11 research outputs found
Gas-phase reactivity of Lewis-adducts and model biochemical systems: Quantun Chemistry and Molecular Dynamics perspectives
Tesis doctoral inĂ©dita cotutelada por la UniversitĂ© DÂŽEvry Val dÂŽEssone y la Universidad AutĂłnoma de Madrid, Facultad de Ciencias. Departamento de QuĂmica. Fecha de lectura: 17-10-2014La reactividad en fase gas, tambin conocida como reactividad intrnseca, tiene un
gran interes ya que la ausencia de interacciones con un solvente puede resultar en
una reactividad muy diferente, permitiendo adems un mejor concimiento de las
propiedades moleculares. Con la aparicin en 1900 de nuevas tcnicas experimenta-
les, concretamente tcnicas de ionizacin ms suaves, la qumica de iones en fase gas
experiment un desarrollo signi cante con el consecuente cambio en cuanto a nues-
tra idea de reactividad qumica. El presente manuscrito est dividido en dos partes
diferentes cada una de las cuales trata un aspecto distinto sobre la reactividad en
fase gas.
La primera parte, Part I, trata sobre el estudio de la acidez intrnseca de una
serie de bases de Lewis pertenecientes al grupo 13 de la tabla peridica. EL principal
tema de estudio durante esta primera parte son los cambios que se producen en
dichas acideces intrnsecas al formase un complejo de Lewis con distintos cidos de
Lewis en los que el centro activo es un elemento del grupo 13 de la Tabla peridica.
Asi, el origen del aumento de acidez observado al formarse el complejo es raciona-
lizado a travs del uso de diferentes mtodos tericos. Se han llevado a cabo calculos
DFT y ab intio de alto nivel con el n de calcular los valores tericos para la acidez
de las moleculas consideradas. Complementariamente, se usaron mtodos para el
anlisis de la poblacin electrnica (AIM, NBO y ELF) con el objetivo de describir
los cambios en la con guracin electrnica que se producen al formarse el complejo y
que son responsables del observado aumento de acidez. Es importante destacar que
parte de los resultados aqu presentados han sido corroborados mediante tcnicas
experimentales.
La seguna parte, Part II, se centra en el estudio de la reactividad unimole-
cular de los iones formamida-M2+ (M = Ca, Sr). En este caso, existan trabajos
experimentales disponibles relacionados con el estudio de la reacticvidad inducida
por colisin (CID, en sus siglas en ingls) de dichos iones. A lo largo de la segunda
parte de este manuscrito, se estudian y caracterizan los mecanismos de fragmen-
tacin de ambos iones, empleando para ello distintas tcnicas tericas que son a la
vez complementarias entre ellas. El primer paso en este estudio es la evaluacin de
distintos mtodos tericos con el objetivo de encontrar el ms adecuado para llevar
a cabo clculos ables a la vez que se mantiene el coste computacional lo ms bajo
posible. Por un lado, hemos realizado un estudio cintico del proceso de fragmen-
tacin usando la teora estadstica conocida como RRKM, con el n de describir
la reactividad \lenta" (en una escala de tiempo > fs). Por otro lado, realizamos
simulaciones dinmicas que permiten describir la reactividad no estadstica en una
escala corta de tiempo (< 2.5 fs). De este modo, usando el descrito procedimiento
multi-escala, hemos sido capaces de racionalizar el origen de todos los productos
observados en los espectros CID de los iones formamida-Ca2+ y formamida-Sr2+
obtenidos experimentalmente, as como las diferencias entre ellos.
En un cuarto capitulo se enumeran y describen brevemente los mtodos utiliza-
dos, tanto tericos como experimentales, a lo largo del trabajo presentado en este
manuscrito.The so-called intrinsic rectivity (gas-phase reactivity) is of great importance since
the absence of interaction with a solvent can result in very di erent reactivity
patterns; allowing for a better understanding of molecular properties. With the
advent in the 1900s of new experimental techniques, notably soft ionization meth-
ods such as electrospray ionization, the gas-phase ion chemistry has signigicantly
developped in the last decades of the 1900s with a concomitant change in our view
of chemical reactivity. The present manuscript is divide in two di erent parts each
one dealing with di erent aspects of gas-phase reactivity.
Part I is concerned with the study of the intrinsic acidity of a series of group
15 Lewis base. The changes on the aforementioned intrinsic acidity as the Lewis
bases form adducts with group 13 Lewis acid is the main subject of this part.
Thus, the origin for the acidity enhancement observed upon adduct formation is
rationalized by means of di erent theoretical methods. High-level DFT and ab
intio calculations were perfomed in order to compute theoretical acidites of the
molecules under survey. Complementary to this, population analysis techniques
such as AIM, ELF, and NBO were used to analyze the changes on the electronic
con gurations of those molecules and therefore provide with an explanation to the
observed acidities. It is worth to stress the fact that part of the results were as
well con rmed by means of experimental measurements.
Part II focuses in unimolecular reactivity of molecular ions, namely, formamide-
M2+ (M = Ca, Sr). In this case, experiments studying the Collision Induced Reac-
tivity (CID) of these ions were already performed and through the second part of
this manuscript the fragmentation mechanism of both ions are studied and char-
acterized using di erent, but complementary, theoretical techniques. It is worth
to mention that in a very rst-step, an assessment of di erent methods to perform
reliable electronic structure calculations while maintaining the lower possible com-
putational cost. On the one hand, a kinetic study of the fragmentation process
using the statistical theory, RRKM, to describe the long-time reactivity (> fs). On
the other hand, direct dynamics simulations are performed in order to describe the
short-time (< 2.5 fs) non-statistical reactivity. This multi-scale approach allowed
us to account for all the products observed in the CID experimental spectra of
formamide-M2+ (M = Ca, Sr), as well as the di erences between them.
In the fourth chapter a summary of the experimental and theoretical proce-
dures used to perform the work presented in this manuscript is provided
Evidence of the torsion of a polyene chain in a strongly hindered molecular environment: The ttbP4 crystal
In this work we provide experimental and theoretical evidence that in a molecular environment as restricted as the crystalline phase, the all-trans ttbP4 (1,1,8,8-tetrakis(tert-butyl)octa-1,3,5,7-tetraene) can undergo a conformational change, by rotating around the second single bond, when it is electronically excited to its 11Bu state. Undoubtedly, this is an interesting step to clarify the viability of the torsional mechanism of retinal pigments in the cavity of bacteriorhodopsin as proposed in the vision mechanism. We show that the fluorescence emission of ttbP4 in the crystalline phase is the combination of two bands corresponding to the emission from two different ttbP4 conformers. Theoretical simulations of absorption and emission spectra allowed us to identify the two conformers as: i) the most stable all-trans ttbP4, giving rise to a structured fluorescence band, and ii) the conformer generated by the torsion around the second single bond of ttbP4 polyene chain, giving rise to an emission band with hardly any structure. Interestingly, experimental data also show that the rotated structure, after deactivating to the ground state, takes a time to return to the all-trans configurationThankful to the Universidad
Autonoma de Madrid for providing the facility to carry out this research.
A.M.S. thanks the CCC-UAM for generous allocation of computing time
and the Madrid Government (Comunidad de Madrid-Spain) under the
Multiannual Agreement with UAM in the line Support to Young Researchers, in the context of the V PRICIT (SI3-PJI-2021-00463). We
acknowledge Javier Cerezo for fruitful discussions and providing help
with FCclases3 program to simulate the spectr
Recommended from our members
Computational Design of a Tetrapericyclic Cycloaddition and the Nature of Potential Energy Surfaces with Multiple Bifurcations
An ambimodal transition state (TS) that leads to formation of four different pericyclic reaction products ([4 + 6]-, [2 + 8]-, [8 + 2]-, and [6 + 4]-cycloadducts) without any intervening minima has been designed and explored with DFT computations and quasiclassical molecular dynamics. Direct dynamics simulations propagated from the ambimodal TS show the evolution of trajectories to give the four cycloadducts. The topography of the PES is a key factor in product selectivity. A good correlation is observed between geometrical resemblance of the products to the ambimodal TS (measured by the RMSD) and the ratio of products formed in the dynamics simulationsWe are grateful to the National Science Foundation (CHE1764328 to K.N.H.) for financial support of this research and
for access to XSEDE and UCLA Hoffman 2 for computer time
and for this study. A.M.S. thanks the Madrid Government
(Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad AutĂłnoma de Madrid in the line
Support to Young Researchers, in the context of the V PRICIT
(SI3-PJI-2021-00463) and âMinisterio de EducaciĂłn Cultura y
Deporteâ for funding (CAS18/00458
2-Hydroxybenzophenone as a Chemical Auxiliary for the Activation of Ketiminoesters for Highly Enantioselective Addition to Nitroalkenes under Bifunctional Catalysis
An organocatalytic system is presented for the Michael addition of monoactivated glycine ketimine ylides with a bifunctional catalyst. The ketimine bears an ortho hydroxy group, which increases the acidity of the methylene hydrogen atoms and enhances the reactivity, thus allowing the synthesis of a large variety of a,g-diamino acid derivatives with excellent stereoselectivit
Enhancing visible-light photocatalysis via endohedral functionalization of single-walled carbon nanotubes with organic dyes
The encapsulation of an organic dye, 10-phenylphenothiazine (PTH), in the inner cavity of single-walled carbon nanotubes (SWNTs) as a breaking heterogenization strategy is presented. The PTH@oSWNT material was microscopically and spectroscopically characterized, showing intense photoemission when illuminated with visible light at the nanoscale. Thus, PTH@oSWNT was employed as a heterogeneous photocatalyst in single electron transfer dehalogenation reactions under visible light irradiation. The material showed an enhanced photocatalytic activity, achieving turnover numbers as high as 3200, with complete recyclability and stability for more than eight cycles. Computational calculations confirm that electronic communication between both partners is established because, upon illumination, an electron of the excited PTH is transferred from the Ïsystem of the molecule to the delocalized Ï-cloud of the SWNT, thus justifying the enhanced photocatalytic activityFinancial support was provided by the European Research Council (ERC-CoG, contract number: 647550), the Spanish Government (RTI2018-095038-B-I00, PID2019-110091GB-I00), and the âComunidad de Madridâ and European Structural Funds (S2018/NMT-4367). M.B. wishes to thank the Spanish Government for a Juan de la Cierva contract (IJC2019-042157-I). A.M.-S. acknowledges support by the Comunidad AutĂłnoma de Madrid under grant 2016-T2/IND166
Intramolecular hydrogen bond activation for kinetic resolution of furanone derivatives by an organocatalyzed [3+2] asymmetric cycloaddition
Herein, a formal highly enantioselective organocatalyzed [3+2] cycloaddition of furanone derivatives and azomethine ylides is presented. The success of this reaction resides in an intramolecular hydrogen bond activation through an o-hydroxy group at aromatic ring of the imine, allowing the formation of highly multifunctional bicyclic adducts with five stereogenic centers in a stereocontrolled manner. Furthermore, the reaction is paired to a highly efficient kinetic resolution of butenolides, achieving selectivity factors above 200. Using this methodology, furan-2(5H)-ones as well as furo[3,4-c]pyrrolidinones were obtained with high enantioselectivities. Quantum chemistry calculations reveal the crucial role of hydrogen bond formed between the catalyst donor-units and the two reagents, which modify their arrangement and promote effective facial discrimination resulting in a highly selective kinetic resolution. In addition, further applicability of the kinetic resolution process is shownPID2019-110091GB-I00, PID2021-122299NB-I00, TED2021-130470B-I00, TED2021-129999B-C32, âComunidad de Madridâ for European Structural Funds (S2018/NMT-4367) and (Y2020/NMT6469), CEX2018-000805-
Intramolecular hydrogen-bond activation for the addition of nucleophilic imines: 2-hydroxybenzophenone as a chemical auxiliary
The addition of nucleophilic imines, using 2-hydroxybenzophenone as a chemical auxiliary, is presented. An intramolecular six-membered ring via hydrogen bonding that enhances the reactivity and selectivity is the key of this strategy, which is supported by DFT calculations and experimental trialsSpanish Government (CTQ2015-64561-R, CTQ2016-76061-P, and MDM-2014-0377), Prodep (UJAT-PTC-247) and CCC-UAM are acknowledged. A. G. thanks MINECO for a PhD fellowship (FPI) and A. M. S. thanks CAM for a postdoctoral contract (2016-T2/IND-1660
Boron Dipyrromethene (BODIPY) as Electron-Withdrawing Group in Asymmetric Copper-Catalyzed [3+2] Cycloadditions for the Synthesis of Pyrrolidine-Based Biological Sensors
This is the peer reviewed version of the following article: Rigotti, T., AsenjoâPascual, J., MartĂnâSomer, A., MilĂĄn Rois, P., Cordani, M., DĂazâTendero, S., ... & AlemĂĄn. Boron Dipyrromethene (BODIPY) as ElectronâWithdrawing Group in Asymmetric CopperâCatalyzed [3+ 2] Cycloadditions for the Synthesis of PyrrolidineâBased Biological Sensors. Advanced Synthesis & Catalysis Volume 362, Issue 6, 17 March 2020, Pages 1345-1355 ,
which has been published in final form at https://doi.org/10.1002/adsc.201901465.
This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsIn this work, we describe the use of Boron Dipyrromethene (BODIPY) as electron-withdrawing group for activation of double bonds in asymmetric copper-catalyzed [3+2] cycloaddition reactions with azomethine ylides. The reactions take place under smooth conditions and with high enantiomeric excess for a large number of different substituents, pointing out the high activation of the alkene by using a boron dipyrromethene as electron-withdrawing group. Experimental, theoretical studies and comparison with other common electron-withdrawing groups in asymmetric copper-catalyzed [3+2] cycloadditions show the reasons of the different reactivity of the boron dipyrromethene derivatives, which can be exploited as a useful activating group in asymmetric catalysis. Additional experiments show that the so obtained pyrrolidines can be employed as biocompatible biosensors, which can be located in the endosomal compartments and do not present toxicity in three cell linesThis work was supported by the Spanish Government (RTI2018â095038âBâI00, CTQ2016â76061âP, SAF2017â87305âR), Comunidad de Madrid (IND2017/INDâ7809), and coâfinanced by European Structural and Investment Fund. We acknowledge the generous allocation of computing time at the CCC (UAM). Financial support from the Spanish Ministry of Economy and Competitiveness, through the ââMaria de Maeztuââ Program of Excellence in R&D (MDMâ2014â0377), is also acknowledged. AsociaciĂłn Española Contra el CĂĄncer, and IMDEA Nanociencia acknowledge support from the âČSevero OchoaâČ Programme for Centres of Excellence in R&D (MINECO, Grant SEVâ2016â0686). P.M.R thanks the Ministry of Economy, Industry and competitiveness of Spain for the FPI grant (BESâ2017.082521). A.M.S. thanks CAM for a postdoctoral contract (2016âT2/INDâ1660
Photodissociation of leucine-enkephalin protonated peptide: An experimental and theoretical perspective
Understanding the competing processes that govern far ultraviolet photodissociation (FUV-PD) of biopolymers such as proteins is a challenge. Here, we report a combined experimental and theoretical investigation of FUV-PD of protonated leucine-enkephalin pentapeptide ([YGGFL + H]+) in the gas-phase. Time-dependent density functional theory (TD-DFT) calculations in combination with experiments and previous results for amino acids and shorter peptides help in rationalizing the evolution of the excited states. The results confirm that fragmentation of [YGGFL + H]+ results mainly from vibrationally excited species in the ground electronic state, populated after internal conversion. We also propose fragmentation mechanisms for specific photo-fragments such as tyrosine side chain loss (with an extra hydrogen) or hydrogen loss. In general, we observe the same mechanisms as for smaller peptides or protonated Tyr and Phe, that are not quenched by the presence of other amino acids. Nevertheless, we also found some differences, as for H loss, in part due to the fact that the charge is solvated by the peptide chain and not only by the COOH terminal grou
Inborn errors of OASâRNase L in SARS-CoV-2ârelated multisystem inflammatory syndrome in children
International audienceMultisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1 , OAS2 , or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)âsensing OAS1 and OAS2 generate 2âČ-5âČ-linked oligoadenylates (2-5A) that activate the single-stranded RNAâdegrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase Lâdeficient cells. Cytokine production in RNase Lâdeficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OASâRNase L deficiencies in these patients unleash the production of SARS-CoV-2âtriggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C