Biomedical subjects

Luigi Cavallo

Publications and source records attributed to Luigi Cavallo.

At least 19 recordsLinked to original sources

PubMed2025

Unveiling the Genomic Landscape of Escherichia coli O1:K1:H7 ST59 in Non-complicated Urinary Infections from Colombia Through Whole-Genome Sequencing.

Escherichia coli (E. coli) is a Gram-negative bacterium known for causing both intestinal and extraintestinal infections in humans. Among extraintestinal infections, urinary tract infections (UTIs) are particularly prevalent and impactful. In Colombia, limited information is available regarding the molecular epidemiology of E. coli. This lack of data hinders the understanding of the local epidemiological landscape and the identification of pathogenic lineages that may contribute to public health concerns. This study aimed to characterize an E. coli strain isolated from a 24-year-old female patient with a community-acquired lower UTI, focusing on genotypic analysis through whole-genome shotgun sequencing (WGSS) and subsequent bioinformatics investigations. The identified strain belongs to phylogroup F, with serotype O1:H7 and sequence type (ST) 59. Several virulence factors, including traT and afimbrial adhesins (afaC), were identified, with afaC being notably uncommon in ST59 phylogroup F. In addition, an antibiotic susceptibility test was performed, and the isolate was found to be sensitive to all the antibiotics tested. This work contributes to the understanding of E. coli phylogroup F in Colombia and provides valuable genomic data, shedding light on the virulence profile of this strain in lower urinary tract infections.

Female↗

PubMed2006

Stereospecificity in metallocene catalyzed acrylate polymerizations: the chiral orientation of the growing chain selects its own chain end enantioface.

The mechanism of stereocontrol in the site-controlled stereospecific polymerization of methyl methacrylate (MMA) with C2- and CS-symmetric zirconocenes is investigated with a DFT based approach. Our model explains the experimentally observed isospecificity in MMA polymerization with the C2-symmetric rac-C2H4(Ind)2Zr-based system as well as the experimentally observed syndiospecificity in MMA polymerization with the CS-symmetric Me2C(Cp)(Flu)Zr-based system. In both cases, the chiral metallocene induces a chiral orientation of the ester enolate growing chain. In turn, the chirally oriented growing chain selects its own enantioface. Comparison with the mechanism of stereocontrol operative in the case of propene polymerization by the same zirconocenes is performed to stress similarities and differences. Although analogies are expected, surprising differences also exist. The most peculiar is that the in the case of 1-olefins, the enantioselective event is selection between the enantiofaces of the prochiral monomer. Instead, in the case of acrylates, the enantioselective event is selection between the enantiofaces of the prochiral growing chain.

Catalysis↗

PubMed2006

The elusive mechanism of olefin metathesis promoted by (NHC)Ru-based catalysts: a trade between steric, electronic, and solvent effects.

The reaction mechanism operative in olefin metathesis has been and still is a challenging area of research. Here we contribute to the discussion showing that the actual mechanism is a balance of the title effects. In particular, we show that the electronic and solvent effects evidenced by experimental studies can be easily counterbalanced by steric effects.

Journal Article↗

PubMed2006

(NHC)Copper(I)-catalyzed [3+2] cycloaddition of azides and mono- or disubstituted alkynes.

A versatile and highly efficient catalyst for the Huisgen cycloaddition reaction has been developed. Previously isolated or in situ generated azides yielded 1,2,3-triazoles with differently substituted alkynes in the presence of a [(NHC)CuBr] complex (NHC = N-heterocyclic carbene). Extremely high reaction rates and excellent yields were obtained in all cases. This catalytic system fulfils the requirements of "click chemistry" with its mild and convenient conditions, notably in water or solvent free reactions and simple isolation with no purification step. Furthermore, for the first time, an internal alkyne was successfully used in this copper-catalyzed cycloaddition reaction. DFT calculations on this particular system allowed for the proposition of a new mechanistic pathway for disubstituted alkynes.

Journal Article↗

PubMed2006

Dynamic properties of metallocenium ion pairs in solution by atomistic simulations.

We report a molecular dynamics study of the dynamics and energetic of the [H(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)], IP1, and [Me(2)Si(Cp)(2)ZrMe(+)][B(C(6)F(5))(4)(-)], IP2, ion pairs in benzene. The metrical parameters obtained for the IP1 ion pair are in excellent agreement with the NMR data reported for the strictly related [Me(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)] ion pair (J. Am. Chem. Soc. 2004, 126, 1448). This validates the molecular modeling protocol we developed. Simulation of the IP2 ion pair suggests that the counterion oscillates between two geometries characterized by a different coordination pattern of the F atoms to the Zr cation. In one case the B(C(6)F(5))(4)(-) coordinates to the metal with two F atoms of the same aryl ring, whereas in the other case two F atoms of different aryl rings are involved in the coordination. Strong solvent reorganization occurs around IP1 and IP2, as well as around the two isolated cations. In the case of the two ion pairs solvent is never coordinated directly to the metal, whereas in the absence of the counterion one benzene molecule is coordinated to the metal through a cation-pi interaction. Free energy calculations result in ion pair free energies of separation of 36.8 and 23.3 kcal/mol for IP1 and IP2, respectively. Simulations with the Zr-B distance fixed at values > 7 A have been also performed. This mimics the situation occurring after counterion displacement by an inserting monomer molecule during olefin polymerization by the title catalysts.

Journal Article↗

PubMed2006

Structure and bonding in monomeric iron(III) complexes with terminal oxo and hydroxo ligands.

We report on the structure and bonding in the title iron(III) complexes, containing the tris[(N'-tert-butylureayl)-N-ethyl]amine ligand, with density functional theory techniques. In agreement with the experimental data, a high-spin electronic state is favored for all of the systems we considered. H bonds between the terminal oxo and hydroxo ligands and NH groups present in the organic ligand coordinated to the metal have a remarkable effect on the overall coordination geometry. In fact, the structure of model complexes without H bonds shows shorter Fe-O bond lengths. This is a consequence of the ability of the H bonds to stabilize a remarkable amount of electron density localized on the terminal oxo and hydroxo ligands. Energy analysis indicates that each H bond stabilizes the nonheme complexes by roughly 35 kJ/mol. Molecular orbital analysis indicates a reduction of two Fe-O bonding electrons on going from a complex with a terminal oxo ligand to a complex with a terminal hydroxo ligand. This reduction in the number of bonding electrons is also supported by frequency analysis.

Ferric Compounds↗

PubMed2006

Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions.

Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis and quantum mechanics approach to calculate accurate energies of the most frequent tRNA tertiary base pairing interactions. Our analysis indicates that six out of the nine classical tertiary interactions are held in place mainly by H-bonds between the bases. In the remaining three cases other effects have to be considered. Tertiary base pairing interaction energies range from -8 to -38 kcal/mol in yeast tRNA(Phe) and are estimated to contribute roughly 25% of the overall tRNA base pairing interaction energy. Six analyzed posttranslational chemical modifications were shown to have minor effect on the geometry of the tertiary interactions. Modifications that introduce a positive charge strongly stabilize the corresponding tertiary interactions. Non-additive effects contribute to the stability of base triplets.

Base Pairing↗

PubMed2005

Interaction of a bulky N-heterocyclic carbene ligand with Rh(I) and Ir(I). Double C-H activation and isolation of bare 14-electron Rh(III) and Ir(III) complexes.

Reactivity and structural studies of unusual rhodium and iridium systems bearing two N-heterocyclic carbene (NHC) ligands are presented. These systems are capable of intramolecular C-H bond activation and lead to coordinatively unsaturated 16-electron complexes. The resulting complexes can be further unsaturated by simple halide abstraction, leading to 14-electron species bearing an all-carbon environment. Saturation of the vacant sites in the 16- and 14-electron complexes with carbon monoxide permits a structural comparison. DFT calculations show that these electrophilic metal centers are stabilized by pi-donation of the NHC ligands.

Journal Article↗

PubMed2005

Steric and electronic properties of N-heterocyclic carbenes (NHC): a detailed study on their interaction with Ni(CO)4.

N-heterocyclic carbene ligands IMes (1), SIMes (2), IPr (3), SIPr (4), and ICy (5) react with Ni(CO)(4) to give the saturated tricarbonyl complexes Ni(CO)(3)(IMes) (8), Ni(CO)(3)(SIMes) (9), Ni(CO)(3)(IPr) (10), Ni(CO)(3)(SIPr) (11), and Ni(CO)(3)(ICy) (12), respectively. The electronic properties of these complexes have been compared to their phosphine analogues of general formula Ni(CO)(3)(PR(3)) by recording their nu(CO) stretching frequencies. While all of these NHCs are better donors than tertiary phosphines, the differences in donor properties between ligands 1-5 are surprisingly small. Novel, unsaturated Ni(CO)(2)(IAd) (13) and Ni(CO)(2)(I(t)()Bu) (14) compounds are obtained from the reaction of Ni(CO)(4) with IAd (6) and I(t)()Bu (7). Complexes 13 and 14 are highly active toward substitution of the NHC as well as the carbonyl ligands. This has allowed the determination of Ni-C(NHC) bond dissociation energies and the synthesis of various unsaturated Ni(0) and Ni(II) complexes. Computational studies on compounds 8-14 are in line with the experimental findings and show that IAd (6) and I(t)()Bu (7) are more bulky than IMes (1), SIMes (2), IPr (3), SIPr (4), and ICy (5). Furthermore, a method based on %V(bur) values has been developed for the direct comparison of steric requirements of NHCs and tertiary phosphines. Complexes 8-14, as well as NiCl(C(3)H(5))(I(t)()Bu) (16) and NiBr(C(3)H(5))(I(t)()Bu) (17), have been characterized by X-ray crystallography.

Journal Article↗

PubMed2004

Origin of enantioselectivity in the asymmetric Ru-catalyzed metathesis of olefins.

The mechanism of enantioselectivity in the asymmetric Ru-catalyzed metathesis of olefins is investigated with a theoretical approach. The models are based on the chiral N-heterocyclic (NHC)-based catalysts developed by Grubbs. Our analysis indicates that the origin of enantioselectivity in the ring-closing metathesis of achiral trienes is correlated to the chiral folding of the N-bonded aromatic groups, which is imposed by the Ph groups in positions 4 and 5 of the imidazole ring of the NHC ligand. This chiral folding of the catalyst imposes a chiral orientation around the Ru=C bond, which, in turn, selects between the two enantiofaces of the substrate. In the ring-closing transition state, the geometry in which additional groups on the forming ring are in pseudoequatorial positions is favored over transition states in which this additional group is in a pseudoaxial position. These combined effects rationalize the enantiomeric excesses experimentally obtained.

Journal Article↗

PubMed2004

Toward a catalytic cycle for the Mn-salen mediated alkene epoxidation: a computational approach.

BP86 density functional calculations for the title reaction are presented, where a model catalyst with hypochlorite as oxygen-containing counter ligand, (ClO)(O)Mn(acacen') (acacen' = -O(CH)3N-C2H4-N(CH)3O-), is employed. The epoxidation reaction on potential energy surfaces corresponding to an overall spin-density of two and four unpaired electrons is investigated. The presence of the hypochlorite ligand is found to cause the reaction to proceed under conservation of spin. Further, the oxygen-containing counter ligand causes reoxidation of the Mn-center, thus closing the catalytic cycle. A catalytic scheme is therefore proposed, which includes a step of regeneration of the catalytically active species. Energetic estimates including corrections for solvent effects are presented for the relevant steps constituting the proposed catalytic scheme.

Journal Article↗

PubMed2004

Do new century catalysts unravel the mechanism of stereocontrol of old Ziegler-Natta catalysts?

Stereoselective polymerization of 1-alkenes was discovered 50 years ago. However, a detailed knowledge of the traditional and industrially used Ziegler-Natta catalytic systems is still missing. Recently, well-defined homogeneous and octahedral complexes that polymerize propene to polypropylenes with microstructures extremely similar to those of polymers produced with the traditional catalysts were discovered. These catalysts offer the exciting opportunity to achieve insights into the mechanism of stereocontrol operative with the traditional catalytic systems.

Journal Article↗

PubMed2003

Electronic effects in (salen)Mn-based epoxidation catalysts.

Presented are density functional calculations on various Mn(salen) systems that are active catalysts in the epoxidation of olefins. Correlation of various structural properties such as Mn=O bond strengths, atomic charges, and C-O distances of evolving bonds in transition state geometries with modified Hammett constants reveal a mechanistic picture of the epoxidation reaction, supporting previous experimental results. Enantioselectivity is tied to the position of a transition state along the reaction coordinate for the first C-O bond formation step, when an olefin is approaching the epoxidation catalyst. Electronic effects exhibited by the 5,5' substituents of the salen ligand manifest themselves in a tuning of the Mn=O bond strength, which in turn influences the C-O distance of the forming bond in the transition state geometry.

Journal Article↗

PubMed2003

POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.

POPS (Parameter OPtimsed Surfaces) is a new method to calculate solvent accessible surface areas, which is based on an empirically parameterisable analytical formula and fast to compute. Atomic and residue areas (the latter represented by a single sphere centered on the C(alpha) atom of amino acids and at the P atom of nucleotides) have been optimised versus accurate all-atom methods. The parameterisation has been derived from a selected dataset of proteins and nucleic acids of different sizes and topologies. The residue based approach POPS-R, has been devised as a useful tool for the analysis of large macromolecular assemblies like the ribosome and it is specially suited for the refinement of low resolution structures. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, which should be particularly useful for the design of new protein-protein and protein-nucleic acid complexes. The program POPS is available at http://mathbio.nimr.mrc.ac.uk/~ffranca/POPS and at the mirror site http://www.cs.vu.nl/~ibivu/programs/popswww.

Algorithms↗

PubMed2003

Origin of the regiochemistry of propene insertion at octahedral column 4 polymerization catalysts: design or serendipity?

The new octahedral column 4 catalysts bearing phenoxy-amine or phenoxy-imine ligands have opposite regioselectivities in propene polymerization. In this Communication, we report on a QM/MM investigation indicating that one of the key factors controlling the regiochemistry of propene insertion is the nature of the N atoms: steric and electronic effects related to the different hybridization synergically favor 1,2 or 2,1 insertion when the said N's are respectively of amine or imine type.

Journal Article↗

PubMed2003

Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin.

A three-dimensional model has been calculated for the discoidin domain of retinoschisin (RS1), the protein involved in the X-linked juvenile retinoschisis. The model allows for a mapping of the pathological retinoschisis missense mutations and a rationale for the structural effects of an evolutionary conserved surface exposed triad (W122-R200-W163). Molecular dynamics simulations of the triad mutants models, together with ab initio energy calculations of the complexes corresponding to the triad show that the observed pathological mutations sensibly destabilize local interactions and the entire fold. Moreover the presented model reveals evidence of a putative site for membrane association.

Amino Acid Sequence↗

PubMed2002

Site chirality as a messenger in chain-end stereocontrolled propene polymerization.

The origin of stereoselectivity in the chain-end controlled syndiospecific polymerization of propene with octahedral Ti-catalysts is unclear. We present a possible mechanism which is based on the site chirality as a messenger of information between the chirality of the chain-end and the chirality of monomer insertion which can operate for secondary propagation. This mechanism could be operative also for the industrially relevant V-based homogeneous catalysts.

Journal Article↗

PubMed2002

Mechanism of ruthenium-catalyzed olefin metathesis reactions from a theoretical perspective.

This paper presents a density functional theory study of the ruthenium-catalyzed olefin metathesis reactions. The ligand binding energy has been calculated in the first generation of Grubbs-type (PCy3)2Cl2Ru=CHPh (pre)catalyst, as well as in the heteroleptic (pre)catalytic systems in which a N-heterocyclic carbene, NHC, ligand substitutes a single phosphine. In agreement with experiments PCy3 coordinates more strongly to Ru in the heteroleptic (pre)catalysts than in the Grubbs-type (pre)catalyst. Moreover, ethene coordination and insertion into the Ru-alkylidene bond in the above-mentioned systems, as well as in the Hofmann type catalytic system with a cis-coordinated phosphane ligand, has been studied. The calculated insertion barrier for the NHC systems are lower than that of the (PCy3)2Cl2Ru=CHPh system. This is consistent with the higher activity experimentally observed for the NHC-based system.

Journal Article↗