Supramolecular Nanosystems based on Molecular Cages Lab

Molecular cages provide a tool to encapsulate diverse guests at the molecular level, allowing the modification of their chemical properties. In our lab, we aim to develop supramolecular systems based on molecular cages for advancing the field of cancer therapy.

In this research line, we aim to develop molecular cage systems to encapsulate drugs for biological applications, for example in cancer therapy. To achieve this ambitious goal we focus on the cage design, starting from the geometry of the building blocks to achieve the desired cage geometry.

All details of the research that is under development are on the Research section of this web.

Work with us

Prospective PhD and postdoctoral researchers are welcome to contact Dr. V. Martí-Centelles by e-mail for further information and how to apply. We are looking for candidates interested in applying to a Marie Sklodowska-Curie Actions Postdoctoral Fellowships (MSCA-PF) and other funding schemes.

Funding

Plan Gen-T: Generació Talent, Generalitat Valenciana

Proyectos de I+D+i 2020 Angencia estatal de investigación y Ministerio de Ciencia e Innovacion

News

Optical Sens SL

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The Universitat Politècnica de València and the Universitat de València constitute the first joint spin-off of the two universities

The Universitat Politècnica de València (UPV) and the Universitat de València (UV) have set up Optical Sens SL, the first joint spin-off of the two universities. This new company is the result of work carried out by researchers at the Inter-University Institute for Molecular Recognition Research and Technological Development (IDM). It will commercialise sensors for the detection of chemical drugs and senescence sensors.

The new spin-off from the UPV and UV aims to offer solutions with chemical sensors and biomarkers that meet the needs of the agri-food sector, health, hygiene-sanitary safety, the pharmacological sector and the chemical industry. It starts its activity with chemical sensors for the detection of drugs and senescence. However, it will work on the development of chemical sensors and biomarkers of high scientific and industrial value.

In this way, it is the first company to propose a technology that detects chemical submissive drugs, which can be used at room temperature and by any user. All of this is in response to statistics showing that around 40% of sexual assaults are caused by chemical submissions, a fact that highlights the need for sensors that can quickly detect these substances.

More info

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The use of chemical submission drugs has become an ever-growing problem for society. In 2019, 14% of sexual crimes were linked to the use of this type of substance. A percentage that in 2021 increased to 31%. Data that could be just the tip of the iceberg and that has already raised concern in the European Union and is even the subject of European projects. With this underlying problem, a group of researchers from the Interuniversity Research Institute for Molecular Recognition and Technological Development (IDM) has created the company Optical Sens, with which they are currently promoting their main project: the development of chemosensors for the detection of drugs of chemical submission at public events such as nightclubs or festivals. An interuniversity spin off in which a total of thirteen researchers from the center participate, in addition to the universities and a technology transfer company. Among the founding team, the Professor of Organic Chemistry at the UV, Margarita Parra, stands out, one of the hundred most influential women in Spain according to Forbes magazine, and the Professor of Inorganic Chemistry at the UPV, Ramón Martínez Máñez, winner of the King Jaume I Prize for New Technologies. The business development team, as a public-private collaboration model, is in the hands of the technology transfer expert company TRL+. "In our research we cover many fields, but the one that interests us at the moment and that we are developing is chemosensors for the detection of chemically induced drugs," explains Margarita Parra. "As a result of considering this issue and doing research, several patents came out, several sensors came out, and the idea of creating a spin off arose." Among the drugs they can detect are GHB, liquid ecstasy, burundanga, ketamine, cathinones and MDMA, among the most common of this type.

More info

Marie Curie Fellowships at UPV

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Attracting talent is essential to maintaining excellence both in universities and research centers and in companies. Horizon Europe, the current Research and Innovation Framework Program of the European Union, includes a powerful tool that promotes the development of talent and excellence in research. This instrument is the Marie Sklodowska-Curie Actions postdoctoral fellowships (MSCA Postdoctoral Fellowships) that offer the possibility of attracting international talent to carry out multidisciplinary research projects that allow extensions in non-academic entities. But, in addition, the so-called MSCA PF offer Universities additional benefits such as the promotion of international collaboration, the transfer of knowledge and the improvement of reputation at an international level. With this objective, the Universitat Politècnica de València (UPV) has deployed through CPI EUROPE a plan to help prepare MSCA PF proposals so that young researchers from all over the world can carry out their postdoctoral projects at the UPV. MSCA PF shares have annual calls, with a closing date of September 11 for this year 2024.

The project won an MSCA PF scholarship in the 2021 call with Antoni Llopis as a postdoctoral researcher, with the supervisor being Vicente Martí, from the Interuniversity Research Institute for Molecular Recognition and Technological Development (IDM) of the UPV. The objective of the project was the development of nanosystems based on molecular cages to give rise to biocompatible nanosystems with the capacity to recognize biomarkers of diseases and induce in situ drug delivery.

The project combined the experience of the IDM (molecular cages: cage-shaped molecular architectures with an internal cavity), that of the candidate (nanotechnology and artificial cells) and that of the Príncipe Felipe Research Center (evaluation of new cancer therapies) to ensure compliance with objectives.

More info

1st Workshop Molecular Cages and Supramolecular Chemistry 2023

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Researchers from the NANOSENS group organize the 1st Workshop Molecular Cages and Supramolecular Chemistry 2023 This event took place on October 25, 2023 in the Grade Room I (Building 5 F), Universitat Politècnica de València The presentations made were "Bio Inspired Cage Catalysis by Prof Paul Lusby University of Edinburgh), Edinburgh), "Metal Organic Polyhedra porous nanoparticles with molecular reactivity by Dr Arnau Carné Universitat de Barcelona), "Dynamic pseudopeptidic molecular cages by Prof Belén Altava Universitat Jaume I), Unlocking the potential of subcomponent self assembly cages in biological applications by Dr Jesús Mosquera (University of A Coruña)

The 1st Workshop Molecular Cages and Supramolecular Chemistry 2023 was a resounding success, with excellent attendance and a high level of engagement from participants. The event provided a stimulating forum for researchers from different disciplines to exchange ideas and collaborate on future projects. The presentations by Prof. Paul Lusby, Dr. Arnau Carné, Prof. Belén Altava, and Dr. Jesús Mosquera covered a wide range of topics in the field of molecular cages and supramolecular self-assembly, and they generated lively discussions among the attendees. The workshop was a valuable contribution to the advancement of this exciting area of research. We are confident that the connections made at the workshop will lead to many fruitful collaborations in the years to come.

Seminar Coordination/metal organic cages: synthesis, formation process, and applications by Dr. Tomoki Tateishi

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The seminar took place on September 22 Coordination /metal organic cages synthesis formation process and applications by Dr Tomoki Tateishi JSPS Postdoctoral Fellow Furukawa Group of the Institute for Integrated Cell Material Sciences Kyoto University Japan This seminar was organized by researchers from the NANOSENS group

Dr. Tomoki Tateishi from Kyoto University, Japan, presented his research on coordination/metal-organic cages at an invited seminar yesterday. Coordination/metal-organic cages are a class of nanomaterials with unique properties, including high surface area, selective adsorption, and catalytic activity. Dr. Tateishi discussed the synthesis of these cages, the formation processes that control their structure and properties, and their potential applications in a variety of fields, including catalysis, medicine, and environmental remediation.

About Vicente Martí Centelles

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Dr. Vicente Martí Centelles
CIDEGENT Distinguished researcher
Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
Universitat Politècnica de València Edificio 5M, Departamento de Química.
Camí de Vera s/n, 46022, Valencia, Spain
Email: vimarce1 -AT- upv.es
Tel. +34 963877000 Ext. 73446
Web page: www.vmarti.es

Vicente obtained a European PhD (Summa Cum Laude) from 2008 to 2012 in supramolecular chemistry with FPU fellowship from the Spanish Ministry of Science and Education at Univ. Jaume I working on the design and synthesis of macrocyclic compounds for molecular recognition. During his PhD he carried out two short research stays at Univ. Zaragoza (Spain, 2009) and Imperial College London (UK, 2010) obtaining a PhD prize from the Univ. Jaume I and preparing more than 10 publications, participate in more than 20 conferences, prepare one patent, participate in teaching at the university and pedagogic research projects (corresponding author of J. Chem. Ed. 2014 with more than 30 citations) and other soft skills acquired.

Then, he was awarded a 2-year postdoctoral VALi+d fellowship (2013–15) funded by the local government (Generalitat Valenciana, Spain) to develop a project involving University Jaume I, Universty of Oxford and a biotechnology company. Postdoctoral work allowed him interdisciplinary research, combining macrocyclic chemistry, interlocked hosts designed for molecular recognition and sensing of anions of biological and environmental importance and sensing of bacteria at the biotechnology company Biotica. This fellowship allowed writing one publication as the corresponding author (J. Org. Chem. 2016), a publication calcified as “Hot Paper” by the journal with an inside back cover (Chem. Eur. J. 2015) and a review on macrocyclization with more than 150 citations (Chem. Rev. 2015, IF=37.37).

The ensemble of these achievements allowed Dr. Martí to obtain the accreditation for assistant professor (2013) and the accreditation for associate professor (2015) from the Spanish National Quality Assessment Agency/Ministry of Education (ANECA). These are prerequisite qualifications for academic positions in Spain. Then he moved to work as Postdoctoral Research Assistant at the Univ. of Edinburgh in the design and synthesis of molecular machines and self-assembled host systems for molecular recognition and catalysis in the Lusby group. Dr. Martí discovered the catalytic properties of the Pd₂L₄ capsules, this key breakthrough shows an example of an artificial “Diels–Alderase” capsule that can overcome the product inhibition paradigm and combining efficient turnover alongside enzyme-like hallmarks (J. Am. Chem. Soc. 2018, IF=13.86, being Dr. Martí the main contributor). In addition to this paper, two more have been published (Chem. Sci. 2017, Chem. Eur. J. 2018) and others are under preparation. In January 2018 Dr. Martí obtained a prestigious Marie Curie IF fellowship (European Union funded) to continue his scientific career at the Nathan McClenaghan research group at the Institut des Sciences Moléculaires (CNRS/Université de Bordeaux) and Laurent Cognet research group focusing in supramolecular systems for fluorescence imaging. More details in the MSCA-IF project web page.

In 2020 Dr. Martí obtained a CIDEGENT Distinguished researcher from Generalitat Valenciana to develop his own project on molecular cages for cancer therapy as principal investigator at Instituto de Reconocimiento Molecular y Desarrollo Tecnologico (IDM), Universidad Politécnica de Valencia.

All details of the research that is under development are on the Research section of this web.

Dr. Martí publication years stared in 2011 and has published >30 papers, 3 of them as the corresponding author, with >700 citations. His J. Am. Chem. Soc. 2018 paper has received 76 citations. The h-index is 14. See the publication list on his web or google scholar.

Awards and Fellowships obtained

• CIDEGENT Distinguished researcher from Generalitat Valenciana, 2020.
• Marie Curie IF Fellowship from the European Union, 2018.
• Honourable mention in the XI Award Scientific-Technical "Ciutat d'Algemesí" for young researchers, 2015.
• Second prize in the XII Premios de innovación y creatividad Cátedra INCREA d'Innovació, Creativitat i Aprenentatge (Univ. Jaume I) for the pedagogical periodic table game ChemMend ( Chem. Ed. 2014), 2015.
• Postdoctoral VALi+d Fellowship from the Generalitat Valenciana, 2013.
• PhD Special Award basic sciences (Premio extraordinario de doctorado en ciencias básicas) Univ. Jaume I, 2013.
• Chemistry Bachelor Honourable Mention in the Chemistry the National Awards for University Studies (Premios Nacionales Terminación Estudios Universitarios) Spain Education Ministry, 2006/7.
• Predoctoral FPU Fellowship from the Spanish Ministry of Science and Education, 2008.
• Chemistry Bachelor Award (Premio extraordinario final de carrera Lic. Química) Universitat Jaume I, 2006/7.
• Chemistry Bachelor Award (Premio al rendimiento académico Generalitat Valenciana), 2006/7.
• Chemistry Bachelor Award Premio Ernest Breva Mallach al esfuerzo y excelencia en los estudios de licenciatura en Química (School of Technology and Experimental Sciences), Universitat Jaume I, 2006/7.
• Chemistry Bachelor Award Premio Colegio de Químicos CV al mejor expediente académico, 2006/7.
• Intitiation to research Fellowship from the Spanish Ministry of Science and Education, 2006.
• Chemistry Bachelor Award Premio al Rendimiento Académico Primer Ciclo Lic. Química, Univ. Jaume I, 2002/5.
• Silver Medal in the 35^th International Chemistry Olympiad, Groningen, The Netherlands, 2002. The highest distinction obtained by Spain in the International Chemistry Olympiad.
• Chemistry Olympiad Silver Medal at 7ª Olimpiada Iberoamericana de Química, Mar del Plata, Argentina, 2002.
• Chemistry Olympiad Gold Medal in the 13ª Olimpiada Nacional de Química, Spain, Oviedo, 2002.
• Physics Olympiad Honourable mention in the 13ª Olimpiada Española de Física, Spain, Burgos, 2002.
• Chemistry Olympiad Gold Medal in the Olimpiada de Química año 2002, Universitat Jaume I, 2002.
• Physics Olympiad Gold Medal in the XIII Olimpiada de Física, Universitat Jaume I, 2002.

Career overview

All details of the research that is under development are on the Research section of this web.

Vicente Martí Centelles research interests are focuses in the applications of supramolecular systems in different fields. Recent research is focused in the design of macrocycles, molecular cages, interlocked molecules, etc. with tailored properties ranging from molecular sensing, catalysis and microscopy.

CIDEGENT: Molecular cages for cancer therapy

Vicente Martí Centelles current research interests focuses on supramolecular systems based on molecular cages for advancing the field of cancer therapy. The project will develop molecular cages with tailored properties for biological applications. Further information can be found on the Research section of this web page.

MSCA-IF: Supramolecular Chemistry for super-resolution microscopy

Vicente MSCA-IF research project focuses on supramolecular systems for advancing the field of fluorescence imaging. This research is carried out through his Marie Curie IF fellowship in the Nathan McClenaghan research group at the Institut des Sciences Moléculaires (CNRS/Université de Bordeaux) and Laurent Cognet research group at the Laboratoire Photonique Numérique et Nanosciences - Institut d'Optique Graduate School (CNRS/Université de Bordeaux). Super-resolution microscopy allows obtaining high resolution images overcoming the light diffraction limit. Thanks to the Marie Curie Individual Fellowship that I obtained, I am developing fluorescent supramolecular systems able to work efficiently in this microscopy techniques. CORDIS EU web page of the MSCA-IF project https://cordis.europa.eu/project/rcn/215464. More details in the MSCA-IF project web page.

This project, indeed allows to integrate all state of the art knowledge acquired during my career to develop functional molecules with tailored properties in microscopy. It is fascinating to be able to detect single molecules using microscopy. This allows studying the individual behavior of molecules that cannot be distinguished using bulk measurements, where it is only possible to measure average values. Single-molecules detection can be performed in a confocal microscope using appropriate fluorescent molecules, excitation laser and a camera. The following image shows differnt frames containing single molecules simulted with ThunderSTORM in ImageJ, and ilustrates the process of detecting single molecules over time to reconstruct a high resolution image by processing all the individual frames. In an interview with the "Sociedad para el Avance Científico" to talk about my Marie Curie Fellowship, you can read the full interview and watch the Youtube video to get further details about the process of getting a Marie Curie Fellowship, the benefits from it and an overview of the project objectives.

Artificial enzymes

Vicente Martí Centelles was previously a postdoctoral researcher in the Lusby group at the University of Edinburgh. His research focused in the design and synthesis of molecular machines and self-assembled host systems for molecular recognition and catalysis. Dr. Martí discovered in his research the catalytic properties of the Pd₂L₄ capsules, and he developed experimental protocols and kinetic models to obtain quantitative thermodynamic data by means of data science programing.

The catalytic hosts have properties similar to the biological systems, in particular, the proteins. The unfolded peptides do not have any activity, and the folded structure has a very efficient activity for a particular reaction. For the cage compounds, a similar effect is observed. The disassembled components do not have any catalytic activity, but the assembled structure has enhanced molecular recognition and catalytic properties. So the catalysis is an emergent property of these sophisticated molecular architectures. Focusing on the design of the cages, why are enzyme active sites buried? If we analyze the size of the active center of an enzyme in comparison to all the structure, this is relatively small with similar size of our cage design. The most important supramolecular interactions present in an enzyme active center are multiple hydrophobic contacts providing selectivity and multiple non-covalent interactions being the main contribution to activity and also providing selectivity.

This research resulted in a key publication J. Am. Chem. Soc. 2018, 140, 2862-2868. IF=13.86, being Dr. Martí the main contributor) reporting an artificial "Diels-Alderase" capsule overcoming the product inhibition paradigm and combining efficient turnover alongside enzyme-like hallmarks. Along the different research topics, Vicente has been involved in the organization of conferences, and being a member of the organizing committee the 3rd edition of the EaStCHEM Conference for Early-Career Researchers ECECR 2018 that was at King's Building Campus, University of Edinburgh.

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Interlocked systems for molecular recognition

Postdoctoral work through the VALi+d fellowship allowed Vicente to diversify his research activities, focusing on macrocyclic chemistry at Univ. Jaume I, synthesis of interlocked hosts designed for molecular recognition and sensing of anions of biological and environmental importance at Univ. of Oxford (Chem. Eur. J. 2015, “Hot Paper”, inside back cover) and sensing of bacteria at Biotica. All the knowledge acquired allowed publication of a review on macrocyclization (Chem. Rev. 2015), and additional participation in two general scientific magazine publications.

The work developed at the University of Oxford focused on the design and preparation of receptors of species of biological, environmental, and medical interest. In this sense, the essential role of anions in these fields must be emphasized. The important role of anions has motivated chemists to develop synthetic anion receptors capable of selective recognition, this research area being an important part of the field of Supramolecular Chemistry.

Nitrate anion plays an important role in environmental and medical contexts: excessive use of fertilizers in agriculture has caused eutrophication and alteration of the natural aquatic ecosystem, while exposure to elevated nitrate levels is a cause of diseases such as methemoglobinemia (blue baby syndrome) in infants. The preparation of selective nitrate receptors is a poorly developed area, with few examples described in the literature, and which mostly operate only in organic solvents. The main challenges to overcome in the design of selective nitrate receptors are the low affinity of the anion to form hydrogen bonds and the high hydration energy of the anion in mixtures of aqueous solvents, which contribute to an association weak in general with the host molecule.

These results were hihghlighted in the news through several interviews. Vicente Martí-Centelles tells to the journal Pan European Networks: Science & Technology about the development of a pioneering method in the evaluation of nitrate pollution Pan European Networks: Science & Technology June 2016, From the UJI to Oxford against water pollution Mediterraneo 22/10/2015, a researcher creates a method that detects nitrates selectively Levante de Castelló 22/10/2015, a researcher designs a pioneering method in the nitrate pollution assessment Universitat Jaume I Science Videos, interview on Radio Voramar esRadio 92.5,in "Es la Mañana" to explain nitrate detection research Radio Voramar esRadio 92.5 29/10/2015, dissemination of research on nitrate detection in Finestra a la Ciència de Vox UJI Radio 30/10/2015, Blog Ciencia TV Universitat Jaume I 2015, and Universitat Jaume I web page 2015.

Whit this work I was able to obtain a honourable mention in the XI Award Scientific-Technical "Ciutat d'Algemesí" for young researchers in 2015. This was hihglhted in the news Algemesi rewards the research work on environmental pollution carried out by Vicente Martí.

Macrocyclic chemistry

Vicente PhD thesis work focused on the design and preparation of pseudopeptidic systems with applications in molecular recognition and self-assembly. Vicente developed this work at Univ. Jaume I, and performing two short research stays in leading research groups at Imperial College London and Univ. Zaragoza in order to gain experience in specific research topics. Vicente developed anion template synthetic strategies to achieve an efficient synthesis of macrocyclic structures through S_N2 reactions in the macrocyclization reaction step (Chem. Eur. J. 2012, J. Org. Chem. 2014, Sci. World J. 2012). Some of these macrocyclic compounds based on acridine had excellent anion recognition and sensing properties, and they were able to selectively recognise dihydrogen phosphate and the tryptophan amino acid by means of fluorescence experiments (Chem. Eur. J. 2014, J. Org. Chem. 2012). In his PhD work he also prepared and characterized novel polymeric metal complexes with appropriately designed pseudopeptidic ligands in my research stay at Imperial College London (CrystEngComm 2011). In these scientific publications he was the main contributor and 1^st author. Additionally, he did further studies in the topic of anion-templated macrocyclization reactions in my postdoctoral project at Univ. Jaume I. In this case, Vicente prepared the macrocycles by means of amide bond formation reactions in the macrocyclization step (J. Org. Chem. 2016). During the PhD, Vicente also participated in a project where a family of organogellating compounds were able to form gels by the self-assembly of the monomers and the gels were stable to high temperatures, these studies resulted in the preparation of one publication (Tetrahedron 2013) and one patent.

Vicente Martí Centelles research in supramolecular chemistry exceptional combination of skills: organic chemistry, supramolecular chemistry, and physical organic chemistry.

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Dissemination of research results and outreach activities

Vicente Martí Centelles has participated in different outreach activities for disseminating his research work targeting a broad audience. These activites include, the european researcher night 2019 in Bordeaux, the "Fete de la Science 2019" at Institut de Sciences Molecularies in Bordeaux and preparing with journalists press releases and journal/radio/video interviews.

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International Chemistry Olympiad

Vicente Martí Centelles has participated in the Chemistry Olympiad over the last years. Dr. Martí's interest in Chemistry began early and in 2002 he obtained a gold medal in the Spanish National Olympiad and a silver medal in both the International Chemistry Olympiad (the highest distinction obtained by Spain in this prestigious competition) and Ibero-American Chemistry Olympiad. The participation in the Chemistry Olympiad includes:

• Member of the Scientific Committee Univ. Jaume I Chemistry Olympiad (2009-13, and 2015).
• Member of the scientific committee of the Spanish National Chemistry Olympiad. 2013 (Alicante), 2012 (Madrid), 2011 (Valencia), 2010 (Seville), 2009 (Avila).
• Head Mentor (head of the Spanish delegation, 2015 Azerbaijan), Mentor (2011 Turkey, 2012 USA, and 2013 Russia) and scientific observer (2009 UK, 2010 Japan), collaborator in training (2008) of the Spanish delegation at the International Chemistry Olympiad (IChO).

The training carried in the Chemistry Olympiad as mentor, cientific observer and collaborator has been succesful, and the students have obtained bronze medals and honourable mentions every year:

• 2008 BUDAPEST (HUNGRÍA): Eduardo Ansaldo Giné, Medalla de Bronce.
• 2009 CAMBRIDGE/OXFORD (INGLATERRA): David Rodriguez San Miguel, Medalla de Bronce; Luca Schneller-Pavelescu, Mención de Honor.
• 2010 TOKIO (JAPON): Pablo Giomi, Medalla de Bronce Jesús Álvaro Gómez Iregui, Medalla de Bronce; Andreu Tortajada Navarro, Medalla de Bronce.
• 2011 ANKARA (TURQUIA): Moisés Maestro López, Medalla de Bronce; Albert Soto Company, Mención de Honor.
• 2012 WASHINGTON (E.U.A.): Sergio Tomás Martínez, Medalla de Bronce.
• 2013 MOSCÚ (RUSIA): Damiá Torres Latorre, Medalla de Bronce; David Prieto Rodríguez, Medalla de Bronce; Sergio Cuesta Galisteo, Mención de Honor.
• 2015 BAKÚ (AZERBAYÁN): Raimon Terricabres Polo, Medalla de Bronce; Jorge Melendo Arrufat, Mención de Honor.

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Vicente whon a Silver Medal at the International Chemistry Olympiad in 1002, and this was highlighted in the news, a complete press dossier is available with all the interviews.

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ChemMend: Learning the periodic table with a card game

Knowing the Periodic Table is essential in the field of chemistry, but its memorisation is often tedious and complex for students. Vicente Martí Centelles and Jenifer Rubio Magnieto, alumni of Chemistry at the Universitat Jaume I, have developed a game for secondary school students and first years of university, and anyone interested in chemistry, to learn the group and period each chemical element belongs to in the Periodic Table in an easy, simple and funny way. Two years of work and experimentation in the classroom have resulted into ChemMend, a game that has been reported on the International Journal of Chemical Education.

ChemMend is the first existing game that allows exploring and gaining knowledge about the groups and periods of elements since; so far, existing games on the Periodic Table are focused on linking the different elements with their symbol. The gameplay is similar to the popular UNO, but this time is to follow the reference card with cards that correspond to the same group of elements or the same period, or to use one of the cards that act as a wildcard and which introduce different instructions as jumping a turn, draw cards from the deck, change direction, make a drawing, etc. All the info can be found in the ChemMend Full Press release document. Also you can found further infomration on www.facebook.com/ChemMend the orignal publication J. Chem. Ed. 2014, 91, 868-871. and the electronic online implementation. www.chemmend.uji.es.

Software

Development of Chemistry Software

I've developed software during my different research process. At the moment I am working on my Vicente GitHub site to share the soruce code, and this sofware will be available to download in due course. I have learned different programming languages that allowed to develop these software. Such languages include C++, Python, Cran-R and Mathematica.

I am also develping a tool to improve the presentation of complex strucutures in poster presentations or meetings. This tool is java script based, and it does not requires the installation of any app and allows displaying a molecule over the AR.Chem recognition motif. The main advantage of this methodology is to allow the user to acces directy to the 3D molecule just using an smartphone to read the QR code, then a web page will be oppened asking to acces the camera and the augmented reality molecule will be displayed over the QR code, simple and efficient. The source code can be accesed from my GitHub page on the following link: Augmented reality for chemistry

You can simply test the this code by acccesing the following link, and then point the camera of you smartphone to the image below: Run the augmented reality for chemistry in your smartphone.

HTML code to implement AR.Chem

<!doctype HTML>
<html>

<script src="aframe.min.js"></script>
<script src="aframe-ar.js"></script>
<script src="aframe-vrml-component.min.js"></script>

<body style='margin : 0px; overflow: hidden;'>
		
        <a-scene embedded 
		vr-mode-ui="enabled: false"
		arjs='debugUIEnabled: false; 
		sourceType: webcam;
		detectionMode: mono_and_matrix; 
		matrixCodeType: 3x3
		trackingMethod: best;'
		renderer="antialias: false; 
		logarithmicDepthBuffer: true; 
		colorManagement: true; 
		sortObjects: true;"
		>
				
		<a-assets>
			<a-asset-item id="3d-wrl" src="rotax_v01.wrl"></a-asset-item>
		</a-assets>
		
		<a-marker type='pattern' url='ar-chem.patt'>
			<a-entity
				vrml="#3d-wrl"
				scale ="0.15 0.15 0.15"
				position="0 0.5 0"
				rotation="-90 0 0"
				>
			</a-entity>
		</a-marker>
		
		<a-entity camera></a-entity>

    </a-scene>
	
</body>

</html>

If you are interested in using any of these contact me by e-mail and I can provide it or we can collaborate to implement it you your particular needs or to solve any particular challenge that you have in your research. For example, I have developed a wide variety of Advanced Kinetic Modelling code with R that allows simulating very complex reactions and perform multivariate fitting.

These sofware has been developed in the Python programming language (using the libraries: SciPy, Matplotlib and PIL Python Image Library) and R. Some of these programs had an user graphical interface (GUI) develped by using the GTK interface wit the aid of glade.

• SEM batch image processing
• Batch image processing to put all the images labeled into the same image and with the correct label
• IR-ATR deconvolution and fitting
• Advanced Kinetic Fitting with R
• UV and CD script to batch process files
• Advanced batch processing of xyz files to create Gaussian input files
• Script to automatically represent a PES from a Gaussian calculation

High Quality Renders for Chemical Structures

We can create high quality renders for our chemical models with Blender. To do this render first we need a pdb file of our molecule. I usually use gaussian to perform my calculantions and I use molden to view the output files. Then I export the molecule in Tinker xyz format. Then I convert the tinker xyz file to pdb wiht xyz2pdb ( the xyz2pdb-src-linux_bin-windows_bin.zip contains the source code (written in C) and binaries compided for linux and windows). To use xyz2pdb open a terminal in linux or the cmd in Windows and execute xyz2pdb -help to obtain a list of help:

$ ./xyz2pdb -help

Usage: ./xyz2pdb [<flags> with arguments, as follows]

 -o <PDB file name>        default is <stdout>
 -xyzfile <XYZ file name>  default is <stdin>
 -debug <level>            0 to 9 [0]
 -backbone                 output backbone only
 -noh                      don't output hydrogen atoms
 -noh2o                    don't output water molecules
 -nourea                   don't output urea molecules
 -usebond                  derive bond info from input file only
 -help                     print this information

Therefore to convert our xyz file we must use:

$ ./xyz2pdb -xyzfile myfile.xyz -o myfile.pdb

Then we will import this pdb file into Blender with pdb2blender.py, this python script is already in a blender file, pdb2blend12.blend. To use the script open the file pdb2blend12.blend in blender, then in the left window right click and execute script, setup the parameters to import and click on Import button to select the pdb file.

Now we can play with blender and modify the properties of the materials, add some reflections... (you can try with this files: ts-tinker.xyz, ts.pdb).

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