The role of glutathione in cadmium ion detoxification: coordination modes and binding properties--a density functional study

In this investigation the reduced form of glutathione molecule (GSH) was considered as a model in the coordination chemistry of Cd²⁺ and group thiol-containing peptides. Three different forms of GSH, corresponding to the prevalent ones in gas-phase and in aqueous solution, were taken into account in the metallation process. The obtained complexes were characterized at the density functional B3LYP level with the purpose to give better insight in the chelation mechanism of GSH with heavy metal ions in living organisms. Solvent effects, whether with explicit water molecules or with polarizable continuum model (PCM), were considered on the most stable cadmium-complexes obtained by every GSH charged species examined.     

Activation energies of selenoxide elimination from Se-substituted selenocysteine

Transition states for selenoxide elimination have been determined for a series of Se-substituted selenocysteine (RSeCys) derivatives that have potential use in the prevention and treatment of cancer, either directly or in conjunction with cisplatin (to reduce its nephrotoxic effects). Reduced activation barriers vs R=Me and R=Ph are found when the alkyl chain length is increased or when activating groups are para to the selenide. Ortho substitution of Lewis bases stabilizes the transition state by directly donating electron density to the selenoxide. The results suggest that RSeCys derivatives incorporating the properties of glutathione peroxidase mimics will, upon oxidation, rapidly eliminate selenenic acid, a precursor to chemopreventative selenols. Scheme Mechanism of selenoxide elimination from Se-substituted SeCys.     

The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation

The geometric and electronic structure of ferrous complexes of bleomycin (Fe(II)BLM) has been investigated by means of density functional theory (DFT) calculations. The active site of this antitumor drug is a highly distorted octahedral complex, with the coordination sphere completed by the five known endogenous ligands, including pyrimidine, imidazole, deprotonated amide, and secondary and primary amines. We have addressed the controversial issue of the nature of the sixth axial ligand, which we have identified as the oxygen of the carbamoyl group. Our conclusions are further validated by a comparison with structural data derived from NMR experiments. Moreover, because of the high sensitivity of structural data on the pH of the environment, we have investigated the effect of a different protonation state of the histidine amide on the geometric structure of the Fe(II)BLM complex. The extensive model of the active site of bleomycin considered in this work allows us to check the limitations of previous investigations based on simplified models.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.An erratum to this article can be found at     

Decarbonylation of As2Co2(CO)6, a binuclear cobalt carbonyl derivative of diarsenic

The structures and relative energies of the As₂Co₂(CO)_n (n = 6, 5, 4) derivatives are predicted by density functional theory to be analogous to those of the corresponding H₂C₂Co₂(CO)_n derivatives. Thus As₂Co₂(CO)₆ is predicted to have three carbonyls on one cobalt atom eclipsed relative to the three carbonyls on the other cobalt atom. The corresponding As₂Co₂(CO)₆ structure with a staggered rather than eclipsed arrangement of the Co(CO)₃ units is a transition state rather than a genuine minimum. For As₂Co₂(CO)₅ the structure in which an equatorial group is removed from the As₂Co₂(CO)₆ structure and a singly bridged As₂Co₂(CO)₄(μ-CO) structure are predicted to have essentially the same energies, within <2 kcal/mol. A higher energy As₂Co₂(CO)₅ structure by 9 ± 2 kcal/mol is derived from the As₂Co₂(CO)₆ structure by removal of an axial carbonyl group. The two unbridged As₂Co₂(CO)₅ structures correspond to those observed experimentally in the photolysis of As₂Co₂(CO)₆ in Nujol matrices at low temperatures. In such photolysis experiments the higher energy isomer is produced initially and then converted to the lower energy isomer upon annealing. A singly bridged structure was found for As₂Co₂(CO)₄. The analogous structure was not observed in the previous work with H₂C₂Co₂(CO)₄. However, such a H₂C₂Co(CO)₃(μ-CO) structure is found here for the acetylene complex. This singly bridged structure is predicted to lie 1.9 kcal/mol below the H₂C₂Co₂(CO)₄4-1S structure by the BP86 method but 3.5 kcal/mol above the latter by the B3LYP method. In addition to the singly bridged As₂Co₂(CO)₄ structure, the same six unbridged structures were located for As₂Co₂(CO)₄ that were previously found for H₂C₂Co₂(CO)₆.     

Binuclear fluoroborylene manganese carbonyls

The lowest energy structure for Mn₂(BF)(CO)₁₀ is predicted to consist of two Mn(CO)₅ groups bridged by a BF group without a manganese-manganese bond. This structure is related to the stable compounds Mn₂(μ-BX)(CO)₁₀ (X = Cl, Br) and [(η⁵-C₅H₅)Ru(CO)₂]₂(μ-BF), which have been synthesized and characterized by X-ray crystallography. The following principles determine the lowest energy structures of the Mn₂(BF)(CO)_n (n = 9, 8, 7, 6) derivatives: (1) two-electron donor bridging μ-BF groups are highly favorable; (2) four-electron donor bridging η²-μ-BF groups are not found and thus appear to be highly unfavorable. Thus the lowest energy structure of Mn₂(BF)(CO)₉ is a doubly bridged structure with bridging CO and BF groups, in contrast to the experimentally observed unbridged structure of Mn₂(CO)₁₀. The lowest energy structures of Mn₂(BF)(CO)₈ have either a four-electron donor η²-μ-CO group or a two-electron donor bridging BF group. Similarly the lowest energy structures of the more highly unsaturated Mn₂(BF)(CO)_n (n = 7, 6) are singlet (for n = 7) or triplet (for n = 6) states in which the BF group is a bridging rather than a terminal ligand.     

Can the stereochemical outcome of glycosylation reactions be controlled by the conformational preferences of the glycosyl donor?

Previous static and dynamical density functional theory studies of the 2,6-di-O-acetyl-3,4-O-isopropylidene-D-galactopyranosyl cations and their methanol adducts has led to an hypothesis that these cations exist in two families of conformers characterized as (2)S(O) and B(2,5), respectively. These families differ by ring inversion, each with its own reactivity. New calculations on the 2,6-di-O-acetyl-3,4-di-O-methyl-D-galactopyranosyl cation confirmed these trends. Removing the isopropylidene group allows more flexibility, but two families of conformers can be discerned with the monocyclic oxocarbenium ions in the E(3) conformation and the bicyclic dioxolenium ions in the (4)H(5) conformation. Attack on the beta-face of these monocyclic cations is favored by hydrogen bonding and the anomeric effect. The experimentally observed high beta-stereoselectivity of mannopyranosyl donors and high alpha-stereoselectivity of glucopyranosyl donors with the 4,6-O-benzylidene protecting groups can be rationalized assuming that the trans-fused 1,3-dioxane ring allows population of only one family of conformers. The combination of hydrogen bonding and conformational changes of the pyranose ring in response to the C-5[bond]O-5[bond]C-1[bond]C-2 torsion angle changes are identified as key factors in stereoselectivity. Based on these observations a strategy to design face discriminated glycosyl donors that exist predominantly in only one family of conformers is proposed.     

The two-conformer hypothesis: 2,3,4,6-tetra-O-methyl-mannopyranosyl and -glucopyranosyl oxacarbenium ions

Computational chemistry can give information about the probable conformations of reactive intermediates that are difficult to determine experimentally. Based on density functional theory (DFT) calculations of tetra-O-methyl-D-mannopyranosyl and -glucopyranosyl oxacarbenium ions, two families of conformations, which we call B0 and B1, were found. For the manno configuration, a 4H3 and 3E almost isoenergetic pair were found, whereas for the gluco-configuration a 4H3 and 5S1 pair favouring 4H3 were calculated. These results corroborate earlier results and suggest that this two or more conformer hypothesis is general. Nucleophilic attack on these pairs of cations was modelled with methanol and led to four cases to consider namely alpha- or beta-attack on B0 or B1. The resulting complexes (G0, G1 and F0, F1) demonstrate facial selectivity. The relative energies of these complexes are dominated by intramolecular hydrogen bonding and the conformational consequences to the pyranose ring of changes in the C-5-O-5-C-1-C-2 torsion angle. Constrained variation of the nucleophilic oxygen (methanol) to C-1 distance shows that these ion dipole complexes are the only minima with this constraint.     

A structural and free energy analysis of Ag complexes to five small peptides

The complexes of Ag⁺ with the peptides MetGly, ProGly, GlyPro, GlyHis and GlyProAla were investigated using hybrid density functional theory at the B3LYP/DZVP level. The silver ion binding free energies at 298 K to each of these peptides was calculated to be 60.8, 52.0, 54.3, 71.2 and 63.3 kcal mol⁻¹, respectively. Structural information and relative free energies are presented for several isomers for each of the five complexes. Each of the global minima found for the five complexes is a charge-solvated ion. An important finding is that the Ag⁺-ProGly is the only complex where a salt bridge structure is energetically favored occurring at 4.0 kcal mol⁻¹ higher in free energy than the global minimum. The Ag⁺ ion in this salt bridge structure is attached to the carboxylate anion of zwitterionic ProGly in which the terminal amino nitrogen is protonated. For all the other complexes studied, the salt bridge structure occurs at much higher energies. All the dipeptide complexes with Ag⁺, but one, exhibit a di- or tri-coordinate metal where the sites of attachment are amino and carbonyl groups. However, the highest coordination numbers are not always the global minima due to steric costs. The global minimum of the Ag⁺-GlyProAla complex is the only structure found in this study where the metal is tetra-coordinated, binding to the terminal amino nitrogen and all three carbonyl oxygen atoms. Silver binding to sulphur and imidazole nitrogen atoms of MetGly and GlyHis, respectively, are present in the three most energetically favored species in each of these cases.     

A theoretical investigation of cytotoxic activity of celastroid triterpenoids

Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds: The energies of the frontier molecular orbitals (E _HOMO and E _LUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6). Figure LUMO of Pristimerin.     

The molecular structure of a curl-shaped retinal isomer

Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted structure in the vicinity of the C₁₁=C₁₂ double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11-cis and all-trans isomers. Rotation around the C₁₀–C₁₁ single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of the C₁₀–C₁₁ bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism (CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation of the β-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the β-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the β-ionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the β-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of the β-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the β-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest that it has a positive torsion angle for the β-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported for the retinal PSB isomers. Figure The figure shows the optimized molecular structure of the curl-shaped retinal isomer. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolution and function of phytochelatin synthases

Both essential and non-essential transition metal ions can easily be toxic to cells. The physiological range for essential metals between deficiency and toxicity is therefore extremely narrow and a tightly controlled metal homeostasis network to adjust to fluctuations in micronutrient availability is a necessity for all organisms. One protective strategy against metal excess is the expression of high-affinity binding sites to suppress uncontrolled binding of metal ions to physiologically important functional groups. The synthesis of phytochelatins, glutathione-derived metal binding peptides, represents the major detoxification mechanism for cadmium and arsenic in plants and an unknown range of other organisms. A few years ago genes encoding phytochelatin synthases (PCS) were cloned from plants, fungi and nematodes. Since then it has become apparent that PCS genes are far more widespread than ever anticipated. Searches in sequence databases indicate PCS expression in representatives of all eukaryotic kingdoms and the presence of PCS-like proteins in several prokaryotes. The almost ubiquitous presence in the plant kingdom and beyond as well as the constitutive expression of PCS genes and PCS activity in all major plant tissues are still mysterious. It is unclear, how the extremely rare need to cope with an excess of cadmium or arsenic ions could explain the evolution and distribution of PCS genes. Possible answers to this question are discussed. Also, the molecular characterization of phytochelatin synthases and our current knowledge about the enzymology of phytochelatin synthesis are reviewed.     

Phenolic esters with potential anticancer activity - the structural variable

The conformational preferences of several potential anticancer dihydroxycinnamic esters with a variable length alkyl chain were studied by quantum-mechanical (DFT) calculations (both for the isolated molecule and for aqueous solutions). The orientation of the hydroxyl ring substituents and of the alkyl ester moiety relative to the carbonyl group showed these to be the most determinant factors for the overall stability of this type of phenolic systems, strongly dependent on an effective π-electron delocalization. Compared to the parent caffeic acid (dihydroxycinnamic acid), esterification was found to lead to a higher conformational freedom, and to affect mainly the energy barrier corresponding to the (O=)C-OR internal rotation. No particular differences were verified to occur upon lengthening of the ester alkyl chain, except when this is branched instead of linear. The vibrational spectra of the whole series of compounds were simulated, based on their calculated harmonic vibrational frequencies, and a preliminary assignment was performed. Figure Schematic representation of the dihydroxycinnamic esters studied in the present work and of the main internal rotations affecting the overall stability of the molecules. (R=(CH₂)_n, n = 0,1,2,3,7,11 for MC, EC, PC, BC, OC and DC, respectively; R=(CHCH₃) for IPC. The atom numbering is included, with the exception of the alkyl ester group)     

Density Functional Theory Calculations of Molecular Hyperpolarizabilities

Recent density functional theory calculations of molecular hyperpolarizabilities are reviewed in order to try to assess the accuracy and reliability of DFT in the specified field by comparison with experiment and with ab initio HF and post-HF methods. In a table [1] (p. 157) containing results from the paper defining the compound electronic structure method Gaussian 2 [2], Foresman presents the relative accuracies of various 'model chemistries' for calculating thermochemical quantities. The Mean Absolute Deviation (MAD) from experiment, its Standard Deviation, and the largest positive and negative errors in the computed values, are the statistical means that allow the various models to be arranged in order of increasing MAD, and thus decreasing overall accuracy. These same statistical quantities, on a percent basis for size consistency and dimensionlessness, are used in this communication for quantifying the accuracies of various combinations of DFT functionals/basis sets/quantum chemical techniques/applied field strengths, in calculations of molecular mean dipole polarizabilities <>, first-order hyperpolarizabilities and second-order hyperpolarizabilities . The relative accuracies of DFT model chemistries are thus surveyed in three tables (including authors/references arranged in chronological order, compounds studied, and program codes employed), and can serve as guidelines for selecting optimal computational methodologies.     

A combined theoretical and spectroscopic study of 4,6-di-O-acetyl-2,3-dideoxy-d-erythro-hex-2-enopyranosyl sulfamide: a novel glycosyl carbonic anhydrase IX inhibitor

The novel 4,6-di-O-acetyl-2,3-dideoxy-d-erythro-hex-2-enopyranosyl sulfamide, which exhibits selectivity for inhibiting isoform IX of carbonic anhydrase as overexpressed in many tumors, has been investigated from a combined theoretical and spectroscopic point of view. The conformational study of the compound shows that the α-anomeric form is more stable than the β-anomeric form from a thermodynamic point of view after including solvent effects. This fact suggests that the synthesis reaction could take place mainly under thermodynamic control as the main experimental product is the α-anomeric form of the sulfamide. Calculated α/β ratio is about 95:5, in excellent agreement with experimental data. Optimized geometries of the α-anomeric form agree quite well with crystallographic data. The inclusion of a solvent has negligible effects on the conformations. A detailed analysis of some geometric parameters shed light into the conformational behavior of the sulfamide in terms of both exo- and endo-anomeric effects and antiperiplanar relationships. Natural bond orbital calculations confirm those findings. Several intramolecular hydrogen bonds, characterized through the Atoms-in-Molecules theory, were found in the stable conformers. They, however, seem to play no relevant role in determining the relative stability of α conformers with respect to the β ones. Calculated ¹H and ¹³C NMR chemical shifts support previous findings concerning configuration and conformation assignments of the title sulfamide. The IR spectrum of the compound is recorded and reported for the first time and the assignment of some of the most important bands is accomplished with the aid of calculated harmonic vibrational frequencies.     

Unsaturation in binuclear cyclopentadienyliron carbonyl thiocarbonyls: Four-electron donor bridging thiocarbonyl groups versus metal-metal multiple bonds

Theoretical studies on the binuclear cyclopentadienyliron carbonyl thiocarbonyl derivatives Cp₂Fe₂(CO)₂(μ-CS)(μ-CO) and Cp₂Fe₂(CO)₂(μ-CS)₂ indicate that the trans and cis isomers are nearly degenerate in energy, consistent with experiment. Structures with bridging CS groups are of lower energy than corresponding structures with bridging CO groups. The corresponding unbridged Cp₂Fe₂(CS)(CO)₃ and Cp₂Fe₂(CS)₂(CO)₂ isomers are predicted to lie 11 and 16 kcal/mol, respectively, above their global minima, indicating increasing activation energies for the cis/trans interconversion as bridging CO groups are replaced by bridging CS groups. The unsaturated species Cp₂Fe₂(μ-CS)(μ-CO)₂ and Cp₂Fe₂(μ-CS)₂(μ-CO) are predicted to have triply bridged triplet spin state structures with FeFe double bonds of lengths 2.26 Å, analogous to the experimentally known triplet (Me₅C₅)₂Fe₂(μ-CO)₃. However, low-lying singlet Cp₂Fe₂(CS)(CO)₂ and Cp₂Fe₂(CS)₂(CO) structures with four-electron donor bridging η²-μ-CS groups and formal Fe-Fe single bonds are also found. The lowest lying Cp₂Fe₂(CS)(CO) and Cp₂Fe₂(CS)₂ structures have two bridging groups and very short FeFe distances of ∼2.14 Å, suggesting formal triple bonds. Several higher energy four-electron donor η²-μ-CS bridged structures are also found for Cp₂Fe₂(CS)(CO) and Cp₂Fe₂(CS)₂. In addition, singlet and triplet structures are found for Cp₂Fe₂(CS)₂ in which the two CS ligands have coupled to form a bridging SCCS group with a carbon-carbon bond. Only a η²-μ-CS bridged singlet structure is predicted for Cp₂Fe₂(CS), rather than the normal bridged structure with a FeFe quadruple bond such as that predicted for the carbonyl analog Cp₂Fe₂(CO).     

m-Terphenylphosphines: Synthesis, structures and coordination properties

A series of m-terphenylphosphines TerphPCl₂, TerphPH₂ and TerphPMe₂ (Terph = 2,6-Mes₂C₆H₃-, 2,6-(4-t-BuC₆H₄)₂C₆H₃-, 2,6-(3,5-Me₂C₆H₃)₂C₆H₃-, 2,6-(2,6-Et₂C₆H₃)₂C₆H₃-, and 2,6-(2,6-i-Pr₂C₆H₃)₂C₆H₃-; Mes = 2,4,6-Me₃C₆H₂-) was prepared and fully characterized. The structural investigation by X-ray crystallography and density functional theory revealed significant distortions in the environment of the ipso carbon and phosphorus centers. These can be traced back to steric interactions and repulsions of the chlorine and methyl substituents on phosphorus with one of the flanking arenes of the m-terphenyl substituents. The primary phosphine 2,6-Mes₂C₆H₃PH₂, 6, and the dimethylphosphine 2,6-(3,5-Me₂C₆H₃)₂C₆H₃PMe₂, 9, readily form complexes with the Cl₂Ru(p-cymene) complex fragment, whereas the larger phosphine 2,6-Mes₂C₆H₃PMe₂, 8, does not. Heating of the complexes TerphPR₂Ru(Cl₂)(p-cymene) 11 and 12 and the mixture of 8 and {(p-cymene)RuCl₂}₂ lead to expulsion of the p-cymene ligand and intramolecular η⁶ coordination of one of the flanking arene rings to the ruthenium center to afford the complexes Cl₂RuP(H₂)C₆H₃-2-η⁶-Mes-6-Mes, 13, Cl₂RuP(Me₂)C₆H₃-2-η⁶-Mes-6-Mes, 14, and Cl₂RuP(H₂)C₆H₃-2-η⁶-(3,5-Me₂C₆H₃)-6-(3,5-Me₂C₆H₃), 15. All complexes were characterized by NMR spectroscopy and complexes 14 and 15 also by X-ray crystallography.     

Electronic analysis of vanadium and iron complexes containing distorted aromatic rings

Aromatic rings can suffer severe distortions upon substituting transition metal centers with certain kinds of organometallic compounds. This property is very interesting because aromaticity can remain despite the deformation. Theoretical calculations at the density functional theory level were carried out on two such structures containing vanadium and iron centres [(C₅H₅-V-H)₂C₆H₆ and (CpFe)₂C₆(CH₃)₆] in order to analyze the nature of the bonds as well as the magnitude of the prevalent aromaticity and how this depends on the electronic characteristics around each metal atom. The analysis of aromaticity was carried out on the basis of known methods, such as HOMA and FLU, with consistent results. The results also show features that suggest a possible catalytic behavior of the species under study. Figure Molecules under study