1,721,093 research outputs found
Chemical concepts of bonding and current research problems, or: Why should we bother to engage in chemical bonding analysis?
No full textlamaGOET : an interface for quantum crystallography
Full text linkIn quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-L-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting
Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data
No full textFrom a high-resolution X-ray data set (sin theta/lambda = 1.1 A(-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
How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine
No full textBergenin, 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
Hirshfeld atom refinement
Full text linkHirshfeld 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 Å2 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
On the temperature dependence of H-U iso in the riding hydrogen model
No full textThe temperature dependence of H-Uiso 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-Uiso 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
Das Wechselspiel von Theorie und Kristallographie
No full textQuantenkristallographie ist mehr als die Summe von Quantenchemie und Kristallographie. Mit ihr lassen sich aus Röntgenbeugungsexperimenten präzise und akkurate molekulare Strukturen sowie eine Wellenfunktion gewinnen, deren Informationsgehalt über den des quantenchemischen Ansatzes hinaus geht
A Comparative Study on the Experimentally Derived Electron Densities of three Protease Inhibitor Model Compounds
No full textIn order to contribute to a rational design of optimised protease inhibitors which can covalently block the nucleophilic amino acids of the proteases' active sites, we have chosen three model compounds (aziridine , oxirane and acceptor-substituted olefin ) for the examination of their electron-density distribution. Therefore, high-resolution low temperature (9, 27 and 100 K) X-ray diffraction experiments on single-crystals were carried out with synchrotron and conventional X-radiation. It could be shown by the analysis of the electron density using mainly Bader's Theory of Atoms in Molecules, Volkov's EPMM method for interaction energies, electrostatic potentials and Gatti's Source Function that aziridine is most suitable for drug design in this field. A regioselective nucleophilic attack at carbon atom C1 could be predicted and even hints about the reaction's stereoselectivity could be obtained. Moreover, the comparison between two data sets of aziridine (conventional X-ray source vs. synchrotron radiation) gave an estimate concerning the reproducibility of the quantitative results
Supramolecular Silanol Chemistry in the Gas Phase. Topological (AIM) and Population (NBO) Analyses of Hydrogen-Bonded Complexes between H 3 SiOH and Selected O- and N-Acceptor Molecules
No full textHydrogen 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)→π conjugation in N(CH3)2C6H5 upon complex formation. EHB shows no correlation with O···A distances and the red shifts Δν(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 ρ(HA) and ρ(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 ΔqNPA(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
- …
