Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective

2010 ◽  
Vol 88 (8) ◽  
pp. 759-768 ◽  
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez

The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.

Author(s):  
Ruben D. Parra ◽  
Álvaro Castillo

The geometries and energetics of molecular self-assembly structures that contain a sequential network of cyclic halogen-bonding interactions are investigated theoretically. The strength of the halogen-bonding interactions is assessed by examining binding energies, electron charge transfer (NBO analysis) and electron density at halogen-bond critical points (AIM theory). Specifically, structural motifs having intramolecular N—X...N (X= Cl, Br, or I) interactions and the ability to drive molecular self-assemblyviathe same type of interactions are used to construct larger self-assemblies of up to three unit motifs. N—X...N halogen-bond cooperativity as a function of the self-assembly size, and the nature of the halogen atom is also examined. The cyclic network of the halogen-bonding interactions provides a suitable cavity rich in electron density (from the halogen atom lone pairs not involved in the halogen bonds) that can potentially bind an electron-deficient species such as a metal ion. This possibility is explored by examining the ability of the N—X...N network to bind Na+. Likewise, molecular self-assembly structures driven by the weaker C—X...N halogen-bonding interactions are investigated and the results compared with those of their N—X...N counterparts.


ChemInform ◽  
2010 ◽  
Vol 27 (40) ◽  
pp. no-no
Author(s):  
R. LOPEZ ◽  
M. F. RUIZ-LOPEZ ◽  
D. RINALDI ◽  
J. A. SORDO ◽  
T. L. SORDO

2001 ◽  
Vol 7 (4-5) ◽  
pp. 303-311 ◽  
Author(s):  
Sophie Hoyau ◽  
Jean-Pierre Pélicier ◽  
Françoise Rogalewicz ◽  
Yannik Hoppilliard ◽  
Gilles Ohanessian

The interaction of glycine with 15 metal cations (M+ or M2+)in the gas phase has been studied by quantum chemical calculations. Three types of complexation have been considered: (i)chelation between nitrogen and the carbonyl oxygen, (ii)attachment to the carboxyl group of neutral glycine and (iii)attachment to the carboxylate group of zwitterionic glycine. It is found that the relative energies of these structures and, therefore, the nature of the lowest energy isomer, depend dramatically upon the metal ion. In several cases, metal ion attachment to glycine results in a switch from the neutral form (the most stable form of gaseous glycine)to the zwitterion (the most stable form of glycine in solution). This occurs with doubly-charged cations and, in some cases, with monocations. Several metal properties are invoked to explain these results: metal charge, size, electron affinity and polarizability. The role of metal–ion polarizability is illustrated by the computed geometries of M(CH3OH)2n+ complexes.


Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 6021
Author(s):  
Miquel Huix-Rotllant

Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.


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