How focussing on hydrogen bonding interactions in amino acids can miss the bigger picture: a high-pressure neutron powder diffraction study of ε-glycine

Moggach, Stephen A.; Marshall, William G.; Rogers, David M.; Parsons, Simon

doi:10.1039/c5ce00327j

Cited by 38 publications

(45 citation statements)

References 75 publications

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“…6 By contrast, β-glycine transforms to δ-glycine at 0.8 GPa, while the γ-form gradually yields the ε-polymorph between 2.0 and 4.3 GPa. 4,7 ε-Glycine transforms back to the γ-form via a, sixth, shortlived ζ-polymorph. 8 L-Serine has four high-pressure polymorphs.…”

Section: Introductionmentioning

confidence: 99%

High-pressure polymorphism inl-threonine between ambient pressure and 22 GPa

et al. 2019

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Section: Introductionmentioning

confidence: 99%

High-pressure polymorphism inl-threonine between ambient pressure and 22 GPa

et al. 2019

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“…In particular, for crystals involving weaker interactions, many calculated energy surfaces are quite flat, so the exact geometry of the synthon may be variable and one-coordinate descriptions in terms of a single atom-atom bond is inadequate. Hence, one must look into interactions between whole molecular charge densities, rather than pairwise atom-atom interactions only, especially at short intermolecular distances or in the presence of highly charged groups [3][4][5][6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

2019

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Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π . . . π stacking and many other kinds of non-covalent atom-atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449-469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (E es ) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to E es . To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (E EML ) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between E EML and E es . However, strong relation between E EML and the charge penetration component of E es is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom-atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

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“…Focusing on prominent interactions can also give a misleading impression of the nature of an overall intermolecular contact. For example, out of 14 molecule-molecule contacts within the first coordination sphere of -glycine, six are destabilizing, including two which involve hydrogen bonds (Moggach et al, 2015).…”

Section: Intermolecular Interactions In Crystal Structuresmentioning

confidence: 99%

MrPIXEL: automated execution of Pixel calculations via the Mercury interface

2020

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The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host–guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule–molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

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How focussing on hydrogen bonding interactions in amino acids can miss the bigger picture: a high-pressure neutron powder diffraction study of ε-glycine

Cited by 38 publications

References 75 publications

High-pressure polymorphism inl-threonine between ambient pressure and 22 GPa

High-pressure polymorphism inl-threonine between ambient pressure and 22 GPa

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

MrPIXEL: automated execution of Pixel calculations via the Mercury interface

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