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Correction for 'Insight at the atomic scale of corrosion inhibition: DFT study of 8-hydroxyquinoline on oxidized aluminum surfaces' by Fatah Chiter et al., Phys. Chem. Chem. Phys., 2023, https://doi.org/10.1039/d2cp04626a.
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8-Hydroxyquinoline (8-HQ) is a promising organic molecule for the corrosion protection of aluminum and its alloys in the replacement of chromate salts. On the aluminum surface, the presence of an oxide layer naturally formed can influence the inhibition efficiency which depends on molecule-surface interactions. In the present study, we performed quantum chemical calculations on native 8-HQ, tautomer and 8-Q (deprotonated, H-abstracted or radical) molecules, adsorbed on an oxidized aluminum surface (γ-Al2O3(111)/Al(111)). All species have the ability to interact strongly with the oxidized aluminum surface and can form stable and dense organic films. The bonding strength of different species of 8-HQ on oxidized aluminum surfaces is more favorable for 8-Q and tautomer species than for the native 8-HQ molecule. On the surface, the native 8-HQ molecule is physisorbed, forming H-bonds, in contrast to the tautomer and 8-Q species that show the predominance of chemisorption modes, involving both H-bonds and covalent bonds at the molecule/substrate interface. The dispersion energy significantly contributes to the adsorption mechanism and increases with increasing molecular surface coverage, due to attractive molecule-molecule interactions. Regardless of surface coverage and considered reaction mechanisms, the 8-Q species is able to enhance the stability of all aluminum sites, and thus to slow down the anodic reaction. In contrast, the native molecule and the tautomeric form have no significant effect or even weakened the stability of aluminum surface atoms.
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Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO2 together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.
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Dióxido de Silício , Água , Adsorção , Leucina/química , Espectroscopia de Ressonância Magnética/métodos , Peptídeos/química , Dióxido de Silício/química , Água/químicaRESUMO
The emergence of antibiotic and anti-inflammatory agents in aquatic and terrestrial systems is becoming a serious threat to human and animal health worldwide. Because pharmaceutical compounds rarely exist individually in nature, interactions between various compounds can have unforeseen effects on their binding to mineral surfaces. This work demonstrates this important possibility for the case of two typical antibiotic and anti-inflammatory agents (nalidixic acid (NA) and niflumic acid (NFA)) bound at goethite (α-FeOOH) used as a model mineral surface. Our multidisciplinary study, which makes use of batch sorption experiments, vibration spectroscopy and periodic density functional theory calculations, reveals enhanced binding of the otherwise weakly bound NFA caused by unforeseen intermolecular interactions with mineral-bound NA. This enhancement is ascribed to the formation of a NFA-NA dimer whose energetically favored formation (-0.5 eV compared to free molecules) is predominantly driven by van der Waals interactions. A parallel set of efforts also showed that no cobinding occurred with sulfamethoxazole (SMX) because of the lack of molecular interactions with coexisting contaminants. As such, this article raises the importance of recognizing drug cobinding, and lack of cobinding, for predicting and developing policies on the fate of complex mixtures of antibiotics and anti-inflammatory agents in nature.
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Compostos de Ferro , Minerais , Adsorção , ÁguaRESUMO
By changing the ultrahigh vacuum (UHV) deposition method, classical sublimation versus electrospray ionization, one can tune the chemistry of a chiral dipeptide molecule (Gly-Pro, GP), when adsorbed on a Cu(110) surface, from anionic to zwitterionic. This chemical shift will influence the adsorption mode of the dipeptide, either in a three-point fashion in the case of anionic GP molecules with a strong interaction among the copper surface, both O atoms of the carboxylate moiety, and the nitrogen atoms, or in the case of zwitterions GP, the adsorption mode relies on the sole interaction of one carboxylate oxygen atom. These different anchoring modes strongly modify the expression of surface 2D chirality and the supramolecular assemblies with two very distinct unit cells.
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Cobre , Dipeptídeos/química , Adsorção , EstereoisomerismoRESUMO
Catalysts based on combinations of copper and cerium oxides are interesting alternatives to noble metal ones for processes involved in the production/purification of hydrogen produced from hydrocarbons or biomass like the water-gas shift or the preferential oxidation of CO reactions. Active sites for such processes have been proposed to correspond to reduced species formed at the interface between both oxides. The present work provides direct evidence of reduced copper species located at the interface and observed during the course of near-ambient XPS experiments performed over samples of copper oxide supported on ceria nanospheres and nanocubes subjected to interaction with CO at different temperatures. The analysis of XPS results is based on DFT+U calculations employed as a complementary method for the analysis of redox properties of the catalysts and core-level shifts produced upon such redox changes. Differences observed in interfacial redox properties as a function of the ceria support morphology appear to be most useful to explain catalytic properties of this type of system for mentioned processes.
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Cobre/química , Espectroscopia Fotoeletrônica/métodos , CatáliseRESUMO
(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [Smerieri, M.; Vattuone, L.; Kravchuk, T.; Costa, D.; Savio, L. (S)-Glutamic Acid on Ag(100): Self-Assembly in the Nonzwitterionic Form. Langmuir2011, 27, 2393-2404]. In particular, two of these structures, referred to as "square" and "flower" geometries, are found to coexist on the surface upon deposition at T = 350 K. The former assembly was fully resolved at the atomic level in the work of Smerieri et al. [Smerieri, M.; Vattuone, L.; Costa, D.; Tielens, F.; Savio, L. Self-Assembly of (S)-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation. Langmuir2010, 26, 7208-7215], in which we proved that the driving force for adsorption is the van der Waals interactions between the molecules and the Ag surface, that is, that molecules are in a physisorbed state. In this paper, we complete our work by presenting the characterization of the "flower" structure. In contrast to the case of the "square" assembly, a strong chemical bond between glutamic acid radicals and the surface is at the basis of the "flowers" geometry. Whereas the chemisorbed central GLU tetramer interacts strongly with the surface, the physisorbed surrounding GLU molecules conserve some degree of freedom in the layer which counterbalances the weak adsorption energy. The "flower" and the "square" assemblies have similar dispersion energy and H-bond interaction energy; as a consequence of the different chemical state of the GLU molecules, however, such contributions have a very different relative weight in the stabilization of the two structures.
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Epoxy-amines are used as structural adhesives deposited on Ti. The amine adhesion to a Ti surface depends highly on the surface state (oxidation, hydroxylation). Amines may adsorb above preadsorbed water molecules or substitute them to bind directly to surface Ti(4+) Lewis acid sites. The adsorption of a model amine molecule, diaminoethane (DAE), on a model surface, hydrated TiO2-anatase (101) surface, is investigated using Density Functional Theory including Dispersive forces (DFT-D) calculations. DAE adsorption and water substitution by DAE are exothermic processes and turn nearly isoenergetic at high coverage with adsorption-substitution energies around -0.3 eV (including dispersion forces and ZPE). Complementary ab initio molecular dynamics studies also suggest that the formation of an amine-water interaction induces water desorption from the surface at room temperature, a preliminary step towards the amine-Ti bond formation. An atomistic thermodynamic approach is developed to evaluate the interfacial free energy balance of both processes (adsorption and substitution). The main contributions to the energetic balance are dispersive interactions between molecules and the surface on the exergonic side, translational and rotational entropic contributions on the endergonic one. The substitution process is stabilized by 0.55 eV versus the adsorption one when free solvation, rotational and vibrational energies are considered. The main contribution to this free energy gain is due to water solvation. The calculations suggest that in toluene solvent with a water concentration of 10(-4) M or less, a full DAE layer replaces a preadsorbed water layer for a threshold concentration of DAE ≥ 0.1 M.
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Etilenodiaminas/química , Titânio/química , Adsorção , Aminas/química , Simulação de Dinâmica Molecular , Pressão , Propriedades de Superfície , Temperatura , Termodinâmica , Água/químicaRESUMO
Intermittent fasting (IF) and physical exercise (PE) have beneficial psychological and physiological effects, improving memory and anxiety-like behavior. However, the impact of this combination on brain electrophysiological patterns is unknown. We aimed to evaluate the behavior and parameters of a brain excitability-related phenomenon named cortical spreading depression (CSD) in young rats (31-87 days of life) submitted to IF and treadmill PE for eight weeks. Sixty-four male and female Wistar rats aged 24 days were randomized into control, IF, PE, and IF+PE groups. Behavioral tests (open field (OF), object recognition, and elevated plus maze (EPM)) were performed, and the CSD propagation features were recorded. IF caused behavioral responses indicative of anxiety (lower number of entries and time spent in the OF center and EPM open arms). IF also reduced the discrimination index for object recognition memory tests and increased the propagation velocity of CSD. PE rats displayed more entries into the OF center and lowered CSD propagation speed. Data suggest that IF worsens anxiety-like behavior and memory and accelerates CSD in young rats. In contrast, PE reverted the unfavorable effects of IF. The brain effects of IF and PE at younger ages are recommended for study.
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Sera from lung cancer patients contain antibodies against tumor-associated antigens. Specific amino acid sequences of the complementarity-determining regions (CDRs) in the antigen-binding fragment (Fab) of these antibodies have potential as lung cancer biomarkers. Detection and identification of CDRs by mass spectrometry can significantly be improved by reduction of the complexity of the immunoglobulin molecule. Our aim was to molecular dissect IgG into κ and λ fragments to reduce the complexity and thereby identify substantially more CDRs than by just total Fab isolation. We purified Fab, Fab-κ, Fab-λ, κ and λ light chains from serum from 10 stage I lung adenocarcinoma patients and 10 matched controls from the current and former smokers. After purification, the immunoglobulin fragments were enzymatically digested and measured by high-resolution mass spectrometry. Finally, we compared the number of CDRs identified in these immunoglobulin fragments with that in the Fab fragments. Twice as many CDRs were identified when Fab-κ, Fab-λ, κ and λ (3330) were combined than in the Fab fraction (1663) alone. The number of CDRs and κ:λ ratio was statistically similar in both cases and controls. Molecular dissection of IgG identifies significantly more CDRs, which increases the likelihood of finding lung cancer-related CDR sequences.
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Regiões Determinantes de Complementaridade/química , Cadeias kappa de Imunoglobulina/análise , Cadeias lambda de Imunoglobulina/análise , Espectrometria de Massas/métodos , Adenocarcinoma/sangue , Adenocarcinoma de Pulmão , Idoso , Estudos de Casos e Controles , Regiões Determinantes de Complementaridade/análise , Eletroforese em Gel de Poliacrilamida , Feminino , Humanos , Cadeias kappa de Imunoglobulina/sangue , Cadeias kappa de Imunoglobulina/química , Cadeias kappa de Imunoglobulina/isolamento & purificação , Cadeias lambda de Imunoglobulina/sangue , Cadeias lambda de Imunoglobulina/química , Cadeias lambda de Imunoglobulina/isolamento & purificação , Neoplasias Pulmonares/sangue , Masculino , Pessoa de Meia-Idade , Razão de Chances , Ensaios Clínicos Controlados Aleatórios como Assunto , Reprodutibilidade dos Testes , Fumar/sangueRESUMO
In cancer and autoimmune diseases, immunoglobulins with a specific molecular signature that could potentially be used as diagnostic or prognostic markers are released into body fluids. An immunomics approach based on this phenomenon relies on the ability to identify the specific amino acid sequences of the complementarity-determining regions (CDR) of these immunoglobulins, which in turn depends on the level of accuracy, resolution, and sensitivity that can be achieved by advanced mass spectrometry. Reproducible isolation and sequencing of antibody fragments (e.g., Fab) by high-resolution mass spectrometry (MS) from seven healthy donors revealed 43 217 MS signals: 225 could be associated with CDR1 peptides, 513 with CDR2 peptides, and 19 with CDR3 peptides. Seventeen percent of the 43 217 MS signals did not overlap between the seven donors. The Fab isolation method used is reproducible and fast, with a high yield. It provides only one Fab sample fraction for subsequent characterization by high-resolution MS. In 17% and 4% of these seven healthy donors, qualitative (presence/absence) and quantitative (intensity) differences in Fab fragments could be demonstrated, respectively. From these results, we conclude that the identification of a CDR signature as biomarker for autoimmune diseases and cancer without prior knowledge of the antigen is feasible.
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Regiões Determinantes de Complementaridade/química , Fragmentos Fab das Imunoglobulinas/sangue , Imunoglobulina G/sangue , Espectrometria de Massas em Tandem/métodos , Idoso , Sequência de Aminoácidos , Análise de Variância , Feminino , Humanos , Fragmentos Fab das Imunoglobulinas/química , Fragmentos Fab das Imunoglobulinas/metabolismo , Imunoglobulina G/química , Imunoglobulina G/metabolismo , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Reprodutibilidade dos Testes , Alinhamento de SequênciaRESUMO
UNLABELLED: Endocardial cushion defects (ECDs) of the cardiac outflow tract are among the most common congenital heart disease phenotypes. VEGF is essential for endocardial cushion formation and derangements in VEGF synthesis lead to ECD. Three functional single nucleotide polymorphisms (SNPs) in the VEGF gene -2578 C>A, -1154 G>A, and -634 G>C play a role in cardiogenesis. In a Dutch case-control family study of triads, 190 case and 317 control children with both parents, we investigated linkage and association between these VEGF SNPs and ECD. Allele frequencies for the three VEGF SNPs were comparable between ECD children and controls. However, VEGF alleles -2578 C and -1154 G were transmitted more frequently to children with ECD (p = 0.003 and p = 0.002), in particular perimembranous ventricular septal defects (p = 0.012 and p = 0.006). The -2578A/-1154A/-634G haplotype was associated with a reduced risk of ECD (OR 0.7; 95% CI, 0.6-1.0) and was significantly less transmitted to children with ECD (p = 0.002). In a Dutch population, we show that the VEGF 2578 C, -1154 G alleles, and the AAG haplotype are associated with ECD. Possible VEGF gene-environment interactions exposures are discussed. ABBREVIATIONS: :
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Endocárdio/patologia , Polimorfismo de Nucleotídeo Único , Fator A de Crescimento do Endotélio Vascular/genética , Estudos de Casos e Controles , Feminino , Frequência do Gene , Humanos , Lactente , MasculinoRESUMO
Nonsyndromic orofacial clefts (OFC) are common birth defects caused by certain genes interacting with environmental factors. Mutations and association studies indicate that the homeobox gene MSX1 plays a role in human clefting. In a Dutch case-control triad study (mother, father, and child), we investigated interactions between MSX1 and the parents' periconceptional lifestyle in relation to the risk of OFC in their offspring. We studied 181 case- and 132 control mothers, 155 case- and 121 control fathers, and 176 case- and 146 control children, in which there were 107 case triads and 66 control triads. Univariable and multivariable logistic regression analyses were applied, and odds ratios (OR), 95% confidence intervals (CI) were calculated. Allele 4 of the CA marker in the MSX1 gene, consisting of nine CA repeats, was the most common allele found in both the case and control triads. Significant interactions were observed between allele 4 homozygosity of the child with maternal smoking (OR 2.7, 95% CI 1.1-6.6) and with smoking by both parents (OR 4.9, 95% CI 1.4-18.0). Allele 4 homozygosity in the mother and smoking showed a risk estimate of OR 3.2 (95% CI 1.1-9.0). If allele 4 homozygous mothers did not take daily folic acid supplements in the recommended periconceptional period, this also increased the risk of OFC for their offspring (OR 2.8, 95% CI 1.1-6.7). Our findings show that, in the Dutch population, periconceptional smoking by both parents interacts with a specific allelic variant of MSX1 to significantly increase OFC risk for their offspring. Possible underlying mechanisms are discussed.
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Fenda Labial/etiologia , Fenda Labial/genética , Fissura Palatina/etiologia , Fissura Palatina/genética , Fator de Transcrição MSX1/genética , Poluição por Fumaça de Tabaco/efeitos adversos , Adulto , Alelos , Estudos de Casos e Controles , Feminino , Fertilização , Predisposição Genética para Doença , Homozigoto , Humanos , Lactente , Masculino , Gravidez , Fatores de RiscoRESUMO
The development of efficient energy conversion systems requires precise engineering of electrochemical interfaces and thus asks for in situ techniques to probe the structure and the composition of the dynamic electrode/electrolyte interfacial region. This work demonstrates the potential of the near ambient pressure X-ray photoelectron spectroscopy (NAPXPS) for in situ studies of processes occurring at the interface between a metal electrode and a liquid electrolyte. By using a model membrane-electrode assembly of a high temperature phosphoric acid-imbibed proton exchange membrane fuel cell, and combining NAPXPS measurements with the density functional theory, it was possible to monitor such fundamental processes as dissociation and migration of the phosphoric acid within a nanostructured Pt electrode under polarization.
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The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface.
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Simulação de Dinâmica Molecular , Teoria Quântica , Dióxido de Silício/química , Água/química , Ligação de Hidrogênio , Modelos Moleculares , Estrutura Molecular , Prótons , Silanos/química , Propriedades de SuperfícieRESUMO
The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far "excluded from biology" metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the protein's sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed.
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Late diagnosis of lung cancer is still the main reason for high mortality rates in lung cancer. Lung cancer is a heterogeneous disease which induces an immune response to different tumor antigens. Several methods for searching autoantibodies have been described that are based on known purified antigen panels. The aim of our study is to find evidence that parts of the antigen-binding-domain of antibodies are shared among lung cancer patients. This was investigated by a novel approach based on sequencing antigen-binding-fragments (Fab) of immunoglobulins using proteomic techniques without the need of previously known antigen panels. From serum of 93 participants of the NELSON trial IgG was isolated and subsequently digested into Fab and Fc. Fab was purified from the digested mixture by SDS-PAGE. The Fab containing gel-bands were excised, tryptic digested and measured on a nano-LC-Orbitrap-Mass-spectrometry system. Multivariate analysis of the mass spectrometry data by linear canonical discriminant analysis combined with stepwise logistic regression resulted in a 12-antibody-peptide model which was able to distinguish lung cancer patients from controls in a high risk population with a sensitivity of 84% and specificity of 90%. With our Fab-purification combined Orbitrap-mass-spectrometry approach, we found peptides from the variable-parts of antibodies which are shared among lung cancer patients.
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Anticorpos/imunologia , Antígenos de Neoplasias/imunologia , Região Variável de Imunoglobulina/imunologia , Neoplasias Pulmonares/imunologia , Peptídeos/imunologia , Idoso , Sequência de Aminoácidos , Anticorpos/química , Anticorpos/genética , Estudos de Casos e Controles , Cromatografia Líquida , Feminino , Humanos , Fragmentos Fab das Imunoglobulinas/química , Fragmentos Fab das Imunoglobulinas/imunologia , Região Variável de Imunoglobulina/química , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/patologia , Masculino , Espectrometria de Massas , Pessoa de Meia-Idade , Dados de Sequência Molecular , Estadiamento de Neoplasias , Peptídeos/química , Reprodutibilidade dos TestesRESUMO
Interactions between biomolecules and inorganic surfaces play an important role in natural environments and in industry, including a wide variety of conditions: marine environment, ship hulls (fouling), water treatment, heat exchange, membrane separation, soils, mineral particles at the earth's surface, hospitals (hygiene), art and buildings (degradation and biocorrosion), paper industry (fouling) and more. To better control the first steps leading to adsorption of a biomolecule on an inorganic surface, it is mandatory to understand the adsorption mechanisms of biomolecules of several sizes at the atomic scale, that is, the nature of the chemical interaction between the biomolecule and the surface and the resulting biomolecule conformations once adsorbed at the surface. This remains a challenging and unsolved problem. Here, we review the state of art in experimental and theoretical approaches. We focus on metallic biomaterial surfaces such as TiO(2) and stainless steel, mentioning some remarkable results on hydroxyapatite. Experimental techniques include atomic force microscopy, surface plasmon resonance, quartz crystal microbalance, X-ray photoelectron spectroscopy, fluorescence microscopy, polarization modulation infrared reflection absorption spectroscopy, sum frequency generation and time of flight secondary ion mass spectroscopy. Theoretical models range from detailed quantum mechanical representations to classical forcefield-based approaches.