Six-coordination in Chlorophylls: The fundamental role of dispersion energy

Fredj, A. Ben; Lakhdar, Z. Ben; Ruiz‐López, Manuel F.

doi:10.1016/j.cplett.2009.03.025

Cited by 25 publications

(40 citation statements)

References 47 publications

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“…Ben Fredj and co-workers [7,8], have previously shown that BSSE contributions to ligation energies are significant. For large basis sets, the wisdom of this approach for hydrogen-bond and ligation interactions has been questioned as often the increase in the correlation energy with increasing basis exceeds the BSSE [41,42].…”

Section: Resultsmentioning

confidence: 97%

“…Single-point energies were then obtained at the 6-31+G(d) geometries using the 6-311++ G(2d,2p) basis sets and corrected for basis-set superposition error (BSSE) using the counterpoise correction method [36]. Its application here is slightly different to that employed by Ben Fredj and co-workers [7,8], however, defining the energy of the second adducts using a simple complexation reaction for the first adduct. Thermodynamic effects were estimated by vibrational frequency calculations at the 6-31G(d) level using the various density functionals.…”

Section: Methodsmentioning

confidence: 99%

“…As Ben Fredj and co-workers [7,8] showed, the free energy corrections associated with complexation reactions in the gas phase are large and variable, playing a key role in the ligation process. At 298 K, the average correction is 12.6 kcal mol −1 , but to some extent these are cancelled by the vaporisation entropy loss when gas-phase molecules are taken into solution and the combined contribution, on average, is just 4.6 kcal mol −1 .…”

Section: Full Solventmentioning

confidence: 97%

“…Here, we consider complexation reactions of chlorophyll-a (Chl-a) with ligand bases. For gas-phase reactions, Ben Fredj et al [7] have demonstrated the importance of dispersion to the binding, as well as the role of entropy effects. They also considered binding in various solvents focusing on water complexation, but did not include the dispersive contributions to solvation [8].…”

Section: Introductionmentioning

confidence: 99%

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Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents

Kobayashi

Reimers

2015

Molecular Physics

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The coordination of bases to chlorophyll magnesium modifies spectroscopic properties in solution as well as in situ in reaction centres. We evaluate the free energies of complexation of one or two pyridine, 1-propanol, diethyl ether or water solvent molecules at 298 and 150 K to rationalise observed phenomena. Various a priori dispersion-corrected density functional theory calculations are performed as well as second-order Møller-Plesset calculations, focusing on the effects of dispersion modifying the intermolecular interactions, of dispersion modifying solvation energies, of entropy, and of basis-set superposition error. A process of particular interest is magnesium complexation in ether at low temperature that is often exploited to assign the Q-band visible absorption spectrum of chlorophyll. Recently, we demonstrated that trace water interferes with this process, but the nature of the resulting complex could not be uniquely determined; here, it is identified as ether.Chlorophyll-a.H 2 O, consistent with interpretations based on our authoritative 2013 assignment.

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Section: Resultsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Section: Full Solventmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents

Kobayashi

Reimers

2015

Molecular Physics

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“…Hyper conjugative [25] interactions have been computed and analyzed using the Natural Bond Orbital (NBO) theory. Throughout this work molecular orbitals and electrostatic potential maps were constructed using Gauss View 5.0.8 visualization program [26].…”

Section: Methodsmentioning

confidence: 99%

Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis

Allehyani¹,

Elroby

Aziz³

et al. 2015

Journal of Biomolecular Structure and Dynamics

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This study aims to identify the origin of the extra stability of alloxan, a biologically active pyrimidine. To achieve this goal, detailed DFT computations and quantum dynamics simulations have been performed to establish the most stable conformation and the global minimum structure on the alloxan potential energy surface. The effects of the solvent, basis set, and DFT method have been examined to validate the theoretical model adopted throughout the work. Two non-covalent intermolecular dimers of alloxan, the H-bonded and dipolar dimers, have been investigated at the ωB97X-D and M06-2X levels of theory using the triple zeta 6-311++G** to establish their relative stability. Quantum chemical topology features and natural bond orbital analysis (NBO) have been performed to identify and characterize the forces that govern the structures and underlie the extra stability of alloxan.

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Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

Fredj

2016

Helvetica Chimica Acta

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Dimeric structures chlorophyll (a) (Chla) and their mono‐ and dihydrated have been suggested to play an important role in the mechanism of photoreaction center chlorophyll special pairs PSI and PSII. Despite their functional importance, the molecular basis structures for interacting two Chla molecules and the structural stabilization role of H2O in the formation of hydrated Chla dimer complexes is poorly understood. In this article, the different coordination modes between two interacting Chla molecules and the configurational (orientation and distance) features between the dimer and bound H2O molecules are characterized by means of super molecule approach the density functional theory DFT. An estimation of the thermodynamic quantities is made for Chla dimerization and hydration processes. The results indicate that structure including ester linkages via H2O hydrogen bonding is the most favorable conformation for the dihydrated chlorophyll (a) dimer at B3LYP/6‐31G*‐DCP level of calculation. The dispersion interaction is shown to be of great significance for the Chla dimer stabilization. In aqueous nonpolar solvent, the thermodynamics show that Chla has a slightly stronger driving force for full hydration than for dimerization and that hydration of the dimers is rather weakly exergonic. The tetrahydrated dimers having a similar arrangement to that in crystals of ethyl chlorophyllide (a) dihydrate are found to be more stable than the Chla dihydrated dimer. The data underscore the key role of H‐bonding in the stability of Chla‐H2O adducts and, in particular, the great importance of the Chla monomeric dihydrated species in the hydration and dimerization of Chla in aqueous media. Clearly, the Chla dihydrates (Chla‐2 H2O) are found more stable than the monohydrates (Chla‐H2O) and the Chla dimers (Chla2), owing to a particular structure in which cooperative interactions occur between the H2O molecules and Chla. Calculations also indicate that the most thermodynamically preferred pathway for the formation of Chla dimer hydrates can be represented by two steps: the first corresponds to the formation of Chla monomeric dihydrates and the second is the dimerization of the dihydrates on to tetrahydrated Chla dimers. These results allow to obtain a new possible pathway for Chla dimer formation processes and could provide new insights to the aggregation of chlorophyll (a) in solution.

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Six-coordination in Chlorophylls: The fundamental role of dispersion energy

Cited by 25 publications

References 47 publications

Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents

Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents

Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis

Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

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