Hydrocarbon Dimers Research Articles

On-Surface Debromination of 2,3-Bis(dibromomethyl)- and 2,3-Bis(bromomethyl)naphthalene: Dimerization or Polymerization?

We describe the on‐surface dehalogenative homocoupling of benzylic bromides, namely bis‐bromomethyl‐ and bis‐gem‐(dibromomethyl) naphthalene as a potential route to either hydrocarbon dimers or conjugated polymers on Au(111). While bis‐gem‐(dibromomethyl) naphthalene affords different dimers with naphthocyclobutadiene as the key intermediate, bis‐bromomethyl naphthalene furnishes a poly(o‐naphthylene vinylidene) as a non‐conjugated polymer which undergoes dehydrogenation toward its conjugated derivative poly(o‐naphthylene vinylene) upon mild annealing. A combination of scanning tunneling microscopy, non‐contact atomic force microscopy and density functional theory calculations provides deep insights into the prevailing mechanisms.

On‐Surface Debromination of 2,3‐Bis(dibromomethyl)‐ and 2,3‐Bis(bromomethyl)naphthalene: Dimerization or Polymerization?

AbstractWe describe the on‐surface dehalogenative homocoupling of benzylic bromides, namely bis‐bromomethyl‐ and bis‐gem‐(dibromomethyl) naphthalene as a potential route to either hydrocarbon dimers or conjugated polymers on Au(111). While bis‐gem‐(dibromomethyl) naphthalene affords different dimers with naphthocyclobutadiene as the key intermediate, bis‐bromomethyl naphthalene furnishes a poly(o‐naphthylene vinylidene) as a non‐conjugated polymer which undergoes dehydrogenation toward its conjugated derivative poly(o‐naphthylene vinylene) upon mild annealing. A combination of scanning tunneling microscopy, non‐contact atomic force microscopy and density functional theory calculations provides deep insights into the prevailing mechanisms.

Deoxygenative Transition-Metal-Promoted Reductive Coupling and Cross-Coupling of Alcohols and Epoxides

AbstractThe prospective utilization of abundant, CO2-neutral, renewable feedstocks is driving the discovery and development of new reactions that refunctionalize oxygen-rich substrates such as alcohols and polyols through C–O bond activation. In this review, we highlight the development of transition-metal-promoted reactions of renewable alcohols and epoxides that result in carbon–carbon bond-formation. These include reductive self-coupling reactions and cross-coupling reactions of alcohols with alkenes and arene derivatives. Early approaches to reductive couplings employed stoichiometric amounts of low-valent transition-metal reagents to form the corresponding hydrocarbon dimers. More recently, the use of redox-active transition-metal catalysts together with a reductant has enhanced the practical applications and scope of the reductive coupling of alcohols. Inclusion of other reaction partners with alcohols such as unsaturated hydrocarbons and main-group organometallics has further expanded the diversity of carbon skeletons accessible and the potential for applications in chemical synthesis. Catalytic reductive coupling and cross-coupling reactions of epoxides are also highlighted. Mechanistic insights into the means of C–O activation and C–C bond formation, where available, are also highlighted.1 Introduction2 Stoichiometric Reductive Coupling of Alcohols3 Catalytic Reductive Coupling of Alcohols3.1 Heterogeneous Catalysis3.2 Homogeneous Catalysis4 Reductive Cross-Coupling of Alcohols4.1 Reductive Alkylation4.2 Reductive Addition to Olefins5 Epoxide Reductive Coupling Reactions6 Conclusions and Future Directions

Nucleation of soot: experimental assessment of the role of polycyclic aromatic hydrocarbon (PAH) dimers

Abstract The irreversible dimerization of polycyclic aromatic hydrocarbons (PAHs) – typically pyrene (C16H10) dimerization – is widely used in combustion chemistry models to describe the soot particle inception step. This paper concerns itself with the detection and identification of dimers of flame-synthesized PAH radicals and closed-shell molecules and an experimental assessment of the role of these PAH dimers for the nucleation of soot. To this end, flame-generated species were extracted from an inverse co-flow flame of ethylene at atmospheric pressure and immediately diluted with excess nitrogen before the mixture was analyzed using flame-sampling tandem mass spectrometry with collision-induced fragmentation. Signal at m/z = 404.157 (C32H20) and m/z = 452.157 (C36H20) were detected and identified as dimers of closed-shell C16H10 and C18H10 monomers, respectively. A complex between a C13H9 radical and a C24H12 closed-shell PAH was observed at m/z = 465.164 (C37H21). However, a rigorous analysis of the flame-sampled mass spectra as a function of the dilution ratio, defined as the ratio of the flow rates of the diluent nitrogen to the sampled gases, indicates that the observed dimers are not flame-born, but are produced in the sampling line. In agreement with theoretical considerations, this paper provides experimental evidence that pyrene dimers cannot be a key intermediate in particle inception at elevated flame temperatures.

An Iterative Fragment Scheme for the ACKS2 Electronic Polarization Model: Application to Molecular Dimers and Chains.

The treatment of electrostatic interactions is a key ingredient in the force field-based simulation of condensed phase systems. Most approaches used fixed, site-specific point charges. Yet, it is now clear that many applications of force fields (FFs) demand more sophisticated treatments, prompting the implementation of charge equilibration methods in polarizable FFs to allow the redistribution of charge within the system. One approach allowing both, charge redistribution and site-specific polarization, while at the same time solving methodological shortcomings of earlier methods, is the first-principles-derived atom-condensed Kohn-Sham density functional theory method approximated to the second order (ACKS2). In this work, we present two fragment approaches to ACKS2, termed f-ACKS2 and a self-consistent version, scf-ACKS2, that treat condensed phase systems as a collection of electronically polarizable molecular fragments. The fragmentation approach to ACKS2 not only leads to a more transferable and less system-specific collection of electronic response parameters but also opens up the method to large condensed phase systems. We validate the accuracies of f-ACKS2 and scf-ACKS2 by comparing polarization energies and induced dipole moments for a number of charged hydrocarbon dimers against DFT reference calculations. Finally, we also apply both fragmented ACKS2 variants to calculate the polarization energy for electron-hole pair separation along a chain of anthracene molecules and find excellent agreement with reference DFT calculations.

Predicting the photoresponse of soot nuclei: Spectroscopic characteristics of aromatic aggregates containing five-membered rings

Establishing the mechanism for soot nucleation will require in situ experimental characterization of the identity and intermolecular interactions of the initial precursors, and electronic spectroscopy methods have the potential to do both. However, the optical response of polycyclic aromatic hydrocarbon (PAH) dimers and complexes differs significantly from that of the constituent monomers, and studies of soot precursor complexes have largely been limited to PAHs containing only six-membered aromatic rings. Hydrocarbons containing unsaturated five-membered rings are also present in high concentration in flames, and the photoresponse of complexes containing five-membered rings has not yet been examined. In this work, we elucidate the spectroscopic properties of small hydrocarbon complexes containing cyclopentadienyl groups or cyclopenta-fused groups, calculating ground- and excited-state binding energies, optimal excited-state geometries, repulsion energies, and fluorescence emission wavelengths. We show that excited-state distortion of cyclopentadienyl groups allows strong binding and low-energy fluorescence emission compared to similar-sized PAHs, and that a cyclopenta-fused group dramatically lowers the absorption and emission energies for acenaphthylene, dominating excited-state noncovalent interactions—findings that could shed light on the complex electronic properties of flames.

Facile biphasic catalytic process for conversion of monoterpenoids to tricyclic hydrocarbon biofuels

Terpenoids have drawn much attention to scientists in synthesizing high-performance bio- jet fuels due to their ring structures, which feature potential high densities. Here, a facile biphasic catalytic process has been developed for the production of high-density tricyclic hydrocarbon biofuels from a monoterpenoid, 1,8-cineole, using sulfuric acid (H2SO4) as the homogeneous catalyst. A ~100% conversion of 1,8-cineole and a > 40% carbon yield of cyclic dimers were achieved at 100 °C within two hours. The mechanism for the acid-catalyzed conversion of 1,8-cineole to cyclic hydrocarbon dimers were explored. In particular, the formation of the diene intermediates and the following dimerization of dienes was essential to synthesize tricyclic terpene dimers. The biphasic catalytic process accelerated the deoxygenation rate and enabled the dimerization with the aid of organic solvent while controlling the reaction rates to avoid the formation of solid residues. Moreover, this process also facilitated the product separation by organic solvent extraction while enabling easy recycle of the homogenous catalysts.

Molecular Helmholtz coils.

How to build a molecular Helmholtz coil? The possibility to create a Helmholtz coil at the molecular level is studied via the induced magnetic responses of several small cyclic hydrocarbon dimers with formula (CnHn)2 and Dnh symmetry (n = 6-10). Our results reveal that for n ≥ 8, π-electrons give rise to a uniform magnetic field within the central region between rings, satisfying the Helmholtz coil condition. This uniformity is independent of the intensity of the induced magnetic field.

Excited states and excitonic interactions in prototypic polycyclic aromatic hydrocarbon dimers as models for graphitic interactions in carbon dots.

The study of electronically excited states of stacked polycyclic aromatic hydrocarbons (PAHs) is of great interest due to promising applications of these compounds as luminescent carbon nanomaterials such as graphene quantum dots (GQDs) and carbon dots (CDs). In this study, the excited states and excitonic interactions are described in detail based on four CD model dimer systems of pyrene, coronene, circum-1-pyrene and circum-1-coronene. Two multi-reference methods, DFT/MRCI and SC-NEVPT2, and two single-reference methods, ADC(2) and CAM-B3LYP, have been used for excited state calculations. The DFT/MRCI method has been used as a benchmark method to evaluate the performance of the other ones. All methods produce useful lists of excited states. However, an overestimation of excitation energies and an inverted ordering of states, especially concerning the bright HOMO-LUMO excitation, are observed. In the pyrene-based systems, the first bright state appears among the first four states, whereas the number of dark states is significantly larger for the coronene-based systems. Fluorescence emission properties are addressed by means of geometry optimization in the S1 state. The inter sheet distances for the S1 state decrease in comparison to the corresponding ground-state values. These reductions are largest for the pyrene dimer and decrease significantly for the larger dimers. Several minima have been determined on the S1 energy surface for most of the dimers. The largest variability in emission energies is found for the pyrene dimer, whereas in the other cases a more regular behavior of the emission spectra is observed.

Atomistic insights into the dynamics of binary collisions between gaseous molecules and polycyclic aromatic hydrocarbon dimers.

Polycyclic aromatic hydrocarbon (PAH) dimers are important intermediates in combustion and soot formation. The scattering dynamics of gaseous molecules colliding with PAH dimers and the subsequent PAH dimer stability are investigated by performing molecular dynamics (MD) simulations. Effects of properties of the surrounding gaseous molecules and PAH dimers as well as temperature are investigated in this study. Depending on the residence time of N2 molecules trapped by the PAH dimers, two scattering types, that is, specular scattering and inelastic scattering, have been observed, which is correlated to the temperature and the type of the PAH dimer. Specifically, specular scattering preferentially takes place at high temperatures on small PAH dimers, while inelastic scattering tends to happen at low temperatures on large PAH dimers. During collision, energy transfer between the gaseous molecule and the PAH dimer changes the thermodynamic stability of the PAH dimer. Statistical analysis indicates that the decomposition rate of a PAH dimer to PAH monomers is sensitive to temperature and the PAH dimer type. Furthermore, effects of the gaseous molecule type on the PAH dimer stability are considered. The molecular mass of the colliding gaseous molecule is a key factor in determining the PAH dimer stability, as heavier gaseous molecules are more effective in promoting the PAH dimer decomposition. Results from this study indicate that collisions with gaseous molecules decrease the PAH dimer stability, while increasing the PAH dimer size and decreasing the collision temperature both decrease the decomposition rate of the PAH dimer.

Mechanistic Features of the Oxidation-Reductive Coupling of Alcohols Catalyzed by Oxo-Vanadium Complexes.

The oxo-vanadium-catalyzed redox disproportionation of activated alcohols (oxidation-reductive coupling, Ox-RC) produces carbonyl compounds and hydrocarbon dimers. A mechanistic study of this novel reaction is reported herein. Following our initial disclosure, new findings include the following: (1) The [(salimin)VO2]--catalyzed Ox-RC of Ph2CHOH in the presence of fluorene affords the products of H-atom abstraction and all possible hydrocarbon dimers. (2) Electronic substituent effects on the relative rates of Ox-RC with respect to 4-X-BnOH reactants and Bu4N[(Y-salimin)VO2] catalysts (1a-c) reveal (a) a correlation of the oxidation rate of X-BnOH reactants with the radical σ parameter and (b) correlation of the oxidation rate for (Y-salimin)VO2- with the standard Hammett σ parameter. (3) The ease of electrochemical reduction of 1a-c is Y = NO2 > OMe > H. (4) Ambient 1H NMR studies of the interaction of 1 with alcohols suggest only a weak equilibrium association. (5) Density functional theory computational modeling of the Ox-RC reaction supports a ping-pong-type catalytic pathway, beginning with alcohol oxidation by (salimin)VO2-, preferably by stepwise-H-atom transfer from the alcohol to 1, affording the carbonyl product and the reduced (salimin)V(III)(OH)2-. The reduction half-reaction likely begins with condensation of the latter species with R2CHOH to give the alkoxide complex (salimin)V(OR)OH-; homolysis of the R···OV(III)(salimin) bond affords (salimin)V(IV)OH(O)- and the R-radical; the latter dimerizes and the former can disproportionate via H-transfer to reform catalyst (salimin)VO2- (1) and (salimin)V(OH)2-.

Pasteur’s Experiment Performed at the Nanoscale: Manual Separation of Chiral Molecules, One by One

Understanding the principles of molecular recognition is a difficult task and calls for investigation of appropriate model systems. Using the manipulation capabilities of scanning tunneling microscopy (STM) we analyzed the chiral recognition in self-assembled dimers of helical hydrocarbons at the single molecule level. After manual separation of the two molecules of a dimer with a molecule-terminated STM tip on a Cu(111) surface, their handedness was subsequently determined with a metal atom-terminated tip. We find that these molecules strongly prefer to form heterochiral pairs. Our study shows that single molecule manipulation is a valuable tool to understand intermolecular recognition at surfaces.

Polarizability of C60 fullerene dimer and oligomers: the unexpected enhancement and its use for rational design of fullerene-based nanostructures with adjustable properties

The high polarizabilities of fullerene and its derivatives cause peculiarities in various physical and chemical processes in fullerene-containing systems. Their polarizabilities have been found to be efficient parameters for the design of nanostructures with desirable behavior. Unfortunately, the appropriate experimental data are scarce for most of the fullerene derivatives, due to their low availability or possible dissociation. At the same time, such information may be useful for C60-based nanotechnologies. We point our attention to the fullerene dimer and oligomers, which are novel and very promising compounds for nano-applications. We have performed the first density-functional theory study on the polarizability of fullerene derivatives (C60)n (n = 1–5) to elucidate how their structure affects the polarizability. In contrast to the concept of additivity, common in physical chemistry, the mean polarizability of (C60)n nonlinearly depends on the number of fullerene cores in their molecules, i.e. it violates the additivity. Similar to the other positive deviations from additive schemes, it has been called exaltation of polarizability. This effect is a result of the interaction of the π-electronic systems of fullerene cores in (C60)n and increases with their maximal remoteness. Experimental evidence of the exaltation is discussed. Thus, it agrees well with the enhancement of the polarizability of crystalline forms of C60 compared to molecular ones measured previously. Also, we have found a strong correlation between the calculated exaltations and the chemical properties of isomeric (C60)3, (C60)2 and its derivatives observed experimentally. The predicted enhancement has not been described previously and may be widespread among various nanostructures (for example, dimers of bowl-shaped hydrocarbons or other fullerenes). Insights into possible applications of the polarizability and its anisotropy to the molecular design and molecular machinery have been provided.

A Density Functional with Spherical Atom Dispersion Terms.

A new hybrid density functional, APF, is introduced, which avoids the spurious long-range attractive or repulsive interactions that are found in most density functional theory (DFT) models. It therefore provides a sound baseline for the addition of an empirical dispersion correction term, which is developed from a spherical atom model (SAM). The APF-D empirical dispersion model contains nine adjustable parameters that were selected based on a very small training set (15 noble gas dimers and 4 small hydrocarbon dimers), along with two computed atomic properties (ionization potential and effective atomic polarizability) for each element. APF-D accurately describes a large portion of the potential energy surfaces of complexes of noble gas atoms with various diatomic molecules involving a wide range of elements and of dimers of small hydrocarbons, and it reproduces the relative conformational energies of organic molecules. The accuracy for these weak interactions is comparable to that of CCSD(T)/aug-cc-pVTZ calculations. The accuracy in predicting the geometry of hydrogen bond complexes is competitive with other models involving DFT and empirical dispersion.

Stable Alkanes Containing Very Long Carbon–Carbon Bonds

The metal-induced coupling of tertiary diamondoid bromides gave highly sterically congested hydrocarbon (hetero)dimers with exceptionally long central C-C bonds of up to 1.71 Å in 2-(1-diamantyl)[121]tetramantane. Yet, these dimers are thermally very stable even at temperatures above 200 °C, which is not in line with common C-C bond length versus bond strengths correlations. We suggest that the extraordinary stabilization arises from numerous intramolecular van der Waals attractions between the neighboring H-terminated diamond-like surfaces. The C-C bond rotational dynamics of 1-(1-adamantyl)diamantane, 1-(1-diamantyl)diamantane, 2-(1-adamantyl)triamantane, 2-(1-diamantyl)triamantane, and 2-(1-diamantyl)[121]tetramantane were studied through variable-temperature (1)H- and (13)C NMR spectroscopies. The shapes of the inward (endo) CH surfaces determine the dynamic behavior, changing the central C-C bond rotation barriers from 7 to 33 kcal mol(-1). We probe the ability of popular density functional theory (DFT) approaches (including BLYP, B3LYP, B98, B3LYP-Dn, B97D, B3PW91, BHandHLYP, B3P86, PBE1PBE, wB97XD, and M06-2X) with 6-31G(d,p) and cc-pVDZ basis sets to describe such an unusual bonding situation. Only functionals accounting for dispersion are able to reproduce the experimental geometries, while most DFT functionals are able to reproduce the experimental rotational barriers due to error cancellations. Computations on larger diamondoids reveal that the interplay between the shapes and the sizes of the CH surfaces may even allow the preparation of open-shell alkyl radical dimers (and possibly polymers) that are strongly held together exclusively by dispersion forces.

Accuracy of Several Wave Function and Density Functional Theory Methods for Description of Noncovalent Interaction of Saturated and Unsaturated Hydrocarbon Dimers.

The proper description of noncovalent complexes is a notoriously difficult problem, especially for complexes dominated by the dispersion energy. Accurate and reliable results can be obtained using computationally demanding methods such as the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)), close to the complete basis set (CBS) limit. The sizes of the noncovalent complexes of interest, however, often exceed the computational capability of available computer facilities and software. Computationally efficient yet accurate and reliable theoretical methods are highly desired. In this work, we assembled a small test set of noncovalent complexes of un/saturated a/cyclic hydrocarbon (HC) dimers in order to inspect the accuracy and reliability of several routinely used low-order scaling wave function (WFT) and density functional theory (DFT) methods. The test set comprises dispersion dominated complexes of two different monomer types, saturated and unsaturated. The unsaturated systems are relatively well populated in one of the most popular training data sets for noncovalent complexes, the S22 set of Jurečka et al. The opposite is true for saturated systems, for which rather poor performance of "approximate" methods has been observed. From the results shown is this work, it is clear that unsaturated, e.g., π···π stacked, covalent complexes are described more accurately on average. With the exception of a few "balanced methods", such as MP2C, MP2.5, SCS-/SCS(MI)-CCSD, or DFT-D3 with the TPSS and PBE functionals, a simultaneous description of saturated and unsaturated HCs introduces serious errors (i.e., more than 1 kcal/mol).

Evaluation of dispersion-corrected density functional theory (B3LYP-DCP) for compounds of biochemical interest

An evaluation of a dispersion-corrected density functional theory method (B3LYP-DCP) [I.D. Mackie, G.A. DiLabio, Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections, J. Phys. Chem. A 112 (2008) 10968–10976] for three systems of biochemical interest is presented. Firstly, structures and energies of isomers of the tripeptide Phe-Gly-Phe have been compared with CCSD(T)/CBS//RI-MP2/cc-pVTZ literature values. In the system aromatic interactions compete with XH–π (X = C, N) interactions and hydrogen bonds which makes it a reliable model for proteins. The resulting mean absolute deviation between B3LYP-DCP and CCSD(T)/CBS relative energies is found to be 0.50 kcal mol −1. Secondly, a phenylalanine derivative featuring a CH–π interaction has been investigated. A comparison between the optimized geometry and X-ray crystal data shows that B3LYP-DCP accurately predicts the interaction between the two aromatic rings. Thirdly, the dipeptide Ac-Phe-Phe-NH 2 which contains an edge-to-face interaction between two aromatic rings has been studied. The study demonstrates the general applicability of the B3LYP-DCP method on systems which features interactions typically present in biochemical compounds.

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.

Cation-aromatic π interaction in the gas phase: an experimental study on relative silver (I) ion affinities of polyaromatic hydrocarbons

Abundant silver (I) ion bound asymmetric dimers of polyaromatic hydrocarbons (PAHs) were easily generated by electrospray ionization. Based on the unimolecular decomposition of the Ag(I) ion bound asymmetric dimers, the relative Ag(I) ion affinities of nine PAHs in the gas phase has been established­as: benzene? <? naphthalene? <? phenanthrene? <? anthracene? <? fluoranthene? <? pyrene? <? triphenylene? <­chrysene < benz[a]anthracene. The observed Ag(I) ion affinities were found to correlate with calculated quadrupole moments of PAHs, indicating that electrostatic charge–quadrupole interaction is important in the cation–aromatic π binding of the polyaromatic systems being studied. However, secondary effects, such as surface area of the aromatic π electrons or intermolecular electronic repulsion and steric repulsion between bay region hydrogens, could also affect the magnitude and relative order of Ag(I) ion affinities of PAHs. © 1998 John Wiley & Sons, Ltd.

Structural Characterization of Aromatic−Aromatic Complexes by Rotational Coherence Spectroscopy

Rotational coherence spectroscopy (RCS) has been applied in structural studies of (a) aromatic−aromatic van der Waals complexes of the form M−X, where M = perylene or fluorene and X = benzene or toluene, and (b) aromatic−aliphatic hydrocarbon dimers of the form M−Y, where M is as above and Y = cyclohexane or methylcyclohexane. For all of the perylene complexes the experimentally determined rotational constants are found to be consistent with centrally bound, parallel-stacked structures in which the monomer planes are separated by a distance of 3.5−4.3 A. Analogous geometries also characterize the fluorene−aliphatic species. However, the two fluorene−aromatic complexes have structures that depart from the parallel-stacked form. Both species have slipped geometries in which the monomer planes are not directly over one another. And, in the case of fluorene−benzene, the two aromatic planes are tilted with respect to one another. These differences are attributed to the significant contribution of electrostatic forces in determining the fluorene−aromatic geometries.