Reactivity differences between α,β-unsaturated carbonyls and hydrazones investigated by experimental and theoretical electron density and electron localizability analyses

It is still a challenge to predict a compound's reactivity from its ground-state electronic nature although Bader-type topological analyses of the electron density (ED) and electron localizability indicator (ELI) give detailed and useful information on electron concentration and electron-pair localization, respectively. Both ED and ELI can be obtained from theoretical calculations as well as high-resolution X-ray diffraction experiments. Besides ED and ELI descriptors, the delocalization index is used here; it is likewise derived from theoretical calculations as well as from experimental X-ray results, but in the latter case, demonstrated here for the first time. We investigate α,β-unsaturated carbonyl and hydrazone compounds because resonance exhibited by these compounds in the electronic ground-state determines their reactive behavior. The degree of resonance as well as the reactivity contrast are quantified with the electronic descriptors. Moreover, competitive mesomeric substituent effects are studied using the two biologically important compounds acrolein and acrylamide. The reactivity differences predicted from the analyses are in line with the known reactivity of these compounds in organic synthesis. Hence, the capability of the ED and ELI for rationalizing and predicting different and competing substituent effects with respect to reactivity is demonstrated.

Effect of electron-withdrawing substituents on the epoxide ring: an experimental and theoretical electron density analysis of a series of epoxide derivatives

A series of acceptor-substituted epoxide derivatives is scrutinized by means of experimental and theoretical electron-density investigations. Due to the possibility of nucleophilic ring-opening, the epoxide ring is not only a very useful functional group in organic synthesis, but acceptor-substituted epoxides are valuable building blocks for the design of protease inhibitors. Therefore, the electron-density analysis in this work focuses on two main aspects that can contribute to rational drug design: (i) the quantification of the electron-withdrawing substituent effects on the epoxide ring and (ii) the intermolecular interactions involving the epoxide ring in combination with different substituents. It can be shown that the electron-withdrawing properties of the substituents cause an elongation of the C-C bonds in the epoxide rings and the loss of electron density can be measured by an analysis of critical points, atomic charges, and the source function. The different strengths of the substituents are reflected in these properties. Covalent and electrostatic contributions to the intermolecular interactions and thus the lattice energies are depicted on different molecular surfaces.

Real-space indicators for chemical bonding. Experimental and theoretical electron density studies of four deltahedral boranes

In an approach combining high-resolution X-ray diffraction at low temperatures with density functional theory calculations, two closo-borates, B(12)H(12)(2-) (1) and B(10)H(10)(2-) (2), and two arachno-boranes, B(10)H(12)L(2) [L = amine (3) or acetonitrile (4)], were analyzed by means of the atoms-in-molecules (AIM) theory and electron localizability indicator (ELI-D). The two-electron three-center (2e3c) bonds of the borane cages are investigated with the focus on real-space indicators for chemical bonding and electron delocalization. In compound 2, only two of the three expected bond critical points (bcp's) are found. However, a weakly populated ELI-D basin is found for this pair of adjacent B atoms and the delocalization index and the Source contributions are on the same order of magnitude as those for the other pairs. The opposite situation is found in the arachno-boranes, where no ELI-D basins are found for two types of B-B pairs, which, in turn, exhibit a bcp. However, again the delocalization index is on the same order of magnitude for this bonding interaction. The results show that an unambiguous real-space criterion for chemical bonding is not given yet for this class of compounds. The arachno-boranes carry a special B-B bond, which is the edge of the crown-shaped molecule. This bond is very long and extremely curved inward the B-B-B ring. Nevertheless, the corresponding bond ellipticity is quite small and the ELI-D value at the attractor position of the disynaptic valence basin is remarkably larger than those for all other B-B valence basins. Furthermore, the value of the ED is large in relation to the B-B bond length, so that only this bond type does not follow a linear relationship of the ED value at the bcp versus B-B bond distances, which is found for all other B-B bcp's. The results indicate that both 2e2c and 2e3c bonding play a distinct role in borane chemistry.

How to easily replace the independent atom model - the example of bergenin, a potential anti-HIV agent of traditional Asian medicine

Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kalpha room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree-Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.

Transferability and reproducibility in electron-density studies--bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine

In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.

Experimental electron density study of ethylene oxide at 100 K

The experimental electron density of ethylene oxide was derived from a multipole refinement of 100 K X-ray data and complemented by density-functional calculations at experimental and optimized geometry. Atomic and bond-topological properties were derived using the atoms-in-molecules (AIM) formalism. The high strain in the three-membered ring molecule is mainly expressed by the high ellipticities of the three bonds in this ring, while the bond paths are only slightly bent for the C—C bond, but are virtually straight for the C—O bond.

Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data

From a high-resolution X-ray data set (sin θ/λ = 1.1 Å−1) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties – about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.

Supramolecular Silanol Chemistry in the Gas Phase. Topological (AIM) and Population (NBO) Analyses of Hydrogen-Bonded Complexes between H3SiOH and Selected O- and N-Acceptor Molecules

Hydrogen bonding of the type SiO-H...A (A = O, N) has been studied in the gas phase for simple H3SiOH.acceptor complexes with the acceptor molecules being O(H)SiH3, OH2, O(H)CH3, O(CH3)2, O(CH3)SiH3, O(SiH3)2, NH3, N(CH3)H2, N(CH3)2H, N(CH3)3, N(CH3)2C6H5, and NC5H5, respectively, at the B3LYP/6-311+(2d,p) level of theory, using Bader's atoms in molecules (AIM) and Weinhold's natural bond orbital (NBO) methodology. For all complexes (except H3SiOH.N(CH3)2C6H5) the complex energy Eadd. is a good estimate for the hydrogen bond energy EHB, which is generally higher in N-acceptor complexes (-5.52 to -7.17 kcal mol-1) than in O-acceptor complexes (-2.09 to -5.06 kcal mol-1). In case of H3SiOH.N(CH3)2C6H5, EHB and Eadd. differ by the energy associated with the loss of n(N)-->pi conjugation in N(CH3)2C6H5 upon complex formation. EHB shows no correlation with O...A distances and the red shifts Deltanu(OH) of the OH-stretching vibrations when different acceptors are compared, although both parameters are commonly used to estimate the strength of the hydrogen bond from spectroscopic and diffraction data. A good linear correlation of the hydrogen bond energy EHB has been established with parameters derived from the AIM and NBO analyses, namely, the electron densities rho(HA) and rho(OH) at the H...A and O-H bond critical points (BCPs) and the NLMO bond orders BONLMO(HA) of the H...A bonds of the H3SiOH.acceptor complexes as well as the change of natural charges DeltaqNPA(O) at the O-donor atom upon H3SiOH.acceptor complex formation. Hydrogen bonding of the type SiO-H...A (A = O, N) has been also studied in the related cyclic multiple H3SiOH.acceptor complexes (H3SiOH)3, (H3SiOH)2.NC5H5, and (H3SiOH)4, respectively, at the same level of theory. Cooperative hydrogen bonding is evident for all cyclic multiple H3SiOH.acceptor complexes, whereby the strongest concomitant strengthening of the hydrogen bonds is observed for (H3SiOH)4 and (H3SiOH)2.NC5H5.