Quentin DuezUniversity of Mons
Quentin Duez
PhD
About
27
Publications
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Introduction
Publications
Publications (27)
The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is...
Chemical reaction networks, such as those found in metabolism and signalling pathways, enable cells to process information from their environment1,2. Current approaches to molecular information processing and computation typically pursue digital computation models and require extensive molecular-level engineering³. Despite considerable advances, th...
![a) IR photodissociation spectrum of [3+H]⁺ measured by helium tagging...](publication/376479368/figure/fig3/AS:11431281246425115@1716361365332/a-IR-photodissociation-spectrum-of-3-H-measured-by-helium-tagging-photodissociation_Q320.jpg)
The Eschenmoser coupling reaction (ECR) of thioamides with electrophiles is believed to proceed via thiirane intermediates. However, little is known about converting the intermediates into ECR products. Previous mechanistic studies involved external thiophiles to remove the sulfur atom from the intermediates. In this work, an ECR proceeding without...
The kinetic enantio-recognition of chiral viologen guests by planar-chiral porphyrin cage compounds, measured in terms of ΔΔG‡on, is determined by the planar-chirality of the host and influenced by the size,...
The flow of information is as crucial to life as the flow of energy1,2. Chemical reaction networks such as those found in metabolism and signalling pathways enable cells to process information from their environment3,4. Current approaches to molecular information processing and computation typically pursue digital computation paradigms and require...
![(a) X-ray structures of [CoC(Cl)] (left) and [CoC(Py)2]Cl (right)....](publication/373370547/figure/fig2/AS:11431281190166379@1695222897359/a-X-ray-structures-of-CoCCl-left-and-CoCPy2Cl-right-Color-code-oxygen_Q320.jpg)
![(a) Relative time evolution of [CoC(PyIN)]⁺ (top lines) and...](publication/373370547/figure/fig4/AS:11431281190157850@1695222898693/a-Relative-time-evolution-of-CoCPyIN-top-lines-and-CoCPyLIN-bottom-lines_Q320.jpg)
![Relative time evolution of [CoC(PyIN)]⁺ (top traces and lines) and...](publication/373370547/figure/fig5/AS:11431281190166384@1695222898972/Relative-time-evolution-of-CoCPyIN-top-traces-and-lines-and-CoCPyLIN-bottom_Q320.jpg)
Complex speciation and exchange kinetics of labile ligands are critical parameters for understanding the reactivity of metal complexes in solution. We present a novel approach to determine ligand exchange parameters based on electrospray ionization mass spectrometry (ESI-MS). The introduction of isotopically labelled ligands to a solution of metal...
The Front Cover illustrates the separation of isomeric manganese oxo‐intermediates by ion mobility mass spectrometry. The manganese oxo‐intermediates are generated during the epoxidation of alkenes by iodosylbenzene, catalyzed by manganese porphyrin cage complexes. These intermediates are formed either on the inside or outside of the cage complex....
Macrocyclic metal porphyrin complexes can act as shape‐selective catalysts mimicking the action of enzymes. To achieve enzyme‐like reactivity, a mechanistic understanding of the reaction at the molecular level is needed. We report a mechanistic study of alkene epoxidation by the oxidant iodosylbenzene, mediated by an achiral and a chiral manganese(...
An increasing number of studies take advantage of ion mobility spectrometry (IMS) coupled to mass spectrometry (IMS‐MS) to investigate the spatial structure of gaseous ions. Synthetic polymers occupy a unique place in the field of IMS‐MS. Indeed, due to their intrinsic dispersity, they offer a broad range of homologous ions with different lengths....
Four trinuclear ruthenium(II) polypyridyl complexes were synthesized, and a detailed investigation of their excited-state properties was performed. The tritopic sexi-pyridine bridging ligands were obtained via para or meta substitution of a central 2,2'-bipyridine fragment. A para connection between the 2,2'-bipyridine chelating moieties of the bri...
Synthetic polymers occupy a unique place in the field of ion mobility mass spectrometry (IMS-MS). Indeed, due to their intrinsic dispersity, they have the asset to offer a broad range of homologous ions with different lengths that can be detected in several charge states. In addition, the gas-phase structure of polymer ions mostly depends on their...
The stereoisomerically pure synthesis of a novel heptanuclear Ru(II)-Os(II) antenna bearing multitopic terpyridine ligands is reported. An unambiguous structural characterization was obtained by 1H NMR spectroscopy and ion mobility spectrometry (IMS-MS). The heptanuclear complex exhibits large molar absorption coefficients (77900 M-1 cm-1 at 497 nm...
Recent advances in molecular dynamics (MD) simulations have made it possible to examine the behavior of large charged droplets that contain analytes such as proteins or polymers, thereby providing insights into electrospray ionization (ESI) mechanisms. In the present study, we use this approach to investigate the release of polylactide (PLA) ions f...
RATIONALE Since their discovery, cyclic polymers have attracted great interest because of their unique properties. Today, the preparation of these macrocyclic structures still remains challenging for polymer chemists and most of the preparation pathways lead to an inescapable contamination by linear by-products. As the properties of the polymers ar...
Electrospray ionization (ESI) is an essential technique for transferring proteins from solution into the gas phase for mass spectrometry and ion mobility spectrometry. The mechanisms whereby [M + zH]z+ protein ions are released from charged nanodroplets during ESI have been controversial for many years. Here we discuss recent computational and expe...
We report a novel class of star-shaped multi-azobenzene photoswitches comprising individual photochromes connected to a central trisubstituted 1,3,5-benzene core. The unique design of such C3 symmetric molecules, consisting of conformationally rigid and pseudo-planar scaffolds, made it possible to explore the role of electronic decoupling in the is...
Several families of polymers possessing various end-groups are characterized by ion mobility mass spectrometry (IMMS). A significant contribution of the end-groups to the ion collision cross section (CCS) is observed, although their role is neglected in current fitting models described in literature. Comparing polymers prepared from different synth...
Recent studies point to an additional stability of metal-complexed functionalized hydrocarbon chains. This additional stabilization is suggested to arise from a bidentate complexation of the metal cation with both the functional group and aliphatic chain, leading to more folded structures. In the present work, this issue is verified for silver comp...
α‐Peptoids are peptido‐mimetic foldamers based on poly‐N‐substituted glycines that currently receive a growing interest due to their larger structural diversity, easier synthetic pathways, and larger thermal stability compared to peptides. An appropriate side chain appended to the nitrogen atoms is often crucial to constrain the peptoids into well‐...
The ion evaporation model (IEM) and the charged residue model (CRM) represent cornerstones of any discussion related to the mechanism of electrospray ionization (ESI). Molecular dynamics (MD) simulations have confirmed that small ions such as Na+ get ejected from the surface of aqueous ESI droplets (IEM), while folded proteins in native ESI are rel...
Recent molecular dynamics (MD) simulations from various laboratories have advanced the general understanding of electrospray ionization (ESI)-related processes. Unfortunately, computational cost has limited most of those previous endeavors to ESI droplets with radii of ~3 nm or less, which represent the low end of the size distribution in the ESI p...
Organic semiconductors are increasingly used in organic-based opto-electronic devices. Since regioselective synthetic approaches are not always controlled, promising compounds are sometimes prepared following non-regioselective routes. Ion Mobility Mass Spectrometry is here introduced as a direct method to distinguish isomers in mixtures, instead o...
One of the main issues when using traveling wave ion mobility spectrometry (TWIMS) for the determination of collisional cross-section (CCS) concerns the need for a robust calibration procedure built from referent ions of known CCS. Here, we implement synthetic polymer ions as CCS calibrants in positive ion mode. Based on their intrinsic polydispers...
Cyclodextrin is commonly used in the formation of supramolecular complexes with an array of targets ranging from metal ion sensing to modulation of peptide properties. Many of the applications of these supramolecular complexes are measured by monitoring the modulation of the optical properties of a chromophore upon formation or breaking of the comp...
In the field of polymer characterization, the use of IMMS (Ion Mobility Mass Spectrometry) remains mainly devoted to the temporal separation of cationized oligomers according to their charge states, molecular masses as well as their macromolecular architectures in order to probe the presence of different structures. When analyzing multiply charged...
Due to the close relationship between the molecular structure of a polymer and the associated physicochemical properties of the material, structural characterization of synthetic macromolecules has become an essential step in the conception of original materials. The aim of this work is to evaluate the performances of ion mobility mass spectrometry...
Questions
Questions (2)
Hello,
I am trying to perform QM/MM simulations using Gromacs 2016.5, especially to model a transition state for a reaction.
I found this tutorial that uses the Linear Transit approach : http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmwater.html#top
However, when I try to use the .mdp file from the tutoral (http://wwwuser.gwdg.de/~ggroenh/EMBO2004/water/LT.mdp), Gromacs returns an error saying that the steep integrator is not supported. Am I missing something and is there a way to perform energy minimization with Gromacs at the QM/MM level, or should I use another package ?
Thank you !
Hello everyone,
I am facing a problem regarding energy minimizations with Gromacs 2016.5.
To provide some context : I am currently parametrizing CHARMM to describe the behavior of polymers. I need thus to pay a lot of attention to Gromacs's energy output during energy minimizations and to compare these energies to high-level calculations.
When performing an energy minimization with the steepest descent algorithm, I obtain an output.gro, output.log file. However, by performing a single-point energy calculation (0step MD with mdrun -rerun without constraints as explained in http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy) and comparing the energies obtained from the single-point energy calculation and from the last step of my output.log file ; I noticed that the energy of output.gro is consistently higher than the energy of the last step of the output.log.
Hence my question : Is the output.gro from a steepest descent EM really the last step of the EM? (And does it thus correspond to the energies reported in the last step of the output.log file?)
For you to have a look, I joined an archive (For those looking at the top file, I am working with three new residues and new atomtypes which are well parametrized and were implemented in pdb2gmx) and all the files obtained with the following procedure.
The EM input are DP5.gro, em.mdp and topol.top
> gmx grompp -f em.mdp -c DP5.gro -p topol.top -o em.tpr
> gmx mdrun -v -deffnm em
I obtain em.gro and em.log.
If I want to perform a single-point energy calculation, I first perform a 0-step MD without constraints and then look at the output energy.
> gmx grompp -f SP.mdp -c em.gro -p topol.top -o SP.tpr
> gmx mdrun -s SP.tpr -rerun em.gro
By looking at md.log, the Epot = 9.02739e+02 kJ/mol
By looking at em.log's last step, the Epot = 8.98943e+02 kJ/mol. The energy difference is not negligible in my opinion and it is striking that the energy of em.gro is higher than the energy of the last step of EM.
Could someone help me with this issue? Is em.gro REALLY the energy-minimized structure?
Thanks a lot!
