Erratum to: Long-range corrected DFT calculations of charge-transfer integrals in model metal-free phthalocyanine complexes

Journal of Molecular Modeling -     

Synthesis, DFT calculations, linear and nonlinear optical properties of binuclear phthalocyanine gallium chloride

The axially substituted binuclear GaCl/GaCl phthalocyanine 1 with an unsymmetrical pattern of substitution has been prepared and its nonlinear optical (NLO) properties determined. The resulting binuclear complex retains approximately the same transition energies of monomeric (RO)₈PcGaCl as far as the linear optical spectrum is concerned, although 1 has a double concentration of central atoms per molecule and an enlarged conjugated ligand. The lack of significant spectral shifts in passing from mononuclear to binuclear complexes has been rationalized theoretically by means of density functional theory calculations. The purpose of the present study is to determine whether binuclearity affects the optical limiting behavior of 1 with respect to monomeric (RO)₈PcGaCl in the NLO regime determined by nanosecond laser pulses. Figure Bis axially substituted binuclear phthalocyanine: synthesis, DFT calculations and NLO properties Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

Theoretical calculations of the permeability of monensin-cation complexes in model bio-membranes

Monensin is one of the best-characterized ionophores; it functions in the electroneutral exchange of cations between the extracellular and cytoplasmic sides of cell membranes. The X-ray crystal structures of monensin in free acid form and in complex with Na(+), K(+) and Ag(+) are known and we have recently measured the diffusion rates of monensin in free acid form (Mo-H) and in complex with Na(+) (Mo-Na) and with K(+) (Mo-K) using laser pulse techniques. The results have shown that Mo-H diffuses across the membrane one order of magnitude faster than Mo-Na and two orders of magnitude faster than Mo-K. Here, we report calculations of the translocation free energy of these complexes across the membrane along the most favorable path, i.e. the lowest free energy path. The calculations show that the most favorable orientation of monensin is with its hydrophobic furanyl and pyranyl moieties in the hydrocarbon region of the membrane and the carboxyl group and the cation at the water-membrane interface. Further, the calculations show that Mo-H is likely to be inserted deeper than Mo-Na into the bilayer, and that the free energy barrier for transfer of Mo-H across the membrane is approximately 1 kcal/mol lower than for Mo-Na, in good agreement with our measurements. Our results show that the Mo-K complex is unlikely to diffuse across lipid bilayers in its X-ray crystal structure, in contrast to the Mo-H and Mo-Na complexes. Apparently, when diffusing across the membrane, the Mo-K complex assumes a different conformation and/or thinning defects in the bilayer lower significantly the free energy barrier for the process. The suitability of the model for treating the membrane association of small molecules is discussed in view of the successes and failures observed for the monensin system.     

The molecular properties of heterocyclic and homocyclic hydrogen-bonded complexes evaluated by DFT calculations and AIM densities

This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C₂H₄O⋯HF and C₂H₅N⋯HF) and homocyclic (C₃H₆⋯HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6–311++G(d,p) level of theory. Subsequently, the interaction energies and polarizabilities were also evaluated, as well as the infrared stretch frequencies and absorption intensities. In addition, by combining intermolecular criteria and charge density concepts, calculations of Bader’s theory of atoms in molecules were used to determine the maxima and minima for electron density in order to measure the strength of the n⋯H and pπ⋯H hydrogen bonds. Finally, the possibility of an F⋯H_α secondary interaction between the fluoride (F) of hydrogen fluoride and the axial hydrogen atoms (H_α) of the C₂H₄O and C₂H₅N heterocyclic rings was explored. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DFT and the electromerism in complexes of iron with diatomic ligands

A reliable procedure is proposed for assigning the electronic structures for large biologically-relevant systems, where the size of the model confines one to the use of density functional theory (DFT) methods, and where the risk of over-interpreting DFT-derived molecular orbitals and spin densities still exists. The proposed approach focuses on the use of the only DFT-derived parameter that is unanimously recognized to be reliable: the geometry. We examine DFT-derived O-O bond lengths in formally ferrous-dioxygen models, and compare them to bond lengths in free, non metal-bound, dioxygen, superoxide and peroxide moieties. Likewise, we compare the N-O bond lengths within ferrous-nitrosyl {FeNO}7 models, with the same parameter in free NO+, NO*, and HNO species. This allows a calibrated, straightforward way of assigning the electronic structure in systems where electromerism makes detailed single-reference molecular orbital analysis unreliable.     

The electrostatic embedding contribution to DFT calculations of ligand-amino acid residues interaction

In this work, we demonstrate that the inclusion of long-range interactions has a significant impact on the estimation of ligand–protein binding energies. Within the scope of the electrostatically embedded adaptation of the molecular fragmentation with conjugated caps (EE-AMFCC) scheme, we unveil the role played by long-range contributions in distinct levels of quantum mechanical calculations. As a prototypical system, we consider ibuprofen coupled to the human serum albumin. In particular, we show that some relevant ligand–residue interaction energies can only be accurately captured in density functional theory (DFT) approaches when the electrostatic background is properly represented by an explicit point charge distribution.

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Graphical Abstract (left) The binding site FA3/FA4 of HSA containing the attached IBU. (right) Absolute value of difference between the biding energies calculated including the electrostatic embedding and the energies calculated without the electrostatic embedding using the HF, B3LYP, CAM-B3LYP, and MP2 methodologies

     

Spontaneous chirality conversion of [5]thiaheterohelicene in charge-transfer complexes in SDS micelles.

Racemic 2-hydroxymethylthieno[3,2-e:4,5-e']di[1]benzothiophene (5HM) with a labile helical structure was incorporated into aqueous SDS micelles containing (R)-2-(2,4,5,7-tetranitrofluoren-9-ylideneaminooxy)propionic acid (TAPA) to exhibit intense induced CD (ICD). Negative Cotton effects of the ICD gradually changed to reversed Cotton effects with time or sonication. This phenomenon of chirality conversion was attributable to conformational alterations of 5HM from an (M) helix to a (P), accompanied by compositional alterations of 5HM-(R)-TAPA charge-transfer (CT) complexes from 1/2 to 1/1. The conversion rate from the (M) enantiomer to the (P) was obtained from the change of the ICD intensities with time and the chiral discrimination energy exerted in the 1:1 CT complex was estimated from the temperature dependence of the ICD intensities.     

The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria

Local damage (mainly burning, heating, and mechanical wounding) induces propagation of electrical signals, namely, variation potentials, which are important signals during the life of plants that regulate different physiological processes, including photosynthesis. It is known that the variation potential decreases the rate of CO₂ assimilation by the Calvin–Benson cycle; however, its influence on light reactions has been poorly investigated. The aim of our work was to investigate the influence of the variation potential on the light energy flow that is absorbed, trapped and dissipated per active reaction centre in photosystem II and on the flow of electrons through the chloroplast electron transport chain. We analysed chlorophyll fluorescence in pea leaves using JIP-test and PAM-fluorometry; we also investigated delayed fluorescence. The electrical signals were registered using extracellular electrodes. We showed that the burning-induced variation potential stimulated a nonphotochemical loss of energy in photosystem II under dark conditions. It was also shown that the variation potential gradually increased the flow of light energy absorbed, trapped and dissipated by photosystem II. These changes were likely caused by an increase in the fraction of absorbed light distributed to photosystem II. In addition, the variation potential induced a transient increase in electron flow through the photosynthetic electron transport chain. Some probable mechanisms for the influence of the variation potential on the light reactions of photosynthesis (including the potential role of intracellular pH decrease) are discussed in the work.     

Novel p-tolylimido rhenium(V) complexes incorporating quinoline-2-carboxylate ion - Synthesis, X-ray studies, spectroscopic characterization and DFT calculations

Novel p-tolylimido rhenium(V) complexes trans-[Re(p-NC₆H₄CH₃)X₂(quin-2-COO)(PPh₃)] and cis-[Re(p-NC₆H₄CH₃)X₂(quin-2-COO)(PPh₃)]·MeCN have been obtained in the reactions of [Re(p-NC₆H₄CH₃)X₃(PPh₃)₂] (X = Cl, Br) with quinoline-2-carboxylic acid. The compounds were identified by elemental analysis IR, UV-Vis spectroscopy and X-ray crystallography. The electronic structures of trans- and cis-halide isomers of [Re(p-NC₆H₄CH₃)Cl₂(quin-2-COO)(PPh₃)] have been calculated with the density functional theory (DFT) method. Additional information about binding in the compounds [Re(p-NC₆H₄CH₃)Cl₂(quin-2-COO)(PPh₃)] with cis- and trans-halide arrangement has been obtained by NBO analysis. The electronic spectra of trans and cis isomers of [Re(p-NC₆H₄CH₃)Cl₂(quin-2-COO)(PPh₃)] were investigated at the TDDFT level employing B3LYP functional in combination with LANL2DZ.     

Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations

Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X?=?D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PP_II and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ₁), along with the computation of ³J(H^αH^β), revealed a preference for the g _? and g ₊ rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl–carbonyl interactions sampled in the PP_II and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.     

Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior

The structure of a previously calculated transition state (TS) was used to design the [tetrahydro-2-(methylthio)furan-2-yl]methyl phosphate dianion (1) as a new scaffold for transition-state analogs of reactions catalyzed by the inverting glycosyltransferases. This scaffold contains relevant features of the donor and acceptor and represents a new type of potential inhibitors for these enzymes. Available conformational space of 1 was explored using DFT quantum chemical methods by means of two-dimensional potential-energy maps calculated as a function of Phi, Psi, and omega dihedral angles at the B3LYP/6-31+G* level. The calculated potential energy surfaces revealed the existence of several low-energy domains. Structures from these regions were refined at the 6-311++G** level and led to 14 conformers. The stability of conformers is influenced by their environment, and in aqueous solution two conformers dominate the equilibrium. A superposition of calculated conformers with the predicted TS structure revealed that the preferred conformers in solution nicely mimic structural features of the TS. These results imply that 1 has structural properties required to mimic the TS and therefore can be used as a scaffold for further development of TS-analog inhibitors for retaining glycosyltransferases.     

Photodynamic activity of water-soluble phthalocyanine zinc(II) complexes against pathogenic microorganisms

Photodynamic activity of tetrakis-(3-methylpyridyloxy)- and tetrakis-(4-sulfophenoxy)-phthalocyanine zinc(II) toward the gram-positive Staphylococcus aureus, the gram-negative Pseudomonas aeruginosa, and the fungi Candida albicans was studied. The drug uptake dependency with an inverse behavior to the cell density was observed. The cationic photosensitizer completely inactivated S. aureus and C. albicans, and with 4 log10 P. aeruginosa. The photoinactivation at mild experimental conditions, such as drug dose of 1.5 microM and fluence of 50 mW cm(-2) for 10 min irradiation time, was shown.     

Redox and fungicidal properties of phthalocyanine metal complexes as related to active oxygen

Some chemical and fungicidal effects of 20 phthalocyanines of Co, Fe, Cu, and Al were studied. Under dark conditions, these complexes reduced nitroblue tetrazolium in the presence of KCN, accelerated the autoxidation of ascorbate or hydroquinone and decomposed hydrogen peroxide. In the later reaction, hydroxyl radical was generated as evidenced with the deoxyribose assay. The inhibition by superoxide dismutase and catalase of catalyzed autoxidation of ascorbate suggests the participation of superoxide anion-radical and hydrogen peroxide in the reaction. Most complexes were toxic to the fungus Magnaporthe grisea which causes blast disease of rice. The toxicity was enhanced by light being diminished by antioxidant reagents sequestering active oxygen species. Some complexes (including nontoxic ones), after 1-day contact with a leaf surface of the disease-susceptible rice cultivar, induced the fungitoxicity of leaf diffusate. This toxicity was also light-activated and sensitive to antioxidant reagents. Several complexes, when added to inocula, decreased 2-3 times the frequency of the compatible symptoms of the blast. It is suggested that in planta, the dark redox activity of phthalocyanines along with their photosensitization promote the generation of active oxygen, which damages the parasite and, therefore, favors disease resistance.     

Interaction of phenols with old yellow enzyme. Physical evidence for charge-transfer complexes.

Evidence is presented that the changes in absorption spectrum obtained on complex formation between Old Yellow Enzyme and phenolic compounds are due to charge-transfer interactions. The positive correlation between the energy of the long wavelength transition and the Hammett para constant with a series of para-substituted phenols indicates that the phenol is the charge-transfer donor and the oxidized flavin of the enzyme is the charge-transfer acceptor. The same conclusion is drawn from studies in which the flavin of the native enzyme, flavin mononucleotide, was replaced by a variety of artificial flavins of different oxidation-reduction potential. The effect of pH on the dissociation constant for the enzyme-ligand binding also indicates that it is the phenolate anion, rather than the conjugate acid, which is responsible for the charge-transfer interaction. The significance of these results is discussed relative to long wavelength absorbing species detected with other flavoproteins.     

DFT calculations of the anomeric and exo-anomeric effect of the hydroperoxy and peroxy groups

DFT calculations were carried out on axially and equatorially oriented 2-hydroperoxy and 2-peroxy tetrahydropyran, cyclohexyl hydroperoxide, hydroperoxides of 2,3-unsaturated hexapyranoses, and hydroperoxides of OMe and OBn substituted derivatives of 2-deoxy-glucopyranose and 2-deoxy-galactopyranose to investigate the anomeric and exo-anomeric effects of these groups. The structure and energy of the conformers were calculated at the B3LYP/6-311++G** level. Calculations showed that the peroxy anion group exhibits a strong anomeric effect, comparable in magnitude to the methoxy group, and that the anomeric effect of the hydroperoxy group is similar to the hydroxyl group. These results revealed that hydroperoxy and peroxy anion groups display an exo-anomeric effect, but the orientation around the C1-O1 bond is also affected by hydrogen bonding and electrostatic interactions.     

The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes

The accuracy of density functional theory with the B3LYP functional is reviewed for systems of relevance to transition-metal-containing enzymes. Calculated energies are commonly within 3–5 kcal/mol of the correct values; however, some exceptions have appeared in the literature and are discussed here. For example, the binding of NO and that of O₂ to metal centers have for some time been known to be underestimated. Most barriers for chemical reactions are overestimated except those involving hydrogen (or proton) transfer, which instead tend to be underestimated. A minor general improvement of the accuracy can probably be obtained by slightly reducing the amount of exact exchange in the B3LYP functional.     

Styrene and ethylbenzene absorption in ionic liquids: comparing DFT affinity calculations with experimental data

Styrene is a widely used bulk chemical produced by dehydrogenation of ethylbenzene (EB). Purification of styrene to contain < 100 ppm EB is not cost-effective by conventional separation methods. One separation method is extractive distillation with an ionic liquid (IL) as a binding agent for one of the components, thereby lowering the vapour pressure of this component. In this study, using quantum density functional theory (DFT), we have simulated 22 IL anion–cation pairs, styrene and EB affinities to them, and ion-pair dimer affinities of the ILs. These are compared with experimental liquid–liquid equilibrium studies of M.T.G. Jongmans, B. Schuur, and A.B. de Haan, Ind. Eng. Chem. Res. 50 (2011), pp. 10800–10810. It is shown that experimental selectivity and distribution coefficients of styrene and EB in the ILs are related to computed gas phase anion–cation stabilisation energies and ion-pair–ion-pair dimer affinities. The inverse of molar volume is found to strongly correlate with the selectivity. The computational results also qualitatively correlate with molar volume, and consequently, it is possible to use DFT calculations as a qualitative prediction tool in screening of ILs for this separation process. This tool does not account for effects caused by long alkyl chains, as the length does not seem to affect dimer stabilisation energy beyond ethyl group.