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Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method.

ABSTRACT: A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal-organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.

SUBMITTER: Ramadhar TR

PROVIDER: S-EPMC4283468 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method.

Ramadhar Timothy R TR Zheng Shao Liang SL Chen Yu Sheng YS Clardy Jon J

Acta crystallographica. Section A, Foundations and advances 20150101 Pt 1

A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal-organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly diff ...[more]

PMID: 25537388

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Project description:Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore-solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography. Major improvements in the method have been made in the guest-soaking and data-collection steps. In the soaking step, obtaining a high site occupancy of the guest is particularly important, and dominant parameters for guest soaking (e.g. temperature, time, concentration, solvents) therefore have to be optimized for every sample compound. When standard conditions do not work, a high-throughput method is useful for efficiently optimizing the soaking conditions. The X-ray experiments are also carefully re-examined. Significant improvement of the guest data quality is achieved by complete data collection at high angle regions. The appropriate disorder treatment of the most flexible ZnI2 portions of the host framework and refinement of the solvents filling the remaining void are also particularly important for obtaining better data quality. A benchmark test for the crystalline sponge method toward an achiral molecule is proposed with a guaiazulene guest, in which the guest structure (with ??100% site occupancy) is refined without applying any restraints or constraints. The obtained data quality with R int = 0.0279 and R 1 = 0.0379 is comparable with that of current conventional crystallographic analysis for small molecules. Another benchmark test for this method toward a chiral molecule is also proposed with a santonin guest. The crystallographic data obtained [R int = 0.0421, R 1 = 0.0312, Flack (Parsons) = -0.0071?(11)] represents the potential ability of this method for reliable absolute structure determination.

Project description:Liquid-filled porous materials exist widely in nature and engineering fields, with the diffusion of substances in them playing an important role in system functions. Although surface evaporation is often inevitable in practical scenarios, the evaporation effects on diffusion behavior in liquid-filled porous materials have not been well explored yet. In this work, we performed noninvasive diffusion imaging experiments to observe the diffusion process of erioglaucine disodium salt dye in a liquid-filled nitrocellulose membrane under a wide range of relative humidities (RHs). We found that evaporation can significantly accelerate the diffusion rate and alter concentration distribution compared with the case without evaporation. We explained the accelerated diffusion phenomenon by the mechanism that evaporation would induce a weak flow in liquid-filled porous materials, which leads to convective diffusion, i.e., evaporation-induced flow and diffusion (EIFD). Based on the EIFD mechanism, we proposed a convective diffusion model to quantitatively predict the diffusion process in liquid-filled porous materials under evaporation and experimentally validated the model. Introducing the dimensionless Peclet (P e) number to measure the relative contribution of the evaporation effect to pure molecular diffusion, we demonstrated that even at a high RH of 95%, where the evaporation effect is usually assumed negligible in common sense, the evaporation-induced diffusion still overwhelms the molecular diffusion. The flow velocity induced by evaporation in liquid-filled porous materials was found to be 0.4-5 μm/s, comparable to flow in many biological and biomedical systems. The present analysis may help to explain the driving mechanism of tissue perfusion and provide quantitative analysis or inspire new control methods of flow and material exchange in numerous cutting-edge technologies, such as paper-based diagnostics, hydrogel-based flexible electronics, evaporation-induced electricity generation, and seawater purification.

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Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method.

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Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method.

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