[Show abstract][Hide abstract] ABSTRACT: The structural characterization of tetraphenylmethane tetrakis-4-phosphonic acid (4a) and its closely related Si-analogue tetraphenylsilane tetrakis-4-phosphonic acid (4b) is reported. Crystals of 4a, obtained by crystallization at 165 °C from water under hydrothermal conditions, comprise a dense threefold interpenetrated hydrogen-bonded network. Lower calculated density cocrystals 4b·4 EtOH, attained by recrystallization from ethanol, give rise to a porous honeycomb network that shows no interpenetration. Isolated from the mother liquor, the encapsulated ethanol is rapidly lost under ambient conditions leaving amorphous 4b. While the amorphous 4b is reasonably soluble in methanol, crystalline 4a is virtually insoluble in common organic solvents.
[Show abstract][Hide abstract] ABSTRACT: In the present study we use quantum-chemical calculations to investigate how the reactivity of vinyl sulfone-based compounds can be modified from an irreversible to a reversible reaction with thiols. Based on the predictions from theory, an array of nine different vinyl sulfones with systematically varying substitution pattern was synthesized and their crystal structures were determined. Subsequent Hirshfeld surface analyses employing the principle of electrostatic complementarity aid the understanding of the crystal packing of the synthesized compounds. Reactivity studies against the nucleophile 2-phenylethanethiol mirror the properties predicted by the quantum-chemical computations in solution.
No preview · Article · Jun 2015 · New Journal of Chemistry
[Show abstract][Hide abstract] ABSTRACT: The paper collects the answers of the authors to the following questions: " What is the significance of topological approach? Can new chemical concepts be found by a topological approach? What is the status of a chemical concept within a topological approach? Should topological approaches provide measurable quantities? Is it possible to predict the outcome of a topological approach without performing a calculation on a computer? What are new domains for which topological approaches would be useful?
Full-text · Article · Feb 2015 · Computational and Theoretical Chemistry
[Show abstract][Hide abstract] ABSTRACT: The energy of interaction between molecules is commonly expressed in terms of four key components: electrostatic, polarization, dispersion, and exchange-repulsion. Using monomer wave functions to obtain accurate estimates of electrostatic, polarization, and repulsion energies along with Grimme’s dispersion corrections, a series of energy models are derived by fitting to dispersion-corrected DFT energies for a large number of molecular pairs extracted from organic and inorganic molecular crystals. The best performing model reproduces B3LYP-D2/6-31G(d,p) counterpoise-corrected energies with a mean absolute deviation (MAD) of just over 1 kJ mol-1 but in considerably less computation time. It also performs surprisingly well against benchmark CCSD(T)/CBS energies, with a MAD of 2.5 kJ mol-1 for a combined data set including Hobza’s X40, S22, A24, and S66 dimers. Two of these energy models, the most accurate and the fastest, are expected to find widespread application in investigations of molecular crystals.Keywords: dispersion-corrected DFT; molecular crystals; intermolecular interaction; dispersion; electrostatic; interaction energy
No preview · Article · Dec 2014 · Journal of Physical Chemistry Letters
[Show abstract][Hide abstract] ABSTRACT: After a long history of use as a prototype cysteine protease inhibitor, the crystal structure of loxistatin acid (E64c) is finally determined experimentally using intense synchrotron radiation, providing insight into how the inherent electronic nature of this protease inhibitor molecule determines its biochemical activity. Based on the striking similarity of its intermolecular interactions with those observed in a biological environment, the electrostatic potential of crystalline E64c is used to map the characteristics of a pseudo-enzyme pocket.
No preview · Article · Nov 2014 · New Journal of Chemistry
[Show abstract][Hide abstract] ABSTRACT: High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of
′ > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O—H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (
) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment,
the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.
No preview · Article · Sep 2014 · Acta Crystallographica Section A: Foundations and Advances
[Show abstract][Hide abstract] ABSTRACT: Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
[Show abstract][Hide abstract] ABSTRACT: The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques . In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.
No preview · Article · Aug 2014 · Acta Crystallographica Section A: Foundations and Advances
[Show abstract][Hide abstract] ABSTRACT: X-ray wavefunction refinement (XWR) is a way of modeling the total aspherical electron density from an X-ray diffraction experiment on a single crystal of a molecular compound. It is a combination of existing quantum-crystallographical techniques: In the first step, geometry is determined using Hirshfeld atom refinement, which is based on a stockholder partitioning of quantum-mechanical aspherical electron densities. In the second step, the same wavefunction is fitted to the experimental data to reproduce the diffraction pattern and simultaneously minimize the molecular energy. The XWR protocol involves embedding the molecule into a field of point charges and dipoles as well as termination strategies to avoid overfitting. Results from an X-ray wavefunction refinement are not restricted to the analysis of electron density: the full reconstructed density matrix is available. Therefore, chemical problems can be tackled with suitable tools for any given question including, e.g., experimentally derived bond orders, electron-pair localisation information, or energetics. We will present first applications of this protocol for a selection of organic (hydrogen maleate salts, sulfur-containing protease inhibitors) and inorganic (siloxanes, sulfur dioxide) compounds, for which we measured high-resolution low-temperature X-ray diffraction data at various synchrotron facilities. We will show geometry improvements, anisotropic displacement parameters for hydrogens, anharmonic motion parameters for sulfur and chlorine atoms, and improved total electron-density distributions in comparison to results from multipole modeling. Moreover, we will discuss the contribution of the experimental data to the final constrained wavefunction (defect density) and demonstrate how the experimentally derived orbital-based descriptors assist in solving fundamental chemical problems.
No preview · Article · Aug 2014 · Acta Crystallographica Section A: Foundations and Advances
[Show abstract][Hide abstract] ABSTRACT: "Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR , Invariom refinement , time-of-flight Neutron diffraction and the TLS+ONIOM approach . In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."
No preview · Article · Aug 2014 · Acta Crystallographica Section A: Foundations and Advances
[Show abstract][Hide abstract] ABSTRACT: The reaction of the intramolecularly coordinated diaryltellurium(IV) oxide (8-Me2NC10H6)2TeO with acetonitrile proceeds with oxygen transfer and gives rise to the formation of the novel zwitterionic diaryltelluronium(IV) acetimidate (8-Me2NC10H6)2-TeNC(O)CH3 (1) in 57% yield. Protolysis of 1 with hydro-chloric acid affords acetamide and the previously known diarylhydroxytelluronium(IV) chloride [(8-Me2NC10H6)2Te(OH)]Cl.
No preview · Article · Jul 2014 · Journal of the American Chemical Society
[Show abstract][Hide abstract] ABSTRACT: The temperature dependence of H-U
iso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U
iso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.
[Show abstract][Hide abstract] ABSTRACT: Single crystal X-ray structure determinations have previously been described for picrate salts of a variety of nitrogen bases. Herein, these have been extended to encompass monoprotonated mono- and oligo-dentate cyclic nitrogen-donor ligand systems derived from pyridine, some via saturation (piperidine and morpholine) and others via lateral extension of the aromatic system (2,2′-bipyridine, 1,10-phenanthroline, 2,9-dimethyl-1,10-phenanthroline, bis(2-pyridyl)amine, 2,2′:6′,2′′-terpyridine, and 8-hydroxyquinoline). Hydrogen-bonding interactions are dominant determinants of the structures, complemented by or in competition with parallel stacking of anion and (aromatic) base planes. Furthermore, nitronitro, nitroπ and phenoxy-Oπ inter-species contacts play a significant role in the crystal packing. It also appears that cationanion interactions arising from CH(adjacent to NH)O(o-nitro) interactions are more important than the available secondary bifurcating component associated with any NHO(o-nitro) approach, resulting, in many cases, in a bidentate NHHC base approach to an (ON)OOO(NO) triadic array. The nature of the anion-cation interactions and their importance are explored using the Hirshfeld surface method. The precision of the structure determinations establishes the quinonoid form of the picrate to be a widespread contributor. Theoretical calculations on picric acid and the parent pyridinium-picrate ion-pair confirm the energetic favourability of the base-triad approach and the dominance of the quinonoid resonance form.
[Show abstract][Hide abstract] ABSTRACT: The case of protease inhibitor model compounds incorporating an aziridine or epoxide ring is used to exemplify how application of experimental electron-density techniques can be used to explain the biological properties of low-molecular weight enzyme ligands. This is furthermore seen in the light of a comparison of crystal and enzyme environments employing QM/MM computations to elucidate to which extent the properties in the crystal can be used to predict behavior in the biological surrounding.
[Show abstract][Hide abstract] ABSTRACT: The syntheses and full characterizations of the peri-substituted naphthalenes (Nap) and acenaphthenes (Ace) 1-Br-8-(Ph2P)-Nap (1a) and 5-Br-6-(Ph2P)-Ace (1b), as well as their derivatives 1-Br-8-[Ph2P(E)]-Nap [E = CH3+ (counterion I–) (2a); E = O (3a); E = S (4a); E = Se (5a)] and 5-Br-6-[Ph2P(E)]-Ace [E = CH3+ (counterion I–) (2b); E = O (3b); E = S (4b); E = Se (5b)] are reported. In order to quantify the energetic and electronic effects of the peri-interactions, an additional set of molecules, 1c–5c, with the bromine atom and the Ph2P(E) fragment on opposite sides of the naphthalene group was generated, which serves as reference because 1c–5c exhibit negligible peri-interactions. The molecular arrangements of all 15 compounds were optimized at the B3PW91/6-311+G(2df, p) level of theory. The analysis of the peri-interactions was not only based on the inspection of the molecular arrangement and energies alone, but extended to a set of real-space bonding indicators (RSBI). These indicators were derived from theoretically calculated electron densities and pair densities, respectively. Particularly, the stockholder, Atoms-In-Molecules (AIM) and Electron-Localizability-Indicator (ELI-D) space partitioning schemes were used to produce Hirshfeld surfaces (HS), bond topological properties and basins of localized bonding and nonbonding electron pairs. Since 1c–5c are 35–58 kJ·mol–1 lower in energy than their counterparts 1a–5a, the hypothesis of a mainly repulsive peri-interaction in 1a/b–5a/b was confirmed. The shapes and contact patterns of the HSs of atoms and fragments involved in the peri-interactions (Br, P, E = CH3+, O, S, Se) reveal that only in 1a and 1b are peri-interactions exhibited between the bromine and the phosphorus atoms. In all other cases (2a/b–5a/b), the interaction mainly occurs between the bromine atom and the E atom/fragment. According to the bond topological properties and the electron populations within the (non)bonding ELI-D basins, which both are almost unaffected by the Br-P/E peri-interaction, sterical interactions are characterized essentially by geometrical and energetical changes.
Full-text · Article · Oct 2013 · Zeitschrift für anorganische und allgemeine Chemie