V. Van Speybroeck

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.

The Conformational Sensitivity of Iterative Stockholder Partitioning Schemes

T. Verstraelen, P. W. Ayers, V. Van Speybroeck, M. Waroquier
Chemical Physics Letters
545, 138-143
2012
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Abstract 

Chemical interpretation and empirical modeling of partial charges requires a robust partitioning scheme to derive these charges from the molecular electronic density. The degree of undesirable conformational sensitivity is assessed for three iterative stockholder partitioning schemes: Hirshfeld-I (HI), Iterative Stockholder Analysis (ISA) and a new Gaussian ISA variant (GISA). GISA has fewer degrees of freedom than ISA and enforces monotonically decaying pro-atoms. These improvements accelerate the converge of GISA as compared to ISA. However, the conformational sensitivity of the charges does not decrease and is still large compared to HI.

Open Access version available at UGent repository

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

M. Van Houteghem, T. Verstraelen, A. Ghysels, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Chemical Physics
137 (2012), 104506
2012
A1

Abstract 

An ecient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in dierent molecules and was calibrated by tting reference BSSE data points computed with the counterpoise method. It is veried that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e. methanol, and more specic on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

Open Access version available at UGent repository

Polycaprolactone and polycaprolactone/chitosan nanofibres functionalised with the pH-sensitive dye Nitrazine Yellow

L. Van der Schueren, T. De Meyer, I. Steyaert, O. Ceylan, K. Hemelsoet, V. Van Speybroeck, K. De Clerck
Carbohydrate Polymers
91 (1), 284-293
2013
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Abstract 

Nanofibres functionalised with pH-sensitive dyes could greatly contribute to the development of stimuli-responsive materials. However, the application of biocompatible polymers is vital to allow for their use in (bio)medical applications. Therefore, this paper focuses on the development and characterisation of pH-sensitive polycaprolactone (PCL) nanofibrous structures and PCL/chitosan nanofibrous blends with 20% chitosan. Electrospinning with added Nitrazine Yellow molecules proved to be an excellent method resulting in pH-responsive non-wovens. Unlike the slow and broad response of PCL nanofibres (time lag of more than 3 h), the use of blends with chitosan led to an increased sensitivity and significantly reduced response time (time lag of 5 min). These important effects are attributed to the increased hydrophilic nature of the nanofibres containing chitosan. Computational calculations indicated stronger interactions, mainly based on electrostatic interactions, of the dye with chitosan (ΔG of -132.3 kJ/mol) compared to the long-range interactions with PCL (ΔG of -35.6 kJ/mol), thus underpinning our experimental observations. In conclusion, because of the unique characteristics of chitosan, the use of PCL/chitosan blends in pH-sensitive biocompatible nanofibrous sensors is crucial.

Open Access version available at UGent repository

Synthesis, Structural Characterization, and Catalytic Performance of a Vanadium-Based Metal-Organic Framework (COMOC-3)

Y-Y Liu, K. Leus, M. Grzywa, D. Weinberger, K. Strubbe, H. Vrielinck, R. Van Deun, D. Volkmer, V. Van Speybroeck, P. Van der Voort
European Journal of Inorganic Chemistry
(16) 2819 - 2827
2012
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Abstract 

A vanadium 2,6-naphthalenedicarboxylate, VIII(OH)(O2C–C10H6–CO2)·H2O, denoted as COMOC-3as (COMOC = Center for Ordered Materials, Organometallics and Catalysis, Ghent University), has been synthesized under hydrothermal conditions by means of both a solvothermal and a microwave synthesis procedure. The structure shows the topology of an aluminium 2,6-naphthalenedicarboxylate, the so-called MIL-69 (MIL = Materials of the Institute Lavoisier). After calcination at 250 °C in air, the VIII center was oxidized to VIV with the structure of VIVO(O2C–C10H6–CO2) (COMOC-3). The oxidation process was verified by cyclic voltammetry and EPR spectroscopy. The crystallinity was investigated by variable-temperature XRD. The title compound is stable against air and moisture. The catalytic performance of COMOC-3 was examined in the liquid-phase oxidation of cyclohexene. COMOC-3 exhibited similar catalytic performance to MIL-47 [VO(O2C–C6H4–CO2)]. The compound is reusable and maintains its catalytic activity through several runs.

New V-IV-Based Metal-Organic Framework Having Framework Flexibility and High CO2 Adsorption Capacity

Y-Y Liu, S. Couck, M. Vandichel, M. Grzywa, K. Leus, S. Biswas, D. Volkmer, J. Gascon, F. Kapteijn, J.F.M. Denayer, M. Waroquier, V. Van Speybroeck, P. Van der Voort
Inorganic Chemistry
52 (1), 113-120
2013
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Abstract 

A vanadium based metal–organic framework (MOF), VO(BPDC) (BPDC2– = biphenyl-4,4′-dicarboxylate), adopting an expanded MIL-47 structure type, has been synthesized via solvothermal and microwave methods. Its structural and gas/vapor sorption properties have been studied. This compound displays a distinct breathing effect toward certain adsorptives at workable temperatures. The sorption isotherms of CO2 and CH4 indicate a different sorption behavior at specific temperatures. In situ synchrotron X-ray powder diffraction measurements and molecular simulations have been utilized to characterize the structural transition. The experimental measurements clearly suggest the existence of both narrow pore and large pore forms. A free energy profile along the pore angle was computationally determined for the empty host framework. Apart from a regular large pore and a regular narrow pore form, an overstretched narrow pore form has also been found. Additionally, a variety of spectroscopic techniques combined with N2 adsorption/desorption isotherms measured at 77 K demonstrate that the existence of the mixed oxidation states VIII/VIV in the titled MOF structure compared to pure VIV increases the difficulty in triggering the flexibility of the framework.

Synthesis, characterization and sorption properties of NH2-MIL-47

K. Leus, S. Couck, M. Vandichel, G. Vanhaelewyn, Y-Y Liu, G.B. Marin, I. Van Driessche, D. Depla, M. Waroquier, V. Van Speybroeck, J.F.M. Denayer, P. Van der Voort
Physical Chemistry Chemical Physics (PCCP)
14, 15562–15570
2012
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Abstract 

An amino functionalized vanadium-containing Metal Organic Framework, NH2-MIL-47 has been synthesized by a hydrothermal reaction in an autoclave. Alternatively, a synthesis route via microwave enhanced irradiation has been optimized to accelerate the synthesis. The NH2-MIL-47 exhibits the same topology as MIL-47, in which the V center is octahedrally coordinated. After an exchange procedure in DMF the V+III center is oxidized to V+IV, which is confirmed by EPR and XPS measurements. The CO2 and CH4 adsorption properties have been evaluated and compared to MIL-47, showing that both MOFs have an almost similar adsorption capacity and affinity for CO2. DFT- based molecular modeling calculations were performed to obtain more insight into the adsorption positions for CO2 in NH2-MIL-47. Furthermore our calculated adsorption enthalpies agree well with the experimental values.

Ab initio parametrized force field for the flexible metal-organic framework MIL-53(Al)

L. Vanduyfhuys, T. Verstraelen, M. Vandichel, M. Waroquier, V. Van Speybroeck
Journal of Chemical Theory and Computation (JCTC)
8 (9), 3217-3231
2012
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Abstract 

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on non-periodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from non-periodic cluster calculations. The new force field, predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behaviour of the MIL-53. Even without the stimulus of external guest molecules the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. JACS 2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters and MM3 dispersion interaction has the tendency to overstabilize the np phase.

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