Are electrophilicity and electrofugality related concepts? A density functional theory study

It is proposed that the electrofugality of a fragment within a molecule is determined by its group nucleophilicity. The variation of electrofugality should be tightly related to the electron releasing ability of the substituent attached to the electrofuge moiety. This contribution closes the set of relationships between philicity and fugality quantities: while nucleofugality appears related to the group electrophilicity of the leaving group, electrofugality is related to the group nucleophilicity of the permanent group.     

Concurrent cyclopropanation by carbenes and carbanions? A density functional theory study on the reaction pathways

The mechanisms for the addition reactions of phenylhalocarbenes and phenyldihalomethide carbanions with acrylonitrile (ACN) and trimethylethylene (TME) have been investigated using an ab initio BH and HLYP/6-31G (d, p) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (THF). These model calculations show that for the addition of phenylhalocarbenes, a TME species may readily undergo addition reactions with carbenes while ACN has a high-energy barrier to overcome. It was also found that phenyldihalomethide carbanions do not readily add to the electron-rich TME. The cyclopropane yields only appear to occur via addition of PhCBr to TME. However, the cyclopropanation proceeds not only via slow addition of phenylhalocarbenes to ACN but also forms through the stepwise reaction of phenyldihalomethide carbanions with ACN. Our calculation results are in good agreement with experimental observations (Moss, R.A.; Tian, J.-Z. J. Am. Chem. Soc. 2005, 127, 8960) that indicate that the cyclopropanation of phenylhalocarbenes and phenyldihalomethide carbanions with ACN are concurrent in THF.     

A density functional theory study of the ��mythic�� Lindlar hydrogenation catalyst

A Lindlar catalyst is a popular heterogeneous catalyst that consists of 5?wt.% palladium supported on porous calcium carbonate and treated with various forms of lead and quinoline. The additives strategically deactivate palladium sites. The catalyst is widely used for the partial hydrogenation of acetylenic compounds in organic syntheses. Alkyne reduction is stereoselective, occurring via syn addition to give the cis-alkene. Even if it has been employed for about 60?years, there is a lack of molecular level understanding of the Lindlar catalyst. We have applied density functional theory simulations to understand the structure and the nature of the interplay between the multiple chemical modifiers in the Lindlar catalyst. Indeed, the poisons influence different parameters controlling selectivity to the alkene: Pb modifies the thermodynamic factor and hinders the formation of hydrides, while quinoline isolates Pd sites thus minimizing oligomerization.     

How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.     

Hydronium ion complex of 18-crown-6: where are the protons? A density functional study of static and dynamic properties

A quantum-chemical study employing the BLYP density functional is reported for the complex of H3O+ with 18-crown-6. According to a Car-Parrinello molecular dynamics (CPMD) study at 340 K, the complex is quite flexible, and is characterized by three quasi-linear (two-center) hydrogen-bond interactions for most of the time. On a time scale of 10 ps, frequent inversions of H3O+ are observed, as well as two 120 degrees rotations switching the hydrogen bonds from one set of crown-ether O atoms to the other. These results are consistent with density-functional studies of stationary points on the potential energy surface, which show how the crown "catalyzes" the guest's inversion. Two close-lying minima are characterized, as well as two distinct transition states connecting them, either via H3O+ inversion or rotation, with barriers of 1.0 and 4.6 kcal/mol, respectively, at the BLYP/II'//BLYP/6-31G level. Orbital interactions between lone pairs on ether O atoms and hydronium sigma(OH) antibonding orbitals are important factors for the directionality of the hydrogen bonds.     

Do penta- and decaphospha analogues of lithocene anion and beryllocene exist? Analysis of stability,structure, and bonding by hybrid density functional study

Stability in penta- and decaphospha analogues of lithocene anion and beryllocene is investigated by complete structural optimization at the B3LYP/6-31G level. Natural bond orbital analysis is carried out to examine the bonding between the metal and the ligands. The heterolytic dissociation energies of 667 and 608 kcal/mol predicted by B3LYP/6-311+G//B3LYP/6-31G calculations for CpBeP(5) and (P(5))(2)Be are comparable with the observed value of 635 +/- 15 kcal/mol in ferrocene. The high stability in CpBeP(5) and (P(5))(2)Be shows that these species are isolable under appropriate conditions. Lithocene anion and its phospha analogues possess lower stability toward dissociation into ionic fragments. A novel observation of the present study is that CpBeP(5) and (P(5))(2)Be have lowest energies when the two planar ligands are arranged perpendicular to each other such that one of the ligands, cyclo-P(5), is eta(1)-coordinated while the second ligand is eta(5)-coordinated to Be. The resulting structure having C(s)() point group (denoted as C(s)()(p)) is predicted to be 22 and 28 kcal/mol lower than the staggered sandwich geometry in CpBeP(5) and (P(5))(2)Be, respectively, at the B3LYP/6-311+G//B3LYP/6-31G level. In the analogous lithocene anions [CpLiP(5)](-) and [(P(5))(2)Li](-) also the C(s)()(p) structures are found to be the lowest energy structures, though their relative stabilities are small. We also characterized the geometry with both ligands eta(1)-coordinated to the metal in a linear arrangement having the D(2)(h)() point group in the decaphospha analogues [(P(5))(2)Li](-) and (P(5))(2)Be. This structure is found to be higher in energy than the C(s)()(p) structure. The D(2)(h)() structure could not be located as a potential minimum in the biscyclopentadienyl complexes and their pentaphospha analogues. Both the C(s)()(p) and D(2)(h)() structures are characterized for the first time in metallocenes. The D(2)(h)() structure seems to be a unique feature in the decaphospha metallocenes under consideration. Covalent bond formation between beryllium and phosphorus atom P(1) of eta(1)-(cyclo-P(5)) is more pronounced (bond orders 0.43-0.49) than that between Be and C(1) of eta(1)-Cp (bond orders 0.24-0.27). Though both eta(1)-coordinated cyclo-P(5) and Cp exhibit C(2)(v)() point groups, bond alternation is less pronounced in the former. The Wiberg P-P bond orders in the eta(1)-(cyclo-P(5)) of CpBeP(5) and (P(5))(2)Be having C(s)()(p) structures are in the range 1.29-1.47. These ring bond orders indicate that the P(5) ring retains aromaticity to a large extent in the eta(1)-mode of bonding with Be. Second-order perturbational energy analysis of the Fock matrix in the natural bond orbital basis reveals that there is a significant stabilizing interaction of approximately 123 kcal/mol between the lone pair orbital of P(1) and the 2s orbital of Be in the C(s)()(p) structures.     

A bond-valence approach to the semicoordination of copper-oxygen and copper–nitrogen complexes

Bond valence as the function of inter-nuclear distance for Cu–O and Cu–N bonds were estimated. Based on the developed bond-valence theory a mutual dependence between the bond length in copper coordination sphere with chromophores CuO₆, CuO₅, CuN₆ and CuN₄O₂ has been derived and compared with the experimental structural correlations. The discontinued transition from chemical bonding to the nonbonding state in the direction of the elongated bond was estimated. The shortest bond lengths are dependent on the copper atom valence. The supreme manifestation of coordination sphere plasticity is estimated as semicoordination. The semicoordinative Cu–O and Cu–N bonds are 3.07 and 2.78 Å long.     

Spectroscopic and electrochemical study of dinuclear and mononuclear copper complexes with the bidentate ligand of the 2,2′-diquinoline series

The newly synthesized complex (2) of copper(I) chloride with di-n-hexyl 2,2′-biquinoline-4,4′-dicarboxylate (L) was spectroscopically and electrochemically characterized. The X-ray diffraction study showed that the crystals of complex 2 consist of the dinuclear moieties [L₂Cu¹ ₂(μ-Cl)₂] containing Cu₂(μ-Cl)₂ clusters. Spectrophotometric studies and ESI-mass spec-trometric measurements showed that after the dissolution of complex 2 in acetonitrile (AN) and N-methyl-2-pyrrolidone (NMP), the solution contained not only the dinuclear complexes [L₂Cu¹ ₂(μ-Cl)₂] but also [L₂Cu¹]Cl, [LCu¹Cl(Sol)], and [Cu¹Cl(Sol)] (Sol is the solvent). The electrochemical data also confirm the conclusion that bridged dinuclear chloride complex 2 dissociates both in NMP and AN to form the tetrahedral bis-biquinoline complex [L₂Cu¹]Cl. In solutions of complex 2 in alcohols and _N,_N-dimethylformamide (DMF), only [L₂Cu¹]Cl and [Cu¹Cl(Sol)] are present. In EtOH, AN, and DMF, [Cu¹Cl(Sol)] undergoes disproportionation to [Cu¹¹Cl(Sol)] and Cu⁰.     

A fluorescence probe study of the mixed surfactant vesicles

Vesicle can be prepared from aqueous mixtures of simple commercially available, single-tailed canonic and anionic surfactants. In this work, the I3/I1 value, Ie/ Im value, and fluorescence lifetime of pyrene in different systems (see the preparation of samples) were determined. Hie essential affecting factors in the formation of vesicle can be deduced from the obtained results. It showed that large vesicle must form naturally before sonication in 0.082 M octyltrimethylammonium bromide and sodium laurate pH = 9.2 aqueous solution. While after sonication, only small vesicle exists, which can be proved further through electron microscope.     

A density functional theory study of the Cu+·(CO)n (n = 1–3) complexes

Density functional theory calculations, with an effective core potential for the copper ion, and large polarized basis set functions have been used to construct the potential energy surface of the Cu⁺·(CO)_n (n = 1–3) complexes. A linear configuration is obtained for the global minimum of the Cu⁺·CO and Cu⁺·(CO)₂ complexes with a bond dissociation energy (BDE) of 35.9 and 40.0 kcal mol^-1, respectively. For the Cu⁺·(CO)₃ complex, a trigonal planar geometry is obtained for the global minimum with a BDE of 16.5 kcal mol^?1. C-coordinated copper ion complexes exhibit stronger binding energy than O-coordinated complexes as a result of C_lp → 4s σ-donation. The computed sequential BDEs of Cu⁺·(CO)_n (n = 1–4) complexes agree well with experimental findings, in which the electrostatic energy and σ-donation play an important role in the observed trend.     

A combined electrochemical and DFT study of the lattice strain effect on the surface reactivity of Pd

We report a combined study of electrochemical experiments and ab initio calculations on tuning the surface reactivity of Pd via a compressive lattice strain achieved by employing nanoparticles of Pd-Cu alloys with a Pd-rich surface.Surface oxygen-containing species were used as the probing molecule for revealing the surface reactivity.Both density functional theory (DFT) calculations and experiments showed linear relationships,with very close slopes,between the adsorption strength of OH_(ads) and the Pd lattice constant.Not only is this work a successful realization of controllable modulation in the surface reactivity,but it also provides valuable information for the rational design of Pd-based catalysts for fuel cell applications.     

How do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.     

A theoretical study of the copper–cysteine bond in blue copper proteins

 The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH₃)₂(SC₂H₅) (CH₃SC₂H₅)^0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order M?ller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-S_Met bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding. Received: 7 July 2000 / Accepted: 17 November 2000 / Published online: 21 March 2001     

Can the replacement of a single atom in the enzyme horseradish peroxidase convert it into a monoxygenase? A density functional study

Density functional calculations on horseradish peroxidase mutants are presented, whereby one or two of the nitrogen atoms of the axial histidine ligand have been replaced by phosphorus atoms. Our calculations show that phosphorus entices a push effect on the oxoiron group, whereas a histidine side chain withdraws electrons. As a result, we predict that a phosphorus-substituted histidine ligand will convert the active form of a peroxidase into a monoxygenase. This subsitution may be useful for the bioengineering of commercially exploitable enzymes.     

Thermodynamic behavior and stability constants of lanthanides–Schiff base complexes in mixed aqueous solvents

The stability constant of complexes of Ln³⁺ ions and butanamide-3-[(2-hydroxyphenyl methylene)amino]ethylimino N-phenyl were determined potentiometrically in 75% (v/v) dioxane?Cwater, 0.1?M (KNO₃) at different temperatures applying the Irving and Rossotti techniques. The nonlinear variation of the thermodynamic parameters (??G, ??H, and ??S) as a function of ionic potential of lanthanide elements was discussed. This behavior was explained in terms of difference in the dehydration of lighter Ln³⁺ from that of heavier ones. In different organic solvents (75% solvent?Cwater media), the stability constant values follow the order: dioxane?>?methanol?>?DMF, depending upon both the dielectric constant and the hydrogen bonding structure of the medium. The thermodynamic parameters at all complexes have been analyzed in terms of their electrostatic (el) and non-electrostatic (non) parts.     

A density functional study on magnetic exchange interaction between Mn(II) ion and nitronyl nitroxide radical in trans- and cis-metal-radical complexes

In the recent few years, transition metal complexeswith radical ligands have received much attentionaiming at a so-called metal-radical approach for novelmolecular magnet design[1]. One of the more popularfamilies is concerned in nitronyl nitroxide radica…