Dmitry I. Sharapa

Conformationally restricted GABA analogs: from rigid carbocycles to cage hydrocarbons

GABA was discovered to play an important role as the major inhibitory neurotransmitter in the adult mammalian CNS 60 years ago. The conformational flexibility of GABA is important for its biological function, as it has been found to bind to different receptors with different conformations. In an effort to increase the lipophilicity and to reduce conformational flexibility of GABA itself, a polycyclic or cage hydrocarbon framework can be introduced into the 3D structure of GABA in order to better control the binding. This article explores the available synthetic methods, properties and activity of carbocyclic (cyclopropanes, cyclobutanes and cyclohexanes) and cage (adamantane and others) hydrocarbons - analogs of GABA with conformationally rigid carbon skeletons.

Accurate Intermolecular Potential for the C60 Dimer: The Performance of Different Levels of Quantum Theory

The self-assembly of molecular building blocks is a promising route to low-cost nanoelectronic devices. It would be very appealing to use computer-aided design to identify suitable molecules. However, molecular self-assembly is guided by weak interactions, such as dispersion, which have long been notoriously difficult to describe with quantum chemical methods. In recent years, several viable techniques have emerged, ranging from empirical dispersion corrections for DFT to fast perturbation and coupled-cluster theories. In this work, we test these methods for the dimer of the prototypical building block for nanoelectronics, C60-fullerene. Benchmark quality data is obtained from DFT-based symmetry-adapted perturbation theory (SAPT), the adiabatic-connection fluctuation dissipation (ACFD) theorem using an adiabatic LDA kernel, and domain-based local pair natural orbital (DLPNO) coupled-pair and coupled-cluster methods. These benchmarks are used to evaluate economical dispersion-corrected DFT methods, double-hybrid DFT functionals, and second-order Møller-Plesset theory. Furthermore, we provide analytical fits to the benchmark interaction curves, which can be used for a coarse-grain description of fullerene self-assembly. These analytical expressions differ significantly from those reported previously based on bulk data.

Highly Regioselective Alkylation of Hexabenzocoronenes - Fundamental Insights into the Covalent Chemistry of Graphene

Abstract Hexa‐peri‐hexabenzocoronides (HBC) was successfully used as a model system for investigating the complex mechanism of the reductive functionalization of graphene. The well‐defined molecular HBC system enabled deeper insights into the mechanism of the alkylation of reductively activated nanographenes. The separation and complete characterization of alkylation products clearly demonstrate that nanographene functionalization proceeds with exceptionally high regio‐ and stereoselectivities on the HBC scaffold. Experimental and theoretical studies lead to the conclusion that the intact basal graphene plane is chemically inert and addend binding can only take place at either preexisting defects or close to the periphery.

Application of classical simulations for the computation of vibrational properties of free molecules

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

Cubic C8: an observable allotrope of carbon?

Ab initio and DFT calculations are used to investigate the structure, electronic properties, spectra and reactivity of cubic C8 , which is predicted to be aromatic according to Hirschs rule. Although highly strained and with a small amount of diradical character, the carbon cube represents a surprisingly deep minimum and should therefore be observable as an isolated molecule. It is, however, predicted to be very reactive, both with itself and triplet oxygen. Calculated IR, Raman, and UV/Vis spectra are provided to aid identification of cubic C8 should it be synthesized.

Nitroxoline Molecule: Planar or Not? A Story of Battle between π–π Conjugation and Interatomic Repulsion

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO2 group from the closest hydrogen, which overcomes the energy gain from the π-π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy

A series of semiempirical PM6* and PM7 methods has been tested in reproducing relative conformational energies of 27 realistic-size complexes of 16 different transition metals (TMs). An analysis of relative energies derived from single-point energy evaluations on density functional theory (DFT) optimized conformers revealed pronounced deviations between semiempirical and DFT methods, indicating a fundamental difference in potential energy surfaces (PES). To identify the origin of the deviation, we compared fully optimized PM7 and respective DFT conformers. For many complexes, differences in PM7 and DFT conformational energies have been confirmed often manifesting themselves in false coordination of some atoms (H, O) to TMs and chemical transformations/distortion of coordination center geometry in PM7 structures. Despite geometry optimization with fixed coordination center geometry leading to some improvements in conformational energies, the resulting accuracy is still too low to recommend explored semiempirical methods for out-of-the-box conformational search/sampling: careful testing is always needed.

Dispersion and polar flattening: noble gas–halogen complexes

AbstractHigh-level ab initio calculations on the complexes between noble gas atoms (He, Ne, Ar, Kr, and Xe) and dihalogen molecules (F2, Cl2, Br2, and I2) reveal trends, both in interaction energies and the energy difference between the linear and T-shaped structures, that can be explained well in terms of dispersion interactions enhanced by polar flattening of the halogens. The partial discrepancies with experimental findings are discussed. Graphical abstractThe molecular electrostatic potential (red positive, blue negative) of Cl2...Br2 projected onto the 0.003 a.u. isodensity surface.

Charge Transport in Organic Materials: Norm-Conserving Imaginary Time Propagation with Local Ionization Energy as the External Potential

An additional charge carrier described as its wave function is propagated in imaginary time using stepwise matrix multiplication and a correction to ensure that the simulation is norm-conserving. The propagation Hamilton operator uses the local ionization energy of a rubrene single crystal, calculated with semiempirical molecular orbital theory, as an external potential for holes to model the interaction with the underlying molecular structure. Virtual electrodes are modeled by setting the potentials in the appropriate areas to constant values with the difference corresponding to the source-drain voltage. Although imaginary time cannot be interpreted directly as time, the simulated gate-dependent imaginary transfer rate is in acceptable qualitative agreement with the experimentally measured gate-dependent hole-transfer rate through a rubrene single crystal.

Synthesis, Structural Characterization, and Crystal Packing of the Elusive Pentachlorinated Azafullerene C59NCl5

We report on the synthesis and the structure elucidation of the elusive azafullerene pentachloride C59 NCl5 , which was obtained by high temperature halogenation of (C59 N)2 . The exceptionally strong host-guest interaction of the title compound in the solid is discussed.