News

SU Papers

A new paper has been published by the NanED PhD student Angelina Vypritskaia of Stockholm University on Acta Crystallographica C titled: “How to use DIALS to process chemical crystallography 3D ED rotation data from pixel array detectors”. In the papers the researchers explain how they have modified the software DIALS, originally developed among others by D. Watermann of UKRI for data analysis of x-ray diffraction, for the analysis of continuous rotation ED data.  The full data analysis with DIALS was successfully tested on one of our round robin samples, natrolite, and on two organic crystals histidine and 1,3,5-triphenylbenzene. The data were collected with a standard TEM set up and with the innovative electron diffractometers Eldico ED-1 and Rigaku Synergy-ED, demonstrating the high flexibility of the software. The article was awarded by the cover of the January issue of Acta Crystallography C.    

CNRS

The 7^th of November 2024 at CNRS-Crismat Laboratory in Caen, France, our ESR Erica Cordero-Oyonarte successfully defended her PhD thesis on "Electrοn crystallοgraphy οf nanοparticles", becoming “Docteur de l’Université de Caen Normandie spécialité Chimie”. Supervised by Philippe Boullay, Erica has investigated the minimum crystal size still suitable for a 3D ED experiment. She has demonstrated that it is possible to collect 3D ED data on nanoparticles as small as 10 nm obtaining a very detail crystal structure using dynamical refinements on these data sets. Remarkable examples of what can be done are the detectability and refinement of lithium sites in Li_xTO₂ nanoparticles or the successful refinement of the partial occupancy in MgTi₂O₅ nanoparticles.   

Well done Erica all the NanED team is proud of you!

CNRS

The 30^th of October 2024 at CNRS-Crismat Laboratory in Caen, France, our ESR Sara Passuti successfully defended her PhD thesis on "Electron crystallography of nanodomains in functional materials", becoming “Docteur de l’Université de Caen Normandie spécialité Chimie”. Supervised by Philippe Boullay, Sara has demonstrated that 3D ED can be used to obtain highly accurate structural data with very high spatial resolution. She has been able to follow the structure relaxation of an epitaxial thin film on its first 20 nanometers from the interface with the substrate. She also observed structure variations on a few nanometers scale in grains of a polycrystalline ceramic compound. All these results are new and unexpected at the accuracy level attained and open a new field of investigation. Well done Sara all the NanED team congratulates you on this remarkable achievement.    

FZU PAPERS

A new paper has been published by the NanED researchers of FZU on Nature Communications titled: “Ionisation of atoms determined by kappa refinement against 3D electron diffraction data”. The group lead by Lukas Palatinus with the participation of NanED PhD students Ashwin Suresh and Chintakindi Hrushikesh demonstrated how, by going beyond the independent atom model (IAM),  3D ED is able to probe the ionization state of the atoms. The authors used the kappa refinement which introduces charge transfers between atoms while assuming a spherical model of the electron density. Five different samples were analyzed: quartz, natrolite, borane, lutecium aluminium garnet, and caesium lead bromide. The dynamical refinements carried out in this way improved the structure with respect to IAM refinement, giving access to charge density information and opening the route to a full multipolar refinement of the electrostatic potential.

SU

Xiaodong Zou, NanED supervisor won the IVA Gold Medal 2024 a prestigious award of Royal Swedish Academy of Engineering Sciences which is awarded every year to people who, through outstanding deeds, have contributed to creating a better society. We read on the Academy motivations that Xiaodong was selected "for her contribution to developing methods for rapid structural determination of small crystals of inorganic, porous and organic materials and for her contribution to the development of porous materials for more efficient chemical and fuel production and carbon capture. She has shown how purposeful realization of a scientific vision can be combined with committed supervision and mentoring of a large number of doctoral students and young researchers”.
All the NanED team, supervisors, researchers and PhD students, congratulate Xiaodong for this remarkable achievement!

IIT Papers

A new paper has been published by the NanED researchers of IIT on ACS Omega titled: “Polymorphism in oxyresveratrol studied by 3D ED”. The group lead by Mauro Gemmi with the participation of NanED PhD student Vincentia Emerson Agbemeh discovered two new polymorphs of the natural compound oxyresveratrol directly in the batch purchased from a chemical company. One of the two is anhydrous and could be easily characterized in the TEM, while the second one contains two molecules of water in the asymmetric unit and was very elusive. In the TEM high vacuum was always transforming into the anhydrous form so its presence could only be detected from powder x-ray diffraction, but its structural characterization was impossible. The researchers had to prepare the sample with a cryo-plunging procedure that was sealing the nanocrystals in amorphous ice to prevent de-hydration in the TEM column. In this way they could collect 3D ED on the hydrated form of oxyresveratrol and solve its structure.

UA Papers

A new paper  has been published by the NanED researchers of EMAT on Chemistry of Materials titled: “In Situ Study of the Activation Process of MOF-74 Using Three-Dimensional Electron Diffraction”. The group lead by Joke Hadermann with the participation of NanED PhD student  Amirhossein Hajizadeh studied in-situ inside a TEM the process in which a MOF releases the residual solvent hosted in its pores to become activated, which means ready to function as an absorber or a catalyst. For the first time the authors have been able to follow this process at high temperature using 3D ED on nanocrystalline grains of the MOF-74 a carbon dioxide absorber. The use of a state-of-the-art direct electron detector enabled rapid acquisition and minimal exposure times, therefore minimizing beam damage of the very electron beam-sensitive MOF-74. The collected data allowed the authors to claim that also after high temperature exposure the pores of the MOF remain filled with some atoms which can impede the effective absorption of gases.  

Workshop SU

From the 3^rd to the 5^th of October NanED had its final meeting at the Arrhenius Laboratoriet in the  Frescati Campus of the Stockholm Universitet Sweden. The meeting was meant to make the final point of the project and to give to all the PhDs the possibility to present all the results of their studies in a kind of “pre defense”. The coordinator and the supervisors in charge of the different work-packages have illustrated the actual stage of development of the project, the milestones achieved and the more to come. Most of Naned partners and several local researchers and students of the Department of Materials and Environmental Chemistry attended the event. The meeting had also two international and one local guests. Prof. Tamir Gonen of UCLA gave a talk on “ A MicroED solution to the MP20 enigma” with an historical point of view of the development of the use of electron diffraction for macromolecular studies from the first 2D structure solutions to MicroED. Prof. Paulina Dominiak of University of Warsaw gave a talk on ““Multipolar scattering factors for 3D electron diffraction” where she explains how 3D ED is sensitive to charge density and can be used to study bonding in molecular crystals. Finally Gerhard Hofer of Stockholm University gave a talk on “Serial electron diffraction” to explain the novel method develop in Stockholm for collecting a large amount of 2D ED patterns on extremely beam sensitive samples like macromolecules. All the participants had also the opportunity to visit all the facilities of the Electron Microscopy Center of Stockholm University.

Workshop FZU

NanED PhD student Hrushikesh Chintakindi won the poster prize sponsored by Nanomegas company at ECM34!  The poster of Hrushikesh was about “Analysing the frame scaling and orientation matrix in the presence of appreciable dynamic diffraction effects utilizing simulated 3D ED data” and describes how dynamical effects strongly affect diffraction patterns that are close to zone axis compared to more random orientation. Hrushikesh proved that both experimental and through dynamical simulations in which the amount of dynamical scattering was tuned by reducing the occupancy factor of each atom. CONGRATULATION HRUSHI!!!!!!  

Workshop JGU FZU UBA CNRS

NanED participation to the last ECM34 meeting in Padova Italy has been amazing. ECM is the annual congress organized by the European Crystallographic Association where all the latest results in crystallography are usually presented. NanED Phd students had a great success with  4 oral contribution and three posters one of which won the Nanomegas poster prize.

Senik Matinyan had an invited talk on “Advancing protein complex analysis with AI and electron diffraction” in the session on AI, software developments and Machine learning applied to MX and CryoEM.

Erica Cordero-Oyonarte had an oral in the session “when can ED challenges XRD in small molecule crystallography?”. Erica’s talk was on 3D electron diffraction for accurate structure analysis of nanoparticles and described the interplay between minimum crystal size and accurate dynamical refinement with 3D ED data.

Sara Passuti had an oral on “Structural analysis of functional materials through Scanning Precession Electron Tomography (SPET)” in the session on advanced and new techniques to study inorganic crystal structures. Sara explained how we can have accurate structure refinement from 3D ED data on both a profile along a line crossing a thin film or on a 2D area. This is the first step towards structure mapping at the nanoscale.

Ashwin Suresh had an oral on “Atomic ionization determined by dynamical kappa refinement against 3D electron diffraction data” in the session on electron diffraction joining forces with quantum crystallography towards materials science and application. Ashwin have shown amazing results of the detection of charge density effects with 3D ED data.

NanED PhD students presented also three posters:

Marco Santucci: “PyFast-ADT: python-driven 3DED data collection and automatic crystal tracking” 

Hrushikesh Chintakindi: ”Analysing the frame scaling and orientation matrix in the presence of appreciable dynamic diffraction effects utilizing simulated 3D ED data”

Laura Gemmrich Hernandez: “Multi method study of calcium-aluminate cement hydration and its crystal structures”

Workshop IIT

NanED participation to the EMC2024 in Copenhagen Denmark congress was numerous. EMC congress joins together all European microscopists to discuss the latest novelties in the field. Apart from several talk delivered by NanED supervisors, Philippe Boullay, Lukas Palatinus and Ute Kolb, NanED PhD student Vincentia Emerson Agbemeh had an oral on “structural study of polyphasic mixtures using 3D Electron Diffraction (3D ED); a case study of oxyresveratrol”. Vincentia summarized in the talk the results published in a recent paper. She showed how by using 3D ED it is possible to study the crystal structure of a nanocrystalline hydrated natural compound by cryo-protecting it in amorphous ice. As a case study she reported the discovery of two new polymorphs of oxyresveratrol, directly identified in the sample batch bought from a chemical company.

Papers UBA

A fourth paper from Senik Matinyan, NanED PhD student,  came out recently on Frontiers on Molecular Biosciences ! In this study, Senik and co-workers present DiffraGAN, a machine learning tool designed to enhance the analysis of protein structures through diffraction methods, which struggle with the loss of phase information. DiffraGAN uses a combination of high-resolution diffraction data and low-resolution images to effectively reconstruct protein structures. Our method leverages a type of artificial intelligence known as a conditional generative adversarial network (cGAN) to predict the missing information from these datasets. We tested DiffraGAN with simulated data, showing that it can accurately phase the high-resolution diffraction data using noisy, low-resolution images. This approach may significantly improve the accuracy and efficiency of protein structure determination in structural biology.

Papers IIT

A new paper by our coordinator Mauro Gemmi appeared recently on Acta Crystallographica C. This paper is a scientific commentary on the paper by Aragon et al. (2024) which discusses the results of a round table on 3D ED/MicroED held during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. In the commentary Dr. Gemmi, in agreement with the above paper, points out how the training of electron crystallographers is one of the bottlenecks that hampers a proper diffusion of the technique. NanED was constructed for this purpose and many crystallographic associations are supporting our view. Both ECA and IUCr through their dedicated organs (the SIG04, Special Interest Group on Electron crystallography for ECA; the CEC Commission on Electron Crystallography for IUCr) sponsor every year the organization of dedicated electron crystallography schools. This year there will be one, Elcrys24, as side event of the ECM34 congress in Padova Italy, while next year the famous International Crystallography School of Erice will be dedicated to electron and quantum crystallography. Very recently, thanks to the great effort of Tatiana Gorelik, ELECTRA was founded in Europe (https://electraec.wordpress.com/), which is a non-profit educational association with the scope of supporting the organization of schools and workshops related to electron crystallography. Therefore, we can consider that the future of electron crystallography will be guaranteed by the new generations that are and will be trained in the next years to come. For what concerns the future development of the technique Dr. Gemmi sees in the complete automation of the method a key point for its diffusion in any crystallography lab. While interesting new science could arise by combining the latest fantastic results obtained by 3D ED, like absolute structure determination and observation of charge density effects, with the high spatial resolution available with bright electron nanobeams.

Papers IIT

A new paper of the NanED IIT group, came out recently on Journal of Crystal Growth & Design! The paper describes the mechanochemical synthesis of a novel MOF built from a bio-ligand that can be found in nature in edible plants: the protocatecuic acid. The MOF is synthesized with a completely green process avoiding any harsh solvent and using copper as metallic center. The mechanosynthesis produces a micro/nanocrystalline powder so the structure determination was only possible by employing the 3D ED technique. 3D ED allowed ab-initio determination of the MOF structure and also its dynamical refinement, which showed the presence of residual water in the channels. The MOF thermal degradation was studied through DSC and in-situ PXRD. Interestingly, after the thermal treatment, the sample, which seemed fully amorphous at PXRD, in the TEM revealed some crystalline residuals that thanks to 3D ED were determined to be a coordination polymer in which the MOF channels have collapsed to form a layered 2D structure. The paper was also awarded a journal cover.

Papers UBA

A third paper from Senik Matinyan, NanED PhD student,  came out recently on Acta Crystallographica A! Deep learning  applications are revolutionizing the field of protein structure prediction by addressing some of its most significant challenges. Some of the architectures are extensively used in different steps of protein crystallography as well. The review from Senik examines how deep learning techniques help in producing high-quality protein crystals, monitoring their growth and extracting accurate structures from complex, noisy, and often incomplete diffraction data.

By leveraging advanced machine learning models, researchers can now analyze the intricate patterns within the data more efficiently, leading to breakthroughs in understanding protein structures and their functions.

The review also provides a brief history of deep learning, clarifies key definitions, and discusses the traditional machine learning methods applied in structural biology, highlighting the impact of these technologies. There is a chapter which discusses key details of the architectures as well.

Course IIT

From the 19^th to the 21^th of February David Waterman and Tarik Drevon of STFC (UKRI) NanED partner gave a course to IIT in Pontedera about how to use Diffraction Integration for Advanced Light Sources software, known as DIALS, for analyzing 3D electron diffraction data. Dials is a software specifically developed and optimized to analyze single crystal diffraction data on macromolecules collected at synchrotron stations. For its wide flexibility and continuous development, it can be easily adapted to be used with other diffraction data and recently it has been specifically modified to work on ED data. We tested together with the help of David Waterman how to analyze with DIALS the 3D ED data produced by NanED ESRs @IIT. David explained the workflow of DIALS from the data import to the final intensity integration step. All the 3D ED data collected at IIT could be positively analyzed and all the structures were successfully solved. During the course the possibility to use DIALS for integrating data coming from 2D materials, where a three-dimensional unit cell does not exist, has been also discussed. We envisaged the possibility to write specific scripts that will allow us to integrate the intensity of each spot as a function of the tilt angle for providing information on the structure of each layers and their stacking modalities.

Workshops JGU

From the 6^th to the 8^th of December 2022, the NanED project had its second workshop, held in Mainz at the Johannes Guthenberg University.  

The workshop's main goal was to teach NanED PhD students how to use powder x-ray diffraction (PXRD) as a complementary tool to 3D ED. The students learned how to solve structures using PXRD and how to refine them with the Rietveld method. As a second topic, the workshop dealt with the problem of investigating disordered structures. The students had the possibility to learn how to treat diffuse scattering both in PXRD and 3DED using the most novel PDF approaches. The workshop hosted several external experts in PXRD and diffuse scattering such as R. Dinnebier of MPI Stuttgart, M. U. Schmidt of Frankfurt University,  N. Barrier of CNRS Caen, J. Plasier of Elettra Sincrotrone Trieste, R. Nieder of Erlangen University, E. Schmidt of Bremen University, C. Cuocci of Istituto di Cristallografia CNR Bari, S. Plana Ruiz of University Rovira I Virgili Tarragona. 

The workshop was designed with theoretical lectures in the morning and practical sessions in the afternoon, where the students could learn how to use the most advanced software for PXRD data analysis and had the opportunity to visit the 3D ED facilities of JGU

In order to expand and improve their soft skills, the students followed a lecture about the intellectual properties and the patent in science held by T. Einfeld of BASF.  

IIT

During the IIT digital festival “Science is ready” broadcasted live on Linkedin the 21^st of October, our coordinator Mauro Gemmi has discussed, together with other two IIT PIs, Annamaria Petrozza and Virgilio Mattoli leading the  PERSEPHONE and the 5DNanoprinting projects respectively, about the most recent advances in realizing new materials that may have a great impact on our life. Mauro had the opportunity to explain to a wide audience the targets and the aim of our project with a strong accent on its importance on the formation of a new generation of scientists that will bring forward the development of electron crystallography.  The discussion was moderated by Valeria delle Cave, head of the Foreign Press Office and Communication of competitive projects Office at IIT.

IIT

NanED PhD students Vincentia Agbemeh and Moussa Faye presented their PhD projects to the wide public in an event organized by IIT in Genova for the 2022 European Researchers’ Night.

Vincentia and Moussa had to explain to people from young children to adults what they do, why their work is important and what it will bring to our everyday life. A difficult task that Vincentia and Moussa carried out successfully. For them it was a really rewarding experience. Well done!

CRISMAT

The first paper involving the work of one of NanED PhD students is already out! A research group led by CRISMAT-CNRS laboratory synthesized a series of self-doped compounds Cu_2+xMn_1-xGeS₄ through Cu substitution to Mn. Using a combination of powder X-ray diffraction, high resolution transmission electron microscopy and precession-assisted electron diffraction tomography, they evidenced that the materials are composed of interconnected enargite- and stannite-type structures, via the formation of nanodomains with a high density of coherent interfaces. The complex crystal chemistry of such nanocomposites rises the issue of the role of the two structures and of their interfaces in the mechanism governing their electrical and thermal conductivities. Sara Passuti (ESR12 working at CRISMAT CNRS in Caen France) has analyzed and identified the structure of both stannite and enargite nanodomains using 3D ED in these complex intergrown nanocomposites. The paper is just out on Angewandte Chemie. Well done Sara!

CRISMAT

Great participation of the NanED team at the 33^rd European Crystallographic Meeting (ECM33) held in Versailles France from the 23rd to the 27th of August 2022. Several supervisors were involved in the congress as chairs and speakers in different sessions and NanED PhD students presented 9 posters in different sessions from electron crystallography to metallorganic framework, from organic crystals to macromolecules. Their posters have attracted a lot of interest and discussion. The participation in the congress has been very fruitful with the opening of possible collaboration.

JGU

Laura Gemmrich Hernandez, NanED PhD student working at Johannes Guthenberg University in Mainz on structural investigation of cement hydration mechanism by electron crystallography, won two poster prizes at ECM33! One in the electron crystallography session shared with the other NanED PhD student Sara Passuti offered by Nanomegas and another offered by CHARMAMAT LABEX in the field of advanced and functional materials.   Laura’s poster was about "Structure solution using 3DED of beam and vacuum sensitive Metal Organic Frameworks" and describes the structure modification of two new porous metal phosphonates built by an organic acid linker in the TEM vacuum. Thanks to 3D ED it has been possible to determine their structures during the transformation process induced by the TEM vacuum and by the electron beam.  Congratulation to Laura!

CRISMAT

Sara Passuti, NanED PhD student working at CNRS in Caen  on electron crystallography of nanodomains in functional materials, won a poster prize at ECM33 in the electron crystallography session offered by Nanomegas! Sara’s poster was about “3D scanning precession electron diffraction analysis of nanodomains in thin films” and describes a procedure about how collect 3D ED data of structure solution quality across a thin film. This procedure should allow to determine the modifications of the crystal structure in different portion of a thin film. Congratulation to Sara!

FZU Workshops

From the 25th to the 27th of May 2022, the NanED project had its first Workshop, held in Prague at the Institute of Physics of the Czech Academy of Sciences.

The workshop's main goal was to teach NanED PhD students how to collect reliable 3D ED data and how to process these data for a successful structure solution and refinement. The workshop was divided into morning theoretical sessions and afternoon practical sessions to learn how to use all the available structure analysis software for 3D ED. Together with most of the NanED supervisors, we had two invited speakers from outside the project, Prof. Tim Gruene from Vienna University a crystallographer expert in the use of SHELX and Dr Gerhard Hofer of Stockholm University a master in protein crystallography. It was the first we gathered together in person and it has been a fantastic experience for all of us.

JGU

Working on beam-sensitive and hydrated samples is a complex process. Therefore, Laura Gemmrich Hernandez (ESR08) is currently focused on optimizing the data acquisition routines and sample preparation to get quality data that can lead to the structure solution of such materials.

Currently, the project is focused on microscope management, cryoEM, and data processing of many different types of challenging, organic as well as inorganic, samples; such as hydrated, beam sensitive, and disordered materials. The cryoEM training has included a visit to the BASF in Ludwigshafen (Germany) to learn and practice the vitrification and cryotransfer procedures for these types of samples.

CRISMAT

Establishing new crystal tracking routines requires a deep understanding of the hardware, software and 3DED technique and its limitations. Due to that, the work of  Marco Santucci (NanED ESR9) is focused in mastering the microscope, with a special eye on the “hidden parameters” that allow the microscope to work. This deep knowledge is necessary to figure out how to handle a basic 3DED experiment, translate it in an automated and technically flexible approach by scripting as well as to improve it.

Marco is focused in the management of the machine, the data collection and processing of organic and inorganic samples, due to their intrinsically different beam stability. Regarding the scripting, Marco is learning Python and DigitalMicrograph© in order to be flexible and synchronize every element of our TEM machines during the data acquisition. Thanks to these acquired competences, Marco will develop a routine to set automatically the best eucentric height, a key parameter for sample mechanical stability during our experiments. At the same time, Marco is also learning how to model disordered crystals and simulate their diffuse scattering using DISCUS, thanks to a visit to the Prof. Rheinard Neder at the FAU in Erlangen.        

CRISMAT

The current objective in the context of Sara Passuti’s (ESR12 @ CNRS) research project is to implement new strategies for diffraction dataset acquisitions for thin films. Differently from a classical Rotation Electron Diffraction (RED) experiment, the beam is scanned across a pre-defined area going from the coating to the substrate of the thin film or vice versa for every tilt angle.

This way, differences in the lattice parameters in distinct areas of the sample could be highlighted and different domains could be identified.

The main issues concern the optimization of the dataset acquisition protocol, making it faster and more efficient, as well as the sorting of the acquired patterns in order to have separated datasets to analyze for different areas of the sample.