Structure, Energetics and Reactivity

Molecular Cryospectroscopy and Biospectroscopy


Brief Description of the Laboratory for Molecular Cryospectroscopy and Biospectroscopy

The Laboratory for Molecular Cryospectroscopy and Biospectroscopy (LMCB) was formally founded in 1994, within the scope of the European Program PRAXIS XXI, and constitutes nowadays one of the leading research units at world scale in the field of low temperature spectroscopy and biospectroscopy. The LMCB has been centring its research on the topic of matrix-isolation infrared spectroscopy and infrared and Raman spectroscopy of biologically relevant chemical systems. Exceptional phenomena such as conformational cooling during matrix deposition, inversion of the lowest energy conformational states upon phase change (including trapping of the molecule under study in a noble gas matrix), conformational selective aggregation, observation of conformer dependent photodegradation pathways upon UV excitation of matrix isolated molecules, in situ photoproduction of Dewar-like bicyclo-lactones, ketenes, nitrilimines, cyanamides, anti-aromatic azirines, carbodiimides and isocyanides (among many other reactive species) in low temperature matrices, first observation of neutral forms of aminoacids in the pure solid state, and production of reactive photoexcitation vibrational spectra of matrix isolated molecules, for example, have been described in the numerous articles and books published by scientists working for the LMCB during the last few years. Observation of tunneling reactions in nitrenes, bond-shift isomeric species, radicals and detailed elucidation of many photochemical mechanistic details of a great number of chemical processes have also been achieved in the LMCB. Moreover, the Laboratory has been working actively in the fields of crystal structure characterization, forensic chemistry, analysis of meteoritic materials, and in the study of pharmaceutical relevant systems. These more applied fields of research have stimulated strong interactions with industry (e.g., the pharmaceutical company BluePharma) and other players (The Laboratory of the Scientific Criminal Nacional Police, Machado de Castro National Museum, the University of Coimbra National Museum, NASA). The international projection of the LMCB can also be evaluated by the numerous collaborations with scientists from different countries, which include USA, Russia, Finland, Germany, Israel, France, Italy, Bulgaria, Spain, Belgium, Argentina, Slovenia, Poland, Ukraine, Romenia, India, Brazil, Turkey, Holland, Algeria, Morocco, Saudi Arabia, Australia, Iran and Romania, among others. The Laboratory is well equipped with top-level spectrometers for research in different spectral regions, cryogenic and vacuum systems, some of them locally developed and having unique capabilities, and computational facilities (computational clusters, direct connection to the main Computer Centre of the University of Coimbra and allowed access to a few international Supercomputer Centres). Sophisticated equipment for narrowband selective irradiation of chemical species exist in the Laboratory, including a high power solid state LASER and an optical parameter oscillator (OPO), and, more recently, the LMCB purchase top-level instrumentation for Raman and infrared imaging. Expansion of the experimental facilities available at LMCB to the domain of time-resolved fs infrared spectroscopy is underway. The Laboratory integrates the European LaserLab Network and the Strategic Scientific Platform for Lasers’ Science of the University of Coimbra. It has also been selected (together with the other laboratories of the LaserLab Coimbra) as a National Strategic Research Infrastructure, within the LaserLab Portugal facility.

Scientific output indicators (last 4 years):

Nº of published Articles: >90
Nº of published books and book chapters: 14
Nº of supervised post-doctoral fellows: >20
Nº of supervised PhD. Theses: 7 (going on: 5)
Nº of supervised MSc. Theses: 11 (going on 3)
Nº of Conferences organized: 16 (international congresses: 12)
Nº of Presentations in Congresses: >120
Nº of Projects funded: >20

Current Members



Shedding light on intramolecular vibrational energy redistribution.

The detailed understanding of photochemical processes at the molecular level requires the investigation of both the excitations as well as the relaxation mechanisms. One direction of our research is dedicated to studies of the processes of intramolecular vibrational energy redistribution (IVR), i.e. how the excess energy of vibrationally excited molecules can be dissipated via intramolecular relaxation pathways.
The monomers of conformationally flexible compounds are captured in cryogenic (typically at 4-15 K) inert matrices, and their isomerizations, induced by selective vibrational excitations, are probed. The detailed characterization of the reactants and products is carried out by infrared spectroscopy. Interpretation of the experiments is aided by fully anharmonic calculations of the fundamental modes, overtones, and combinations up to two quanta, including their infrared intensities.
In this way we have been gaining insight into the IVR processes and contributing to development of vibrationally controlled molecular switches.
Selected Recent References:

  1. “Conformational Switching in Pyruvic Acid Isolated in Ar and N2 Matrixes: Spectroscopic Analysis, Anharmonic Simulation, and Tunneling”, I. Reva, C. M. Nunes, M. Biczysko and R. Fausto, J. Phys. Chem. A, 119 (2015) 2614.
  2. “Conformational Switching by Vibrational Excitation of a Remote NH Bond”, A. J. Lopes Jesus, I. Reva, C. Araujo-Andrade and R. Fausto, J. Am. Chem. Soc. 137 (2015) 14240. (Front cover, JACS).
  3. “Near-Infrared In Situ Generation of the Higher-Energy Trans Conformer of Tribromoacetic Acid: Observation of a Large-Scale Matrix-Site Changing Mediated by Conformational Conversion”, R. F. G. Apóstolo, G. Bazsó, G. O. Ildiz, G. Tarczay and R. Fausto, J. Chem. Phys. 148 (2018) 044303.
  4. “Investigation of Long-Range Intramolecular Vibrational Energy Redistribution by NIR Irradiation Induced Conformational Transformation of E-Glutaconic Acid”, B Kovács, N. Kus, G. Tarczay and R. Fausto, J. Phys. Chem. A. 121 (2017) 3392.

Development of electronically controlled molecular switches.

Parent azobenzene (AB) and 2,2'-substituted AB (R=OH, CH3) were isolated in argon and xenon matrices and their molecular structures and photochemical transformations were characterized by infrared spectroscopy and theoretical calculations. All these compounds can adopt the E and Z isomeric forms around the central CNNC moiety. For AB, both E → Z and Z → E isomerizations were observed upon irradiations with UV and visible light. The studies of isomerization between the two 2,2'‑substituted AB derivatives provided a direct experimental observation of an E → E isomerization. The latter type of photoisomerization provides evidence for a small‑amplitude pedal motion in azobenzene-type molecules.
Selected Recent References:

  1. “Structural and Spectroscopic Characterization of E- and Z- Isomers of Azobenzene”, L. Duarte, I. Reva and R. Fausto, Phys. Chem. Chem. Phys. 16 (2014) 16919 (inside Front cover, PCCP).
  2. “Photoisomerization of Azobenzenes Isolated in Cryogenic Matrices”, L. Duarte, L. Khriachtchev, R. Fausto and I. Reva, Phys. Chem. Chem. Phys. 18 (2016) 16802.
  3. “Controlled Light-driven Switching in 2-Thiobenzimidazole”, E. M. Brás and R. Fausto, J. Photochem. Photobiol. A: Chemistry 357 (2018) 185.

Mechanistic insights on the generation and photochemistry of reactive species.

Generation followed by stabilization in cryogenic matrices of reactive species like radicals and many other usually short-living reaction intermediates has been achieved, alowing their detailed structural, spectroscopic and photochemical characterization, and the investigation of their reactivity. Following our seminal work on the photogeneration and photochemistry of the phenoxy radical, we shed light on the photochemistry of its sulphur analogue. Also, our work on the photochemical reactivity of tetrazoles explored strategies to generate a substantial number of rare, highly-reactive molecules, which were reviewed in a publication in JPP C – Photochem. Reviews.
Selected Recent References:

  1. “Photogeneration of the Thione Forms of Thiophenol”, I. Reva, M. J. Nowak, L. Lapinski and R. Fausto, Phys. Chem. Chem. Phys. 17 (2015) 4775. (inside fromt cover, PCCP)
  2. “Genesis of Rare Molecules Using Light-Induced Reactions of Matrix-Isolated Tetrazoles”, L.M.T. Frija, M.L.S. Cristiano, A. Gómez-Zavaglia, I. Reva and R. Fausto, J. Photochem. Photobiol. C: Photochem. Reviews, 18 (2014) 71.
  3. “Infrared Spectra and UV-Tunable Laser Induced Photochemistry of Matrix-Isolated Phenol and Phenol-d5”, I.D. Reva, B. M. Giuliano, L. Lapinski and R. Fausto, J. Chem. Phys. 136 (2012) 024505.

Experimental observation of bond-shift isomers.

Bond-shift isomers have been theoretically postulated for many years, but escaped to experimental observation. We were able to produce and observed experimentally bond-shift isomers of phenylnitrile imine, the allenic and  propargylic forms, and study their reactivity in details.

  1. “Bond-Shift Isomers: The Co-existence of Allenic and Propargylic Phenylnitrile Imines”, C. M. Nunes, I. Reva, R. Fausto, D. Bégué and C. Wentrup, Chem. Comm. 51 (2015) 14712. (front cover, Chem. Comm.)

Production of small aggregates and energetic crystals made by rare conformers.

Preparation and characterization of high-energy conformers, dimers and complexes of these species has been achieved by controled conformational changes induced by narrow band selective excitation of low-energy common conformers isolated in cryogenic matrices, followed by thermal mobilization under temperature controled conditions. Procedures were  developed for subsequent preparation of high-energy crystals based on these high-energy rare conformers.
Selected Recent References:

  1. “Formic Acid Dimers in a Nitrogen Matrix”, S. Lopes, R. Fausto and L. Khriachtchev, J. Chem. Phys. 148 (2018) 034301.
  2. “Acetic Acid - Water Complex: The first Observation of Structures Containing the Higher -Energy Acetic Acid Conformer”, S. Lopes, R. Fausto and L. Khriachtchev, J. Chem. Phys. 144 (2016) 084308.
  3. “The Birth of High-Energy Crystals from Isolated Molecules – The Unsuspected Parenthood of Rare Conformers”, Project PTDC/QEQ-QFI/3284/2014. (P. I. – Rui Fausto).

Development of “Vibrational Antennas” to induce structural changes at distance.

We demonstrated that intramolecular vibrational energy relaxation can be transferred to long distance, through several bonds in a molecule, providing a mechanism for promoting highly selective, most of times reversible, structural transformations in a region of  molecule (target group) far away from that initially excited vibrationally (antenna). These results opening the gate for using infrared excitation to selectively promote chemical reactions, not just of conformational isomerization, but also involving bond breaking/bond forming processes.
Selected Recent References:

  1. “Conformational Control over an Aldehyde Fragment by Selective Vibrational Excitation of Interchangeable Remote Antennas”, A. J. Lopes Jesus, C. M. Nunes, R. Fausto and I. Reva, Chem. Comm. 54 (2018) 4778. (front cover, Chem. Comm.)
  2. “UV-Induced Transformatins in Matrix-Isolated 6-Methoxyindole”, A. J. Lopes Jesus, I. Reva and R. Fausto, J. Photochem. Photobiol. A: Chemistry 336 (2017) 123.
  3. “Conformational Switching by Vibrational Excitation of a Remote NH Bond”, A. J. Lopes Jesus, I. Reva, C. Araujo-Andrade and R. Fausto, J. Am. Chem. Soc. 137 (2015) 14240. (front cover, JACS)

Exploring the chemistry of nitrenes and tunneling reactions:

We have been investigating nitrenes reactive intermediates (open‑shell R‒N species) and their slippery potential energy surface using a combination of a cryogenic matrix environment and a tunable narrowband radiation source to selectively produce and induce photochemistry of the different species resulting from suitable initial nitrene precursors. In this way, we have unraveled new gateways to nitrenes, characterized new challenging species and discovered fascinating cases of tunneling reactions. Direct spectroscopic observations of heavy-atom tunneling reactions and competitive tunneling events have put our research group in the forefront of this research filed.
Selected Recent References:

  1. “Competitive Nitrogen vs Carbon Tunneling”, C. M. Nunes, I. Reva,  R. Fausto, A. K. Eckhardt  and  P. R. Schreiner,  under preparation.
  2. “Photochemistry of 2-Formylphenylnitrene: A Doorway to Heavy-Atom Tunneling of a Benzazirine to a Cyclic Ketenimine”, C. M. Nunes, I. Reva, S. Kozuch, R. J. McMahon and R. Fausto , J. Am. Chem. Soc. 139 (2017) 17649.
  3. “Evidence of a Nitrene Tunneling Reaction: Spontaneous Rearrangement of 2-Formyl Phenylnitrene to an Imino Ketene in Low-Temperature Matrices”, C. M. Nunes, S. N. Knezz, I. Reva, R. Fausto and R. J. McMahon, J. Am. Chem. Soc. 138 (2016) 15287.

LMCB Photos