scholarly journals lamaGOET: an interface for quantum crystallography

2021 ◽  
Vol 54 (3) ◽  
Author(s):  
Lorraine A. Malaspina ◽  
Alessandro Genoni ◽  
Simon Grabowsky
Keyword(s):  
Least Squares ◽  
Quantum Chemical ◽  
Theoretical Calculations ◽  
Molecular Orbitals ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
Localized Molecular Orbitals ◽  
Quantum Crystallography

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.

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

2021 ◽  
Vol 77 (5) ◽  
pp. 695-705
Author(s):  
Giovanni Macetti ◽  
Piero Macchi ◽  
Alessandro Genoni
Keyword(s):  
Excited State ◽  
Gas Phase ◽  
Structure Factor ◽  
Theoretical Calculations ◽  
Molecular Orbitals ◽  
Reference Structure ◽  
Structural Refinement ◽  
Excitation Energies ◽  
X Ray ◽  
Localized Molecular Orbitals

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.

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

Conformational Study of 2,4-Diaryl-3-azabicyclo[3.3.1]nonan-9-ones and Their 3-Methyl Derivatives by Quantum Mechanical Calculations, NMR, and X-ray Crystallography

1994 ◽  
Vol 59 (9) ◽  
pp. 2565-2569 ◽  
Author(s):  
Maria-Selma Arias ◽  
Yves G. Smeyers ◽  
Maria-Jose Fernandez ◽  
Nadine J. Smeyers ◽  
Enrique Galvez ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Conformational Study ◽  
X Ray ◽  
X Ray Crystallography ◽  
Methyl Derivatives

Molecular X-ray Spectra of Sulfur and Chlorine Bearing Substances

1970 ◽  
Vol 14 ◽  
pp. 453-486 ◽  
Author(s):  
G. Andermann ◽  
H. C. Whitehead
Keyword(s):  
Theoretical Models ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Molecular Models ◽  
X Ray ◽  
Starting Point ◽  
State Models ◽  
Basic Features ◽  
Photon Spectra ◽  
Molecular Bonding

AbstractThe interpretation and use of x-ray photon spectra of substances containing second row elements has utilized a number of theoretical models. These models may be divided into three basic categories, namely, the isolated atom model, various molecular models, and a number of solid state models, it is the purpose of this paper to examine critically the validity and limitations of molecular models for interpreting published x-ray photon spectra and spectra obtained by this group on chlorine and sulfur bearing substances.Chlorine and sulfur bearing substances were chosen for at least three important reasons. First, a great deal of published experimental data already exists on the Kα, Kβ, and L2, 3 transitions of these substances. Second, motivated in part by the long standing controversy concerning possible 3d orbital participation in the bonding of second row elements, there are extensive quantum mechanical calculations for ions containing sulfur and chlorine via simple molecular orbital concepts. Thirdj the availability of accurate photoelectron spectroscopic data on these substances now permits a detailed quantitative comparison of x-ray photon transitions with quantum mechanical calculations.Detailed evaluation along these lines indicates that for many substances the theoretically calculated energy values are frequently within a few electron volts (or less) of the experimentally observed energies. This study, therefore, tends to substantiate a viewpoint suggested by some recently; namely, that for many substances the starting point in interpreting most of the basic features of soft x-ray spectra should be based upon molecular bonding approaches.

scholarly journals Determination of the electron density in methyl (±)-(1S,2S,3R)-2-methyl-1,3-diphenylcyclopropanecarboxylate using refinements with X-ray scattering factors from wavefunction calculations of the whole molecule

2013 ◽  
Vol 69 (8) ◽  
pp. 910-914 ◽  
Author(s):  
John Bacsa ◽  
John Briones
Keyword(s):  
Electron Density ◽  
Title Compound ◽  
Cyclopropane Ring ◽  
Topological Analysis ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
Compound C ◽  
X Ray Scattering

The molecule of the title compound, C18H18O2, is a substituted cyclopropane ring. The electron density in this molecule has been determined by refining single-crystal X-ray data using scattering factors derived from quantum mechanical calculations. Topological analysis of the electron densities in the three cyclopropane C—C bonds was carried out. The results show the effects of this substitution on these C—C bonds.

Crystal Structure and Tautomerism of 1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone

2001 ◽  
Vol 56 (10) ◽  
pp. 1003-1008 ◽  
Author(s):  
H. Ünver ◽  
M. Kabak ◽  
D. M. Zengin ◽  
T. N. Durlu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Quantum Mechanical ◽  
Monoclinic Space Group ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
H Nmr ◽  
Mechanical Methods ◽  
Intramolecular Hydrogen ◽  
Semi Empirical

1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone (1) (C17H12NOI) has been studied by X-ray analysis, IR, 1H NMR, UV and AM1 semi-empirical quantum mechanical methods. It crystallises in the monoclinic space group P21/n with a = 4.844(3), b = 21.428(2), c = 13.726(2) Å, ß = 93.07(2)° (R1 =0.032 for 4132 reflections [I > 2σ(I)]). The title compound is not planar and an intramolecular hydrogen bond connects O1 and N1 [2.530(4) Å]. Complementary IR, 1H NMR and UV measurements out. Tautomerism and conformations of the title semi-empirical quantum mechanical calculations and the results are compared with the X-ray data.

Molecular electronic structure of subphthalocyanine macrocycles

2000 ◽  
Vol 04 (06) ◽  
pp. 611-620 ◽  
Author(s):  
V. R. FERRO ◽  
L. A. POVEDA ◽  
R. H. GONZÁLEZ-JONTE ◽  
J. M. GARCIA DE LA VEGA ◽  
T. TORRES ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Ab Initio ◽  
Central Region ◽  
Quantum Chemical ◽  
Theoretical Calculations ◽  
Molecular Electronic ◽  
X Ray ◽  
Compositional Changes ◽  
Molecular Electronic Structure ◽  
Semiempirical Mndo

Quantum chemical calculations at semiempirical (MNDO methods) and ab initio (6-31G and STO-3G basis ses) levels have been performed on boron(III) subphthalocyanines 1-10. Theoretical calculations predict a cone-shaped structure for these compounds independently of the kind of peripheral substitution and even of compositional changes in the central region of the macrocycle (for example, substitution of the boron atom by two hydrogens). The theoretical calculations are in excellent agreement with previous X-ray determinations.

scholarly journals Unconstrained and X-ray constrained extremely localized molecular orbitals: analysis of the reconstructed electron density

2014 ◽  
Vol 70 (6) ◽  
pp. 532-551 ◽  
Author(s):  
Leonardo H. R. Dos Santos ◽  
Alessandro Genoni ◽  
Piero Macchi
Keyword(s):  
Dipole Moments ◽  
Topological Analysis ◽  
Molecular Orbitals ◽  
Basis Sets ◽  
Electron Densities ◽  
X Ray ◽  
Localized Molecular Orbitals ◽  
New Strategy ◽  
Electron Distributions ◽  
Detailed Assessment

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.

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