<i>xINTERPDF</i>: a graphical user interface for analyzing intermolecular pair distribution functions of organic compounds from X-ray total scattering data

Shi, Chenyang

doi:10.1107/s1600576718012359

Cited by 11 publications

(7 citation statements)

References 9 publications

(8 reference statements)

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“…More accurate fits can be achieved with programs that can accomplish this including DISCUS, ,, Diffpy-CMI, , or TOPAS v6 and up . A graphical use interface for Diffpy-CMI for fitting molecular materials is also available . DISCUS and Diffpy-CMI both provide options to also generate PDFs through the use of the Debye scattering equation, eq , and then propagate to F ( Q ) to be Fourier transformed.…”

Section: Modeling Strategiesmentioning

confidence: 99%

“…483 A graphical use interface for Diffpy-CMI for fitting molecular materials is also available. 614 DISCUS and Diffpy-CMI both provide options to also generate PDFs through the use of the Debye scattering equation, eq 6, 34 and then propagate to F(Q) to be Fourier transformed. This is particularly useful for nonperiodic models such as discrete nanoparticles or single molecules.…”

Section: In Situ Structural Transformationsmentioning

confidence: 99%

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Structural Analysis of Molecular Materials Using the Pair Distribution Function

2021

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This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short-and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.

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Section: Modeling Strategiesmentioning

confidence: 99%

Section: In Situ Structural Transformationsmentioning

confidence: 99%

Structural Analysis of Molecular Materials Using the Pair Distribution Function

2021

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“…Simulated TS-PDF of Form I andForm II single-crystal structures were calculated using the xINTERPDF software. 79 High energy X-ray (58 keV, λ = 0.2128 Å) scattering measurements were performed in transmission mode at beamline 11-ID-B of the Advanced Photon Source (APS) located at Argonne National Laboratory (ANL) using facilities and procedures described in the literature. 45 A PerkinElmer amorphous Si 2D image plate detector was placed perpendicular to the high energy X-ray beam, 170 mm behind the capillary samples.…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior

et al. 2021

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Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å 2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.

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“…Simulated TS-PDF of varying water Form II experimental structures were calculated using the xINTERPDF software. 57 High energy X-ray (58 keV, λ = 0.2128 Å) scattering measurements were performed in transmission mode at beamline 11-ID-B of the Advanced Photon Source (APS) located at Argonne National Laboratory (ANL) using facilities and procedures described in the literature. 58 The raw total scattering data obtained from these measurements were Fourier transformed to determine the experimental PDF plots.…”

Section: ■ Conclusionmentioning

confidence: 99%

Distinct Hybrid Hydrates of Paritaprevir: Combined Experimental and Computational Assessment of their Hydration–Dehydration Behavior and Implications for Regulatory Controls

Hong

Bhardwaj

Henry

et al. 2021

Crystal Growth & Design

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Paritaprevir is a first-generation direct-acting antiviral and, as a conformationally flexible molecule containing a 15-membered macrocyclic ring, has unique chameleonic and solidstate features. The two commercially relevant forms (Forms I and II) are clearly differentiated wherein Form I benefits from strong intermolecular interactions, whereas weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an intramolecular hydrogen bond, which significantly lowers the conformational energy. Both forms are hydrated and exhibit hybrid features of stoichiometric and nonstoichiometric hydrates, albeit differently. Form I exhibits strong host−host and weak host−water interactions and contains stable channels that do not substantially change upon hydration/dehydration. Form II contains weak host−host and strong host−water interactions and a host−water hydrogen bonding planar network that evolves with the hydration state. Furthermore, periodic density functional theory calculations for potential energy differences show that a transition from enthalpic stabilization of the structure to entropic stabilization occurs at 2.5 mol equiv of water in Form II. Since the paritaprevir drug substance is manufactured as Form II, implications of its features for nomenclature and testing within the regulatory context are also discussed.

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xINTERPDF: a graphical user interface for analyzing intermolecular pair distribution functions of organic compounds from X-ray total scattering data

Abstract: A new software program, xINTERPDF, that analyzes the intermolecular correlations in organic compounds via measured X-ray total scattering data is described.

Cited by 11 publications

References 9 publications

Structural Analysis of Molecular Materials Using the Pair Distribution Function

Structural Analysis of Molecular Materials Using the Pair Distribution Function

Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior

Distinct Hybrid Hydrates of Paritaprevir: Combined Experimental and Computational Assessment of their Hydration–Dehydration Behavior and Implications for Regulatory Controls

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