries and interaction energies is appreciably smaller than the magnitude of BSSE in the conventional CCSD(T) results. We decompose the CCSD(T) and CCSD(T)-F12b interaction energies into the constituent HF or HF CABS, CCSD or CCSD-F12b, and (T) contributions. We find that the complementary auxiliary basis set (CABS) singles correction and the F12b approximation significantly reduce the magnitude of BSSE at the HF and CCSD levels of theory, respectively. For a given cardinal number, we find that non-CP corrected, unscaled triples CCSD(T)-F12b/VXZ-F12 interaction energies are in overall best agreement with the CBS limit.

Synthesis and Crystal Structures of 1,4,8,11-Tetraalkyl-6,13-diphenylpentacenes

Abstract Two 1,4,8,11-tetraalkyl-6,13-diphenylpentacenes were prepared. X-ray analysis revealed that the methyl derivative had a herringbone arrangement with π-overlap, while the propyl derivative had a slipped-parallel structure without π-overlap. The solid-state order reflected UV–vis absorption spectra in the solid state.

Interactions in Large, Polyaromatic Hydrocarbon Dimers: Application of Density Functional Theory with Dispersion Corrections

The interactions within two models for graphene, coronene and hexabenzocoronene (HBC), and (H 3C(CH 2) 5) 6-HBC, a synthesizable model for asphaltenes, were studied using density functional theory (DFT) with dispersion corrections. The corrections were implemented using carbon atom-centered effective core-type potentials that were designed to correct the erroneous long-range behavior of several DFT methods. The potentials can be used with any computational chemistry program package that can handle standard effective core potential input, without the need for software modification. Testing on a set of common noncovalently bonded dimers shows that the potentials improve calculated binding energies by factors of 2-3 over those obtained without the potentials. Binding energies are predicted to within ca. 15%, and monomer separations to within ca. 0.1 A, of high-level wave function data. The application of the present approach predicts binding energies and structures of the coronene dimer that are in excellent agreement with the results of other DFT methods in which dispersion is taken into account. Dimers of HBC show extensive binding in pi-stacking arrangements, with the largest binding energy, 44.8 kcal/mol, obtained for a parallel-displaced structure. This structure is inline with the published crystal structure. Conformations in which the monomers are perpendicular to one another are much more weakly bound and have binding energies less than 10 kcal/mol. For dimers of (H 3C(CH 2) 5) 6-HBC, which contain 336 atoms, we find that a slipped-parallel structure with C s symmetry has a binding energy of 52.4 kcal/mol, 8.9 kcal/mol lower than that of a bowl-like, C 6 v -symmetric structure.

Infrared spectra of the polar and nonpolar N 2O dimers in the 1280 cm −1 region of the ν3 fundamental

The high-resolution infrared spectrum of the polar N 2O dimer has been observed in the region of the N 2O ν 3 fundamental (∼1280 cm −1) using a tunable diode laser to probe a pulsed supersonic slit jet. About 120 rotational transitions were assigned in terms of an a/b hybrid band of a planar asymmetric top molecule with a slipped parallel structure. The vibrational origin was determined to be 1290.21 cm −1, showing a blue shift of 5.31 cm −1 with respect to the monomer band origin. In addition, the spectrum of the nonpolar isomer at 1279.71 cm −1 has been remeasured and analyzed in improved detail. Small but widespread perturbations are noted in this band, which appear somewhat similar to larger effects observed previously in the ν 1 + ν 3 region for nonpolar (N 2O) 2.

Nitrous oxide dimer: Observation of a new polar isomer

Spectra of the nitrous oxide dimer (N2O)2 are studied in the region of the N2O nu1 fundamental band around 2230 cm-1 using a rapid-scan tunable diode laser spectrometer to probe a pulsed supersonic jet expansion. The previously known band of the centrosymmetric nonpolar dimer is analyzed in improved detail, and a new band is observed and assigned to a polar isomer of (N2O)2. This polar form of the dimer has a slipped parallel structure, rather similar to the slipped antiparallel structure of the nonpolar form but with a slightly larger intermolecular distance. The accurate rotational parameters determined here should enable a microwave observation of the polar N2O dimer. The need for a modern ab initio investigation of the N2O-N2O intermolecular potential energy surface is emphasized.

The Molecular Structure of CO2–N2O

The rotational spectra of the weakly bound acetonitrile-carbon dioxide complex have been recorded using a pulsed-nozzle Fourier transform microwave spectrometer. In a supersonic expansion using helium as the carrier gas, the two lowest energy conformers were observed. A T-shaped structure where the nitrogen end of CH3CN donates electron density to the C center of CO2, and a slipped-parallel structure where the CO2 and CH3CN are aligned such that the linear heavy atom backbones are parallel. Spectra were also recorded for the CD3CN∙∙∙CO2 and the CH313CN∙∙∙CO2 isotopologues which help to confirm the structures observed. The spectra show hyperfine splitting due to nitrogen quadrupole coupling which could be resolved. The CH3CN∙∙∙CO2 complex offers the possibility to study the tetrel bond involving the three C atoms of the system. The observed T-shaped structure is bound by a N∙∙∙C carbon/tetrel bond. The Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses are used to identify the non-covalent interactions present in this complex and investigate different types of tetrel bonds.

Optimum geometry of CO dimer and FT-IR spectra of CO in solid argon

To gain insight into the optimum geometry of the CO dimer, conventional ab initio and density functional calculations have been carried out. The potential energy surface of the CO dimer appeared to be very flat. Nonetheless, the planar distorted T-shaped structure was computed to be the most stable structure. The slipped antiparallel structure was also computed to be a local minimum. Both the linear and the nonplanar crossed structures seemed unstable. The slipped parallel structure was calculated to correspond to a saddle point. In addition to computing the optimum geometry of (CO) 2, the matrix isolated infrared spectra were taken for CO dispersed in solid argon. Three peaks were identified at 2136.4, 2138.4, and 2139.9 cm −1. The most distinct peak at 2138.4 cm −1 could be assigned to monomeric CO. The other two peaks were attributed to distorted T-shaped dimeric CO species, the 2136.4 cm −1 peak due to (CO) 2 bound through the CO…OC interaction and the 2139.9 cm −1 peak due to (CO) 2 bound through the OC…CO interaction.

Infrared diode laser jet spectroscopy of the van der Waals complex (N2O)2

The rotationally resolved spectrum of the dimer (N2O)2 has been recorded in the region of the monomer N2O υ3 vibrational band using a diode laser absorption spectrometer which incorporates a multiple-pass cell and a pulsed-jet expansion. A double-modulation technique involving a fast modulation of the laser frequency and a slow modulation of the gas pulse has been developed in the experiments. The spectrum is completely analysed and the rotational constants and effective structures are accurately determined for both the ground and the excited vibrational states. The centrosymmetric slipped parallel structure of (N2O2 is well explained by an intermolecular potential containing a combination of electrostatic interactions between distributed multipoles of different monomers and atom–atom Lennard-Jones potentials to describe the repulsion and dispersion interactions.

Infrared diode laser jet spectroscopy of the van der Waals complex (N2O)2

The rotationally resolved spectrum of the dimer (N2O)2 has been recorded in the region of the monomer N2O υ3 vibrational band using a diode laser absorption spectrometer which incorporates a multiple-pass cell and a pulsed-jet expansion. A double-modulation technique involving a fast modulation of the laser frequency and a slow modulation of the gas pulse has been developed in the experiments. The spectrum is completely analysed and the rotational constants and effective structures are accurately determined for both the ground and the excited vibrational states. The centrosymmetric slipped parallel structure of (N2O2 is well explained by an intermolecular potential containing a combination of electrostatic interactions between distributed multipoles of different monomers and atom–atom Lennard-Jones potentials to describe the repulsion and dispersion interactions.

Free-jet infrared absorption spectroscopy of the (N 2O) 2 van der Waals complex in the 8 μm region

The vibration-rotation spectrum of (N 2O) 2 has been studied in the monomer ν 1 region (≈ 1280 cm −1) by free-jet absorption spectroscopy. The rotational constants determined are consistent with the centrosymmetric slipped parallel structure reported recently by Huang and Miller and by Howard. The band origin, 1279.7107 (6) cm −1, is red-shifted from that of the monomer by 5.1926(6) cm −1.

Collisional energy transfer and fragmentation of size selected CO2 clusters

Carbon dioxide clusters are generated in a supersonic molecular beam and size selected by scattering from a He beam. By analyzing the measured time-of-flight spectra as a function of the deflection angle, differential energy loss spectra for (CO2)2 — He are obtained which show a rotational rainbow structure with a maximal energy transfer of ΔE/E=0.4. This result is compatible with the slipped parallel structure of dimer but not with theT-shaped geometry. The scattering analysis is also used to derive information about the pressure dependence of cluster formation and the fragmentation by electron impact ionisation. The latter process leads preferably to the monomer product ion CO2+ with a small but finite probability for other ionic channels.

Pulsed molecular beam infrared absorption spectroscopy of CO 2 dimer

The rotationally resolved spectrum of the carbon dioxide dimer has been obtained in the region of the ν 3 CO 2 monomer vibration by diode laser absorption spectroscopy of a pulsed molecular beam. Rotational and centrifugal distortion constants within a Watson S-reduced Hamiltonian are determined and interpreted in terms of a centrosymmetric slipped parallel structure. The ground-state geometrical parameters are R (CC) = 3.602 Å and ∠ CCO = 57.9°. This effective structure is explained by a potential including distributed multipole and dispersion interactions and a cylindrical hard-core repulsion.