Publications by authors named "Valentin P Nicu"

11 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

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

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

Interplay of Exciton Coupling and Large-Amplitude Motions in the Vibrational Circular Dichroism Spectrum of Dehydroquinidine.

Chemistry 2016 Jan 27;22(2):704-15. Epub 2015 Nov 27.

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

A detailed analysis of the computed structure, energies, vibrational absorption (VA) and circular dichroism (VCD) spectra of 30 low-energy conformers of dehydroquinidine reveals the existence of families of pseudo-conformers, the structures of which differ mostly in the orientation of a single O-H bond. The pseudo-conformers in a family are separated by very small energy barriers (i.e., 1.0 kcal mol(-1) or smaller) and have very different VCD spectra. First, we demonstrate the unreliable character of the Boltzmann factors predicted with DFT. Then, we show that the large differences observed between the VCD spectra of the pseudo-conformers in a family are caused by large-amplitude motions involving the O-H bond, which trigger the appearance/disappearance of strong VCD exciton-coupling bands in the fingerprint region. This interplay between exciton coupling and large-amplitude-motion phenomena demonstrates that when dealing with flexible molecules with polar bonds, vibrational averaging of VCD spectra should not be neglected. In this regard, the dehydroquinidine molecule considered here is expected to be a typical example and not the exception to the rule.
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http://dx.doi.org/10.1002/chem.201503250DOI Listing
January 2016

Determination of the Absolute Configurations Using Exciton Chirality Method for Vibrational Circular Dichroism: Right Answers for the Wrong Reasons?

J Phys Chem A 2015 Oct 7;119(42):10589-601. Epub 2015 Oct 7.

Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235 United States.

Quantum chemical (QC) predictions of vibrational circular dichroism (VCD) spectra for the keto form of 3-benzoylcamphor and conformationally flexible diacetates of spiroindicumide A and B are presented. The exciton chirality (EC) model has been briefly reviewed, and a procedure to evaluate the relevance of the EC model has been presented. The QC results are compared with literature experimental VCD spectra as well as with those obtained using the EC model for VCD. These comparisons reveal that the EC contributions to bisignate VCD couplets associated with the C═O stretching vibrations of benzoylcamphor, spiroindicumide A diacetate, and spiroindicumide B diacetate are only ∼30%, ∼3%, and ∼15%, respectively. With such meager EC contributions, the correct absolute configurations (ACs) suggested in the literature for spiroindicumide A diacetate and spiroindicumide B diacetate molecules using the EC concepts can be considered fortuitous. The possibilities for obtaining wrong AC predictions using the EC concepts for VCD are identified, and guidelines for the future use of this model are presented.
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http://dx.doi.org/10.1021/acs.jpca.5b07940DOI Listing
October 2015