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The Mo/Cu-dependent CO dehydrogenase from Oligotropha carboxidovorans is an enzyme that is able to catalyze CO oxidation to CO2; moreover, it can also oxidize H2, thus eliciting a characteristic EPR signal. Interestingly, the Ag-substituted enzyme form proved unable to catalyze H2 oxidation. In the present contribution, we characterized the reactivity of the enzyme with H2 by quantum-chemical calculations. It was found that dihydrogen binding to the wild-type enzyme requires significant structural rearrangements of the active site Theoretical EPR spectra for plausible H2-bound models of the partially reduced, paramagnetic active site are also presented and compared with the experimental counterpart. Finally, density functional theory modeling shows that Ag substitution impairs H2 binding at the active site.

International audience; [FeFe] hydrogenases are H2-evolving enzymes that feature a diiron cluster in their active site (the [2Fe]H cluster). One of the iron atoms has a vacant coordination site that directly interacts with H2, thus favoring its splitting in cooperation with the secondary amine group of a neighboring, flexible azadithiolate ligand. The vacant site is also the primary target of the inhibitor O2. The [2Fe]H cluster can span various redox states. The active-ready form (Hox) attains the Fe(II)Fe(I) state. States more oxidized than Hox were shown to be inactive and/or resistant to O2. In this work, we used density functional theory to evaluate whether azadithiolate-to-iron coordination is involved in oxidative inhibition and protection against O2, a hypothesis supported by recent results on biomimetic compounds. Our study shows that Fe-N(azadithiolate) bond formation is favored for an Fe(II)Fe(II) active-site model which disregards explicit treatment of the surrounding protein matrix, in line with the case of the corresponding Fe(II)Fe(II) synthetic system. However, the study of density functional theory models with explicit inclusion of the amino acid environment around the [2Fe]H cluster indicates that the protein matrix prevents the formation of such a bond. Our results suggest that mechanisms other than the binding of the azadithiolate nitrogen protect the active site from oxygen in the so-called H ox (inact) state.

The presence of amyloid is a hallmark of Gerstmann-Straussler-Scheinker (GSS) disease, which is a prion disease caused by germ line mutations in the PRNP gene. The major component of amyloid is a fragment spanning residues from 81-82 to 144-153, part of the minimal sequence thought to play a crucial role in the conversion reaction and to sustain prion replication. We present here a molecular dynamics study on the 82-146 peptide from the human prion protein. The aim is to identify its aggregation-prone folds. The 82-146 prion sequence corresponds to a naturally occurring prion peptide able to form fibrils rich in parallel beta-sheets. A spontaneous right-handed beta-helical arrangement with 13 residues per turn can be observed in the 103-135 segment of the 82-146 peptide. The observed fold is in accordance with the evidence of a parallel beta-sheet organization in amyloid and with experiments on 82-146 discussed in the literature. To elucidate the conformational properties that trigger this peptide’s aggregation propensity, the conformational behavior of peptides of different length (106-126 and 113-120 prion segments) was also investigated. Simulation analysis has led to some interesting considerations on sequence specific flexibility and the effects of growth. Comparing peptides of different length allows the localization of the origin of the beta-helix conformational propensity in the 106-126 segment, though longer sequences appear necessary for a clear beta-helical arrangement. Structural features of the observed 82-146 beta-helical fold are compatible with the ‘‘dock and lock’’ mechanism proposed to interpret peptide aggregation kinetics.

There is evidence that Tetracyclines are potentially useful drugs to treat prion disease, the fatal neurodegenerative disease in which cellular prion proteins change in conformation to become a disease-specific species (PrPSc). Based on an in vitro anti-fibrillogenesis test, and using the peptide PrP106-126 in the presence of tetracycline and 14 derivatives, we carried out a three-dimensional quantitative structure-activity relationship (3D-QSAR) study to investigate the stereoelectronic features required for anti-fibrillogenic activity. A preliminary variable reduction technique was used to search for grid points where statistical indexes of interaction potential distributions present local maximum (or minimum) values. Variable selection genetic algorithms were then used to search for the best 3D-QSAR models. A 6-variable model showed the best predictability of the anti-fibrillogenic activity that highlighted the best tetracycline substitution patterns: hydroxyl group presence in positions 5 and 6, electrodonor substituents on the aromatic D-ring, alkylamine substituent at the amidic group in position 2 and non-epi configuration of the NMe2 group. © Springer-Verlag 2008.

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007.

Calculations on [Gd-(H 2 O) 9 ] 3+ at the restricted Hartree-Fock (RHF), density functional theory (DFT) and Moller- Plesset 2 (MP2) levels were performed using an effective core potential (ECP) including 4f electrons in the core for gadolinium. An optimized valence basis set with different contraction schemes for the metal, and the STO-3G, 3-21G, 6-31G ∗ , 6-31G ∗∗ and D95 ∗∗ basis sets for water molecules were used. Geometry optimization provided three main conformations: a minimum and two saddle points, each corresponding to a tricapped trigonal prism arrangement of the coordinated water molecules. The minimum energy conformation is of D 3 symmetry and does not correspond to any known experimental structure. The geometries of the two saddle points are of C 3 h and D 3 h symmetry, respectively, and correspond to two different crystallographic structures. At the DFT/D95 ∗∗ (RHF/D95 ∗∗ ) level these are respectively 4.95 (4.92) and 6.97 (6.26) kcal mol −1 above the global minimum. The results show that the major structural features of the coordination cage observed in the crystallographic structures are mainly due to intramolecular interactions between the coordinated water molecules. Intermolecular interactions, such as crystal packing forces and hydrogen-bond networks, should be responsible for the energy stabilization of the C 3 h and D 3 h structures in the solid state. At the RHF level, the STO-3G basis set is very sensitive to the choice of basis set on the metal center and, even in the best cases, provides unsatisfactory results. On the contrary, the 3-21G basis set provides, independently of the metal basis set, quite reliable geometries and conformational energies in qualitative agreement with those obtained using polarized basis sets. The results from the polarized basis sets themselves are consistent; further, inclusion of the electron correlation causes only a little shortening of the gadolinium-oxygen bond distances with respect to RHF and the conformational energies are substantially unaffected. These results highlight that calculations with the adopted ECP for the metal can provide reliable results in the study of gadolinium complexes also at the RHF level; further, a satisfactory representation of the potential energy surface of these systems can be obtained by 6-31G ∗ single point energy calculations on optimized 3-21G geometries.

Detailed ab initio characterization of the stereoelectronic properties of syn -blocked bithiophenes can qualitatively contribute to the rationalization of the conductivity differences observed in the related doped polymers. In particular, the inter-ring torsional angle and the electrostatic effects due to the presence of heteroatoms other than sulphur can play important roles in intra- and inter-chain electric conduction.

11 páginas, 8 figuras, 4 tablas, 3 esquemas -- PAGS nros. 21-31, Magnetic Resonance Imaging (MRI) using paramagnetic systems as contrast agents is receiving increased attention as diagnostic tool in the clinic. At the same time, NMR of paramagnetic systems can also be applied in biochemical fields; for example, the use of Paramagnetic Relaxation Enhancement (PRE) allows structure refinement and the analysis of transient dynamic processes involved in macromolecular complex formation. Herein we report the synthesis and computational characterization of a new DOTA-like sialic acid conjugate, which can be used both in MRI and PRE applications when coordinated to a suitable paramagnetic metal, We gratefully acknowledge financial supports from the University of Milano-Bicocca (FAR2008) and computational facilities from CILEA (Consorzio Interuniversitario Lomabardo per l’Elaborazione Automatica), Programma Operativo Regione Lombardia Ob. 3 Fondo Sociale Europeo 2000–2006, Sovvenzione Globale Progetto Ingenio A0001127/2007 and Consorzio Interuniversitario Nazionale ‘Metodologie e Processi Innovativi di Sintesi’ (C.I.N.M.P.I.S.).

The role of multivariate analysis methods in evaluating, rationalizing, and working out complex environmental problems is discussed. The discussion is organized in two sections; a literature analysis of the application of chemometric methods to PCDD/PCDF data interpretation and source correlation and a review of the role of chemometric methods in analysing the results obtained by the Authors studying PCDD/PCDF formation and destruction mechanisms in MSW combustion processes.

The conformational and electronic properties of 11 5-HT 3 receptor antagonists, were investigated to rationalize their biological activity. All compounds fulfill the previously reported geometrical requirements for the pharmacophore, although they show a wide spectrum of activities. Quantitative structure-activity relationships (QSAR) models were searched using the cross-validated partial least squares technique. The results of the QSAR analysis show that a unique model can rationalize both the in vitro (affinity, K d ) and the in vivo (50% inhibitory dose, ID 50 ) activities. This model includes the value of the molecular electrostatic potential minimum above the aromatic fragment, used as an index of the π-electron density, as well as the relative population of the anti-periplanar (app, the “active”) conformation. Two other models were also obtained that include electrophilic superdelocalizability indexes. Although these models give a more satisfactory value of the cross-validated correlation coefficient ( R 2 cv ), they represent two different models for K d and ID 50 which is in contrast with the experimental evidence that a correlation exists between these two activities. It is concluded that the use of electronic and conformational properties in addition to the geometrical characteristics may better describe and predict the activity of 5-HT 3 receptor antagonists, than the use of geometrical characteristics alone.

A model which makes use of the complete perturbative treatment of Salem and Devaquet is proposed for the interpretation of regio-, sito- and stereo-selectivity of cycloaddition reactions. The van der Waals intermolecular interaction potential-energy surface minima relevant to the hypothesized alternative reaction paths are suggested as model structures (perturbed states) for the corresponding weakly interacting complexes in the early stages of the reaction. It is shown how results are affected by the increase in the degrees of freedom for the approach of the two interacting molecules, by the choice of a particular atom-atom potential and by the two-partner internal-geometry relaxation which occurs at the perturbed state. The results obtained for some sample reactions (butadiene and ethylene, penta-1,3-diene and acrolein, penta-1,3 -diene and 2,5-dimethyl-1,4-benzoquinone) corroborate our previous choice of a Lennard-Jones function and of an undistorted reagent geometry to localize the non-bonding minima. The inclusion of a greater number of intermolecular variables and their simultaneous optimization during the non-bonding minima localization is a marked improvement for the definition of the perturbed state. The results obtained for the reactions of mono- and di-substituted dienes with unsymmetrically substituted quinones confirm the predictive ability of our improved procedure.

The conformational behavior of four [Ln(DOTA)(H(2)O)](-) systems (Ln = La, Gd, Ho, and Lu) has been characterized by means of ab initio calculations performed in vacuo and in aqueous solution, the latter by using the polarizable continuum model (PCM). Calculated molecular geometries and conformational energies of the [Ln(DOTA)(H(2)O)](-) systems, and interconversion mechanisms, barriers, and (13)C NMR spectra of the [Lu(DOTA)](-) complex are compared with experimental values. For each system, geometry optimizations, performed in vacuo and in solution at the HF/3-21G level and using a 46+4f(n) core electron effective core potential (ECP) for lanthanides, provide two minima corresponding to a square antiprismatic (A) and an inverted antiprismatic (IA) coordination geometry. All the systems are nonacoordinated, with the exception of the IA isomer of the Lu complex that, from in solution calculations, is octacoordinated, in agreement with experimental data. On comparing the in vacuo relative free energies calculated at different theory levels it can be seen that the nonacoordinated species dominates at the beginning of the lanthanide series while the octacoordinated one does so at the end. Furthermore, on passing along the series the IA isomer becomes less and less favored with respect to A and for the Lu complex a stabilization of the IAisomer is observed in solution (but not in vacuo), in agreement with the experimental data. Investigation of the A--IA isomerization process in the [Lu(DOTA)](-) system provides two different interconversion mechanisms: a single-step process, involving the simultaneous rotation of the acetate arms, and a multistep path, involving the inversion of the cyclen cycle configuration. While in vacuo the energy barrier for the acetate arm rotation is higher than that involved in the ring inversion (23.1 and 13.1 kcal mol(-)(1) at the B3LYP/6-311G level, respectively), in solution the two mechanisms present comparable barriers (14.7 and 13.5 kcal mol(-)(1)), in fairly good agreement with the experimental values. The NMR shielding constants for the two isomers of the [Lu(DOTA)](-) complex have been calculated by means of the ab initio GIAO and CSGT methods, and using a 46-core-electron ECP for Lu. The calculated (13)C NMR chemical shifts are in close agreement with the experimental values (rms 3.3 ppm, at the HF/6-311G level) and confirm the structural assignment of the two isomers based on experimental NMR spectra in solution. The results demonstrate that our computational approach is able to predict several physicochemical properties of lanthanide complexes, allowing a better characterization of this class of compounds for their application as contrast agents in medical magnetic resonance imaging (MRI).

BF3-OEt2 mediated thioester silylketene acetal additions to aldehydes are stereoconvergent and give high anti-syn ratios and good chemical yields. An acyclic transition state model was hypothesized in order to account for the observed selectivity. Theoretical methods (MNDO) were used to evaluate the ground-state conformations of thioester silylketene acetals and to model the acyclic transition states. Lewis acid mediated additions of thioester silylketene acetals to 2-phenylpropion-aldehyde (BF3-OEt2), O-benzyl lactic aldehyde (SnCl4), 2,3-0,O-dibenzyl glyceraldehyde (SnCl4), and 3-benzyloxy-2-methylpropionaldehyde (TiCl4) were found to be highly diastereoface selective so that three contiguous stereocenters could be established. With α-, β- , or α,β-alkoxy aldehydes, relative stereoselection (chelation) effectively controls internal stereolection. The ground state conformations of the chiral aldehydes were studied using molecular mechanics (MM2).

The most stable conformations of four pyrrolidin-2-one derivatives, biologically active compounds, have been determined using the molecular mechanics method with different parametrizations and the quantum mechanical semiempirical AM1 method; the minima of the four potential energy hypersurfaces thus obtained were verified by SCF ab-initio calculations at the 3–21G level. Results indicate that the different methods single out minimum energy conformations characterized by similar geometries with the exception of the AM1 method which predicts a planar ring geometry instead of an envelope one. The geometries of the absolute minimum conformations are confirmed at the ab-initio level, while the relative minima, which generally have rather elevated relative energies (even larger then 4 kcal mol−1) and modest rotational interconversion barriers (< 0.5 kcal mol−1), are not confirmed.

The dipole moment, molar Kerr constant (in CCl 4 ) and electronic absorption spectrum (in n-hexane) of 2-carbomethoxy-1,4-benzoquinone have been measured at 25°C. MNDO calculations indicate that the preferred gas-phase conformation has the carbomethoxy group nearly perpendicular to the plane of the benzoquinone skeleton. The theoretical molar Kerr constant and that of the parent 1,4-benzoquinone, have been evaluated by a new method which incorporates the exaltation of polarizability in the bond polarizabilities. The preferred conformation of 2-carbomethoxy-1,4-benzoquinone in solution, as deduced from the experimental and calculated dipole moments and the molar Kerr constant, is consistent with the theoretical prediction. The theoretical interpretation of the electronic spectrum using the CNDO/CI calculation is in line with the configurational and conformational results obtained by the preceding analysis. Calculated values of the first ionization potential and electronic affinity are also reported.

The dipole moment, molar Kerr constant and electronic spectra of 1-vinylcyclohexene were measured at 25°C. Using the molecular mechanics method, modified for diene systems, the equilibrium geometries of the possible conformers have been determined. It is found that the half-chair form is always more stable than the corresponding boat form. Ab initio SCF calculations using the STO-3G basis set and the force field geometries have been performed on the rotamers of the half-chair vinylcyclohexene to estimate the relative energies. The potential energy curve obtained for vinyl group rotation reveals s- trans (absolute minimum) and nearly s- cis minima, 0.53 kcal mol −1 apart, with a barrier of 2.5 kcal mol −1 from s- trans to s- cis . The model system cyclohexene is used to test the applicability of the previously proposed “variable bond polarizabilities” approach to the calculation of the molar Kerr constant: the estimated value is in excellent agreement with experiment. The preferred solution-state conformation of 1-vinylcyclohexene indicated by the analysis of experimental and calculated dipole moment, molar Kerr constant and electronic spectra is shown to be consistent with the theoretical predictions: the s- trans form seems to be preferred but the presence of a 20–30% population of s- cis or nearly s- cis rotamers cannot be ruled out. An estimate of the first ionization potential is also given.