Paweł Lipkowski

Characteristics of X-H · · · π Interactions: Ab Initio and QTAIM Studies

The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.

Electronic Structure, Bonding, Spectra, and Linear and Nonlinear Electric Properties of Ti@C28

The potential energy surface (PES) of Ti@C(28) has been revisited, and the stationary points have been carefully characterized. In particular, the C(2v) symmetry structure considered previously turns out to be a transition state lying 2.3 kcal/mol above the ground state of C(3v) symmetry at the MP2/6-31G(d) level. A large binding energy of 181.3 kcal/mol is found at the ROMP2/6-31G(d) level. Topological analysis of the generalized Ti@C(28) density reveals four bond paths between Ti and carbon atoms of the host. The character of all four contacts corresponds to a partially covalent closed shell interaction. UV-vis, IR, and Raman spectra are calculated and compared with C(28)H(4). The dipole moment and the static electronic and double harmonic vibrational (hyper)polarizabilities have been obtained. Distortion of the fullerene cage due to encapsulation leads to nonzero diagonal components of the electronic first hyperpolarizability β, and to an increase in the diagonal components of the electronic polarizability α and second hyperpolarizability γ. However, introduction of the Ti atom causes a comparable or larger reduction in most cases due to localized bonding interactions. At the double harmonic level, the average vibrational β is much larger than its electronic counterpart, but the opposite is true for α and for the contribution to γ that has been calculated. There is also a very large anharmonic (nuclear relaxation) contribution to β which results from a shallow PES with four minima separated by very low barriers. Thus, the vibrational γ (and α) may, likewise, become much larger when anharmonicity is taken into account.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

On the Nature of Intermolecular Interactions in Nucleic Acid Base-Amino Acid Side-Chain Complexes

Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated using the second-order Møller-Plesset perturbation theory and coupled clusters approach with single and double excitations, while their components have been determined by means of a hybrid variational-perturbational decomposition scheme. Additionally, the topological analysis of an electron density distribution of the studied complexes has been performed. In the case of all of the studied neutral complexes, the main source of stabilization is the delocalizaction energy associated with the electron density deformation upon the interaction which contributes almost half of the total interaction energy. Furthermore, analysis of the interaction induced difference density maps of complexes containing neutral amino acid side chains reveals that the delocalization component involves the electron density changes localized in the double-hydrogen-bonded ring structures. A relatively good correlation between the sum of densities at hydrogen-bond critical points and the Hartree-Fock intermolecular interaction energy components (electrostatic, delocalization, and exchange) has been observed for the two independently considered sets of complexes, containing positively charged and neutral amino acid side chains.

Solvatochromism of BODIPY-Schiff Dye

A boron-dipyrrin chromophore connected with an o-hydroxyaryl aldimine by a diazo bridge (BODIPY-Schiff dye) has been developed. The photophysical properties of the BODIPY-Schiff dye have been investigated with UV, steady-state, and time-resolved fluorimetry. The spectral features have been characterized with respect to density functional theory and time-dependent density functional theory. The conformational analysis of the studied compound has been accomplished both in the ground and excited states. A scheme of the processes occurring in the BODIPY-Schiff dye has been proposed.

Electron-topological, energetic and π-electron delocalization analysis of ketoenamine-enolimine tautomeric equilibrium

The ketoenamine-enolimine tautometic equilibrium has been studied by the analysis of aromaticity and electron-topological parameters. The influence of substituents on the energy of the transition state and of the tautomeric forms has been investigated for different positions of chelate chain. The quantum theory of atoms in molecules method (QTAIM) has been applied to study changes in the electron-topological parameters of the molecule with respect to the tautomeric equilibrium in intramolecular hydrogen bond. Dependencies of the HOMA aromaticity index and electron density at the critical points defining aromaticity and electronic state of the chelate chain on the transition state (TS), OH and HN tautomeric forms have been obtained.

Comparison of resonance assisted and charge assisted effects in strengthening of hydrogen bonds in dipyrrins.

This paper deals with the study of two types of hydrogen bonding: a quasi-aromatic hydrogen bonding in dipyrromethene and the ionic one in dipyrromethane. The study focuses on two phenomena-the proton transfer process and tautomeric equilibrium. Metric parameters and spectroscopic assignments have been calculated; this allowed a further comparison of spectral features calculated with four methods (Car-Parrinello molecular dynamics (CPMD), ab initio, density functional theory (DFT), and numerical calculation of anharmonic vibrational levels via a solution of the corresponding 1D Schrödinger equation). A significant dynamics of the bridged proton and bent vibration of pyrrole fragments in dipyrromethane have been exposed by the CPMD calculations. The prevailing of the ionic effect over the π-electronic coupling in the strengthening of the hydrogen bonding has been shown on the basis of the calculated structural, electron-topological, and spectral data as well as potential energy surface (PES). The analysis of the aromaticity and electronic state of pyrrole and chelate moieties depending on the tautomeric equilibrium by the quantum theory of atoms in molecules (QTAIM) method was conducted. The principle divergence in the behavior of aromaticity of the chelate chains in the analyzed compounds was demonstrated.

Impact of the Keto–Enol Tautomeric Equilibrium on the BODIPY Chromophore

An intramolecular tautomeric fluorescent BODIPY sensor has been designed and synthesized. The obtained BODIPY dye is a combination of the 4-bora- 3a, 4a-diaza- s-indacene core and a diketone fragment. The study of conformational equilibria in the ground and excited states has been completed for a broad range of solvent polarity by steady state and NMR methods as well as by DFT and TD-DFT calculations. The interpretation of the unique emission observed in hydrogen bond accepting solvents upon the excitation of the fluorescent dye in the S0-S2 transition has been accomplished. The Jablonski diagram has been analyzed for the observed processes in the BODIPY dye studied on the basis of DFT and TD-DFT calculations.

Photochromic cycle of 2′-hydroxyacetophenone azine studied by absorption and emission spectroscopy in different solvents

This paper reports on the investigations of the synthesized di-(o-hydroxyaryl ketoimine) compound by the steady state absorption and emission techniques as well as picosecond time resolved emission and femtosecond transient absorption methods in different solvents. The results of the experimental observation have been supported by the theoretical DFT and TD-DFT calculations. The theoretical data have revealed the completed influence of the environmental polarity on particular conformers of studied compound. Dependencies between the activation rate constant and polarizability function as well as Kamlet-Abbond-Taft hydrogen-bonding parameter have been obtained in different solvent. The mechanism of photodynamic changes of di-(o-hydroxyaryl ketoimine) is presented.