Embed Size (px)
Citation preview
Book of Abstracts
XXXIII reunió de la
Xarxa de Referència de Química Teòrica i Computacional
5-6 de Juliol, Tarragona
Plenary talks
Natalie Fey, Computational Inorganic Chemistry, University of Bristol, UK
Computational Expeditions into Chemical Space
Sonsoles Martín-Santamaría, Biological Research Center (CIB-CSIC), Madrid
Pattern recognition receptors: A computational approach
Henrik Koch, Departement of Chemistry, NTNU Trondheim, Norway
Novel multi-level coupled cluster methods for valence and core excited states
Nicolas Ferré, Université d'Aix-Marseille, France
New models for pH-dependent absorption spectrum of photoactive biomolecules
Scott Mitchell, Institute of Materials Science of Aragón, Zaragoza
Molecular and hybrid nanomaterials for applications in health and cultural heritage
Computational Expeditions into Chemical Space
Natalie Fey
School of Chemistry, University of Bristol, UK Email: [email protected]
Computational studies of organometallic homogeneous catalysis play an increasingly important role in furthering (and changing) our understanding of catalytic cycles and can help to guide the discovery and evaluation of new catalysts (Dalton Trans., 2014, 43, 13545; Angew. Chem. Int. Ed. 2012, 51, 118). While a truly “rational design” process remains out of reach, detailed mechanistic information from both experiment and computation can be combined successfully with suitable parameters characterising catalysts and substrates to predict outcomes and guide screening (Chem. Asian J., 2014, 9, 1714-1723). Rather than pursuing a purely computational solution of in silico catalyst design and evaluation, an iterative process of mechanistic study, data analysis, prediction and experimentation can accommodate complicated mechanistic manifolds and lead to useful predictions for the discovery and design of suitable catalysts. The computational inputs to this process rely on large databases of parameters characterising ligand and complex properties in a range of different environments (Organometallics, 2014, 33, 1751-1791; Organometallics, 2010, 29, 6245; ibid.2012, 31, 5302; Dalton Trans., 2013, 42, 172). More recently, we have started to develop a database designed to capture the properties of redox-switchable catalysts of interest to the Diaconescu group (UCLA), where the metallocene backbone is the primary redox switch, but the catalytically active metal centre may also be able to access different oxidation states. Such maps of ligand space are combined with detailed computational mechanistic studies (Dalton Trans., 2014, 43, 13545; Dalton Trans., 2010, 39, 10833), using the best available computational approaches for synthetically-relevant complexes, on carefully selected subsets of ligands, as well as large-scale data analysis. This presentation will use examples drawn from recent work on a range of transition metal-catalysed reactions to illustrate this process and identify key challenges and bottlenecks to computational predictions. Website: https://feygroupchem.wordpress.com/
Pattern Recognition Receptors. A Computational Approach
Sonsoles Martín-Santamaría
Computational Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC. C/ Ramiro de Maeztu, 9. 28040-Madrid, Spain. [email protected]
The pattern recognition receptor (PRR) Toll-Like Receptor 4 (TLR4), together with the MD-2 protein, forms a heterodimer responsible of the specific recognition of lipopolysaccharides (LPS) from the outer membrane of Gram-negative bacteria. However, the mechanism at the atomic level for such activation/inactivation process remains unknown, pointing to fascinating questions related to: i) the ligand-receptor interactions pattern governing the binding of some glycolipids; ii) the dynamics of the MD-2 binding pocket and its ability to accommodate lipid A (1); iii) the glycolipid-mimetic mechanism of non LPS-like molecules (2); iv) the activation of the human TLR4/MD-2 complex by natural under-acylated LPS (3). We have applied a combination of different computational techniques, such as MD simulations, NMA, docking calculations, virtual screening, and membrane simulations to address some of these questions (Figure 1). Other PRRs have also been studied (lectins) by means of computational techniques to address the design of glycomimetics with enhanced selectivity.
Figure 1. Representation of some computational studies of the TLR4/MD-2 system.
References
1. Vašl, J.; Oblak, A.; Peternelj, T. T.; Klett, J.; Martín-Santamaría, S.; Gioannini, T. L.; Weiss, J. P.; Jerala, R. J. Immunol. 2016, 196, 2309-18. 3. Sestito, S. E.; Facchini, F. A.; Billod, J.-M.; Martin-Santamaria, S.; Casnati, A.; Sansone, F.; Peri, F. J. Med. Chem. 2017, in press. 3. Di Lorenzo, F.; Kubik, Ł.; Oblak, A.; Lorè, N. I.; Cigana, C.; Lanzetta, R.; Parrilli, M.; Hamad, M. A.; De Soyza, A.; Silipo, A.; Jerala, R.; Bragonzi, A.; Valvano, M. A.; Martín-Santamaría, S.; Molinaro, A. J. Biol. Chem. 2015, 290, 21305-19.
Noveldevelopmentsofmulti-levelcoupledclustermethodsforvalenceandcoreexcitations
HenrikKoch,1,2RolfH.Myhre,1,2Ida-MarieHøyvik1andSoniaCoriani3
1.DepartmentofChemistry,NTNU,7491Trondheim,Norway.2.StanfordPULSEInstitute,SLACNationalAcceleratorLaboratory,MenloPark,CA94025,USA.3.DepartmentofChemistry,TechnicalUniversityofDenmark,2800Kgs.Lyngby,[email protected]
Accurate calculation of core-excited states requires use of high-level electron correlationmethods.Ontheotherhand,thechangeintheelectronicstructurecomparedtothegroundstateishighlylocalizedaroundtheatominvolvedinthecore-excitation.Thiscanbeefficientlyusedtodevise approximation schemes with significant reduced cost and without compromising theaccuracy.Iwillfocusonourrecentdevelopmentsofthecorevalenceseparation(CVS)[1],multi-levelcoupledclustermodels(MLCC)[2,3],correlatednaturaltransitionorbitals(CNTOs)[4]andrelateddevelopments.Theperformanceofthedevelopedtechniqueswillbeillustratedbytheresultsfromourrecentcollaborationonnewcutting-edgeexperimentsperformedatSLAC[5].
[1]S.CorianiandH.Koch,J.Chem.Phys.143,181103(2015).��[2]R.H.Myhre,A.M.J.SánchezdeMerásandH.Koch,J.Chem.Phys.141,224105(2014).��[3]R.H.Myhre,S.CorianiandH.Koch,J.Chem.TheoryComput.,12,2633(2016).[4]I.-M.Høyvik,R.H.MyhreandH.Koch,J.Chem.Phys.146,144109(2017).[5]T.J.A.Wolf,R.H.Myhre,J.P.Cryan,S.Coriani,R.J.Squibb,A.Battistoni,N.Berrah,C.Bostedt,P.Bucksbaum,G.Coslovich,R.Feifel,K.J.Gaffney,J.Grilj,T.J.Martinez,S.Miyabe,S.P.Moeller,M.Mucke,A.Natan,R.Obaid,T.Osipov,O.Plekan,S.Wang,H.KochandM.Gühr,2016,Nat.Commun.(inpress)
New models for pH-dependent absorption spectrum of photoactive biomolecules
Elisa Pieri; Michael Stenrup; Vincent Ledentu; Nicolas Ferré
Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, Marseille, France
Like many other molecular properties, photophysical properties of complex systems often depend on pH.
From the theoretical chemistry point of view, the modeling of this dependence relies on the correct description
of the protonation states for all the possible ionizable sites present in the system.
In this talk, I will report different models which deal with the absorption spectrum of two photoactive
biomolecules: i) a photochromic microbial protein, Anabaena Sensory Rhodopsin, whose retinal
chromophore behaves as a unidirectional biological rotor1 and ii) a polypeptide featuring a Trp-Tyr dyad.2
Going from a simple electrostatic model3 to a sophisticated multi-scale approach involving molecular dynamics
simulations and QM/MM calculations,4 we show that not only protonation states of amino-acids matter but also
that several distributions of protonation micro-states need to be considered to analyse the pH-dependency of
their UV-visible absorption spectrum.
References
1. (a) R. Rozin, A. Wand, K.-H. Jung, S. Ruhman, M. Sheves, J. Phys. Chem. B 2014, 118, 8995. (b) O.
A. Sineshchekov, V. D. Trivedi, J. Sakaki, J. L. Spudich, Biol. Chem. 2005, 280, 14663.
2. C. V. Pagba, T. G. McCaslin, G. Veglia, F. Porcelli, J. Yohannan, Z. Guo, M. McDaniel, B. A. Barry,
Nat. Commun. 2015, 6, 20010.
3. M. Stenrup, E. Pieri, V. Ledentu, N. Ferré, Phys. Chem. Chem. Phys. 2017, 19, 14073.
4. (a) A. Strambi, B. Durbeej, N. Ferré, M. Olivucci, Proc. Nat. Acad. Sci. USA 2010, 107, 21322. (b) I.
Schapiro, S. Ruhman, Biochim. Biophys. Acta 2013, 1837, 589.
Molecular and hybrid nanomaterials for applications in health and cultural heritage
Scott G. Mitchell
Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Cientificas-Universidad de Zaragoza and CIBER-BBN, Zaragoza, Spain. [email protected]
Microorganisms are highly proficient at inhabiting and decaying paper, leather and stone objects, generating serious problems for the conservation of paintings, textiles and sculptures. The associated health risks coupled with the cost of decontaminating infected artefacts, exhibition rooms and depots make this a pertinent topic for museums, local authorities and private collectors alike. Moreover, our shared cultural heritage is a social, economic and environmental resource for Europe.1 The overall aim of our current research efforts is to engineer a range of nanohybrid materials with enhanced antimicrobial properties that will act as biocidal agents to help prevent biodeterioration in objects of cultural heritage. As an example, Figure 1 (below) illustrates how modular and tuneable ionic liquid materials can be constructed from the combination of two component parts: polyoxometalates (POMs) and quaternary ammonium cations.2 The ability to tailor each of these two constituents offers a unique opportunity to produce precision biocides that meet the specific needs of cultural heritage conservation (e.g highly applicable colourless gels, waxes, sols etc.).3 Our research also demonstrates how comprehensive antimicrobial functional screening programmes can be used to assess the activity of nanomaterials against bacterial and fungal strains commonly found infecting objects of cultural heritage. Thereafter the most active and applicable materials are evaluated against biodeteriorative microorganism contaminants on in real cultural heritage artefacts from libraries and museums.
Figure 1. Use of POM-ILs as biocidal coatings on stone surfaces.
References
1. K. Sterflinger and G. Piñar, Appl. Microbiol. Biotechnol., 2013, 97, 9637–9646. 2. S. Herrmann, L. De Matteis, S. G. Mitchell, and C. Streb, Angew. Chem. Int. Ed. 2017, 56, 1667–1670. 3. “Heritage Microbiology and Science”, RSC Publishing (Ed. E. May, M. Jones and J. Mitchell) 2008.
Contributed talksCristina Roncero, UB: Spin interactions and magnetism in Cu(hfac)2LR “breathing crystal”. A static vs dynamicalapproach.
Pau Armengol, UAB: Ultrafast Action Chemistry in Slow Motion: Atomistic Description of the Excitation and Fluorescence Processes in an Archetypal Fluorescent Protein
Roberto Robles, ICN2: Ferrocene molecules on metal surfaces: self-assembly and magnetic doping
Steven Roldan, UdG: Trifluoromethylation of a well defined square planar aryl-Ni(II)-Complex: A computational insight into its mechanism.
Fèlix Llovell, IQS: Transferable models of ionic liquids and deep eutectic solvents with a molecular-based equation
Carolina Estarellas, UB: It is possible allosteric modulation mechanism of AMPK?
Roser Morales, URV: Uranium endofullerenes
Giuseppe Sciortino, UAB: Prediction of coordination sites of metal complexes with proteins through theoretical calculations
Enrique Marcos, IRB: Computational design of protein structures from scratch
Adrian Romero, UdG: Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase
Zhongling Lang, URV: DFT studies on polyoxometalate-gold composites: From structure to catalysis
Antonio Moreno, URV: Halogenated endohedral metallofullerenes: Can they be synthesized?
Ferran Acuña, ICIQ: Computational study of the hydrogen production mechanism by a cobalt-aminopyridine catalyst
Masoud Shahrohki, ICIQ: Hybrid Palladium Nanoparticles for Direct Hydrogen Peroxide Synthesis: The Key Role of the Ligand
Egil Sa, UAB: σ-Donating ligands containing Fe=CH2 : a path towards iron-based olefin metathesis
Sergio Illero, ICN2: Thermal conductivity of 2D materials from first principles
Estefanía López, UB: Experimental and Theoretical points of view of Li+ + i-C3H7Br gas-phase reaction
Rositha Kuniyil, ICIQ: Mechanistic insights into the Palladium catalysed stereoselective formation of allylic amines
Enric Fortin, UB: On-Lattice Monte Carlo simulation of enzyme kinetics in crowded intracellular environments
Spin interactions and magnetism in Cu(hfac)2LR “breathing crystal”. A static vs dynamical approach.
Cristina Roncero; Mercè Deumal; Jordi Ribas-Ariño; Juan J. Novoa
Secció Química Física, Dept. Ciència Materials i Química Física, & IQTCUB, Universitat de Barcelona.
The family of heterospin Cu(hfac)2LR complexes has the ability to undergo reversible, thermally induced structural rearrangements that produce a spin crossover-like transition. Due to these structural and magnetic changes, the Cu(hfac)2LR family of complexes is known as “breathing crystals”.
The Cu(hfac)2LBu crystal with butylpyrazolyl-substituted nitronyl nitroxides (NN) [1] exhibits a polymeric-chain crystal structure formed by the alternation of two units: a one-spin Cu(hfac)2 unit (enclosed in blue) and a three-centres-three-spins NN-Cu(hfac)2-NN unit, known as triad (enclosed in red). The main structural and magnetic changes that this switchable material experiences are mostly localised within the triad. We have demonstrated that the JAB interaction within the triads cannot be evaluated at DFT level, due to being multiconfigurational at low temperature. Our study corroborates that the intra-triad exchange coupling (JCu·NN) changes from weak ferromagnetic (FM) at room temperature to antiferromagnetic (AFM) at low temperature upon spin transition.
Contrary to what the crystal packing appears to indicate, the triads are magnetically connected due to direct through-space NN-NN magnetic interactions (see green rectangle in Figure). A full static study at CASSCF level of the magnetic pathways in the system has thus proved that the system presents a one-dimensional magnetic topology. At 100 K, the magnetic topology consists of strongly AFM coupled NN-Cu(hfac)2-NN triads that interact between them antiferromagnetically. This picture becomes an alternant chain topology with intra-FM-triad interactions coupling again antiferromagnetically connected upon phase transition at room temperature. The simulation of the magnetic susceptibility clearly highlights that different magnetic topology translates into different χT(T) behaviour. These static results correctly reproduce the two extreme behaviors: low and high temperature. However, the calculations done using the 145 K data do not agree at all with the experimental data, showing a lack of information of how the transition occurs. Our dynamical study throws some light on this transition and shows the importance of considering the thermal fluctuations in this kind of systems.
References
1. S. L. Veber et al., “High-Field EPR Reveals the Strongly Temperature-Dependent Exchange Interaction in ‘Breathing’ Crystals Cu (hfac)2LR,” pp. 2444–2445, 2008.
Figure. Crystal packing of polymeric chains and magnetic
topology. Note the triad and the CuO4N2 unit are enclosed in red and blue, respectively. The exchange interaction pathways are highlighted (blue arrows). The green rectangle envelopes
the NN radicals involved in the intra-triad JAB. Hydrogen and fluorine atoms have been omitted for clarity.
Ultrafast Action Chemsitry in Slow Motion: Atomistic Description of the Excitation and Fluorescence Processes in an Archetypal Fluorescent
Protein
Pau Armengola, Ricard Gelaberta, Miquel Morenoa and J.M. Llucha,b
aDepartament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
bInstitut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
Corresponding autor: [email protected]
The development of Fluorescent Proteins (PFs) has set a milestone in modern bioimaging techniques, since de discovery of the Green Fluorescent Protein (GFP) in the early 1960s. They can be used as non-invasive labels for protein observation in living cells due to their unique characteristics: they are small, very resistant and easy-to-replicate proteins and, on the top, they are autofluorescent.1 GFP displays two absorption peaks at room temperature, commonly labelled A (395 nm) and B (475 nm), which correspond to the neutral and the ionized form of the chromophore. Upon excitation, GFP emits radiation at 508 nm with a QY of 0.8 after an internal excited State proton transfer takes place. The GFP variant S65T/H148D has been widely studied due to its unique spectroscopic characteristics. It absorbs at 415 nm and emits green light at 508 nm with a QY of 0.21, but the rise of the emission band could not be resolved experimentally and it has set to be under 50 fs. After a sudden decay of the excitation energy (< 50 fs), a second component of decay is experimentally detected, which occurs in the order of picosecods. 2
In this work we have performed extensive quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations in order to reproduce the experimental data and shed light to the processes associated to the 2-component decay of the excitation energy. We have been able to associate the first component to a direct proton transfer between the chromophore and the proton acceptor (Asp148), which occurs in about 20 fs, and the second component to a complex coordinate composed by the lengthen of the chromophore-Asp148 distance, the approach of the residue Tyr145 and the loss of planarity of the chromophore. Furthermore, we have found two different non-radiative relaxation channels that can explain the loss of QY and the mismatch between the decay of the emission of the form A* and the rise of the I* form.
References
1. R. Y. Tsien, Annu. Rev. Biochem., 1998, 67, 509-44.
2. Kondo, M.; Heisler, I. A.; Stoner Ma, D.; Tonge, P. J.; Meech, S. R. J. Am. Chem. Soc. 2010, 132, 1452-1453.
Ferrocene molecules on metal surfaces: self-
assembly and magnetic doping
Roberto Robles1, Paula Abufager2, Nicolas Lorente31 Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The BarcelonaInstitute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain.2 Instituto de Fısica de Rosario, Consejo Nacional de Investigaciones Cientıficas y Tecnicas(CONICET) and Universidad Nacional de Rosario, Av. Pellegrini 250 (2000) Rosario,Argentina.3Centro de Fısica de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardi-
zabal 5, 20018 Donostia-San Sebastian, Spain, and Donostia International Physics Center
(DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain.
Metallocenes wires have recently attracted considerable interest for their usein molecular spintronics. However, this interest is hampered by our incom-plete knowledge of the metallocene interaction with a metal. Here we presenta study of di↵erent aspects of ferrocene molecules on metal surfaces. First,combining low-temperature scanning tunneling microscopy and density func-tional theory calculations we study the self-assembly of ferrocene moleculeson copper surfaces. We show two di↵erent configurations and we proposethat they are stabilized by arrangements formed by vertical- and horizontal-lying molecules. Second, we explore the magnetic doping of the moleculesby Co atoms, showing two di↵erent on-surface procedures to build isolatedand layer-integrated Co-ferrocene molecules. We show that, unlike singleferrocene, the formed molecule has a magnetic moment. Our results pavethe way for a controlled procedure towards the development of metallocene-based nanowires with tailored magnetic properties.
References1. M. Ormaza, P. Abufager, N. Bachellier, R. Robles, M. Verot, T. Le Bahers,M.- L. Bocquet, N. Lorente, and L. Limot, J. Phys. Chem. Lett. 6, 395(2015).2. M. Ormaza, R. Robles, N. Bachellier, P. Abufager, N. Lorente, and L.Limot, Nano Lett. 16, 588 (2016).
Trifluoromethylation of a well defined square planar aryl-Ni(II)-Complex: A computational insight into its mechanism.
Steven Roldán-Gómez;1 Mireia Rovira;1 Vlad Martin-Diaconescu;1 Christopher J. Whiteoak,1.2 Anna Company;1 Josep M. Luis;1 Xavi Ribas.1
1 Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Facultat Ciències, E17071 Girona (Catalonia, Spain); 2 Biomolecular Sciences Research Centre, Faculty of Health and Wellbeing, Sheffield Hallam University, City Campus, Sheffield S1 1WB, England
[email protected]; [email protected]; [email protected]
The interest for the chemistry of the trifluoromethyl functional group has grown in the last decades due to its capability to module properties related to solubility and stability in organic compounds, having important applications in the pharmaceutical and agrochemical industry. (1)(2) While the vast majority of these transformations use palladium based catalysts,(2)(3) the development of nickel cross-coupling reactions have surge during the last decade(4) motivated by the envision of nickel catalysts as a low-cost/ less-toxic alternative to palladium. Mechanistic studies have shown that Ni-catalyzed reactions can occur via organometallic Ni(0), Ni(I), Ni(II), Ni(III) and, as reported very recently, Ni(IV) intermediates.(5)(6) Using density functional theory (DFT), we study a well-defined aryl-Ni(II) complex, which undergoes an aryl-CF3 bond forming cross-coupling reactions in the presence of (S-trifluoromethyl)dibenzothiophenium triflate (TDTT). In this work, we analyze two plausible mechanism based on the amount of electrons tranferered durind the reaction (1 electron transfer, Ni(II)/Ni(III), 2 electron transfer, Ni(II)/Ni(IV)). Interestingly, the result enlighted us with a third option, a combined mechanism of the two proposed (Ni(II)/Ni(III)/Ni(IV). Afterwards, we move to study the reactivity of some derivatives of the well-defined aryl-Ni(II) complex with intentions of finding a more reactive system.
References
1. Ritter, T. Nature, 2011,473, 470- 477 2. Buchwald, S.L. Science, 2010, 328, 1679-1681 3. Sanford, M. Organometallics, 2014, 33, 2653−2660 4. Jamison, T.F. Nature. 2014, 509, 299 5. Sanford, M. Science, 2015, 347, 1218-1220 6. Sanford, M. J. Am. Chem. Soc. 2015, 137, 8034−8037
NNN
H H NNN
NiIIIH H
·CF3
NNN
CF3H H
NiII CF3
NiII
NNN
NiIVH H
CF3
+> 99%
SET
radical – NiIIIrecombination
reductive elimination
Development of transferable models to describe the physicochemical behavior of ionic liquids and deep eutectic solvents with a molecular-based equation
Joel O. Lloret1; Lourdes F. Vega2; Fèlix Llovell1
1Department of Chemical Engineering and Materials Science, IQS School of Engineering, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain; 2Gas Research Center and Chemical Engineering Department, Khalifa University of Science and Technology, The Petroleum Institute, P.O. Box 2533, Abu Dhabi, United Arabs Emirates.
[email protected] ; [email protected]; [email protected]
The potential to reduce the environmental impact in industrial processes has led to investigations on ionic liquids (ILs) and Deep Eutectic Solvents (DESs) as an alternative for a variety of applications that conventionally use organic compounds. The popularity of ILs grew rapidly due to their almost inexistent vapor phase (in the range of application) and wide liquid range, although their expensive synthesis has become a limiting factor. Recently, DESs have appeared as a new class of compounds, with similar properties but with a very low cost. DESs are systems formed from a eutectic mixture of Lewis or Brønsted acids and bases, which can contain a variety of anionic and/or cationic species. Due to a strong hydrogen-bonding effect, their melting point is significantly lower than the melting point of the individual components. Unfortunately, the mechanisms behind the physicochemical properties of ILs and, particularly, DESs are still not well understood. Consequently, there are almost no available theoretical models describing the main physicochemical properties of these compounds. Recent computational studies1 have revealed a considerable network of hydrogen bonding interactions in ILs and DESs. In this regard, molecular modeling techniques and, in particular, molecular-based equations of state (EoSs), provide an attractive option to screen DESs properties, based on the fact that hydrogen bonding is explicitly considered in those equations by means of the Wertheim’s theory. The purpose of an advanced EoSs is to build coarse-grained simple molecular models, able to capture the basic features occurring in the molecule, in order to obtain fast and qualitative results that give quick answers to guide the experiments, becoming a crucial tool for process design. This work illustrates several practical examples based on the solubility of greenhouse gases on several ILs and DESs, in order to evaluate their feasibility for gas separation and carbon capture. A coarse-grained molecular model, within the framework of the soft-SAFT equation of state2 is presented for each molecule based on structural information. The absorption of relevant gases is modeled and compared with experimental data using a minimum amount of data, trying to assess the most appropriate solvent and the optimal operating conditions to maximize each gas separation.3-4 Particular attention is paid to the hydrogen-bonding effects and the transferability of the molecular parameters on ILs and DESs.
References
1. C. R. Ashworth, R. P. Matthews, T. Welton, P. A. Hunt, Phys. Chem. Chem. Phys. 18 (2016) 18145−18160.
2. F. J. Blas, L. F. Vega, Mol. Phys. 92 (1997) 135-150.
3. F. Llovell, M. B. Oliveira, J.A.P. Coutinho, L. F. Vega, Catalysis Today 255 (2015) 87–96.
4. J. O. Lloret, L.F. Vega, F. Llovell, Fluid Phase Equilibria, doi.org/10.1016/j.fluid.2017.04.013
Molecular dynamics simulations of AMPK: Mechanism of allosteric regulation by direct activators
C. Estarellas 1; E. Fara 1; S. Quesada-Sánchez 2; A. Castro 2; F.J. Luque 1
Departamento de Nutrición, Ciencias de la Alimentación y Gastronomia, Facultad de Frmacia e Instituto de Biomedicina, Campus de la Alimentación de Torribera, Universidad de Barcelona, Av. Prat de la Riba, 171, 08921 Santa Coloma de Gramenet; Instituto de Química Médica (IQM-CSIC), C/ Juan de la Cieva, 3, 28006, Madrid
Mammalian AMP-activated protein kinase (AMPK) is a Ser108/Thr132 protein kinase with a key role as sensor in the cellular energy homeostasis (1). This function confers AMPK a major role in numerous metabolic disorders, such as type 2 diabetes, obesity and cancer, and explains the progressive interest as a therapeutic target. AMPK is a heterotrimeric enzyme complex composed by a catalytic α-subunit and two regulatory subunits, β and γ. It is regulated by several mechanisms, including indirect activators such as metformin, rosiglitazone and resveratrol, and direct activators, such as compound A-769662 (2). The X-ray structure of AMPK bound to the direct activator A-769662 has been recently reported (PDB entry: 4CFF), providing a structural basis for the regulation of AMPK activation thanks to the phosphorylated Ser108 (pSer108) located at the CBM of the β subunit (2).
We have carried out a series of molecular dynamic simulations of AMPK in apo and holo states, as well as the holo in presence of ATP to gain insight into the mechanism of AMPK activation. The results point out an overall reduction in the conformational flexibility of holo systems compared to apo, especially significant in the N-lobe region. This fact is most likely due to the strong interactions formed between pSer108 and Lys29/Lys31 upon binding of the activator. Furthermore, the presence of the activator leads to a significant alteration in the protein flexibility, particularly regarding the motion of the N-terminus of the catalytic α-subunit and the regulatory domain of the β-subunit, as deduced from analysis of the essential motions. The net effect is that the shape and size of the ATP-binding pocket is altered and tends to pre-organize the ATP binding site. Thus, we hypothesize that the activator would act like a glue, filling the space between the N-terminal domain of the α subunit and transferring the movement of these regions to the ATP-binding site. This effect would rearrange the ATP-binding site, specifically leading to a conformational change in the mouth of the binding pocket, favouring the binding of ATP. Current efforts address the design of novel compounds that may act as activators of the enzyme.
References
1. D. Carling, F.V. Mayer, M.J. Sanders, S.J. Gamblin. Nat. Chem. Biol. 2011, 7, 512–518.
2. B. Xiao, M.J. Sanders, D. Carmena, N.J. Bright, L.F. Haire, E. Underwood, B.R. Patel, R.B. Heath, P.A. Walker, S. Hallen, F. Giordanetto, S.R. Martin, D. Carling, S.J. Gamblin. Nat. Commun. 2013, 4, 3017.
Computations on uranium endohedral metallofullerenes: Oxidation states for U dependent on the cage isomer
Roser Morales-Martínez, Antonio Rodríguez-Fortea, Josep M. Poblet
Departament de Química Física i Inorgànica, Universitat Rovira i Virgili
[email protected]; [email protected]; [email protected];
Fullerenes are allotropic forms of carbon formed by pentagonal and hexagonal rings. Their spherical geometry generates a cavity inside which makes them able to encapsulate atoms or clusters to form endohedral fullerenes with potential applications in biomedicine and photovoltaics. These molecules are stabilized by a formal transfer of electrons from the encapsulated atom or cluster to the fullerene cage. Since the detection of the first endohedral metallofullerene (EMF), La@C82, in 1991, it has always been observed that the oxidation state of a given encapsulated metal is always the same, regardless of the cage size. Here we present a recent study on some uranium mono-metallofullerenes, in collaboration with L. Echegoyen (UTEP) and N. Chen (Soochow Univ.), providing theoretical and experimental evidence for cage isomer dependent oxidation states for U. From DFT calculations we have found that U@D3h-C74 and U@C2(5)-C82 have tetravalent electronic configurations, whereas the isomeric U@C2v(9)-C82 has a trivalent electronic configuration. These are the first X-Ray crystallographic structures of uranium EMFs and this is first observation of metal oxidation state dependence on carbon cage isomerism for mono-EMFs.
References
1. W. Cai, R. Morales-Martínez, X. Zhang, D. Najera, E. L. Romero, A. Metta-Magaña, A. Rodríguez-Fortea, S. Fortier, N. Chen, J. M. Poblet and L. Echegoyen, Chem. Sci., 2017, Advance Article
2. A. Rodriguez-Fortea, A. L. Balch and J. M. Poblet, Chemical Society Reviews, 2011, 40, 3551- 3563.
3. A. A. Popov, S. F. Yang and L. Dunsch, Chem. Rev., 2013, 113, 5989-6113
Prediction of coordination sites of metal complexes with proteins through theoretical calculations
Giuseppe Sciortino,#,§ Daniele Sanna,† Jaime Rodríguez-Guerra,# Valeria Ugone,§ Giovanni Micera,§ Agustí Lledós,# Jean-Didier Maréchal,*,# and Eugenio Garribba*,§
# Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain
§ Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy
† Istituto CNR di Chimica Biomolecolare, Trav. La Crucca 3, I-07040 Sassari, [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected].
We present a new approach for expanding the range of application of protein-ligand docking methods to accurately predict the interaction of coordination complexes (i.e. metallodrugs but also physiologically relevant metal species) with proteins. We assume that, from a pure computational point of view, hydrogen bond functions could be related to coordination bonds. The hard work consists therefore in generating the convenient atom types and scoring functions to adapt this idea to docking software without using any geometrical constraint or energy restrain. To test this approach, we applied our model to 39 high-quality X-ray structures with transition and main group metal complexes bound to proteins using our implementation in the protein-ligand docking GOLD suite. The results are excellent: the percentage in which the RMSD of the simulated pose is smaller than the X-ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0, showing that the method could be used as a new tool to predict metal complexes-proteins interactions also when the X-ray structure is not available. This work could put the first steps for novel applicability of dockings in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most of protein-ligand docking programs nowadays available. Finally, the theoretical method were applied to the study of the interaction of two VIVO complexes with anti-diabetic activity1, [VIVO(pic)2(H2O)] and [VIVO(ma)2(H2O)] where pic is picolinate and ma is maltolate, with lysozyme (Lyz) for which EPR spectroscopy suggests the binding of the moieties VO(pic)2 and VO(ma)2 through a carboxylate group of an amino acid residue (Asp or Glu).2
References
1. (a) Thompson, K. H.; McNeill, J. H.; Orvig, C. Chem. Rev. 1999, 99, 2561-2572. (b) Thompson, K. H.; Orvig, C. Coord. Chem. Rev. 2001, 219–221, 1033-1053. (c) Shechter, Y.; Goldwaser, I.; Mironchik, M.; Fridkin, M.; Gefel, D. Coord. Chem. Rev. 2003, 237, 3-11.
2. Santos, M. F. A.; Correia, I.; Oliveira, A. R.; Garribba, E.; Costa Pessoa, J.; Santos-Silva, T. Eur. J. Inorg. Chem. 2014, 3293-3297.
Computational Design of Protein Structures from Scratch
Enrique Marcos1,2; Benjamin Basanta2; Tamuka M.Chidyausiku2; Gaetano T. Montelione3; David Baker2; Modesto Orozco1
1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; 2Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA; 3Department of Biochemistry and Molecular Biology, The State University of New Jersey, Piscataway, NJ, 08854, USA.
Computational design of new functional proteins relies on finding existing proteins having both the desired geometry and the stability to tolerate mutations needed for the new function. Despite successes of this approach for developing new enzymes and binding proteins, this dependence on existing protein structures can be a limitation for certain applications and, instead, building proteins de novo with custom-made structures should be more effective1. In a step toward custom-tailored ligand-binding proteins, our work focuses on the de novo design of protein folds suited for small-molecule binding2. We computationally designed a series of protein folds with curved β-sheets shaping cavities and verified them experimentally. We have also applied the de novo design approach to build chimeric proteins for nucleosomal DNA recognition.
References
1. P.-S. Huang, S.E. Boyken, D. Baker. The coming of age of de novo protein design. Nature, 537, 320-327 (2016).
2. E. Marcos, B. Basanta, T.M. Chidyausiku, et al. Principles for designing proteins with cavities formed by curved β sheets. Science, 355, 201-206 (2017).
!!
Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase
Adrian Romero-Rivera,1 Miguel A. Maria-Solano,1 and Sílvia Osuna1
1. Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, 17003 Girona, Spain.
Billions of years of evolution have made enzymes the best catalysts on Earth. They are capable of accelerating reactions by many orders of magnitude. This rate acceleration is achieved by decreasing the activation barriers of reactions, making them possible at ambiental conditions. Among all known catalysts, enzymes (i.e., biocatalysts) are the most efficient, specific and selective. The metal-dependent enzymes are really interesting due to their implication on oxidation-reduction reactions, these metalloenzymes have been studied since decades experimentally and computationally. Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets (Fig. 1), which dictate their substrate scope and stereoselectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site pockets, which has a great impact on the substrate–enzyme interactions and stereopreferences. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME (1) and NCIplot (2,3) corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants. (4)
Figure 1: Volume of the small and big pockets.
References
1. J. D. Durrant, L. Votapka, J. Sørensen and R. E. Amaro, J. Chem. Theory Comput. 2014, 10, 5047–5056. 2. J. Contreras-García, E. R. Johnson, S. Keinan, R. Chaudret, J.-P. Piquemal, D. N. Beratan and W. Yang, J. Chem. Theory Comput. 2011, 7, 625–632. 3. E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contrerasgarcía, A. J. Cohen and W. Yang, J. Am. Chem. Soc. 2010, 132, 6498–6506
4. M. A. Maria-Solano, A. Romero-Rivera, S. Osuna, Org. Biomol. Chem., 2017, 15, 4122-4129.
DFT Studies on Polyoxometalate-gold Composites: From Structure to Catalysis
Zhongling Lang, Anna Clotet,� Josep M. Poblet�
Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
Because of the charged nature of polyoxometalates (POMs) to model the interaction between POMs and surfaces is not forward. Previous studies for moderately (PW12O403-, SiW12O404-) and highly charged systems on the silver or gold surfaces, have demonstrated that the incorporation of counterions in the calculations is strictly necessary to have reasonable electronic properties.1 Initial attempts in the modeling of POMs deposited on surfaces used classical MDs to know the distribution of cations and explicit solvent molecules around the POM. This approach allows to evaluate redox properties1 or the orientation of a lacunary anion in contact with metal surface,2 but does permit to compute the energy profile associate to a catalytic reaction.
Here we report the first computational study on a catalytic reaction, where a POM acts as a co-catalyst. We have selected the water gas shift reaction catalyzed by the polyoxomolybdate [PMo12O40]3- in contact with a gold surface.3 We have taken the advantage of continuum solvent models to model the super-system. 4
References
1. X. Aparicio-Angles, P. Miro, A. Clotet, C. Bo, J. M. Poblet, Chem. Sci., 2012, 3, 2020–2027.
2. Z. L. Lang, X. Aparicio-Angles, I. Weinstock, A. Clotet, J. M. Poblet, Inorg. Chem. 2017, 56, 3961−3969.
3. W. B. Kim, T. Voitl, G. J. Rodriguez-Rivera, S. T. Evans, A. Dumesic, Angew. Chem. Int. Ed. 2005, 44, 778 – 782.
4. K. Mathew, R. Sundararaman, K. Letchworth-Weaver, T. A. Arias and R. G. Hennig, J. Chem. Phys. 2014, 140, 084106-1−084106-8.
Halogenated Endohedral Metallofullerenes: Can They Be Synthesized?
Antonio Moreno-Vicente, Marc Mulet-Gas, Paul W. Dunk,* Josep M. Poblet* and Antonio Rodríguez-Fortea*
Departament de Química Física i Inorgànica, Universitat Rovira i Virgili; National High Magnetic Field Laboratory, Florida State University
[email protected]; [email protected]; [email protected]
Endohedral metallofullerenes (EMFs), i.e. those fullerenes that contain metal atoms or clusters in their interior, show exceptional properties and potential applications in biomedicine and photovoltaics. Formation of halogenated EMFs, systems that might serve as precursors for tailored functionalizations of fullerene cages, is predicted to be feasible based on thermodynamic grounds. We have computed bond energies for the halogenation and hydrogenation of a wide range of empty fullerenes and EMFs (C50, C60, C66, C68, C70, C72, C80, C82 and C84). Besides, we have analyzed the stability for the fluorination of the prototypical Sc3N@Ih(7)-C80 cage by means of Car-Parrinello molecular dynamics simulations. In parallel, in situ halogenation of metallofullerenes is investigated (Dunk and Mulet-Gas at FSU) by use of a pulsed laser vaporization cluster source to experimentally corroborate our theoretical predictions. We propose that halogenation, as well as hydrogenation, might be possible for EMFs.
References
1. A. A. Popov, S. F. Yang and L. Dunsch, Chem. Rev., 2013, 113, 5989-6113
2. A. Rodriguez-Fortea, A. L. Balch and J. M. Poblet, Chemical Society Reviews, 2011, 40, 3551-3563.
COMPUTATIONAL STUDY OF THE HYDROGEN PRODUCTION MECHANISM BY A
COBALT-AMINOPYRIDINE CATALYST
Ferran Acuña Parés;a Josep M. Luis Luis;b,* Julio Lloret Fillola,*
aInstitute of Chemical Research of Catalonia (ICIQ), Tarragona, 43007, Spain; bInstitut de
Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona,
Campus Montilivi, Girona, 17071, Spain. [email protected]; [email protected]
Water splitting reaction promoted by sunlight is the most desired energetic pathway for molecular
hydrogen production and was recognized as a convenient solution to the long-run storage of renewable
energies through a particularly clean way. The development of water-splitting devices with catalysts
based on earth-abundant materials may become the most cheap and sustainable way to achieve this
process.1 Therefore, many efforts have been made to develop first row transition metal catalytic systems
capable to produce H2 from water or organic acids, by using light as a source of energy or at low
overpotentials.2
Lloret-Fillol and co-workers reported the synthesis, characterization and proton reduction activity of a
cobalt(II) complex based on the pentadentate ligand 1,4-di(picolyl)-7-(p-toluenesulfonyl)-1,4,7-
triazacyclononane (Py2Tstacn).3 This cobalt complex has excellent electrocatalytic proton reduction
activity in acetonitrile when using trifluoroacetic acid as a proton source, and it is also photochemically
active in a 7:3 H2O/CH3CN solvent mixture using the iridium photosensitizer [IrIII(ppy)2(bpy)]+ and Et3N
as a sacrificial electron donor. In order to understand how this catalyst work, we have carried DFT
calculations to: i) propose a viable catalytic cycle consistent with our experimental results for the photo-
and electrochemically driven H2 generation and ii) to elucidate the role of the ligand and the reaction
conditions on the H2 evolution activity. The computational mechanistic analysis supported by
experimental data unravel which factors make feasible the proton reduction process. This information
may guide the synthesis of more efficient proton reduction catalysts.
References
1. J. H. Alstrum-Acevedo, M. K. Brennaman, T .J. Meyer, Inorg. Chem. 2005, 44, 6802.
2. a) V. Artero, M. Chavarot-Kerlidou, M. Fontecave, Angew. Chem. Int. Ed. 2011, 50, 7238; b) M. L. Helm, M. P.
Stewart, R. M. Bullock, M. R. DuBois, D. L. DuBois, Science 2011, 333, 863; c) Z. Han, F. Qiu, R. Eisenberg, P. L.
Holland, T. D. Krauss, Science 2012, 338, 1321; d) Z. Han, W. R. McNamara, M.-S. Eum, P. L. Holland, R. Eisenberg,
Angew. Chem. Int. Ed. 2012, 51, 1667; e) F.Gärtner, A. Boddien, E. Barsch, K. Fumino, S. Losse, H. Junge, D. Hollmann,
A. Bruckner, R. Ludwig, M. Beller, Chem. Eur. J. 2011, 17, 6425; f) T. Matsumoto, H.-C. Chang, M. Wakizaka, S. Ueno,
A. Kobayashi, A. Nakayama, T. Taketsugu, M. Kato, J. Am. Chem. Soc. 2013, 135, 8646; g) H. I. Karunadasa, C. J.
Chang, J. R. Long, Nature 2010, 464, 1329; h) H. I. Karunadasa, E. Montalvo, Y. Sun, M. Majda, J. R. Long, C. J. Chang,
Science 2012, 335, 698.
3. A. Call, Z. Codolà, F. Acuña-Parés, J. Lloret-Fillol, Chem Eur J. 2014, 20, 6171.
Hybrid Palladium Nanoparticles for Direct Hydrogen Peroxide
Synthesis: The Key Role of the Ligand
Giacomo M. Lari[a], Begoña Puértolas[a], Masoud Shahrokhi[b], Núria López[b], and
Javier Pérez-Ramírez[a]
[a] Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich (Switzerland)
[b] Institute of Chemical Research of Catalonia (ICIQ) and Barcelona Institute of Technology (BIST), Av. Països Catalans 16, 43007 Tarragona (Spain)
[email protected]; [email protected]
Ligand-modified palladium nanoparticles deposited on a carbon carrier efficiently catalyze the direct synthesis of H2O2 and the unique performance is due to their hybrid nanostructure. Catalytic testing demonstrated that the selectivity increases with the HHDMA ligand content from 10% for naked nanoparticles up to 80%, rivalling that obtained with state-of-the-art bimetallic catalysts (HHDMA=C20H46NO5P). Furthermore, it remains stable over five consecutive reaction runs owing to the high resistance towards leaching of the organic moiety, arising from its bond with the metal surface. As rationalized by density functional theory, this behavior is attributed to the adsorption mode of the reaction intermediates on the metal surface. Whereas they lie flat in the absence of the organic shell, their electrostatic interaction with the ligand results in a unique vertical configuration which prevents further dissociation and over-hydrogenation. These findings demonstrate the importance of understanding substrate–ligand interactions in capped nanoparticles to develop smart catalysts for the sustainable manufacture of hydrogen peroxide.
References
1. Y. Yi, L. Wang, G. Li, H. Guo, Catal. Sci. Technol. 2016, 6, 1593 –1610.
2. A. Plauck, E. E. Stangland, J. A. Dumesic, M. Mavrikakis, Proc. Natl. Acad. Sci. USA 2016, 113, E1973–E1982.
3. C.-J. Jia, F. Schgth, Phys. Chem. Chem. Phys. 2011, 13, 2457 – 2487.
4.P. T. Witte, P. H. Berben, S. Boland, E. H. Boymans, D. Vogt, J. W. Geus, J. G. Donkervoort, Top. Catal. 2012, 55, 505–511.
5. M. Garc&a-Mota, N. Llpez, Phys. Chem. Chem. Phys. 2011, 13, 5790–5797.
6. S. Shaik, D. Mandal, R. Ramanan, Nat. Chem. 2016, 8, 1091 – 1098.
σ-Donating ligands containing Fe=CH2 : a path towards iron-based olefin metathesis
Égil de Brito Sá1,2, Luis Rodríguez-Santiago1, Mariona Sodupe1, Xavier Solans-Monfort1 1 Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 080290, Barcelona-Espanya 2 Universidade Federal do Piauí, Campus Ministro Reis Velloso, Parnaíba, 64202-020, Piauí-Brasil [email protected]; [email protected]; [email protected]; [email protected] Olefin Metathesis (OM) is one of the most efficient and elegant tools for carbon-carbon double bond formation. It takes place, necessarily, in the presence of [M]=CR2 species, performing as catalyst. The most successful metals to such catalysts are Mo, W and Ru (1). One of the nowadays task for the organometallic chemistry is to perform the chemistry of hard and precious metals with metals of the first row, because they are more abundant, eco-friendly and, usually, less toxic (2). In our case a Fe carbene appears to be a good alternative to olefin metathesis reaction, once it belongs to the same family of ruthenium, besides of be inexpensive and show a low toxicity. Unfortunately, so far, the synthetized [Fe]=CR2 drives basically to the side reaction cyclopropanation, instead of the desirable olefin metathesis (Fig. 1) (3). In this work we use a theoretical approach, based on DFT level of theory, to understand the electronic structure and the reactivity of the known existing [Fe]=CR2, plus a large set of possible in silico designed iron carbenes. We analysed the factors which make olefin cyclopropanation more feasible than OM, regarding the different spin states, thermodynamic and kinetics, focusing in determine the coordination sphere and oxidation state of the iron that could lead toward a potential OM catalysts. The alkyl-containing σ-donating tridentate ligands, which, at the same time, promotes the iron carbene to the singlet state and destabilize the triplet state cyclopropanation products seems to be a way to be followed (4).
Fig. 1
References
[1] Grubbs, R. H. Angew. Chem., Int. Ed. 2006, 45, 3760– 3765. [2] Chirik, P.; Morris, R. Acc. Chem. Res. 2015, 48, 2495. [3] Du, G.; Andrioletti, B.; Rose, E.; Woo, L. K. Organometallics 2002, 21, 4490– 4495. [4] de Brito Sá, E.; Rodríguez-Santiago, L.; Sodupe, M.; Solans-Monfort, X. Organometallics 2016, 35, 3914-3923.
Thermal conductivity of 2D materials from �rst principles
S. Illera1, L. Colombo2, M. Pruneda3, P. Ordejón3
1 Institut Català de Nanociència i Nanotecnologia (ICN2) and Institut de Ciència de Materials de Barcelona (ICMAB), CSIC and BIST, Campus de la UAB, 08193 Bellaterra (Barcelona), Spain
2 Dipartamento di Fisica, Università di Cagliari Cittadella Universitaria, 09042 Monserrato (Ca), Italy
3Institut Català de Nanociència i Nanotecnologia (ICN2), CSIC and BIST, Campus de la UAB, 08193 Bellaterra (Barcelona), Spain
From the fundamental science point of view, the heat transport properties are strongly
related to the material's structure and composition down to the atomic scale. When
the dimensionality is reduced or nanometric scales are reached, novel thermal
properties emerge. Concerning 2D materials, graphene (GN) has shown exceptional
electrical and thermal properties stimulating the interest in similar isomorphic
materials, such boron nitride (BN). Regarding the BN nanoribons (BNNRs), it has been
recently shown that the thermal conductivity is strongly dependent on the transport
direction in contrast to the GNRs1. Here, we present the study from :rst-principles of
the thermal transport properties of BN using the methodology of "Approach to
Equilibrium Molecular Dynamics" (AEMD)2 from a pure Density Functional Theory (DFT)
approach as implemented in the SIESTA program3. The SIESTA MD module was
modi:ed to perform AEMD simulations, allowing the determination of the thermal
conductivity from a purely :rst-principles description, without assumptions on the
interatomic potentials or :ts to experimental information. This is the :rst time that
both approaches (DFT AEMD) are used in combination opening the possibility to
determine accurately the thermal conductivity in structures whose force :elds are not
available or su?ciently accurate (defective materials, doped systems or surfaces with
adsorbates). The anisotropy of the thermal conductivity of BN was studied in order to
demonstrate the capabilities of the proposed methodology, and to test the validity of
the recent force :eld studies1, quantifying the variation of the thermal conductivity as
a function of the transport direction.
References
[1] Yin-Chung Chen, Shang-Chin Lee, Te-Huan Liu, and Chien-Cheng Chang,
International Journal of Thermal Sciences 94,72-78 (2015)
[2[ C. Melis, R. Dettori, S. Vandermeulen, and L. Colombo, Eur. Phys. J. B 87:96
(2014)
[3] J. Soler, E. Artacho, J. D. Gale, A. García, J. Junquera, P. Ordejón, and D.
Sánchez-Portal, J. Phys.: Condens. Matter. 14, 2745 (2002)
Experimental and Theoretical points of view of Li+ + i-C3H7Br gas-phase reaction
E. López1; J.M. Lucas1; J. de Andrés1; M. Albertí1; J.M. Bofill2; A. Aguilar1.
1: Departament de Ciència de Material I Química Física, IQTC.
2: Departament de Química Inorgànica I Orgànica, IQTC.
The study of gas-phase reactions plays an important role in the knowledge of many types of chemicalreactions that happen on our planet, and also in other bodies of the Solar System1,2. Based on this idea, in theGDRQ at UB we study gas phase reactions between different types of reagents using a Radio FrequencyGuided Ion Beam(RF-GIB) apparatus3, to provide an experimental point of view. These are complementedwith a theoretical-computational approach that allow us to develop a complete analysis of multiple systems.In this work we present the results of the gas phase reaction between Li+ cations and organic iso-bromopropane neutral molecules, as an example of the type of studies carried out over many years in ourlaboratory4.
For the system treated herein, several reaction products corresponding to different reactive channels havebeen experimentally detected, as well as the formation of the collision adduct between the cation and theorganic molecule5, which has a long enough lifetime to be detected and quantified. These laboratorymeasurements are complemented by a later theoretical-computational study, determining and characterizingfirst the reactive system stationary points on the SEP by ab initio calculations. These stationary points will laterbe joined by the IRC method to form a reaction path and giving a vision about the reaction mechanism.Finally, through the use of the Venus-NWChem program, a sufficient number of dynamic trajectories havebeen performed in order to obtain satisfactory results for all the experimentally detected reaction channelsand for the adduct formation, too.
So, in this way, the study of this type of reactions is completed through treatments from different points ofview that provide us with information and details that allow a more extensive understanding of the processcarried out.
References
1. D. Kim, S. Hu, P. Tarakeshwar, and K. S. Kim, J. Phys. Chem. A 107(8),1228 (2003). 2. T. B. McMahon and G. Ohanessian, Chem. Eur. J. 6, 2931-294 (2000).3. M. Sabidó, J.M. Lucas, J. de Andrés, J. Sogas, M. Albertí, A. Aguilar, D. Bassi, D. Ascenzi, P. Franceschi, P. Tosi, andF. Pirani, Chem. Phys. Lett. 442, 28 (2007).4. J. M. Lucas, J. de Andrés, E. López, M. Albertí, J. M. Bofill, D. Bassi, D. Ascenzi, P. Tosi, and A. Aguilar, J. Phys.Chem. A. 113 , 14766 (2009).5. E. López, J.M. Lucas, J. de Andrés, M. Albertí, J.M. Bofill, and A. Aguilar, The Journal of Chemical Physics, 146,134301 (2017).
MECHANISTIC INSIGHTS INTO THE PALLADIUM CATALYSED STEREO-
SELECTIVE FORMATION OF ALLYLIC AMINES
Rositha Kuniyil;
a
Feliu Maserasa,b
a
Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and
Technology , Av. Països Catalans, 16, Tarragona (Spain); b
Departament de Química, Universitat
Autònoma de Barcelona, 08193 Bellaterra (Spain)
e-mail:[email protected]
Allylic amines, representing a class of functional olefins, are fundamental building blocks in organic chemistry,
and their synthesis is an important industrial and synthetic goal (1).
Significant progress has been observed in
recent years in the synthesis of allylic amines which has limited potential to introduce three or four different
substituents (2).
Pd-catalyzed conversion of allyl surrogates which are readily obtained from cyclic vinyl carbonates to
multisubstituted allylic amines are characterized by excellent stereoselectivity, operational simplicity, mild
reaction conditions, and wide scope in reaction partners(3). DFT studies were performed to rationalize the
stereocontrol in these allylic amine formation reactions, and evidence is provided that the formation of a six-
membered palladacyclic intermediate leads toward the formation of (Z)-configured allylic amine products.
Scheme1. Conversion of cyclic vinyl carbonates to allylic amines
The detailed mechanism for the palladium catalyzed conversion of cyclic vinyl carbonates to allylic amines will
be presented.
References
1. L. Huang, M. Arndt, K. Gooßen, H. Heydt, L. J. Gooßen, Chem. Rev. 115 (2015) 2596. (b)
B. M. Trost, M. L. Crawley, Chem. Rev. 103 (2003) 2921. (c) M. Tsuyoshi, H. Yuki, Y. Sato,
Org. Lett. 16 (2014) 14.
2. N. A. Butt, W. Zhang, Chem. Soc. Rev. 44 (2015) 7929. (b) B. M. Trost, T. Zhang, J. D.
Sieber, Chem. Sci. 1 (2010) 427.
3. W. Guo, L. Martínez-Rodríguez, R. Kuniyil, E. Martin, E. C. Escudero-Adán, F. Maseras, A.
W. Kleij, J. Am. Chem. Soc. 138 (2016) 11970.
On-Lattice Monte Carlo simulation of enzyme kinetics incrowded intracellular environmentsEnric Fortin; Sergio Madurga; Eudald Vilaseca; Francesc Mas
Material Science and Physical Chemistry Department & Institute of Theoretical and Compu-
tational Chemistry (IQTCUB), University of Barcelona (UB)
Reference Network on Theoretical and Computational Chemistry of Catalonia (XRQTC)
[email protected]; [email protected]
The cellular cytosol and the cellular membrane are highly structured environ-
ments with a great concentration of biological macromolecules that, through
nonspecific interactions, significantly a↵ect the processes of di↵usion and reac-
tion that occur within
1,2. Current theoretical models allow us to describe these
processes in diluted solution, but fail to explain their behaviour in intracellular
environments. In order to achieve it, the e↵ects of this macromolecular crowding
must be accounted for.
A lattice-based Monte Carlo algorithm has been generalized from previous
di↵usion
3and reaction
4Monte Carlo algorithms by our group. The program
simulates reaction-di↵usion processes with an irreversible Michaelis Menten
mechanism, by combination of a random walk and a stochastic sampling of
the reactive event. Addition of obstacles in the system enabled us to sim-
ulate macromolecular crowding and observe its e↵ects. The probabilities for
the stochastic events were chosen to represent an enzyme with realistic kinetic
constants
5, whereas the concentrations of enzyme and substrate are within the
physiological range.
Although this model is not as accurate as Brownian Dynamics, it allows us to
simulate at longer timescales. The results show a significant enhancement of
the bimolecular rate constants with increasing excluded volume.
References1. Zhou H-X, Rivas G, Minton AP. Annu. Rev. Biophys. (2008), 37:375–397.
2. Pastor, I. et al. Biophys. Chem. (2014), 185:8–13.
3. Vilaseca, E. et al. Phys. Chem. Chem. Phys. (2011), 13:7396–7407
4. Pitulice, L. et al. Biosci. (2014), 251:72–82.
5. Bar-Even, A. et al. Biochemistry (2011), 50:4402–4410.
