Publications related to Revealing Single-Bond Anomeric Selectivity in Carbohydrate-Protein Interactions

Palladium‐Based Dyotropic Rearrangement Enables A Triple Functionalization of Gem‐Disubstituted Alkenes: An Unusual Fluorolactonization Reaction

Qian Wang, Jieping Zhu, Qiang Feng, Chenxu Liu

We report in this paper a Pd(II)-catalyzed migratory gem-fluorolactonization of ene-carboxylic acids. Reaction of 4-methylenealkanoic acid derivatives with Selectfluor in the presence of Pd(OAc)2 (1.0 mol %) at room temperature affords fluorolactones in go ...

Wiley-VCH Verlag GmbH2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

Gas/Surface reactions probed by reflection absorption infrared spectroscopy

Harmina Vejayan

In my thesis, I present an investigation of the dissociation reactions of gas phase molecules on single crystal metal surfaces studied by a molecular beam in combination with Reflection Absorption Infrared Spectroscopy (RAIRS). Two gas/surface systems were ...

EPFL2023

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

Tunnel junction sensing of TATP explosive at the single-molecule level

Radomir Zikic, Helena Miljkovic

Triacetone triperoxide (TATP) is a highly potent homemade explosive commonly used in terrorist attacks. Its detection poses a significant challenge due to its volatility, and the lack of portability of current sensing techniques. To address this issue, we ...

Royal Soc Chemistry2023

Mechanism of Reduction of Aqueous U(V)-dpaea and Solid-Phase U(VI)-dpaea Complexes: The Role of Multiheme c-Type Cytochromes

Marinella Mazzanti, Rizlan Bernier-Latmani, Karin Lederballe Meibom, Radmila Faizova, Margaux Camille Andréa Molinas

The biological reduction of soluble U(VI) complexes to form immobile U(IV) species has been proposed to remediate contaminated sites. It is well established that multiheme c-type cytochromes (MHCs) are key mediators of electron transfer to aqueous phase U( ...

2023

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging

Klaus Kern, Stephan Rauschenbach, Uta Schlickum

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. ...

Wiley-VCH Verlag GmbH2023

Supramolecular Polymer Brushes

Friederike Katharina Metze

Thin polymer coatings present a method to modify the surface properties of underlying substrates. Polymer-coated surfaces have been used as anticorrosive materials, surfaces with special wetting properties, antifriction materials, and as materials for biom ...

EPFL2023

Salt Bridge Structure of Microhydrated Arginine Kinetically Trapped in the Gas Phase by Evaporative Cooling

Oleg Boyarkine, Andrei Zviagin

Aminoacids and peptides generally exhibit zwitterionic forms withsalt bridge (SB) structures in solution but charge-solvated (CS) motifsin the gas phase. Here, we report a study of non-covalent complexesof the protonated amino acid arginine, ArgH(+)(H2O)( ...

2023

Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

Second-order Moller-Plesset perturbation theory (MP2) is the most expedient wave function-based method for considering electron correlation in quantum chemical calculations and, as such, provides a cost-effective framework to assess the effects of basis se ...

Amer Chemical Soc2023

Multistage Ion Mobility Spectrometry Combined with Infrared Spectroscopy for Glycan Analysis

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Priyanka Bansal

The structural complexity of glycans makes their characterization challenging, not only because of the presence of various isomeric forms of the precursor molecule but also because the fragments can themselves be isomeric. We have recently developed an IMS ...

2023

Combining multi-stage ion mobility spectrometry with cryogenic infrared spectroscopy for glycan analysis

Priyanka Bansal

Structural analysis of biomolecules is essential to understanding biological processes. Among the various classes of biomolecules, glycans have gained significant attention recently due to their ubiquitous roles in biological systems. However, study of gly ...

EPFL2022

Identification of Mobility-Resolved N-Glycan Isomers

Thomas Rizzo, Ahmed Ben Faleh, Robert Paul Pellegrinelli, Stephan Warnke, Priyanka Bansal

Glycan analysis has evolved considerably during the last decade. The advent of high-resolution ion-mobility spectrometry has enabled the separation of isomers with only the slightest of structural differences. However, the ability to separate such species ...

AMER CHEMICAL SOC2022

Structures of the (Imidazole)(n)H+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations

Valeriu Scutelnic

Here, we present new cryogenic infrared spectra of the (Imidazole) H-n(+) (n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. ...

SPRINGER/PLENUM PUBLISHERS2023

Urea Derivative-Promoted CsPbl(2)Br Perovskite Solar Cells with High Open-Circuit Voltage

Xin Guo, Bowen Yang, Yang Liu, Chen Li

Inorganic perovskite solar cells (PSCs) have witnessed extraordinary advances owing to their prominent stability against thermal aging. However, they suffer from a phase transition from black phase to yellow phase under ambient conditions and serious energ ...

WILEY-V C H VERLAG GMBH2022

A New Strategy Coupling Ion-Mobility-Selective CID and Cryogenic IR Spectroscopy to Identify Glycan Anomers

Thomas Rizzo, Ahmed Ben Faleh, Robert Paul Pellegrinelli, Stephan Warnke, Priyanka Bansal, Eduardo Carrascosa Casado, Lei Yue

Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) ...

2022

Modeling non-covalent interactions in condensed phase

Veronika Juraskova

The modeling of non-covalent interactions, solvation effects, and chemical reactions in complex molecular environment is a challenging task. Current state-of-the-art approaches often rely on static computations using implicit solvent models and harmonic ap ...

EPFL2022

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Anne-Clémence Corminboeuf, Veronika Juraskova, Rubén Laplaza Solanas, Frédéric Célerse

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry, and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environme ...

2022