Katarzyna N. Jarzembska

New version of the theoretical databank of transferable aspherical pseudoatoms, UBDB2011 – towards nucleic acid modelling

The theoretical databank of aspherical pseudoatoms (UBDB) was recently extended with over 100 new atom types present in RNA, DNA and in some other molecules of great importance in biology and pharmacy. The atom-type definitions were modified and new atom keys added to provide a more precise description of the atomic charge-density distribution. X-H bond lengths were updated according to recent neutron diffraction studies and implemented in the LSDB program as well as used for modelling the appropriate atom types. The UBDB2011 databank was extensively tested. Electrostatic interaction energies calculated on the basis of the databank of aspherical atom models were compared with the corresponding results obtained directly from wavefunctions at the same level of theory (SPDFG/B3LYP/6-31G** and SPDFG/B3LYP/aug-cc-pVDZ). Various small complexes were analysed to cover most of the different interaction types, i.e. adenine-thymine and guanine-cytosine with hydrogen bonding, guanine-adenine with stacking contacts, and a group of neutral and charged species of nucleic acid bases interacting with amino acid side chains. The energy trends are well preserved (R(2) > 0.9); however the energy values differ between the two methods by about 4 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) on average. What is noticeable is that the replacement of one basis set by another in a purely quantum chemical approach leads to the same electrostatic energy difference, i.e. of about 4 kcal mol(-1) in magnitude. The present work opens up the possibility of applying the UBDB2011 for macromolecules that contain DNA/RNA fragments. This study shows that on the basis of the UBDB2011 databank electrostatic interaction energies can be estimated and structure refinements carried out. However, some method limitations are apparent.

Is the Hoveyda–Grubbs Complex a Vinylogous Fischer‐Type Carbene? Aromaticity‐Controlled Activity of Ruthenium Metathesis Catalysts

Three naphthalene-based analogues (4 a-c) of the Hoveyda-Grubbs metathesis catalyst exhibited immense differences in reactivity. Systematic structural and spectroscopic studies revealed that the ruthenafurane ring present in all 2-isopropoxyarylidene chelates possesses some aromatic character, which inhibits catalyst activity. This aromatic stabilization within the chelate ring may be controlled by variation of the polycyclic core topology as was demonstrated for tetraline and phenanthrene derivatives (4 d, e). General conclusions about a new mode of ligand-structure tuning in catalytic systems are presented.

Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition.

Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor ( approximately -300 kJ mol(-1) for -COO(-) in non-aromatic inhibitors, approximately -120-210 kJ mol(-1) for -COO(-) in aromatic inhibitors and approximately -450 kJ mol(-1) for -PO(3)(2-)) and with the amino and guanidine groups at C4 ( approximately -250 kJ mol(-1)). Other groups contribute less than approximately 100 kJ mol(-1). Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292-->Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing inhibitors compared with the more hydrophobic derivatives.

Photoelectrochemical Hole Injection Revealed in Polyoxotitanate Nanocrystals Functionalized with Organic Adsorbates

We find that crystallographically resolved Ti17O24(OPr(i))20 nanoparticles, functionalized by covalent attachment of 4-nitrophenyl-acetylacetonate or coumarin 343 adsorbates, exhibit hole injection into surface states when photoexcited with visible light (λ = 400-680 nm). Our findings are supported by photoelectrochemical measurements, EPR spectroscopy, and quantum dynamics simulations of interfacial charge transfer. The underlying mechanism is consistent with measurements of photocathodic currents generated with visible light for thin layers of functionalized polyoxotitanate nanocrystals deposited on FTO working electrodes. The reported experimental and theoretical analysis demonstrates for the first time the feasibility of p-type sensitization of TiO2 solely based on covalent binding of organic adsorbates.

Statistical analysis of multipole-model-derived structural parameters and charge-density properties from high-resolution X-ray diffraction experiments.

A comprehensive analysis of various properties derived from multiple high-resolution X-ray diffraction experiments is reported. A total of 13 charge-density-quality data sets of α-oxalic acid dihydrate (C2H2O4·2H2O) were subject to Hansen-Coppens-based modelling of electron density. The obtained parameters and properties were then statistically analysed yielding a clear picture of their variability across the different measurements. Additionally, a computational approach (CRYSTAL and PIXEL programs) was utilized to support and examine the experimental findings. The aim of the study was to show the real accuracy and interpretation limits of the charge-density-derived data. An investigation of raw intensities showed that most of the reflections (60-70%) fulfil the normality test and the lowest ratio is observed for weak reflections. It appeared that unit-cell parameters are determined to the order of 10(-3) Å (for cell edges) and 10(-2) ° (for angles), and compare well with the older studies of the same compound and with the new 100 K neutron diffraction data set. Fit discrepancy factors are determined within a 0.5% range, while the residual density extrema are about ±0.16 (3) e Å(-3). The geometry is very well reproducible between different data sets. Regarding the multipole model, the largest errors are present on the valence shell charge-transfer parameters. In addition, symmetry restrictions of multipolar parameters, with respect to local coordinate systems, are well preserved. Standard deviations for electron density are lowest at bond critical points, being especially small for the hydrogen-bonded contacts. The same is true for kinetic and potential energy densities. This is also the case for the electrostatic potential distribution, which is statistically most significant in the hydrogen-bonded regions. Standard deviations for the integrated atomic charges are equal to about 0.1 e. Dipole moments for the water molecule are comparable with the ones presented in various earlier studies. The electrostatic energies should be treated rather qualitatively. However, they are quite well correlated with the PIXEL results.

How Does Substitutional Doping Affect Visible Light Absorption in a Series of Homodisperse Ti11 Polyoxotitanate Nanoparticles

Homodisperse doped polyoxotitanate nanoclusters with formulae Ti11 (MX)O14 (OiPr)17 (M=Mn, Fe or Co; X=Cl, Br or I, OiPr=isopropoxide) display strongly dopant-dependent properties. Spectroscopic solution and reflectance measurements backed up by density of states and time-dependent DFT calculations based on the determined structures, show the prominent effect of FeX substitution by decreasing the HOMO-LUMO gap of the particles. The effect is attributed to the presence of an occupied Fe β orbital halfway up the bandgap, leading to long-wavelength absorption with electron transfer to the titanium atoms of the cluster. Whereas the light absorption varies significantly with variation of the transition metal dopant, its dependency on the nature of the halogen atom or the change in dipole moment across the series is minor.

CLUSTERGEN: a program for molecular cluster generation from crystallographic data

A new program, CLUSTERGEN, for molecular cluster generation is introduced. CLUSTERGEN provides the quantum mechanics/molecular mechanics (QM/MM) input files for program packages such as ADF [Baerends et al. (2012). Vrije Universiteit, Amsterdam, The Netherlands] and GAUSSIAN [Frisch et al. (2009). Gaussian Inc., Pittsburgh, Pennsylvania, USA]. Additionally, it prints out a standard CRYSTAL [Dovesi et al. (2009). University of Turin, Italy] input and, in general, facilitates file-format manipulation. The CLUSTERGEN program is supported by an extensive manual and a user-friendly graphical interface. The code is freely available and carefully commented, which makes it easily modifiable. Exemplary applications of CLUSTERGEN concerning QM/MM calculations and derivation of nucleus-independent chemical shift indices are demonstrated.

Sunitinib: from charge-density studies to interaction with proteins.

Protein kinases are targets for the treatment of a number of diseases. Sunitinib malate is a type I inhibitor of tyrosine kinases and was approved as a drug in 2006. This contribution constitutes the first comprehensive analysis of the crystal structures of sunitinib malate and of complexes of sunitinib with a series of protein kinases. The high-resolution single-crystal X-ray measurement and aspherical atom databank approach served as a basis for reconstruction of the charge-density distribution of sunitinib and its protein complexes. Hirshfeld surface and topological analyses revealed a similar interaction pattern in the sunitinib malate crystal structure to that in the protein binding pockets. Sunitinib forms nine preserved bond paths corresponding to hydrogen bonds and also to the C-H···O and C-H···π contacts common to the VEGRF2, CDK2, G2, KIT and IT kinases. In general, sunitinib interacts with the studied proteins with a similar electrostatic interaction energy and can adjust its conformation to fit the binding pocket in such a way as to enhance the electrostatic interactions, e.g. hydrogen bonds in ligand-kinase complexes. Such behaviour may be responsible for the broad spectrum of action of sunitinib as a kinase inhibitor.

Shedding Light on the Photochemistry of Coinage-Metal Phosphorescent Materials: A Time-Resolved Laue Diffraction Study of an AgI–CuI Tetranuclear Complex

The triplet excited state of a new crystalline form of a tetranuclear coordination d(10)-d(10)-type complex, Ag2Cu2L4 (L = 2-diphenylphosphino-3-methylindole ligand), containing Ag(I) and Cu(I) metal centers has been explored using the Laue pump-probe technique with ≈80 ps time resolution. The relatively short lifetime of 1 μs is accompanied by significant photoinduced structural changes, as large as the Ag1···Cu2 distance shortening by 0.59(3) Å. The results show a pronounced strengthening of the argentophilic interactions and formation of new Ag···Cu bonds on excitation. Theoretical calculations indicate that the structural changes are due to a ligand-to-metal charge transfer (LMCT) strengthening the Ag···Ag interaction, mainly occurring from the methylindole ligands to the silver metal centers. QM/MM optimizations of the ground and excited states of the complex support the experimental results. Comparison with isolated molecule optimizations demonstrates the restricting effect of the crystalline matrix on photoinduced distortions. The work represents the first time-resolved Laue diffraction study of a heteronuclear coordination complex and provides new information on the nature of photoresponse of coinage metal complexes, which have been the subject of extensive studies.

Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole

Multi-temperature single-crystal and powder diffraction experiments on 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole show that this crystal undergoes an isomorphic phase transition with the coexistence of two phase domains over a wide temperature range. The anharmonic approach was the only way to model the resulting disorder.