Periodic Reporting for period 4 - SEMICOMPLEX (Divide and conquer ab initio semiclassical molecular dynamics for spectroscopic calculations of complex systems)
Reporting period: 2020-05-01 to 2022-04-30
The main idea of this project is based on an ancient military Rome’s strategy, the divide-and-conquer technique. SEMICOMPLEX is the adaption of such approach to semiclassical calculations and it paved the way to new and more accurate chemical research of large molecular systems allowing us to detect fundamental quantum mechanical properties. Unfortunately, both theory and experiments in vibrational spectroscopy, the field of SEMICOMPLEX, was facing serious challenges when treating large molecular systems, since computer simulations entirely based on quantum dynamics are prohibitively expensive and experiments are difficult to interpret. The computer simulations performed in this project demonstrate that the spectroscopy of large systems (for instance solvated biomolecules) may be successfully implemented to address these problems. By combining classical dynamics simulations with semiclassical mathematical tools, we recovered the essential quantum features and projected the original problem onto a set of smaller ones. The main beneficial outcomes for the society are in economic and technological terms. This project prospects for the near future the possibility to avoid expensive and sometimes even dangerous lab practices in favor of computer simulations. The main overall objectives consisted in providing the scientific community with a new computational tool to solve the open scientific issue of quantum spectroscopy for large systems, and in providing experimental and industrial partners with an efficient rationalization of the physical and chemical mechanisms at the heart of the production of new compounds. For example,in synergy with experimental partners we devised nanomaterials made of titania to promote the photo-degradation of pollutants.
Overall SEMICOMPLEX has generated a computational tool able to reproduce the widespread Raman and IR experiments and that will be implemented for the community in a starting ERC POC project.
Overall SEMICOMPLEX has generated a computational tool able to reproduce the widespread Raman and IR experiments and that will be implemented for the community in a starting ERC POC project.
SEMICOMPLEX activities are structured onto different levels that can be seen as concentric spheres.
At the core, there is the scientific research, aimed at developing new theoretical chemistry methods that allow for both the correct interpretation and the prediction of spectroscopic experiments.The codes are tested on significant real systems to be compared with well-known experimental results. Small amino-acids, such as glycine and proline, water cluster up to 21 molecules, microhydrated glycine molecules, fullerene, nucleobasis, nucleotides, G-quadruplex in water, have been target systems where exact calculations are not available but there are accurate experimental results to compare with.
At the outer sphere there is the scientific dissemination activity. This activity is mainly composed of oral or poster presentations at scientific meetings plus peer-reviewed journal publications.Our publications of highest impact have appeared in Nature Communications, Physical Review Letters and Chemical Science. We participated at several national and international meetings to have the ERC project SEMICOMPLEX well known within the chemistry and physics community. Also, the PI organized in June 2016 a CECAM-sponsored meeting in Lausanne, named “Different Routes to Quantum Molecular Dynamics”, and three SEMICOMPLEX team members presented their work to the experts of the field. The new theory and results have been positively accepted by the international community. This has permitted the exploitation of the SEMICOMPLEX project.
At the outermost sphere, we performed some outreach activities. These actives were aimed at impacting on the general public and can be divided into multimedia ones, such as a movie describing the project (https://video.unimi.it/media/1770/) and an interview (https://www.chemistryworld.com/news/how-many-water-molecules-make-a-droplet/4013080.article) to the PI which appeared in Chemistry World, the most important chemistry English magazine. Also, the SEMICOMPLEX team invited and organized at the University of Milan the lecture of the 2013 Nobel Laureate Prof. Martin Karplus. Prof. Karplus is nowadays the world’s most eminent theoretical chemist. The choice of Prof. Karplus is motivated by the fact that a Nobel Laureate can be easily identified by common people as the top representative of the discipline with the possibility to reach a very broad audience. People attending the lecture were composed of colleagues, graduate and undergraduate students, people from private companies, as well as high school students, for a total of about 1000 people. Prof. Karplus' visit was important also for the scientific part of the project. In fact, he is considered the father of modern molecular dynamics, the branch of theoretical chemistry to which the ERC SEMICOMPLEX project belongs to. He was hosted by the SEMICOMPLEX team group and we gathered his positive feedback on the project. His visit was fully sponsored by the private company “Linea Energia” and the team wrote a newspaper article for Nuova Energia, a periodic journal about events related to an environmental-friendly approach to chemistry.
The team also worked as “ERC Community ambassadors” by diffusing the mission of the ERC to high school students. Frequently, the young EU citizens are not fully aware of how the national taxpayers’ money is invested at the EU level in research and how each EU citizen can benefit from that. The goal of the “ERC Community ambassador” is to educate high school students toward the importance of the ERC, illustrate its activity and explain why the theoretical and computational project SEMICOMPLEX has been financed. Several aspects have been illustrated. These include what theoretical and computational chemistry is (with specific reference to molecular dynamics), the role of the ERC institution and how it works, and the SEMICOMPLEX project. We visited high schools and the Museum of Science in Milan and met students from different grades. They demonstrated a strong interest about both theoretical chemistry and the ERC institution.
The main scientific take home message from SEMICOMPLEX is that quantum mechanical effects are present also in large molecular systems.
At the core, there is the scientific research, aimed at developing new theoretical chemistry methods that allow for both the correct interpretation and the prediction of spectroscopic experiments.The codes are tested on significant real systems to be compared with well-known experimental results. Small amino-acids, such as glycine and proline, water cluster up to 21 molecules, microhydrated glycine molecules, fullerene, nucleobasis, nucleotides, G-quadruplex in water, have been target systems where exact calculations are not available but there are accurate experimental results to compare with.
At the outer sphere there is the scientific dissemination activity. This activity is mainly composed of oral or poster presentations at scientific meetings plus peer-reviewed journal publications.Our publications of highest impact have appeared in Nature Communications, Physical Review Letters and Chemical Science. We participated at several national and international meetings to have the ERC project SEMICOMPLEX well known within the chemistry and physics community. Also, the PI organized in June 2016 a CECAM-sponsored meeting in Lausanne, named “Different Routes to Quantum Molecular Dynamics”, and three SEMICOMPLEX team members presented their work to the experts of the field. The new theory and results have been positively accepted by the international community. This has permitted the exploitation of the SEMICOMPLEX project.
At the outermost sphere, we performed some outreach activities. These actives were aimed at impacting on the general public and can be divided into multimedia ones, such as a movie describing the project (https://video.unimi.it/media/1770/) and an interview (https://www.chemistryworld.com/news/how-many-water-molecules-make-a-droplet/4013080.article) to the PI which appeared in Chemistry World, the most important chemistry English magazine. Also, the SEMICOMPLEX team invited and organized at the University of Milan the lecture of the 2013 Nobel Laureate Prof. Martin Karplus. Prof. Karplus is nowadays the world’s most eminent theoretical chemist. The choice of Prof. Karplus is motivated by the fact that a Nobel Laureate can be easily identified by common people as the top representative of the discipline with the possibility to reach a very broad audience. People attending the lecture were composed of colleagues, graduate and undergraduate students, people from private companies, as well as high school students, for a total of about 1000 people. Prof. Karplus' visit was important also for the scientific part of the project. In fact, he is considered the father of modern molecular dynamics, the branch of theoretical chemistry to which the ERC SEMICOMPLEX project belongs to. He was hosted by the SEMICOMPLEX team group and we gathered his positive feedback on the project. His visit was fully sponsored by the private company “Linea Energia” and the team wrote a newspaper article for Nuova Energia, a periodic journal about events related to an environmental-friendly approach to chemistry.
The team also worked as “ERC Community ambassadors” by diffusing the mission of the ERC to high school students. Frequently, the young EU citizens are not fully aware of how the national taxpayers’ money is invested at the EU level in research and how each EU citizen can benefit from that. The goal of the “ERC Community ambassador” is to educate high school students toward the importance of the ERC, illustrate its activity and explain why the theoretical and computational project SEMICOMPLEX has been financed. Several aspects have been illustrated. These include what theoretical and computational chemistry is (with specific reference to molecular dynamics), the role of the ERC institution and how it works, and the SEMICOMPLEX project. We visited high schools and the Museum of Science in Milan and met students from different grades. They demonstrated a strong interest about both theoretical chemistry and the ERC institution.
The main scientific take home message from SEMICOMPLEX is that quantum mechanical effects are present also in large molecular systems.
Within the computational chemistry community, a very small fraction of people is devoted to quantum molecular dynamics because of the inherent difficulties, while a majority of people employ classical molecular dynamics. However, classical molecular dynamics simulations do not include ubiquitous quantum mechanical effects and are heavily limited in the possibility to faithfully reproduce experiments and reliably simulate chemical, physical and biological processes. The SEMICOMPLEX project went beyond the state of the art by introducing semiclassical methodologies that employ classical molecular dynamics information to reproduce quantum mechanical effects in high dimensional molecular systems.We proved that large molecular complexes, such as water clusters, amino-acids in solution and supra-molecular systems in general, are ruled by quantum mechanics laws.
In the near future, our codes will be available as a tool to perform quantum dynamics simulations for a detailed and precise understanding of how matter is behaving by the exploitation of a ERC POC project. There will be socio-ecomomic implications in the medium-long term, when our computational tools are employed in laboratories for detection of compounds and are interfaced with IR and Raman experiments.
In the near future, our codes will be available as a tool to perform quantum dynamics simulations for a detailed and precise understanding of how matter is behaving by the exploitation of a ERC POC project. There will be socio-ecomomic implications in the medium-long term, when our computational tools are employed in laboratories for detection of compounds and are interfaced with IR and Raman experiments.