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Mateusz Marianski, Ph.D.

Computational & Theoretical Chemistry, Biomolecular Simulations, Carbohydrates, IR Spectroscopy



Contact Information:

Office Location: Hunter North Building, Room 1321B

Office Telephone: 212-772-5343

E-mail: mmarians@hunter.cuny.edu

Education:

M.Sc. University of Wroclaw, Poland (Robert Wieczorek)
Ph.D. Graduate Center and Hunter College, CUNY (Joseph J. Dannenberg)
Postdoc Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany (Carsten Baldauf and Gert von Helden)

Research Summary:

Structure formation and dynamics in carbohydrates:

Carbohydrates, one of the three important classes of biopolymers, are involved in a range of biological processes: they serve as structural polymer, energy storage and recognition module in immune system or cell-cell communication. Their multiple functions in living organism are facilitated by properties of the monomer: whereas other biopolymers assembles in a linear fashion, several distinct possibilities for glycosidic bond formation bolster the accessible structural space of carbohydrates over those available for nucleotides and peptides. Moreover, carbohydrates frequently differ only in spatial configuration of atoms, they carry the same mass-over-charge ratio and, hence, they are indistinguishable in a conventional mass spectrometry analysis and requires more elaborate techniques. These complications in glycoanalitics caused that glycomics lags behind more mature fields of genomics and proteomics. In the consequence, the relation between the carbohydrate sequence and the structure (hence function) it adopts remains largely unknown.

In recent years novel glycosynthesis and glycoanalytic techniques initiated a rapid development in glycomics. Especially two analytic techniques promise to become the new standard: Ion Mobility-mass spectrometry (IM-MS) and cold-ion gas-phase infrared spectroscopy. These two methods are complementary in their very nature; the IM-MS conveniently reduces the structural information to a single number - the collision cross section - that describes an overall molecular shape, whereas the vibrational spectroscopy extracts in-depth details of the molecular structure and conformation. However, in order to fully benefit from these novel experimental techniques and advance our understanding of the carbohydrate structural space, the data needs to be cracked by theoretical chemistry methods.

In the lab, we focus on theoretical understanding of in-depth relation between the carbohydrate sequence and its molecular properties. Our set of tools, selection of which depends on a particular problem we want to tackle, ranges from simple force-field based molecular modeling to high-level quantum chemistry methods. Despite this flexibility, our workhorse is the density-functional theory which provides excellent balance between accuracy and computational tractability for carbohydrate-sized molecules and enables to access their dynamic properties using ab initio molecular dynamics.

The research provides excellent opportunity to gain an understanding of concepts ubiquitous in all branches of chemistry like basics of bio- and glycochemistry, as well as more advanced concepts of quantum mechanics, molecular energy landscapes and reaction mechanisms. Moreover, research in the theoretical chemistry lab will teach basics of scripting/programing (linux, bash, python, perl, C++...) and data-analysis skills.

Selected Publications:

V. Scutelnic, M. A. S. Perez, M. Marianski, S. Warnke, A. Gregor, U. Rothlisberger, M. T. Bowers, C. Baldauf, G. von Helden, T. Rizzo, J. Seo, J. Am. Chem. Soc, 2018, Article ASAP, doi: 10.1021/jacs.8b02118: "The Structure of the Protonated Serine Octamer"

E. Mucha, A. I. Gonzalez Flores, M. Marianski, D. A. Thomas, W. Hoffmann, W. B. Struwe, H. S. Hahm, S. Gewinner, W. Schoellkopf, P. H. Seeberger, G. von Helden and K. Pagel, Angew. Chem. Int. Ed., 2017, 56, pp. 11248-11251: "Glycan fingerprinting using cold-ion infrared spectroscopy"

M. Marianski, A. Supady, T. Ingram, M. Schneider and C. Baldauf, J. Chem. Theory Comput., 2016, 12, pp. 6157-6168: "Assessing the accuracy of across-the scale methods for predicting carbohydrate conformational energies on the example of glucose and α-maltose"

P. Chen, M. Marianski and C. Baldauf, ACS Macro Lett, 2016, 5, pp. 50-54: ``H-Bond isomerization in crystalline cellulose IIII: Proton hopping versus hydroxyl flip-flop``