D.D. Claeys

Accurate prediction of 1H-chemical shifts in interstrand cross-linked DNA

E. Pauwels, D.D. Claeys, J. Martins, M. Waroquier, G. Bifulco, V. Van Speybroeck, A. Madder
RSC Advances
2013 (3), 3925-3938
2013
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Abstract 

Structural analysis of modified DNA with NMR is becoming ever more difficult with increasingly complex compounds under scrutiny for use in medical diagnosis, therapeutics, material science and chemical synthesis. To facilitate this process, we develop a molecular modeling approach to predict proton chemical shifts in sufficient agreement with experimental NMR measurements to guide structure elucidation. It relies on a QM/MM partitioning scheme and first principle calculations to predict the spatial structure and calculate corresponding proton chemical shifts. It is shown that molecular dynamics simulations that take into account solvent and temperature effects properly are of utmost importance to sample the conformational space sufficiently. The proposed computational procedure is universally applicable to modified oligonucleotides and DNA, attaining a mean error for the proton chemical shifts of less than 0.2 ppm. Here, it is applied on the Drew-Dickerson d(CGCGAATTCGCG)2 dodecamer as a benchmark system and the mispair-aligned N3T-ethyl-N3T cross-linked d(CGAAAT*TTTCG)2 undecamer, illustrating its universal use as computational tool to assist in structure elucidation. For the proton chemical shifts in the cross-linked system our methodology yields a strikingly superior description, surpassing the predictive power of (semi-)empirical methods. In addition, our methodology is the only one available to make an accurate prediction for the protons in the actual cross-link. To the best of our knowledge, this is the first computational study that attempts to determine the chemical shifts of oligonucleotides of this size and at this level of complexity.

Synthesis of Tricyclic Phosphonopyrrolidines via IMDAF: Experimental and Theoretical Investigation of the Observed Stereoselectivity

D.D. Claeys, K. Moonen, B.I. Roman, V.N. Nemykin, V.V. Zhdankin, M. Waroquier, V. Van Speybroeck, C.V. Stevens
Journal of Organic Chemistry
73 (20), 7921-7927
2008
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Abstract 

During the synthesis of tricyclic phosphonopyrrolidines via intramolecular Diels−Alder reactions of 1-acylamino(furan-2-yl)methyl phosphonates, two isomers are formed in most cases. The presence of a short three-atom tether together with spectroscopic data, including difference NOE, revealed that the cycloaddition occurred exo, but the phosphonate substituent on the tether had an exo or endo orientation. This was confirmed via X-ray analysis. A thermodynamic preference for the product with the phosphonate function in the endo position was observed experimentally and was confirmed theoretically. Density functional theory methods and several high-level post Hartree−Fock procedures were used to rationalize the observed isomer ratio of the IMDAF-reactions. This was done for two different types of reagents: with the activating carbonyl group in the tether or as a substituent on the tether. For the first type of molecules there is a large steric hindrance of the bulky tether substituents that disfavors the exo-isomer. In the latter case, there was a very small energy difference between the transition states causing a mixture of epimers being formed.

The Formation of trans-Fused Macrocycles from N3,N3′-Polymethylenebis(hydantoins) by Ring-Closing Metathesis

D.D. Claeys, C.V. Stevens, N. Dieltiens
European Journal of Organic Chemistry
(1), 171–179
2008
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Abstract 

A straightforward ring transformation giving polymethylenebis(hydantoins) was extended, as these are HMBA analogues. Firstly, ethyl or allyl pyroglutamate was carbamoylated with a diisocyanate. Upon treatment with KOtBu in allyl alcohol the bis(carbamoyllactam) rearranged to give the hydantoin, which was followed by the ring-opening of the pyrrolidinone with formation of the allyl ester. These compounds were subsequently ring-closed in the presence of second-generation Grubbs' catalyst to form macrocycles containing the ester functionality in the ring. It was established by HSQC experiments with inverse detection that only the E isomers were formed in the cases of the 24- and 26-membered heterocycles. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Exploiting the regioselectivity of pyroglutamate alkylations for the synthesis of 6-azabicyclo[3.2.1]octanes and 4-azabicyclo[3.3.0]octanes

K.G.R. Masschelein, C.V. Stevens, N. Dieltiens, D.D. Claeys
Tetrahedron
63 (22), 4712–4724
2007
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Abstract 

Depending on the N-protecting group of pyroglutamates, the reactivity can be directed to the formation of 6-azabicyclo[3.2.1]octanes or 4-azabicyclo[3.3.0]octanes, which are conformationally restricted glutamate analogues.

The Pyroglutamate Hydantoin Rearrangement

N. Dieltiens, D.D. Claeys, V.V. Zhdankin, V.N. Nemykin, B. Allaert, F. Verpoort, C.V. Stevens
European Journal of Organic Chemistry
2006 (11), 2649–2660
2006
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Abstract 

When a mixture of a pyroglutamate and an isocyanate in THF is treated with NaH, a ring transformation occurs leading to functionalised hydantoins. The novel reaction involves a ring-closing ring-opening sequence providing a new and straightforward access to an interesting class of heterocyclic compounds. Furthermore, starting from pyroglutamates allows the synthesis of highly substituted hydantoins under very mild conditions. This ring transformation in combination with ring-closing metathesis is used in a four-step reaction sequence for the synthesis of multi-functionalised bicyclic hydantoin derivatives.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Synthesis of N(3),N‘(3)-Polymethylene-bis-hydantoins and Their Macrocyclic Derivatives

N. Dieltiens, D.D. Claeys, C.V. Stevens
Journal of Organic Chemistry
71(10), 3863–3868
2006
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Abstract 

An efficient and straightforward two-step approach toward N(3),N‘(3)-polymethylene-bis-hydantoins was developed. As a first step, a pyroglutamate is reacted with a diisocyanate to produce a bis-carbamoyllactam. The second step is a double-ring transformation by treatment of this bis-carbamoyllactam with KOtBu in ethanol. In this fashion N(3),N‘(3)-polymethylene-bis-hydantoins are produced in two quantitative steps and under very mild conditions. When properly derivatized, these compounds can be converted to their macrocyclic derivatives upon treatment with 5 mol % of second-generation Grubbs' catalyst. These macrocyclic derivatives are so far not described in the literature. It was proven that exclusively (E)-isomers are formed.

Synthesis of 1,3-dioxo-hexahydropyrido[1,2-c][1,3]diazepine carboxylates, a new bicyclic skeleton formed by ring expansion–RCM methodology

N. Dieltiens, D.D. Claeys, B. Allaert, F. Verpoort, C.V. Stevens
Chemical Communications
(35), 4477
2005
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Abstract 

A short and elegant synthetic pathway was developed for the synthesis of 1,3-dioxo-hexahydropyrido[1,2-c][1,3]diazepine carboxylates, a new 1,3-diazepan-2,4-dione containing bicyclic moiety, starting from pyroglutamate esters.

Straightforward Ring Expansion of Pyroglutamates to Perhydro-1,3-diazepine-2,4-diones

C.V. Stevens, N. Dieltiens, D.D. Claeys
Organic Letters
7 (6), 1117–1119
2005
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Abstract 

Perhydro-1,3-diazepine-2,4-diones are rare and can only be prepared, up to now, by special methods. A new one-step protocol was developed, comprising N-carbamoylation using an isocyanate followed by intramolecular ring expansion. This new methodology provides a straightforward access to this interesting seven-membered skeleton.

(Additions and corrections: Org. Lett., 2005, 7, 5347), 2005

Conformational Sampling of Macrocyclic Alkenes Using a Kennard−Stone-Based Algorithm

D.D. Claeys, T. Verstraelen, E. Pauwels, C.V. Stevens, M. Waroquier, V. Van Speybroeck
Journal of Physical Chemistry A
114 (25), 6879–6887
2010
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Abstract 

The properties and functions of (bio)molecules are closely related to their molecular conformations. A variety of methods are available to sample the conformational space at a relatively low level of theory. If a higher level of theory is required, the computational cost can be reduced by selecting a uniformly distributed set of conformations from the ensemble of conformations generated at a low level of theory and by optimizing this selected set at a higher level. The generation of conformers is performed using molecular dynamics runs which are analyzed using the MD-Tracks code [ J. Chem. Inf. Model. 2008, 48, 2414]. This article presents a Kennard−Stone-based algorithm, with a distance measure based on the distance matrix, for the selection of the most diverse set of conformations. The method has been successfully applied to macrocyclic alkenes. The correct thermodynamic stability of the double-bond isomers of a flexible macrocyclic alkene containing two chiral centers is reproduced. The double-bond configuration has a limited effect on the conformation of the whole macrocycle. The chirality of the stereocenters has a larger effect on the molecular conformations.

Experimental and computational study of the ring opening of tricyclic oxanorbornenes to polyhydro isoindole phosphonates

D.D. Claeys, C.V. Stevens, B.I. Roman, P. Van De Caveye, M. Waroquier, V. Van Speybroeck
Organic & Biomolecular Chemistry
8, 3644-3654
2010
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Abstract 

Phosphonylated azaheterocycles are an important class of compounds with high biological potential as conformationally restricted bioisosteres of amino acids. Therefore, it is of interest to synthesize conformationally constrained amino phosphonates. We wanted to investigate possible routes via ring opening of α-amino phosphonates with an oxanorbornene skeleton, as these can be synthesized with high stereoselectivity. This was achieved using different Lewis acids, leading to a range of products. The reaction with TiCl4 and FeCl3 was modelled at a DFT level of theory to get insight in the pathways towards the corresponding products. To ease the work up, the Fe(III) catalyst was coated on montmorillonite clay, but this accelerated aromatization after ring opening. Quenching the FeCl3 catalyzed reaction mixture on celite caused complete aromatization.

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