Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine

In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.

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Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768111041747 ◽

2011 ◽

Vol 67 (6) ◽

pp. 569-581 ◽

Cited By ~ 24

Author(s):

Lilianna Chęcińska ◽

Simon Grabowsky ◽

Magdalena Małecka ◽

Agnieszka J. Rybarczyk-Pirek ◽

Andrzej Jóźwiak ◽

...

Keyword(s):

Electron Density ◽

Intermolecular Interactions ◽

Crystal Packing ◽

Theoretical Calculations ◽

Topological Analysis ◽

Theoretical Models ◽

Hirshfeld Surface ◽

Data Sets ◽

Dft Methods ◽

Geometric Function

A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C—H...C(π), C,N(π)...C,N(π) and H...H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.

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Weak interactions in chain polymers [M(μ-X)2 L 2]∞ (M = Zn, Cd; X = Cl, Br; L = substituted pyridine) – an electron density study

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768109028626 ◽

2009 ◽

Vol 65 (5) ◽

pp. 600-611 ◽

Cited By ~ 26

Author(s):

Ruimin Wang ◽

Christian W. Lehmann ◽

Ulli Englert

Keyword(s):

Hydrogen Bonds ◽

Electron Density ◽

Critical Points ◽

Weak Interactions ◽

Data Sets ◽

X Ray Diffraction ◽

Density Distributions ◽

The One ◽

Experimental Electron Density ◽

Density Study

The experimental electron-density distributions in crystals of five chain polymers [M(μ-X)2(py)2] (M = Zn, Cd; X = Cl, Br; py = 3,5-substituted pyridine) have been obtained from high-resolution X-ray diffraction data sets (sin θ/λ > 1.1 Å−1) at 100 K. Topological analyses following Bader's `Atoms in Molecules' approach not only confirmed the existence of (3, −1) critical points for the chemically reasonable and presumably strong covalent and coordinative bonds, but also for four different secondary interactions which are expected to play a role in stabilizing the polymeric structures which are unusual for Zn as the metal center. These weaker contacts comprise intra- and inter-strand C—H...X—M hydrogen bonds on the one hand and C—X...X—C interhalogen contacts on the other hand. According to the experimental electron-density studies, the non-classical hydrogen bonds are associated with higher electron density in the (3, −1) critical points than the halogen bonds and hence are the dominant interactions both with respect to intra- and inter-chain contacts.

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Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520616010581 ◽

2016 ◽

Vol 72 (5) ◽

pp. 775-786 ◽

Cited By ~ 14

Author(s):

Chinnasamy Kalaiarasi ◽

Mysore S Pavan ◽

Poomani Kumaradhas

Keyword(s):

Electron Density ◽

Intermolecular Interactions ◽

Electrostatic Potential ◽

Theoretical Calculations ◽

Topological Analysis ◽

X Ray Diffraction ◽

Topological Characterization ◽

Data Set ◽

X Ray ◽

Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

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The influence of the type of halogen substituent and its position on the molecular conformation, intermolecular interactions and crystal packing for a series of 1-benzoyl-3-(halogenophenyl)thioureas

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229620015594 ◽

2021 ◽

Vol 77 (1) ◽

pp. 11-19

Author(s):

Damian Rosiak ◽

Andrzej Okuniewski ◽

Jarosław Chojnacki

Keyword(s):

Intermolecular Interactions ◽

Phenyl Ring ◽

Benzoyl Chloride ◽

Molecular Conformation ◽

Crystal Packing ◽

Theoretical Calculations ◽

The Novel ◽

X Ray Diffraction ◽

X Ray ◽

C Nmr

By the reaction of benzoyl chloride, potassium isothiocyanate and the appropriate halogenoaniline, i.e. 2/3/4-(bromo/iodo)aniline, we have obtained five new 1-benzoyl-3-(halogenophenyl)thioureas, namely, 1-benzoyl-3-(2-bromophenyl)thiourea and 1-benzoyl-3-(3-bromophenyl)thiourea, C14H11BrN2OS, and 1-benzoyl-3-(2-iodophenyl)thiourea, 1-benzoyl-3-(3-iodophenyl)thiourea and 1-benzoyl-3-(4-iodophenyl)thiourea, C14H11IN2OS. Structural and conformational features of the compounds have been analyzed using X-ray diffraction and theoretical calculations. The novel compounds were characterized by solid-state IR and 1H/13C NMR spectroscopy. The conformations and intermolecular interactions, such as hydrogen bonds, π–π and S(6)...π stacking, and X...O (X = I or Br), I...S and I...π, have been examined and rationalized, together with four analogous compounds described previously in the literature. The set of nine compounds was chosen to examine how a change of the halogen atom and its position on the phenyl ring affects the molecular and crystal structures.

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Electron density distribution and Madelung potential in α-spodumene, LiAl(SiO3)2, from two-wavelength high-resolution X-ray diffraction data

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768198013536 ◽

1999 ◽

Vol 55 (3) ◽

pp. 273-284 ◽

Cited By ~ 11

Author(s):

Sandrine Kuntzinger ◽

Nour Eddine Ghermani

Keyword(s):

High Resolution ◽

Density Distribution ◽

Electron Density ◽

Electron Density Distribution ◽

Data Sets ◽

X Ray Diffraction ◽

Net Charge ◽

X Ray ◽

Madelung Potential ◽

Net Charges

The electron density distribution in α-spodumene, LiAl(SiO3)2, was derived from high-resolution X-ray diffraction experiments. The results obtained from both Mo Kα- and Ag Kα-wavelength data sets are reported. The features of the Si—O and Al—O bonds are related to the geometrical parameters of the Si—O—Al and Si—O—Si bridges on the one hand and to the O...Li+ interaction on the other. Kappa refinements against the two data sets yielded almost the same net charges for the Si (+1.8 e) and O (−1.0 e) atoms in spodumene. However, the Al net charge obtained from the Ag Kα data (+1.9 e) is larger than the net charge derived from the Mo Kα data (+1.5 e). This difference correlates with a more contracted Al valence shell revealed by the shorter X-ray wavelength (κ = 1.4 for the Ag Kα data set). The derived net charges were used to calculate the Madelung potential at the spodumene atomic sites. The electrostatic energy for the chemical formula LiAl(SiO3)2 was −8.60 e2 Å−1 (−123.84 eV) from the net charges derived from the Ag Kα data and −6.97 e2 Å−1 (−100.37 eV) from the net charges derived from the Mo Kα data.

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A First Experimental Electron Density Study on a C70 Fullerene: (C70C2F5)10

Zeitschrift für Naturforschung B ◽

10.1515/znb-2010-0101 ◽

2010 ◽

Vol 65 (1) ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Roman Kalinowski ◽

Manuela Weber ◽

Sergey I. Troyanov ◽

Carsten Paulmann ◽

Peter Luger

Keyword(s):

High Resolution ◽

Electron Density ◽

Theoretical Calculations ◽

Asymmetric Unit ◽

Data Set ◽

X Ray ◽

Atomic Properties ◽

Density Methods ◽

Experimental Electron Density ◽

Density Study

The electron density of the C70 fullerene C70(C2F5)10 was determined from a high-resolution X-ray data set measured with synchrotron radiation (beamline F1 of Hasylab/DESY, Germany) at a temperature of 100 K. With 140 atoms in the asymmetric unit this fullerene belongs to the largest problems examined until now by electron density methods. Using the QTAIM formalism quantitative bond topological and atomic properties have been derived and compared with the results of theoretical calculations on the title compound and on free C70

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Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K

Acta Crystallographica Section B Structural Science ◽

10.1107/s010876810501637x ◽

2005 ◽

Vol 61 (4) ◽

pp. 443-448 ◽

Cited By ~ 21

Author(s):

S. Scheins ◽

M. Messerschmidt ◽

P. Luger

Keyword(s):

Electron Density ◽

Electron Density Distribution ◽

Theoretical Calculations ◽

Topological Analysis ◽

Theoretical Studies ◽

X Ray Diffraction ◽

X Ray ◽

Resolution Single ◽

Experimental Electron Density ◽

Experimental Charge Density

The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

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Is It Conjugated or Not? The Theoretical and Experimental Electron Density Map of Bonding in p-CH3CH2COC6H4-C≡C-C≡C-p-C6H4COCH3CH2

Molecules ◽

10.3390/molecules25194388 ◽

2020 ◽

Vol 25 (19) ◽

pp. 4388 ◽

Cited By ~ 1

Author(s):

Przemysław Starynowicz ◽

Sławomir Berski ◽

Nurbey Gulia ◽

Karolina Osowska ◽

Tadeusz Lis ◽

...

Keyword(s):

Electron Density ◽

Theoretical Calculations ◽

Topological Analysis ◽

Carbon Chain ◽

Small Contribution ◽

X Ray Diffraction ◽

X Ray ◽

Density Map ◽

Electron Density Map ◽

Experimental Electron Density

The electron density of p-CH3CH2COC6H4-C≡CC≡C-p-C6H4COCH3CH2 has been investigated on the basis of single-crystal X-ray diffraction data collected to high resolution at 100 K and from theoretical calculations. An analysis of the X-ray data of the diyne showed interesting “liquidity” of electron distribution along the carbon chain compared to 1,2-diphenylacetylene. These findings are compatible with the results of topological analysis of Electron Localization Function (ELF), which has also revealed a larger (than expected) concentration of the electron density at the single bonds. Both methods indicate a clear π-type or “banana” character of a single bond and a significant distortion from the typical conjugated structure of the bonding in the diyne with a small contribution of cumulenic structures.

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Electron density of a benzoylated tetrafructopyranose

Zeitschrift für Naturforschung B ◽

10.1515/znb-2021-0178 ◽

2022 ◽

Vol 0 (0) ◽

Author(s):

Peter Luger ◽

Birger Dittrich

Keyword(s):

Electron Density ◽

X Ray Diffraction ◽

X Ray ◽

Atomic Properties ◽

Phenyl Rings ◽

Structural Database ◽

Non Covalent Interactions ◽

Weak Surface ◽

Average Bond ◽

Covalent Interactions

Abstract The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge Structural Database (CSD). Bond topological and atomic properties were obtained by application of Bader’s QTAIM formalism. From a large number of 105 C–C bonds in the molecule average bond orders for 33 single and 72 aromatic bonds were calculated yielding values of 1.33 and 1.61. Molecular Hirshfeld and electrostatic potential (ESP) surfaces show that only weak non-covalent interactions exist. The phenyl rings of the benzoyl fragments in the outer regions of the molecule generate a positive ESP shell with repulsive properties between adjacent molecules. Weak surface interactions result in a rather unusual low density around 1.3 g cm−3, which is understandable when compared to other carbohydrates where strong O–H⋯O hydrogen bonds allow a 20% more dense packing with densities >1.5 g cm−3 as determined by single crystal X-ray diffraction.

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Electron density study of 2H-chromene-2-thione

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768102018712 ◽

2002 ◽

Vol 58 (6) ◽

pp. 1011-1017 ◽

Cited By ~ 21

Author(s):

Parthapratim Munshi ◽

T. N. Guru Row

Keyword(s):

Dipole Moment ◽

Electron Density ◽

Goodness Of Fit ◽

Theoretical Calculations ◽

X Ray Diffraction ◽

Molecular Electron ◽

Ccd Detector ◽

The Difference ◽

Difference Fourier ◽

Density Study

The charge-density distribution in 2H-chromene-2-thione (2-thiocoumarin), C9H6OS, has been determined from X-ray diffraction data measured at 90 K using a CCD detector, to a resolution of sinθ/λ < 1.08 Å−1. A multipolar-atom density model was fitted against 6908 reflections with I > 2σ(I) [R(F) = 0.021, wR(F) = 0.022, goodness of fit = 1.81] in order to generate the difference Fourier maps. The topological properties of the molecular electron density in terms of the bond critical points and the evaluation of the dipole moment show that the molecular dipole moment in the crystal is higher than the corresponding value derived from theoretical calculations.

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