24 results on '"Rafael Grande-Aztatzi"'
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2. Structural evolution of small gold clusters doped by one and two boron atoms.
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Rafael Grande-Aztatzi, Paulina R. Martínez-Alanis, José Luis Cabellos, Edison Osorio, Ana Martínez, and Gabriel Merino
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- 2014
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Catalog
3. Front Cover: Reversible Stereoisomer‐Specific Cotton Effect of the Ligand Field Transitions at a Copper(II) Binding Site of the Prion Protein (Eur. J. Inorg. Chem. 2/2022)
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Lina Rivillas‐Acevedo, Rafael Grande‐Aztatzi, Eusebio Juaristi, Alberto Vela, and Liliana Quintanar
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Inorganic Chemistry - Published
- 2021
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4. Reversible Stereoisomer‐Specific Cotton Effect of the Ligand Field Transitions at a Copper(II) Binding Site of the Prion Protein
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Lina Rivillas-Acevedo, Alberto Vela, Eusebio Juaristi, Rafael Grande-Aztatzi, and Liliana Quintanar
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Inorganic Chemistry ,Ligand field theory ,Circular dichroism ,chemistry ,Stereochemistry ,chemistry.chemical_element ,Prion protein ,Binding site ,Copper ,Cotton effect - Published
- 2021
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5. Does phosphorylation increase the binding affinity of aluminum? A computational study on the aluminum interaction with serine and O-phosphoserine
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Elena Formoso, Rafael Grande-Aztatzi, and Xabier Lopez
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inorganic chemicals ,010405 organic chemistry ,Atoms in molecules ,Hyperphosphorylation ,Phosphoproteins ,010402 general chemistry ,complex mixtures ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Inorganic Chemistry ,Serine ,Phosphoserine ,chemistry.chemical_compound ,chemistry ,Biophysics ,Quantum Theory ,Phosphorylation ,Density functional theory ,Chelation ,Solvent effects ,Aluminum ,Chelating Agents ,Protein Binding - Abstract
Several toxic effects arise from aluminum's presence in living systems, one of these effects is to alter the natural role of enzymes and non-enzyme proteins. Aluminum promotes the hyperphosphorylation of normal proteins. In order to assess the aluminum-binding abilities of phosphorylated proteins and peptides, the interaction of aluminum at different pH with serine and phosphoserine is studied by a Density Functional Theory study, combined with polarizable continuum models to account for bulk solvent effects, and the electronic structure of selected complexes are analyzed by Quantum Theory of "Atoms in Molecules". Our results confirm the high ability of aluminum to bind polypeptides as the pH lowers. Moreover, the phosphorylation of the building blocks increases the affinity for aluminum, in particular at physiological pH. Finally, aluminum shows a tendency to be chelated forming different size rings. more...
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- 2019
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6. Theoretical characterization of Al(III) binding to KSPVPKSPVEEKG: Insights into the propensity of aluminum to interact with key sequences for neurofilament formation
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Jon I. Mujika, Elena Formoso, Rafael Grande-Aztatzi, Xabier Lopez, and David De Sancho
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Phosphopeptides ,Neurofilament ,Protein Conformation ,Binding energy ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Coordination complex ,Inorganic Chemistry ,Molecular dynamics ,Coordination Complexes ,Neurofilament Proteins ,Humans ,Binding site ,Protein secondary structure ,Density Functional Theory ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Solvation ,Peptide Fragments ,0104 chemical sciences ,Models, Chemical ,Biophysics ,Thermodynamics ,Density functional theory ,Aluminum ,Protein Binding - Abstract
Classical molecular dynamic simulations and density functional theory are used to unveil the interaction of aluminum with various phosphorylated derivatives of the fragment KSPVPKSPVEEKG (NF13), a major multiphosphorylation domain of human neurofilament medium (NFM). Our calculations reveal the rich coordination chemistry of the resultant structures with a clear tendency of aluminum to form multidentate structures, acting as a bridging agent between different sidechains and altering the local secondary structure around the binding site. Our evaluation of binding energies allows us to determine that phosphorylation has an increase in the affinity of these peptides towards aluminum, although the interaction is not as strong as well-known chelators of aluminum in biological systems. Finally, the presence of hydroxides in the first solvation layer has a clear damping effect on the binding affinities. Our results help in elucidating the potential structures than can be formed between this exogenous neurotoxic metal and key sequences for the formation of neurofilament tangles, which are behind of some of the most important degenerative diseases. more...
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- 2020
7. Aluminum's preferential binding site in proteins: sidechain of amino acids versus backbone interactions
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Jon I. Mujika, Xabier Lopez, Christopher Exley, Sławomir J. Grabowski, Rafael Grande-Aztatzi, Gabriele Dalla Torre, and Elena Formoso
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Models, Molecular ,inorganic chemicals ,Protein Conformation ,Stereochemistry ,Amino Acid Motifs ,Static Electricity ,Binding energy ,Aluminum Hydroxide ,Peptide ,Ligands ,010402 general chemistry ,complex mixtures ,01 natural sciences ,Biochemistry ,Inorganic Chemistry ,Phosphoserine ,chemistry.chemical_compound ,Coordination Complexes ,Aspartic acid ,Humans ,Computer Simulation ,QD ,Denaturation (biochemistry) ,Phosphorylation ,Protein secondary structure ,Chelating Agents ,chemistry.chemical_classification ,Amyloid beta-Peptides ,Binding Sites ,010405 organic chemistry ,Computational Biology ,Preferential binding ,Carbonyl group ,Peptide Fragments ,0104 chemical sciences ,Amino acid ,Kinetics ,Energy Transfer ,chemistry ,Quantum Theory ,Thermodynamics ,Environmental Pollutants ,Oligopeptides ,Aluminum - Abstract
The interaction of aluminum ion Al(III) with polypeptides is a subject of paramount importance, since it is a central feature to understand its deleterious effects in biological systems. Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. In the present paper, we use computational methods to discuss the possibility of aluminum to interact with the backbone of peptides and compare it with the known ability of aluminum to interact with amino acid sidechains. To do so, we compare the thermodynamics of formation of prototype aluminum-backbone structures with prototype aluminum-sidechain structures, and compare these results with previous data generated in our group in which aluminum interacts with various types of polypeptides and known aluminum biochelators. Our results clearly points to a preference of aluminum towards amino acid sidechains, rather than towards the peptide backbone. Thus, structures in which aluminum is interacting with the carbonyl group are only slightly exothermic, and they become even less favorable if the interaction implies additionally the peptide nitrogen. However, structures in which aluminum is interacting with negatively-charged sidechains like aspartic acid, or phosphorylated serines are highly favored thermodynamically. more...
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- 2018
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8. Aromaticity, the Hückel 4 n+2 Rule and Magnetic Current
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Gernot Frenking, Rafael Grande-Aztatzi, Cina Foroutan-Nejad, Lili Zhao, and Jesus M. Ugalde
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010405 organic chemistry ,Chemistry ,Chemical shift ,Hückel's rule ,Aromaticity ,General Chemistry ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Molecular physics ,Aromatic ring current ,0104 chemical sciences ,Delocalized electron ,Computational chemistry ,Physics::Atomic and Molecular Clusters ,Density functional theory ,Physics::Chemical Physics ,Ring current - Abstract
Quantum chemical calculations using density functional theory and correlated ab initio methods of the 10 π-electron systems (N6H6)2+ and C2N4H6 show that the planar forms are no minima on the potential energy surfaces. The twisted ring structures of the two species are energy minima, but acyclic isomers are much lower in energy. The planar geometries sustain strong diamagnetic ring current comparable with that of benzene. In contrast, the calculated multicenter normalized Giambiagi electron delocalization index ING suggests that π-delocalization in planar (N6H6)2+ and C2N4H6 is much weaker than in benzene. Since aromaticity is synonymous for a particular stability of cyclic delocalized systems, it may be stated that calculation or measurement of magnetic chemical shifts due to induced ring currents is not a reliable method to ascertain the aromatic character of a molecule. Aromatic compounds exhibit ring current induced magnetic shielding, but the reverse conclusion that ring current induced magnetic shielding identifies aromaticity is not justified. Furthermore, the 4n+2 rule as indicator of aromatic stabilization should only be used in conjunction with the ring size; the nature of the occupied π orbitals must always be examined. more...
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- 2017
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9. Spectroscopic and Theoretical Study of CuI Binding to His111 in the Human Prion Protein Fragment 106–115
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Alberto Vela, Claudio O. Fernández, Edward I. Solomon, Lina Rivillas-Acevedo, Trinidad Arcos-López, Marco C. Miotto, Liliana Quintanar, Keith O. Hodgson, Britt Hedman, Rafael Grande-Aztatzi, and Munzarin F. Qayyum more...
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0301 basic medicine ,Stereochemistry ,Biophysics ,chemistry.chemical_element ,Plasma protein binding ,Prion Protein ,010402 general chemistry ,Endocytosis ,01 natural sciences ,Article ,Prion Proteins ,Inorganic Chemistry ,Metal ,03 medical and health sciences ,chemistry.chemical_compound ,Humans ,Molecule ,Physical and Theoretical Chemistry ,Nuclear Magnetic Resonance, Biomolecular ,Methionine ,Superoxide ,Otras Ciencias Químicas ,Ciencias Químicas ,Sulfoxide ,Hydrogen-Ion Concentration ,Models, Theoretical ,Copper ,Peptide Fragments ,nervous system diseases ,0104 chemical sciences ,3. Good health ,Kinetics ,Crystallography ,X-Ray Absorption Spectroscopy ,030104 developmental biology ,chemistry ,visual_art ,visual_art.visual_art_medium ,Cu(I) ,Oxidation-Reduction ,CIENCIAS NATURALES Y EXACTAS ,Protein Binding - Abstract
The ability of the cellular prion protein (PrPC) to bind copper in vivo points to a physiological role for PrPC in copper transport. Six copper binding sites have been identified in the nonstructured N-terminal region of human PrPC. Among these sites, the His111 site is unique in that it contains a MKHM motif that would confer interesting CuI and CuII binding properties. We have evaluated CuI coordination to the PrP(106–115) fragment of the human PrP protein, using NMR and X-ray absorption spectroscopies and electronic structure calculations. We find that Met109 and Met112 play an important role in anchoring this metal ion. CuI coordination to His111 is pH-dependent: at pH >8, 2N1O1S species are formed with one Met ligand; in the range of pH 5–8, both methionine (Met) residues bind to CuI, forming a 1N1O2S species, where N is from His111 and O is from a backbone carbonyl or a water molecule; at pH, CuI coordination to the His111 site in the HuPrP protein is highly dependent on the pH: at pH 8, 2N1O1S species are formed with only a Met ligand. The CuI-1N1O2S species activates dioxygen, and in this process, the Met residues are partially oxidized to sulfoxide. more...
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- 2016
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10. Oxidation of Acid, Base, and Amide Side-Chain Amino Acid Derivatives via Hydroxyl Radical
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Jon I. Mujika, Jon Uranga, Jon M. Matxain, and Rafael Grande-Aztatzi
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chemistry.chemical_classification ,High concentration ,010405 organic chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Surfaces, Coatings and Films ,Amino acid ,Solvent ,chemistry.chemical_compound ,Amino acid derivative ,chemistry ,Amide ,Materials Chemistry ,Side chain ,Density functional theory ,Hydroxyl radical ,Physical and Theoretical Chemistry - Abstract
Hydroxyl radical (•OH) is known to be highly reactive. Herein, we analyze the oxidation of acid (Asp and Glu), base (Arg and Lys), and amide (Asn and Gln) containing amino acid derivatives by the consecutive attack of two •OH. In this work, we study the reaction pathway by means of density functional theory. The oxidation mechanism is divided into two steps: (1) the first •OH can abstract a H atom or an electron, leading to a radical amino acid derivative, which is the intermediate of the reaction and (2) the second •OH can abstract another H atom or add itself to the formed radical, rendering the final oxidized products. The studied second attack of •OH is applicable to situations where high concentration of •OH is found, e.g., in vitro. Carbonyls are the best known oxidation products for these reactions. This work includes solvent dielectric and confirmation’s effects of the reaction, showing that both are negligible. Overall, the most favored intermediates of the oxidation process at the side chain cor... more...
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- 2018
11. Correction: The stability of biradicaloid versus closed-shell [E(μ-XR)]
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Rafael, Grande-Aztatzi, Jose M, Mercero, and Jesus M, Ugalde
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Correction for 'The stability of biradicaloid versus closed-shell [E(μ-XR)]
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- 2018
12. The stability of biradicaloid versus closed-shell [E(μ-XR)]2 (E = P, As; X = N, P, As) rings. Does aromaticity play a role?
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Rafael Grande-Aztatzi, Jose M. Mercero, and Jesus M. Ugalde
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Field (physics) ,010405 organic chemistry ,Chemistry ,General Physics and Astronomy ,Aromaticity ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Crystallography ,Planar ,Molecular geometry ,Ab initio quantum chemistry methods ,Computational chemistry ,Physical and Theoretical Chemistry ,Perturbation theory ,Open shell ,Basis set - Abstract
High-level multiconfigurational self-consistent field calculations, supplemented with multiconfigurational quasi-degenerate perturbation theory ab initio calculations with the aug-cc-pVTZ basis set, demonstrate that the [E(μ-XH)]2 (E = P, As; X = N, P, As) compounds possess one planar and one butterfly-like isomer. The calculations predict that for X = N, planar isomers, which bear substantial biradicaloid character, are more stable than their butterfly-like counterpart isomers, which feature closed-shell electronic structures. This has been ascribed to the fact that the increased bond angle strain at E-N-E is not compensated by the E-E σ (deformed) bond formation in the butterfly-like isomers, yielding the planar structures, which hold wider E-N-E bond angles, as the most stable isomers. As N is substituted by heavier atoms, either P or As, the E-P(As)-E bond angle strain is released and, additionally, as the formed E-E σ-bond is less deformed, the butterfly isomer becomes the most stable isomer. Subsequent evaluation of the normalized Giambiagi multicenter electron delocalization indices revealed no sign of electron delocalization in the four-membered rings and consequently, it is concluded that aromaticity does not play any role in the stabilization of the planar isomers. more...
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- 2016
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13. Correction: The aromaticity of dicupra[10]annulenes
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Jose M. Mercero, Rafael Grande-Aztatzi, Jesus M. Ugalde, Gernot Frenking, and Eduard Matito
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Chemistry ,Computational chemistry ,General Physics and Astronomy ,Aromaticity ,Physical and Theoretical Chemistry ,Annulene - Abstract
Correction for ‘The aromaticity of dicupra[10]annulenes’ by Rafael Grande-Aztatzi et al., Phys. Chem. Chem. Phys., 2017, 19, 9669–9675.
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- 2017
14. The aromaticity of dicupra[10]annulenes
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Jesus M. Ugalde, Rafael Grande-Aztatzi, Gernot Frenking, Jose M. Mercero, and Eduard Matito
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010405 organic chemistry ,Chemistry ,Chemical shift ,General Physics and Astronomy ,Aromaticity ,Electronic structure ,Annulene ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,0104 chemical sciences ,Delocalized electron ,chemistry.chemical_compound ,Crystallography ,Organic chemistry ,Molecular orbital ,Molecular graph ,Physical and Theoretical Chemistry - Abstract
An extensive theoretical investigation of the electronic structure of a tested fair model dicupra[10]annulene compound, based on the analysis of atom-pair delocalization indices, Bader's molecular graph, the inspection of the canonical molecular orbitals, the z components of their Nuclear Independent Chemical Shifts, NICS(0)zz, and the normalized Giambiagi multicenter delocalization indices, concludes that the perimeter aromaticity of the dicupra[10]annulene ring is consistent with both 10 and 14 π-electron Huckel aromatic 10-membered rings. In either case, the 10-membered ring encloses two 6 π-electron aromatic inner rings, hinged at the Cu-Cu bond. This work demonstrates that the aromaticity of dicupra[10]annulenes closely resembles that of naphthalene. Hence, they are best regarded as metalla-polyacenes, which could make the building blocks of extended structures such as metalated nanotubes. more...
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- 2017
15. Copper coordination to the prion protein: Insights from theoretical studies
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Liliana Quintanar, Rafael Grande-Aztatzi, Carlos Z. Gómez-Castro, Lina Rivillas-Acevedo, Alberto Vela, and Trinidad Arcos-López
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chemistry.chemical_classification ,Car–Parrinello molecular dynamics ,Chemistry ,chemistry.chemical_element ,Copper ,Coordination complex ,Inorganic Chemistry ,Molecular dynamics ,Crystallography ,chemistry.chemical_compound ,Covalent bond ,Amide ,Materials Chemistry ,Protein folding ,Physical and Theoretical Chemistry ,Binding site - Abstract
The cellular prion protein (PrP C ) has emerged as an important copper binding protein. The interaction of copper with PrP C may play important roles in both the physiological function of the protein, and in the pathogenesis of prion diseases. The copper coordination chemistry of PrP C is complex, as different Cu(II) coordination modes can be formed depending on pH and copper to protein ratios, and involving six different His residues in the N-terminal region of the protein. The nature of these Cu(II) binding sites has been studied using theoretical tools, which expand on the information obtained from experimental results and provide important insights into Cu–PrP C interactions. This article provides a general overview of the different Cu(II) binding sites in PrP C and their redox properties, highlighting the contributions from electronic structure calculations and molecular dynamics simulations. Particular emphasis is placed in discussing the electronic structure of each Cu binding mode, as it is intimately related to redox properties. For most Cu binding modes, the dominating Cu(II) bonding interactions involve deprotonated amide nitrogens, which yield Cu N amide bonds that are significantly more covalent than the Cu N His bond. The key factors that determine the direction of Cu(II) binding to backbone amides in the vicinity of the anchoring His are discussed. Additionally, the impact of Cu–PrP C interactions in protein folding and in the potential initiation of PrP C aggregation is discussed. more...
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- 2013
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16. Structural and optical properties of the naked and passivated Al5Au5 bimetallic nanoclusters
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Jose M. Mercero, Jesus M. Ugalde, Rafael Grande-Aztatzi, Sławomir J. Grabowski, Elena Formoso, and Jon M. Matxain
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Passivation ,Chemistry ,Ab initio ,General Physics and Astronomy ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Alkali metal ,01 natural sciences ,0104 chemical sciences ,Nanoclusters ,chemistry.chemical_compound ,Crystallography ,Nucleophile ,Ionic liquid ,Density functional theory ,Physical and Theoretical Chemistry ,0210 nano-technology ,Bimetallic strip - Abstract
The structural and optical properties of both the naked and passivated bimetallic Al5Au5 nanoclusters have been analyzed based on data obtained from ab initio density functional theory and quantum molecular dynamics simulations. It has been found that the Al5Au5 nanocluster possesses a hollow shaped minimum energy structure with segregated Al and Au layered domains, the former representing the electrophilic domain and the latter the nucleophilic domain. In particular, it has been shown that alkali metal cations attach in the nucleophilic domain and hop from one Au site to the next one in the picoseconds time scale, while anions are bound tightly to the Al atoms of the electrophilic domain. Simulating annealing studies are very suggestive of the proneness of the nanocluster towards coalescence into large cluster units, when the cluster is left unprotected by appropriate ligands. Further passivation studies with NaF salt suggest, nonetheless, the possibility of the isolation of the Al5Au5 cluster in molten salts or ionic liquids. more...
- Published
- 2016
17. Phosphorylation promotes Al(iii) binding to proteins: GEGEGSGG as a case study
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Jesus M. Ugalde, Jon I. Mujika, Elena Formoso, Xabier Lopez, and Rafael Grande-Aztatzi
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Neurofilament ,General Physics and Astronomy ,Peptide ,Plasma protein binding ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Molecular dynamics ,0103 physical sciences ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Phosphorylation ,Peptide sequence ,Protein secondary structure ,Nuclear Magnetic Resonance, Biomolecular ,chemistry.chemical_classification ,010304 chemical physics ,Chemistry ,Proteins ,0104 chemical sciences ,Biochemistry ,Biophysics ,Density functional theory ,Aluminum ,Protein Binding - Abstract
Aluminum, the third most abundant element in the Earth's crust and one of the key industrial components of our everyday life, has been associated with several neurodegenerative diseases due to its ability to promote neurofilament tangles and β-amyloid peptide aggregation. However, the experimental characterization of aluminum speciation in vivo is a difficult task. In the present study, we develop a theoretical protocol that combines molecular dynamics simulations, clustering of structures, and density functional theory for the characterization of the binding of aluminum to the synthetic neurofilament analogue octapeptide GEGEGSGG and its phosphorylated variant. Our protocol is tested with respect to previous NMR experimental data, which allows for a full interpretation of the experimental information available and its relationship with key thermodynamic quantities. Our results demonstrate the importance of phosphorylation in the ability of a peptide to bind to aluminum. Thus, phosphorylation: (i) changes the binding pattern of aluminum to GEGEGSGG, shifting the preferential binding site from the C-terminal to S6(P); (ii) increases the binding affinity by a factor of around 15 kcal mol(-1) in free energy; and (iii) may cause significant changes in the secondary structure and stiffness of the polypeptide chain, specially in the case of bidentate binding modes. Our results shed light on the possibility of aluminum to induce aggregation of β-amyloid proteins and neurofilament tangles. more...
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- 2016
18. Inducing magnetic communication in caged dinuclear Co(II) systems
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Yasmi Reyes-Ortega, Judith Caballero-Jiménez, Ilia Korobkov, Muralee Murugesu, Daniel Ramírez-Rosales, Gopalan Rajaraman, Rafael Grande-Aztatzi, Gabriel Merino, Mukesh Kumar Singh, and Fatemah Habib
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Transition-Metal-Complexes ,Stereochemistry ,Chemistry ,Bridging Ligands ,Intermetallic ,Azacryptand ,Bases Hsab ,Magnetic exchange ,Ion ,Inorganic Chemistry ,Crystallography ,Single-Molecule Magnets ,Density-Functional Theory ,Zero-Field Splittings ,Superexchange ,State Perturbation-Theory ,Antiferromagnetism ,Binuclear Complexes ,Organic Cages ,Cobalt(Ii) Complexes - Abstract
The synthesis, structural, electronic and magnetic characterization of five dinuclear Co(II) azacryptand compounds (1-5) bridged through different ions are reported. The magnetic exchange interactions, 2J values, obtained from theoretical computations show that the variation of the intermetallic angles and distances lead to antiferromagnetic behaviours. Magneto-structural correlations show a trend, where the angles Co(II)-bridge-Co(II) closer to 180 degrees favour an increase in the superexchange pathway leading to higher AF interaction values. more...
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- 2015
19. Frontiers in Computational Chemistry
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Kazutaka Hirakawa, Patrizia Calaminici, Zuojun Guo, María V. Castillo, Emiliano Laudadio, Rafik Karaman, Zaheer Ul-Haq, Jeffry D. Madura, Gabriel del Rio, Elida Romano, Tzonka Mineva, Silvia Antonia Brandán, Roberta Galeazzi, Rafael Grande-Aztatzi, Alberto Vela, Andreas M. Köster, Dennis R. Salahub, José M. Vásquez-Pérez, Pradip Bhattacharyya, Raschi Ana B., Carlos Z. Gómez-Castro, Kunal Roy, Carlos Polanco González, Jianwei Che, Miguel Arias-Estrada, Bernardo Zuniga-Gutierrez, Aurelio Alvarez-Ibarra, Nabajit Sarmah, Annick Goursot, Supratik Kar, Sourab Sinha, Luca Massaccesi, Bhabesh Chandra Deka, and Yang Zhong more...
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Computer science ,Biochemical engineering - Published
- 2015
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20. Structural evolution of small gold clusters doped by one and two boron atoms
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Gabriel Merino, Edison Osorio, Paulina R. Martínez-Alanis, José Luis Cabellos, Rafael Grande-Aztatzi, and Ana Martínez
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Stochastic Processes ,Molecular Structure ,Doping ,Static Electricity ,chemistry.chemical_element ,General Chemistry ,Potential energy ,Structural evolution ,Computational Mathematics ,Chemical bond ,chemistry ,Chemical physics ,Natural density ,Quantum Theory ,Reactivity (chemistry) ,Molecular orbital ,Gold ,Atomic physics ,Boron ,Algorithms - Abstract
The potential energy surfaces (PES) of a series of gold-boron clusters with formula Aun B (n = 1-8) and Aum B2 (m = 1-7) have been explored using a modified stochastic search algorithm. Despite the complexity of the PES of these clusters, there are well-defined growth patterns. The bonding of these clusters is analyzed using the adaptive natural density partitioning and the natural bonding orbital analyses. Reactivity is studied in terms of the molecular electrostatic potential. more...
- Published
- 2014
21. Insights into the oxygen-based ligand of the low pH component of the Cu(2+)-amyloid-β complex
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Carlos Z. Gómez-Castro, Liliana Quintanar, Annick Goursot, Rafael Grande-Aztatzi, Tzonka Mineva, Alberto Vela, Departamento de Quimica - Cinvestav, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), CONACYT Grant Nos. 128369 and 128255, and GENCI HPC resources of CCRT allocations t2011036031 and t20110818 more...
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inorganic chemicals ,Stereochemistry ,Coordination number ,Molecular Conformation ,Peptide ,Ligands ,chemistry.chemical_compound ,Coordination Complexes ,Materials Chemistry ,Side chain ,Molecule ,Humans ,Carboxylate ,Physical and Theoretical Chemistry ,Conformational isomerism ,chemistry.chemical_classification ,Amyloid beta-Peptides ,Hydrogen bond ,Ligand ,Electron Spin Resonance Spectroscopy ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,[CHIM.MATE]Chemical Sciences/Material chemistry ,Hydrogen-Ion Concentration ,Surfaces, Coatings and Films ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Oxygen ,chemistry ,Oxidation-Reduction ,Copper - Abstract
In spite of significant experimental effort dedicated to the study of Cu(2+) binding to the amyloid beta (Aβ) peptide, involved in Alzheimer's disease, the nature of the oxygen-based ligand in the low pH component of the Cu(2+)-Aβ(1-16) complex is still under debate. This study reports density-functional-theory-based calculations that explore the potential energy surface of Cu(2+) complexes including N and O ligands at the N-terminus of the Aβ peptide, with a focus on evaluating the role of Asp1 carboxylate in copper coordination. Model conformers including 3, 6, and 17 amino acids have been used to systematically study several aspects of the Cu(2+)-coordination such as the Asp1 side chain conformation, local peptide backbone geometry, electrostatic and/or hydrogen bond interactions, and number and availability of Cu(2+) ligands. Our results show that the Asp1 peptide carbonyl binds to Cu(2+) only if the coordination number is less than four. In contrast, if four ligands are available, the most stable structures include the Asp1 carboxylate in equatorial position instead of the Asp1 carbonyl group. The two lowest energy Cu(2+)-Aβ(1-17) models involve Asp1 COO(-), the N-terminus, and His6 and His14 as equatorial ligands, with either a carbonyl or a water molecule in the axial position. These models are in good agreement with experimental data reported for component I of the Cu(2+)-Aβ(1-16) complex, including EXAFS- and X-ray-derived Cu(2+)-ligand distances, Cu(2+) EPR parameters, and (14)N and (13)C superhyperfine couplings. Our results suggest that at low pH, Cu(2+)-Aβ species with Asp1 carboxylate equatorial coordination coexist with species coordinating the Asp1 carbonyl. Understanding the bonding mechanism in these species is relevant to gain a deeper insight on the molecular processes involving copper-amyloid-β complexes, such as aggregation and redox activity. more...
- Published
- 2014
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22. Structural models for Cu(II) bound to the fragment 92-96 of the human prion protein
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Liliana Quintanar, Alberto Vela, Lina Rivillas-Acevedo, and Rafael Grande-Aztatzi
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Circular dichroism ,Coordination sphere ,Stereochemistry ,animal diseases ,chemistry.chemical_element ,Electronic structure ,law.invention ,Metal ,law ,Materials Chemistry ,Molecule ,Humans ,PrPC Proteins ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Binding Sites ,Chemistry ,Circular Dichroism ,Electron Spin Resonance Spectroscopy ,Water ,Hydrogen-Ion Concentration ,Copper ,nervous system diseases ,Surfaces, Coatings and Films ,Crystallography ,visual_art ,visual_art.visual_art_medium ,Absorption (chemistry) ,Protein Binding - Abstract
The prion protein (PrP(C)) binds Cu(II) in its N-terminal region, and it is associated to a group of neurodegenerative diseases termed transmissible spongiform encephalopaties (TSEs). The isoform PrP(Sc), derived from the normal PrP(C), is the pathogenic agent of TSEs. Using spectroscopic techniques (UV-vis absorption, circular dichroism, and electron paramagnetic resonance) and electronic structure calculations, we obtained a structural description for the different pH-dependent binding modes of Cu(II) to the PrP(92-96) fragment. We have also evaluated the possibility of water molecule ligation to the His96-bound copper ion. Geometry-optimized structural models that reproduce the spectroscopic features of these complexes are presented. Two Cu(II) binding modes are relevant at physiological pH: 4N and 3NO equatorial coordination modes; these are best described by models with no participation of water molecules in the coordination sphere of the metal ion. In contrast, the 2N2O and N3O coordination modes that are formed at lower pH involve the coordination of an axial water molecule. This study underscores the importance of including explicit water molecules when modeling copper binding sites in PrP(C). more...
- Published
- 2012
23. Spectroscopic and electronic structure studies of copper(II) binding to His111 in the human prion protein fragment 106-115: evaluating the role of protons and methionine residues
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Italia Lomelí, Erika Barrios, Lina Rivillas-Acevedo, Sarai Teloxa, Liliana Quintanar, Javier García, Alberto Vela, and Rafael Grande-Aztatzi
- Subjects
Circular dichroism ,Methionine ,Ligand ,Stereochemistry ,Prions ,Circular Dichroism ,Electron Spin Resonance Spectroscopy ,Protonation ,Inorganic Chemistry ,Turn (biochemistry) ,Crystallography ,chemistry.chemical_compound ,Deprotonation ,chemistry ,Amide ,Humans ,Histidine ,Spectrophotometry, Ultraviolet ,Physical and Theoretical Chemistry ,Binding site ,Protons ,Copper - Abstract
The prion protein (PrP(C)) is implicated in the spongiform encephalopathies in mammals, and it is known to bind Cu(II) at the N-terminal region. The region around His111 has been proposed to be key for the conversion of normal PrP(C) to its infectious isoform PrP(Sc). The principal aim of this study is to understand the role of protons and methionine residues 109 and 112 in the coordination of Cu(II) to the peptide fragment 106-115 of human PrP, using different spectroscopic techniques (UV-vis absorption, circular dichroism, and electron paramagnetic resonance) in combination with detailed electronic structure calculations. Our study has identified a proton equilibrium with a pK(a) of 7.5 associated with the Cu(II)-PrP(106-115) complex, which is ascribed to the deprotonation of the Met109 amide group, and it converts the site from a 3NO to a 4N equatorial coordination mode. These findings have important implications as they imply that the coordination environment of this Cu binding site at physiological pH is a mixture of two species. This study also establishes that Met109 and Met112 do not participate as equatorial ligands for Cu, and that Met112 is not an essential ligand, while Met109 plays a more important role as a weak axial ligand, particularly for the 3NO coordination mode. A role for Met109 as a highly conserved residue that is important to regulate the protonation state and redox activity of this Cu binding site, which in turn would be important for the aggregation and amyloidogenic properties of the protein, is proposed. more...
- Published
- 2011
24. Insightsinto the Oxygen-Based Ligand of the Low pHComponent of the Cu2+-Amyloid-β Complex.
- Author
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CarlosZ. Gomez-Castro, Alberto Vela, Liliana Quintanar, Rafael Grande-Aztatzi, Tzonka Mineva, and Annick Goursot
- Published
- 2014
- Full Text
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