Density functional theory investigation of the active site of Fe-hydrogenases. systematic study of the effects of redox state and ligands hardness on structural and electronic properties of complexes related to the [2Fe](H) subcluster

Density functional theory has been used to investigate complexes related to the [2Fe](H) subcluster of [Fe]-hydrogenases. In particular, the effects on structural and electronic properties of redox state and ligands with different sigma-donor pi-acceptor character, which replace the cysteine residue coordinated to the [2Fe](H) subcluster in the enzyme, have been investigated. Results show that the structural and electronic properties of fully reduced Fe(I)Fe(I) complexes are strongly affected by the nature of the ligand L, and in particular, a progressive rotation of the Fe(d)(CO)(2)(CN) group, with a CO ligand moving from a terminal to a semibridged position, is observed going from the softest to the hardest ligand. For the partially oxidized Fe(I)Fe(II) complexes, two isomers of similar stability, characterized either by a CO ligand in a terminal or bridged position, have been observed. The switching between the two forms is associated with a spin and charge transfer between the two iron atoms, a feature that could be relevant in the catalytic mechanism of dihydrogen activation. The structure of the fully oxidized Fe(II)Fe(II) models is extremely dependent on the nature of the L ligand; one CO group coordinated to Fe(d) switches from terminal to bridging position going from complexes characterized by neutral to anionic L ligands.     

Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR

Summary An example of a CoMFA study is described with the aim to discuss one of the major problems of this 3D QSAR method: lack of variable selection. It is shown that the use of nonrelevant energy parameters might produce CoMFA contour maps which poorly reflect the actual nature of the binding site and are in part statistical artefacts. The data set employed in our analysis comparises triazine inhibitors of dihydrofolate reductase (DHFR), isolated from chicken liver, which have already been the object of a QSAR study by other authors. Since three-dimensional structures of triazine-DHFR complexes are known, it was possible not only to reduce ambiguities in the superimposition of the ligands, but also to compare the resulting CoMFA contour maps with the enzyme active site.Supplementary material available: The Cartesian coordinates and the atomic charges of the PM3-optimized structures used in the CoMFA study are available as MOL2 files upon request.To whose memory this paper is dedicated.     

Multireference perturbation CI I. Extrapolation procedures with CAS or selected zero-order spaces

We discuss the “three class” approximation to full multireference perturbation CI, which greatly reduces the computational effort by restricting the summation of diagrams to determinants belonging to a subspace of the zero-order space. In the framework of the CIPSI algorithm, we propose a new extrapolation procedure allowing recovery of the full “two class” results. The new procedure is applied to complete active spaces (CAS) and to individually selected zero-order spaces. Comparison with a full two class calculation on a CAS shows a reduction of computer time of one or two orders of magnitude in the tests presented here, with an accuracy in the order of 0.1 kcal/mol. Our procedure can thus compete with the CASPT2 algorithm, specifically conceived to deal with CAS. In the case of selected zero-order spaces, the speed-up is less dramatic but the method still retains its advantages. Received: 12 June 1997 / Accepted: 31 July 1997     

A Theoretical Study of Amine Bonding in Titanium Alkoxide Adducts

Summary. DFT calculations were carried out on Ti₂(OCH₃)₈ (NH₂CH₃)₂ and Ti₂(OCH₃)₈(NH₃)₂, which are model compounds for the previously isolated amine adducts Ti₂(OR)₈(NH₂ R′)₂. The calculations show that the Ti–N bond strength is weak; however, coordination of the amine to the metal center is supported by a N–H···O hydrogen bond of the amine with the neighboring alkoxo ligand. The Ti–N interaction is purely σ in nature, while the Ti–O interactions include both σ and π contributions. The lowest unoccupied molecular orbitals are mainly localized on Ti t_2g-like orbitals.     

Unprecedented eta(1)-P(basal) coordination of P(4)X(3) molecules (X = S, Se). An experimental and theoretical study of the apical vs basal complexation dichotomy

Reaction of [(triphos)Re(CO)(2)(OTf)] (1) [triphos = MeC(CH(2)PPh(2))(3); OTf = OSO(2)CF(3)] with P(4)S(3) and P(4)Se(3) yields pairs of coordination isomers, namely, [(triphos)Re(CO)(2)[eta(1)-P(apical)-P(4)X(3)]](+) (X = S, 2; Se, 5) and [(triphos)Re(CO)(2)[eta(1)-P(basal)-P(4)X(3)]](+) (X = S, 3; Se, 6). The latter represent the first examples of the eta(1)-P(basal) coordination achieved by the P(4)X(3) molecular cage. Further reaction of 2/3 and 5/6 mixtures with 1 affords the dinuclear species [[(triphos)Re(CO)(2)](2)[mu,eta(1:1)-P(apical,)P(basal)-P(4)X(3)]](2+) (X = S, 4; Se, 7) in which the unprecedented M-eta(1)-P(basal)/eta(1)-P(apical)-M' bridging coordination of the P(4)X(3) molecule is accomplished. A theoretical analysis of the bonding properties of the two coordination isomers is also presented. The directionality of apical vs basal phosphorus lone pairs is also discussed in terms of MO arguments.     

Binding and condensation of plasmid DNA onto functionalized carbon nanotubes: toward the construction of nanotube-based gene delivery vectors

Carbon nanotubes (CNTs) constitute a class of nanomaterials that possess characteristics suitable for a variety of possible applications. Their compatibility with aqueous environments has been made possible by the chemical functionalization of their surface, allowing for exploration of their interactions with biological components including mammalian cells. Functionalized CNTs (f-CNTs) are being intensively explored in advanced biotechnological applications ranging from molecular biosensors to cellular growth substrates. We have been exploring the potential of f-CNTs as delivery vehicles of biologically active molecules in view of possible biomedical applications, including vaccination and gene delivery. Recently we reported the capability of ammonium-functionalized single-walled CNTs to penetrate human and murine cells and facilitate the delivery of plasmid DNA leading to expression of marker genes. To optimize f-CNTs as gene delivery vehicles, it is essential to characterize their interactions with DNA. In the present report, we study the interactions of three types of f-CNTs, ammonium-functionalized single-walled and multiwalled carbon nanotubes (SWNT-NH3+; MWNT-NH3+), and lysine-functionalized single-walled carbon nanotubes (SWNT-Lys-NH3+), with plasmid DNA. Nanotube-DNA complexes were analyzed by scanning electron microscopy, surface plasmon resonance, PicoGreen dye exclusion, and agarose gel shift assay. The results indicate that all three types of cationic carbon nanotubes are able to condense DNA to varying degrees, indicating that both nanotube surface area and charge density are critical parameters that determine the interaction and electrostatic complex formation between f-CNTs with DNA. All three different f-CNT types in this study exhibited upregulation of marker gene expression over naked DNA using a mammalian (human) cell line. Differences in the levels of gene expression were correlated with the structural and biophysical data obtained for the f-CNT:DNA complexes to suggest that large surface area leading to very efficient DNA condensation is not necessary for effective gene transfer. However, it will require further investigation to determine whether the degree of binding and tight association between DNA and nanotubes is a desirable trait to increase gene expression efficiency in vitro or in vivo. This study constitutes the first thorough investigation into the physicochemical interactions between cationic functionalized carbon nanotubes and DNA toward construction of carbon nanotube-based gene transfer vector systems.     

Metal-induced assembling/disassembling of fluorescent naphthalenediimide derivatives signalled by excimer emission

The new quadridentate bischelating ligands 2 and 3 display in solution the typical absorption and emission properties expected for naphthalenediimide derivatives. Spectrophotometric studies show that systems 2 and 3 interact with Zn(II), Cd(II) and Cu(I) in CHCl3 or MeCN according to an apparent 1:1 stoichiometry. Molecular modelling, ESI-MS and 1H NMR experiments indicate that the complex species formed in the presence of stoichiometric amounts of metal ion are nonhelical [2 + 2] adducts. The metal-induced self-assembling process is signalled by an intense excimer-type emission caused by the intramolecular interaction of two naphthalenediimide subunits that face each other in the [2 + 2] adduct, as shown by molecular modelling studies. In the presence of excess metal ion, a disassembling process takes place, leading to a dinuclear complex with a 2:1 metal/ligand stoichiometry, in which the intramolecular excimer is no longer allowed to form because the interaction between the naphthalenediimide subunits has been lost. Thus, the overall metal-induced assembling/disassembling process is signalled by the appearance and disappearance of the excimer band in the emission spectrum.     

Allopurinol and its interactions with Cu<Superscript>2+</Superscript> ions: radical reactions and complex structure

Allopurinol (ALP), an inhibitor of the xanthine oxidase enzime, is reported to provide protection against free-radical mediated damage by various mechanisms, including free-radical scavenging and metal chelation (i.e. Cu(II)). To obtain a wider insight into the molecular aspects of the beneficial action of ALP, free ALP and the Cu(II)- ALP system were investigated by radiation chemical and spectroscopic studies. Pulse radiolysis experiments show that ALP is a good · OH scavenger (1.8 × 10⁹ and 5.4 × 10⁹ M^-1 s^-1 at pH 6.0 and 11.0, respectively), leading to · OH-adducts and transient semi-oxidized species, such as phenoxyl radicals. The latter are also formed by the reaction of ALP with some specific one-electron oxidizing radicals (i.e. N₃ and SO₄ ^-). The semi-oxidized species are stabilized by their resonance properties and scarcely react with oxygen. In addition, the chelation of Cu(II) by ALP does not significantly affect the reactivity of the drug towards ·OH (2.5×0⁹ M^-1 s^-1). Raman and the IR spectra support the good chelating ability of ALP, indicating the formation of two Cu(II)- ALP complexes with a slightly different structure. Depending on the metal/ligand ratio, pyrimidine nitrogens may take part to the Cu(II) co-ordination in addition to the N pyrazolic atoms and the C O groups of some ALP molecules. These results suggest that ALP may inhibit oxidative damage both through the direct radical scavenging and the copper-chelation mechanism. In fact, both the conversion of a harmful radical, such as ·OH, into a less reactive transient species, and the capture of copper ions, which play a relevant role in metal-catalysed generation of reactive oxygen species, will prove beneficial for the cell protection.     

On the direct calculation of the time evolution of excited molecular states in the presence of nonadiabatic interactions

The possibility is explored of calculating the time evolution of a given initial molecular state, in the presence of sufficiently strong nonadiabatic interactions, with a fully quantum-mechanical approach. Two methods are presented. The first one is based on the determination of the molecular eigenstates, with expansion of the nuclear wavefunctions on a Hermite basis. The second method is based on the Padé 1,1 approximation of the time evolution operator and on a finite difference representation of the time-dependent nuclear wavefunctions. Both methods are applied to simple models of a diatomic molecule.     

Standard pH values for potassium hydrogenphthalate reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water mixed solvents at temperatures from 288.15 to 318.15 K

Standard pH(S) values for 0.05 mol kg^?1 potassium hydrogenphthalate (KHpH) reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water solvent mixtures within the temperature range 288.15–318.15 K are determined from e.m.f. measurements of the cell without transference Pt|H₂|KHPh + KCl|AgCl|Ag|Pt. The consistency of the results is analysed by a recently described method of multilinear regression of the quantity p(a_Hγ_Cl) as a function of both solution composition and temperature. The standard pH(S) determined can be reproduced to within ±0.01 by the equation pH(S) - 4.004 + 3.309w + 0.408z + 1.037w³ - 14.95zw² + 27.1zw³, where w is the weight fraction of dioxane in the solvent mixture,z = (T –θ)/θ, and θ - 298.15 K. Values of the first ionization constant of phthalic acid (H₂Ph; benzene-1,2-dicarboxylic acid) in the above solvent mixtures are also determined from e.m.f. measurements of the cell without transference Pt|H₂|H₂Ph + KHPh + KCl|AgCl|Ag|Pt.