Publications by authors named "Mark A J Koenis"

13 Publications

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Vibrational circular dichroism spectroscopy for probing the expression of chirality in mechanically planar chiral rotaxanes.

Chem Sci 2020 Jul 23;11(32):8469-8475. Epub 2020 Jul 23.

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands

Mechanically interlocked molecules can exhibit molecular chirality that arises due to the mechanical bond rather than covalent stereogenic units. Developing applications of such systems is made challenging by the absence of techniques for assigning the absolute configuration of products and methods to probe how the mechanical stereogenic unit influences the spatial arrangements of the functional groups in solution. Here we demonstrate for the first time that Vibrational Circular Dichroism (VCD) can be used to not only discriminate between mechanical stereoisomers but also provide detailed information on their (co)conformations. The latter is particularly important as these molecules are now under investigation in catalysis and sensing, both of which rely on the solution phase shape of the interlocked structure. Detailed analysis of the VCD spectra shows that, although many of the signals arise from coupled oscillators isolated in the covalent sub-components, intercomponent coupling between the macrocycle and axle gives rise to several VCD bands.
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http://dx.doi.org/10.1039/d0sc02485fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8163398PMC
July 2020

Vibrational circular dichroism studies of exceptionally strong chirality inducers in liquid crystals.

Phys Chem Chem Phys 2021 Apr;23(16):10021-10028

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

7,7'-Disubstituted 2,2'-methylenedioxy-1,1'-binaphthyls are highly efficient chirality inducers in nematic liquid crystals. The absolute configuration of these compounds is, however, hard to determine as they only crystallize as racemic mixtures. In this work a Vibrational Circular Dichroism (VCD) study is reported that provides an unambiguous determination of the absolute configuration of these compounds. An in-depth General Coupled Oscillator (GCO) analysis of the source of the VCD signal reveals that the unusual structure of these binaphthyl compounds inherently leads to strong and robust VCD bands. Combined with linear transit calculations, our VCD studies allow for the determination of key structural parameters.
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http://dx.doi.org/10.1039/d1cp00854dDOI Listing
April 2021

Analysis of Vibrational Circular Dichroism Spectra of Peptides: A Generalized Coupled Oscillator Approach of a Small Peptide Model Using VCDtools.

J Phys Chem B 2020 03 21;124(9):1665-1677. Epub 2020 Feb 21.

Department of Environmental Science, Physics, Physical Education and Sport, Lucian Blaga University of Sibiu, loan Ratiu Street, Nr. 7-9, 550012 Sibiu, Romania.

Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intramolecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that the contributions to the rotational strengths, considered to be insignificant in standard VCD models, may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of the amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies-and in particular, the decomposition of the rotational strength made possible by the GCO analysis-it becomes clear that one should be cautious when employing measures of robustness as proposed previously.
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http://dx.doi.org/10.1021/acs.jpcb.9b11261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061330PMC
March 2020

Self-Assembly of Supramolecular Polymers of N-Centered Triarylamine Trisamides in the Light of Circular Dichroism: Reaching Consensus between Electrons and Nuclei.

J Am Chem Soc 2020 01 7;142(2):1020-1028. Epub 2020 Jan 7.

Van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands.

The self-assembly of chiral supramolecular polymers is an intricate process that spans a wide range of length scales. Circular dichroism techniques are ideal to study this process as they provide information on the molecular scale but are at the same time also sensitive probes of the long-range interactions that control the growth and morphology of these polymers. As yet, Electronic Circular Dichroism that uses electronic transitions as a probe has by far been the method of choice while Vibrational Circular Dichroism, which uses vibrational transitions to probe structure, is much less employed. Here, we report experimental and theoretical studies of the self-assembly of helical supramolecular polymers of ()-triarylamine tris-amides (()-TATA) in which both techniques are applied in concert. Theoretical studies based on quantum chemical calculations and on simplified models that allow for extrapolation to "infinitely" long polymers provide a solid basis for interpreting results from each of the two techniques that on their own would appear to be contradictory. In the particular case of ()-TATA it is shown that upon equilibration the initially formed fibers undergo a conformational transition that becomes only "visible" by the combination of the two techniques. Our studies thus show that combining electronic and vibrational domains offers a unique and complementary means to probe these polymers, precisely because they are sensitive to different aspects of molecular and polymeric structure.
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http://dx.doi.org/10.1021/jacs.9b11306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966911PMC
January 2020

GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra.

J Chem Inf Model 2020 01 2;60(1):259-267. Epub 2020 Jan 2.

Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street, Number 7-9 , 550012 Sibiu , Romania.

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.
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http://dx.doi.org/10.1021/acs.jcim.9b00956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988127PMC
January 2020

Taming conformational heterogeneity in and with vibrational circular dichroism spectroscopy.

Chem Sci 2019 Sep 9;10(33):7680-7689. Epub 2019 Jul 9.

Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street Nr. 7-9 , 550012 Sibiu , Romania . Email:

The flexibility of a molecule has important consequences on its function and application. Vibrational Circular Dichroism (VCD) is intrinsically an excellent experimental technique to get a hold on this flexibility as it is highly sensitive to key conformational details and able to distinguish rapidly interconverting conformers. One of the major challenges in analyzing the spectra by comparison to theoretical predictions is the uncertainty in the computed energies of the multitude of conformations. This uncertainty also affects the reliability of the stereochemical assignment it is normally used for. We present here a novel approach that explicitly takes the energy uncertainties into account in a genetic algorithm based method that fits calculated to the experimental spectra. We show that this approach leads to significant improvements over previously used methodologies. Importantly, statistical validation studies provide quantitative measures for the reliability of relevant parameters used such as the energy uncertainty and the extent to which conformational heterogeneity can be determined. Similarly, quantitative measures can be obtained for the possibility that the flexibility that is introduced in the fit might lead to an incorrect assignment of the stereochemistry. These results break new ground for different techniques based on VCD to elucidate conformational flexibility.
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http://dx.doi.org/10.1039/c9sc02866hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6844231PMC
September 2019

Analytical chemistry on many-center chiral compounds based on vibrational circular dichroism: Absolute configuration assignments and determination of contaminant levels.

Anal Chim Acta 2019 Dec 14;1090:100-105. Epub 2019 Sep 14.

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands; Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525, ED, Nijmegen, the Netherlands. Electronic address:

The absolute configuration of a chiral molecule is key to its biological activity. Being able to find out what this configuration is, is thus crucial for a wide range of applications. The difficulties associated with such a determination steeply rise as the number of chiral centers in a given compound becomes larger. Concurrently, it becomes increasingly more challenging to determine the levels and identity of potential stereochemical contaminants in a given sample with one and the same technique, leading in practice to extensive and laborious efforts employing multiple analytical techniques. Here, experimental and theoretical studies based on Vibrational Circular Dichroism (VCD) are presented for dydrogesterone, a synthetic drug employed in reproductive medicine that is a prototypical example of such a multi-center chiral compound. We show that our approach allows us to distinguish and assign its absolute configuration without prior knowledge to one of the 64 possible stereoisomers associated with the six chiral centers. Studies on mixtures of dydrogesterone and 6-dehydroprogesterone, one of the diastereomers of dydrogesterone and generally the dominant impurity of dehydrogesterone, show that we can identify the presence of both compounds from one single VCD spectrum. Moreover, we find that we can determine diastereomeric contamination levels as low as 5% from the experimental VCD spectra.
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http://dx.doi.org/10.1016/j.aca.2019.09.021DOI Listing
December 2019

Temperature Control of Sequential Nucleation-Growth Mechanisms in Hierarchical Supramolecular Polymers.

Chemistry 2019 Oct 9;25(56):13008-13016. Epub 2019 Sep 9.

SAMS Research Group, University of Strasbourg-Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France.

Upon cooling in solution, chiral triarylamine tris-amide unimers produce organogels by stacking into helical supramolecular polymers, which subsequently bundle into larger fibers. Interestingly, circular dichroism, vibrational circular dichroism, and AFM imaging of the chiral self-assemblies revealed that monocolumnar P-helical fibrils formed upon fast cooling, whereas bundled M-superhelical fibers formed upon slow cooling. The mechanistic study of this structural bifurcation reveals the presence of a strong memory effect, reminiscent of a complex stepwise combination of primary and secondary nucleation-growth processes. These results highlight the instrumental role of sequential self-assembly processes to control supramolecular architectures of multiple hierarchical order.
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http://dx.doi.org/10.1002/chem.201902898DOI Listing
October 2019

A Tunable, Fullerene-Based Molecular Amplifier for Vibrational Circular Dichroism.

Chemistry 2019 Sep 23;25(54):12560-12566. Epub 2019 Aug 23.

Molecular Photonics Group, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.

Vibrational circular dichroism (VCD) studies are reported on a chiral compound in which a fullerene C moiety is used as an electron acceptor and local VCD amplifier for an alanine-based peptide chain. Four redox states are investigated in this study, of which three are reduced species that possess low-lying electronic states as confirmed by UV/Vis spectroelectrochemistry. VCD measurements in combination with (TD)DFT calculations are used to investigate (i) how the low-lying electronic states of the reduced species modulate the amplification of VCD signals, (ii) how this amplification depends on the distance between oscillator and amplifier, and (iii) how the spatial extent of the amplifier influences amplification. These results pave the way for further development of tailored molecular VCD amplifiers.
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http://dx.doi.org/10.1002/chem.201902190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6790965PMC
September 2019

Taming the Complexity of Donor-Acceptor Stenhouse Adducts: Infrared Motion Pictures of the Complete Switching Pathway.

J Am Chem Soc 2019 05 24;141(18):7376-7384. Epub 2019 Apr 24.

Van 't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands.

Switches that can be actively steered by external stimuli along multiple pathways at the molecular level are the basis for next-generation responsive material systems. The operation of commonly employed molecular photoswitches revolves around one key structural coordinate. Photoswitches with functionalities that depend on and can be addressed along multiple coordinates would offer novel means to tailor and control their behavior and performance. The recently developed donor-acceptor Stenhouse adducts (DASAs) are versatile switches suitable for such applications. Their photochemistry is well understood, but is only responsible for part of their overall photoswitching mechanism. The remaining thermal switching pathways are to date unknown. Here, rapid-scan infrared absorption spectroscopy is used to obtain transient fingerprints of reactions occurring on the ground state potential energy surface after reaching structures generated through light absorption. The spectroscopic data are interpreted in terms of structural transformations using kinetic modeling and quantum chemical calculations. Through this combined experimental-theoretical approach, we are able to unravel the complexity of the multidimensional ground-state potential energy surface explored by the photoswitch and use this knowledge to predict, and subsequently confirm, how DASA switches can be guided along this potential energy surface. These results break new ground for developing user-geared DASA switches but also shed light on the development of novel photoswitches in general.
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http://dx.doi.org/10.1021/jacs.9b00341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509641PMC
May 2019

Publisher Correction: O-O and O-N collision-induced absorption mechanisms unravelled.

Nat Chem 2018 05;10(5):573

Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.

In the version of this Article originally published, Figures 3 and 4 were erroneously swapped, this has been corrected in all versions of the Article.
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http://dx.doi.org/10.1038/s41557-018-0063-2DOI Listing
May 2018

O-O and O-N collision-induced absorption mechanisms unravelled.

Nat Chem 2018 05 9;10(5):549-554. Epub 2018 Apr 9.

Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.

Collision-induced absorption is the phenomenon in which interactions between colliding molecules lead to absorption of light, even for transitions that are forbidden for the isolated molecules. Collision-induced absorption contributes to the atmospheric heat balance and is important for the electronic excitations of O that are used for remote sensing. Here, we present a theoretical study of five vibronic transitions in O-O and O-N, using analytical models and numerical quantum scattering calculations. We unambiguously identify the underlying absorption mechanism, which is shown to depend explicitly on the collision partner-contrary to textbook knowledge. This explains experimentally observed qualitative differences between O-O and O-N collisions in the overall intensity, line shape and vibrational dependence of the absorption spectrum. It is shown that these results can be used to discriminate between conflicting experimental data and even to identify unphysical results, thus impacting future experimental studies and atmospheric applications.
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http://dx.doi.org/10.1038/s41557-018-0015-xDOI Listing
May 2018

Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α-Hydroxysilane.

Chemphyschem 2018 03 29;19(5):561-565. Epub 2018 Jan 29.

Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.

Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum-a region that provides important marker bands-cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.
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http://dx.doi.org/10.1002/cphc.201701335DOI Listing
March 2018