research article on x ray crystallography

Journal of Materials Chemistry C

Development of high-performance direct x-ray detector materials: from hybrid halide perovskites to all-inorganic lead-free perovskites.

X-rays Detection plays a vital role in medical imaging, industrial defect detection, security screening and scientific research. Direct X-ray detectors are of greater interest to researchers because they offer the advantages of faster imaging, higher resolution and simpler construction than indirect detectors. Due to their intrinsic properties, traditional materials have inherent problems that limit their performance in detector applications. Perovskite is a new material with excellent properties that has great potential in the field of X-ray detectors. This paper summaries the research progress of perovskite materials in the field of X-ray detectors. First, the problems of traditional materials are listed according to the principle and material requirements of X-ray detectors. Then, the problems and challenges of different types of perovskite materials are divided from the classification of perovskite materials, from organic to inorganic materials, and from halide perovskite to lead-free perovskite. The intention is to provide ideas for the development of more environmentally friendly and higher performance X-ray detectors.

  • This article is part of the themed collection: Journal of Materials Chemistry C Recent Review Articles

Article information

Download citation, permissions.

research article on x ray crystallography

X. Wu, A. Li, M. Yang, X. Hao, L. Wu, R. Su and J. Zhang, J. Mater. Chem. C , 2024, Accepted Manuscript , DOI: 10.1039/D4TC00423J

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page .

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page .

Read more about how to correctly acknowledge RSC content .

Social activity

Search articles by author.

This article has not yet been cited.

Advertisements

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • View all journals
  • My Account Login
  • Explore content
  • About the journal
  • Publish with us
  • Sign up for alerts
  • Open access
  • Published: 09 May 2024

Computational study of diffraction image formation from XFEL irradiated single ribosome molecule

  • Michal Stransky 1 , 2 , 3 ,
  • Juncheng E 1 ,
  • Zoltan Jurek 4 , 5 ,
  • Robin Santra 4 , 5 , 6 ,
  • Richard Bean 1 ,
  • Beata Ziaja 2 , 4 &
  • Adrian P. Mancuso 1 , 7 , 8  

Scientific Reports volume  14 , Article number:  10617 ( 2024 ) Cite this article

208 Accesses

Metrics details

  • Atomic and molecular interactions with photons
  • Imaging techniques
  • Macromolecules and clusters

Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.

Similar content being viewed by others

research article on x ray crystallography

Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser

research article on x ray crystallography

Serial protein crystallography in an electron microscope

research article on x ray crystallography

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Introduction.

Single particle imaging (SPI) at atomic resolution is one of the most vaunted research goals for X-ray free-electron laser (XFEL) facilities 1 , 2 , 3 . Such a capability has the potential for a transformative impact in biological and medical sciences, as high-resolution structural information on biosamples is essential for many research areas therein. This is because the structure of many biologically important particles (macromolecules, viruses, etc.) has not yet been sufficiently explored with conventional X-ray diffraction techniques, due to the lack of successful crystallization 4 . Nevertheless, key challenges to this method remain, and computational explorations of its viability and best use are helpful to optimize the technique towards being valuable to samples of scientific interest 4 .

High-resolution single-particle cryo-EM has been largely developed to reach atomic resolution with new detector technology and image processing algorithms in the past few years 5 , 6 . However, its limitations in the sample environment and temporal resolution prevent it from investigating the dynamics of proteins under physiological conditions, where the XFEL has the potential 7 .

While the serial femtosecond crystallography (SFX) method 8 , 9 , 10 , 11 , 12 , which operates on nano- and micro-crystals, and therefore bridges between conventional crystallography and SPI, has proven to be very successful, high-resolution imaging of single non-periodic objects still remains a challenge 4 . Therefore, theoretical studies are necessary to guide further development of single-particle imaging techniques towards their optimization, and also for identifying and overcoming the existing physical and technical limitations of SPI (see, e.g. Ref. 13 ).

Such an effort has already led to the development of the start-to-end (S2E) computer simulation pipeline dedicated for computational studies of SPI at the European XFEL facility 14 , 15 . The pipeline was later developed into the SIMEX platform 16 for multidisciplinary applications, and a simplified python interface SimEx-lite 17 for easy user access was added. In Ref. 18 , 19 , this platform was used to investigate the SPI of a small hydrated protein molecule, 2NIP, containing around 5000 non-hydrogen atoms. However, a realistic SPI study of biological objects containing at least hundreds of thousands of atoms (i.e. of scientific relevance and size which can yield sufficiently strong signal during experimental imaging studies), could not be performed so far with this simulation tool, due to the too-high computational costs. As straightforward extrapolation of SIMEX predictions for small samples to large samples is not possible, due to the differently progressing radiation damage in small and large samples (e.g., Ref. 20 ), dedicated computer simulations are necessary to explore this regime. In this paper, we perform a comprehensive analysis of radiation damage during a realistic SPI study of a ribosome macromolecule, containing 142,429 non-hydrogen atoms. For the simulation, we use the SIMEX framework 16 , with a dedicated software for modeling X-ray induced radiation damage in large finite-size samples, the tree-code-extended XMDYN tool 21 , 22 , 23 . With these codes, we estimate the minimal number of simulated molecular-dynamics realizations of the X-ray irradiated molecule (performed under typical experimental conditions) needed to reliably compute its time-integrated and realization-averaged diffraction image. We compare the actual prediction to that obtained previously for the small 2NIP protein in Ref. 18 . We do the same for the prediction on the measure of degradation of diffraction image quality: the R-factor. Discussion and outlook then follow.

Our results demonstrate the feasibility of computational SPI studies for biological samples of realistic size. This is very important as it shows that the SIMEX platform can be used for simulations of SPI experiments preceding practical experiments, and help to establish optimal parameters for these experiments. This can stimulate more efficient SPI studies at XFEL facilities worldwide.

Simulation setup

Simulation framework.

The S2E/SIMEX modeling framework was discussed in detail in Ref. 16 , 18 . In short, an SPI experiment (Fig. 1 ) is modeled using a virtual simulation pipeline. It consists of consecutive modules providing: (1) simulations of SASE X-ray pulses (the X-ray source), (2) description of beam propagation through the XFEL optics, (3) modeling of the interaction between X-rays and the irradiated sample, (4) formation of X-ray scattering patterns, (5) processing of individual diffraction patterns, and (6) real-space structure determination from X-ray scattering patterns assembled in the reciprocal space.

figure 1

Schematic of a typical single-particle imaging experiment, modeled within our start-to-end simulation framework 18 . X-rays propagate from the source to the sample through the beamline optics and then interact with the sample. The scattering pattern is recorded by the detector on the right.

Irradiation conditions

For our simulations, we used the set of 55 SASE X-ray pulses generated for our earlier studies 15 , 18 . The nominal X-ray pulse parameters were: 4.96 keV photon energy, \(5 \times 10^{11}\) photons per pulse, 9 fs FWHM pulse duration and 250 nm \(\times\) 160 nm FWHM focal size. The simulation parameters match the ones from the earlier simulation work 15 to aid comparison. The values represent an achievable, though not optimal performance of the accelerator and SPB/SFX instrument at the European XFEL.

Molecule description

Ribosomes are key molecules in living cells. They are responsible for assembling amino acids into protein chains, using information carried by m-RNA molecules. Ribosomes consist of a large subunit and a small subunit. In some studies the subunits are investigated separately; in this study, however, the entire assembly is considered. The imaged ribosome is taken from the E. Coli bacteria, indexed as 4V6C in the PDB database 24 . It includes 243,324 atoms in total, out of which 100,895 atoms are hydrogen atoms. The largest atom-atom separation is about 300 Å which defines an upper limit for the size of this inhomogeneous molecule of irregular shape.

X-ray—molecule interaction

We used the tree-code-extended XMDYN code 21 , 22 , 23 to simulate the dynamics of the irradiated ribosome molecule. XMDYN follows the ionization dynamics of atoms and ions, using a Monte Carlo scheme combined with first-principle atomic-structure calculations. When an orbital of an atom is ionized, the corresponding occupation number is updated and all orbitals of the atom are reoptimized. Simultaneously, an electron is ejected in the immediate vicinity of the ionized atom. The ejected electron is then treated as a classical particle.

XMDYN captures the real-space dynamics of the atoms/ions and of free electrons using the molecular dynamics (MD) scheme. Only Coulomb forces between charged particles are considered because chemical bonds are expected to break up early in the exposure due to the rapid sample ionization. As atoms and electrons are treated as classical particles and information on the specific atomic configuration of each ion is provided by the code, one can easily calculate scattering patterns from the atomic snapshots.

The ribosome molecule containing over two hundred thousand atoms and a very high number of excited electrons could not be simulated using the original n -body solvers for Coulomb interaction and secondary ionization implemented in XMDYN. Both of the solvers had O( \(n^2\) ) computation time complexity (where n is the number of particles). In order to simulate such a large system, we incorporated the Pretty Efficient Parallel Coulomb-solver (PEPC) developed in Forschungszentrum Jülich 25 , and developed a more efficient secondary ionization solver (based on tree code search for nearest neighbors), reducing the time complexity to O( \(n \cdot \textrm{log}(n)\) ). A detailed description of the solver can be found in Ref.  23 .

In total, we have generated 100 different molecular-dynamics realizations (trajectories) of the stochastic dynamics within the X-ray irradiated ribosome molecule, randomly oriented with respect to the incoming X-ray beam. Calculation of one MD trajectory took about 45 days. Calculation of all MD trajectories took about 17,000 CPU days.

X-ray induced radiation damage in ribosome

During the exposure to the 9 fs FWHM duration free-electron laser X-ray pulse, atoms undergo photoionization from core levels, with subsequent Auger decay of core holes. The released electrons cause further radiation damage by collisional ionization of atoms/ions. Incoming X-rays scatter coherently and incoherently on the electrons bound on atoms/ions within the molecule and incoherently on the free electrons, producing a diffraction image with a fluctuating background which encode the information on the molecule structure.

The ionization process reduces the number of bound electrons. As a result, the coherent scattering signal from the sample decreases (e.g. Ref. 11 , 26 , 27 ). In addition, ionized atoms start to repel each other due to mutual repulsive Coulomb forces. This leads to atomic displacement and, eventually, to sample expansion. The progressing atomic displacements also reduce the quality of the diffraction image.

In order to quantify the effect of X-ray induced radiation damage in the ribosome molecule, we first show the average number of bound electrons for each atomic species as a function of time (Fig.  2 ). The average was calculated from 100 XMDYN simulations, as discussed in the subsection on “X-ray - molecule interaction”.

figure 2

Average number of bound electrons per atom as a function of time calculated for various atomic species within the ribosome molecule. The average was taken from 100 XMDYN simulations. The average over the SASE pulses employed is peaked at 0 fs.

The most abundant non-hydrogen atoms, C, N and O, yield the strongest contribution to the elastic scattering signal. With increasing time, their ionization progresses very similarly, reducing the scattering cross sections at the time of the pulse maximum to about two thirds of their respective initial values. For time references, we define the time zero here as the time of the maximum of the average temporal envelope of the 55 SASE pulses, each 9-fs long that we used in the simulations. The element zinc is a trace element with only one atom present in the entire molecule. Therefore, it has the largest error bars. However, zinc does not have a measurable effect on the overall scattering signal.

Figure  3 shows average atomic displacements for various atomic species during the X-ray pulse. At the maximum of the pulse (time zero), the sample’s ability to scatter X-rays has already been somewhat reduced due to ionization, so that the strongest contribution to the time-integrated signal registered at the detector occurs shortly before this maximum, yet the displacement for the C, N and O elements up to the time zero is still below 1 Å.

figure 3

Average atomic displacement calculated for different atomic species within the ribosome molecule. Pulse and simulation parameters are the same as in Fig.  2 .

In Ref. 18 , the small 2NIP protein was studied. It was observed that the sample ionization was mostly driven by collisional ionization induced by photo- and Auger electrons. The ionization was reduced at the sample edge, due to the electron density gradient. Similar behavior has also been found for the ribosome molecule. Figure  4 shows that at time zero the average number of electrons bound to carbon ions is larger at the sample edge than in its central region. The example of carbon is shown as it is the most abundant non-hydrogen element in biological molecules. Similar behavior was observed for nitrogen and oxygen atoms (not shown here). There are two main reasons for higher ionization degree in the center of molecule: first, electrons ejected close to the edge are more likely to leave the molecule without triggering secondary ionization events and second, slower excited electrons get trapped in the molecule’s central region causing further ionization therein. The resulting non-uniformity in the spatial distribution of bound electrons reduces the quality of imaging in the 50–100 Å resolution region. As mentioned above, this reduced ionization damage at the sample edge is very similar to that of the non-hydrated 2NIP sample discussed in 18 .

figure 4

Average number of electrons bound to carbon ions at time zero as a function of distance from the molecule’s center of mass at time zero. Pulse and simulation parameters are the same as in Fig.  2 .

Similar analysis can be performed for the average atomic displacement. Figure  5 shows the average atomic displacement at time zero obtained from 100 XMDYN realizations for carbon atoms/ions.

figure 5

Average displacement of carbon ions at time zero as a function of distance from the molecule’s center of mass at time zero. Pulse and simulation parameters are the same as in Fig  2 .

The displacement is relatively small in the central molecule region, where ion charges are screened by free electrons. In the region close to the molecule edge, it becomes up to three times larger due to the decreased electron density which stimulates surface expansion. However, even then, the displacement still remains only a fraction of an Ångstrom.

Conditions for statistically reliable description of radiation damage in SPI simulations

During the SPI experiments, one obtains hundreds of thousands of diffraction images. Each image results from X-ray diffraction from a randomly oriented particle, with stochastically progressing radiation damage. It is computationally not possible to simulate that many MD realizations, therefore a reasonable simplification must be applied, in order to reduce the computational effort.

The most natural way is to try to reduce the number of calculated MD realizations. However, in such a case, multiple images must be calculated at different (random) sample orientation, using the same molecular-dynamics realization. This strategy was used in earlier studies 14 , 18 . However, for ribosome, the XMDYN simulations take a very long time. Therefore, it becomes critical to find a minimal number of MD realizations that yields statistically reliable average diffraction patterns.

In order to establish a lower limit for the number of required MD realizations, we studied the convergence of the average 3D reciprocal-space time-integrated image of the simulated molecule (later referred to as “time-integrated 3D image”, or “3D image”). The analysis performed in the reciprocal space gave us the immediate advantage of addressing directly different resolution regimes.

First, we obtained a time-integrated 3D image for each of the simulated MD realizations. The time integration used the time-resolved photon count rate for the SASE pulse that was used for the calculation of that realization. The time integration was performed using 10 diffraction images taken at 10 selected time steps in the same way as stated in Ref. 18 . They were all calculated on a preselected 3D q -grid with the oversampling ratio of 2.8 and the edge full-period resolution of 3.5 Å. At the end, each of the 3D time-integrated images was normalized by dividing the signal by the total incident photon count of the respective pulse. From the 100 real-space realizations obtained for the X-ray irradiated ribosome molecule, we calculated 100 time-integrated 3D-reciprocal-space images. From them, we calculated a mean 3D reciprocal space image on the selected q -grid. This 3D image served as the reference image in our analysis.

Further, for each of the voxels on this grid we also calculated the standard deviation of the signal. The voxel intensity varies in the volume over six orders of magnitude; however, the same is true for the estimate of the standard deviation of the voxel intensity, so one is naturally led to define a relative standard deviation in each voxel as \(\sigma _{px} / I_{px}\) . To facilitate the interpretation of the results, we averaged these relative standard deviations of the signal on spheres of constant q and plotted those as a function of q (see Fig.  6 ). This enabled us to better judge the quality of convergence at different reciprocal resolution scales.

In our previous work 18 , we simulated 1000 XMDYN realizations for 2NIP (which has diameter of 70 Å) using the same set of X-ray pulse parameters (same SASE pulses). We took 100 of these realizations, so we could compare the relative standard deviation for molecules of different sizes. In Fig.  6 , we show the relative standard deviation of the signal as a function of q , obtained for both molecules. The relative standard deviation rapidly increases with increasing q and then stabilizes at a value close to 0.2. This implies that if we calculate the mean reciprocal-space image from \(N\ge 25\) realizations, the relative standard deviation of this mean would be less than 4% in the entire q -range (assuming the validity of the central limit value theorem in this case).

Perhaps surprisingly, the relative standard deviations of the signal are comparable for both molecules, with the relative standard deviations of the signal for 2NIP being slightly higher than that for the ribosome. This implies that one would need a similar number of realizations for both the small 2NIP and the large ribosome, in order to achieve a similar accuracy for the time-integrated 3D diffraction image.

figure 6

The relative standard deviation of the intensity signal as a function of q for 2NIP and ribosome molecules. It was calculated from 100 XMDYN realizations for both molecules.

Below we also show the resolution-dependent R-factor for ribosome and 2NIP molecules (see Figs.  7 , 8 respectively). The R-factor is calculated from reciprocal-space intensity distributions. It measures the degradation of the diffraction image quality due to radiation damage and Compton scattering with respect to the diffraction from an undamaged molecule (elastic signal only; see e.g. Ref. 18 ). We found that the R-factor was already converged when 25 MD realizations were used for its calculation, both for the ribosome and 2NIP molecules.

One has to mention that for calculating the R-factor we used 2000 diffraction images. They were created from 100 MD realizations of X-ray irradiated ribosome, after rotating them randomly 20 times for each realization. This was possible due to the observation that the damage of the molecule negligibly depends on the orientation of the molecule with respect to the incoming X-ray beam. This is discussed in detail in the supplementary material. This procedure significantly reduced otherwise very extensive computational costs.

figure 7

R-factor as a function of full-period resolution. It measures the degradation of diffraction image quality with respect to the diffraction image from undamaged 2NIP molecule. It was calculated with: (i) all 100 simulated MD realizations, and (ii) with 25 realizations randomly selected.

figure 8

R-factor as a function of full-period resolution. It measures the degradation of diffraction image quality with respect to the diffraction image from undamaged ribosome molecule. It was calculated with: (i) all 100 simulated MD realizations, and (ii) with 25 realizations randomly selected.

In the previous work 18 , the image quality degradation (due to radiation damage and compton scattering) quantified using the R-factor, was studied for the 2NIP molecule, which contains only \(\sim\) 5000 non-hydrogen atoms. Our current analysis has provided the R-factor for a much larger molecule, ribosome, with \(\sim\) 150,000 non-hydrogen atoms. As the R-factor values are very similar for both molecules (Figs.  7 and 8 ) despite the very different molecule size, one can expect that the R-factor for molecules of a size located between these two values will be similar for the same set of X-ray pulse parameters.

Conclusions

In this work, we studied computationally the conditions for statistically reliable description of radiation damage in SPI simulations, in particular the convergence with respect to the realization number and the image quality degradation. We showed that in order to meaningfully characterize image quality degradation during SPI of small and large molecules, one only needs to simulate a few tens of realizations. Also, we demonstrated that for the same set of X-ray pulse parameters, the R-factors, measuring the image quality degradation, are very similar, both for the \(\sim\) 150-thousand-non-hydrogen-atom large ribosome molecule and \(\sim\) 5-thousand-atom large 2NIP molecule. One can then expect that the realization-number convergence and R-factor for a molecule of a size located between these two limiting cases will behave similarly for the same set of X-ray pulse parameters. Our study shows that computational SPI studies for biological samples of realistic size are feasible, and the SIMEX platform can be efficiently used for the simulations of SPI experiments preceding real experiments, helping to estimate optimal parameters for these experiments.

Data availability

Data are available from the corresponding author M. S. upon reasonable request.

Bogan, M. J. et al. Single particle X-ray diffractive imaging. Nano Lett. 8 , 310–316. https://doi.org/10.1021/nl072728k (2008).

Article   ADS   CAS   PubMed   Google Scholar  

Seibert, M. M. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470 , 78–81. https://doi.org/10.1038/nature09748 (2011).

Article   ADS   CAS   PubMed   PubMed Central   Google Scholar  

Sobolev, E. et al. Megahertz single-particle imaging at the European XFEL. Commun. Phys. https://doi.org/10.1038/s42005-020-0362-y (2020).

Article   Google Scholar  

Bielecki, J., Maia, F. R. N. C. & Mancuso, A. P. Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources. Struct. Dynam. 7 , 040901. https://doi.org/10.1063/4.0000024 (2020).

Article   CAS   Google Scholar  

Cheng, Y. Single-particle cryo-em-how did it get here and where will it go. Science 361 , 876–880. https://doi.org/10.1126/science.aat4346 (2018).

Nogales, E. The development of cryo-em into a mainstream structural biology technique. Nat. Methods 13 , 24–27. https://doi.org/10.1038/nmeth.3694 (2016).

Article   CAS   PubMed   PubMed Central   Google Scholar  

Sun, Z., Fan, J., Li, H. & Jiang, H. Current status of single particle imaging with x-ray lasers. Appl. Sci. https://doi.org/10.3390/app8010132 (2018).

Barty, A. et al. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat. Photonics 6 , 35–40. https://doi.org/10.1038/nphoton.2011.297 (2012).

Xu, R. et al. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat. Commun. 5 , 4061. https://doi.org/10.1038/ncomms5061 (2014).

Mancuso, A. P. et al. The single particles, clusters and biomolecules and serial femtosecond crystallography instrument of the European XFEL: Initial installation. J. Synchrotron Radiat. 26 , 660–676. https://doi.org/10.1107/S1600577519003308 (2019).

Nass, K. et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 11 , 1814. https://doi.org/10.1038/s41467-020-15610-4 (2020).

Chapman, H. N. et al. Femtosecond x-ray protein nanocrystallography. Nature 470 , 73–77. https://doi.org/10.1038/nature09750 (2011).

Ziaja, B. et al. Towards realistic simulations of macromolecules irradiated under the conditions of coherent diffraction imaging with an x-ray free-electron laser. Photonics 2 , 256–269. https://doi.org/10.3390/photonics2010256 (2015).

Yoon, C. H. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray free-electron laser. Sci. Rep. https://doi.org/10.1038/srep24791 (2016).

Article   PubMed   PubMed Central   Google Scholar  

Fortmann-Grote, C. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray free-electron laser. IUCrJ 4 , 560–568. https://doi.org/10.1107/S2052252517009496 (2017).

Fortmann-Grote, C. & E, J. C. Simex. howpublished https://github.com/PaNOSC-ViNYL/SimEx (2020).

Juncheng, E. et al. Simex-lite: Easy access to start-to-end simulation for experiments at advanced light sources. Proc. SPIE https://doi.org/10.1117/12.2677299 (2023).

Juncheng, E. et al. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray free-electron laser. Sci. Rep. 11 , 17976. https://doi.org/10.1038/s41598-021-97142-5 (2021).

Juncheng, E. et al. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Sci. Rep. 13 , 16359. https://doi.org/10.1038/s41598-023-43298-1 (2023).

Ziaja, B., Wabnitz, H., Wang, F. & Weckert, E. Energetics, ionization, and expansion dynamics of atomic clusters irradiated with short intense vacuum-ultraviolet pulses. Phys. Rev. Lett. 102 , 205002 (2009).

Jurek, Z., Son, S.-K., Ziaja, B. & Santra, R. XMDYN and XATOM: Versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter. J. Appl. Crystallogr. 49 , 1048–1056 (2016).

Article   ADS   CAS   Google Scholar  

Murphy, B. F. et al. Femtosecond X-ray-induced explosion of C 60 at extreme intensity. Nat. Commun. 5 , 4281. https://doi.org/10.1038/ncomms5281 (2014).

Stransky, M., Jurek, Z., Santra, R., Mancuso, A. & Ziaja, B. Tree-code based improvement of computational performance of the X-ray-matter-interaction simulation tool XMDYN. Molecules 27 , 4206. https://doi.org/10.3390/molecules27134206 (2022).

Zhang, W., Dunkle, J. A. & Cate, J. H. D. Structures of the ribosome in intermediate states of ratcheting. Science 325 , 1014–1017. https://doi.org/10.1126/science.1175275 (2009).

Gibbon, P. PEPC: Pretty Efficient Parallel Coulomb-solver. Technical Report, FORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte Mathematik FZJ-ZAM-IB-2003-05 (2003).

Inoue, I. et al. Femtosecond reduction of atomic scattering factors triggered by intense x-ray pulse. Phys. Rev. Lett. 131 , 163201 (2023).

Abdullah, M. M., Son, S.-K., Jurek, Z. & Santra, R. Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description. IUCrJ 5 , 699–705. https://doi.org/10.1107/S2052252518011442 (2018).

Download references

Acknowledgements

We thank J. Bielecki for insightful comments. A.P.M. and B.Z. gratefully acknowledge the funding received from the R & D grant provided by the European XFEL, with the contribution of IFJ PAN in Krakow.

Open Access funding enabled and organized by Projekt DEAL.

Author information

Authors and affiliations.

European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany

Michal Stransky, Juncheng E, Richard Bean & Adrian P. Mancuso

Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland

Michal Stransky & Beata Ziaja

Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21, Prague 8, Czech Republic

Michal Stransky

Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany

Zoltan Jurek, Robin Santra & Beata Ziaja

The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany

Zoltan Jurek & Robin Santra

Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany

Robin Santra

Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK

Adrian P. Mancuso

Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia

You can also search for this author in PubMed   Google Scholar

Contributions

The concept of the paper was proposed by A.P.M. and B.Z.; M.S. performed the molecular dynamics simulation; M.S. and J.E. analyzed its results, with the support of Z.J. and B.Z.; M.S., J.E., Z.J., B.Z. wrote the first draft of the manuscript. All authors discussed and interpreted the data, and contributed to writing the manuscript.

Corresponding authors

Correspondence to Michal Stransky , Juncheng E or Adrian P. Mancuso .

Ethics declarations

Competing interests.

The authors declare no competing interests.

Additional information

Publisher's note.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Supplementary information., rights and permissions.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ .

Reprints and permissions

About this article

Cite this article.

Stransky, M., E, J., Jurek, Z. et al. Computational study of diffraction image formation from XFEL irradiated single ribosome molecule. Sci Rep 14 , 10617 (2024). https://doi.org/10.1038/s41598-024-61314-w

Download citation

Received : 14 February 2024

Accepted : 03 May 2024

Published : 09 May 2024

DOI : https://doi.org/10.1038/s41598-024-61314-w

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

By submitting a comment you agree to abide by our Terms and Community Guidelines . If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Quick links

  • Explore articles by subject
  • Guide to authors
  • Editorial policies

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

research article on x ray crystallography

Controlled morphology of a new 3D Co(II) metal–organic framework (Co-MOF) via green sonochemical synthesis: crystallography, Hirshfeld surface analysis

  • Published: 09 May 2024
  • Volume 26 , article number  100 , ( 2024 )

Cite this article

research article on x ray crystallography

  • Seyedeh Elahe Hosseini 1 ,
  • Mohammad Kazem Mohammadi 1 ,
  • Payam Hayati 2 ,
  • Haman Tavakkoli 1 &
  • Ayeh Rayatzadeh 1  

Nanostructures of a cobalt(II) metal–organic framework (MOF), denoted as 4,4′,4″-s-triazin-1,3,5-triyltri-p-aminobenzoate (TATAB) [[Co 2 (TATAB)(OH)(H 2 O) 2 ].H 2 O.0.6O] n {1 } , were successfully synthesized using two different experimental techniques: solvothermal and sonochemical strategies. Remarkably, both methods yielded an identical crystal structure. Various characterization techniques, including powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR), were employed to analyze all the compounds. Compound contains cobalt ions (Co 2+ ) that were determined to be six-coordinated through the analysis of single-crystal X-ray diffraction (SCXRD). The effect of various factors such as temperature, reaction time, reactant concentration, and ultrasonic energy on the synthesis and final morphology of the compounds obtained by sonochemical method was investigated. Finally, Hirshfeld surface analysis (HAS) of compound was conducted. The molecular descriptors obtained at the BLYP/6–311 +  + g (d, p) level of theory framework indicate a unique electronic structure for this complex, characterized by low chemical hardness ( η  = 1.702 eV), high electrophilicity ( ω  = 3.637 eV), and a narrow HOMO–LUMO gap (1.55 eV). These descriptors suggest that this complex can be considered a favorable nucleophile in interactions with proteins.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price includes VAT (Russian Federation)

Instant access to the full article PDF.

Rent this article via DeepDyve

Institutional subscriptions

research article on x ray crystallography

Marandi F et al (2017) Synthesis, spectral and X-ray diffraction of two new 2D lead (II) coordination polymers formed by nicotinic acid N-oxide linkers. J Mol Struct 1149:92–98

Article   CAS   Google Scholar  

Yang Y et al (2009) Supramolecular networks of hexanuclear cadmium (II): synthesis, crystal structure and emission property. Inorg Chim Acta 362(9):3065–3068

Moon D et al (2006) Face-driven corner-linked octahedral nanocages: M6L8 cages formed by C 3-symmetric triangular facial ligands linked via C 4-symmetric square tetratopic PdII Ions at truncated octahedron corners. J Am Chem Soc 128(11):3530–3531

Article   CAS   PubMed   Google Scholar  

Norjmaa G et al (2021) Modeling kinetics and thermodynamics of guest encapsulation into the [M4L6] 12–supramolecular organometallic cage. J Chem Inf Model 61(9):4370–4381

Article   CAS   PubMed Central   PubMed   Google Scholar  

Evans OR, Lin W (2002) Crystal engineering of NLO materials based on metal− organic coordination networks. Acc Chem Res 35(7):511–522

Rashidi N et al (2021) Antibacterial and cytotoxicity assay of two new Zn (ii) complexes: synthesis, characterization, X-ray structure, topology, Hirshfeld surface and thermal analysis. J Mol Struct 1231:129947

Hanifehpour Y et al (2015) Sonochemical syntheses of two new flower-like nano-scale high coordinated lead (II) supramolecular coordination polymers. Ultrason Sonochem 23:282–288

Sharifzadeh Z, Morsali A (2022) Amine-functionalized metal-organic frameworks: from synthetic design to scrutiny in application. Coord Chem Rev 459:214445

Caneschi A et al (2001) Cobalt (II)-nitronyl nitroxide chains as molecular magnetic nanowires. Angew Chem Int Ed 40(9):1760–1763

Tanatani A, Mio MJ, Moore JS (2001) Chain length-dependent affinity of helical foldamers for a rodlike guest. J Am Chem Soc 123(8):1792–1793

Zhang Z et al (2023) Coordination-driven self-assembly of dibenzo-18-crown-6 functionalized Pt (II) metallacycles. Chin Chem Lett 34(2):107521

Roesky HW, Andruh M (2003) The interplay of coordinative, hydrogen bonding and π–π stacking interactions in sustaining supramolecular solid-state architectures: a study case of bis (4-pyridyl)-and bis (4-pyridyl-N-oxide) tectons. Coord Chem Rev 236(1–2):91–119

Das D, Roy S, Biradha K (2018) Crystal engineering with isosteric triether and triamine linked aromatic tri-carboxylic acids: iso-structurality and synthon interplay in their co-crystals and salts with bis (pyridyl) derivatives. New J Chem 42(24):19953–19962

Chen XM, Liu GF (2002) Double-stranded helices and molecular zippers assembled from single-stranded coordination polymers directed by supramolecular interactions. Chem A Eur J 8(20):4811–4817

Emerson AJ et al (2018) High-connectivity approach to a hydrolytically stable metal–organic framework for CO2 capture from flue gas. Chem Mater 30(19):6614–6618

Nabipour H et al (2020) Metal-organic frameworks for flame retardant polymers application: a critical review. Compos A Appl Sci Manuf 139:106113

Karimi M et al (2021) Metal–organic framework. Interface Science and Technology. Elsevier, pp 279–387

Google Scholar  

Liu W et al (2018) Cobalt complexes as an emerging class of catalysts for homogeneous hydrogenations. Acc Chem Res 51(8):1858–1869

Rahpeyma M, MJ Soltanian Fard, and P Hayati, Green chemistry syntheses of different morphology novel nano-sized cobalt (II) supramolecular: as a precursor for the synthesis of cobalt (II) oxide nanoparticles, thermal, Hirshfeld surface analysis, and biological activities . Iran J Chem Chem Eng 2023

Lin W, Rieter WJ, Taylor KM (2009) Modular synthesis of functional nanoscale coordination polymers. Angew Chem Int Ed 48(4):650–658

Spokoyny AM et al (2009) Infinite coordination polymer nano-and microparticle structures. Chem Soc Rev 38(5):1218–1227

Li H et al (2015) Multi-component coordination-driven self-assembly toward heterometallic macrocycles and cages. Coord Chem Rev 293:139–157

Article   Google Scholar  

Zheng S-L et al (2001) Toward designed assembly of microporous coordination networks constructed from silver (I)− hexamethylenetetramine layers. Inorg Chem 40(14):3562–3569

Kirillov AM (2011) Hexamethylenetetramine: an old new building block for design of coordination polymers. Coord Chem Rev 255(15–16):1603–1622

Barcikowski S et al (2019) Materials synthesis in a bubble. MRS Bull 44(5):382–391

Qiu L-G et al (2008) Facile synthesis of nanocrystals of a microporous metal–organic framework by an ultrasonic method and selective sensing of organoamines. Chem Commun 31:3642–3644

Sabouni R, Kazemian H, Rohani S (2010) A novel combined manufacturing technique for rapid production of IRMOF-1 using ultrasound and microwave energies. Chem Eng J 165(3):966–973

Safarifard V, Morsali A, Joo SW (2013) Sonochemical synthesis and characterization of nano-sized lead (II) 3D coordination polymer: precursor for the synthesis of lead (II) oxybromide nanoparticles. Ultrason Sonochem 20(5):1254–1260

Paulusse JM, Huijbers JP, Sijbesma RP (2006) Quantification of ultrasound-induced chain scission in PdII–phosphine coordination polymers. Chem Eur J 12(18):4928–4934

Suslick KS (1991) The sonochemical hot spot. J Acoust Soc Am 89:1885–1886

Haque E et al (2010) Synthesis of a metal–organic framework material, iron terephthalate, by ultrasound, microwave, and conventional electric heating: a kinetic study. Chem Eur J 16(3):1046–1052

Jung D-W et al (2010) Facile synthesis of MOF-177 by a sonochemical method using 1-methyl-2-pyrrolidinone as a solvent. Dalton Trans 39(11):2883–2887

Alavi MA, Morsali A (2010) Syntheses and characterization of Sr (OH) 2 and SrCO3 nanostructures by ultrasonic method. Ultrason Sonochem 17(1):132–138

Rigaku, C.-S., Expert 2.1 b43. The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan, 2014

Sheldrick GM (2015) SHELXT–integrated space-group and crystal-structure determination. Acta Crystallogr A Found Adv 71(1):3–8

Article   PubMed Central   PubMed   Google Scholar  

Spek AL (2009) Structure validation in chemical crystallography. Acta Crystallogr D Biol Crystallogr 65(2):148–155

Nonius, B., SADABS. Bruker Nonius, Delft, The Netherlands, 2002

Altomare A et al (1999) SIR97: a new tool for crystal structure determination and refinement. J Appl Crystallogr 32(1):115–119

Turner, M., et al., CrystalExplorer17; University of Western Australia, 2017. (b) Spackman, MA; Jayatilaka, D. CrystEngComm, 2009 11 19

Blatov VA, Shevchenko AP, Proserpio DM (2014) Applied topological analysis of crystal structures with the program package ToposPro. Cryst Growth Des 14(7):3576–3586

Farrugia LJ (2012) WinGX and ORTEP for Windows: an update. J Appl Crystallogr 45(4):849–854

Abbasi A, Moradpour T, Van Hecke K (2015) A new 3D cobalt (II) metal–organic framework nanostructure for heavy metal adsorption. Inorg Chim Acta 430:261–267

Pakiari AH, Eshghi F (2017) Geometric and electronic structures of vanadium sub-nano clusters, Vn (n= 2–5), and their adsorption complexes with CO and O2 ligands: a DFT-NBO study. Phys Chem Res 5(3):601–615

CAS   Google Scholar  

Frisch M et al., Gaussian 09, Revision D. 01, Gaussian, Inc., Wallingford CT . See also: URL: http://www.gaussian.com , 2009

Wang YA, Liu S, Parr RG (1997) Laurent series expansions in density functional theory. Chem Phys Lett 267(1–2):14–22

Molegro A, MVD Molegro Virtual Docker 5.0. Molegro: Aarhus C, Denmark, 2011

Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49(11):3315–3321

Li CG et al (2022) Novel zinc (II) and nickel (II) complexes of a quinazoline-based ligand with an imidazole ring: Synthesis, spectroscopic property, antibacterial activities, time-dependent density functional theory calculations and Hirshfeld surface analysis. Appl Organomet Chem 36(5):e6622

Tyula YA et al (2018) A new supramolecular zinc (II) complex containing 4-biphenylcarbaldehyde isonicotinoylhydrazone ligand: nanostructure synthesis, catalytic activities and Hirshfeld surface analysis. Appl Organomet Chem 32(3):e4141

Chai YM et al (2022) Antimicrobial activities of two 1-D, 2-D, and 3-D mononuclear Mn (II) and dinuclear Bi (III) complexes: X-ray structures, spectroscopic, electrostatic potential, Hirshfeld surface analysis, and time-dependent/density functional theory studies. Appl Organomet Chem 36(6):e6682

Tasi G et al (1993) Calculation of electrostatic potential maps and atomic charges for large molecules. J Chem Inf Comput Sci 33(3):296–299

Download references

Acknowledgements

Support of this investigation by Islamic Azad University, Ahvaz Branch, is gratefully acknowledged.

Author information

Authors and affiliations.

Advanced Surface Engineering and Nano Materials Research Center, Department of Chemistry, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran

Seyedeh Elahe Hosseini, Mohammad Kazem Mohammadi, Haman Tavakkoli & Ayeh Rayatzadeh

Organic and Nano Group, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran

Payam Hayati

You can also search for this author in PubMed   Google Scholar

Contributions

Elahe Hosseini worked on the synthesis of nanocomposite. Mohammad Kazem Mohammadi, Haman Tavakkoli, and Ayeh Rayatzadeh characterized the synthesized nanostructure and theory.

Corresponding author

Correspondence to Mohammad Kazem Mohammadi .

Ethics declarations

Competing interests.

The author(s) declare no competing interests.

Additional information

Publisher's note.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 260 KB)

Rights and permissions.

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Hosseini, S.E., Mohammadi, M.K., Hayati, P. et al. Controlled morphology of a new 3D Co(II) metal–organic framework (Co-MOF) via green sonochemical synthesis: crystallography, Hirshfeld surface analysis. J Nanopart Res 26 , 100 (2024). https://doi.org/10.1007/s11051-024-05991-8

Download citation

Received : 09 February 2024

Accepted : 12 April 2024

Published : 09 May 2024

DOI : https://doi.org/10.1007/s11051-024-05991-8

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

  • Metal–organic framework
  • Sonochemical Synthesis
  • Crystallography
  • Hirshfeld Surface Analysis
  • Find a journal
  • Publish with us
  • Track your research

Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.

Volume 30, Number 6—June 2024

Chest radiograph screening for detecting subclinical tuberculosis in asymptomatic household contacts, peru.

Main Article

research article on x ray crystallography

Figure 4 . Association between degree of baseline chest radiograph severity and time to developing incident TB among persons with abnormal radiograph findings by age group, Peru. Gray shading indicates 95% CIs. A) 16–24-year age group (n = 12). Mean difference −0.004 (95% CI −0.007 to −0.001); p < 0.001, ρ = −0.71; B) 25–44-year age group (n = 6). Mean difference −0.0002 (95% CI −0.015 to 0.015); p = 0.96, ρ = −0.025; C) > 45-year age group (n = 9). Mean difference 0.0006 (95% CI −0.004 to 0.005); p = 0.73, ρ = 0.14. ρ, Pearson correlation coefficient.

1 These authors contributed equally to this article.

Exit Notification / Disclaimer Policy

  • The Centers for Disease Control and Prevention (CDC) cannot attest to the accuracy of a non-federal website.
  • Linking to a non-federal website does not constitute an endorsement by CDC or any of its employees of the sponsors or the information and products presented on the website.
  • You will be subject to the destination website's privacy policy when you follow the link.
  • CDC is not responsible for Section 508 compliance (accessibility) on other federal or private website.

IMAGES

  1. X-ray crystallography

    research article on x ray crystallography

  2. X-Ray Crystallography

    research article on x ray crystallography

  3. X-Ray Crystallography

    research article on x ray crystallography

  4. Using X-Ray Crystallography to Simplify and Accelerate Biologics Drug

    research article on x ray crystallography

  5. PPT

    research article on x ray crystallography

  6. Home

    research article on x ray crystallography

VIDEO

  1. Scientists Used DNA To Create World's Smallest Antenna Ever For an Unusual Reason

  2. X-ray Crystallography: Principles

  3. X ray Crystallography method of determination of the structure of protein

  4. What is X-ray crystallography?

  5. X-ray Crystallography: Crystal Symmetry

  6. X-ray Crystallography: Production of X-ray and its properties

COMMENTS

  1. X-ray crystallography

    X-ray crystallography is a technique that uses X-ray diffraction patterns to determine high-resolution, three-dimensional structures of molecules such as proteins, small organic molecules, and ...

  2. X-ray crystallography articles within Scientific Reports

    Non contrast enhanced volumetric histology of blood clots through high resolution propagation-based X-ray microtomography. Somayeh Saghamanesh. , Daniela Dumitriu LaGrange. & Robert Zboray.

  3. (PDF) Crystallography applications: A comprehensive review

    X-ray crystallography has had a revolutionary impact in the f ields of chemistry and biology in particular. For example, the determination of the double helix structure of DNA in 1953 was achieved

  4. X-ray crystallography

    Read the latest Research articles in X-ray crystallography from Nature. ... X-ray crystallography, cryo-electron microscopy, structural modelling, biochemistry, cell biology, and evolutionary ...

  5. A review of basic crystallography and x-ray diffraction applications

    Although various researched works have been carried out in x-ray crystallography and its applications, but there are still limited number of researches on crystallographic theories and industrial application of x-ray diffraction. ... Introduction to X-ray powder, Research note, EPS 400-001, p 10. Alejandro BR (2007) Fast quantification of avion ...

  6. X-Ray Crystallography and its Role in Understanding the ...

    Over the past century, the role of X-ray crystallography as a tool to probe the structure and function of materials has greatly been acknowledged. Prediction of properties of a material based solely on its crystal structure is an emerging area of research and efforts in this direction further underscore the importance of X-ray crystallography.

  7. X-ray crystallography over the past decade for novel drug discovery

    X-ray crystallography typically requires a homogeneous fraction of macromolecules to obtain diffraction quality crystals (and/or the process of crystallization naturally selects for a homogenous fraction of the molecule). ... The authors' research was supported with federal funds from the National Institute of Allergy and Infectious Diseases ...

  8. New developments in crystallography: exploring its technology, methods

    Introduction. To first set a historical context, of especial significance is that the Protein Data Bank (PDB) was launched nearly five decades ago (in 1971) by the Cambridge Structure Database (CSD) and the Brookhaven National Laboratory [] and which now has more than 120,000 depositions.The majority of these are from X-ray crystallography and 90% of these are from synchrotron radiation beamlines.

  9. 248929 PDFs

    Explore the latest full-text research PDFs, articles, conference papers, preprints and more on X-RAY CRYSTALLOGRAPHY. Find methods information, sources, references or conduct a literature review ...

  10. X-ray Crystallography: One Century of Nobel Prizes

    The year 1962 witnessed another Nobel Prize involving X-ray crystallography, that awarded in Medicine to Crick, Watson, and Wilkins for the molecular structure of nucleic acids. While examining DNA-oriented films for UV dichroism, Wilkins noted extremely uniform fibers, serendipitously produced while manipulating DNA gel.

  11. Protein X-ray Crystallography and Drug Discovery

    1. Introduction. The first X-ray diffraction by protein crystals was reported in the early thirties [1,2], but nearly 30 years passed before the atomic crystallographic structure of myoglobin was published [].Yet, the potential of X-ray crystallography was already evidenced as it allowed the unambiguous structure determination of penicillin [].X-ray diffraction, either on crystalline material ...

  12. A Fluorinated Chaperone Gives X‐ray Crystal Structures of Acyclic

    Research Article. A Fluorinated Chaperone Gives X-ray Crystal Structures of Acyclic Natural Product Derivatives up to 338 Molecular Weight. Tim Berking, ... Crystallizing molecules with long flexible chains is a challenge, making it difficult to perform X-ray crystallography. Chaperones can assist in the crystallization of compounds that do not ...

  13. X-Ray Crystallography

    X-ray crystallography is a tool used for determining the atomic and molecular structure of a crystal. The underlying principle is that the crystalline atoms cause a beam of X-rays to diffract into many specific directions (Fig. 2.10).By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a 3D picture of the density of electrons within the crystal.

  14. Journal of Applied Crystallography

    December 2023. Volume 56, Pages: 1313-1615. October 2023. Many research topics in condensed matter research, materials science and the life sciences make use of crystallographic methods to study crystalline and non-crystalline matter with neutrons, X-rays and electrons. Articles published in Journal of Applied Crystallography focus on these ...

  15. X-Ray Crystallography and the Elucidation of the Structure of DNA

    X-ray crystallography is an imaging technique first described in 1913 by the father-and-son duo of William Henry Bragg (1862-1942) and William Lawrence Bragg (1890-1971), in which x-rays are projected onto a crystalline solid to determine atomic positioning and molecular structure. Two key characteristics of x-rays and crystalline materials ...

  16. X-ray crystallography

    High-speed fixed-target serial virus crystallography. A new sample-delivery method for serial X-ray crystallography exploits the full repetition rate of the X-ray free-electron laser at the LCLS ...

  17. The Nobel Science: One Hundred Years of Crystallography

    A new kind of ray. The story of X-ray crystallography begins with a professor at the University of Würzburg, Wilhelm Conrad Röntgen. As a child Röntgen did not show any notable outstanding academic ability, besides in mathematics (Simmons 2002), however he was very skilled in building mechanical contraptions, an attribute which proved particularly useful during his research career ...

  18. Developments in X-ray Crystallographic Structure ...

    These Nobel Prizes signal the effect that crystallography has had and continues to have in the world of cutting-edge research. Fig. 1 Visualization of macromolecular structures. (A) ... , x-ray crystallography has seen many developments that have moved it into center stage as an essential discipline contributing to a broad portfolio of ...

  19. X-ray crystallography

    A powder X-ray diffractometer in motion. X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract in specific directions. By measuring the angles and intensities of the X-ray diffraction, a crystallographer can produce a three-dimensional picture of the ...

  20. Picoplatin binding to proteins: X-ray structures and mass spectrometry

    X-ray crystallography identifies different binding sites on the two proteins, highlighting a different behaviour of picoplatin in the absence or presence of dimethyl sulfoxide (DMSO). Metal-containing fragments bind to HEWL close to the side chains of His15, Asp18, Asp119 and both Lys1 and Glu7, whereas they bind to RNase A on the side chain of ...

  21. X-Ray Crystallography of Chemical Compounds

    Crystallographic studies play a vital role in many disciplines including materials science, chemistry, pharmacology, and molecular biology. X-ray crystallography is the most comprehensive technique available to determine molecular structure. A requirement for the high accuracy of crystallographic structures is that a 'good crystal' must be ...

  22. Development of high-performance direct X-ray detector materials: from

    X-rays Detection plays a vital role in medical imaging, industrial defect detection, security screening and scientific research. Direct X-ray detectors are of greater interest to researchers because they offer the advantages of faster imaging, higher resolution and simpler construction than indirect detector Journal of Materials Chemistry C Recent Review Articles

  23. X-ray crystallographic analyses of 14 IPMK inhibitor complexes

    Inositol polyphosphate multikinase (IPMK) is a ubiquitously expressed kinase that has been linked to several cancers. Here, we report 14 new co-crystal structures (1.7 Å - 2.0 Å resolution) of human IPMK complexed with various IPMK inhibitors developed by another group. The new structures reveal two ordered water molecules that participate in hydrogen-bonding networks, and an unoccupied ...

  24. Computational study of diffraction image formation from XFEL ...

    Single particle imaging (SPI) at atomic resolution is one of the most vaunted research goals for X-ray free-electron laser (XFEL) facilities 1,2,3.Such a capability has the potential for a ...

  25. X-Ray Crystallography: The Past and Present of the Phase Problem

    X-Ray Crystallography: The Past and Present of the Phase Problem. Published: February 2002. Volume 13 , pages 81-96, ( 2002 ) Cite this article. Download PDF. David Sayre. 412 Accesses. 27 Citations.

  26. x Ray crystallography

    The aim of x ray crystallography is to obtain a three dimensional molecular structure from a crystal. A purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam. The resulting diffraction patterns can then be processed, initially to yield information about the crystal packing symmetry and the size of the repeating unit that forms the crystal.

  27. Accelerating material characterization: Machine learning meets X-ray

    In a new study in ACS Chemistry of Materials, LLNL scientists Wonseok Jeong and Tuan Anh Pham developed a new approach that combines machine learning with X-ray absorption spectroscopy (XANES) to elucidate the chemical speciation of amorphous carbon nitrides. The research offers profound new insights into the local atomic structure of the ...

  28. Controlled morphology of a new 3D Co(II) metal-organic ...

    As shown in Figs. 4 and 5, hydrogen bonds between hydrogen atoms of water molecules and oxygen atoms of carboxylate groups in the ligand 4,4′,4″-s-triazin-1,3,5-triyltri-p-aminobenzoate (TATAB) is formed, and the distance between two aromatic rings is 4.092 Å.Figure 6 also shows that this three-dimensional coordination complex is connected through intramolecular interactions and expands ...

  29. Progress in protein crystallography

    Two pioneers of protein crystallography, Max Perutz and John Kendrew, were winners of the Nobel Prize in Chemistry in 1962 for solving the first ever X-ray crystal structures of proteins, those of hemoglobin [ 4] and myoglobin [ 5 ]. X-ray crystallography played an important role in deciphering the structure of fibrous DNA, for which James ...

  30. Figure 4

    Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released. Volume 30, Number 6—June 2024 Research Chest Radiograph Screening for Detecting Subclinical Tuberculosis in Asymptomatic Household Contacts, Peru