Benzene Dimer Research Articles

The 1,4-phenylenediisocyanide dimer: gas-phase properties and insights into organic self-assembled monolayers

The 1,4-phenylenediisocyanide (PDI) dimer serves as an intriguing case of the substituted benzene dimer, as well as a prototype system for self-assembled monolayers of organic isocyanide complexes. Structures and binding energies are explored using recently developed dual-basis second-order Møller-Plesset perturbation theory energies and gradients. The structures are dictated by a combination of dispersion and electrostatics, a combination not properly treated with local or gradient-corrected density functionals. The PDI dimer binds more than twice as strongly as unsubstituted benzene dimers in several configurations, and greater directional specificity between parallel-displaced and T-shaped structures is observed. A rotated-parallel structure is the predicted lowest-energy, gas-phase configuration, in which the isocyanide ligands are staggered on the monomers. Relevant potential energy curves of the dimer are also presented, and insights into PDI monolayer formation on metal surfaces are explored via simple two-body models. Based on the adsorbate interaction alone, a high-coverage configuration and non-vertical tilt are predicted to be favorable, although the total binding for PDI in these configurations is still insufficient to form ordered monolayers, a result consistent with previous experimental findings. Additional phenyl rings (biphenyldiisocyanide, triphenyldiisocyanide) significantly stabilize the interaction and provide the additional dispersion necessary for an ordered monolayer.

Binding of polycyclic aromatic hydrocarbons and graphene dimers in density functional theory

An early van der Waals density functional (vdW-DF) described layered systems (such as graphite and graphene dimers) using a layer-averaged electron density in the evaluation of nonlocal correlations. This early vdW-DF version was also adapted to approximate the binding of polycyclic aromatic hydrocarbons (PAHs) (Chakarova S D and Schröder E 2005 J. Chem. Phys.122 054102). In parallel to that PAH study, a new vdW-DF version (Dion M, Rydberg H, Schröder E, Langreth D C and Lundqvist B I 2004 Phys. Rev. Lett. 92 246401) was developed that provides accounts of nonlocal correlations for systems of general geometry. We apply here the latter vdW-DF version to aromatic dimers of benzene, naphthalene, anthracene and pyrene, stacked in sandwich (AA) structure, and the slipped-parallel (AB) naphthalene dimer. We further compare the results of the two methods as well as other theoretical results obtained by quantum-chemistry methods. We also compare calculations for two interacting graphene sheets in the AA and the AB structures and provide the corresponding graphene-from-graphite exfoliation energies. Finally, we present an overview of the scaling of the molecular–dimer interaction with the number of carbon atoms and with the number of carbon rings.

Theoretical analysis of intermolecular interactions of selected residues of triosephosphate isomerase from Trypanosoma cruzi with its inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid

The interaction between selected amino acid residues of the homodimeric enzyme triosephosphate isomerase from Trypanosoma cruzi with the inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid (BTT) was investigated by means of high level quantum chemical methods. The amino acids phe75A, arg71A and tyr102B from the enzyme monomers A and B were selected using experimental X-ray structural data. The ab initio intermolecular energies for the association of the inhibitor with the individual amino acids were calculated in two forms, namely, with a supermolecular approach and using the symmetry adapted perturbation theory. The latter also provided the contributions to the interaction energies, which were interpreted in terms of the usual van der Waals forces. The electron density for the specific interactions between BTT and the amino acids and the charge redistribution due to complex formation were also analyzed. It was found that for phe75A and tyr102B the dispersion energy is the dominant contribution to the complex stabilization followed by the induction and electrostatic energies. In addition, whereas the face-edge complex of BTT with phe75A exhibits a C-H pi bond similar to that observed for the benzene dimer, the complex with arg71A shows an important charge redistribution on the amino acid in regions far removed from those where the intermolecular specific interactions occur.

Stacking of polycyclic aromatic hydrocarbons as prototype for graphene multilayers, studied using density functional theory augmented with a dispersion term

The interlayer pi-pi interaction between finite-size models of graphene sheets was investigated by using a density functional theory method, augmented with an empirical R(-6) term for the description of long-range dispersive interaction; these were calibrated by studying the pi-pi interaction between various benzene dimer configurations and comparing the results with previous calculations. For stacked bilayers (dimers) and multilayers of polyaromatic hydrocarbons, which serve as molecular models of graphene sheets, we found that binding energies and energy gaps are strongly dependent on their sizes, while the stacking order and the number of stacked layers have a minor influence. The remarkably broad variation of the energy gap, ranging from 1.0 to 2.5 eV, due mainly to variation of the model size, suggests the potential of broadband luminescence in the visible range for carbon-based nanomaterials that have pi-pi interacting.

Linear response coupled cluster study of the benzene excimer

The hierarchy CC2, CCSD and CCSDR(3) of linear response coupled cluster methods is used to study the electronic states of the benzene dimer related with the emission, absorption and interaction energy of the benzene excimer. Differential electron density plots are used to give insights into the stabilizing interactions within the benzene excimer. The CC2 level describes properly most of the addressed spectroscopic parameters, partially due to error cancellations. High accuracy is obtained if the triple excitations are considered at the CCSDR(3) approximation together with corrections for large basis sets. A detailed and critical comparison between theory and experiment is presented.

Benchmark Data for Noncovalent Interactions in HCOOH···Benzene Complexes and Their Use for Validation of Density Functionals.

We present benchmark energetic data for the HCOOH···benzene complexes. The benchmark data were determined by a composite approach based on CCSD(T) calculations. Final binding energies (kcal/mol) are in the range of 1.6-4.8 kcal/mol, and they were used as reference data to test density functionals in the literature. Among the tested local density functionals without empirical dispersion corrections, M06-L is the best performing functional, and M06-L/6-31+G(d,p) gives a mean unsigned error (MUE) of only 0.15 kcal/mol. PBEsol and SOGGA also show promising performance. The best local DFT-D methods are BLYP-D and PBEsol-D, and they give an MUE of 0.15 kcal/mol after removing basis set superposition errors by the counterpoise approach. Empirical dispersion corrections greatly improve the descriptions of noncovalent interactions in HCOOH···benzene dimers. The calculated benchmark data and intermolecular potential are useful for the parametrizations of new force fields and coarse-grained models for chemical species such as the acrylic polymers.

Novel Benzene-Bridged Triphenylene-Based Discotic Dyads

We report the synthesis and characterization of two series of novel triphenylene-based benzene-bridged symmetric discotic dimers. Two triphenylene discotics have been connected to a rigid benzene ring via flexible methylene spacers. In one series, triphenylene moiety was tethered with benzene via an ester linkage, while in the second series it is via an ether linkage. Within each series, the orientation of the linkage of the triphenylene core around the benzene core has been changed by substituting the benzene ring at o-, m-, and p-positions. These materials have been characterized from their spectral and elemental analysis. The thermotropic liquid crystalline properties were investigated by polarizing optical microscopy, differential scanning calorimetry, and X-ray diffraction studies. All the virgin compounds do not display any mesomorphism; however, their charge transfer complexes with trinitrofluorenone, an electron acceptor, exhibited columnar mesophases. The direct current (dc) conductivity of charge transfer complexes at two ratios has been studied at variable temperature. The small conductivity value demonstrates that long spacers as well as connectivity to the rigid benzene ring dilute the column packing, hence making pi-pi interaction less efficient for the entire column length. A hexagonal assembly of triphenylene-benzene dimer 12 on a highly oriented pyrolytic graphite (HOPG) surface has been visualized with scanning tunneling microscopy (STM).

Signatures of molecular recognition from the topography of electrostatic potential

The recognition of interaction between two molecules is analysed via the topography of their molecular electrostatic potentials (MESP). The point of recognition between two species is proposed to be the geometry at which there is a change in the nature of the set of MESP critical points of one of the molecules vis-a-vis with its MESP topography at infinite separation. These results are presented for certain model systems such as pyridine and benzene dimers, cytosine-guanine and adenine-thymine base pairs in various orientations of approach of the two species.

Assessment of standard force field models against high‐qualityab initiopotential curves for prototypes of π–π, CH/π, and SH/π interactions

Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechanical potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH(4) complex, and the benzene-H(2)S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions) are employed for the empirical force fields.

An Assessment of Theoretical Methods for Nonbonded Interactions: Comparison to Complete Basis Set Limit Coupled-Cluster Potential Energy Curves for the Benzene Dimer, the Methane Dimer, Benzene−Methane, and Benzene−H2S

Large, correlation-consistent basis sets have been used to very closely approximate the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] complete basis set potential energy curves of several prototype nonbonded complexes, the sandwich, T-shaped, and parallel-displaced benzene dimers, the methane-benzene complex, the H2S-benzene complex, and the methane dimer. These benchmark potential energy curves are used to assess the performance of several methods for nonbonded interactions, including various spin-component-scaled second-order perturbation theory (SCS-MP2) methods, the spin-component-scaled coupled-cluster singles and doubles method (SCS-CCSD), density functional theory empirically corrected for dispersion (DFT-D), and the meta-generalized-gradient approximation functionals M05-2X and M06-2X. These approaches generally provide good results for the test set, with the SCS methods being somewhat more robust. M05-2X underbinds for the test cases considered, while the performances of DFT-D and M06-2X are similar. Density fitting, dual basis, and local correlation approximations all introduce only small errors in the interaction energies but can speed up the computations significantly, particulary when used in combination.

Protonated Benzene Dimer: An Experimental and Ab Initio Study

The excitation spectrum of the protonated benzene dimer has been recorded in the 415-600 nm wavelength range. In contrast to the neutral iso-electronic benzene dimer, its absorption spectrum extends in the visible spectral region. This huge spectral shift has been interpreted with ab initio calculations, which indicate that the first excited states should be charge transfer states.

A quantum chemistry study of Diels–Alder dimerizations in benzene and anthracene

There is considerable experimental evidence of covalent dimerization of aromatic compounds occurring under shock conditions. Because of their endothermicity, these reactions could play a large role in the shock initiation process of aromatic molecular explosives such as 2,4,6-trinitrotoluene and 1,3,5-triamino-2,4,6-trinitrobenzene by withdrawing energy from the shock compression. Very little is known about the energetics, however, and this knowledge is crucial for the design of empirical force fields that can treat shock-induced chemistry. We have employed ab initio electronic structure and density functional methods to study the Diels-Alder (DA) dimerizations of benzene and anthracene. The enthalpy of reaction for DA benzene dimerization is predicted to be +35.9 kcal/mol. The stepwise pathway to this dimer involves formation of a stable triplet intermediate that requires 71.8 kcal/mol of energy. Transition states along both the concerted and stepwise pathways were optimized and the energetics of the reaction pathways are detailed. The former is found to be the energetically preferred mechanism. Nine DA dimers of anthracene were found, with six predicted to have dimerization DeltaH(rxn)'s of 24-55 kcal/mol, two with dimerization energies near zero and one that is formed through an exothermic reaction. Twelve triplet dimers of anthracene, with DeltaH(rxn)'s ranging from 33-50 kcal/mol, are also described. Finally, the potential importance of these reactions in the context of shock compression of these materials is discussed.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Origin of Stacked-Ring Aromaticity

Although strong diatropic currents run in the pi-stacked dimers of 4n pi annulenes, they are still antiaromatic with negative topological resonance energies (TREs). The TRE difference between two annulene molecules and the pi-stacked annulene dimer can be used as a practical measure of stacked-ring aromaticity. As predicted by Corminboeuf et al., all pi-stacked 4n pi annulene dimers exhibit marked stacked-ring aromaticity. In contrast, the TRE for the entire conjugated system of a pi-stacked benzene dimer is much smaller than twice the TRE for benzene. The analysis of circuit contributions to energetic and magnetic properties shows that such stacked-ring aromaticity and diatropicity arise from many (4n + 2)-site circuits created by the stacking of two antiaromatic rings. Tetragonal faces formed in the dimers are responsible for the creation of these (4n + 2)-site circuits.

Origin of substituent effects in edge-to-face aryl–aryl interactions

Substituent effects in the edge-to-face configuration of the benzene dimer have been studied using modern density functional theory. An accurate interaction potential energy curve has been computed for the unsubstituted dimer using ab initio methods with large basis sets. The recommended binding energy for the edge-to-face benzene dimer is 2.31 kcal mol−1, estimated at the counterpoise-corrected CCSD(T)/aug-cc-pVTZ level of theory. For both edge-ring and face-ring-substituted dimers, interaction energies correlate with σm for the substituents, indicating that substituent effects can be understood qualitatively in terms of simple electrostatic effects, although in the latter case dispersion results in some scatter in the data. In contrast to prevailing models of substituent effects in benzene dimers, polarization of the π-system of the substituted ring does not induce substituent effects. For edge-ring-substituted dimers, substituent effects arise from differential electrostatic interactions between the hydrogens on the substituted ring and the π-cloud of the face ring and direct interactions of the substituents with the unsubstituted ring. For face-ring-substituted dimers, substituent effects arise from direct electrostatic and dispersion interactions of the substituents with the edge ring. Substituents with σm > 0.12 favour edge ring substitution while for σm < 0.12 substitution on the face ring is preferred.

Accurate Methods for Large Molecular Systems

Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g., protein, liquid, zeolite) into small subunits (fragments) in very different ways that are designed to both retain the high accuracy of the chosen quantum mechanical level of theory while greatly reducing the demands on computational time and resources. Each of these methods is inherently scalable and is therefore eminently capable of taking advantage of massively parallel computer hardware while retaining the accuracy of the corresponding electronic structure method from which it is derived. The effective fragment potential (EFP) method is a sophisticated approach for the prediction of nonbonded and intermolecular interactions. Therefore, the EFP method provides a way to further reduce the computational effort while retaining accuracy by treating the far-field interactions in place of the full electronic structure method. The performance of the methods is demonstrated using applications to several systems, including benzene dimer, small organic species, pieces of the alpha helix, water, and ionic liquids.

Novel structural motif for stabilization of polyacene systems

It was shown that, in these systems, the limiting values of the energy gaps between the frontier molecular orbitals ( ∆ E HOMO-LUMO ) do not exceed 1 eV [1] (calculated for acenes up to C 200 ) and 1.8 eV at n → ∞ [2]. Because of the destabilizing four-electron repulsions of bonding π MOs [3, 4], formation of three-dimensional layered π stacking structures is possible only due to van der Waals interactions, which leads to weakly bound adducts with nonparallel orientation of the planes of conjugated systems of type 3 and has no effect on ∆ E values [5, 6]. In particular, the most stable benzene dimer has a T -shape configuration [7, 8], typical also of the dimers of other arenes [8, 9], and pentacene molecules have a herringbone crystal packing [6]. Previously, we found that polyacene chains 2 ( n = 1–6) can be stabilized in the form of sandwich structures 4 interlayered with lithium (M = Li) or transition metal atoms [10]. Double polyacene chains 4 are characterized by narrower energy gaps between the frontier orbitals and, hence, by better current-conducting properties [2, 11]. Polyacene structures can have magnetic properties [12]. Another approach to the formation of stable polyacene aggregates, suggested in this work, is based on binding of radical pairs of polyacene structures 5 , mimicking the graphene structural motif. Great interest in graphene systems stems from potential possibilities of using them as materials for molecular electronics [13]. M M

A new electronic structure method for doublet states: Configuration interaction in the space of ionized 1h and 2h1p determinants

An implementation of gradient and energy calculations for configuration interaction variant of equation-of-motion coupled cluster with single and double substitutions for ionization potentials (EOM-IP-CCSD) is reported. The method (termed IP-CISD) treats the ground and excited doublet electronic states of an N-electron system as ionizing excitations from a closed-shell N+1-electron reference state. The method is naturally spin adapted, variational, and size intensive. The computational scaling is N(5), in contrast with the N(6) scaling of EOM-IP-CCSD. The performance and capabilities of the new approach are demonstrated by application to the uracil cation and water and benzene dimer cations by benchmarking IP-CISD against more accurate IP-CCSD. The equilibrium geometries, especially relative differences between different ionized states, are well reproduced. The average absolute errors and the standard deviations averaged for all bond lengths in all electronic states (58 values in total) are 0.014 and 0.007 A, respectively. IP-CISD systematically underestimates intramolecular distances and overestimates intermolecular ones, because of the underlying uncorrelated Hartree-Fock reference wave function. The IP-CISD excitation energies of the cations are of a semiquantitative value only, showing maximum errors of 0.35 eV relative to EOM-IP-CCSD. Trends in properties such as dipole moments, transition dipoles, and charge distributions are well reproduced by IP-CISD.

An efficient algorithm for the density-functional theory treatment of dispersion interactions

The quasi-self-consistent-field dispersion-corrected density-functional theory formalism (QSCF-DC-DFT) is developed and presented as an efficient and reliable scheme for the DFT treatment of van der Waals dispersion complexes, including full geometry optimizations and frequency calculations with analytical energy derivatives in a routine way. For this purpose, the long-range-corrected Perdew-Burke-Ernzerhof exchange functional and the one-parameter progressive correlation functional of Hirao and co-workers are combined with the Andersson-Langreth-Lundqvist (ALL) long-range correlation functional. The time-consuming self-consistent incorporation of the ALL term in the DFT iterations needed for the calculation of forces and force constants is avoided by an a posteriori evaluation of the ALL term and its gradient based on an effective partitioning of the coordinate space into global and intramonomer coordinates. QSCF-DC-DFT is substantially faster than SCF-DC-DFT would be. QSCF-DC-DFT is used to explore the potential energy surface (PES) of the benzene dimer. The results for the binding energies and intermolecular distances agree well with coupled-cluster calculations at the complete basis-set limit. We identify 16 stationary points on the PES, which underlines the usefulness of analytical energy gradients for the investigation of the PES. Furthermore, the inclusion of analytically calculated zero point energies reveals that large-amplitude vibrations connect the eight most stable benzene dimer forms and make it difficult to identify a dominating complex form. The tilted T structure and the parallel-displaced sandwich form have the same D(0) value of 2.40 kcal/mol, which agrees perfectly with the experimental value of 2.40+/-0.40 kcal/mol.

Borazine and Benzene Homo- and Heterodimers

The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) and one borazine (bor) molecule are investigated using MP2, SCS-MP2, and CCSD(T) theories in conjunction with basis sets of up to quadruple-zeta quality. Dimer geometries were completely optimized using the resolution of the identity approximation of MP2 with a QZVPP basis set and characterized by computation of harmonic vibrational frequencies using triple-zeta basis sets. While significant higher order correlation effects beyond MP2 are important for the benzene dimer, these are very small for the borazine dimer and intermediate for the heterodimer. The spin-component scaling (SCS) correction of MP2 produces binding energies for the borazine dimer that are too low but yields very good agreement with CCSD(T) for the heterodimer. The decrease in the intermolecular distance in the sandwich (S) configurations from bz(2) via bz-bor to bor(2) is accompanied by an increased binding energy and a change from second-order stationary points to a minimum for bor(2). The T isomer is less stable than the S configuration for bor(2), but it is preferred over the S and a parallel-displaced (PD) arrangement in the heterodimer. The following order of stability is obtained for the minima at the extrapolated CCSD(T) level: T(bz-bor) > S(bor(2)) > PD(bz-bor) > PD(bor(2)) > T(bor(2)) > PD(bz(2)). The most stable isomer at all levels of theory, T(bz-bor), features a NH...pi interaction.