1,721,059 research outputs found
Remarks on X-ray constrained/restrained wavefunction fitting
No full textX-ray constrained/restrained wavefunctions (XCWs/XRWs) result from a combination of theory and experiment and are therefore affected by experimental errors and model uncertainties. The present XCW/XRW procedure does not take this into account, thus limiting the meaning and significance of the obtained wavefunctions
Critical assessment of the x-ray restrained wave function approach: Advantages, drawbacks, and perspectives for density functional theory and periodic ab initio calculations
No full textThe x-ray restrained wave function (XRW) method is a quantum crystallographic technique to extract wave functions compatible with experimental x-ray diffraction data. The approach looks for wave functions that minimize the energies of the investigated systems and also reproduce sets of x-ray structure factors. Given the strict relationship between x-ray structure factors and electron distributions, the strategy practically allows determining wave functions that correspond to given (usually experimental) electron densities. In this work, the capabilities of the XRW approach were further tested. The aim was to evaluate whether the XRW technique could serve as a tool for suggesting new exchange-correlation functionals for density functional theory or refining existing ones. Additionally, the ability of the method to address the influences of the crystalline environment was also assessed. The outcomes of XRW computations were thus compared to those of traditional gas-phase, embedding quantum mechanics/molecular mechanics, and fully periodic calculations. The results revealed that, irrespective of the initial conditions, the XRW computations practically yield a consensus electron density, in contrast to the currently employed density functional approximations (DFAs), which tend to give a too large range of electron distributions. This is encouraging in view of exploiting the XRW technique to develop improved functionals. Conversely, the calculations also emphasized that the XRW method is limited in its ability to effectively address the influences of the crystalline environment. This underscores the need for a periodic XRW technique, which would allow further untangling the shortcomings of DFAs from those inherent to the XRW approach
Quantum crystallography
No full textApproximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated tool. The development of quantum crystallographic research is reviewed. Some results obtained by quantum crystallography illustrate the potential and limitations of this field
Analysis of crystal field effects and interactions using X-ray restrained ELMOs
No full textThe purpose of this study is to assess the capability of X-ray restrained molecular wavefunction methods to reproduce the perturbation due to the crystal field. The effect of the crystal environment on the molecular charge densities has been thoroughly investigated experimentally and theoretically. However, the same analysis in terms of molecular orbitals is unprecedented. We specifically analysed the extremely localized molecular orbitals (ELMOs) because they allow for a valence bond like interpretation that is closer to the typical chemical reasoning. For a set of test molecules, we calculated first principles wavefunctions (called primary wavefunctions) and the corresponding scattered intensities (primary structure factors), which we afterwards used for X-ray restrained Hartree-Fock and ELMO calculations. This mimics the typical procedure of modelling wavefunctions from experimental X-ray diffraction, having the primary wavefunction as benchmark. This study follows a previous investigation concerning the effects of electron correlation, where it was shown that those subtle features could be retrieved only to a minor extent. The electric field generated by surrounding molecules is instead more substantial. Therefore, retrieving this information should be more successful and, in case, extremely useful for supramolecular chemistry and crystal engineering. The work also provides useful indications to experimentalists who want to exploit the potentialities offered by the X-ray restrained wavefunction methods
Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks
No full textIn a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints
Atomic level description of the protecting effect of osmolytes against thermal denaturation of proteins
No full textThe protecting effect of the osmolyte molecule taurine against thermal denaturation of the protein Chimotripsin Inhibitor 2 was modelled using Molecular Dynamics simulations. The protein was simulated in denaturing conditions at different taurine concentrations. Analysis of the molecular details of its behaviour shows that the protective effect of the osmolyte is concentration dependent. Moreover, the influence of taurine on the solvent structure was studied. A concentration dependent ordering effect of taurine on water molecules emerges from solvent structure analysis and is well correlated to the protecting effect observed. Based on these observations an interpretation of the osmoprotective effect is proposed. © 2007 Elsevier B.V. All rights reserved
A novel extremely localized molecular orbitals based technique for the one-electron density matrix computation
No full textThe 'nearsightedness' of electronic structure is an underlying principle in many of the linear scaling methods recently developed to study large systems. Among them, there are strategies based on the transfer of orbitals strictly localized on molecular fragments, such as the extremely localized molecular orbitals (ELMOs). Unfortunately, due to the non-orthogonal nature of these orbitals, the density matrix calculation is computationally demanding, so preventing a straightforward application to very large molecules. In this Letter, we show how this problem can be overcome by a proper application of the 'Divide and Conquer' strategy to the ELMO approach. © 2005 Elsevier B.V. All rights reserved
Extremely localized molecular orbitals: Theory and applications
No full textOrbitals that are extremely localized on molecular fragments represent a powerful tool for a number of purposes: to cite a few examples, they allow to reduce strongly the complexity of calculations on large systems and are easily transferable from one molecule to another, providing a suitable and efficient way to build up the electronic structure of large molecules. Recently, we have developed efficient algorithms to determine extremely localized molecular orbitals (ELMOs), which will be reviewed in this paper. As a rigorous localization is strictly connected to a reduction in the number of variational parameters, which reflects into an increased value of the associated energy with respect to the Hartree Fock value, we have developed a number of strategies to relax the wavefunction built up using transferred localized orbitals. The extreme localization has also been exploited in connection with the "Divide and Conquer" technique to determine the electron densities of large polypeptides assembled from orbitals computed on small model molecules. Moreover, we will discuss the recent application of the ELMOs in the framework of the hybrid QM/MM methods to describe the frontier region. We will also show that the ELMOs can be used to extract chemical interpretations from numerical results. A variety of applications will be presented. © Springer-Verlag 2007
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