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Molecular Interactions in Chemical and Biological Systems

Molecular interactions are of key importance to many chemical and biological processes such as protein folding and function, peptide aggregation, enzymatic reactions, or the stabilization of reactive species, to name but a few. Intermolecular interactions between solvent (water in most cases of biological relevance) and solute molecules determine the aggregation of proteins into fibrils, enzyme catalysis, and other biological processes. In our group we use state of the art computational tools and the construction of new models of complex systems to investigate molecular interactions of proteins, organic molecules, solvents, co-solvents and lipid bilayers. The focus of our research is to explore the properties, reactivity, and applications of complex systems consisting of a large number of interacting molecules.



Elsa Sánchez-García

Dr. Elsa Sánchez-García

since 2010
Nachwuchsgruppenleiterin at the Max-Planck-Institut für Kohlenforschung (Liebig Stipendium des Fonds der Chemischen Industrie)
Postdoc at the Max-Planck-Institut für Kohlenforschung (W. Thiel)
Postdoc, Ruhr University Bochum; Assistentin im Chemiepraktikum für Medizin- und Biologiestudenten
Dr. rer. nat., University of Bochum (M. Havenith-Newen)
Research Scientist, Max Planck Institute für Strahlenchemie (now Max Planck Institute für Bioanorganische Chemie) (S. Braslavsky)
Ph.D studies at the Laboratory of Theoretical and Computational Chemistry (L.A. Montero) at the University of Havana
Junior teacher of General Chemistry and Quantum Chemistry at the University of Havana
Diploma of Chemistry at the University of Havana
Born in Havana, Cuba
Member of the Global Young Faculty
Liebig-Stipendium, Fonds der Chemischen Industrie
Forschungsstipendium, MPI für Kohlenforschung
Book Prize of the Faculty of Chemistry, University of Bochum
PhD with Summa cum laude (mit Auszeichnung), University of Bochum, Germany
Award of a Scholarship of the DAAD (German Academic Exchange Service)
Award in the category of "Best Novel Lecturer (Reserva Científica)". Faculty of Chemistry, University of Havana
Best graduated student of the University of Havana
Summa cum laude Diploma, University of Havana
Best graduated student of Chemistry

Costa, Paolo; Fernandez Oliva, Miguel; Sanchez-Garcia, Elsa* and Sander, Wolfram * “Isolation and Stabilization of the Highly Reactive Benzhydryl Cation in Water Ice” Journal of the American Chemical Society (2014) doi: 10.1021/ja507894x.

Bravo-Rodriguez, Kenny; Ismail-Ali, Ahmed F.; Klopries, Stephan; Ismail, Shehab; Wittinghofer, Alfred; Schulz, Frank* and Sánchez-García, Elsa* “Predicted Incorporation of Non-Native Substrates by a Polyketide Synthase yields Bioactive Natural Product Derivatives”, ChemBioChem (2014), 15, 1991–1997.

Crespo-Otero, Rachel; Mardyukov, Artur; Sanchez-Garcia, Elsa; Sander, Wolfram and Barbatti, Mario “Photo-stability of Peptide-bond Aggregates: N-methylformamide dimers”, Physical Chemistry Chemical Physics (2014), 16 (35), 18877–18887.

Sander, Wolfram*; Roy, Saonli; Bravo-Rodriguez, Kenny; Grote, Dirk and Sánchez-García, Elsa* “The Benzylperoxy Radical as a Source of Hydroxyl and Phenyl Radicals”, Chemistry–A European Journal (2014) doi: 10.1002/chem.201402459.
Klopries, Stephan; Koopmans, Kyra R. M.; Sánchez-García, Elsa* and Schulz, Frank*. “Biosynthesis with Fluorine”. ChemBioChem (2014), 15, 495–497.

Merten, Christian; Li, Fee; Bravo-Rodriguez, Kenny; Sanchez-Garcia, Elsa; Xu, Yunjie and Sander, Wolfram. “Solvent-induced Conformational Changes in Cyclic Peptides: A Vibrational Circular Dichroism Study”. Physical Chemistry Chemical Physics (2014), 16(12), 5627–5633.


Li, Fee; Bravo-Rodriguez, Kenny; Fernandez-Oliva, Miguel; Ramirez-Anguita, Juan M.; Merz, Klaus; Winter, Manuela; Lehmann, Christian W.; Sander, Wolfram* and Sanchez-Garcia, Elsa*. “Stereochemistry Rules: A Single Stereocenter Changes the Conformation of a Cyclic Tetrapeptide”, Journal of Physical Chemistry B (2013), 117, 10785–10791.

Hernández-Rodríguez, Erix W.;  Montero-Alejo, Ana L.; López, Rafael; Sánchez-García, Elsa; Montero-Cabrera, Luis A. and García de la Vega, José M. “Electron Density Deformations provide new Insights into the Spectral Shift of Rhodopsins”, Journal of Computational Chemistry (2013), 34, 2460–2471.

Dutt, Som; Wilch, Constanze; Gersthagen, Thomas; Talbiersky, Peter; Bravo-Rodriguez, Kenny; Hanni, Matti; Sanchez-Garcia, Elsa*; Ochsenfeld, Christian*; Klärner, Frank* and Schrader, Thomas*. “Molecular Tweezers with Varying Anions: A Comparative Study”, Journal of Organic Chemistry (2013), 78, 6721–6734.

Li, Fee; Bravo-Rodriguez, Kenny; Phillips, Charlotte; Seidel, Rüdiger W.; Wieberneit, Florian; Stoll, Raphael; Doltsinis, Nikos L.; Sanchez-Garcia, Elsa* and Sander, Wolfram*. “Conformation and Dynamics of a Cyclic Disulfide-Bridged Peptide: Effects of Temperature and Solvent”, Journal of Physical Chemistry B (2013), 117, 3560–3570.

Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, C.; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa*; Schrader, Thomas* and Ottmann, Christian*. “Molecular tweezers modulate 14-3-3 protein-protein interactions”, Nature Chemistry (2013), 5, 234–239.

Sundermann, Uschi; Bravo-Rodriguez, Kenny; Klopries, Stephan; Kushnir, Susanna; Gomez, Hansel; Sanchez-Garcia, Elsa* and Schulz, Frank*. “Enzyme-Directed Mutasynthesis: A Combined Experimental and Theoretical Approach to Substrate Recognition of a Polyketide Synthase”, ACS Chemical Biology (2013), 8, 443–450.

Crespo-Otero, Rachel; Bravo-Rodriguez, Kenny; Roy, Saonli; Benighaus, Tobias; Thiel, Walter; Sander, Wolfram and Sánchez-García, Elsa*. “Interactions of Aromatic Radicals with Water”, ChemPhysChem, special issue (2013), 14, 805–811.

Crespo-Otero, Rachel;  Mardyukov, Artur; Sánchez-García, Elsa; Barbatti, Mario and Sander, Wolfram. "Photochemistry of N-Methylformamide: Matrix Isolation and Nonadiabatics Dynamics”,  ChemPhysChem, special issue (2013), 14, 827–836.


Sander, Wolfram*; Roy, Saonli; Polyak, Iakov Ramirez-Anguita, Juan Manuel and Sanchez-Garcia, Elsa*. “The Phenoxyl Radical−Water Complex – A Matrix Isolation and Computational Study”, Journal of the American Chemical Society (2012), 134, 8222–8230.

Sánchez-García, Elsa* and Jansen, Georg*. “Competition between H•••π and H•••O Interactions in Furan Heterodimers”, Journal of Physical Chemistry A (2012), 116 (23), 5689–5697.

Hernández-Rodríguez, Erix Wiliam; Sánchez-García, Elsa*; Crespo-Otero, Rachel; Montero Alejo, Ana Lilian; Montero, Luis Alberto and Thiel, Walter. “Understanding Rhodopsin Mutations Linked to the Retinitis Pigmentosa Disease: A QM/MM and DFT/MRCI Study”, Journal of Physical Chemistry B (2012), 116, 1060–1076.

Metzelthin, Anja; Sánchez-García, Elsa; Birer, Özgür; Schwaab, Gerhard; Thiel, Walter; Sander, Wolfram and Havenith, Martina. “Acetylene•••Furan Trimer Formation at 0.37 K as a Model for Ultracold Aggregation of Non- and Weakly Polar Molecules”, ChemPhysChem (2011), 12 (10), 2009–2017.

Hsiao, Ya-Wen; Sánchez-García, Elsa; Doerr, Markus and Thiel, Walter. “Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein DsRed.M1”, Journal of Physical Chemistry B (2010), 114, 15413–15423.

Mardyukov, Artur; Crespo-Otero, Rachel; Sánchez-García, Elsa and Sander, Wolfram. “Photochemistry and Reactivity of the Phenyl Radical – Water System: A Matrix Isolation and Computational Study”, Chemistry – A European Journal  (2010), 16 (29), 8679–8689.


Research Topics

Molecular interactions in peptides and proteins

Molecular interactions in peptides and proteins

Amyloidogenic peptides are systems of high biological and medical relevance. For instance, the islet amyloid polypeptide (IAPP) is involved in the development of type-II diabetes mellitus. The amyloid beta peptide (Aβ) has been identified as a causative agent in Alzheimer disease (AD). Aβ40 and Aβ42 are the most common forms, Aβ42 being the most fibrillogenic and neurotoxic. The principal toxic species in AD are the soluble oligomeric aggregates of Aβ; therefore the search of oligomerization inhibitors agents is one of the targets of therapeutical intervention against AD and other amyloid diseases. We use molecular dynamics (MD), QM/MD, and quantum mechanics/molecular mechanics (QM/MM) techniques to investigate the aggregation of amyloidogenic peptides and proteins and their interactions with several inhibitors of oligomerization. Solvents and lipid bilayers are explicitly treated.

Cyclic polypeptides containing a photocleavable disulfide (S-S) bridge are model systems for the study of the dynamical conformational changes that convert a polypeptide chain into a three-dimensional protein structure. The interactions between the peptides and various solvents results in drastic conformational changes that are not well understood. In addition, conformational changes that result from the S-S photocleavage are investigated.

Reactive and unusual species

Reactive and unusual species

The concept of hydrogen bonding in open-shell complexes has gained relevance during the last years, but still it is much less investigated in comparison to the hydrogen bond in closed shell and ionic systems. Non-covalent interactions between the phenyl radical and water are of special interest since hydrogen bonds involving the singly occupied molecular orbitals (SOMOs) of the radical might play a role in hydrogen transfer reactions.

The phenyl radical is a reactive intermediate of fundamental importance to organic chemistry. It has been shown to play a key role in the combustion of hydrocarbon fuels to produce polycyclic aromatic hydrocarbons and soot. It has also been discussed as an intermediate in the chemistry of the interstellar medium, especially for the formation of polycyclic aromatic hydrocarbons, and in tropospheric chemistry.

We study complexes between various radicals and water. Of special interest is the structure and reactivity of the non-covalent complexes formed during this aggregation.


Photoreceptors: fluorescent proteins, rhodopsin

Photoreceptors: fluorescent proteins, rhodopsin

Rhodopsin is the visual pigment in rods and a heptahelical transmembrane receptor protein expressed in the retina. Mutations affecting rhodopsin can lead to loss of the outer field of vision. Over 120 point mutations have been discovered in the rhodopsin gene. We study the effect of mutations on the structural and spectroscopic properties of bovine and human rhodopsin models including the effect of the solvent and lipid bilayers.

Fluorescent proteins are very much used in molecular biology and biomedical research. Similar to green fluorescent protein (GFP), in the red fluorescent proteins (RFP) the chromophore is formed autocatalytically from the Gln66-Tyr67-Gly68 peptide in the presence of molecular oxygen. This reaction is commonly assumed to pass through a  GFP-like green chromophore with a trans-peptide bond between Phe65 and Gln66. This is followed by a so-called maturation step that yields the DsRed chromophore with a cis-acylimine group between Phe65 and Gln66, which extends the conjugation of the system and thus causes a red shift compared to GFP. We use QM/MM, QM/MM - MD, and MRCI methods, among others, to investigate the structural, mechanistic and spectroscopic features of RFPs





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