103 results on '"Carles Bo"'
Search Results
2. Chemical reaction network knowledge graphs: the OntoRXN ontology
- Author
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Diego Garay-Ruiz and Carles Bo
- Subjects
Ontologies ,Reaction networks ,Semantics ,Reactivity ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows. Graphical Abstract
- Published
- 2022
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3. Grafting of Anionic Decahydro-Closo-Decaborate Clusters on Keggin and Dawson-Type Polyoxometalates: Syntheses, Studies in Solution, DFT Calculations and Electrochemical Properties
- Author
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Manal Diab, Ana Mateo, Joumada El Cheikh, Zeinab El Hajj, Mohamed Haouas, Alireza Ranjbari, Vincent Guérineau, David Touboul, Nathalie Leclerc, Emmanuel Cadot, Daoud Naoufal, Carles Bo, and Sébastien Floquet
- Subjects
polyoxometalate ,hybrid ,decaborate ,DFT ,NMR ,hydrogen evolution reaction ,Organic chemistry ,QD241-441 - Abstract
Herein we report the synthesis of a new class of compounds associating Keggin and Dawson-type Polyoxometalates (POMs) with a derivative of the anionic decahydro-closo-decaborate cluster [B10H10]2− through aminopropylsilyl ligand (APTES) acting as both a linker and a spacer between the two negatively charged species. Three new adducts were isolated and fully characterized by various NMR techniques and MALDI-TOF mass spectrometry, notably revealing the isolation of an unprecedented monofunctionalized SiW10 derivative stabilized through intramolecular H-H dihydrogen contacts. DFT as well as electrochemical studies allowed studying the electronic effect of grafting the decaborate cluster on the POM moiety and its consequences on the hydrogen evolution reaction (HER) properties.
- Published
- 2022
- Full Text
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4. Tuning and mechanistic insights of metal chalcogenide molecular catalysts for the hydrogen-evolution reaction
- Author
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James McAllister, Nuno A. G. Bandeira, Jessica C. McGlynn, Alexey Y. Ganin, Yu-Fei Song, Carles Bo, and Haralampos N. Miras
- Subjects
Science - Abstract
While hydrogen offers a potential carbon neutral fuel, its production from water using earth-abundant, heterogeneous materials has proven challenging to understand. Here, authors present a series of molecular electrocatalysts based on molybdenum, sulphur, and oxygen for aqueous hydrogen evolution.
- Published
- 2019
- Full Text
- View/download PDF
5. A redox-active inorganic crown ether based on a polyoxometalate capsule
- Author
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Nanako Tamai, Naoki Ogiwara, Eri Hayashi, Keigo Kamata, Toshiyuki Misawa, Takeru Ito, Tatsuhiro Kojima, Mireia Segado, Enric Petrus, Carles Bo, and Sayaka Uchida
- Subjects
General Chemistry - Abstract
The POM capsule functions as a redox-active inorganic crown ether. Specifically, Cs+ ions are captured in the crown-ether-like pores {Mo3Fe3O6}, which exist on the surface of the capsule, and electrons are stored in the Mo atoms of the capsule.
- Published
- 2023
6. Domino Synthesis of Bicyclic 3,5-Anhydro Furanose Mimics Using a Binary Al(III) Complex/Halide Catalyst
- Author
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Chang Qiao, Alba Villar-Yanez, Diego Garay-Ruiz, Jordi-Benet Buchholz, Carles Bo, and Arjan W. Kleij
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General Chemistry ,Catalysis - Published
- 2022
7. Elucidating Sulfide Activation Mode in Metal-Catalyzed Sulfoxidation Reactivity
- Author
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Diego Garay-Ruiz, Cristiano Zonta, Silvia Lovat, Joan González-Fabra, Carles Bo, and Giulia Licini
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Inorganic Chemistry ,Physical and Theoretical Chemistry - Abstract
Interest in the catalytic activation of peroxides, together with the requirement of stereoselectivity for the production of enantiopure sulfoxides, has made sulfoxidation the ideal playground for theoretical and experimental physical organic chemists investigating oxidation reactivity. Efforts have been dedicated for elucidating the catalytic pathway regarding these species and for dissecting out the dominant factors influencing the yield and stereochemistry. In this article, Ti(IV) and Hf(IV) aminotriphenolate complexes have been prepared and investigated as catalysts in the presence of peroxides in sulfide oxidation. Experimental results have been combined with theoretical calculations obtaining detailed mechanistic information on oxygen transfer processes. The study revealed that steric issues are mainly responsible for the formation of intermediates in the oxidation pathway. In particular, we could highlight the occurrence of a blended situation where the steric effects of sulfides, ligands, and oxidants influence the formation of different intermediates and reaction pathways.
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- 2022
8. Cascade Transformation of Carbon Dioxide and Alkyne-1,n-diols into Densely Substituted Cyclic Carbonates
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Xuetong Li, Alba Villar-Yanez, Charlene Ngassam Tounzoua, Jordi Benet-Buchholz, Bruno Grignard, Carles Bo, Christophe Detrembleur, and Arjan W. Kleij
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General Chemistry ,Catalysis - Published
- 2022
9. New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited
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Diego Garay-Ruiz, Moises Álvarez-Moreno, Carles Bo, and Emilio Martínez-Núñez
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General Medicine - Published
- 2022
10. Mechanistic insights of molecular metal polyselenides for catalytic hydrogen generation
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Alexander Elliott, James McAllister, Liudvika Masaityte, Mireia Segado-Centellas, De-Liang Long, Alexey Y. Ganin, Yu-Fei Song, Carles Bo, and Haralampos N. Miras
- Subjects
Molybdenum ,Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,General Chemistry ,Catalysis ,Hydrogen ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
Molecular metal chalcogenides have attracted great attention as electrocatalysts for the hydrogen evolution reaction (HER). However, efficient utilisation of the active sites and catalytic performance modulation has been challenging. Here we explore the design of immobilized molecular molybdenum polyselenides [Mo2O2S2(Se2)(Sex)]2– that exhibit efficient hydrogen evolution at low overpotential and stability over 1000 cycles. Density functional calculations provide evidence of a unimolecular mechanism in the HER process via the exploration of viable reaction pathways. The discussed findings are of a broad interest in the development of efficient molecular electrocatalytic materials.
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- 2022
11. A new series of bioactive Mo(V)2O2S2-based thiosemicarbazone complexes: Solution and DFT studies, and antifungal and antioxidant activities
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Diana Cebotari, Jordi Buils, Olga Garbuz, Greta Balan, Jérôme Marrot, Vincent Guérineau, David Touboul, Mohamed Haouas, Mireia Segado-Centelles, Carles Bo, Aurelian Gulea, and Sébastien Floquet
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Inorganic Chemistry ,Biochemistry - Published
- 2023
12. Unlocking Phase Diagrams for Molybdenum and Tungsten Nanoclusters and Prediction of their Formation Constants
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Enric Petrus and Carles Bo
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Aqueous solution ,010304 chemical physics ,Chemistry ,chemistry.chemical_element ,Tungsten ,010402 general chemistry ,01 natural sciences ,Chemical reaction ,0104 chemical sciences ,Nanoclusters ,Chemical physics ,Molybdenum ,0103 physical sciences ,Genetic algorithm ,Density functional theory ,Physical and Theoretical Chemistry ,Phase diagram - Abstract
Understanding and controlling aqueous speciation of metal oxides are key for the discovery and development of novel materials, and challenge both experimental and computational approaches. Here we present a computational method, called POMSimulator, which is able to predict speciation phase diagrams (Conc. vs pH) for multi-species chemical equilibria in solution, and which we apply to molybdenum and tungsten isopolyoxoanions (IPAs). Starting from the MO4 monomers, and considering dimers, trimers, and larger species, the chemical reaction networks involved in the formation of [H32Mo36O128]8- and [W12O42]12- are sampled in an automatic manner. This information is used for setting up ~105 speciation models, and from there, we generate the speciation phase diagrams, which show an insightful picture of the behavior of IPAs in aqueous solution. Furthermore, we predict the values for 107 formation constants for a diversity of molybdenum and tungsten molecular oxides. Among these species, we could include several pentagonal shaped species and very reactive tungsten intermediates as well. Last but not least, the calibration employed for correcting the DFT Gibbs energies is remarkably similar for both metals, which suggests that a general rule might exist for correcting computed free energies for other metals.
- Published
- 2021
13. Computational Prediction of Speciation Diagrams and Nucleation Mechanisms: Molecular Vanadium, Niobium, and Tantalum Oxide Nanoclusters in Solution
- Author
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Carles Bo, Mireia Segado-Centellas, and Enric Petrus
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Inorganic Chemistry ,Physical and Theoretical Chemistry - Abstract
Understanding the aqueous speciation of molecular metal-oxo clusters plays a key role in different fields such as catalysis, electrochemistry, nuclear waste recycling, and biochemistry. To accurately describe the speciation, it is essential to elucidate the underlying self-assembly processes. Herein, we apply a computational method to predict the speciation and formation mechanisms of polyoxovanadates, -niobates and -tantalates. While polyoxovanadates have been widely studied, polyoxoniobates and -tantalates lack the same level of understanding. In the first place, we proposed a pentavanadate cluster ([V5O14]3-) as a key intermediate for the formation of the decavanadate. Our computed phase speciation diagram is in particularly good agreement with the experiments. Secondly, we report the formation constants of the heptaniobate, [Nb7O22]9-, decaniobate, [Nb10O28]6-, and tetracosaniobate [H9Nb24O72]9-. Additionally, we have computed the speciation and phase diagram of niobium, which so far was restricted to Lindqvist derivates. Finally, we have predicted the formation constant of the decatantalate ([Ta10O26]6-) in water, even though it had only been synthetized in toluene. Furthermore, the corresponding speciation and phase diagrams for polyoxotantalates have been also calculated. Overall, we show that our method can be successfully applied to different families of molecular metal oxides without any need for readjustments; therefore, it can be regarded as a trustworthy tool for exploring polyoxometalates’ chemistry.
- Published
- 2022
14. Dimension-Controlled Dewetting in Hydrophobic Porous Nanocapsules
- Author
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Josep Bonet Avalos, Carles Bo, Bin Wu, Lionel Porcar, Ira A. Weinstock, Sourav Chakraborty, Qianjie Zhou, Dolores Melgar, and Panchao Yin
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Materials science ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Nanocapsules ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,General Energy ,Dimension (vector space) ,Dewetting ,Physical and Theoretical Chemistry ,0210 nano-technology ,Porosity - Abstract
Water in different physical states has been attracting great interest for decades for its strong association with the origin of life, the biophysical behaviors of biomacromolecules, and the transpo...
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- 2020
15. Predicting the Solubility of Inorganic Ion Pairs in Water
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Tasnim Rahman, Enric Petrus, Mireia Segado, Nicolas P. Martin, Lauren N. Palys, Mark A. Rambaran, C. Andre Ohlin, Carles Bo, and May Nyman
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General Chemistry ,General Medicine ,Catalysis - Abstract
Polyoxometalates (POMs), ranging in size from 1 to 10's of nanometers, resemble building blocks of inorganic materials. Elucidating their complex solubility behavior with alkali-counterions can inform natural and synthetic aqueous processes. In the study of POMs ([Nb
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- 2022
16. Ni-Catalyzed Decarboxylative Silylation of Alkynyl Carbonates: Access to Chiral Allenes via Enantiospecific Conversions
- Author
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Kun Guo, Qian Zeng, Alba Villar-Yanez, Carles Bo, and Arjan W. Kleij
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Organic Chemistry ,Physical and Theoretical Chemistry ,Biochemistry - Abstract
A Ni-mediated decarboxylative silylation of alkynyl cyclic carbonates used as versatile propargylic surrogates is reported affording a wide range of highly substituted 2,3- and 3,4-allenol products in good yields. The formal cross-coupling between a tentative intermediate Ni(allenyl) and the silyl reagent was further extended to enantiospecific conversions providing access to chiral allene synthons. This protocol marks the first Ni-catalyzed propargylic silylation proceeding through an S
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- 2022
17. Nucleation mechanisms and speciation of metal oxide clusters
- Author
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Mireia Segado, Carles Bo, and Enric Petrus
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Reaction mechanism ,Materials science ,Nucleation ,Oxide ,Ionic bonding ,General Chemistry ,chemistry.chemical_compound ,Chemical species ,Chemistry ,chemistry ,Stability constants of complexes ,Chemical physics ,Genetic algorithm ,Molecular graph ,Chemical equilibrium - Abstract
The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. We present a new computational methodology that identifies the reaction mechanism for the formation of metal-oxide clusters and provides a speciation model from first-principles and in an automated manner. As a first example, we apply our method to the formation of octamolybdate. In our model, we include variables such as pH, temperature and ionic force because they have a determining effect on driving the reaction to a specific product. Making use of graphs, we set up and solved 2.8 × 105 multi-species chemical equilibrium (MSCE) non-linear equations and found which set of reactions fitted best with the experimental data available. The agreement between computed and experimental speciation diagrams is excellent. Furthermore, we discovered a strong linear dependence between DFT and empirical formation constants, which opens the door for a systematic rescaling., The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. The POMSimulator deals with that complexity in an automated manner.
- Published
- 2021
18. Aggregation Patterns in Low- and High-Charge Anions Define Opposite Solubility Trends
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May Nyman, Mireia Segado, and Carles Bo
- Subjects
animal structures ,Aqueous solution ,010304 chemical physics ,Chemistry ,Hydrogen bond ,Charge density ,Charge (physics) ,Ion pairs ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Molecular dynamics ,Solvation shell ,Chemical physics ,0103 physical sciences ,Materials Chemistry ,sense organs ,Physical and Theoretical Chemistry ,Solubility - Abstract
Molecular dynamics simulations in aqueous solution reveal the existence of two distinct patterns of aggregation in low and high charge density Lindqvist-type polyoxometalates (POMs). Our results indicate the presence of contact and solvent-shared ion pairs and specific and preferential interactions of alkalis with POMs. Highly charged POMs are capable of breaking apart the Li+ and Cs+ solvation shell, thus enhancing the formation of long-lived alkali–POM contact ion pairs, where alkalis act as an electrostatic “glue” forming large oligomers. Stronger ion pair interactions for Li+ than for Cs+ promote lower solubility for Li+ than for Cs+, evoking anomalous solubility trends. Lower charge density POMs are not capable of disrupting the Li+ solvation shell and only solvent-shared ion pairs are formed, whereas for Cs+, contact ion pairs exist. The large number of oxygen atoms in the POM surface enhances the hydrogen bonds between POM and water, thus promoting aggregation. In this case, aggregation follows nor...
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- 2019
19. Strategic Capture of the {Nb 7 } Polyoxometalate
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Enric Petrus, Mireia Segado, May Nyman, Nicolas P. Martin, Lev N. Zakharov, Carles Bo, and Ana Arteaga
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Aqueous solution ,010405 organic chemistry ,media_common.quotation_subject ,Organic Chemistry ,Niobium ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Uranyl ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Metal ,Crystallography ,Speciation ,chemistry.chemical_compound ,chemistry ,visual_art ,Polyoxometalate ,visual_art.visual_art_medium ,Transect ,media_common - Abstract
Group V Nb-polyoxometalate (Nb-POM) chemistry generally lacks the elegant pH-controlled speciation exhibited by group VI (Mo, W) POM chemistry. Here three Nb-POM clusters were isolated and structurally characterized; [Nb14 O40 (O2 )2 H3 ]14- , [((UO2 )(H2 O))3 Nb46 (UO2 )2 O136 H8 (H2 O)4 ]24- , and [(Nb7 O22 H2 )4 (UO2 )7 (H2 O)6 ]22- , that effectively capture the aqueous Nb-POM species from pH 7 to pH 10. These Nb-POMs illustrate a reaction pathway for control over speciation that is driven by counter-cations (Li+ ) rather than pH. The two reported heterometallic POMs (with UO22+ moieties) are stabilized by replacing labile H2 O/HO-Nb=O with very stable O=U=O. The third isolated Nb-POM features cis-yl-oxos, prior observed only in group VI POM chemistry. Moreover, with these actinide-heterometal contributions to the burgeoning Nb-POM family, it now transects all major metal groups of the periodic table.
- Published
- 2019
20. Tuning and mechanistic insights of metal chalcogenide molecular catalysts for the hydrogen-evolution reaction
- Author
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Alexey Y. Ganin, Jessica C. McGlynn, Yu-Fei Song, Carles Bo, Haralampos N. Miras, James McAllister, and Nuno A. G. Bandeira
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0301 basic medicine ,Materials science ,Hydrogen ,Chalcogenide ,Science ,General Physics and Astronomy ,chemistry.chemical_element ,02 engineering and technology ,Overpotential ,7. Clean energy ,General Biochemistry, Genetics and Molecular Biology ,Article ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,Chalcogen ,lcsh:Science ,Multidisciplinary ,General Chemistry ,021001 nanoscience & nanotechnology ,030104 developmental biology ,chemistry ,Chemical engineering ,13. Climate action ,Linear sweep voltammetry ,Water splitting ,lcsh:Q ,0210 nano-technology ,Stoichiometry - Abstract
The production of hydrogen through water splitting using earth-abundant metal catalysts is a promising pathway for converting solar energy into chemical fuels. However, existing approaches for fine stoichiometric control, structural and catalytic modification of materials by appropriate choice of earth abundant elements are either limited or challenging. Here we explore the tuning of redox active immobilised molecular metal-chalcoxide electrocatalysts by controlling the chalcogen or metal stoichiometry and explore critical aspects of the hydrogen evolution reaction (HER). Linear sweep voltammetry (LSV) shows that stoichiometric and structural control leads to the evolution of hydrogen at low overpotential with no catalyst degradation over 1000 cycles. Density functional calculations reveal the effect of the electronic and structural features and confer plausibility to the existence of a unimolecular mechanism in the HER process based on the tested hypotheses. We anticipate these findings to be a starting point for further exploration of molecular catalytic systems., While hydrogen offers a potential carbon neutral fuel, its production from water using earth-abundant, heterogeneous materials has proven challenging to understand. Here, authors present a series of molecular electrocatalysts based on molybdenum, sulphur, and oxygen for aqueous hydrogen evolution.
- Published
- 2019
21. Entropic corrections for the evaluation of the catalytic activity in the Al(<scp>iii</scp>) catalysed formation of cyclic carbonates from CO2 and epoxides
- Author
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W. M. C. Sameera, Arjan W. Kleij, Joan González-Fabra, Gunnar Nyman, Carles Bo, and Fernando Castro-Gómez
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Aluminum Complex ,Addition reaction ,Reaction mechanism ,010405 organic chemistry ,Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Catalytic cycle ,Physical chemistry ,Density functional theory ,Binary system - Abstract
The reaction mechanism for formation of cyclic carbonates from CO2 and 1,2-epoxyhexane catalyzed by an [Al(amino-triphenolate)]/NBu4I binary system has been investigated by using density functional theory (DFT) based methods. A monometallic mechanism is proposed and the main steps of the reaction are described in detail. The energetic span model (δE) was used to theoretically determine the turnover frequencies (TOFs) of the catalytic cycle and to evaluate the efficiency of the aluminum complex in mediating the CO2 addition reaction. Our findings indicate that entropy changes in solution must be included in order to compute the TOF values in line with the experimental results.
- Published
- 2019
22. Human-Readable SMILES: Translating Cheminformatics to Chemistry
- Author
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Diego Garay-Ruiz, Carles Bo, and Diego Garay Ruiz
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Set (abstract data type) ,business.industry ,Cheminformatics ,Human–computer interaction ,String (computer science) ,GRASP ,Big data ,Web application ,business ,Asset (computer security) ,De facto standard - Abstract
Molecular string representations are a key asset in cheminformatics and are becoming increasingly relevant to the general chemical community, due to the steadily growing impact of Big Data and Machine Learning. Among all of the existing string representations that have been proposed, SMILES (Simplified Molecular Input Line Entry Specification) are probably the de facto standard as of today. Despite their convenience as a way to store unique molecular structures in data-bases, however, SMILES are not easy to understand for most chemists: that is, it is difficult for an untrained chemist to grasp the molecule that a SMILES is describing. To mitigate this, we propose the HumanSMILES algorithm: a simple pro-cedure that can translate a SMILES string into a more interpretable name, inspired by common abbreviations and names employed in general organic chemistry. The Human-Readable SMILES can describe linear structures and general non-fused cyclic structures, with a set of naming rules that combines automated processing and chemical knowledge. The code is available open-source, as well as a web application.
- Published
- 2021
23. Human-Readable SMILES: Translating Cheminformatics to Chemistry
- Author
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Carles Bo and Diego Garay-Ruiz
- Abstract
Molecular string representations are a key asset in cheminformatics and are becoming increasingly relevant to the general chemical community, due to the steadily growing impact of Big Data and Machine Learning. Among all of the existing string representations that have been proposed, SMILES (Simplified Molecular Input Line Entry Specification) are probably the de facto standard as of today. Despite their convenience as a way to store unique molecular structures in data-bases, however, SMILES are not easy to understand for most chemists: that is, it is difficult for an untrained chemist to grasp the molecule that a SMILES is describing. To mitigate this, we propose the HumanSMILES algorithm: a simple pro-cedure that can translate a SMILES string into a more interpretable name, inspired by common abbreviations and names employed in general organic chemistry. The Human-Readable SMILES can describe linear structures and general non-fused cyclic structures, with a set of naming rules that combines automated processing and chemical knowledge. The code is available open-source, as well as a web application.
- Published
- 2021
24. Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge
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Xavier Barril, Carles Bo, and Dylan Serillon
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Binding free energy ,Protein Conformation ,Distributed computing ,Binding energy ,Molecular dynamics ,Molecular Dynamics Simulation ,Degrees of freedom (mechanics) ,Ligands ,010402 general chemistry ,01 natural sciences ,Article ,Machine Learning ,Semi-empirical methods ,Xtb GFN2B ,0103 physical sciences ,Drug Discovery ,Molecular mechanics ,Physical and Theoretical Chemistry ,Binding free energy calculations ,Binding Sites ,010304 chemical physics ,Proteins ,Computational drug design ,Pipeline (software) ,0104 chemical sciences ,Computer Science Applications ,Molecular Docking Simulation ,Identification (information) ,Docking (molecular) ,Solvents ,Thermodynamics ,Host (network) ,Software ,Scope (computer science) ,Protein Binding - Abstract
The design of new host–guest complexes represents a fundamental challenge in supramolecular chemistry. At the same time, it opens new opportunities in material sciences or biotechnological applications. A computational tool capable of automati- cally predicting the binding free energy of any host–guest complex would be a great aid in the design of new host systems, or to identify new guest molecules for a given host. We aim to build such a platform and have used the SAMPL7 challenge to test several methods and design a specific computational pipeline. Predictions will be based on machine learning (when previous knowledge is available) or a physics-based method (otherwise). The formerly delivered predictions with an RMSE of 1.67 kcal/mol but will require further work to identify when a specific system is outside of the scope of the model. The latter is combines the semiempirical GFN2B functional, with docking, molecular mechanics, and molecular dynamics. Correct predictions (RMSE of 1.45 kcal/mol) are contingent on the identification of the correct binding mode, which can be very challenging for host–guest systems with a large number of degrees of freedom. Participation in the blind SAMPL7 challenge provided fundamental direction to the project. More advanced versions of the pipeline will be tested against future SAMPL challenges.
- Published
- 2021
- Full Text
- View/download PDF
25. Revisiting Catalytic Cycles: A Broader View Through the Energy Span Model
- Author
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Diego Garay-Ruiz and Carles Bo
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Reaction mechanism ,Materials science ,010405 organic chemistry ,Homogeneous catalysis ,General Chemistry ,010402 general chemistry ,Span (engineering) ,Heterogeneous catalysis ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Chemical physics ,Energy (signal processing) ,Level of detail - Abstract
The computational study of catalytic processes allows discovering really intricate and detailed reaction mechanisms that involve many species and transformations. This increasing level of detail can even result detrimental when drawing conclusions from the computed mechanism, as many co-existing reaction pathways can be in close com- petence. Here we present a reaction network-based implementation of the energy span model in the form of a computational code, gTOFfee, capable of dealing with any user-specified reaction network. This approach, compared to microkinetic simulations, enables a much easier and straightforward analysis of the performance of any catalytic reaction network. In this communication, we will go through the foundations and appli- cability of the underlying model, and will tackle the application to two relevant catalytic systems: homogeneous Co-mediated propene hydroformylation and heterogeneous CO2 hydrogenation over Cu(111).
- Published
- 2020
26. Organocatalytic Trapping of Elusive Carbon Dioxide based Heterocycles through a Kinetically Controlled Cascade Process
- Author
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Chang Qiao, Alba Villar-Yanez, Josefine Sprachmann, Bart Limburg, Carles Bo, and Arjan. W. Kleij
- Abstract
A conceptually novel approach is described for thesynthesis of larger-ring cyclic carbonates derived from carbon dioxide. The approach utilizes homoallylic precursors that are converted into five-membered cyclic carbonates having a beta-positioned alcohol group in one of the ring substituents. The activation of the pendent alcohol group through an N-heterocyclic base allows for equilibration towards a thermodynamically disfavored six-membered carbonate analogue that can be conveniently trapped by an acylation agent. Various control experiments and computational analysis of this manifold are in line with a process that is primarily dictated by a kinetically controlled acylation step. This cascade process delivers an ample diversity of novel six-membered cyclic carbonates in excellent yields and chemoselectivities under remarkably mild reaction conditions. This newly developed protocol helps to expand the repertoire of CO2-based heterocycles that are otherwise difficult to generate by conventional approaches.
- Published
- 2020
27. Organocatalytic Trapping of Elusive Carbon Dioxide Based Heterocycles by a Kinetically Controlled Cascade Process
- Author
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Carles Bo, Bart Limburg, Chang Qiao, Josefine Sprachmann, Alba Villar-Yanez, and Arjan W. Kleij
- Subjects
Reaction mechanism ,010405 organic chemistry ,Alcohol ,Homogeneous catalysis ,General Medicine ,General Chemistry ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Acylation ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Organocatalysis ,Carbon dioxide ,Carbonate - Abstract
A conceptually novel approach is described for the synthesis of six-membered cyclic carbonates derived from carbon dioxide. The approach utilizes homoallylic precursors that are converted into five-membered cyclic carbonates having a β-positioned alcohol group in one of the ring substituents. The activation of the pendent alcohol group through an N-heterocyclic base allows equilibration towards a thermodynamically disfavored six-membered carbonate analogue that can be trapped by an acylating agent. Various control experiments and computational analysis of this manifold are in line with a process that is primarily dictated by a kinetically controlled acylation step. This cascade process delivers an ample diversity of six-membered cyclic carbonates in excellent yields and chemoselectivities under mild reaction conditions.
- Published
- 2020
28. Unprecedented coupling reaction between two anionic species of a closo -decahydrodecaborate cluster and an Anderson-type polyoxometalate
- Author
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Manal Diab, Daoud Naoufal, Mohamed Haouas, Flavien Bourdreux, Joumada Al Cheikh, Ana Mateo, Carles Bo, Emmanuel Cadot, Alireza Ranjbari, Sébastien Floquet, Institut Lavoisier de Versailles (ILV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Lebanese University [Beirut] (LU)
- Subjects
Inorganic Chemistry ,Crystallography ,010405 organic chemistry ,Chemistry ,Polyoxometalate ,Cluster (physics) ,Decahydrodecaborate ,[CHIM.INOR]Chemical Sciences/Inorganic chemistry ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,Coupling reaction ,0104 chemical sciences - Abstract
International audience; Two decahydrodecaborate-functionalized Anderson-Evans polyoxometalates have been synthesized. The compounds have been characterized in solution by ESI-MS, various NMR techniques and electrochemistry, while DFT calculation bring strong support to understand their properties.
- Published
- 2020
29. Regioselective Catalysis by the {Mo 132 } Nanocapsule: A Computational Inspection
- Author
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Nuno A. G. Bandeira and Carles Bo
- Subjects
Inorganic Chemistry ,chemistry ,010405 organic chemistry ,Molybdenum ,Regioselectivity ,chemistry.chemical_element ,Nanoreactor ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences ,Catalysis - Published
- 2018
30. Hydrogen Generation via Activation of X-H Bonds in Ammonia and Water by an MoI Complex
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Luis F. Veiros, Nuno A. G. Bandeira, and Carles Bo
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Ammonia ,chemistry.chemical_compound ,chemistry ,Hydrogen ,010405 organic chemistry ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,Hydrogen production - Published
- 2017
31. Crystallizing Elusive Chromium Polycations
- Author
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Lauren B. Fullmer, Carles Bo, Nuno A. G. Bandeira, Wei Wang, May Nyman, Lev N. Zakharov, Sara Goberna-Ferrón, and Douglas A. Keszler
- Subjects
Metal hydroxide ,010405 organic chemistry ,Precipitation (chemistry) ,General Chemical Engineering ,Biochemistry (medical) ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,Zinc ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,law.invention ,Metal ,chemistry ,law ,visual_art ,Polyoxometalate ,Materials Chemistry ,visual_art.visual_art_medium ,Cluster (physics) ,Environmental Chemistry ,Crystallization ,Dissolution - Abstract
Summary Metal-oxo clusters are commonly isolated from water with ligands for preventing the precipitation of metal hydroxides. However, unligated clusters are important for both mechanistic studies and applications. Isolating open-shell transition-metal clusters is especially difficult without ligation. Herein, we elucidate a cluster-isolation process that yields an unligated Zn 2+ -Al 3+ -Cr 3+ polyoxocation. For decades, Cr 3+ -polyoxocations have proved elusive synthetic targets because of hydrolytic instability. We overcame the synthetic challenges by the following strategies: (1) pH-driven hydrolysis by oxidative dissolution of zinc; (2) metal nitrate concentrations 10× higher than conventional syntheses, suppressing cluster assembly; and (3) azeotropic evaporation of HNO 3 -H 2 O, driving cluster assembly and crystallization at the solution surface. Contrary to common cluster growth, the fully assembled cluster is never detected in the reaction solution. Because these reactive clusters do not persist in solution, uncontrolled precipitation of metal hydroxide is avoided. The proposed formation pathway opens opportunities to expand the composition space of metal-oxo clusters.
- Published
- 2016
32. On the Mechanism of the Nickel-Catalyzed Boron Insertion into the C−O Bond of Benzofuran
- Author
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Hideki Yorimitsu, Carles Bo, Hayate Saito, and Ana Mateo-Martínez
- Subjects
Reaction mechanism ,chemistry.chemical_compound ,Nucleophile ,Chemistry ,Reagent ,Aryl ,Boranes ,Benzofuran ,Medicinal chemistry ,Reductive elimination ,Catalysis - Abstract
The reaction of benzofurans with diboron reagents and Cs2CO3catalyzed by Ni(0) complexes results in the insertion of boron into the C-O bond. The reaction conditions mimic those reported by Martin and Hosoya for borylating aryl C-F bonds, but neither the role of the base nor the sequence of elementary steps is clear. Herein we report on the mechanism of such transformation on the basis of DFT studies, which suggest that the base activates the diboron reagent and generates a reactive boryl group, that Ni(II) is reduced back to Ni(0) during the boryl insertion into the Ni-O bond, and that the classical reductive elimination step is best viewed as a ring-contracting nucleophilic attack.
- Published
- 2019
33. Strategic Capture of the {Nb
- Author
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Nicolas P, Martin, Enric, Petrus, Mireia, Segado, Ana, Arteaga, Lev N, Zakharov, Carles, Bo, and May, Nyman
- Abstract
Group V Nb-polyoxometalate (Nb-POM) chemistry generally lacks the elegant pH-controlled speciation exhibited by group VI (Mo, W) POM chemistry. Here three Nb-POM clusters were isolated and structurally characterized; [Nb
- Published
- 2019
34. The role of computational results databases in accelerating the discovery of catalysts
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Núria López, Feliu Maseras, and Carles Bo
- Subjects
Database ,010405 organic chemistry ,Computer science ,Process Chemistry and Technology ,Bioengineering ,010402 general chemistry ,computer.software_genre ,01 natural sciences ,Biochemistry ,Catalysis ,0104 chemical sciences ,Metadata ,computer ,Reliability (statistics) - Abstract
Databases of computational results hold high promise for accelerating catalysis research. Still, many challenges remain and consensus on facets such as metadata, reliability and curation is crucial to transform the hype into an attractive technology
- Published
- 2018
35. Alkali-Driven Disassembly and Reassembly of Molecular Niobium Oxide in Water
- Author
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Dylan J. Sures, Mireia Segado, May Nyman, and Carles Bo
- Subjects
chemistry.chemical_classification ,Aqueous solution ,010405 organic chemistry ,Chemistry ,General Chemistry ,Pourbaix diagram ,010402 general chemistry ,Alkali metal ,01 natural sciences ,Biochemistry ,Chloride ,Catalysis ,0104 chemical sciences ,Colloid and Surface Chemistry ,Polyoxometalate ,medicine ,Physical chemistry ,Niobium oxide ,Solubility ,Counterion ,medicine.drug - Abstract
Counterions are deemed “spectators” in aqueous solutions of cationic or anionic molecular metal-oxo clusters. While pH and concentration drive aqueous metal speciation as a first approximation, the important effect of counterions is usually overlooked and never considered in standard Pourbaix databases. Alkali counterions for polyoxometalate (POM) clusters control solubility with distinct periodic trends, but evidence for alkali control over speciation is ambiguous. Here we show that a simple Nb-POM, [Nb10O28]6– ({Nb10}), converts to oligomers of (HxNb24O72)(24–x)– ({Nb24}) upon adding only alkali chloride salts, even in buffered neutral solutions. Raman and X-ray scattering reveal that the rate of {Nb10} to {Nb24} conversion increases with alkali cation radius and cation concentration. Cation-bridged oligomers of {Nb24}y (y = 2,4) are defined by comparing experimental to computed small-angle X-ray scattering spectra. Computational studies and mass spectrometry indicate that the alkalis open the compact {...
- Published
- 2018
36. Selective Lanthanide Distribution within a Comprehensive Series of Heterometallic [LnPr] Complexes
- Author
-
Leoní A. Barrios, Olivier Roubeau, Verónica Velasco, Simon J. Teat, Carles Bo, David Aguilà, Guillem Aromí, Joan González-Fabra, Generalitat de Catalunya, Agencia Estatal de Investigación (España), European Research Council, European Commission, Ministerio de Economía y Competitividad (España), and Ministerio de Ciencia, Innovación y Universidades (España)
- Subjects
Lanthanide ,Ions ,Complex systems ,Distribution (number theory) ,Series (mathematics) ,010405 organic chemistry ,Ligand ,Chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,3. Good health ,Inorganic Chemistry ,Crystallography ,Sistemes complexos ,Physical and Theoretical Chemistry ,Isostructural - Abstract
The preparation of heterometallic, lanthanide-only complexes is an extremely difficult synthetic challenge. By a ligand-based strategy, a complete isostructural series of dinuclear heterometallic [LnPr] complexes has been synthesized and structurally characterized. The two different coordination sites featured in this molecular entity allow study of the preferences of the praseodymium ion for a specific position depending on the ionic radii of the accompanying lanthanide partner. The purity of each heterometallic moiety has been evaluated in the solid state and in solution by means of crystallographic and spectrometric methods, respectively, revealing the limits of this strategy for ions with similar sizes. DFT calculations have been carried out to support the experimental results, confirming the nature of the site-selective lanthanide distribution. The predictable selectivity of this system has been exploited to assess the magnetic properties of the [DyPr] and [LuPr] derivatives, showing that the origin of the slow dynamics observed in the former arises from the dysprosium ion., G.A. thanks the Generalitat de Catalunya for the prize ICREA Academia 2008 and 2013 and the ERC for a Starting Grant (258060 FuncMolQIP). The authors acknowledge funding by the Spanish MINECO through CTQ2012-32247 and CTQ2015-68370-P (G.A., L.A.B., D.A., and V.V.), MAT2014-53961-R and MAT2017-86826-R (O.R.), and CTQ2017-88777-R (C.B. and J.G.-F.) as well as through the Juan de la Cierva program IJCI-2016-29901 (D.A.) and the Severo Ochoa Excellence Accreditation SEV-2013-0319 (C.B. and J.G.-F.). We also thank the Generalitat de Catalunya for financial support through the CERCA Program and 2017 SGR 290 grant.
- Published
- 2018
37. Deciphering key intermediates in the transformation of carbon dioxide into heterocyclic products
- Author
-
Eduardo C. Escudero-Adán, Atsushi Urakawa, Arjan W. Kleij, Carles Bo, Eddy Martin, Joan González-Fabra, Jeroen Rintjema, and Rui Huang
- Subjects
chemistry.chemical_classification ,010405 organic chemistry ,Hydrogen bond ,Process Chemistry and Technology ,Intermolecular force ,Infrared spectroscopy ,Substrate (chemistry) ,Bioengineering ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Combinatorial chemistry ,Catalysis ,Cycloaddition ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Carbonate ,Alkyl - Abstract
The identification of catalytic intermediates in the conversion of carbon dioxide is vital for improved catalyst design and optimization of structure–reactivity relationships, but remains elusive. Here, we report that intermolecular hydrogen bonding interactions between an epoxy alcohol, water and the catalyst structure are crucial towards the formation of a cyclic carbonate from carbon dioxide. A combination of multiple in situ and ex situ techniques including substrate labelling, kinetic studies, computational analysis, operando infrared spectroscopy and X-ray diffraction was applied to identify and support the structural connectivities of several previously unknown intermediates. An epoxy alcohol–water cluster formed by hydrogen bonding was identified as the initial intermediate able to trap CO2 and an elusive alkyl carbonate anion was also detected. The synergistic spectroscopic and computational analysis shown here offers a unique insight under operando conditions, as well as a useful analytical blueprint for key suggested intermediates in other mechanistically related CO2 conversion processes. One of the major routes for the use of CO2 in chemical production is the formation of carbonates via cycloaddition of CO2 to epoxides. This work uses a range of experimental and computational techniques to map out the elusive key intermediates in this process.
- Published
- 2018
38. Reconèixer la diversitat per a la millora de l’accés digital. Fonaments i accions del Laboratori d’Innovació Social Digital
- Author
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Mar Beneyto Seoane, Núria Simó-Gil, Carles Bosch-Geli, and Ramon Reig-Bolaño
- Subjects
desigualtat social ,tecnologia de l’educació ,educació social ,educació informal ,igualtat d'oportunitats ,Education (General) ,L7-991 ,Psychology ,BF1-990 - Abstract
Les tecnologies digitals formen part de la nostra vida quotidiana de forma extensiva des de fa més d’una dècada. Tot i que l’accés material a la tecnologia s’ha anat popularitzant, part de la població es troba, encara, en risc d’exclusió digital. Davant d’aquest pretext, aquest article descriu els fonaments i les accions del Laboratori d’Innovació Social Digital (LISD) de la Universitat de Vic - Universitat Central de Catalunya (Uvic-UCC), el qual aposta pel desenvolupament de pràctiques digitals inclusives i, a través de la investigació-acció, acompanya processos de millora digital i social amb i per a la comunitat, concretament de la població jove. La metodologia utilitzada pretén reconèixer les necessitats sociodigitals del territori i treballar, juntament amb la comunitat, en la construcció d’accions de millora des d’una perspectiva pedagògica. En aquesta línia i fins ara, el LISD ha treballat en quatre accions per al desenvolupament de les competències digitals de la població jove, especialment aquella més vulnerable, i l’intercanvi de coneixements entre persones de contextos diversos. Els resultats evidencien que cal orientar la funció del LISD cap a la implementació d’accions sistèmiques contextuals vinculades a facilitar l’accés i l’ús de les tecnologies, així com al desenvolupament de les competències digitals amb la població del municipi.
- Published
- 2023
- Full Text
- View/download PDF
39. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
- Author
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Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje, and ENCODE Imputation Challenge Participants
- Subjects
Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research.
- Published
- 2023
- Full Text
- View/download PDF
40. Ynones Merge Activation/Conjugate Addition of Chalcogenoborates ArE-Bpin (E=Se, S)
- Author
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Christopher M. Vogels, Stephen A. Westcott, Carles Bo, Xavier Sanz, Marc G. Civit, and Elena Fernández
- Subjects
Chemistry ,Stereochemistry ,General Chemistry ,Merge (version control) ,3. Good health ,Conjugate - Published
- 2015
41. AlIII-Catalysed Formation of Poly(limonene)carbonate: DFT Analysis of the Origin of Stereoregularity
- Author
-
Leticia Peña Carrodeguas, Joan González-Fabra, Carles Bo, Arjan W. Kleij, Fernando Castro-Gómez, Química Física i Inorgànica, and Universitat Rovira i Virgili
- Subjects
0947-6539 ,Green chemistry ,Oxide ,DFT ,Alumini ,Catalysis ,chemistry.chemical_compound ,Nucleophile ,Polymer chemistry ,Organic chemistry ,polymers ,chemistry.chemical_classification ,Limonene ,Densitat funcional ,aluminium ,Organic Chemistry ,Substrate (chemistry) ,Química ,General Chemistry ,Polymer ,Chemistry ,polycarbonate ,chemistry ,density functional calculations ,CO2 ,limonen ,Cis–trans isomerism - Abstract
Amino-triphenolate derived Al(III) complexes combined with suitable nucleophiles have been investigated as binary catalysts for the coupling of limonene oxide and carbon dioxide to afford alternating polycarbonates. These catalysts are able to produce stereo-regular, perfectly alternating trans-polymers from cis-limonene oxide, whereas the pure trans isomer and cis/trans mixture give rise to lower degrees of stereo-regularity. The best Al(III) catalyst shows the potential to mediate the conversion of both stereo-isomers of limonene oxide with high conversion levels of up to 71% under neat conditions indicating a high robustness and atom-efficiency of this catalytic process. Computational studies have revealed unique features of the binary catalyst system among which is the preferred nucleophilic attack on the quaternary carbon centre in the limonene oxide substrate.
- Published
- 2015
- Full Text
- View/download PDF
42. An atomistic insight into light-sensitive polymers with methylstilbene building blocks
- Author
-
Nuno A. G. Bandeira, Carles Bo, Bartosz Tylkowski, Krzysztof Artur Bogdanowicz, and Marta Giamberini
- Subjects
chemistry.chemical_classification ,Materials science ,Polymers and Plastics ,Double bond ,Organic Chemistry ,Nanotechnology ,Polymer ,Copolyester ,Spectral line ,chemistry ,Chemical physics ,Materials Chemistry ,Periodic boundary conditions ,Isomerization ,Excitation ,Cis–trans isomerism - Abstract
Controlled release of photosensitive systems is widely studied because of its numerous applications. However, just a few descriptions of the mechanism of this phenomenon have been reported. The aim of this study was to investigate the behaviour of a real system based on light-sensitive α-methylstilbene-based copolyester microcapsules with vanillin as an upload under UV irradiation. For this purpose we aimed to elucidate some of the structural features of the chains by means of quantum chemical calculations applying periodic boundary conditions. Additionally, the excitation energy of an approximated model was used to verify the influence of large size and various functionalities of attached groups on the system. From the optimized structure of trans and cis isomers, it was proved that trans-to-cis isomerization can be responsible for a main chain length reduction by 20% in comparison to the initial state, thus confirming the experimental findings. Moreover, the major influence of double bonds on photoactivity of the system was justified by comparison of the calculated UV-visible spectra of both forms with empirically obtained data which were in good agreement. © 2015 Society of Chemical Industry
- Published
- 2015
43. Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform
- Author
-
Moises Álvarez-Moreno, Feliu Maseras, Carles Bo, Josep M. Poblet, Núria López, and C. de Graaf
- Subjects
Big Data ,Computer science ,XSL ,General Chemical Engineering ,Computational Chemsitry ,Big data ,Library and Information Sciences ,computer.software_genre ,User-Computer Interface ,Databases ,Upload ,Software ,Computational chemistry ,computer.programming_language ,Structure (mathematical logic) ,Internet ,HTML5 ,Database ,business.industry ,Open data ,General Chemistry ,Computer Science Applications ,Key (cryptography) ,The Internet ,business ,computer ,Databases, Chemical - Abstract
We present the ioChem-BD platform (www. iochem-bd.org) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers’ needs in the form of HTML5 reports, supporting information, and other research media.  
- Published
- 2014
44. Depletion Interactions at Interfaces Induced by Ferromagnetic Colloidal Polymers
- Author
-
Joan Josep Cerdà, Josep Batle, Carles Bona-Casas, Joan Massó, and Tomàs Sintes
- Subjects
colloidal polymers ,magnetism ,numerical simulations ,Organic chemistry ,QD241-441 - Abstract
The pair-interaction force profiles for two non-magnetic colloids immersed in a suspension of ferromagnetic colloidal polymers are investigated via Langevin simulations. A quasi-two-dimensional approach is taken to study the interface case and a range of colloidal size ratios (non-magnetic:magnetic) from 6:1 up to 20:1 have been considered in this work. Simulations show that when compared with non-magnetic suspensions, the magnetic polymers strongly modify the depletion force profiles leading to strongly oscillatory behavior. Larger polymer densities and size ratios increase the range of the depletion forces, and in general, also their strength; the force barrier peaks at short distances show more complex behavior. As the length of the ferromagnetic polymers increases, the force profiles become more regular, and stable points with their corresponding attraction basins develop. The number of stable points and the distance at which they occur can be tuned through the modification of the field strength H and the angle θ formed by the field and the imaginary axis joining the centers of the two non-magnetic colloids. When not constrained, the net forces acting on the two colloids tend to align them with the field till θ=0∘. At this angle, the force profiles turn out to be purely attractive, and therefore, these systems could be used as a funneling tool to form long linear arrays of non-magnetic particles. Torsional forces peak at θ=45∘ and have minimums at θ=0∘ as well as θ=90∘ which is an unstable orientation as slight deviations will evolve towards θ→0∘. Nonetheless, results suggest that the θ=90∘ orientation could be easily stabilized in several ways. In such a case, the stable points that the radial force profiles exhibit for this orthogonal orientation to the field could be used to control the distance between the two large colloids: their position and number can be controlled via H. Therefore, suspensions made of ferromagnetic colloidal polymers can be also useful in the creation of magnetic colloidal tweezers or ratchets. A qualitative explanation of all the observed phenomena can be provided in terms of how the geometrical constraints and the external field modify the conformations of the ferromagnetic polymers near the two large particles, and in turn, how both factors combine to create unbalanced Kelvin forces that oscillate in strength with the distance between the two non-magnetic colloids.
- Published
- 2024
- Full Text
- View/download PDF
45. Mechanistic Insights into the Carbon Dioxide-Cyclohexene Oxide Copolymerization reaction: Is one Metal Center enough?
- Author
-
Fernando Castro-Gómez, Carles Bo, Arjan W. Kleij, and Joan González-Fabra
- Subjects
Models, Molecular ,General Chemical Engineering ,Molecular Conformation ,Homogeneous catalysis ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Catalysis ,Polymerization ,Metal ,chemistry.chemical_compound ,symbols.namesake ,Cyclohexenes ,Copolymer ,Organometallic Compounds ,Environmental Chemistry ,General Materials Science ,Bimetallic strip ,010405 organic chemistry ,Chemistry ,Carbon Dioxide ,0104 chemical sciences ,Gibbs free energy ,General Energy ,visual_art ,visual_art.visual_art_medium ,symbols ,Physical chemistry ,Epoxy Compounds ,Quantum Theory ,Thermodynamics ,Density functional theory ,Cyclohexene oxide ,Aluminum - Abstract
A detailed study on the mechanism for the alternating copolymerization of cyclohexene oxide (CHO) and CO2 mediated by a [Al{amino‐tri(phenolate)}]/NBu4I binary catalyst system has been carried out using density functional theory (DFT) based methods. Four potential mechanisms (one monometallic and three bimetallic) were considered for the first propagation cycle of the CHO/CO2 copolymerization. The obtained Gibbs free-energies provide a rational for the relative high activity of a non-covalent dimeric structure formed in situ and thus the feasibility of a bimetallic mechanism to obtain polycarbonates quantitatively. Gibbs free energies also indicate that the alternating copolymerization was favoured over the cyclic carbonate formation.
- Published
- 2017
46. Metal-Free Synthesis of N-Aryl Amides using Organocatalytic Ring-Opening Aminolysis of Lactones
- Author
-
Arjan W. Kleij, Carles Bo, Luis Martínez-Rodríguez, Nuno A. G. Bandeira, Wusheng Guo, and José Enrique Gómez
- Subjects
Bicyclic molecule ,010405 organic chemistry ,General Chemical Engineering ,Aryl ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Amides ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,Lactones ,General Energy ,Aminolysis ,chemistry ,Amide ,Organocatalysis ,Environmental Chemistry ,Organic chemistry ,General Materials Science ,Amines ,Guanidine - Abstract
Catalytic ring-opening of bio-sourced non-strained lactones with aromatic amines can offer a straightforward, 100 % atom-economical, and sustainable pathway towards relevant N-aryl amide scaffolds. Herein, the first general, metal-free, and highly efficient N-aryl amide formation is reported from poorly reactive aromatic amines and non-strained lactones under mild operating conditions using an organic bicyclic guanidine catalyst. This protocol has high application potential as exemplified by the formal syntheses of drug-relevant molecules.
- Published
- 2017
47. Anions coordinating anions: analysis of the interaction between anionic Keplerate nanocapsules and their anionic ligands
- Author
-
Dolores Melgar, Carles Bo, Nuno A. G. Bandeira, and Josep Bonet Avalos
- Subjects
010405 organic chemistry ,Inorganic chemistry ,Solvation ,Oxide ,General Physics and Astronomy ,Phosphinate ,010402 general chemistry ,01 natural sciences ,Selenate ,Nanocapsules ,0104 chemical sciences ,Metal ,chemistry.chemical_compound ,chemistry ,visual_art ,Polymer chemistry ,visual_art.visual_art_medium ,Carbonate ,Dipolar bond ,Physical and Theoretical Chemistry - Abstract
Keplerates are a family of anionic metal oxide spherical capsules containing up to 132 metal atoms and some hundreds of oxygen atoms. These capsules holding a high negative charge of −12 coordinate both mono-anionic and di-anionic ligands thus increasing their charge up to −42, even up to −72, which is compensated by the corresponding counter-cations in the X-ray structures. We present an analysis of the relative importance of several energy terms of the coordinate bond between the capsule and ligands like carbonate, sulphate, sulphite, phosphinate, selenate, and a variety of carboxylates, of which the overriding component is contributed by solvation/de-solvation effects.
- Published
- 2017
48. Thermodynamic Stability of Heterodimetallic [LnLn'] Complexes: Synthesis and DFT Studies
- Author
-
Leoní A. Barrios, David Aguilà, Simon J. Teat, Carles Bo, Joan González-Fabra, Nuno A. G. Bandeira, Guillem Aromí, Verónica Velasco, Olivier Roubeau, Fundação para a Ciência e a Tecnologia (Portugal), Generalitat de Catalunya, European Commission, European Research Council, Ministerio de Economía y Competitividad (España), Department of Energy (US), and Consejo Superior de Investigaciones Científicas (España)
- Subjects
Lanthanide ,Supramolecular chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,Dissociation (chemistry) ,Química supramolecular ,supramolecular chemistry ,Coordination complex ,chemistry.chemical_compound ,Pyridine ,Molecule ,lanthanides ,functional molecules ,Density functionals ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Teoria del funcional de densitat ,General Chemistry ,3. Good health ,0104 chemical sciences ,Crystallography ,Chemical Sciences ,density functional calculations ,coordination chemistry ,Chemical stability ,Coordination compounds ,Compostos de coordinació ,Selectivity - Abstract
The solid‐state and solution configurations of the heterodimetallic complexes (Hpy)[LaEr(HL)3(NO3)(py)(H2O)] (1), (Hpy)[CeEr(HL)3(NO3)(py)(H2O)] (2), (Hpy)[CeGd(HL)3(NO3)(py)(H2O)] (3), (Hpy)[PrSm(HL)3(NO3)(py)(H2O)] (4), and (Hpy)2[LaYb(HL)3(NO3)(H2O)](NO3) (5), in which H3L is 6‐(3‐oxo‐3‐(2‐hydroxyphenyl)propionyl)pyridine‐2‐carboxylic acid and py is pyridine, were analyzed experimentally and by using DFT calculations. Complexes 3, 4, and 5 are described here for the first time, and were analyzed by using single‐crystal X‐ray diffraction and mass spectrometry. The theoretical study was also extended to the [LaCe] and [LaLu] analogues. The results are consistent with a remarkable selectivity of the metal distribution within the molecule in the solid state, enhanced by the size difference between the different ions. This selectivity was reduced in solution, particularly for ions with the most similar radii. This unique entry into 4f–4f′′ heterometallic chemistry establishes for the first time the difference between the selectivity in solution and that in the solid state, as a result of changes to the coordination that follow the dissociation of terminal ligands upon dissolution of the complexes., G.A. thanks the Generalitat de Catalunya for the prize ICREA Academia 2008 and 2013 and the ERC for a Starting Grant (258060 FuncMolQIP). The authors thank the Spanish MINECO for funding through CTQ2012‐32247, CTQ2015‐68370‐P (GA, LAB, DA, VV), CTQ2014‐52824‐R (CB, JGF, NAGB), and MAT2014‐53961‐R (OR), the Marie Curie Co‐funding of Regional, National, and International Programs (COFUND) for funding scheme 291787‐ICIQ‐IPMP, Fundação para a Ciência e Tecnologia Grant SFRH/BPD/110419/2015 (NAGB), and the Severo Ochoa Excellence Accreditation SEV‐2013‐0319 (CB). Also we thank Generalitat de Catalunya for financial support through the CERCA Program and grant no. 2014SGR409. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under contract no. DE‐AC02‐05CH11231.
- Published
- 2017
49. Magneto-Structural Analysis of Iron(III) Keggin Polyoxometalates
- Author
-
Jürgen Schnack, Yuan-Zhu Zhang, Toby J. Woods, Carles Bo, Kim R. Dunbar, Nuno A. G. Bandeira, Omid Sadeghi, and May Nyman
- Subjects
Stereochemistry ,Chemistry ,1. No poverty ,Magnetism ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Magnetic susceptibility ,DFT ,Homonuclear molecule ,0104 chemical sciences ,Ion ,Crystallography ,Antiferromagnetism ,polyoxometalates ,Computational analysis ,Physical and Theoretical Chemistry ,0210 nano-technology ,Spin (physics) ,Keplerates ,Magneto - Abstract
A computational study and magnetic susceptibility measurements of three homonuclear Fe(III) Keggin structures are herein presented: the [FeO4@Fe12F24(μ−OCH3)12]5− anion (1), the [Bi6{FeO4@Fe12O12(OH)12}(μ-O2CCCl3)12]+ cation (2) and its polymorph [Bi6
- Published
- 2017
50. Photochromism and Dual-Color Fluorescence in a Polyoxometalate\textendashBenzospiropyran Molecular Switch
- Author
-
Anna Proust, Arnaud Parrot, Guillaume Izzet, Stefano A. Serapian, Aurélie Jacquart, Anne Dolbecq, Aurélie Bernard, Carles Bo, Pierre Mialane, Olivier Oms, Rémi Métivier, Etienne Derat, Institut Parisien de Chimie Moléculaire (IPCM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Barcelona Institute of Science and Technology (BIST), Méthodes et Application en Chimie Organique (MACO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Lavoisier de Versailles (ILV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Edifices PolyMétalliques (E-POM), Laboratoire de Photophysique et Photochimie Supramoléculaires et Macromoléculaires (PPSM), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universitat Rovira i Virgili, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Cachan (ENS Cachan)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan), and Química Física i Inorgànica
- Subjects
Polioxometal·lats ,POLE 2 ,POLE 1 ,Population ,02 engineering and technology ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Catalysis ,Photochromism ,Density functional calculations, E-POM, fluorescence, MACO, molecular photoswitches, photochromism, POLE 1, POLE 2, Polyoxometalates ,[CHIM]Chemical Sciences ,polyoxometalates ,education ,1433-7851 ,Molecular switch ,education.field_of_study ,010405 organic chemistry ,Chemistry ,Polyoxometalates ,molecular photoswitches ,General Medicine ,General Chemistry ,Química ,021001 nanoscience & nanotechnology ,photochromism ,Fluorescence ,E-POM ,Fluorescència ,0104 chemical sciences ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Density functional calculations ,Covalent bond ,Polyoxometalate ,density functional calculations ,fluorescence ,0210 nano-technology ,MACO ,Two-dimensional nuclear magnetic resonance spectroscopy ,Excitation ,Fisicoquímica - Abstract
The photophysical properties of a Keggin-type polyoxometalate (POM) covalently bounded to a benzospir- opyran (BSPR) unit have been investigated. These studies reveal that both closed and open forms are emissive with distinct spectral features (lem (closed form) = 530 nm, lem (open form) = 670 nm) and that the fluorescence of the BSPR unit of the hybrid is considerably enhanced compared to BSPR parent compounds. While the fluorescence excitation energy of the BSPR reference compounds (370 nm) is close to the intense absorption responsible of the photochromic character (350 nm), the fluorescence excitation of the hybrid is shifted to lower energy (400 nm), improving the population of the emissive state. Combined NOESY NMR and theoretical calculations of the closed form of the hybrid give an intimate understanding of the conformation adopted by the hybrid and show that the nitroaryl moieties of the BSPR is folded toward the POM, which should affect the electronic properties of the BSPR.  
- Published
- 2017
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