66 results on '"Carmen Sousa"'
Search Results
2. Portuguese Neonatal Screening Program: A Cohort Study of 18 Years Using MS/MS
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Maria Miguel Gonçalves, Ana Marcão, Carmen Sousa, Célia Nogueira, Helena Fonseca, Hugo Rocha, and Laura Vilarinho
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Portuguese neonatal screening program ,neonatal screening ,inborn errors of metabolism (IEM) ,second-tier testing (2TT) ,Pediatrics ,RJ1-570 - Abstract
The Portuguese Neonatal Screening Program (PNSP) conducts nationwide screening for rare diseases, covering nearly 100% of neonates and screening for 28 disorders, including 24 inborn errors of metabolism (IEMs). The study’s purpose is to assess the epidemiology of the screened metabolic diseases and to evaluate the impact of second-tier testing (2TT) within the PNSP. From 2004 to 2022, 1,764,830 neonates underwent screening using tandem mass spectrometry (MS/MS) to analyze amino acids and acylcarnitines in dried blood spot samples. 2TT was applied when necessary. Neonates with profiles indicating an IEM were reported to a reference treatment center, and subsequent biochemical and molecular studies were conducted for diagnostic confirmation. Among the screened neonates, 677 patients of IEM were identified, yielding an estimated birth prevalence of 1:2607 neonates. The introduction of 2TT significantly reduced false positives for various disorders, and 59 maternal cases were also detected. This study underscores the transformative role of MS/MS in neonatal screening, emphasizing the positive impact of 2TT in enhancing sensitivity, specificity, and positive predictive value. Our data highlight the efficiency and robustness of neonatal screening for IEM in Portugal, contributing to early and life-changing diagnoses.
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- 2024
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3. Phenylketonuria in Portugal: Genotype–phenotype correlations using molecular, biochemical, and haplotypic analyses
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Filipa Ferreira, Luísa Azevedo, Raquel Neiva, Carmen Sousa, Helena Fonseca, Ana Marcão, Hugo Rocha, Célia Carmona, Sónia Ramos, Anabela Bandeira, Esmeralda Martins, Teresa Campos, Esmeralda Rodrigues, Paula Garcia, Luísa Diogo, Ana Cristina Ferreira, Silvia Sequeira, Francisco Silva, Luísa Rodrigues, Ana Gaspar, Patrícia Janeiro, António Amorim, and Laura Vilarinho
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biochemical and genetic findings ,haplotypic study ,mutation spectrum ,phenylketonuria ,Portuguese population ,Genetics ,QH426-470 - Abstract
Abstract Background The impairment of the hepatic enzyme phenylalanine hydroxylase (PAH) causes elevation of phenylalanine levels in blood and other body fluids resulting in the most common inborn error of amino acid metabolism (phenylketonuria). Persistently high levels of phenylalanine lead to irreversible damage to the nervous system. Therefore, early diagnosis of the affected individuals is important, as it can prevent clinical manifestations of the disease. Methods In this report, the biochemical and genetic findings performed in 223 patients diagnosed through the Portuguese Neonatal Screening Program (PNSP) are presented. Results Overall, the results show that a high overlap exists between different types of variants and phenylalanine levels. Molecular analyses reveal a wide mutational spectrum in our population with a total of 56 previously reported variants, most of them found in compound heterozygosity (74% of the patients). Intragenic polymorphic markers were used to assess the haplotypic structure of mutated chromosomes for the most frequent variants found in homozygosity in our population (p.Ile65Thr, p.Arg158Gln, p.Leu249Phe, p.Arg261Gln, p.Val388Met, and c.1066‐11G>A). Conclusion Our data reveal high heterogeneity at the biochemical and molecular levels and are expected to provide a better understanding of the molecular basis of this disease and to provide clues to elucidate genotype–phenotype correlations.
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- 2021
- Full Text
- View/download PDF
4. LPS Modulates the Expression of Iron-Related Immune Genes in Two Antarctic Notothenoids
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Danixa Pamela Martínez, Carmen Sousa, Ricardo Oyarzún, Juan Pablo Pontigo, Adelino V. M. Canario, Deborah Mary Power, Luis Vargas-Chacoff, and Pedro Miguel Guerreiro
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Notothenia coriiceps ,Notothenia rossii ,iron metabolism ,Antarctic fish ,nutritional immunity ,Physiology ,QP1-981 - Abstract
The non-specific immunity can induce iron deprivation as a defense mechanism against potential bacterial pathogens, but little information is available as to its role in Antarctic fish. In this study the response of iron metabolism related genes was evaluated in liver and head kidney of the Antarctic notothenoids Notothenia coriiceps and Notothenia rossii 7 days after lipopolysaccharide (LPS) injection. Average plasma Fe2+ concentration was unaffected by treatment in any of the species. The gene expression response to LPS varied between tissues and species, being stronger in N. coriiceps and more prominent in the head kidney than liver. The reaction to LPS was marked by increased individual variability in most genes analyzed, even when the change in expression was not statistically significant, suggesting different individual sensitivity and coping responses in these wild fish. We found that iron related genes had an attenuated and homogenous response to LPS but there was no detectable relationship between plasma Fe2+ and gene expression. However, overall in both tissues and species LPS exposure set a multilevel response that concur to promote intracellular accumulation of iron, an indication that Antarctic Notothenoids use innate nutritional immunity as a resistance mechanism against pathogens.
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- 2020
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- View/download PDF
5. Role of RNA in Molecular Diagnosis of MADD Patients
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Célia Nogueira, Lisbeth Silva, Ana Marcão, Carmen Sousa, Helena Fonseca, Hugo Rocha, Teresa Campos, Elisa Leão Teles, Esmeralda Rodrigues, Patrícia Janeiro, Ana Gaspar, and Laura Vilarinho
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glutaric aciduria type II ,MADD ,β-oxidation ,ETFDH ,NBS ,RNA ,Biology (General) ,QH301-705.5 - Abstract
The electron-transfer flavoprotein dehydrogenase gene (ETFDH) encodes the ETF-ubiquinone oxidoreductase (ETF-QO) and has been reported to be the major cause of multiple acyl-CoA dehydrogenase deficiency (MADD). In this study, we present the clinical and molecular diagnostic challenges, at the DNA and RNA levels, involved in establishing the genotype of four MADD patients with novel ETFDH variants: a missense variant, two deep intronic variants and a gross deletion. RNA sequencing allowed the identification of the second causative allele in all studied patients. Simultaneous DNA and RNA investigation can increase the number of MADD patients that can be confirmed following the suggestive data results of an expanded newborn screening program. In clinical practice, accurate identification of pathogenic mutations is fundamental, particularly with regard to diagnostic, prognostic, therapeutic and ethical issues. Our study highlights the importance of RNA studies for a definitive molecular diagnosis of MADD patients, expands the background of ETFDH mutations and will be important in providing an accurate genetic counseling and a prenatal diagnosis for the affected families.
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- 2021
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6. The Role of Vibrational Anharmonicity in the Computational Study of Thermal Spin Crossover
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Jianfang Wu, Carmen Sousa, and Coen de Graaf
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spin crossover ,iron complexes ,vibrational frequencies ,transition temperature ,DFT ,anharmonicity ,Chemistry ,QD1-999 - Abstract
Spin crossover in transition metal complexes can be studied in great detail with computational chemistry. Over the years, the understanding has grown that the relative stability of high-spin (HS) versus low-spin (LS) states is a subtle balance of many factors that all need to be taken into account for a reliable description. Among the different contributions, the zero-point energy (ZPE) and the entropy play key roles. These quantities are usually calculated assuming a harmonic oscillator model for the molecular vibrations. We investigated the impact of including anharmonic corrections on the ZPE and the entropy and indirectly on the critical temperature of spin crossover. As test systems, we used a set of ten Fe(II) complexes and one Fe(III) complex, covering different coordination modes (mono-, bi-, and tri-dentate ligands), decreasing coordination number upon spin crossover, coordination by second- and third-row atoms, and changes in the oxidation state. The results show that the anharmonicity has a measurable effect, but it is in general rather small, and tendencies are not easily recognized. As a conclusion, we put forward that for high precision results, one should be aware of the anharmonic effects, but as long as computational chemistry is still struggling with other larger factors like the influence of the environment and the accurate determination of the electronic energy difference between HS and LS, the anharmonicity of the vibrational modes is a minor concern.
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- 2019
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7. Toward a Rigorous Theoretical Description of Photocatalysis Using Realistic Models
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Ángel Morales-García, Francesc Viñes, Carmen Sousa, and Francesc Illas
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Electronic structure ,Titanium dioxide ,Estructura electrònica ,General Materials Science ,Superfícies (Física) ,Diòxid de titani ,Physical and Theoretical Chemistry ,Surfaces (Physics) - Abstract
This Perspective aims at providing a road map to computational heterogeneous photocatalysis highlighting the knowledge needed to boost the design of efficient photocatalysts. A plausible computational framework is suggested focusing on static and dynamic properties of the relevant excited states as well of the involved chemistry for the reactions of interest. This road map calls for explicitly exploring the nature of the charge carriers, the excited-state potential energy surface, and its time evolution. Excited-state descriptors are introduced to locate and characterize the electrons and holes generated upon excitation. Nonadiabatic molecular dynamics simulations are proposed as a convenient tool to describe the time evolution of the photogenerated species and their propagation through the crystalline structure of photoactive material, ultimately providing information about the charge carrier lifetime. Finally, it is claimed that a detailed understanding of the mechanisms of heterogeneously photocatalyzed reactions demands the analysis of the excited-state potential energy surface.
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- 2023
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8. Understanding kinetically controlled spin transitions in bistable spin crossover materials
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Sergi Vela, Maria Fumanal, and Carmen Sousa
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Materials Chemistry ,General Chemistry - Abstract
Kinetic rate constants are evaluated computationally for the spin-forbidden thermal relaxations of SCO complexes, unveiling their mechanism, and retrieving accurate TLIESST predictions.
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- 2023
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9. Deconstruir una imagen. Algunas notas sobre la iconografía del (des)amor maternal en el surrealismo
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Carmen Sousa-Pardo
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History ,Affect theory ,Visual Arts and Performing Arts ,Motherhood ,Amor ,Mujeres ,Love ,Maternidad ,Teoría de los afectos ,Iconography ,Woman ,Surrealismo ,Iconografía ,Surrealism - Abstract
El propósito del presente artículo es revisitar, desde otra perspectiva, la de la maternidad, el papel que dos de las temáticas centrales del Surrealismo, las mujeres y el amor, tuvieron en el movimiento. Para el Surrealismo, la maternidad, necesariamente opuesta al deseo, constituía una barrera para la liberación absoluta de las pasiones a la que confiaban el proyecto revolucionario. Desde el punto de vista femenino, la anulación del sujeto que suponía la maternidad era también la de sus deseos y, por tanto, una limitación para su desarrollo como artistas. Ironizando sobre las fórmulas anteriores y creando otras nuevas, la iconografía surrealista de la maternidad será ante todo la de una deconstrucción: la de la imagen que la presentaba como sinónimo de felicidad femenina., The aim of this article is to revise the role of women and love in surrealism from another perspective: that of motherhood. For the surrealists, motherhood, inevitably opposed to desire, was a barrier to the absolute liberation of the passions, a liberation on which they relied in their revolutionary project. From the feminine point of view, the annulment of the subject that motherhood entailed was also an annulment of her desires and so a limitation for the development of artists. While ironizing on previous iconographies and establishing new formulas, the surrealist iconography of motherhood will be, above all, that of a deconstruction: that of the image presenting the mother as a synonym of female happiness.
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- 2022
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10. Bandgap Engineering of MXene Compounds for Water Splitting
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Diego Ontiveros, Francesc Viñes, and Carmen Sousa
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Renewable Energy, Sustainability and the Environment ,General Materials Science ,General Chemistry - Abstract
MXenes compounds, a recently discovered family of 2D materials, have been found to become semiconductors and photoactive when their pristine surfaces are functionalized with an electronegative termination. MXenes may present...
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- 2023
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11. EDUCOMUNICAÇÃO: UMA EXPERIÊNCIA TEÓRICO-PRATICO NA ASSOCIAÇÃO DE JUVENTUDES, CULTURA E CIDADANIA EM SÃO JOSÉ DA MATA, CAMPINA GRANDE – PB
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Lígia Beatriz Carvalho de Almeida, Camila Eduarda Travassos Silva, Ramon Araújo de Souza, Carmen Sousa, Leonardo Pereira Tavares, and Anderson de Albuquerque Gomes
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- 2021
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12. Role of RNA in Molecular Diagnosis of MADD Patients
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Elisa Leão Teles, Carmen Sousa, Helena Fonseca, Ana Maria Minarelli Gaspar, Ana Marcão, Patrícia Janeiro, Laura Vilarinho, Esmeralda Rodrigues, Teresa Campos, Lisbeth Silva, Célia Regina Nogueira, and Hugo Rocha
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0301 basic medicine ,QH301-705.5 ,Genetic counseling ,Medicine (miscellaneous) ,Case Report ,Prenatal diagnosis ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,NBS ,Genotype ,Medicine ,Missense mutation ,Allele ,Biology (General) ,Gene ,Genetics ,Newborn screening ,business.industry ,RNA ,MADD ,ETFDH ,030104 developmental biology ,glutaric aciduria type II ,β-oxidation ,business ,030217 neurology & neurosurgery - Abstract
The electron-transfer flavoprotein dehydrogenase gene (ETFDH) encodes the ETF-ubiquinone oxidoreductase (ETF-QO) and has been reported to be the major cause of multiple acyl-CoA dehydrogenase deficiency (MADD). In this study, we present the clinical and molecular diagnostic challenges, at the DNA and RNA levels, involved in establishing the genotype of four MADD patients with novel ETFDH variants: a missense variant, two deep intronic variants and a gross deletion. RNA sequencing allowed the identification of the second causative allele in all studied patients. Simultaneous DNA and RNA investigation can increase the number of MADD patients that can be confirmed following the suggestive data results of an expanded newborn screening program. In clinical practice, accurate identification of pathogenic mutations is fundamental, particularly with regard to diagnostic, prognostic, therapeutic and ethical issues. Our study highlights the importance of RNA studies for a definitive molecular diagnosis of MADD patients, expands the background of ETFDH mutations and will be important in providing an accurate genetic counseling and a prenatal diagnosis for the affected families.
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- 2021
13. Phenylketonuria in Portugal: Genotype-Phenotype Correlations Using Molecular, Biochemical, and Haplotypic Analyses
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Francisco Silva, Sónia Ramos, Helena Fonseca, Luísa Azevedo, Filipa Ferreira, Raquel Neiva, Carmen Sousa, Ana Marcão, Laura Vilarinho, Paula Garcia, Patrícia Janeiro, Sílvia Sequeira, Esmeralda Martins, António Amorim, Esmeralda Rodrigues, Luísa Diogo, Anabela Bandeira, Hugo Rocha, Ana C. Ferreira, Ana Maria Minarelli Gaspar, Teresa Campos, Célia Carmona, Luísa C. Rodrigues, and Instituto de Investigação e Inovação em Saúde
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0301 basic medicine ,Male ,Phenylalanine hydroxylase ,HDE MTB ,biochemical and genetic findings ,Population ,phenylketonuria ,Phenylalanine ,Disease ,QH426-470 ,030105 genetics & heredity ,Biology ,Compound heterozygosity ,Biochemical ,03 medical and health sciences ,Portuguese population ,Neonatal Screening ,Gene Frequency ,Liver enzyme ,Phenylketonurias ,Genetics ,Humans ,Phenylketonuria ,Haplotypic Study ,Mutation Spectrum ,education ,Molecular Biology ,Genotype-Phenotype Correlations ,Genetics (clinical) ,haplotypic study ,education.field_of_study ,Portugal ,Homozygote ,Infant, Newborn ,Phenylalanine Hydroxylase ,Original Articles ,Biochemical and genetic findings ,030104 developmental biology ,Phenotype ,Haplotypes ,Genetic marker ,Mutation ,biology.protein ,mutation spectrum ,Genetic Findings ,Female ,Original Article - Abstract
Background The impairment of the hepatic enzyme phenylalanine hydroxylase (PAH) causes elevation of phenylalanine levels in blood and other body fluids resulting in the most common inborn error of amino acid metabolism (phenylketonuria). Persistently high levels of phenylalanine lead to irreversible damage to the nervous system. Therefore, early diagnosis of the affected individuals is important, as it can prevent clinical manifestations of the disease. Methods In this report, the biochemical and genetic findings performed in 223 patients diagnosed through the Portuguese Neonatal Screening Program (PNSP) are presented. Results Overall, the results show that a high overlap exists between different types of variants and phenylalanine levels. Molecular analyses reveal a wide mutational spectrum in our population with a total of 56 previously reported variants, most of them found in compound heterozygosity (74% of the patients). Intragenic polymorphic markers were used to assess the haplotypic structure of mutated chromosomes for the most frequent variants found in homozygosity in our population (p.Ile65Thr, p.Arg158Gln, p.Leu249Phe, p.Arg261Gln, p.Val388Met, and c.1066‐11G>A). Conclusion Our data reveal high heterogeneity at the biochemical and molecular levels and are expected to provide a better understanding of the molecular basis of this disease and to provide clues to elucidate genotype–phenotype correlations., The present study identify and characterize the variants underlying PKU in affected individuals in the Portuguese PKU/HPA cohort. Biochemical data, haplotic analysis and genetic findings performed in 223 patients diagnosed through the Portuguese Neonatal Screening Program (PNSP) is presented. The information obtained will improve the diagnostic applicability of mutational analysis and the capacity to predict the evolution of the disease.
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- 2021
14. Galanin isoforms by alternative splicing: Structure, expression, and immunohistochemical location in the gonads of European sea bass
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Carmen Sousa, Rute S.T. Martins, Patrícia Pinto, Adelino V.M. Canario, Silvia Zanuy, Ana M. Gómez, Gregorio Molés, André R. Andrade, European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Economía y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), and Universidade do Algarve
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Gene isoform ,Male ,LH ,endocrine system ,Sea bass ,Neuropeptide ,030209 endocrinology & metabolism ,Ovary ,Galanin ,Biology ,Oogenesis ,03 medical and health sciences ,0302 clinical medicine ,Endocrinology ,FSH ,medicine ,Animals ,Protein Isoforms ,Gonads ,Spermatogenesis ,Gametogenesis ,030304 developmental biology ,0303 health sciences ,Galanin receptors ,Cell biology ,Alternative Splicing ,medicine.anatomical_structure ,Theca ,Animal Science and Zoology ,Bass ,Female ,Immunostaining - Abstract
Galanin (Gal) is a neuropeptide with multiple functions that is widely expressed in the central and peripheral nervous systems of vertebrates. Anatomical and functional evidence suggests a possible role in regulating reproduction in fishes. To test this possibility, we have isolated and characterized two gal alternative transcripts in European sea bass (Dicentrarchus labrax) that encode two prepropeptides, respectively of 29 (gal_MT853221) and 53 (gal_MT853222) amino acids. The two gal transcripts are highly expressed in brain, pituitary and gonads, and appear to be differentially regulated in males and females. In males, gal_MT853222 in the hypothalamus and gal_MT853221 in the pituitary were downregulated with the progression of spermatogenesis (stages I-III). Both transcripts are downregulated in testicles of 1-year (precocious) and 2-year spermiating males compared to immature fish of the same age. Gal peptides and receptors are expressed throughout ovarian development in the hypothalamic-pituitary-gonadal (HPG) axis of females. In the testis, immunoreactive Gal-29 and Gal-53 peptides were detected in blood vessels and Leydig cells during the spermatogenesis stages I-III but Gal immunostaining was barely undetected in more advanced stages. In the ovary, both peptides localized in interstitial cells and blood vessels and in theca cells surrounding the maturing oocytes. The immunolocalization of galanin in Leydig and theca cells suggests a possible role in steroid production regulation. The different pattern of gal expression and Gal localization in the testis and ovary may suggest the possibility that androgens and estrogens may also regulate Gal gene transcription and translation. Altogether, this study showed evidence for the possible involvement of locally produced Gal in gametogenesis and that its production is differentially regulated in male and female gonads., This research was funded by the Portuguese national funds from FCT (Foundation of Science and Technology, I.P.) through projects UIDB/04326/2020 and PTDC/MAR-BIO/3890/2012 and by the European Union Seventh Framework Programme AQUAEXCEL (Grant Agreement 262336, TNA project 318). AG and GM were supported by Spanish MINECO (AGL2015-67477-C2-1-R) and CSIC (201640E073). R.S.T.M and P.I.S.P were supported by FCT under contracts of Norma transitória (DL 57/2016/CP1361/CT0021 and DL57/2016/CP6321/CT0015, respectively) with Universidade do Algarve. We acknowledge Zélia Velez for the help during sampling, Deborah Power for IHC advice and Victoria Alvarado and Alicia Felip for providing hypothalamus and pituitary RNA panels.
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- 2021
15. Clinical, biochemical and molecular findings of 24 Brazilian patients with glutaric acidemia type 1: 4 novel mutations in the GCDH gene
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Carmen Regla Vargas, Carmen Sousa, Gilian Guerreiro, Angela Sitta, Vitoria Volfart da Rocha, Laura Vilarinho, Bianca Gomes dos Reis, Daniella de Moura Coelho, and Moacir Wajner
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Male ,0301 basic medicine ,medicine.medical_specialty ,Pediatrics ,Late Diagnosis ,Neurology ,DNA Mutational Analysis ,Glutaric aciduria type 1 ,Disease ,Gene mutation ,medicine.disease_cause ,Biochemistry ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,0302 clinical medicine ,medicine ,Humans ,Amino Acid Metabolism, Inborn Errors ,Dystonia ,Newborn screening ,Mutation ,Glutaryl-CoA Dehydrogenase ,Brain Diseases, Metabolic ,business.industry ,Infant, Newborn ,Infant ,medicine.disease ,Doenças Genéticas ,030104 developmental biology ,GCDH gene ,Female ,Neurology (clinical) ,business ,030217 neurology & neurosurgery ,Glutaric Acidemia Type 1 ,Brazil ,Mutations - Abstract
Glutaric aciduria type 1 (GA-1) is a rare but treatable inherited disease caused by deficiency of glutaryl-CoA dehydrogenase activity due to GCDH gene mutations. In this study, we report 24 symptomatic GA-1 Brazilian patients, and present their clinical, biochemical, and molecular findings. Patients were diagnosed by high levels of glutaric and/or 3-hydroxyglutaric and glutarylcarnitine. Diagnosis was confirmed by genetic analysis. Most patients had the early-onset severe form of the disease and the main features were neurological deterioration, seizures and dystonia, usually following an episode of metabolic decompensation. Despite the early symptomatology, diagnosis took a long time for most patients. We identified 13 variants in the GCDH gene, four of them were novel: c.91 + 5G > A, c.167T > G, c.257C > T, and c.10A > T. The most common mutation was c.1204C > T (p.R402W). Surprisingly, the second most frequent mutation was the new mutation c.91 + 5G > A (IVS1 ds G-A + 5). Our results allowed a complete characterization of the GA-1 Brazilian patients. Besides, they expand the mutational spectrum of GA-1, with the description of four new mutations. This work reinforces the importance of awareness of GA-1 among doctors in order to allow early diagnosis and treatment in countries like Brazil where the disease has not been included in newborn screening programs. info:eu-repo/semantics/publishedVersion
- Published
- 2020
16. Limitations of the equivalent core model for understanding core-level spectroscopies
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Paul S. Bagus, Carmen Sousa, and Francesc Illas
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Physics ,General Physics and Astronomy ,02 engineering and technology ,Electronic structure ,State (functional analysis) ,Fotoelectrons ,Espectroscòpia ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Spectrum analysis ,0104 chemical sciences ,Interpretation (model theory) ,Core level ,Statistical physics ,Relaxation (approximation) ,Physical and Theoretical Chemistry ,Core model ,0210 nano-technology ,Photoelectrons - Abstract
The equivalent core model, or the Z + 1 approximation, has been used to interpret the binding energy, BE, shifts observed in X-ray photoelectron spectroscopy, XPS; in particular to relate these shifts to their origin in the electronic structure of the system. Indeed, a recent paper has claimed that the equivalent core model provides an intuitive chemical view of XPS BE shifts. In the present paper, we present a detailed comparison of the electronic structure provided from rigorous core-hole theory and from the equivalent core model to assess the validity and the utility of the use of the equivalent core model. This comparison shows that the equivalent core model provides a qualitative view of the different properties of initial and core-hole electronic structure. It is also shown that a very serious limitation of the equivalent core model is that it fails to distinguish between initial and final state contributions to the shifts of BEs which seriously reduces the utility of the information obtained with the equivalent core model. Indeed, there is a danger of making an incorrect assignment of the importance of relaxation because the equivalent core model appears to stress the role of final state effects. Given the importance of the distinction of initial and final state effects, we provide rigorous definitions of these two effects and we discuss an example where an incorrect interpretation was made based on the use of the equivalent core model.
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- 2020
17. [Portuguese Newborn Screening Program.]
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Hugo, Rocha, Ana, Marcão, Carmen, Sousa, Helena, Fonseca, Lurdes, Lopes, Ivone, Carvalho, and Laura, Vilarinho
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Neonatal Screening ,Portugal ,Infant, Newborn ,Humans ,Program Evaluation - Abstract
The Portuguese Newborn Screening Program is a public health program that started in 1979, screening for PKU, being totally supported by public funds. It's a non-mandatory well implemented program that testes about 99.9% of Portuguese newborns. In the actual screening panel encompasses 26 disorders, including inborn errors of metabolism, congenital hypothyroidism and cystic fibrosis. Sample collection is advised to be made at 3rd day of life and treatment begins in average by the 10th day. Every testes are performed in one single national laboratory, that processes about 88,000 samples/year. In the 41 years of program existence, more than 3,800,000 newborns were screened and 2,130 affected newborns detected, reflecting the positive impact of the Program in the population. Future perspectives include the increase of program value in terms of public health by optimizing the screening of the disorders already screened and evaluation the possibility of adding others.El Programa Portugués de Cribado Neonatal es un programa de Salud Pública a nivel nacional, que tuvo su inicio en 1979 con el cribado de la fenilcetonuria y es financiado totalmente por el Estado portugués. Se trata de un programa no obligatorio, con una tasa de cobertura del 99,8%, en el que hoy en día se criban veintiséis enfermedades, incluyendo metabolopatías, hipotiroidismo congénito y fibrosis quística. La toma de muestra se hace al 3er día de vida y el tratamiento de los neonatos afectos empieza en torno al 10º día. Todos los análisis están centralizados en un único laboratorio, que procesa aproximadamente 88.000 muestras al año. En los últimos cuarenta y un años se cribaron más de 3.800.000 neonatos y se detectaron 2.130 niños afectados, lo que es un indicador del impacto del programa en la población. Los desafíos futuros incluyen la búsqueda de nuevas estrategias para incrementar el valor del programa, donde se evalúen nuevas enfermedades a cribar y la optimización del cribado actual.
- Published
- 2020
18. Effect of electron correlation in the decomposition of core level binding energy shifts into initial and final state contributions
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Marc Figueras, Francesc Illas, and Carmen Sousa
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Nanoestructures ,Materials science ,Electronic correlation ,Binding energy ,General Physics and Astronomy ,02 engineering and technology ,Electron ,Espectroscòpia de raigs X ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Decomposition ,Nanostructures ,0104 chemical sciences ,Chemical bond ,X-ray photoelectron spectroscopy ,Chemical physics ,Ionization ,X-ray spectroscopy ,Molecule ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
The influence of electron correlation into the decomposition of core level binding energy shifts, measured by X-ray photoelectron spectroscopy (XPS), into initial and final effects is analysed for a series of molecules where these effects are noticeable. Moreover, the series of molecules is chosen in such a way that electron delocalization and increasing number of electrons may provide a large screening of the core hole. A detailed analysis shows that the Hartree-Fock decomposition is biased whereas a physically meaningful decomposition is obtained when electron correlation effects are taken into account. The results show that in this case, trends in core level binding energy shifts are driven by initial state effects thus providing further support to the use of these observable quantities to interpret changes in the chemical bond in the neutral molecule rather than on the core ionized cation. Consequences for the theoretical interpretation of XPS data in materials and surface science are discussed.
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- 2019
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19. Erratum: LPS Modulates the Expression of Iron-Related Immune Genes in Two Antarctic Notothenoids
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Danixa Pamela Martínez, Carmen Sousa, Ricardo Oyarzún, Juan Pablo Pontigo, Adelino V. M. Canario, Deborah Mary Power, Luis Vargas-Chacoff, and Pedro Miguel Guerreiro
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0301 basic medicine ,Lipopolysaccharide ,Physiology ,Antarctic fish ,Notothenia coriiceps ,nutritional immunity ,lcsh:Physiology ,Notothenia rossii ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Immunity ,Physiology (medical) ,Gene expression ,iron metabolism ,Immune gene ,Gene ,Original Research ,Head Kidney ,lcsh:QP1-981 ,biology ,04 agricultural and veterinary sciences ,Metabolism ,biology.organism_classification ,Nutritional immunity ,Iron metabolism ,Cell biology ,030104 developmental biology ,chemistry ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Erratum ,Intracellular - Abstract
The non-specific immunity can induce iron deprivation as a defense mechanism against potential bacterial pathogens, but little information is available as to its role in Antarctic fish. In this study the response of iron metabolism related genes was evaluated in liver and head kidney of the Antarctic notothenoids Notothenia coriiceps and Notothenia rossii 7 days after lipopolysaccharide (LPS) injection. Average plasma Fe2+ concentration was unaffected by treatment in any of the species. The gene expression response to LPS varied between tissues and species, being stronger in N. coriiceps and more prominent in the head kidney than liver. The reaction to LPS was marked by increased individual variability in most genes analyzed, even when the change in expression was not statistically significant, suggesting different individual sensitivity and coping responses in these wild fish. We found that iron related genes had an attenuated and homogenous response to LPS but there was no detectable relationship between plasma Fe2+ and gene expression. However, overall in both tissues and species LPS exposure set a multilevel response that concur to promote intracellular accumulation of iron, an indication that Antarctic Notothenoids use innate nutritional immunity as a resistance mechanism against pathogens. FCT-NSFC/0002/2016; CCMAR/Multi/04326/2013; PTDC/BIAANM/3484/2014 info:eu-repo/semantics/publishedVersion
- Published
- 2020
20. Deactivation of Excited States in Transition-Metal Complexes: Insight from Computational Chemistry
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Alex Domingo, Coen de Graaf, Marc Alías, and Carmen Sousa
- Subjects
Photochemistry ,010405 organic chemistry ,Process (engineering) ,Chemistry ,Scale (chemistry) ,Organic Chemistry ,Time evolution ,Transition metals ,General Chemistry ,Metalls de transició ,010402 general chemistry ,01 natural sciences ,Quantum chemistry ,Catalysis ,0104 chemical sciences ,Fotoquímica ,Computational chemistry ,Spin crossover ,Excited state ,Nuclear spin ,Energy transformation ,Spin (Física nuclear) ,Química quàntica ,Spin-½ - Abstract
Investigation of the excited state decay dynamics of transition metal systems is a crucial step for the development of photoswitchable molecular based ma- terials with applications in growing fields as energy conversion, data storage or molecular devices. The photophysics of these systems is an entangled problem arising from the interplay of electronic and geometrical rearrangements that take place on a short time scale. Several factors play a role in the process: various electronic states of di↵erent spin and chemical character are involved, the system undergoes important structural variations and several nonradiative processes can occur. Computational chemistry is a useful tool to get insight into the micro- scopic description of the photophysics of these materials since it provides unique information about the character of the electronic spin states involved, the ener- getics and time evolution of the system. In this review article, we present an overview of the state of the art methodologies available to address the several aspects that have to be incorporated to properly describe the deactivation of excited states in transition metal complexes. The most recent developments in theoretical methods are discussed and illustrated with examples.
- Published
- 2018
- Full Text
- View/download PDF
21. Theoretical Study of the Light-Induced Spin Crossover Mechanism in [Fe(mtz)6]2+ and [Fe(phen)3]2+
- Author
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Coen de Graaf, Carmen Sousa, Ria Broer, Andrii Rudavskyi, and Theoretical Chemistry
- Subjects
Ligand field theory ,Iron ,RELAXATION ,Ligands ,010402 general chemistry ,01 natural sciences ,ISOLATED IRON(II) COMPLEX ,DENSITY-FUNCTIONAL THEORY ,Spin crossover ,Singlet state ,Physical and Theoretical Chemistry ,Wave function ,Wave functions ,Density functionals ,BASIS-SETS ,TRANSIENT ABSORPTION-SPECTROSCOPY ,010405 organic chemistry ,Ligand ,Chemistry ,Relaxation (NMR) ,Teoria del funcional de densitat ,LIGAND-FIELD ,STATE ,0104 chemical sciences ,Lligands ,Chemical physics ,Molecular vibration ,PERTURBATION-THEORY ,Condensed Matter::Strongly Correlated Electrons ,Density functional theory ,TRANSITION ,PHOTOPHYSICS ,Ferro ,Funcions d'ona - Abstract
The deactivation pathway of the light-induced spin crossover process in two Fe(II) complexes has been studied by combining density functional theory calculations for the geometries and the normal vibrational modes and highly correlated wave function methods for the energies and spin orbit coupling effects. For the two systems considered, the mechanism of the photoinduced conversion from the low-spin singlet to the high-spin quintet state implies two intersystem crossings through intermediate triplet states. However, for the [Fe(mtz)(6)](2+) complex, the process occurs within few picoseconds and involves uniquely metal-centered electronic states, whereas for the [Fe(phen)(3)](2+) system the deactivation channel involves both metal to ligand charge transfer and metal-centered states and takes place in a femtosecond time scale.
- Published
- 2017
- Full Text
- View/download PDF
22. Correcting flaws in the assignment of nitrogen chemical environments in N-doped graphene
- Author
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Francesc Illas, Víctor A. de la Peña O’Shea, Carmen Sousa, Marc Figueras, Francesc Viñes, and Ignacio J. Villar-Garcia
- Subjects
Materials science ,Grafè ,Binding energy ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Molecular physics ,Spectral line ,law.invention ,Interpretation (model theory) ,X-ray photoelectron spectroscopy ,law ,Physical and Theoretical Chemistry ,Oligòmers ,Graphene ,Espectroscòpia de raigs X ,021001 nanoscience & nanotechnology ,Nitrogen ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,General Energy ,chemistry ,Electrocatàlisi ,Oligomers ,X-ray spectroscopy ,Core level ,Doped graphene ,0210 nano-technology ,Electrocatalysis - Abstract
X-ray Photoelectron Spectroscopy (XPS) applied to N-doped graphene leads to a rather broad N(1s) core level signal that, based on different sources available in the literature, is most often interpreted by fitting the experimental spectra to three peaks. The resulting N(1s) features are assigned to graphitic, pyrrolic, and pyridinic nitrogen, even if these are far from being uniquely defined in the literature. This broadly accepted interpretation has been questioned by recent accurate Hartree-Fock calculations concluding that graphitic and pyrrolic N(1s) core level binding energies are too close to be distinguished. Consideration of models with N in other so far unexplored environments such as N dimers or N at defects show some variations in the calculated core level binding energies. However, these are not large enough to justify a third peak and suggest that the usual three peaks interpretation of the N(1s) XPS in N-doped graphene may be an artefact caused by the fitting procedure. New measurements have been carried out for samples of N-doped graphene and the obtained N(1s) spectra fitted to two or three peaks. It turns out that the spectra can be equally fitted using two or three peaks but only the former is consistent with the results of the unbiased ab initio calculations which calls for a revision of the usual assignment.
- Published
- 2019
23. Approaching multiplet splitting in X-ray photoelectron spectra by density functional theory methods: NO and O2 molecules as examples
- Author
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Paul S. Bagus, Carmen Sousa, and Francesc Illas
- Subjects
Physics ,Nanoestructures ,Binding energy ,General Physics and Astronomy ,Teoria del funcional de densitat ,02 engineering and technology ,Espectroscòpia de raigs X ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,Spectral line ,Spin contamination ,0104 chemical sciences ,Nanostructures ,Ionization ,X-ray spectroscopy ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,0210 nano-technology ,Multiplet ,Open shell ,Density functionals - Abstract
The ability of density functional theory (DFT) based methods to predict the multiplet splitting arising from the core hole ionization of molecules such as NO and O2, exhibiting an open shell grounds state, is explored. In the NO molecule, N(1s) or O(1s) ionization leads to 3Π and 1Π multiplets whereas for O2, the presence of an O(1s) core hole leads to doublet and quartet multiplets with distinct BEs. Multiplet splittings obtained using different exchange-correlation functionals show an overall good agreement with experiment and minor variations within the functionals studied when spin contamination resulting from unrestricted DFT calculations is accounted for.
- Published
- 2019
24. Differential many-body effects for initial and core-ion states: impact on XPS spectra
- Author
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Francesc Illas, Paul S. Bagus, and Carmen Sousa
- Subjects
Physics ,Nanoestructures ,010304 chemical physics ,Binding energy ,Ionic bonding ,Espectroscòpia de raigs X ,010402 general chemistry ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Ion ,Nanostructures ,X-ray photoelectron spectroscopy ,0103 physical sciences ,Atom ,X-ray spectroscopy ,Molecule ,Singlet state ,Physical and Theoretical Chemistry ,Wave function - Abstract
In this paper, the contribution of many body effects to the X-ray photoelectron spectroscopy, XPS, of an NO molecule are studied using wavefunction theory where the specific consequences of different many-body terms are examined and contrasted. It is shown that there is a differential importance of the many-body effects for the different configurations involved in the XPS. These are the ground, initial state configuration and final, N(1s) and O(1s) core-hole ionic configurations. The consequences of the many-body effects are examined for the binding energies, BEs, to the two final state multiplets, triplet and singlet, for each of the core ions and for the relative intensities of the XPS transitions to these multiplets. The many body effects examined are those described as static effects that arise for individual terms that are important. The objective is to understand the chemical and physical origins that determine the importance of the correlation effects for the XPS, rather than to obtain very accurate predictions of the BEs. An important theoretical construct that is tested and justified is the equivalent core approximation where the core ionized atom is replaced by the next higher element in the periodic table. This construct allows us to establish a correlation for the relative importance of the many-body effects in terms of effective charges of the different atoms. This is a correlation that has not been considered before and that we expect may have general relevance. The potential of the effects that we have identified for the XPS of NO to be relevant for the XPS of more complex, condensed phase systems is considered.
- Published
- 2019
25. Effect of second-order spin-orbit coupling on the interaction between spin states in spin-crossover systems
- Author
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Coen de Graaf, Alex Domingo, and Carmen Sousa
- Subjects
Spin states ,010402 general chemistry ,01 natural sciences ,Catalysis ,Reaccions químiques ,Spin crossover ,Computational chemistry ,Metallic composites ,Quantum mechanics ,Chemical reactions ,0103 physical sciences ,Spin (Física nuclear) ,Singlet state ,Spin-½ ,Coupling ,010304 chemical physics ,Spin polarization ,Chemistry ,Organic Chemistry ,General Chemistry ,Spin–orbit interaction ,0104 chemical sciences ,Excited state ,Nuclear spin ,Condensed Matter::Strongly Correlated Electrons ,Compostos metàl·lics - Abstract
Investigation of the excited state decay dynamics of transition metal systems is a crucial step for the development of photoswitchable molecular based ma- terials with applications in growing fields as energy conversion, data storage or molecular devices. The photophysics of these systems is an entangled problem arising from the interplay of electronic and geometrical rearrangements that take place on a short time scale. Several factors play a role in the process: various electronic states of di↵erent spin and chemical character are involved, the system undergoes important structural variations and several nonradiative processes can occur. Computational chemistry is a useful tool to get insight into the micro- scopic description of the photophysics of these materials since it provides unique information about the character of the electronic spin states involved, the ener- getics and time evolution of the system. In this review article, we present an overview of the state of the art methodologies available to address the several aspects that have to be incorporated to properly describe the deactivation of excited states in transition metal complexes. The most recent developments in theoretical methods are discussed and illustrated with examples.
- Published
- 2018
26. On the prediction of core level binding energies in molecules, surfaces and solids
- Author
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Francesc Viñes, Francesc Illas, and Carmen Sousa
- Subjects
Materials science ,Nanoestructures ,010304 chemical physics ,Binding energy ,General Physics and Astronomy ,Teoria del funcional de densitat ,02 engineering and technology ,Espectroscòpia de raigs X ,021001 nanoscience & nanotechnology ,01 natural sciences ,Nanostructures ,Fotoemissió ,X-ray photoelectron spectroscopy ,Chemical physics ,0103 physical sciences ,Theoretical methods ,X-ray spectroscopy ,Core level ,Molecule ,Physical and Theoretical Chemistry ,0210 nano-technology ,Photoemission ,Density functionals - Abstract
Core level binding energies, directly measured by X-ray photoelectron spectroscopy (XPS), provide unique information regarding the chemical environment of atoms in a given system. However, interpretation of XPS in extended systems may not be straightforward and requires assistance from theory. The different state-of-the-art theoretical methods commonly used to approach core level binding energies and their shifts with respect to a given reference are reviewed and critically assessed with special emphasis on recently developed theoretical methods and with a focus on future applications in materials and surface sciences.
- Published
- 2018
27. Theoretical evidence for the direct 3MLCT-HS deactivation in the light-induced spin crossover of Fe(II)-polypyridyl complexes
- Author
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Carmen Sousa, Miquel Llunell, Coen de Graaf, and Alex Domingo
- Subjects
education.field_of_study ,Materials science ,010405 organic chemistry ,Magnetism ,Iron ,Population ,General Physics and Astronomy ,010402 general chemistry ,Ligands ,01 natural sciences ,0104 chemical sciences ,Molecular dynamics ,Intersystem crossing ,Lligands ,Transition metal ,Chemical physics ,Spin crossover ,Metastability ,Nuclear spin ,Direct coupling ,Spin (Física nuclear) ,Physical and Theoretical Chemistry ,education ,Ferro - Abstract
Spin-orbit couplings have been calculated in twenty snapshots of a molecular dynamics trajectory of [Fe(bpy)3]2+ to address the importance of geometrical distortions and second-order spin-orbit coupling on the intersystem crossing rate constants in the light-induced spin crossover process. It was found that the effective spin-orbit coupling between the 3MLCT and 5T2 state is much larger than the direct coupling in the symmetric structure, which opens the possibility of a direct 3MLCT-5T2 deactivation without the intervention of triplet metal-centered states. Based on the calculated deactivation times, we conclude that both the direct path- way and the one involving intermediate triplet states are active in the ultrafast population of the metastable HS state, bringing in agreement two experimental observations that advocate for either deactivation mechanism. This resolves a long-standing dispute about the deactivation mechanism of Fe(II)-polypyridyl complexes in particular, and about light-induced magnetism in transition metal complexes in general.
- Published
- 2018
28. Theoretical Study of the Light-Induced Spin Crossover Mechanism in [Fe(mtz)
- Author
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Carmen, Sousa, Coen, de Graaf, Andrii, Rudavskyi, and Ria, Broer
- Abstract
The deactivation pathway of the light-induced spin crossover process in two Fe(II) complexes has been studied by combining density functional theory calculations for the geometries and the normal vibrational modes and highly correlated wave function methods for the energies and spin-orbit coupling effects. For the two systems considered, the mechanism of the photoinduced conversion from the low-spin singlet to the high-spin quintet state implies two intersystem crossings through intermediate triplet states. However, for the [Fe(mtz)
- Published
- 2017
29. Responsiveness of pituitary to galanin throughout the reproductive cycle of male European sea bass (Dicentrarchus labrax)
- Author
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Alicia Felip, Soraia Santos, Zélia Velez, Carmen Sousa, M. V. Alvarado, André R. Andrade, Silvia Zanuy, Adelino V.M. Canario, Patrícia Pinto, Foundation for Science and Technology, European Commission, Ministerio de Economía y Competitividad (España), Generalitat Valenciana, Andrade, A., Felip, Alicia, Zanuy, Silvia, Canário, Adelino V. M., Andrade, A. [0000-0002-5900-8782], Felip, Alicia [0000-0003-4708-9754], Zanuy, Silvia [0000-0002-8231-8260], and Canário, Adelino V. M. [0000-0002-6244-6468]
- Subjects
Male ,0301 basic medicine ,Sexual-dimorphism ,Immunoreactive neurons ,Autoradiographic distribution ,Gametogenesis ,Follicle-stimulating hormone ,Endocrinology ,Cyclic AMP ,Gene-expression ,Luteinizing-hormone secretion ,Receptor ,biology ,Reproduction ,Carassius-auratus ,Lh-release ,Hypothalamus ,Pituitary Gland ,Dicentrarchus ,Luteinizing hormone ,hormones, hormone substitutes, and hormone antagonists ,medicine.medical_specialty ,endocrine system ,Neuropeptide ,Galanin ,03 medical and health sciences ,Internal medicine ,medicine ,Animals ,RNA, Messenger ,14. Life underwater ,Sea bass ,European sea bass ,Gene Expression Profiling ,Colforsin ,Binding-sites ,Luteinizing Hormone ,biology.organism_classification ,030104 developmental biology ,Pituitary ,Bass ,Animal Science and Zoology ,Follicle Stimulating Hormone ,Receptors, Galanin ,Teleost fish ,Gonadotropins ,Knockout mice - Abstract
The neuropeptide galanin (Gal) is a putative factor regulating puberty onset and reproduction through its actions on the pituitary. The present study investigated the pituitary responsiveness to galanin and the patterns of galanin receptors (Galrs) expression throughout the reproductive cycle of two years old male European sea bass (Dicentrarchus labrax), an important aquaculture species. Quantitative analysis of pituitary and hypothalamus transcript expression of four galr subtypes revealed differential regulation according to the testicular developmental stage, with an overall decrease in expression from the immature stage to the mid-recrudescence stage. Incubation of pituitary cells with mammalian 1–29 Gal peptide induced significant changes in cAMP concentration, with sensitivities that varied according to the testicular development stages. Furthermore 1–29 Gal was able to stimulate both follicle stimulating hormone (Fsh) and luteinizing hormone (Lh) release from pituitary cell suspensions. The magnitude of the effects and effective concentrations varied according to reproductive stage, with generalized induction of Fsh and Lh release in animals sampled in January (full spermiation). The differential expression of galrs in pituitary and hypothalamus across the reproductive season, together with the differential effects of Gal on gonadotropins release in vitro strongly suggests the involvement of the galaninergic system in the regulation the hypothalamus-pituitary-gonad axis of male sea bass. This is to our knowledge the first clear evidence for the involvement of galanin in the regulation of reproduction in non-mammalian vertebrates., This work was supported by the Portuguese Foundation for Science and Technology [grant numbers SFRH/BPD/84033/2012, PTDC/MAR-BIO/3890/2012, UID/Multi/04326/2013]; the European Union Seventh Framework Programme [AQUAEXCEL grant number 262336]; the Spanish Ministry of Science and Innovation (MICINN) and the Spanish Ministry of the Economy and Competitiveness (MINECO) [KISSCONTROL project, AGL2009-11086]; the Spanish Ministry of the Economy and Competitiveness and the Regional Government of Valencia (REPROBASS project, PROMETEOII/2014/051).
- Published
- 2017
30. Assessing the ability of DFT methods to describe static electron correlation effects: CO core level binding energies as a representative case
- Author
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Francesc Illas, Noèlia Pueyo Bellafont, Carmen Sousa, Paul S. Bagus, and Universitat de Barcelona
- Subjects
Better than average ,010304 chemical physics ,Electronic correlation ,Chemistry ,Binding energy ,General Physics and Astronomy ,Teoria del funcional de densitat ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,Surface chemistry ,Química de superfícies ,0103 physical sciences ,Core level ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,Atomic physics ,Total energy ,0210 nano-technology ,Wave function ,Density functionals - Abstract
We use a total energy difference approach to explore the ability of various density functional theory based methods in accounting for the differential effect of static electron correlation on the C(1s) and O(1s) core level binding energies (BEs) of the CO molecule. In particular, we focus on the magnitude of the errors of the computed C(1s) and O(1s) BEs and on their relative difference as compared to experiment and to previous results from explicitly correlated wave functions. Results show that the different exchange-correlation functionals studied here behave rather erratically and a considerable number of them lead to large errors in the BEs and/or the BE shifts. Nevertheless, the TPSS functional, its TPSSm and RevTPSS derivations, and its corresponding hybrid counterpart, TPSSh, perform better than average and provide BEs and BE shifts in good agreement with experiment.
- Published
- 2017
31. Molecular picture of cobalamin C/D defects before and after newborn screening era
- Author
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Célia Nogueira, H. Rocha, Helena Fonseca, Carla Valongo, Ana Marcão, Laura Vilarinho, and Carmen Sousa
- Subjects
Male ,0301 basic medicine ,Pediatrics ,medicine.medical_specialty ,Expanded Newborn Screening ,Mitochondrial Membrane Transport Proteins ,Cobalamin ,03 medical and health sciences ,chemistry.chemical_compound ,Neonatal Screening ,Genotype ,Ethnicity ,Prevalence ,medicine ,Humans ,Vitamin B12 ,MMACHC ,Early onset ,MMADHC ,Newborn screening ,Portugal ,business.industry ,Health Policy ,Blood Spots ,Infant, Newborn ,Intracellular Signaling Peptides and Proteins ,Public Health, Environmental and Occupational Health ,Quality Improvement ,Doenças Genéticas ,Vitamin B 12 ,030104 developmental biology ,chemistry ,Mutation ,Immunology ,Cohort ,Female ,CBLC ,Carrier Proteins ,Oxidoreductases ,business ,Metabolism, Inborn Errors - Abstract
Objective Birth prevalence of Cobalamin (Cbl) C or D defects in Portugal is an estimated 1:85,000, one of the highest worldwide. We compared the genotype/phenotype of patients identified with CblC or CblD before and after the implementation of expanded newborn screening. Methods Twenty-five Portuguese CblC/D patients, 14 symptomatic and 11 identified through screening, were diagnosed using gas chromatography or tandem mass spectrometry. Molecular characterization was performed through the study of MMACHC and MMADHC genes. Results The most common MMACHC mutation, c.271dupA, was present in 100% of MMACHC alleles of all CblC screened patients, in contrast with the 61% identified before expanded newborn screening. All studied cases (except one, who presented a CblD deficiency) presented a CblC defect. More CblC late-onset patients were diagnosed before the introduction of newborn screening than in the post newborn screening era, probably because some early onset patients died without a definitive diagnosis. Conclusion The molecular data found in this cohort contribute to the improvement of screening and diagnosis of Cbl defects and would enable a confirmatory diagnosis of these patients, reducing the need for complex, costly, laborious, and time-consuming biochemical/enzymatic tests.
- Published
- 2017
32. Explanation of the site-specific spin crossover in Fe(mtz)(6)(BF4)(2)
- Author
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Carmen Sousa, Coen de Graaf, Andrii Rudavskyi, Ria Broer, Remco W. A. Havenith, Química Física i Inorgànica, Universitat Rovira i Virgili., Theoretical Chemistry, and Zernike Institute for Advanced Materials
- Subjects
chemistry.chemical_classification ,AB-INITIO ,DENSITY-FUNCTIONAL METHODS ,Spin states ,Condensed matter physics ,Double bond ,CASPT2 ,STATE ENERGETICS ,STRUCTURAL DYNAMICS ,Ab initio ,EXCITED-STATE ,Crystal structure ,Electronic structure ,TRANSITION-METAL-COMPLEXES ,Inorganic Chemistry ,chemistry.chemical_compound ,ELECTRONIC-STRUCTURE ,chemistry ,Chemical physics ,Spin crossover ,SYSTEMS ,Excited state ,Tetrazole ,BASIS-SETS - Abstract
10.1039/c3dt52027g The spin crossover behavior of the two [Fe(mtz)6](2+) complexes occupying different lattice sites in Fe(mtz)6(BF4)2 is addressed by combining quantum chemical calculations with a careful analysis of the crystal structure. It is first established from the calculations that the energy difference between high spin and low spin states depends on the orientation of the tetrazole ligands; small rotation angles favor the low spin state, while for angles larger than ~20° the high spin state is more stable. The crystal structure shows that the two complexes have different average rotation angles of the ligands. It is larger for the site that remains HS down to low temperatures and smaller for the site that shows spin crossover to LS. The origin of the different rotation angles is found to be determined by a subtle interplay amongst steric repulsion between the ligands, HF interactions between the complex and the counterions, and intersite interactions involving NH contacts and p-p interactions between the N[double bond, length as m-dash]N double bonds of the tetrazole rings.
- Published
- 2013
- Full Text
- View/download PDF
33. 3-Methylcrotonyl-CoA carboxylase deficiency: Mutational spectrum derived from comprehensive newborn screening
- Author
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Ana Marcão, Luísa Azevedo, Laura Vilarinho, Carmen Sousa, Helena Fonseca, and Catarina Serrano
- Subjects
0301 basic medicine ,Male ,Context (language use) ,Biology ,Bioinformatics ,Mutational spectra ,Organic aciduria ,03 medical and health sciences ,Unknown Significance ,Genetics ,medicine ,Humans ,Mass Screening ,Gene ,Newborn screening ,Portugal ,Infant, Newborn ,Infant ,General Medicine ,3-Methylcrotonyl-CoA carboxylase deficiency ,medicine.disease ,Pyruvate carboxylase ,030104 developmental biology ,Carbon-Carbon Ligases ,Child, Preschool ,Mutation ,Female ,Metabolism, Inborn Errors - Abstract
The deficiency of 3-methycrotonyl-CoA carboxylase (3-MCC; EC 6.4.1.4) is an autosomal recessive organic aciduria that is included in the newborn screening programs of several countries. This study reports data mainly obtained from the Portuguese newborn screening program collected over a ten-year period. Analysis of the MCCC1 and MCCC2 genes yielded 26 previously unreported mutations and a variant of clinically unknown significance. These mutations are discussed in the context of their likely impact on the function of the 3-MCC enzyme, with a view to exploring whether a phenotype-genotype correlation might be discerned. Further, these mutations were analysed in the context of what is known of the MCCC1 and MCCC2 mutational spectra, information that will be useful in both clinical and laboratory practice.
- Published
- 2016
34. Cover Feature: Effect of Second-Order Spin-Orbit Coupling on the Interaction between Spin States in Spin-Crossover Systems (Chem. Eur. J. 20/2018)
- Author
-
Coen de Graaf, Alex Domingo, and Carmen Sousa
- Subjects
Spin states ,Condensed matter physics ,Cover (topology) ,Chemistry ,Ab initio quantum chemistry methods ,Spin crossover ,Organic Chemistry ,Order (ring theory) ,General Chemistry ,Spin–orbit interaction ,Femtochemistry ,Catalysis - Published
- 2018
- Full Text
- View/download PDF
35. Four years of expanded newborn screening in Portugal with tandem mass spectrometry
- Author
-
Rui Vaz Osório, Mário Bogas, Carmen Sousa, Laura Vilarinho, Ana Marcão, Helena Fonseca, and Hugo Rocha
- Subjects
Pediatrics ,medicine.medical_specialty ,Time Factors ,Tandem mass spectrometry ,Screening programme ,Neonatal Screening ,Predictive Value of Tests ,Tandem Mass Spectrometry ,Carnitine ,Prevalence ,Genetics ,medicine ,Humans ,False Positive Reactions ,Genetic Predisposition to Disease ,Amino Acids ,Genetics (clinical) ,Newborn screening ,Portugal ,business.industry ,Glutaric aciduria ,Infant, Newborn ,Prognosis ,medicine.disease ,Doenças Genéticas ,Congenital hypothyroidism ,Early Diagnosis ,Phenotype ,Predictive value of tests ,National laboratory ,business ,Biomarkers ,Metabolism, Inborn Errors ,Program Evaluation ,medicine.drug - Abstract
INTRODUCTION: The Portuguese Neonatal Screening Programme (PNSP) was started in 1979 for phenylketonuria (2,590,700 newborns screened; prevalence 1:11,031) and, shortly after, for congenital hypothyroidism (2,558,455 newborns screened; prevalence 1:3,174). In 2004, expanded neonatal screening was implemented in the National Laboratory. The programme is not mandatory and has 99.8% coverage of the country (including Madeira and the Azores islands). MATERIAL AND METHODS: In the past 4 years, 316,243 neonates were screened with the use of tandem mass spectrometry (MS/MS) to test for selected amino acids and acylcarnitines. RESULTS: During this time, 132 patients were identified with 24 different inherited metabolic diseases (classic forms and variants). To date, the global frequency for all disorders integrated into the PNSP is estimated to be 1:1,380, with 1:2,396 for metabolic disorders. A total of 379 tests (0.12%) were classified as having false positive results, yielding an overall specificity of 99.9%. Despite the low frequency of several disorders, the positive predictive value of the overall MS/MS screening was found to be 26%, reflecting high diagnostic specificity of the method. Diagnostic sensitivity of extended screening for the different groups of disorders was 100%. Eight cases of maternal disorders [three glutaric aciduria type I, one carnitine transporter defect, and four 3-methylcrotonyl coenzyme A (CoA) carboxylase deficiency] were also detected through newborn screening. CONCLUSIONS: Our data support the advantage of a centralised laboratory for screening an elevated number of samples and making decisions if relying on a clinical network able to provide fast treatment and a good outcome in the screened cases.
- Published
- 2010
- Full Text
- View/download PDF
36. Promoter and poisoning effects on NO-catalyzed dissociation on bimetallic RhCu(111) surfaces
- Author
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Carmen Sousa, Silvia González, and Francesc Illas
- Subjects
Chemistry ,Inorganic chemistry ,chemistry.chemical_element ,Catalysis ,Dissociation (chemistry) ,Transition state ,Rhodium ,Adsorption ,Transition metal ,Physical chemistry ,Physical and Theoretical Chemistry ,Bimetallic strip ,Single crystal - Abstract
A systematic density functional study of NO dissociation on Rh(111), Cu(111), and two different RhCu(111) bimetallic surfaces was conducted using a periodic supercell approach. Properties of the transition states, energy barriers, and transition state theory reaction rates were obtained for relevant situations involving NO adsorbed on different compositions of fcc and hcp sites. The results demonstrate that the superior activity of Rh versus Cu toward NO dissociation has its origin in the stronger adsorption on the former surface, which permits NO dissociation without the need for extra energy to the system. Moreover, the presence of Cu atoms on a Rh surface exerts a promoter effect by decreasing the energy barrier with respect to the value for the single crystal surface. In contrast, the presence of Rh atoms on a Cu surface has a poisoning effect. Analysis of the adsorption energies provides some important clues as to the modification of the corresponding energy barriers induced by the presence of the second metal. The results indicate that it is possible to improve the catalytic properties of Rh surfaces by adding small quantities of Cu, in agreement with previous experimental findings.
- Published
- 2006
- Full Text
- View/download PDF
37. Assessing the zero-field splitting in magnetic molecules by wave function-based methods
- Author
-
Carmen Sousa and Coen de Graaf
- Subjects
Electronic correlation ,Chemistry ,Dimer ,Ionic bonding ,Zero field splitting ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Ion ,chemistry.chemical_compound ,Complete active space ,Physical and Theoretical Chemistry ,Atomic physics ,Wave function ,Quantum - Abstract
The effect of spin-orbit coupling is assessed through the spin-orbit state interaction method. This method involves a two-step procedure to include both dynamical electron correlation effects and spin-orbit effects on the relative energies of the low-lying electronic states. Accurate energies of the spin free states are obtained with the complete active space self-consistent field/complete active space second-order perturbation theory (CASSCF/CASPT2) procedure. Second, the spin-orbit coupling is taken into account by interaction of the CASSCF states using the CASPT2 relative energies. The method is validated on the Co2+ ion in vacuum and in the ionic insulator CoO. Afterward the method is applied to CoCl2(PPh3)2 and the dinuclear complexes [TM2Cl6]2− (TM = Mn, Fe, Co). For the monomeric species, the results compare favorable with experimental data or fully relativistic benchmarks. We discuss the difficulties to interpret the dimer results in terms of the parameters that are usually derived from experiment. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
- Published
- 2006
- Full Text
- View/download PDF
38. Hopping matrix elements from first-principles studies of overlapping fragments: Double exchange parameters in manganites
- Author
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Ria Broer, C. de Graaf, Carmen Sousa, A. Stoyanova, and Theoretical Chemistry
- Subjects
Ab initio ,Electron ,manganites ,CASCI ,state interaction ,DENSITY-FUNCTIONAL THEORY ,ATOMS ,Matrix (mathematics) ,Atomic orbital ,SYSTEMS ,WAVE-FUNCTIONS ,Cluster (physics) ,SPECTRA ,Physical and Theoretical Chemistry ,LAMNO3 ,Wave function ,AB-INITIO ,EXCITATIONS ,Electronic correlation ,Chemistry ,double exchange ,COMPOUND ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Condensed Matter::Strongly Correlated Electrons ,Density functional theory ,Atomic physics ,TRANSITION - Abstract
We recently developed a scheme for first-principles calculations of hopping matrix elements between localized states in extended systems. We apply the scheme to the determination of double exchange (DE) parameters in lightly hole-doped LaMnO(3) and electron-doped CaMnO(3). DE is one of the important factors for understanding the properties of doped manganites. The calculations are based on the construction of wave functions for localized hole states or localized electron states for large embedded clusters. The wave functions of these clusters are expressed in terms of localized orbitals, obtained from calculations on smaller units, or "fragments," centered around a transition metal ion. The starting point of electronic states expressed in terms of localized orbital sets is conceptually attractive. It also allows for a rigorous treatment of local electron correlation and electronic relaxation effects. In the present study, the fragments are embedded [MnO(6)] units. The large clusters contain either two or four Mn ions and all neighboring oxygen ligands. The results are compared with conventional embedded cluster calculations. In both compounds, the effective hopping matrix elements, or "double exchange" (DE) parameters, in the ab planes (in the Pbnm space group) are larger than along the c axes. We found nearly perfect agreement with the Anderson-Hasegawa model for the spin dependence of the DE parameters. Nearest-neighbor parameters are more than one order of magnitude larger than next nearest-neighbor parameters. In LaMnO(3) the DE in the ab planes is approximate to -0.26 eV. If there were no Jahn-Teller distortion present in the material, it would have been twice as large. In CaMnO(3), the corresponding nearest-neighbor DE parameter for hopping of a doped electron in the ab planes is only approximate to -0.17 eV, due to the antiparallel spin coupling. However, since this interaction is much larger than the exchange coupling, we suggest that it induces local ferromagnetic clusters around the doped electrons. (C) 2006 Wiley Periodicals, Inc.
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- 2006
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39. Effect of the surface model on the theoretical description of the chemisorption of atomic hydrogen on Cu()
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David Dominguez-Ariza, Nicholas M. Harrison, Carmen Sousa, Francesc Illas, and Maria Veronica Ganduglia-Pirovano
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Work (thermodynamics) ,Chemistry ,Binding energy ,Charge density ,Surfaces and Interfaces ,Hydrogen atom ,Condensed Matter Physics ,Surfaces, Coatings and Films ,Adsorption ,Chemical physics ,Chemisorption ,Materials Chemistry ,Cluster (physics) ,Supercell (crystal) ,Physical chemistry - Abstract
Adsorption at surfaces can be modelled using a periodic supercell approach or using finite clusters. For many systems and properties these models are complementary and often the most productive way to work is to use a combination of these techniques. If reliable data is to be obtained it is essential that convergence is achieved with respect to the size of supercell and cluster. This work discusses the convergence of chemisorption properties of H on Cu(0 0 1) with respect to the cluster size. To this end,calculations of the H binding energy and equilibrium distance are reported for cluster models of increasing size containing up to 77 metal atoms. Likewise,periodic slab model calculations are used to provide the corresponding values towards which the cluster approach should converge. In many previous studies of a wide variety of systems it has been established that computed equilibrium distances converge rapidly with respect to cluster size. Here,a systematic study of the dependence on cluster size shows that,for adsorption in the fourfold site,convergence is not achieved even for very large clusters. The reason for this poor convergence is seen to be the inability of the cluster model to reproduce accurately the charge density and electrostatic potential of the crystalline surface. 2002 Elsevier Science B.V. All rights reserved.
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- 2003
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40. A Quantum Chemical Model for Electric Field Induced Electron Transfer at Metal Electrodes. Application to Halide Oxidation on Cu(100)
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David Domfnguez-Ariza, Francesc Illas, and Carmen Sousa
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Field (physics) ,Chemistry ,Halide ,Electron ,Half-cell ,Surfaces, Coatings and Films ,Electron transfer ,Chemical physics ,Electric field ,Electrode ,Materials Chemistry ,Physical and Theoretical Chemistry ,Atomic physics ,Electrode potential - Abstract
A model based on the use of ab initio quantum chemical explicitly correlated wave functions is proposed to study the electronic transfer reaction between an adsorbate and a metallic electrode. In this model, the effects of the electrode potential are simulated through the application of a uniform external electric field. This field exerts an influence on the relative stability of the two electronic states that are mainly involved in the electron transfer. These electronic states have the transferred electron localized either in the electrode or in the adsorbate. The model has been applied to the electron transfer between halides and a cluster model representation of the Cu(100) single-crystal electrode. A linear correlation between the electric field intensity at which the two electronic states involved in the charge-transfer process become degenerate and the normal reduction electrode potential is found. The existence of this linear correlation indicates that the proposed model contains the essential physics governing the trend of halide oxidation at a metal electrode.
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- 2002
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41. Theoretical Study of the Catalytic Activity of Bimetallic RhCu Surfaces and Nanoparticles toward H2 Dissociation
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Marcos Fernández-García, Virineya Bertin, Carmen Sousa, Silvia González, and Francesc Illas
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biology ,Hydrogen ,Chemistry ,Inorganic chemistry ,Theoretical models ,Active site ,chemistry.chemical_element ,Nanoparticle ,Photochemistry ,Dissociation (chemistry) ,Surfaces, Coatings and Films ,Catalysis ,Adsorption ,Materials Chemistry ,biology.protein ,Physical and Theoretical Chemistry ,Bimetallic strip - Abstract
First principles based density functional methods and theoretical models have been used to investigate the reactivity of different RhCu alloys toward molecular hydrogen dissociation. For pure Rh(111), it is predicted that H2 can either dissociate spontaneously or be physisorbed as molecular hydrogen. These predictions agree with recent experimental findings. The simple addition of a Cu atom to a Rh-rich environment is enough to eliminate the presence of the energy minimum associated with molecularly adsorbed hydrogen and to convert H2 dissociation in an activated process. From the present results it is concluded that increasing the Cu content may lead to a change in the active site and permits us to speculate about the enhancement on the irreversible hydrogen uptake on going from Rh to RhCu alloys with a small Cu content.
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- 2002
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42. Multiconfigurational Perturbation Theory: An Efficient Tool to Predict Magnetic Coupling Parameters in Biradicals, Molecular Complexes, and Ionic Insulators
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Francesc Illas, Ibério de P. R. Moreira, Coen de Graaf, and Carmen Sousa
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Condensed matter physics ,Chemistry ,Statistical physics ,Function (mathematics) ,Perturbation theory (quantum mechanics) ,Complete active space ,Symmetry breaking ,Physical and Theoretical Chemistry ,Configuration interaction ,Inductive coupling ,Anderson impurity model ,Spin-½ - Abstract
The performance of the complete active space second-order perturbation theory (CASPT2) to accurately predict magnetic coupling in a wide series of molecules and solid state compounds has been established. It is shown that CASPT2, based on a reference wave function that only includes the effects described by the Anderson or Hay−Thibeault−Hoffmann model, correctly reproduces all experimental trends. For a complete quantitative agreement with experiment (or with accurate results arising from the difference dedicated configuration interaction method), it is necessary to include effects that go beyond the Anderson model in the reference wave function. The CASPT2 method is computationally less demanding than CI based methods and, hence, allows us to extend the study of magnetic coupling parameters to larger molecules or systems with elevated spin moments. Moreover, CASPT2 provides a reliable and accurate alternative to density functional based methods that require the use of a broken symmetry approach.
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- 2001
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43. Optical properties of peroxy radicals in silica: Multiconfigurational perturbation theory calculations
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Coen de Graaf, Gianfranco Pacchioni, and Carmen Sousa
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Optical properties ,Chemistry ,Radical ,Ab initio ,General Physics and Astronomy ,Infrared spectroscopy ,Paramagnetism ,Atomic electron transition ,Ab initio quantum chemistry methods ,Excited state ,Compostos de silici ,Silicon compounds ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Perturbation theory ,Atomic physics ,Propietats òptiques - Abstract
The low-lying electronic transitions in a peroxy radical, wSi-O-O¿, a fundamental radiation induced point defect in silicon dioxide, have been investigated by means of ab initio multiconfiguration perturbation theory calculations, CASPT2, and cluster models. The accuracy of the computed transition energies and intensities as predicted by the CASPT2 approach has been checked by studying the exited state properties of two molecular analogues, the HOO¿ and CH3OO¿ radicals, and of a well-characterized paramagnetic defect in silica, the nonbridging oxygen center, wSi-O¿, for which unambiguous assignments exist. We found that the peroxy radical gives rise to two optical absorption bands, a very weak one at 0.7 eV and an intense one at 5.49 eV, in agreement with the experimental assignments of Radzig [V. A. Radzig, Chem. Phys. Reports 14, 1206 (1995)].
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- 2001
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44. Theoretical Study of the Interaction of Molecular Hydrogen with PdCu(111) Bimetallic Surfaces
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Francesc Illas, and Virineya Bertin, and Carmen Sousa
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biology ,Chemistry ,Ligand ,Hydrogen molecule ,Active site ,Surfaces, Coatings and Films ,Catalysis ,Chemical physics ,Computational chemistry ,Atom ,Materials Chemistry ,biology.protein ,Cluster (physics) ,Reactivity (chemistry) ,Physical and Theoretical Chemistry ,Bimetallic strip - Abstract
A density functional cluster model approach has been applied to the study of the interaction of molecular hydrogen with two different cluster models of the PdCu(111) surface corresponding to a different formal alloy composition both having a single Pd atom in the surface. Despite the similar surface morphology of the two bimetallic clusters, they exhibit a rather different reactivity toward molecular hydrogen. The coordination of the surface Pd atom to other Pd atoms in the second layer appears to be necessary for this atom be able to trap and dissociate molecular hydrogen with a very low energy cost, thus being a potential active site for catalysis. This important result points out that electronic, or ligand, effects do also play an important role in the activity of the PdCu(111) surface sites toward molecular hydrogen.
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- 2001
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45. Neutral atoms in ionic lattices: Excited states ofKCl:Ag0
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Carmen Sousa, J. A. Aramburu, M. T. Barriuso, Miguel Moreno, C. de Graaf, and Francesc Illas
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Range (particle radiation) ,Materials science ,Energetic neutral atom ,Atomic orbital ,Impurity ,Excited state ,Atom ,Ionic bonding ,Atomic physics ,Molecular physics ,Ion - Abstract
due to the presence of the Ag 0 impurity. Moreover, from the present results, it is predicted that on passing to NaCl:Ag 0 the CT onset would be out of the optical range while the 5s-5p transition would undergo a redshift of 0.3 eV. These conclusions, which underline the different character of involved orbitals, are consistent with experimental findings. The existence of a CT transition in the optical range for an atom inside an ionic host is explained by a simple model, which also accounts for the differences with the more common 3d systems. The present study sheds also some light on the R dependence of the s 2 - sp transitions due to s 2 ions like Tl 1 .
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- 2000
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46. Neutral atoms in ionic lattices: Stability and ground-state properties ofKCl:Ag0
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J. A. Aramburu, Miguel Moreno, C. de Graaf, Francesc Illas, Carmen Sousa, M. T. Barriuso, and I. Cabria
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Materials science ,Unpaired electron ,Ab initio quantum chemistry methods ,Atom ,Physics::Atomic and Molecular Clusters ,Ab initio ,Cluster (physics) ,Ionic bonding ,Atomic physics ,Ground state ,Molecular physics ,Ion - Abstract
The equilibrium geometry of Ag 0 centers formed at cation sites in KCl has been investigated by means of total-energy calculations carried out on clusters of different sizes. Two distinct methods have been employed: First, an ab initio wave-function based method on embedded clusters and second, density-functional theory ~DFT! methods on clusters in vacuo involving up to 117 atoms. In the ab initio calculations the obtained equilibrium Ag 0 -Cl 2 distance Re is 3.70 A, implying a large outward relaxation of 18%, along with 7% relaxation for the distance between Ag 0 and the first K 1 ions in ^100& directions. A very similar result is reached through DFT with a 39-atom cluster. Both approaches lead to a rather shallow minimum of the total-energy surface, the associated force constant of the A1g mode is several times smaller than that found for other impurities in halides. These conclusions are shown to be compatible with available experimental results. The shallow minimum is not clearly seen in DFT calculations with larger clusters. The unpaired electron density on silver and Cl ligands has been calculated as function of the metal-ligand distance and has been compared with values derived from electron-paramagnetic resonance data. The DFT calculations for all cluster sizes indicate that the experimental hyperfine and superhyperfine constants are compatible whenRe is close to 3.70 A. The important relation between the electronic stability of a neutral atom inside an ionic lattice and the local relaxation is established through a simple electrostatic model. As most remarkable features it is shown that ~i! the cationic Ag 0 center is not likely to be formed inside AgCl, ~ii! in the Ag 0 center encountered in SrCl2, the silver atom is probably located at an anion site, and ~iii! the properties of a center-like KCl:Ag 0 would experience significant changes under hydrostatic pressures of the order of 6 GPa.
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- 2000
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47. Core exciton energies of bulk MgO,Al2O3,andSiO2from explicitly correlatedab initiocluster model calculations
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Coen de Graaf, Carmen Sousa, and Francesc Illas
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Physics ,Electronic correlation ,Atomic theory ,Excited state ,Exchange interaction ,Ab initio ,Atomic physics ,Wave function ,Energy (signal processing) ,Excitation - Abstract
Ab initio cluster model wave functions are used to predict the existence of localized excited states in MgO, ${\mathrm{Al}}_{2}{\mathrm{O}}_{3},$ and ${\mathrm{SiO}}_{2}$ arising from metal $2p$ core-level excitations. Theoretical values obtained at different levels of theory result in a quantitative agreement with experiment, and the use of different models permits us to quantify the different contributions to the final excitation energy. The most important contribution is atomic in nature; a meaningful zero-order approximation is that in MgO and ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ the exciton can be assigned to a ${M(2p}^{6})\ensuremath{\rightarrow}{M(2p}^{5}{3s}^{1})$-like excitation, where $M=\mathrm{Mg}$ or Al. For the atomic models, the singlet-triplet exchange in the excited configuration is in good agreement with experiment. In addition, the solid-state effects on this exchange energy predicted by experiment are well reproduced by the cluster models representing MgO and ${\mathrm{SiO}}_{2},$ whereas a less clear situation appears in ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}.$ The open-shell orbital in the final state has, however, important contributions from the ions near the atomic site where excitation occurs. Nevertheless, the final state appears to be localized in space without any a priori assumption, the localization following from the hole-particle interaction implicitly induced in the final-state wave function. The Madelung field reduces the excitation energy with respect to the atomic value; the effect of neighboring atoms, mainly Pauli repulsion, acts in the opposite way; and electronic correlation effects decrease it again. In agreement with the covalent nature of ${\mathrm{SiO}}_{2},$ the exciton cannot be simply understood as arising from a $\mathrm{Si}{(2p}^{6})\ensuremath{\rightarrow}\mathrm{Si}{(2p}^{5}{3s}^{1})$ in a fully oxidized Si cation.
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- 2000
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48. Computational approach to the study of thermal spin crossover phenomena
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Carmen Sousa, Ria Broer, Coen de Graaf, Remco W. A. Havenith, Andrii Rudavskyi, Química Física i Inorgànica, Universitat Rovira i Virgili., Universitat de Barcelona, Theoretical Chemistry, and Zernike Institute for Advanced Materials
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Entropy ,Spin transition ,General Physics and Astronomy ,Molecular physics ,COMPLEX FE(PHEN)(2)(NCS)(2) ,ELECTRONIC-STRUCTURE CALCULATIONS ,DENSITY-FUNCTIONAL THEORY ,symbols.namesake ,RAMAN-SPECTROSCOPY ,Spin crossover ,Simulació per ordinador ,Termodinàmica ,CRYSTAL-STRUCTURE ,Spin (Física nuclear) ,Physical and Theoretical Chemistry ,Entropy (energy dispersal) ,Wave function ,ZETA VALENCE QUALITY ,BASIS-SETS ,0021-9606 ,Condensed matter physics ,Chemistry ,Transition temperature ,STATE ENERGETICS ,Transition metals ,Metalls de transició ,Computer simulation ,IRON(III) COMPOUNDS ,Molecular vibration ,Entropia ,symbols ,Nuclear spin ,PERTURBATION-THEORY ,Thermodynamics ,Density functional theory ,Raman spectroscopy - Abstract
The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low-and high-spin states. From these values, the transition temperature, T-1/2, is estimated for different compounds. (C) 2014 AIP Publishing LLC.
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- 2014
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49. Theoretical characterization of the low-lying excited states of the CuCl molecule
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Ria Broer, W. A. de Jong, W. C. Nieuwpoort, and Carmen Sousa
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SPECTRUM ,Chemistry ,General Physics and Astronomy ,Diatomic molecule ,Spectral line ,Ion ,ATOMS ,2ND-ORDER PERTURBATION-THEORY ,ELECTRONIC STATES ,Excited state ,ANO BASIS-SETS ,WAVE-FUNCTIONS ,EXCITATION-ENERGIES ,Complete active space ,RADIATIVE LIFETIMES ,Physical and Theoretical Chemistry ,Atomic physics ,Wave function ,Valence electron ,Relativistic quantum chemistry ,CUF MOLECULE ,TRANSITION - Abstract
The character of the low-lying excited states of diatomic CuCl is studied primarily by means of the complete active space self-consistent field (CASSCF), method and a second order perturbation approach with the CASSCF wave function as reference state [complete active space perturbation theory to second order (CASPT2)]. Far comparison, the lower levels of the spectra of the Cu+ ion are also analyzed. A first order treatment of the scalar relativistic effects, the mass-velocity and Darwin terms, is included in the calculations. The importance of spin-orbit interactions is investigated by comparing our nonrelativistic valence shell CI (VCI) and relativistic results obtained with our four-component program suite MOLFDIR. The six lowest excited states of the CuCl molecule, which are related to the Cu+(3d(9)4s(1))Cl-(3s(2)3p(6)) ionic configuration, are assigned. The assignments agree with earlier theoretical work. Where they can be compared, the calculated spectroscopic constants are in good agreement with the experimental data. (C) 1997 American Institute of Physics.
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- 1997
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50. On modelling the interaction of CO on the MgO(100) surface
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Marcos Fernández-García, Antonio M. Márquez, Josep M. Ricart, José A. Mejías, Carmen Sousa, Francesc Illas, and J.Fernández Sanz
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Chemistry ,Hartree–Fock method ,Ab initio ,Ionic bonding ,Surfaces and Interfaces ,Interaction energy ,Condensed Matter Physics ,Surfaces, Coatings and Films ,Ab initio quantum chemistry methods ,Chemisorption ,Chemical physics ,Physics::Atomic and Molecular Clusters ,Materials Chemistry ,Cluster (physics) ,Atomic physics ,Cluster expansion - Abstract
In this work we discuss the interaction of an adsorbate on an ionic surface taking as representative example CO on a perfect MgO(100) surface. The main goal is to investigate the different contributions to the interaction and how to model them by using a finite cluster model. To this end we use three different ab initio Hartree-Fock approaches. First, we discuss the convergence properties of the array of point charges used to simulate the Madelung potential. Next, we use large cluster models to show that there is an oscillatory behavior of the interaction energy. We show that rather large clusters are needed to avoid such oscillations. Also, we discuss how to represent these large clusters by using model potentials and compare the results with those obtained from periodic Hartree-Fock calculations. The interaction of CO on MgO is found to be weak and of electrostatic origin, with no noticeable chemical contributions.
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- 1995
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