X-ray restrained extremely localized molecular orbitals for the embedding of quantum mechanical calculations

Author(s):  
Giovanni Macetti ◽  
Piero Macchi ◽  
Alessandro Genoni

The X-ray restrained wavefunction (XRW) method is a quantum crystallographic technique that allows the calculation of molecular wavefunctions adapted to minimize the difference between computed and reference structure factor amplitudes. The latter result from experimental measurements on crystals or from advanced theoretical calculations with periodic boundary conditions, and are used as external restraints in a traditional least-squares structural refinement. Detailed investigations have shown that the technique is able to reliably capture the effects of the crystal field on the molecular electron density. In a recent application, electron distributions obtained from preliminary X-ray restrained wavefunction calculations have been employed in the framework of frozen density embedding theory to embed excited state computations of well defined subsystems. Inspired by these results, it was decided to test, for the first time, the X-ray restrained extremely localized molecular orbitals (XR-ELMOs) along with the recently developed quantum mechanics/extremely localized molecular orbital multiscale embedding approach. By exploiting XR-ELMOs obtained through XRW calculations that used structure factor amplitudes resulting from periodic ab initio computations, excited state calculations of acrylamide in an environment mimicking the one of the crystal structure were performed. In all these computations, the QM region coincides with the crystal asymmetric unit and the ELMO subsystem consisted of two other acrylamide molecules involved in direct hydrogen bonds with the reference unit. The shifts of the excitation energies with respect to the corresponding gas-phase values were evaluated as a function of different parameters on which the computations with XR-ELMOs depend. For instance, the dependence on the resolution of the sets of structure factors that were used to determine the embedding XR-ELMOs were assessed in particular. The results have shown that the use of XR-ELMOs slightly (but not negligibly) improves the description of excited states compared to the gas-phase ELMOs. Once again, these results demonstrate the efficiency of the XRW approach in incorporating environment effects into the calculated molecular orbitals and, hence, into the corresponding electron densities.

2021 ◽  
Vol 54 (3) ◽  
Author(s):  
Lorraine A. Malaspina ◽  
Alessandro Genoni ◽  
Simon Grabowsky

In 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.


1973 ◽  
Vol 4 (40) ◽  
Author(s):  
SAUL WOLFE ◽  
LUIS M. TEL ◽  
W. J. HAINES ◽  
M. A. ROBB ◽  
I. G. CSIZMADIA

2013 ◽  
Vol 42 (32) ◽  
pp. 11497 ◽  
Author(s):  
Brenno A. D. Neto ◽  
Barbara F. L. Viana ◽  
Thyago S. Rodrigues ◽  
Priscila M. Lalli ◽  
Marcos N. Eberlin ◽  
...  

2020 ◽  
Author(s):  
Haiwang Yong ◽  
Andrés Moreno Carrascosa ◽  
Lingyu Ma ◽  
Brian Stankus ◽  
Michael P Minitti ◽  
...  

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-Ångstrom resolution from time-resolved gas-phase scattering signals. The method,...


2014 ◽  
Vol 70 (6) ◽  
pp. 532-551 ◽  
Author(s):  
Leonardo H. R. Dos Santos ◽  
Alessandro Genoni ◽  
Piero Macchi

The recently developed X-ray constrained extremely localized molecular orbital (XC-ELMO) technique is a potentially useful tool for the determination and analysis of experimental electron densities. Molecular orbitals strictly localized on atoms, bonds or functional groups allow one to combine the quantum-mechanical rigour of the wavefunction-based approaches with the easy chemical interpretability typical of the traditional multipole models. In this paper, using very high quality X-ray diffraction data for the glycylglycine crystal, a detailed assessment of the capabilities and limitations of this new method is given. In particular, the effects of constraining the ELMO wavefunctions to experimental X-ray structure-factor amplitudes and the ability of the method to reproduce benchmark electron distributions have been accurately investigated. Topological analysis of the XC-ELMO electron densities and of the zero-flux surface-integrated charges and dipole moments shows that the new strategy is already reliable, provided that sufficiently flexible basis sets are used. These analyses also raise new questions and call for further improvements of the method.


2014 ◽  
Vol 70 (a1) ◽  
pp. C284-C284 ◽  
Author(s):  
Alessandro Genoni

The accurate determination of electron densities in crystals from high-resolution X-ray diffraction data has become more and more important over the years. The existing techniques to accomplish this task can be subdivided into two great families: the multipole models and the wave function-based strategies. The former, which are the most widely used, are essentially linear scaling and allow an easy chemical interpretation of the obtained molecular charge densities, but they are also characterized by some drawbacks, such as the possible presence of unphysical negative regions in the resulting electron distributions. On the contrary, the latter always provide quantum mechanically rigorous electron densities, but they are more computationally expensive and, above all, the ease of chemical interpretation is almost completely lost. In this context, in order to combine the easy chemical interpretability of the multipole models with the quantum mechanical rigor of the wave-function based methods, we have recently extended the X-ray constrained wave function approach proposed by Jayatilaka in the framework of a quantum chemistry technique for the a priori determination of Extremely Localized Molecular Orbitals (ELMOs), namely we have developed a new strategy that allows to extract from X-ray diffraction data a single Slater determinant built up wit Molecular Orbitals strictly localized on small molecular fragments (e.g., atoms, bonds or functional groups). Preliminary tests have shown that the determination of X-ray constrained ELMOs is really straightforward. Furthermore, given the reliable transferability of the obtained Molecular Orbitals, we are constructing new ELMOs databases that can be used as alternative to the existing pseudo-atoms libraries for refining crystallographic structures and electron distributions of large systems. A detailed comparison between the new technique and the multipole models is also currently under investigation.


2017 ◽  
Vol 32 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Yury Teterin ◽  
Konstantin Maslakov ◽  
Mikhail Ryzhkov ◽  
Anton Teterin ◽  
Kirill Ivanov ◽  
...  

On the basis of the X-ray photoelectron spectroscopy data and results of theoretical calculations for the NpO2Cl4 (D4h) cluster, the electronic structure and the chemical bond nature in , was done in the binding Cs2NpO2Cl4 single crystal, containing the neptunyl group NpO2 energy range of 0 eV to ~35 eV. The filled Np 5f electronic states were established to form in the valence band of Cs2NpO2Cl4. This was attributed to the direct participation of the Np 5f electrons in the chemical bonding. The Np 6p electrons were shown to participate in formation of both the inner valence band (~15 eV-~35 eV) and the outer valence band (0 eV-~15 eV). The filled Np 6p and the O 2s, Cl 3s electronic shells were found to make the largest contribution to the formation of the inner valence molecular orbitals. The molecular orbitals composition and the sequence order in the binding energy range 0 eV-~35 eV in Cs2NpO2Cl4, were established. For the first time the quantitative scheme of molecular orbitals for the NpO2Cl4 cluster in the binding energy range 0 eV-~35 eV, was built. This scheme reflects neptunium close environment in the studied compound and is fundamental for both understanding the chemical bond nature in Cs2NpO2Cl4 and the interpretation of other X-ray spectra of Cs2NpO2Cl4. The contributions to the chemical binding for the NpO2Cl4 cluster were evaluated to be: the outer valence molecular orbitals contribution - 73 %, and the inner valence molecular orbitals contribution - 27 %.


Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 236
Author(s):  
Si-Hai Wu ◽  
Dian-Xue Ma ◽  
Zhong-Liang Gong ◽  
Junjie Ma ◽  
Jiang-Yang Shao ◽  
...  

An IrIII-PtII heterodimetallic complex [(ppy)2Ir(dapz)PtCl2]Cl (4), together with the corresponding monometallic complexes [(dapz)PtCl2] (2) and [(ppy)2Ir(dapz)]Cl (3) was designed and prepared, where dapz is 2,5-di(N-methyl-N′-(pyrid-2-yl)amino)pyrazine and ppy is 2-phenylpyridine, respectively. Single-crystal X-ray analysis was carried out for complex 4, displaying the intermolecular Pt∙∙∙Pt and aromatic plane∙∙∙plane distances of 3.839 and 3.886 Å, respectively. The monometallic complex 2 exhibits a single emission maximum at 432 nm with a shorter excited-state lifetime (τ) of 6 ns, while complex 3 exhibits an emission band at 454 nm with a longer excited-state lifetime of 135 ns in CH3CN (N2-saturated) under ambient conditions. In contrast, the heterodimetallic complex 4 displays intriguing excitation wavelength-dependent dual singlet and triplet emissions. Theoretical calculations of the electronic structures and absorption spectra of these complexes were carried out to assist the interpretation of these experimental findings.


1993 ◽  
Vol 03 (01) ◽  
pp. 45-61 ◽  
Author(s):  
RAVINDER KAUR ◽  
SATINDER SINGH

Photon-induced L X-ray production cross sections have been calculated for even Z in the region Z=40–92 at different excitation energies. The results have been compared with the experimental values, and the effects of the choice of atomic parameters — like fluorescence yields, Coster-Kroning transition probabilities and relative emission rates — used in calculating L X-ray production cross sections have been discussed.


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