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Tailoring the activity of an organometallic catalyst usually requires a targeted ligand design. Tuning the ligand bulkiness and tuning the electronic properties are popular approaches, which are somehow interdependent because substituents of different sizes within ligands can determine inter alia the occurrence of different degrees of inductive effects. Ligand basicity, in particular, turned out to be a key property for the modulation of protonation reactions occurring in vacuo at the metals in complexes bearing organophosphorus ligands; however, when the same reactions take place in a polar organic solvent, their energetics becomes dependent on the trade-off between ligand basicity and bulkiness, with the polarity of the solvent playing a key role in this regard [Bancroft et al., Inorg. Chem., 1986, 25, 3675; Rovaletti et al., J. Phys. Org. Chem., 2018, 31, e3748]. In the present contribution, we carried out molecular dynamics and density functional theory calculations on water-soluble Mo-based catalysts for proton reduction, in order to study the energetics of protonation reactions in complexes where the incipient proton binds a catalytically active ligand (i.e., an oxide or a disulphide). We considered complexes either soaked in water or in a vacuum, and featuring N-based ancillary ligands of different bulkiness (i.e. cages constituted either by pyridine or isoquinoline moieties). Our results show that the energetics of protonation events can be affected by ancillary ligand bulkiness even when the metal center does not play the role of the H+ acceptor. In vacuo, protonation at the O or S atom in the α position relative to the metal in complexes featuring the bulky isoquinoline-based ligand is more favored by around 10 kcal mol−1 when compared to the case of the pyridine-based counterparts, a difference that is almost zero when the same reactions occur in water. Such an outcome is rationalized in light of the different electrostatic properties of complexes bearing ancillary ligands of different sizes. The overall picture from theory indicates that such effects of ligand bulkiness can be relevant for the design of green chemistry catalysts that undergo protonation steps in water solutions.

The Suzuki-Miyaura reaction between the aryl halide (1) and the phenyl boronic acid (2), in the presence of the palladium(0) complex (3) as catalyst, gives the cross-coupling product (4) in quantitative yield when performed in basic aqueous solution of the nonionic surfactant Kolliphor-EL (K-EL). The partition between the aqueous and micellar environments of the species of this reaction has been investigated by means of Molecular Dynamics (MD) simulations. Starting from the K-EL molecules dispersed in water, a micelle model has been generated by MD simulations, adopting the 2016H66 force field. Reagent and product species have been described with the same force field, once the reliability of this force field has been tested comparing the n-octanol/water partition free energies calculated from the MD and Free Energy Perturbation (FEP) method with those obtained from the quantum-mechanical SMD method. The potential of mean force for the transfer process between water and the micellar phase of the different species has been calculated by the MD simulations and the Umbrella Sampling (US) method. The overall picture that emerges from these results confirms that the molecular species involved in this reaction prefers the micellar environment and concentrates in different but close zones of the micelle. This supports the experimental evidence that the use of suitable surfactant agents promotes reactivity, allowing micelles to behave as nanoreactors in which reactive species are solubilized and enhance their local concentration.

The photogeneration of electricity and solar fuels by solar irradiation in photoelectrochemical cells is one of the sectors with the highest growth potential in the decarbonised society. However, the use of different components, in particular photosensitizers and catalysts, can present problems of charge transfer efficiency at the interface, leading to lower final efficiencies. In this work we present novel integrated photosensitizer-catalyst dyads based on robust and, at the same time, flexible host-guest non-covalent interactions through the use of calix[4]arene cavities. Current photogeneration in photoelectrochemical cells showed twice greater efficiency in the integrated calixarene-based host-guest dyads compared to the traditional architecture based on the separate photosensitizer-catalyst pair. Molecular dynamics studies have shown that the enhanced performance originates from an optimization of the distances between the centres of the photosensitizer, catalyst and semiconductor involved in the charge transfer processes, thus allowing a higher final efficiency of the charge photogeneration process.

The aerobic CO dehydrogenase from Oligotropha carboxidovorans is an environmentally crucial bacterial enzyme for maintenance of subtoxic concentration of CO in the lower atmosphere, as it allows for the oxidation of CO to CO2 which takes place at its Mo−Cu heterobimetallic active site. Despite extensive experimental and theoretical efforts, significant uncertainties still concern the reaction mechanism for the CO oxidation. In this work, we used the hybrid quantum mechanical/molecular mechanical approach to evaluate whether a water molecule present in the active site might act as a nucleophile upon formation of the new C−O bond, a hypothesis recently suggested in the literature. Our study shows that activation of H2O can be favoured by the presence of the Mo=Oeq group. However, overall our results suggest that mechanisms other than the nucleophilic attack by Mo=Oeq to the activated carbon of the CO substrate are not likely to constitute reactive channels for the oxidation of CO by the enzyme.

Some microorganisms, like the aerobic soil bacteria, Oligotropha carboxidovorans, have the capability to oxidize the highly toxic atmospheric gas carbon monoxide (CO) into CO2 through CO dehydrogenase enzymes, whose active site contains a bimetallic MoCu center. Over the last decades, a number of experimental and theoretical investigations were devoted to understanding the mechanism of CO oxidation and, in particular, the role of a very stable thiocarbonate intermediate that may be formed during the catalytic cycle. The occurrence of such an intermediate was reported to make the CO2 release step kinetically difficult. In this work, by using an accurate QM/MM approach and energy refinement by means of the BigQM method, we were able to determine the role of such an intermediate and propose a novel mechanism for the oxidation of CO into CO2 by Mo/Cu CO dehydrogenase. Surprisingly, we found that the detachment of CO2 occurs directly from the product of the Mo=O nucleophilic attack reaction on the carbon of CO aided by the transient coordination of the active site glutamate to the Mo ion. The estimated activation barrier is in good agreement with the experimental one, while the thiocarbonate turned out to not interfere with the CO-oxidation catalytic cycle. The results highlight the importance of the environmental effects in the assembly of the molecular model and in the choice of the computational protocol. Our accurate modeling of the enzyme also allowed us to exclude the involvement of a frustrated Lewis pair in the CO-oxidation mechanism, which has recently been suggested based on an analysis of structural and electronic features of synthetic mimics of the Mo/Cu CO dehydrogenase active site.

Intrinsically Disordered Peptides and Proteins (IDPs) in solution can span a broad range of conformations that often are hard to characterize by both experimental and computational methods. However, obtaining a significant representation of the conformational space is important to understand mechanisms underlying protein functions such as partner recognition. In this work, we investigated the behavior of the Sic1 Kinase-Inhibitor Domain (KID) in solution by Molecular Dynamics (MD) simulations. Our results point out that application of common descriptors of molecular shape such as Solvent Accessible Surface (SAS) area can lead to misleading outcomes. Instead, more appropriate molecular descriptors can be used to define 3D structures. In particular, we exploited Weighted Holistic Invariant Molecular (WHIM) descriptors to get a coarse-grained but accurate definition of the variegated Sic1 KID conformational ensemble. We found that Sic1 is able to form a variable amount of folded structures even in absence of partners. Among them, there were some conformations very close to the structure that Sic1 is supposed to assume in the binding with its physiological complexes. Therefore, our results support the hypothesis that this protein relies on the conformational selection mechanism to recognize the correct molecular partners.

The Mo/Cu-dependent CO dehydrogenase from O. carboxydovorans is an enzyme that is able to catalyse CO oxidation to CO 2, moreover, it also expresses hydrogenase activity, as it is able to oxidize H 2 . Here, we have studied the dihydrogen oxidation catalysis by this enzyme using QM/MM calculations. Our results indicate that the equatorial oxo ligand of Mo is the best suited base for catalysis. Moreover, extraction of the first proton from H 2 by means of this basic centre leads to the formation of a Mo&ndash, OH&ndash, Cu I H hydride that allows for the stabilization of the copper hydride, otherwise known to be very unstable. In light of our results, two mechanisms for the hydrogenase activity of the enzyme are proposed. The first reactive channel depends on protonation of the sulphur atom of a Cu-bound cysteine residues, which appears to favour the binding and activation of the substrate. The second reactive channel involves a frustrated Lewis pair, formed by the equatorial oxo group bound to Mo and by the copper centre. In this case, no binding of the hydrogen molecule to the Cu center is observed but once H 2 enters into the active site, it can be split following a low-energy path.

Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which-differently from other enzyme classes with similar function-retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.

The chemical groups present at the surface of graphite have been thought for a long time to be mainly responsible for its catalytic activity in the oxygen reduction reaction. Recently, it was proposed that the surface defects of graphite also significantly contribute to promote this reaction. Although the behaviour of surface defects has been reported, only few comments have been dedicated to their involvement in the mechanism and the possible intermediate species in the oxygen reduction reaction. Herein, we aim to present a more detailed explanation of the catalytic activity of graphite particles based on the structure of their defects and their size. Structural, spectroscopic and magnetic investigation (X-ray diffraction, Raman and electron spin resonance) and electrochemical measurements were performed to describe the nature of the defects and their aptitude to transfer electrons. Computational description supplied precise details of the energy of the different defects and their ability to promote the reduction, also suggesting the structure of the intermediate adduct in the oxygen reduction. The results indicated that molecular oxygen preferentially interacts with graphite defects, which involve the π-electron system and accumulation of the spin density on the edges of the grains, in particular, on the zig-zag edges present on ball-milled graphite. This promotes the reactivity of this nanomaterial. Furthermore, the activation increases by decreasing the particle size.

We present a theoretical investigation providing key insights on a long-standing controversial issue that dominated the debate on carbon monoxide oxidation by Mo–Cu CO-dehydrogenases. Previous investigations gravitate around the possible occurrence of a thiocarbonate intermediate, that was repeatedly reported to behave as a thermodynamic sink on the catalytic energy landscape. By using a hierarchy of quantum mechanical and hybrid quantum/classical models of the enzyme, we show that no such energy sink is present on the catalytic energy profile. Consequent perspectives for the definition of a novel mechanistic proposal for the enzyme-catalyzed CO-oxidation are discussed in light of the recent literature.

The adiabatic transition energies from the lowest triplet states of four Europium tris β-diketonate/phenantroline complexes have been determined in vacuo and in dicholomethane solution by the ΔSCF approach at the density functional theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals. The calculated adiabatic transition energies have been compared with the experimental 0-0 transitions of each complex determined from phosphorescence spectra of the corresponding Gd3+ complexes and followed by direct comparison between simulated and experimental spectra line shapes.For compound 1, the Eu(TTA)3Phen system, triplet states other than the lowest one and conformational isomers other than the one present in the crystallographic structure have been considered. In the crystallographic structure, this compound presents three quasi-degenerate low energy triplet states, differing for the TTA ligand where the two unpaired electrons are localized and showing close adiabatic transition energies. For compound 1, the lowest triplet states of the four investigated conformational isomers show similar characteristics and close adiabatic transition energies. On the basis of these results, an investigation of compounds 2-4 (Eu(Br-TTA)3Phen, Eu(DTDK)3Phen, and Eu(MeT-TTA)3) has been performed by considering only the isomer present in the crystallographic structure and only the lowest triplet state of each compound. For compounds 1-3, the energies of the lowest triplet states calculated by both functionals in solution including zero-point energy corrections well reproduce the experimental trends as well as the values of the adiabatic transition energies: CAM-B3LYP, the best performing functional, provides energies of the lowest triplet state with deviations from experiments lower than 1200 cm-1. Also, the calculated vibrationally resolved phosphorescence spectra and UV-vis absorptions well reproduce the main features of their experimental counterparts. Significant differences between calculated and experimental results are observed for compound 4, for which difficulties in the experimental determination of the triplet state energy were encountered: our results show that the negligible photoluminescence quantum yield of this compound is due to the fact that the energy of the most stable triplet state is significantly lower than that of the resonance level of the Europium ion, and thus the energy transfer process is prevented.These results confirm the reliability of the adopted computational approach in calculating the energy of the lowest triplet state energy of these systems, a key parameter in the design of new ligands for lanthanide complexes presenting large photoluminescence quantum yields. © 2013 American Chemical Society.

DFT calculations were used to investigate the cycloaddition reaction of CO2 to styrene oxide for the formation of styrene carbonate. The uncatalyzed process alongside the reactions assisted by tetrabutylammonium bromide (TBAB), the novel nonsymmetrical single-center aluminum(III) salen-acac hybrid complex (salenac) (Al1cat) and the binary Al1cat/TBAB system were all investigated and for all of them the optimized structures, rate-determining steps, and lowest energy barrier reaction pathways were intercepted for both gas-phase and solvent environments. For the catalyzed systems, the reaction mechanism consists of three key elementary steps: 1) epoxy ring opening; 2) CO2 electrophilic attack and 3) intramolecular cyclization. In the presence of Al1cat, the central metal of the catalyst coordinates with an oxygen atom of the epoxide, activating it towards a nucleophilic attack by the halide. An oxyanion species is formed that affords the corresponding cyclic carbonate after reaction with CO2. Our results provide important hints on the cycloaddition of CO2 and epoxides promoted by nonsymmetrical aluminum complex containing a single metal center, and can satisfactorily explain the previous experimental observations allowing the development of more efficient catalysts for organic carbonate production.

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.

Environmentally persistent free radicals (EPFRs) are toxic products deriving from incomplete combustion and are able to generate DNA damage and pulmonary dysfunction. They are formed on particulate matter through interaction with aromatic hydrocarbons, catalyzed by transition metal oxides, and produce reactive oxygen species (ROS) in aquatic media. The processes are already described for substituted aromatic molecules, for example, phenol, but not for unsubstituted aromatic systems, such as benzene. This Article reports on the reaction of benzene with molecular oxygen in the presence of CuxO/SiO2, suggesting a mechanism based on cluster and periodic computational models. The activation of O2 by interaction with silica coordinated Cu(I) centers leads to a peroxy species that yields the phenoxy radical upon reaction with benzene. Dissociation of OH• radical eventually allows for the recovery of the catalyst. The experimental characterization of the CuxO/SiO2 catalyst regarded morphology, crystal structure, copper electronic state, and crystal field around Cu(II). Electron paramagnetic resonance (EPR) spectroscopy revealed the formation of phenoxy radical entrapped in the catalyst upon reaction between benzene and CuxO/SiO2. Moreover, EPR investigation of ROS in aqueous solution evidenced the generation of OH• radicals by benzene-contacted CuxO/SiO2. All of the experimental results nicely fit the outcomes of the computational models.

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.

Ad hoc quantum chemical modeling of the acetyl-CoA synthase local structure and folding allowed us to identify an unprecedented coordination mode of histidine sidechain to protein-embedded metal ions. This journal is

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.

Extensive molecular dynamic simulations (similar to 240 ns) have been used to investigate the conformational behavior of PrP106-126 prion peptide in four different environments (water, dimethyl sulfoxide, hexane, and trifluoroethanol) and under both neutral and acidic conditions. The conformational polymorphism of PrP106-126 in solution observed in the simulations supports the role of this fragment in the structural transition of the native to the abnormal form of prion protein in response to changes in the local environmental conditions. The peptide in solution is primarily unstructured. The simulations show an increased presence of helical structure in an apolar solvent, in agreement with the results from circular dichroism spectroscopy. In water solution, beta-sheet elements were observed between residues 108-112 and either residues 115-121 or 121-126. An alpha-beta transition was observed under neutral conditions. In DMSO, the peptide adopted an extended conformation, in agreement with nuclear magnetic resonance experiments.

Needle biopsy samples were taken from vastus lateralis muscle (VL) of five male body builders (BB, age 27.4 ± 0.93 years; mean ±s.e.m.), who had being performing hypertrophic heavy resistance exercise (HHRE) for at least 2 years, and from five male active, but untrained control subjects (CTRL, age 29.9 ± 2.01 years). The following determinations were performed: anatomical cross-sectional area and volume of the quadriceps and VL muscles in vivo by magnetic resonance imaging (MRI); myosin heavy chain isoform (MHC) distribution of the whole biopsy samples by SDS-PAGE; cross-sectional area (CSA), force (Po), specific force (Po/CSA) and maximum shortening velocity (Vo) of a large population (n= 524) of single skinned muscle fibres classified on the basis of MHC isoform composition by SDS-PAGE; actin sliding velocity (Vf) on pure myosin isoforms by in vitro motility assays. In BB a preferential hypertrophy of fast and especially type 2X fibres was observed. The very large hypertrophy of VL in vivo could not be fully accounted for by single muscle fibre hypertrophy. CSA of VL in vivo was, in fact, 54% larger in BB than in CTRL, whereas mean fibre area was only 14% larger in BB than in CTRL. MHC isoform distribution was shifted towards 2X fibres in BB. Po/CSA was significantly lower in type 1 fibres from BB than in type 1 fibres from CTRL whereas both type 2A and type 2X fibres were significantly stronger in BB than in CTRL. Vo of type 1 fibres and Vf of myosin 1 were significantly lower in BB than in CTRL, whereas no difference was observed among fast fibres and myosin 2A. The findings indicate that skeletal muscle of BB was markedly adapted to HHRE through extreme hypertrophy, a shift towards the stronger and more powerful fibre types and an increase in specific force of muscle fibres. Such adaptations could not be fully accounted for by well known mechanisms of muscle plasticity, i.e. by the hypertrophy of single muscle fibre (quantitative mechanism) and by a regulation of contractile properties of muscle fibres based on MHC isoform content (qualitative mechanism). Two BB subjects took anabolic steroids and three BB subjects did not. The former BB differed from the latter BB mostly for the size of their muscles and muscle fibres.

Molecular dynamics simulations of a variety of polymeric systems provide the evidence for two different kinds of conformational transitions: independent single bond transitions and cranklike transitions (or correlated bond transitions). While single bond transitions can be rationalized according to standard theories of activated processes controlled by the saddle point crossing, a more complex description is required for the other type of transitions. In a recent work devoted to the analysis of the simplified chain model with three rotors [B. Nigro and G. J. Moro, J. Phys. Chem. B 106, 7365 (2002)], a theory has been proposed for cranklike transitions represented as a kinetic process between equilibrium states differing by two torsional angles (i.e., two bond transitions). Moreover their rate coefficients were estimated on the basis of a local expansion about the bifurcation of the separatrices departing from the potential function maximum. In the present work the same theory is applied to a model for long alkyl chains in solution, in order to rationalize the behavior of cranklike transitions in polyethylene and to recognize the molecular features controlling them. We obtain probabilities of occurrence of cranklike transitions in substantial agreement with simulation results. Furthermore, the theory is capable of explaining the dependence of the rate on the separation between the two reactive bonds, as well as the dependence on the conformational state of the starting configuration. In particular, selection rules for next-to-nearest neighbor transitions are recovered from the shape of the separatrices and the location of the corresponding bifurcations.

The conformational behavior in aqueous solution of four complexes of the Eu(III) ion with bis (R-amide) derivatives (R = H, methyl, ethyl, butyl) of diethylentriamine pentacetate ligands has been characterized at the ab initio level to rationalize the experimentally observed influence of alkyl substituents on the rate of the exchange process of the water molecule coordinated to the ion with the bulk water. Calculations were performed in vacuo and for aqueous solution, the latter by using the polarizable continuum model. Geometry optimizations provide, for each system, four isomers as stable conformations, all presenting a distorted tricapped trigonal prism coordination geometry around the ion. No significant influence of the alkyl substitution on the coordination geometry, nor on the europium-water distance, was observed. Moreover, increasing the length of the alkyl chain had no significant effect on the relative isomer population in solution. Thus, these results lead us to suppose that other effects, like those deriving from lateral chain folding in solution, should be considered to explain the increased rate of the water-exchange process with alkyl chain lengthening. © Springer-Verlag 2003.

Transverse nuclear spin relaxation experiments, employing the Carr-Purcell-Meiboom-Gill (CP) sequence, are analyzed under slow-motional conditions for deuterated probes experiencing order director fluctuations in nematic phases. The pulse-spacing dependent transverse relaxation rate is expressed as a function of all the viscoelastic parameters of the liquid crystal. The theory describes the effects of the anisotropy of the viscoelastic parameters on the dispersion profile beyond the commonly applied one-constant approximation.

The orientational order parameters of four aromatic solutes in nematic solvents, derived from proton dipolar couplings in NMR spectra, show a correlation with the dielectric anisotropy of the solvents. Explanation of the experimental behaviour is provided by a molecular theory based on the reaction field approximation.

It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H-2, O-2, and N-2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

Dendritic cells (DCs) are strong activators of primary T cell responses. Their priming ability is acquired upon encounter with maturation stimuli. To identify the genes that are differentially expressed upon maturation induced by exposure to Gram-negative bacteria, a kinetic study of DC gene expression was done with microarrays representing 11,000 genes and ESTs (expressed sequence tags). Approximately 3000 differentially expressed transcripts were identified. We found that functional interleukin 2 (IL-2) mRNA, which gave rise to IL-2 production, was transiently up. regulated at early time-points after bacterial encounter. In contrast, macrophages did not produce IL-2 upon bacterial stimulation. Thus, IL-2 is an additional key cytokine that confers unique T cell stimulatory capacity to DCs.

A new methodology for 3D-QSAR studies, based on the combined use of global and local approaches, is proposed. Information on the whole molecular electrostatic potential distribution is obtained from a global approach and used to build global models, based on the grid weighted holistic invariant molecular (G-WHIM) descriptors, as well as to define an alignment criterion for developing local models. Moreover, a new technique based on local correlation indexes is proposed to perform the variable reduction. Both the global and the local models are obtained by a variable selection genetic algorithms technique. The methodology is applied to a benchmark steroid data set. The molecular electrostatic potential and the experimental binding affinity constants for the corticosteroid-binding globulin are used as variables. The QSAR models obtained compared with those obtained by the CoMFA method show higher predictive ability and give insight into the local molecular features that determine high binding affinity.

A set of atomic radii used for the construction of solute cavities in the framework of the polarizable continuum model (PCM) is extended and validated with the aim of supporting the investigation of lanthanide(III) complexes in aqueous solution. The parameterization of the atomic radii for the whole Ln(III) series is performed by minimizing the differences between the experimental and the calculated standard hydration free energies of the ions calculated at the HF level. The optimized radii show a remarkable linear relationship with effective ionic radii and well reproduce the experimental hydration free energies also when electron correlation effects are included in the calculations. We have next validated a mixed discrete continuum model in which a supermolecule formed by the ion and by water molecules in the first hydration shell is immersed in a polarizable continuum. The molecular structures, the relative stability of the octa- with respect to the nonahydrated species, and the ion hydration free ener...

The conformational properties of five gadolinium(III) complexes with polyamino carboxylate (PAC) ligands used as magnetic resonance imaging contrast agents have been investigated by ab initio and molecular mechanics (MM) methods. Ab initio calculations were performed using an effective core potential (ECP) that includes 4f electrons in the core and an optimized valence basis set for the metal. To test the reliability of ECP calculations, full geometry optimizations of Gd complexes were performed at the RHF and DFT (B-LYP) levels using the 3-21G and the 6-31G* basis sets for the ligands. Comparison with experimental data shows that ab initio calculations provide quite accurate geometries and correct conformational energies at the RHF level. Within the framework of a valence force fields, parameters for Gd−ligand interactions were determined by fitting the empirical potential to the ab initio potential energy surface (PES) of the [Gd−DOTA(H2O)]-1 complex. Sampling of the PES was performed by moving the ion ...

The neutral and dication species of thiophene oligomers of increasing size (2 to 12 rings) have been examined and a study made of structural modifications occurring due to the increase in molecular charge; molecular properties such as charge-density distribution have been calculated. Preliminary results concerning the effect of electron correlation included at the density functional theory level are reported. Significant differences with respect to Hartree-Fock results are observed: the whole bipolaronic defect shape changes so that in the longer oligomers the bond-length alternation is no longer present.

A critical review of the receptor model based on Target Transformation Factor Analysis is presented. A new way of scaling the data set and evaluating the number of independent sources is proposed. The model applied to particulate matter samples collected at a receptor site in the Milan city-center leads to the identification of five sources contributing to air pollution.

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.

A new method is proposed for the calculation of kinetic coefficients from Fokker–Planck (FP) equations. Starting from the time scale separation between the kinetic modes of the FP operator and the other faster eigenmodes associated to the local equilibration of the coordinates, a set of site‐localizing functions is introduced for the ensemble of stable states of the system by means of linear combinations of the kinetic eigenfunctions. They allow the mapping of a nonequilibrium distribution onto a set of site populations which obey to rate equations of kinetic type. Such a procedure is easily implemented by using numerical eigenfunctions of the time evolution operator, so providing a set of transition rates which leads to the same decay rates of the FP kinetic modes. Several examples are considered in order to illustrate the typical results of the method. Particularly interesting is a two‐dimensional model for the chain of two bistable oscillators bound to a wall. A new kind of kinetic processes is recovered, besides ordinary transitions associated to saddle point crossings. They represent displacements localized within the chain without saddle point crossing, with analogy to crank‐shaft transitions of polymers.

The dominating route to polychlorinated Dibenzo-p-dioxin and Dibenzofuran formation in the ‘‘cold zones’’ of flue gas cleaning systems of municipal solid waste incinerators is the so-called de novo synthesis, that is, carbonaceous matrix burnoff with simultaneous oxidation and chlorination reactions. Pyrene (1) and Benzodibenzofuran (2) were chosen as the model compounds of carbonaceous material present in fly ash. Possible routes of Dibenzofuran formation by oxidative pathways of compounds (1) and (2) were investigated by theoretical calculations at the density functional theory level. The key intermediate peroxy radical, formed by reaction with molecular oxygen, can follow three main paths leading to Dibenzofuran. In the kinetically favourite path, the highest energetic barriers (25–30 kcal mol-1) are encountered in the steps where CO molecules are released from ketenelike structures. These findings agree with previously reported temperature-programmed desorption results on CO desorption. Moreover, along this path, phenanthrene and biphenyl intermediates are formed, in agreement with the detection of these products in previously reported experimental Pyrene oxidation. Along the preferred path, different steric constraints in compounds (1) and (2) play a role in determining the relative stability of the intermediates, while they have less influence on the energetic barriers. As a consequence, compounds (1) and (2) should present similar kinetic behaviour as they present similar energetic barriers.

A new oxyiminopyrazole-based ytterbium chelate enables NIR emission upon UV excitation in colorless single layer luminescent solar concentrators for building integrated photovoltaics. © the Owner Societies 2012.

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 cage variables describing solute–solvent interactions have been introduced in part I of the work. Moreover, the equilibrium distribution and the relaxation times for both solute and cage variables were derived from the analysis of a molecular dynamics (MD) simulation of liquid argon. In the second part of the work, a stochastic model for the cage is developed on the basis of these informations. The model is characterized by a particular choice for the set of independent stochastic variables and for the evolution operators describing each elementary process. Accurate solutions are derived numerically, while analytical solutions are obtained by separating the cage frame rotations from fast variables like the solute velocity. The calculation of correlation functions allows the comparison with MD results. A substantial agreement is found except for the displacement between solute and cage center. The examined cage model, because of its simple structure, allows a straightforward analysis of the effects of ...

Stochastic cage models require a choice for the cage variables suitable to describe the restoring forces generated by the solvent on the solute. A set of cage variables is introduced from the parametrization of the cage potential which is defined as the solute–solvent interaction energy considered as a function of the solute position for a fixed solvent configuration. This is an operative definition of cage variables that allows their identification at each time step of molecular dynamics simulations. Therefore, quantitative information about the equilibrium properties and the dynamics of cage variables can be extracted from molecular dynamics simulations. This procedure is applied to liquid argon near the triple point, in order to recognize the different processes contributing to the cage diffusion. The equilibrium distribution and the characteristic correlation times are derived as ingredients for the stochastic cage model developed in part II of the work.

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.

Spectroscopic and electrical properties of conformationally syn-blocked bithiophene monomers 1–3 and polymers are shown to be strongly dependent on the infer-ring torsional angle θ.

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.