The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon... Show moreThe formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post-)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations' unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability. Show less
1,4‐Naphthoquinone (1,4‐NQ) is an important product of naphthalene oxidation, and it appears as a motif in many biologically active compounds. We have investigated the structure of 1,4‐NQ using... Show more1,4‐Naphthoquinone (1,4‐NQ) is an important product of naphthalene oxidation, and it appears as a motif in many biologically active compounds. We have investigated the structure of 1,4‐NQ using chirped‐pulse Fourier transform microwave spectroscopy and quantum chemistry calculations. The rotational spectra of the parent species, and its 13C and 18O isotopologues were observed in natural abundance, and their spectroscopic parameters were obtained. This allowed the determination of the substitution rs, mass‐weighted rm and semi‐experimental reSE structures of 1,4‐NQ. The obtained structural parameters show that the quinone moiety mainly changes the structure of the benzene ring where it is inserted, modifying the C−C bonds to having predominantly single or double bond character. Furthermore, the molecular electrostatic surface potential reveals that the quinone ring becomes electron deficient while the benzene ring remains a nucleophile. The most electrophilic areas are the hydrogens attached to the double bond in the quinone ring. Knowledge of the nucleophilic and electrophilic areas in 1,4‐NQ will help understanding its behaviour interacting with other molecules and guide modifications to tune its properties. Show less
Son, M. van; Schilder, J.T.; Di Savino, A.; Blok, A.J.; Ubbink, M.; Huber, M.I. 2020
Anion binding to a receptor based on stiff‐stilbene, which is equipped with a urea hydrogen bond donating group and a phosphate or phosphinate hydrogen bond accepting group, can be controlled by... Show moreAnion binding to a receptor based on stiff‐stilbene, which is equipped with a urea hydrogen bond donating group and a phosphate or phosphinate hydrogen bond accepting group, can be controlled by light. In one photoaddressable state (E isomer) the urea binding site is available for binding, while in the other (Z isomer) it is blocked because of an intramolecular interaction with its hydrogen bond accepting motif. This intramolecular interaction is supported by DFT calculations and 1H NMR titrations reveal a significantly lower anion binding strength for the state in which anion binding is blocked. Furthermore, the molecular switching processhas been studied in detail by UV/Vis and NMR spectroscopy. The presented approach opens up new opportunities toward the development of photoresponsive anion receptors. Show less
Granda Marulanda, L.P.; Builes, S.; Koper, M.T.M.; Calle-Vallejo, F. 2019
Solvation can significantly modify the adsorption energy of species at surfaces, thereby influencing the performance of electrocatalysts and liquid‐phase catalysts. Thus, it is important to... Show moreSolvation can significantly modify the adsorption energy of species at surfaces, thereby influencing the performance of electrocatalysts and liquid‐phase catalysts. Thus, it is important to understand adsorbate solvation at the nanoscale. Here we evaluate the effect of van der Waals (vdW) interactions described by different approaches on the solvation energy of *OH adsorbed on near‐surface alloys (NSAs) of Pt. Our results show that the studied functionals can be divided into two groups, each with rather similar average *OH solvation energies: (1) PBE and PW91; and (2) vdW functionals, RPBE, PBE‐D3 and RPBE‐D3. On average, *OH solvation energies are less negative by ∼0.14 eV in group (2) compared to (1), and the values for a given alloy can be extrapolated from one functional to another within the same group. Depending on the desired level of accuracy, these concrete observations and our tabulated values can be used to rapidly incorporate solvation into models for electrocatalysis and liquid‐phase catalysis. Show less
Ham, A. van der; Hansen, T.; Lodder, G.; Codée, J.D.C.; Hamlin, T.A.; Filippov, D.V. 2019
Lithium ion selective crown ethers have been the subject of much research for a multitude of applications. Current research is aimed at structurally rigidifying crown ethers, as restructuring of... Show moreLithium ion selective crown ethers have been the subject of much research for a multitude of applications. Current research is aimed at structurally rigidifying crown ethers, as restructuring of the crown ether ring upon ion binding is energetically unfavorable. In this work, the lithium ion binding ability of the relatively rigid 8‐crown‐4 was investigated both computationally by density functional theory calculations and experimentally by 1H and 7Li NMR spectroscopy. Although both computational and experimental results showed 8‐crown‐4 to bind lithium ion, this binding was found to be weak compared to larger crown ethers. The computational analysis revealed that the complexation is driven by enthalpy rather than entropy, illustrating that rigidity is only of nominal importance. To elucidate the origin of the favorable interaction of lithium ion with crown ethers, activation strain analyses and energy decomposition analyses were performed pointing to the favorable interaction being mainly electrostatic in nature. 8‐crown‐4 presents the smallest crown ether reported to date capable of binding lithium ion, possessing two distinct conformations from which it is able to do so. Show less
The determination of the appropriate local‐field factor for quantifying the response of a molecule to an external electric field is of major importance in optical spectroscopy. Although numerous... Show moreThe determination of the appropriate local‐field factor for quantifying the response of a molecule to an external electric field is of major importance in optical spectroscopy. Although numerous studies have dealt with the evolution of the optical properties of emitters as a function of their environment, the choice of the model used to quantify local fields is still ambiguous, and sometimes even arbitrary. In this paper, we review the Onsager–Böttcher model, which introduces the polarizability of the probe molecule as the determinant parameter for the local field factor, and we establish a simple conceptual framework encompassing all commonly used models. Finally, a discussion of published experimental research illustrates the potential of the measurement of local electric fields in dense dielectric media, as well as the subtleties involved in their interpretation. Show less
A structural characterization of the products formed in the dissociative electron ionization of adamantane (C10H16) is presented. Molecular structures of product ions are suggested based on... Show moreA structural characterization of the products formed in the dissociative electron ionization of adamantane (C10H16) is presented. Molecular structures of product ions are suggested based on multiple‐photon dissociation spectroscopy using the Free Electron Laser for Infrared eXperiments (FELIX) in combination with quantum‐chemical calculations. Product ions are individually isolated in an ion trap tandem mass spectrometer and their action IR spectra are recorded. Atomic hydrogen loss from adamantane yields the 1‐adamantyl isomer. The IR spectrum of the C8H11+ product ion is best reproduced by computed spectra of 2‐ and 4‐protonated meta‐xylene and ortho‐ and para‐protonated ethylbenzenes. The spectrum of the product ion at m/z 93 suggests that it is composed of a mixture of ortho‐protonated toluene, para‐protonated toluene and 1,2‐dihydrotropylium, while the spectrum of the m/z 79 ion is consistent with the benzenium ion. This study thus suggests that adamantane is efficiently converted into aromatic species and astrophysical implications for the interstellar medium are highlighted. Show less
