Molecular Clusters of pi-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Solvent effects in the GIAO-DFT calculations of the 15N NMR chemical shifts of azoles and azines

The calculation of (15)N NMR chemical shifts of 27 azoles and azines in 10 different solvents each has been carried out at the gauge including atomic orbitals density functional theory level in gas phase and applying the integral equation formalism polarizable continuum model (IEF-PCM) and supermolecule solvation models to account for solvent effects. In the calculation of (15)N NMR, chemical shifts of the nitrogen-containing heterocycles dissolved in nonpolar and polar aprotic solvents, taking into account solvent effect is sufficient within the IEF-PCM scheme, whereas for polar protic solvents with large dielectric constants, the use of supermolecule solvation model is recommended. A good agreement between calculated 460 values of (15)N NMR chemical shifts and experiment is found with the IEF-PCM scheme characterized by MAE of 7.1 ppm in the range of more than 300 ppm (about 2%). The best result is achieved with the supermolecule solvation model performing slightly better (MAE 6.5 ppm).

Competitive pi interactions and hydrogen bonding within imidazolium ionic liquids

In this paper we have explored the structural and energetic landscape of potential π(+)-π(+) stacked motifs, hydrogen-bonding arrangements and anion-π(+) interactions for gas-phase ion pair (IP) conformers and IP-dimers of 1,3-dimethylimidazolium chloride, [C1C1im]Cl. We classify cation-cation ring stacking as an electron deficient π(+)-π(+) interaction, and a competitive anion on-top IP motif as an anion-donor π(+)-acceptor interaction. 21 stable IP-dimers have been obtained within an energy range of 0-126 kJ mol(-1). The structures have been found to exhibit a complex interplay of structural features. We have found that low energy IP-dimers are not necessarily formed from the lowest energy IP conformers. The sampled range of IP-dimers exhibits new structural forms that cannot be recovered by examining the ion-pairs alone, moreover the IP-dimers are recovering additional key features of the local liquid structure. Including dispersion is shown to impact both the relative energy ordering and the geometry of the IPs and IP-dimers, however the impact is found to be subtle and dependent on the underlying functional.

Cation-π interactions in protonated phenylalkylamines

Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.

Anisotropic charge distribution and anisotropic van der Waals radius leading to intriguing anisotropic noncovalent interactions

Although group (IV–VII) nonmetallic elements do not favor interacting with anionic species, there are counterexamples including the halogen bond. Such binding is known to be related to the charge deficiency because of the adjacent atom's electron withdrawing effect, which creates σ/π-holes at the bond-ends. However, a completely opposite behavior is exhibited by N₂ and O₂, which have electrostatically positive/negative character around cylindrical-bond-surface/bond-ends. Inspired by this, here we elucidate the unusual features and origin of the anisotropic noncovalent interactions in the ground and excited states of the 2^nd and 3^rd row elements belonging to groups IV–VII. The anisotropy in charge distributions and van der Waals radii of atoms in such molecular systems are scrutinized. This provides an understanding of their unusual molecular configuration, binding and recognition modes involved in new types of molecular assembling and engineering. This work would lead to the design of intriguing molecular systems exploiting anisotropic noncovalent interactions.

Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene

IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).

Double-hybrid density functionals free of dispersion and counterpoise corrections for non-covalent interactions

We have optimized two double-hybrid density functionals (DHDFs) within the frameworks of B2PLYP and mPW2-PLYP against the S22B database. These two functionals are denoted as B2NC-PLYP and mPW2NC-PLYP, where "NC" represents noncovalent interaction. The DHDFs of B2NC-PLYP and mPW2NC-PLYP are optimized free of dispersion and counterpoise corrections with triple-ζ quality basis sets. Combined with the aug-cc-pVTZ basis set, these two functionals are further assessed with the S66 database. According to our computations, both the B2NC-PLYP and mPW2NC-PLYP functionals seem to be competent for investigating noncovalent interactions. Note that the triple-ζ quality basis sets with adequate polarization and diffuse functions should be employed for practical applications. However, different exchange and correlation functionals may be selected and/or modified to reduce the amount of the Fock-exchange in the future.

Precise tuning of cationic cyclophanes toward highly selective fluorogenic recognition of specific biophosphate anions

Cationic cyclophanes with bridging and spacer groups possess well-organized semirigid cavities and are able to encapsulate and stabilize anionic species through diverse molecular interactions. We highlight the precise tuning of functionalized cyclophanes toward selective recognition of AMP, GTP, and pyrophosphate (PPi) using fluorescence, NMR spectroscopy, and density functional theory (DFT).

Selective detection of guanosine-5'-triphosphate and iodide by fluorescent benzimidazolium-based cyclophanes

New fluorescent benzimidazolium-based receptors selectively display the effective fluorescence quenching effect for biologically important anions, GTP and I(-), in aqueous solution of physiological pH 7.4. These affinities can be attributed to the strong ionic H-bonding along with additional interactions of fluorophore moieties with the nucleic base of GTP and I(-).

Blind prediction of binding affinities for charged supramolecular host-guest systems: achievements and shortcomings of DFT-D3

Association free energies ΔGa are calculated for two different types of host-guest systems, the rigid cucurbit[7]uril (CB7) and the basket shaped octa-acid (OA), and a number of charged guest molecules each by quantum chemical methods from first principles in the context of a recent blind test challenge (SAMPL4). For CB7, the overall agreement between theory and experiment is excellent. In comparison with all other submitted calculated relative ΔGa,rel values for this part of the blind test, our results ranked on top. Modeling the binding free energy in the case of the OA host mainly suffers from the problem that the binding situation is undefined with respect to the charge state and due to its intrinsic flexibility the host-guest complex is not represented well by a single configuration, but qualitative features of the binding process such as the proper binding orientation and the order of magnitude of ΔGa are represented in accord with the experimental expectations even though an accurate ranking is not possible.

Stable platinum nanoclusters on genomic DNA-graphene oxide with a high oxygen reduction reaction activity

Nanosize platinum clusters with small diameters of 2–4 nm are known to be excellent catalysts for the oxygen reduction reaction. The inherent catalytic activity of smaller platinum clusters has not yet been reported due to a lack of preparation methods to control their size (<2 nm). Here we report the synthesis of platinum clusters (diameter ≤1.4 nm) deposited on genomic double-stranded DNA–graphene oxide composites, and their high-performance electrocatalysis of the oxygen reduction reaction. The electrochemical behaviour, characterized by oxygen reduction reaction onset potential, half-wave potential, specific activity, mass activity, accelerated durability test (10,000 cycles) and cyclic voltammetry stability (10,000 cycles) is attributed to the strong interaction between the nanosize platinum clusters and the DNA–graphene oxide composite, which induces modulation in the electronic structure of the platinum clusters. Furthermore, we show that the platinum cluster/DNA–graphene oxide composite possesses notable environmental durability and stability, vital for high-performance fuel cells and batteries.

Platinum nanoclusters are well-known catalysts for the oxygen reduction reaction, although the performance of clusters smaller than 2 nm is poorly studied. Here, the authors report 1.4 nm platinum clusters supported on DNA–graphene oxide composites and demonstrate promising electrochemical activity and stability.

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Secondary stereocontrolling interactions in chiral Brønsted acid catalysis: study of a Petasis–Ferrier-type rearrangement catalyzed by chiral phosphoric acids

Guided by computational studies, the involvement of non-classical C–H⋯O hydrogen bonds and π–π stacking interactions were found to be crucial for high stereocontrol in a chiral phosphoric acid-catalyzed reaction.

Supramolecular electron donor–acceptor complexes formed by perylene diimide derivative and conjugated phenazines

The nanostructure and binding mode of the perylene diimide–phenazine complex can be modulated by the phenazine derivative substituents.

Characterization of NTCDI supra-molecular networks on Au(111); combining STM, IR and DFT calculations

In this paper, we investigate the self-organization of NTCDI molecules on Au(111) surface by combining Density Functional Theory (DFT) and experiments based on scanning tunneling microscopy (STM) and infrared spectroscopy measurements.

A combined experimental and computational study of supramolecular assemblies in ternary copper(ii) complexes with a tetradentate N4donor Schiff base and halides

Three new copper(ii) Schiff base complexes have been prepared and characterized. DFT calculations were employed to estimate the contribution of different non-covalent interactions in the extended supra-molecular networks.

Fourier transform microwave spectrum of the nitrogen molecule-ethylene oxide complex: intracomplex motions

The rotational spectra of the N2-ethylene oxide (EO) complex were measured in the frequency region from 4 to 27 GHz by Fourier transform microwave spectroscopy, paying particular attention to intracomplex motions. The isotopologues with enriched (15)N2 or (15)NN as a moiety were also investigated. We have observed spectra of a strong/weak pair for each of the ortho and para states of the (14)N2-EO and (15)N2-EO species, which indicated that the complex existed in four distinct states. We interpreted, on the basis of the observed relative intensities, that these states were generated primarily by the exchange of the nitrogen atoms of the N2 moiety, followed by that of the two CH2 groups in the EO molecule. The (15)NN-EO species was found to consist of two isomers, one with the (15)N in the inner expressed as N(15)N-EO and the other in the outer position designated as (15)NN-EO, and the spectra of both isomers were accompanied by one weak set of satellites. The observed spectra were rotationally assigned by using sum rules and were analyzed by the asymmetric-rotor program of S-reduction, with the standard deviation of less than 10 kHz. We have found some of the molecular parameters like A, D(JK), and D(K) to be correlated between the two pairs of the spectra, and also, to much less extent, between the strong and weak members. The differences in these molecular parameters between the four sets were explained by the first-order Coriolis interaction between the "ground" and "excited" states generated by a combination of the two internal motions corresponding to the exchanges of the equivalent atoms and/or groups in the N2 and EO constituents of the complex. These internal motions were simulated by the 2-fold internal rotations of the two moieties. We have carried out ab initio molecular orbital calculations at the level of MP2 with basis sets 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ, to complement the information on the intracomplex motions obtained from the observed rotational spectra.