Mansour Zahedi

Unique 1∶2 adduct formation of meso-tetraarylporphyrins and meso-tetraalkylporphyrins with BF3: a spectroscopic and ab initio study

The interaction of a series of free base meso-tetraarylporphyrins (arylpor) and meso-tetraalkylporphyrins (alkylpor) with BF3·Et2O, with different molar ratios ( 1∶2) in chloroform, immediately and exclusively yielded the 1∶2 adducts (BF3)2por. The close spectral correlation between the corresponding (BF3)2por and (CF3COOH)2por were suggestive of similar saddled porphyrin core structures with BF3 molecules coordinated to the two pyrrolenine nitrogen donors, and simultaneously hydrogen bonded to the pyrrole NH groups of the porphyrin macrocycle from above and below the plane of the porphyrins. The complexation of various arylpor and alkylpor with BF3 and their protonation with CF3COOH caused red shifts of the Soret bands (3 to ∼30 nm). The interaction of arylpor (except H2tmp) and also H2t(tert-Bu)p with BF3·OEt2 and CF3COOH demonstrated red shifts of the Q(0,0) bands (5.4 to 40 nm). In contrast, reactions of the alkylpor (alkyl = Me, Et, n-Pr, n-Bu) and H2tmp with BF3 or CF3COOH displayed blue shifts of the Q(0,0) bands (−13.5 to −31.8 nm). The observed differences in the Q(0,0) bands shifts for the complexation of arylpor versus alkylpor are presumably related to the relative co-planarity of the meso-aryl groups with the porphyrin core, and the possible π-interactions in the former. It is noteworthy that while the UV-vis spectrum of H4t(tert-Bu)p2+ was very sensitive to excess amounts of CF3COOH, the UV-vis spectrum of (BF3)2H2t(tert-Bu)p showed no changes in the presence of additional BF3·Et2O. The 1H and 13C NMR spectra of the 1∶2 adducts demonstrated a general correspondence with those of the related protonated porphyrins. However, the pyrrole NH signals of the (BF3)2por were upfield shifted to an unusual extent as compared to those of the diprotonated H2por2+ species. This effect presumably is due to the weaker NH hydrogen bonding of the 1∶2 molecular complexes compared to the protonated porphyrins. It was also observed that, in contrast to the gradual upfield shifts of the NH signals of H2por2+ with increasing CF3COOH concentration, the NH signals of (BF3)2por complexes remained fixed and independent of BF3·OEt2 concentration. 19F and 11B NMR spectra of various (BF3)2por showed upfield shifts of both 11B and 19F signals relative to those of BF3·OEt2. The observed larger upfield shifts of 11B (−6.48 to −6.71 ppm) signals than those of 19F (−3.53 to −4.20 ppm), apparently reflect direct coordination of the B atoms to the nitrogen donors and their closer proximity to the porphyrin core. The results of ab initio calculations illustrated that in (BF3)2H2tpp the two BF3 molecules are coordinated to the pyrrolenine nitrogen donors and are hydrogen-bonded to the pyrrole NH groups. Also calculations indicated that the addition of a BF3 molecule to the 1∶1 species, BF3H2tpp, is more favorable (2.4 kcal mol−1) than its coordination to H2tpp, and the 1∶2 molecular complex is more stable (14.5 kcal mol−1) than the 1∶1 adduct. A mechanism is proposed to explain the absence of the 1∶1 adduct and the observed symmetric NMR spectra of the pyrrole rings and fluorines in (BF3)2por.

A Theoretical Elucidation of Glucose Interaction with HSA's Domains

Abstract The interaction of different domains belonging to Human Serum Albumin (HSA) with open form of glucose have been investigated using molecular dynamics simulation methods. Applying docking, primary structures involving interaction of some residues with glucose have been obtained. Subsequently, equilibrium geometries at 300 K and minimum geometries have been determined for each of aforementioned structures by employing MD simulation and simulated annealing. The stability of species has been evaluated using a SAWSA v2.0 model. Ultimately, NBO analysis has been carried out to specify possible hydrogen bonding regarding the HSA interaction with glucose. Results obtained show that glucose can interact with Lys195, Lys199, and Glu153. In these interactions, each lysine forms an H-bonding with glucose. The H-bonding is obtained by stretching of N-H bond belonging to NH3+ group of lysine along an oxygen atom of glucose. In addition, the above mentioned lysines are protonated, and there is an electrostatic interaction between glucose with Lys195 or Lys199. In addition, an H-bonding is formed between O atom of -COO group belonging to Glu153 and H atom of OH group belonging to glucose. Because, the N-H group of Lys195 interacts with the O atom of latter OH group, reaction of Lys195 is more desirable than that of Lys199. In fact, glucose is placed in the vicinity of Lys195 along with electrostatic interaction and H-bonding to Lys195 and Lys199 as well as H-bonding with Glu153, which subsequently reacts with Lys195. Thus, Lys195 is the primary site in reaction of glucose with HSA.

Quantum chemical investigation of intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives

The one step intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives has been studied through the use of electronic structure methods. Due to the absence of experimental data for the parent molecule of 1,2,4-triazole-3-thione the structure and energetics of aforementioned tautomers were derived using various basis sets and levels including HF, B3LYP, and MP2 methods. The gas phase results show that in all different levels of theory the most stable tautomer is the thione form. It has also been revealed that B3LYP/6-31G(d,p) level is quite well suited and reliable to investigate these kinds of tautomerism. To account the influence of substituents on the mentioned tautomerization, the tautomerism and conformational properties as well as vibrational analysis of 20 halophenyl and isopyridyl derivatives were investigated using B3LYP/6-31G(d,p) calculations. In all cases the calculations indicate that substituents have no considerable effects on relative stabilities and energy barriers for the thione-thiol proton transfer and the thione forms are the predominant species in the gas phase. In order to figure out the relative stabilities of the species involved in the tautomerism, geometrical and natural bond orbital (NBO) analyses have been employed. It has also been shown that the computed vibrational frequencies of tautomers with different scaling factors could be used to interpret the vibrational frequencies in IR spectrum of similar species.

Density Functional Theory (B3LYP) Study of Substituent Effects on O–H Bond Dissociation Enthalpies of trans-Resveratrol Derivatives and the Role of Intramolecular Hydrogen Bonds

In this paper, 23 substituents with various electron-donating and electron-withdrawing characters were placed in available positions of trans-resveratrol in order to study their effect on the three O-H bond dissociation enthalpies (BDEs) via density functional theory (DFT) with Becke three-parameter exchange and Lee-Yang-Parr correlation (B3LYP). It has been found that the mutual positions of substituents and OH groups affect investigated BDEs substantially. Formation of strong intramolecular hydrogen bonds and suitable spin density distributions in several radicals result in low BDEs. Calculated BDEs have been correlated with Hammett constants, selected geometry parameters, and charge on phenoxy radical oxygen q(O). Found dependences are satisfactorily linear.

Effect of Axial Ligand on the Electronic Configuration, Spin States, and Reactivity of Iron Oxophlorin

Iron-oxophlorin is an intermediate in heme degradation, and the nature of the axial ligand can alter the spin, electron distribution, and reactivity of the metal and the oxophlorin ring. The structure and reactivity of iron-oxophlorin in the presence of imidazole, pyridine, and t-butyl isocyanide as axial ligands was investigated using the B3LYP and OPBE methods with the 6-31+G* and 6-311+G** basis sets. OPBE/6-311+G** has shown that the doublet state of [(Py)(2)Fe(III)(PO)] (where pyridines are in perpendicular planes and PO is the oxophlorin trianion) is 3.45 and 5.27 kcal/mol more stable than the quartet and sextet states, respectively. The ground-state electronic configuration of the aforementioned complex is π(xz)(2) π(yz)(2) a(2u)(2) d(xy)(1) at low temperatures and changes to π(xz)(2) π(yz)(2) d(xy)(2) a(2u)(1) at high temperatures. This latter electronic configuration is consistently seen for the [(t-BuNC)(2)Fe(II)(PO(•))] complex (where PO(•) is the oxophlorin dianion radical). The complex [(Im)(2)Fe(III)(PO)] adopted the d(xy)(2) (π(xz) π(yz))(3) ground state and has low-lying quartet excited state which is readily populated when the temperature is increased.

An ab initio/hybrid (ONIOM) investigation of biliverdin isomers and metal–biliverdin analogue complexes

Ab initio HF and DFT (BLYP, B3LYP) methods have been applied to the computation of three isomeric forms, diketo, keto– enol and dienol of biliverdin. The fully optimized structures so obtained are compared and the most stable isomer (diketo form) agrees well with the structure determined from X-ray crystallographic studies. Results of the calculations based on three methods, HF, BLYP and B3LYP have been compared with the experimental parameters. B3LYP method results are determined to be closest to the experimental results. Octaethyl dimethyl amido biliverdin as a free ligand while complexed with zinc(II) which forms a metal – biliverdin analogue complex Zn II (OEBNMe2) has been fully optimized using PM3 and B3LYP methods. Comparison of calculated parameters for this complex with X-ray results has proved the capability of the ab initio method in accurately predicting fine details of the complex. Results obtained by employing a hybrid (ONIOM) calculation method on such system for the first time has established the applicability as well as low computational cost of the technique. q 2003 Elsevier B.V. All rights reserved.

Comparative DFT study to determine if α-oxoaldehydes are precursors for pentosidine formation.

We report a comprehensive density functional theory (DFT) study of the mechanism of pentosidine formation. This work is a continuation of our earlier studies in which we proposed pathways for formation of glucosepane (J. Mol. Model. 2011, pp 1-15, DOI 10.1007/s00894-011-1161-x), GODIC (glyoxal-derived imidazolium cross-link), and MODIC (methyl glyoxal-derived imidazolium cross-link; J. Phys. Chem. 2011, 115, pp 13542-13555). Here we show that formation of pentosidine via reaction of α-oxoaldehydes with lysine and arginine in aqueous solution is possible thermodynamically and kinetically, in good agreement with the available experimental evidence. Five pathways, A-E, were characterized, as in our previous GODIC and MODIC work. In pathways A and B, a Schiff base is first formed from lysine and methyl glyoxal (MGO), and this is followed by addition of arginine and glyoxal (GO). By contrast, in pathways C, D, and E, addition of arginine to MGO occurs first, resulting in the formation of imidazolone, which then reacts with lysine and GO to give pentosidine. Our calculations show that the reaction process is highly exergonic and that the three pathways A, C, and E are competitive. These results serve to underline the potentially important role that α-oxoaldehydes play as precursors in pentosidine formation in the complex field of glycation.

Cross-Linking Mechanisms of Arginine and Lysine with α,β-Dicarbonyl Compounds in Aqueous Solution

Cross-linking in proteins by α,β-dicarbonyl compounds is one of the most damaging consequences of reactive carbonyl species in vivo and in foodstuffs. In this article we investigate computationally the cross-linking of glyoxal and methylglyoxal with lysine and arginine residues using density functional theory and the wB97XD dispersion-corrected functional. Five pathways, A-E, have been characterized. In pathways A and B, the reaction proceeds via formation of the Schiff base, aldimine, followed by addition of arginine. In contrast, in pathways C-E, direct addition of arginine to the dicarbonyl compounds occurs first, leading to a dihydroxyimidazolidine intermediate, which then reacts with lysine after dehydration and proton transfer reactions. The results reveal that pathways A, C, and E are competitive whereas reactions via pathways B and D are much less favorable. Inclusion of up to five explicit water molecules in the proton transfer and dehydration steps is found to lower the energy barriers in the feasible pathways by about 5-20 kcal/mol. Comparison of the mechanisms of methylglyoxal-derived imidazolium cross-linking (MODIC) and glyoxal-derived imidazolium cross-linking (GODIC) shows that the activation barriers are lower for GODIC than MODIC, in agreement with experimental observations.

An ab initio investigation of sulfur diimides: stability of various conformers and conformational analysis Part I. parent sulfur diimide

In this paper various properties of parent sulfur diimides (PSD) as the simplest member of sulfur diimides family have been considered with aid of B3LYP method and correlation consistent basis set hierarchies. According to these calculations ZZ conformer is predicted to be the most stable conformer while the difference with EZ conformer is completely minute. Also comparison of experimental microwave spectra with theoretical calculations have been carried out and good agreement have been observed. The properties of EE conformer have also been anticipated although no experimental data exist for this conformer. The possible pathways for interconversion between different conformers have been investigated and a pseudo-rotation mechanism has been determined as the best candidate.

Conclusive evidence for delayed autocatalytic behavior of Mn(II) ions at a critical concentration

The kinetics of the permanganic oxidation process of glycine, L-alanine and L-leucine in strong acid media were investigated using a spectrophotometric technique. Conclusive evidence has proven that the autocatalytic activity of Mn(II) in these reactions in strong acidic media is analogous to that of weak acid media, but in the former, Mn(II) ions should acquire a critical concentration for them to show autocatalytic characteristics. This critical concentration depends on the nature of the amino acid used. Considering the delayed autocatalytic behavior of Mn(II) ions, we herein present the rate equations and mechanisms satisfying observations for both catalytic and noncatalytic routes. The correspondence of the pseudo-order rate constants of the catalytic and noncatalytic pathways to Eyring law verify both the critical concentration as well as the delayed autocatalytic behavior concepts. In general, the onset of delayed behavior can be attributed to the concentration ratio of Mn(II) to amino acid which can be of a certain value for any particular amino acid.