Publications by Natalia Nagornova

Waste-to-Taste: Transforming Wet Byproducts of the Food Industry into New Nutritious Foods

Food and beverage production generates enormous amounts of spent residues in the form of pomaces, pulps, grains, skins, seeds, etc. Although these sidestreams remain nutritious, their conversion to foods can be complicated by issues of digestibility and pr ...

2024

Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy

Oleg Boyarkine, Natalia Nagornova, Manuel Dömer, Andrei Zviagin, Ruslan Yamaletdinov

The geometry of biomolecules isolated in the gas phaseusuallydiffers substantially from their native structures in aqueous solution,which are the only ones truly relevant to life science. To connectthe high resolution of cold ion spectroscopy that can be a ...

2023

Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles

Majed Chergui, Natalia Nagornova, Thomas Charles Henry Rossi, Hui-Yuan Chen

The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) s ...

Aip Publishing2023

Tracking local and global structural changes in a protein by cold ion spectroscopy

Oleg Boyarkine, Natalia Nagornova, Vladimir Kopysov, Andrei Zviagin

Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated pro ...

ROYAL SOC CHEMISTRY2022

Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy

Oleg Boyarkine, Natalia Nagornova, Vladimir Kopysov

The early stages of fibril formation are difficult to capture in solution. We use cold-ion spectroscopy to examine an 11-residue peptide derived from the protein transthyretin and clusters of this fibre-forming peptide containing up to five units in the ga ...

Wiley-Blackwell2018

A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy

Oleg Boyarkine, Natalia Nagornova, Robert Benny Gerber

The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic le ...

American Chemical Society2017

The LOUVRE Laboratory: State-of-the-Art Ultrafast Ultraviolet Spectroscopies for Molecular and Materials Science

Majed Chergui, Frank van Mourik, Natalia Nagornova, Lars-Hendrik Mewes, Thomas Charles Henry Rossi, Tania Palmieri, Edoardo Baldini, Malte Oppermann, Benjamin Bauer, Aurelio Oriana

We describe the facilities for ultraviolet studies in the femtosecond to nanosecond time domain. These facilities consist of: i) a set-up for deep-ultraviolet spectroscopy in the 260–380 nm range in both pump and probe pulses for transient absorption/refle ...

2017

Vibrational Signatures of Conformer-Specific Intramolecular Interactions in Protonated Tryptophan

Oleg Boyarkine, Natalia Nagornova, Aleksandr Pereverzev

Because of both experimental and computational challenges, protonated tryptophan has remained the last aromatic amino acid for which the intrinsic structures of low-energy conformers have not been unambiguously solved. The IR-IR UV hole-burning spectroscop ...

Amer Chemical Soc2016

Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy

Oleg Boyarkine, Thomas Rizzo, Natalia Nagornova, Vladimir Kopysov, Robert Benny Gerber

Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculat- ed from first- principles and measured in a wide spectral range using infr ...

Wiley-V C H Verlag Gmbh2015

Exploring the Mechanism of IR–UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins

Oleg Boyarkine, Thomas Rizzo, Natalia Nagornova

Wiley-VCH Verlag GmbH2013

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Oleg Boyarkine, Thomas Rizzo, Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Natalia Nagornova, Manuel Dömer

We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test ...

Wiley-Blackwell2013

Interplay of Intra- and Intermolecular H-Bonding in a Progressively Solvated Macrocyclic Peptide

Oleg Boyarkine, Thomas Rizzo, Natalia Nagornova

Studying solvation of a large molecule on an atomic level is challenging because of the transient character and inhomogeneity of hydrogen bonding in liquid water. We studied water clusters of a protonated macrocyclic decapeptide, gramicidin S, which were p ...

American Association for the Advancement of Science2012

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

Oleg Boyarkine, Thomas Rizzo, Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Natalia Nagornova, Manuel Dömer

Wiley-VCH Verlag GmbH2011

Cold Ion Spectroscopy of Biological Molecules in the Gas Phase

Natalia Nagornova

The three-dimensional (3D) structures of proteins and peptides in vivo largely determine their biological functions. In vitro these native structures and their heterogeneity reflect a subtle balance between noncovalent intramolecular interactions and those ...

EPFL2011

Structure and Bonding of Isoleptic Coinage Metal (Cu, Ag, Au) Dimethylaminonitrenes in the Gas Phase

Oleg Boyarkine, Thomas Rizzo, Peter Chen, Natalia Nagornova

Dimethylaminonitrene complexes of IMesM+ (IMes = 1,3-bis(2,4,6-trimethylphenyl)- imidazol-2-ylidene; M = Cu, Ag, Au) were prepared in the gas phase and structurally characterized by high-resolution infrared spectroscopy of the cold species, ion-molecule re ...

American Chemical Society2010

Highly-resolved Spectra of Gas-phase Gramicidin S: A Benchmark for Peptide Structure Calculations

Oleg Boyarkine, Thomas Rizzo, Natalia Nagornova

We have measured a vibrationally-resolved UV spectrum of doubly-protonated gramicidin S (GS) in the gas phase and, subsequently, a highly-resolved, conformer-specific infrared spectra in the 6 μm fingerprint region, using a cold ion trap in combination wit ...

American Chemical Society2010