Qualification for the practice as chemist 2003
PhD Chemistry, Cagliari University 2002
MS Graduation in Chemistry (mark 110/110 cum laude) 1999
Erasmus Teacher at PJ Šafárik University Kosice 2016, Sept
Visiting Professor at Stockholm University 2011- 2016
Visiting Scientist, short periods, at Université Libre de Bruxelles 2010
Researcher, Cagliari University, Pharmacy Faculty 2006-present
Aggr. Prof. In Physical Method in Organic Chemistry 2007-present
Aggr. Prof. In Organic Chemistry 2016-present
Post-Doctoral Fellow, Sezione di Microbiologia e Virologia Generale e Biotecnologie Microbiche, Cagliari University, 2004-2005
Post-Doctoral Fellow, Dipartimento Scienze Chimiche, Cagliari University, 2003-2004
Visiting Scientist at Stockholm University 2003
Predoctoral stay at Stockholm University 2001
- The scientific activity is mainly directed to the study of conformational preferences of organic and bio-organic molecules and of their interactions with other molecules and ions; these researches are carried out by means of modeling techniques often combined with NMR techniques. The employed computational techniques are based either on quantum or classical mechanics, and recently she became involved in the development of coarse grained models. Part of these studies involve collaborations either with national or international groups. More in details the following collaborations are active:Cagliari University (Prof. G. Cerioni, Prof G. Saba, Dr F. Cesare Marincola, Dr S. Porcedda, Dr Massimiliano Porcu, Ms Marianna Usula)
Stockholm University (Prof. A. Laaksonen, Prof. A. Lyubartsev, Dr Y.L. Wang, Miss T.Y. Sun Mr G. Todde)
Université Libre de Bruxelles (Prof. M. Luhmer, Dr L. Fusaro),
Sassari University (Prof. U. Azzena, Dr L. Pisano)
Biomolecular Chemistry Institute, CNR, Sassari (Dott. P. Spanu, Dott.ssa F. Ulgheri),
Vilnius University (Dr K. Aidas)
Universita’ di Roma La Sapienza (Prof. Ruggero Caminiti, Dr Lorenzo Gontrani),
Safarik University, Kosice (Prof. Jozef Ulicny & Mr Matúš Rebič) and
“Gheorghe Asachi” Technical University of Iasi (Dr E.S. Băcăiţă)Her research activity started in 1999 with a PhD in chemistry under the supervision of Prof. Giuseppe Saba, studying the effects of the nucleotides sequence on its local structure and on interactions with ions. In 2001 a collaboration has been started, and still is active, with Prof. Laaksonen, with the aim of combining the molecular dynamics technique with the study of the magnetic relaxation of quadrupolar ions, in complex solutions like those of oligomeric DNA. Quadrupolar relaxation has been, and still is, widely employed to study ionic distribution around charged molecules, like DNA, and their structural and dynamical properties or their binding modes with other molecules. By calculating the electric field gradient at the quadrupolar nuclei during the simulated molecular dynamics, it has been possible to calculate their relaxation parameters from the trajectories. This study allowed rationalizing the effect of Na/DNA direct and water mediated binding on static and dynamic parameters of the quadrupolar relaxation. These studies are now being extended to other quadrupolar ions and to different DNA sequences. Presently the validation of the NMR calculations is also being performed using QM/MM methods on simple electrolyte systems and on ionic liquids, in collaboration with Dr Aidas of Vilnius University, Prof. Laaksonen and Dr Wang of Stockholm University. The studies of nucleic acids are now extended to quadruplexes of DNA, in collaboration with the group of Prof. Laaksonen and Lyubartsev at Stockholm University, and that of Prof. Ulicny of Safarik University. The collaboration is aimed at the development of nucleic acid coarse-grained model capable of well reproducing the interactions with ions.Recently she has extended her investigations to the Modeling of Enzymatic Fuel Cell. More in details, she is currently using MD to study the denaturation process of the most used enzyme at the anode (Glucose Oxidase), in order to propose modifications which would lead to a more stable protein. Within the same project QM/MM calculations are being used to study the reaction in the active site, and the effect of protein modification on the catalytic action. This activity is carried on in collaboration with Prof. Laaksonen, and in the framework of this project she has been Visiting Professor at Stockholm University.Another important part of her research activity concerns the study of structural, dynamical and chemical properties of organic molecules by means of quantum mechanical calculations usually combined with NMR experimental data, mainly using the O-17 nuclide. Different classes of compounds have been studied with this combined approach, comprising β-diketones, vic-triketones, α-β unsaturated carbonyl compounds, λ-3 and λ-5 iodanes, acetoxysilanes and others. These studies are carried out in collaboration, for the experimental part, with Prof. Cerioni of Cagliari University, Prof. Luhmer and Dr Fusaro of Université Libre de Bruxelles.Within a collaboration with Dr Bacaita of Technical University of Iasi and Prof Laaksonen of Stockholm University, Dr Mocci is extending her interest in the simulations of polymeric systems of biological interest (so far limited to DNA and proteins) to amylose and amylopectine systems, which are to be used as drug delivery vehicles.
Teaching Experience: Courses
- Pharmacy and Biology Faculty
- 2006- present
“Physical Methods in Organic Chemistry” for Chemistry and Pharmaceutical Science Students
an undergraduate course covering the following topics: H-1 NMR, C-13 NMR, Two Dimensional NMR, Dynamic NMR, UV.
Developed quizzes, exams, and homework, diagnostic and self assessment tests.
- 2006- 2009
“Computational Methods in Organic Chemistry” for Chemistry and Pharmaceutical Science Students
an undergraduate course covering the following topics:
Introduction to the investigation of organic molecules properties
by quantum chemistry and force field calculations.
“Organic Chemistry” for Biology Students
an undergraduate course covering the following topics:
Introduction to organic molecules and their reactivity
Teaching for teachers
Since the academic year 2012/2013 I am delivering courses for developing professional teaching competencies of High School Science Teachers.
In my courses I show how the computational modeling tools can be used by high school teachers to prepare their lessons, to capture student attention, to let them perceive chemistry as a funny subject, and to easily show in a pictorial way concepts that are often considered by the students as too abstract. The courses are mostly developed by myself by combining my expertise in molecular modeling software with the chemistry problems that high school students have to solve.
“Chemistry with the Computers”
8 hrs A postgraduate course for high school chemistry teachers candidates
(TFA AMBITO SCIENTIFICO)
19 hrs A postgraduate for chemistry teachers with 3 years experience in teaching in high school
(PAS AMBITO SCIENTIFICO)
23 hrs A postgraduate course for high school chemistry teachers candidates
(TFA AMBITO SCIENTIFICO)
- As PhD student (2000-2002):
Tutoring in Chemistry undergraduate courses
- “Biological chemical physics”
- “Theoretical chemistry”
Division of Physical Chemistry:
2010, Erasmus teacher: “Computational methods in the study of organic molecules ”
Universidade Federal do ABC, Santo Andre (San Paolo) Brazil
- 2013 “II Escola Brasileira de Modelagem Molecular”: 01/02 Lecture entitled “Coarse Grained Modeling of DNA”
- 2015 “III Escola Brasileira de Modelagem Molecular“: 29/06 – 03/07 12 hrs Course “Solvation in simulations: models and applications.”
Safarik University, Kosice, Slovakia
2016, Erasmus+ teaching activity (20-26 Sept, Introduction to NMR spectroscopy)
- 2015, The Course of Molecular Modeling 2015 24/02 – 8 hours course on “Molecular Dynamics of Biopolymers”
Teaching Activity: Student Supervising
Masters Students Supervised
Luca Fusaro, “Studi di Dinamica Molecolare di Quadruplex di DNA” (Molecular dynamics studies of DNA Quadruplexes), 2004
Laura Caboni “Studi acido-base via spettroscopica e computazionale (Spectroscopic and Computational Studies of Acid-Base properties)”, 2006
Sonia Liggi, “Idratazione del DNA: uno studio di dinamica molecolare della dipendenza dalla sequenza” (DNA hydration: a molecular dynamics study of sequence dependence), 2009
- Alessio Atzori, “Studio delle Interazioni tra DNA e controioni mediante simulazioni di Dinamica Molecolare” DNA/counterions interactions studied by molecular dynamics simulations), 2009
- Giulia Mameli, “Carattere flussionale degli acetossi silani: uno studio DFT e 17O NMR dinamico” (Fluxional character of acetoxy silanes: a DFT and 17O Dynamic NMR study), 2010
- Valentina Porcu, “Studi FTIR della denaturazione di proteine” (FTIR studies of protein denaturation), 2014
- Sara Massidda, “Sviluppo di un modello Coarse Grained per duplex di DNA” (Duplex DNA coarse grained model development), 2015
- Olga Becconi, “Studio delle interazioni specifiche tra Li+, Na+, K+ e l’albumina del siero bovino mediante dinamica molecolare”, 2016
- Federico Conticchio “Modellazione Molecolare della Glucosio Ossidasi – Studio della sua denaturazione tramite simulazioni di Dinamica Molecolare”, 2016
Vladimir Banovic “QM/MM computer simulations of the catalytic action of Glucose Oxidase- as part of a prototype enzymatic fuel cell”, 2011
- Emelie Ertan “Molecular Dynamics computer simulations of Glucose Oxidase
– as part of prototype Enzymatic Fuel Cell”, 2011
Federico Conticchio “Molecular Modelling of Glucose Oxidase – Deep inside its denaturation through MD simulation”, 2012
PhD Students Supervised:
Massimiliano Porcu “Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica”, 2015
High School Teachers Candidates Supervised:
Vincenzo Brundu, “Le reazioni di sostituzione nucleofila”, 2014
Daniela Satta, “Gli enzimi: ciclossigenasi e aspirina”, 2014
Evita Bella, Final Report on the one year preschool teacher course, 2015
Invited Lectures / Seminars (Since 2010)
Helsinki (Finland), Molecules in Motion Symposium, ” On the interactions of monoatomic ions in charged organic and biomolecular systems: Insight from Molecular Dynamics simulations”, Invited Lecture, August 23, 2016
Sassari (Italy), “Docking studies for inhibition of Caspase-3”, Giornata di Presentazione dei Risultati del Progetto: Individuazione di Nuovi Lead per la Cura di Patologie Neurodegenerative. Invited Lecture, July 6, 2016
Honolulu (USA) Pacifichem2015, Symposium on Synergistic Relationships between Computational Chemistry and Experiment, Invited Lecture “CompChem & NMR studies of quadrupolar nuclei in solution”, December 19, 2015.
Novy Smokovec, High Tatras (Slovakia) Conference on X-ray for cellular imaging, Invited Lecture “DNA Simulations beyond the atomistic scale” November 5th, 2015
Bratislava, CoDECS Meeting of Bratislava Conference on ADVANCES IN COMPUTATIONAL SPECTROSCOPY 2014: Invited Lecture “MD studies of quadrupolar relaxation in solution”, October 27th, 2014
University of Eastern Finland, Kuopio, Invited Lecture “Molecular modeling combined with O-17 and Na-23 NMR in the study of (bio)-organic molecules in solution” August 20th, 2014
Kosice, Velka Trna, Slovakia , The Multi-scale Modelling Workshop, Invited Lecture “Binding preferences of ions to DNA surface: models dependence” July 7th, 2014
Sassari, Italy, Italian Organic Chemistry Division Conference, Contributed talk, “Glucose Oxidase from Penicillium Amagasakiense: insight on the thermally-induced structural modification from Molecular Dynamics Simulations” September 12th, 2014
Pula, (Ca, Italy) –INTERNATIONAL CONFERENCE IIC Contributed talk, “Water and ion parameters effects on the base sequence specificity of ion binding to DNA in MD simulations” April 29th, 2013
Santo Andre’ (SP, Brasil) – III Escola Brasileira de modelagem molecular. Invited Lecture “Coarse Grained model of DNA”, January 31st, 2013
Ribeirao Preto, (SP, Brasil) –.“Coarse Grained Modeling of DNA” FCFRP – Invited Lecture at the Universidade de São Paulo, Feb, 4th 2013
Munchen, September 22nd, 2010, (Muenster, Germany) Contributed Talk “Fluxional Character of Carboxylates: DFT & 17O NMR Investigations”
Parigi, April 15th, TheTIS 2011-Theoretical Tools for In Silico Spectroscopy, Invited talk “Molecular modeling combined with O-17 and Na-23 NMR in the study of (bio)-organic molecules in solution”
Stockholm, Sweden “Base Sequence Specificity of Counterion Binding to DNA: what simulation can tell us?” Invited Seminar at Karolinska Institutet, September, 21st 2011
Reviewer of Applications for
2015, Swedish Research Council ( > 30 applications )
2010, Natural Sciences and Engineering Research Council of Canada (2010)
Symposium & Conferences Organization
Chair of the international conference THEOBIO2015 “VII International Theoretical Biophysics Symposium”. Cagliari, June 8-12, 2015.
FM has been involved in the organization of the following symposium:
La Parola ai Giovani, 2008, Cagliari
Centenary celebration of the Italian Chemistry Society, Cagliari, 2009
Scienza-società-scienza 2013, Cagliari
Reviewer of Articles for several journals, such as:
Journal of Organic Chemistry (ACS)
Inorganic Chemistry (ACS)
Journal of Molecular Structure (Elsevier)
Journal of Thermal Analysis and Calorimetry (Springer)
Proteins: Structure, Function, and Bioinformatics (Wiley)
Nucleic Acids Research (Oxford Journals)
Physical Chemistry Chemical Physics (RSC)
Member of the reviewer panel of Frontier in Chemistry
Member of the Italian Chemical Society (2007 – present)
Member of the steering committee of the Italian Chemical Society, Sardinia Section, and treasurer of the same (2008-2010).
European Union Networks and Projects
Member of the COST action: CMST Action CM1002 – CODECS: COnvergent Distributed Environment for Computational Spectroscopy (2010-2014)
Member of the COST action: CMST Action CM1402 – MOLIM: MOLecules In Motion (2015-2018)
Member of the panel of experts which provides important complementary know-how to the FP7 Project “CELIM: Fostering Excellence in Multiscale Cell Imaging ” Grant agreement no: 316310 (2013-2016)
Host of foreign researchers/students
Long Stays in my group
- Prof. Aatto Laaksonen (2008, 2009, 2012, 2015), Stockholm University, Sweden, 20 months
Dr Simona Bacaita (2012), Technical University of Iasi, Romania, 3 months
Mr Matus Rebic (2014), Safarik University, Kosice, Slovakia, 3 months
Miss Dovile Lengivinaite (2015-2016), Vilnius University, Lithuania, 9 months
Prof. Christopher Gunaseelan (2016), University of Malaya, 8 months
Mr Mathieu Fossepre (2009), Namur University, 3 months
Mr Aymeric Naome (2009), Namur University
Dr Yoaquan Tu (2009), Orebro University, Sweden
- Prof. Jozef Ulicny (2009, 2015), Safarik University, Kosice, Slovakia
Prof. Klaus Koch (2015), Stellenboch University, South Africa
Prof. Michel Luhmer (2010), Université libre de Bruxelles, Belgium
Kestutis Aidas (2012, 2013), Vilnius University, Lithuania
Yong Lei Wang (2013), Stockholm University, Sweden
Dr Nikolay Korolev (2009) Nanyang Technological University, Singapore
Prof Igor Svishchev, (2009) Trent University Peterborough, Canada
Prof Alexander Lyubartsev (2009) Stockholm University, Sweden
Mr Alexander Mirzoev (2009) Stockholm University
Miss Tianyang Sun, (2013, 2014, 2015) Zhejiang University, Hangzhou, P. R. China
Dr Katarína Stroffekova (2016) Department of Biophysics, PJ Safarik University, Slovakia
Italian: Native Language
English: Fluent English
Swedish: Novice reading and listening.
French, Spanish: Good in Reading and Intermediate in Listening
Sardinian: Advanced listening and reading
Mocci F, Laaksonen A, (2015)
“Combining MD simulations and NMR spectroscopy for molecular insight and methodological synergy: the integrated MD-NMR method”
Book Chapter in Nuclear Magnetic Resonance (Eds Kamienska-Trela K, Wojcik J) Volume 44, 592-616, DOI:10.1039/9781782622758-00592. Series: Specialist Periodical Reports; Royal Society of Chemistry Publishing.
- Mocci F, Laaksonen A, Wang Y-L, Saba G, Lai A, Cesare Marincola F, (2014)
“CompChem and NMR Probing Ionic Liquids”
Chapt. 4 in “The Structure of Ionic Liquids” (Eds. Caminiti R & Gontrani L), pp 97-126, ISBN: 978-3-319-01697-9 (Print) 978-3-319-01698-6 (Online) DOI 10.1007/978-3-319-01698-6_4, Springer International Publishing Switzerland
- Laaksonen A, Lyubartsev A, Mocci F, (2012)
“M.DynaMix Studies of Solvation, Solubility and Permeability”
in “Molecular Dynamics / Book 2″, p. 85-106, ISBN: 978-953-51-0444-5, doi: 10.5772/35955 Wang L. Editor
- Cerioni G, Mocci F (2006)
“17O NMR spectroscopy of organic compounds containing the -O-O- group”,
Chapter 5 in “The Chemistry of Peroxides” (Ed. Z. Rappaport), Wiley
Atzori A, Liggi S, Laaksonen A, Porcu M, Lyubartsev AP, Saba G, Mocci F (2016, in press. )
“Base Sequence Specificity of Counterion Binding To DNA: What Can MD Simulations Tell Us?”
Canadian Journal of Chemistry, Corresponding Author
Invited paper for the special issue in honour of Russ Boyd and Arvi Rauk
Rebič M, Laaksonen A, Šponer J, Uličný J, Mocci F (2016)
“Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models”
The Journal of Physical Chemistry B 120 (30), 7380-7391 Corresponding Author
Azzena U, Carraro M, Pisano L, Mocci F, Antonello S, Maran F (2016)
“Reducing properties of 1, 2-dipyridyl-1, 2-disodioethanes: chemical validation of theoretical and electrochemical predictions”
RSC Advances 6 (52), 46813-46821 Corresponding Author
Chiriu D, Ricci PC, Carbonaro CM, Nadali D, Polcaro A, Mocci F (2016)
“Drying oil detected in mid-third Millennium B.C. Mesopotamian clay artifacts: Raman spectroscopy and DFT simulation study”
Microchemical Journal, 124, 386–395
Benetis NP, Dmitriev Y, Mocci F, Laaksonen A.(2015)
“Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra”
The Journal of Physical Chemistry A 119(35):9385-9404.
Rebic M, Mocci F, Laaksonen A, Ulicny J (2015)
“Multiscale Simulations of Human Telomeric G-Quadruplex DNA”
Journal of Physical Chemistry B (2015), 119(1), 105-113 Corresponding Author
Usula M, Matteoli E, Leonelli F, Mocci F, Cesare Marincola F, Gontrani L (2014)
Thermo-physical properties of ammonium-based ionic liquid + N-methyl-2-pyrrolidone mixtures at 298.15 K.
Fluid Phase Equilibria 383, 49-54
Usula M, Porcedda S, Mocci F, Gontrani L, Caminiti R (2014)
“NMR, calorimetry, and computational studies of aqueous solutions of N-methyl-2-pyrrolidone”
The Journal of Physical Chemistry B 118 (35), 10493-10502
Todde G, Hovmöller S, Laaksonen A and Mocci F (2014)
“Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations.”
Proteins. doi: 10.1002/prot.24596 Corresponding Author
Usula M, Mocci F, Cesare Marincola F, Porcedda S, Gontrani L, Caminiti R (2014)
“The Structural Organization of N-Methyl-2-pyrrolidone + Water Mixtures: A Densitometry, X-ray Diffraction and Molecular Dynamics Study”,
J. Chem. Phys., 140, 124503; doi: 10.1063/1.4869235d. Corresponding Author
Wang Y-L, Hedman F, Porcu M, Mocci F, Laaksonen A (2014)
“Non-Uniform FFT and Its Applications in Particle Simulations”
Applied Mathematics, 2014, Vol. 5, 520-541 DOI: 10.4236/am.2014.53051
Jämbeck J P M, Mocci F, Lyubartsev A P, Laaksonen A (2013).
Partial atomic charges and their impact on the free energy of solvation.
Journal of Computational Chemistry, Vol 34(3), p 187-197
Aidas K, Ågren H, Kongsted J, Laaksonen A, Mocci F (2013)
“A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution”.
Physical Chemistry Chemical Physics. Vol 15, 1621-1631 Corresponding Author
Fusaro L, Mameli G, Luhmer M, Mocci F, Cerioni G (2012).
Dynamic NMR of low-sensitivity fast-relaxing nuclei: 17O NMR and DFT study of acetoxysilanes.
Magnetic Resonance in Chemistry, vol. 50, p. 152-158 Corresponding Author
Mocci F, Laaksonen A (2012).
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”.
Soft Matter, vol. 8, p. 9268-9284 Corresponding Author
Fusaro L, Mocci F, Muller R N, Luhmer M (2012).
Insight into the Dynamics of Lanthanide-DTPA Complexes As Revealed by Oxygen-17 NMR.
Inorganic Chemistry, vol. 51, p. 8455-8461
Fusaro L, Mocci F, Luhmer M, Cerioni G, (2012)
17O-Dynamic NMR and DFT Investigation of Bis(acyloxy)iodoarenes.
Molecules, Vol. 17, 12718-12733. Corresponding Author
Azzena U, Dettori G, Mocci S, Pisano L, Cerioni G, Mocci F, (2010)
”Active-sodium-promoted Reductive Cleavage of Halogenated Benzoic Acids”
Tetrahedron, vol. 66, pp 9171-9174.
Fusaro L, Luhmer M, Cerioni G, Mocci F. (2009)
“On the Fluxional Behavior of Dess−Martin Periodinane: A DFT and 17O NMR Study”,
The Journal of Organic Chemistry, vol. 74 (22), pp. 8818-8821. Corresponding Author
Mocci F, Usai M, Cerioni G (2009).
“DFT and multinuclear magnetic resonance studies of diazenedicarboxylates and related compounds.”
Magnetic Resonance in Chemistry, vol. 47, pp. 31-37 ISSN: 0749-1581. Corresponding Author
Cerioni G, Maccioni E, Cardia M.C, Vigo S, Mocci F. (2009)
“Characterization of 2,5-diaryl-1,3,4-oxadiazolines by multinuclear magnetic resonance and DFT calculations. Investigation on a case of very remote Hammett correlation”
Magnetic Resonance in Chemistry. Vol. 47(9), pp 727 – 733. Corresponding Author
Cesare Marincola F, Virno A, Randazzo A, Mocci F, Saba G, Lai A, (2009)
“Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR Study.”
Magnetic Resonance in Chemistry. Vol. 47(12), pp. 1036 – 1042.
Mocci F, (2009)
“Torsion angle relationship of the 17O NMR chemical shift in α,β-unsaturated carbonyl compounds.”
Magnetic Resonance in Chemistry, vol. 47(10), pp 862 – 867. Corresponding Author
Mocci F, Uccheddu G, Frongia A, Cerioni G. (2007).
“Solution Structure of Some λ3 Iodanes: An 17O NMR and DFT Study.”
Journal of Organic Chemistry. vol. 72, pp. 4163-4168. Corresponding Author
Mocci F, Laaksonen A, Lyubartsev A, Saba G. (2004)
“A molecular dynamics investigation of 23Na relaxation in oligomeric DNA aqueous solution”,
Journal of Physical Chemistry B, vol. 108(41), pp. 16295 – 16302.
Mocci F, Saba G. (2003)
“MD simulations of AT rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA.”
Biopolymers, vol. 68, pp 471-485.
Cerioni G, Plumitallo A, Mocci F, Rappoport Z, Rubin M.R. (2001)
“Conformation of vicinal-triketones: A theoretical and 17O NMR approach”
Journal of the Chemical Society, Perkin Transactions 2, vol 5, pp. 774-777.