Abstracts of the CTTC 2019

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Frederik Tielens

Vrije Universiteit Brussel Faculteit Wetenschappen en Bio-ingenieurswetenschappen Pleinlaan 2, B-1050 Brussel, Belgium frederik.tielens@vub.be

Characterization of Self-Assembled Monolayers on Noble Metal Surfaces

Self-assembled monolayers (SAMs) consist of a layer of functionalized long-chain molecules tethered to a solid substrate. SAMs have attracted significant interest of both the fundamental and applied scientific communities. Their presence as a “coating” on a surface is attractive in a number of applications due to the possibility to provide tuning of the surface properties by selectively modifying functional groups on the SAM. Alkanethiols (CH3(CH2)nSH) and alkylthiolate radicals (CH3(CH2)nS∙) adsorption on Au(111) surface is one of the most studied and best-known SAM systems, but also other bioorganic molecules such as amino acids organize at the surface. The nature of the corresponding structure at the surface has been controversial for a long time, as well as other aspects such as the adsorption site on which the thiol chain is anchored, and if the thiol adsorbs by S-H bond breaking process or not. Experimental studies shed some light on both questions, indicating that surface thiol species are attached to Au adatoms, rather than Au atoms in such a bulk-terminated layer, and that it is the movement of these Au-adatom-thiolate moieties that order to produce the SAM structure. Still, some questions remain unsolved such as: At which coverage does this happen, and for which chain length? What is the influence of the presence of defect sites (vacancy and adatoms) on the S-H bond breaking process? The thiols adsorb in a laying down geometry at low coverage, but at which coverage do they straighten up or stand up? In this context we will show here a series of results on the characterization of alkyl thiol SAMs investigated in detail by means of periodic density functional calculations.

References I. Lorenzo Geada, I. Petit, M. Sulpizi and F. Tielens, Surf.Sci. 677 (2018) 271. E. Colombo, G. Belletti, F. Tielens, P. Quaino, Appl. Surf. Sci. 452, (2018) 141. S. Kumar Meena, C. Goldmann, D. Nassoko, M. Seydou, T. Marchandier, S. Moldovan, O. Ersen, F. Ribot, C. Chanéac, C. Sanchez, D. Portehault, F. Tielens, M. Sulpizi, ACS Nano, 11, 7371 (2017). D. Nassoko, M. Seydou, C. Goldmann, C. Chanéac, C. Sanchez, D. Portehault, F. Tielens, Materials Today Chemistry 5, 34, (2017). C. Goldmann, F. Ribot, L.F. Peiretti, P. Quaino, F. Tielens, C. Sanchez, C. Chanéac, D. Portehault, Small, 13, 1604028, (2017) H. Guesmi, N. Luque, E. Santos, F. Tielens, Chem.Eur.J, 23, 1402, (2017). D. Costa, C.-M. Pradier, F. Tielens, L. Savio, Surface Science Reports, 70, 449 (2015).

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Sam Trickey

Dept. of Physics and Quantum Theory Project, Univ. of Florida

Less is More – or – Back to Kohn-Sham

Simplification of widely used meta-generalized-gradient approximation (mGGA) exchange-correlation functionals by removal of their explicit orbital dependence is valuable because it re-incorporates mGGA calculations in the Kohn-Sham framework. Returning to the pure Kohn-Sham local potential framework (rather than the generalized K-S approach almost always used with orbital-dependent mGGA functionals) aids interpretability and improves computational efficiency in large-scale simulations. The talk will summarize how the Laplacian level of refinement can be achieved by use of suitably constructed approximate kinetic energy density functionals (KEDFs). The existence of Laplacian-level deorbitalizations which yield better performance than the original mGGA will be illustrated for molecules with the meta-GGA-made-very-simple functional. Results on standard molecular and condensed-phase test sets obtained from the deorbitalized version of the SCAN functional (“SCAN-L” for SCAN with Laplacian) reproduce the original SCAN error patterns rather well. However, the magnetization of bcc Fe is quite different, an important distinction that will be discussed.

Supported by U.S. Dept. of Energy grants DE-SC 0002139 and DE-SC 0019330.

References D. Mejía-Rodríguez and S.B. Trickey, Phys. Rev. B 98, 115161 (2018); Phys. Rev. A 96, 052512 (2017).

Adrienn Ruzsinszky

Department of Physics, Temple University, Philadelphia, PA 19122, USA

Going beyond the random phase approximation for materials

The Random Phase Approximation (RPA) has become a standard method beyond semilocal Density Functional Theory (DFT) that naturally incorporates weak interactions and eliminates self-interaction error in the exchange energy [1]. RPA is not completely perfect, however, and suffers from self- correlation error as well as an incorrect description of short-ranged correlation. To improve upon RPA, various beyond-RPA approximations were developed in the past decade. The most familiar approximations are the RPA+ [2], SOSEX (second-order screened exchange) [3] along with model exchange-correlation kernels within the time-dependent DFT framework [4]. Exchange-correlation kernels can be applied to excited states and optical spectra [4]. In this talk I will reveal the strengths and limitations of these methods. In addition, I will introduce new alternative routes which can deliver further improvement beyond the already existing techniques [5,6]. Applications will be also discussed.

Work is supported by NSF DMR–1553022 and DOE BES DE-SC0012575.

References:[1] H. Eshuis, J. E. Bates, F. Furche, Theor. Chem. Acc., 131, 1084 (2012) [2] S. Kurth and J. P. Perdew, Phys. Rev. B, 59, 10461, (1999) [3] A. Grüneis, M. Marsman, J. Harl, L. Schimka, and G. Kresse, J. Chem. Phys. 131, 154115 (2009) [4] J.E. Bates, S. Laricchia, and A. Ruzsinszky, Phys. Rev. B 93, 045119, (2016) [5] T. Gould, J. P. Perdew and A. Ruzsinszky, to be submitted [6] P.D. Mezei, A. Ruzsinszky, to be submitted.

Luis Rincon

Universidad San Francisco de Quito, Quito, Ecuador

The information content of the Fermi and Coulomb holes

This presentation summarizes two recently proposed information quantities which are employed to visualize the Fermi and Coulomb holes in the real space. The first one is the information content of the Exchange-Correlation hole, calculated from the Kullback–Leibler divergence of the same-spin conditional pair density respect to the marginal probability (χXC). As reported, χXC, can be used to reveal the regions of the space associated to the classical electron pair model [1-3]. The second one is the information content of the correlation hole, which is computed in terms of the Kullback–Leibler divergence of a correlated same-spin conditional pair density respect to the uncorrelated Hartree–Fock pair density (χC) [4-5]. These two information quantities are discussed on the light of the results for high-spin clusters of alkali metals.

1. L. Rincon, R. Almeida, P. L. Contreras and F.J. Torres “The information content of the conditional pair probability” Chem. Phys. Lett. 635, 116 (2015). 2. A.S. Urbina, F.J. Torres and L. Rincon “The electron localization as the information content of the conditional pair probability” J. Chem. Phys. 144, 244104 (2016). 3. L. Rincon, F.J. Torres and R. Almeida “Is the Pauli exclusion the origin of electron localization?” Mol. Phys. 116, 518 (2018) 4. L. Rincon, F.J. Torres, M. Becerra, S. Liu, A. Fritsch and R. Almeida “On the separation of the information content of the Fermi and Coulomb holes and their influence on the electronic properties of molecular systems” Mol. Phys. 117, 610 (2019) 5. F.J. Torres, L. Rincon, C. Zambrano, J.R. Mora and M.A. Mendez “A review on the information content of the pair density as a tool for the description of the electronic properties of molecular systems” Int. J. Quantum Chem. 119, e25763 (2019)

Ángel Martín Pendás

Dpto. Química Física y Analítica. Universidad de Oviedo. Oviedo, Spain

Should charge-shift bonding be reconsidered?

Charge-shift bonding (CSB) was introduced as a distinct third family of electron-pair links that adds to the covalent and ionic tradition. However, the full battery of orbital invariant tools provided by modern real space artillery shows that it is difficult to find CSB signatures outside the original valence-bond framework in which CSB was developed. Here we show that this concept should probably be further investigated.

References J. Luis Casals-Sainz, F. Jiménez-Grávalos, E. Francisco, A. Martín Pendás, Chem. Commun. (2019), DOI: 10.1039/C9CC02123J

Dennis R. Salahub

Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Canada

Towards free-energy profiles for nano-catalyzed chemical reactions in complex environments

I will review our attempts to build somewhat realistic models of nanocatalysis at finite temperature. Current thoughts are to bring in machine-learning techniques to, ideally, define the relevant reaction coordinates/collective variables. Significant progress has been made on such questions in the bio- modeling literature and I would like to understand the new ML methodologies better and to, hopefully, adapt them to the field of nanocatalysis. I am a neophyte, eager for any guidance that CTTC participants might offer, once I have exposed my state of knowledge/ignorance.

Josep M. Luis

University of Girona

Density Functional Theory and Nonlinear Optical Properties

The design of new molecular materials with large nonlinear optical properties (NLOP) remains a challenging task for computational chemistry due to the necessity of accurately computing both electronic and vibrational hyperpolarizabilities of individual molecules as well as the effects of intermolecular interactions. Density Functional Theory (DFT) has proven to be a powerful tool for solving various quantum mechanical problems in a cost-effective way, but DFT performance in the area of NLOP has been under active assessment. We have performed an extensive study of the performance of a diverse set of density functional approximations in predicting the NLOP of hydrogen-bonded complexes using the CCSD(T)/aug-cc-pVTZ level of theory as reference.[1] For all the studied properties, the average absolute errors below 20% can only be obtained using the CAM-B3LYP functional, while LC-BLYP and MN15 are shown to be only slightly less accurate. We reported huge errors in predicting the vibrational second hyperpolarizability by B97X, M06 and M06-2X functionals. This large failure is traced down to a poor determination of third- and fourth-order energy derivatives with respect to normal modes. These results reveal serious flaws of some DFT methods and suggest caution in selecting the appropriate functional to calculate any molecular property that contains vibrational anharmonic contributions.

We have also analyzed the optimal tuning of range-separatiod LC-BLYP functional based on adjusting the attenuating function parameters to satisfy ionization potential theorem. Our results revealed that this approach does not bring any systematic improvement in the predictions of NLOPs. However, we have explored new strategies to tune the range-separation parameter to provide a correct description of NLOP, performing an exhaustive study of the dependency of this parameter in terms of simply quantities.[2] We have found a simple expressions for the optimal value of the attenuating parameter in terms of the second hyperpolarizability values computed at LC-BLYP level that reproduce the CCSD(T) second hyperpolarizabilities. The hyperpolarizabilities obtained with our NLOP-tailored new optimal tuned LC-BLYP are more accurate than the ones obtained with CAM-B3LYP and LC-BLYP functionals. .

References [1] Robert Zalesny, Miroslav Medved,Sebastian Sitkiewicz, Eduard Matito, Josep M. Luis, “Can Density Functional Theory Be Trusted for High-Order Electric Properties? The Case of Hydrogen-Bonded Complexes”, J. Chem. Theory Comput., submitted. [2] Pau Besalú, Sebastian Sitkiewicz, Pedro Salvador, Eduard Matito, Josep M. Luis, in preparation.

Joakim Halldin Stenlid

Department of Physics, Stockholm University, Sweden

Chemical interaction behaviour probed by the local electron attachment energy

The ability to make swift and reliable predictions of chemical interaction behavior and reactivity lies at the heart of theoretical chemistry. This presentation will examine the performance of a new DFT-based ground-state property, the local electron attachment energy [E(r)] [1], for the prediction of global and local electrophilicity/Lewis acidity. E(r) is a property based on a multi-orbital analysis of the unoccupied KS-DFT electronic states. It is found that this joint-orbital picture outperforms the frontier molecular orbital approach (FMO) for predictions of both regioselectivity and intermolecular reactivity trends. E(r) furthermore complements the electrostatic potential probe by reflecting also local contributions to charge-transfer and polarization. Examples of the use of E(r) are taken from molecular reaction theory including conjugate addition and aromatic substitution, as well as from materials science with emphasis on heterogeneous catalysis of transition metal and transition metal oxide nanoparticles and surfaces [2]. Comparisons are made to both experimental and computational data. Future directions for the efficient screening of new catalytic materials based on the new property will be discussed.

References

[1] T Brinck, P Carlqvist, JH Stenlid, Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding, The Journal of Physical Chemistry A 120, 10023-10032, 2016 [2] T Brinck, JH Stenlid, The Molecular Surface Property Approach: A Guide to Chemical Interactions in Chemistry, Medicine, and Material Science, Advanced Theory and Simulations, 2, 1800149, 2019

Juan E. Peralta

Department of Physics, Central Michigan University, Mount Pleasant MI 49959

The FLO-SIC route to self-interaction-free DFT

The effect of DFT self-interaction error (SIE) on calculated molecular and solid-state properties has been known for a long time. The most widely accepted framework for removing SIE in DFT is due to Perdew and Zunger (PZ) [1]. However, due to the high computational cost associated with minimizing the PZ energy expression, the calculation of explicitly self-interaction free molecular properties remains elusive. Recently, an efficient implementation for SIE removal based on Fermi orbitals was proposed [2]. This method explicitly avoids the unitary transformation from canonical to localized orbitals that is needed in standard PZ, and replaces it by a Fermi-Löwdin transformation which depends only on one vector descriptor per orbital, or Fermi orbital descriptor (FOD). The Fermi-Löwdin orbital self-interaction correction (FLO-SIC) provides an computationally efficient alternative to the traditional PZ methods. [2] I will describe the FLO-SIC methodology and its advantages and caveats compared to PZ-SIC. I will show our recent efforts to make FLO-SIC more efficient and user-friendly. [3] As an illustration of the capabilities of the FLO-SIC method, I will show some recent results of diverse properties in cases where SIC is important and discuss the opportunities to move FLO-SIC forward.[4-6]

References

[1] J. P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981).
[2] M. R. Pederson, A. Ruzsinszky, and J. P. Perdew, J. Chem. Phys. 140, 121103 (2014).
[3] K. Trepte, S. Schwalbe, T. Hahn, J. Kortus, D. Kao, Y. Yamamoto, T. Baruah, R. R. Zope , K. P. K. Withanage, J. E. Peralta, and, K. A. Jackson, J. Comp. Chem. 40, 820 (2019).
[4] K. P. K. Withanage, K. Trepte, J. E. Peralta, T. Baruah, R. Zope, and Koblar A. Jackson, J. Chem. Theory Comput. 14, 4122 (2018).
[5] R. P. Joshi, K. Trepte, K. P. K. Withanage, K. Sharkas, Y. Yamamoto, L. Basurto, R. R. Zope, T. Baruah, K. A. Jackson, and J. E. Peralta, J. Chem. Phys. 149, 164101 (2018).
[6] K. Sharkas, L. Li, K. Trepte, K. P. K. Withanage, R. P. Joshi, R. R. Zope, T. Baruah, J. K. Johnson, K. A. Jackson, and J. E. Peralta, J. Phys. Chem. A 122, 9307 (2018).

Emmanuel Fromager

Université de Strasbourg, Laboratoire de Chimie Quantique, Institut Le Bel, 4 rue Blaise Pascal, 67000 Strasbourg, FRANCE

Density matrix functional embedding theory based on the Householder transformation

In the increasingly popular density matrix embedding theory (DMET) [1], a fragment (also referred to as impurity) of the full electronic system of interest is embedded into an effective reduced-in-size environment (referred to as bath). A Schrödinger-like equation can then be solved accurately (if not exactly) for the embedded cluster (impurity+bath). Despite the name of the method, the embedding procedure of standard DMET essentially relies on a state-specific and approximate (mean-field) wavefunction. Consequently, its improvement as well as its extension to finite temperatures is not straightforward.

In this talk, I will present an in-principle-exact DMET-like approach where the embedding is fully driven by the (one-electron reduced) density matrix. In such a density matrix functional embedding theory (DMFET), the bath is determined by applying a Householder transformation to the density matrix [2]. The method is in principle systematically improvable since electron correlation in the (so-called Householder) cluster environment is described by a functional of the density matrix. Exact and approximate single-impurity formulations of DMFET will be presented for the one-dimensional Hubbard model. Extensions to multiple impurities and connections with standard DMET will also be discussed.

References

[1] G. Knizia and G. K.-L. Chan, Phys. Rev. Lett. 109, 186404 (2012). [2] M. Saubanère, L. Mazouin, M. Tsuchiizu, and E. Fromager, in preparation (2019).

Daniel Finkelstein-Shapiro

Department of Chemical Physics, Lund University, Sweden

Constructing effective operators for open quantum systems using ancillary continua

Open quantum system master equations implicitly capture the effect an environment or bath (e.g. vibrational modes of a molecule, protein, solvent) on a central system of interest (e.g. electronic levels of a molecule) in the form of effective transitions that account for energy exchange between system and bath. This shifts the problem from calculating explicitly the nuclear degrees of freedom – a prohibitively expensive problem computationally – to that of finding accurate master equations. Equally important is the invaluable insight provided by simplified master equations in the form of analytically solvable toy models.

In this talk we present the solution to a family of toy models where one or more of the levels has been replaced by a continuum. These models with Hamiltonians with discrete-continuous spectrum capture real systems such as molecules on surfaces, and have a mathematical structure that affords a more transparent understanding of effective operators for open quantum systems. The solution to these problems is in the form of a nonlinear Liouville equation that describes a partition of the system that can exchange not only energy but also particle density with a generalized environment (including other levels of the electronic manifold). We use this formalism to classify the approximations used in adiabatic elimination techniques and improve them, and to formally connect the phenomenon of particle decay and Markovian dissipation.

References

[1] Finkelstein-Shapiro, D.; Urdaneta, I.; Calatayud-Antonino, M.; Atabek, O.; Mujica, V.; Keller, A. Fano-Liouville Spectral Signatures in Open Quantum Systems. Phys. Rev. Lett., 2015, 115, 113006 [2] Finkelstein-Shapiro, D.; Calatayud-Antonino, M.; Atabek, O.; Mujica, V.; Keller, A. Nonlinear Fano Interferences in Open Quantum Systems: an Exact Solution. Phys. Rev. A, 2016, 93, 063414 [3] Finkelstein-Shapiro, D.; Keller, A. Ubiquity of Beutler-Fano profiles: from scattering to dissipative processes. Phys. Rev. A. 2018, 97, 023411

Thibault Terencio

School of Chemical Science and Engineering, Yachay Tech University, Yachay City of Knowledge, 100650 Urcuqui, Ecuador.

Chemoselectivity in the oxidation of cycloalkenes with a non-heme iron(IV)-oxo-chloride complex: Epoxidation vs. hydroxylation selectivity

We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]+, which models the active species in iron dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways – allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze 4 different factors : effects of the substrate, effect of the complex conformation, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase. Finally, this study allows us to propose a strategy for the design of iron(IV)oxo complex that would be selective for hydroxylation over epoxidation.

References

Mark E. Tuckerman

Department of Chemistry and Courant Institute of Mathematical Science, New York University

Molecular simulation and Machine Learning as Routes to Exploring Structure and Phase Behavior in Atomic and Molecular Crystals

Organic molecular crystals frequently exist in multiple forms known as polymorphs. Structural differences between crystal polymorphs can affect desired properties, such as bioavailability of active pharmaceutical formulations, lethality of pesticides, or electrical conductivity of organic semiconductors. Crystallization conditions can influence polymorph selection, making an experimentally driven hunt for polymorphs difficult. Such efforts are further complicated when polymorphs initially obtained under a particular experimental protocol “disappear” in favor of another polymorph in subsequent repetitions of the experiment. Consequently, theory and computational can potentially play a vital role in mapping the landscape of crystal polymorphism. However, traditional theoretical methods face their own challenges, and new approaches are needed. In this talk, I will show, by leveraging concepts from statistical mechanics in combination with techniques of molecular simulation and machine learning, a that new paradigm in crystal structure prediction may be emerging.

Andy Teale

School of Chemistry, University of Nottingham, UK

All electron approaches to orbital-free density-functional theory

Andy Teale, Matt Ryley and Tom Irons: School of Chemistry, University of Nottingham, UK

Trygve Helgaker: Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Norway

The development of an accurate orbital-free approach to density-functional theory for general finite and periodic systems has long been an elusive goal for quantum chemists. Much progress has been made for periodic systems with local pseudopotentials, e.g. PROFESS [1] and ATLAS [2]. However, robust all electron treatments have lagged behind these developments. Recently, Lopez-Acevedo [3, 4] has shown how an all electron implementation (GPAW) of OF-DFT calculations can be achieved for the Thomas-Fermi von Weisacker family (ɣTFλW) of kinetic energy density functionals (KEDFs). This approach uses ideas based on work by Levy, Perdew and Sahni [5], who identified the equivalence between the solution of the Euler equation and a one-orbital analogue of the Kohn-Sham equations. To achieve convergence using the approach of Ref. [3] it is necessary to employ simple Pulay-type density matrix damping, rather than conventional SCF accelerators such as Pulay’s C1-DIIS; leading to a large number of iterations, see Fig. 1. In addition, as discussed by Karasiev and Trickey [6], extension of this approach to other KEDFs is unclear. Furthermore, differing conclusions as to the stability of different KEDFs have been reached using different programs.

Earlier Chan, Cohen and Handy [7] proposed an all electron approach for finite systems using Gaussian functions, which is applicable to general KEDFs. In their initial publication only applications to ɣTFλW functionals were presented. This approach uses a nested optimization of the OF-DFT Langrangian to determine the ground state energy and chemical potential μ. Here we present a new implementation of this scheme [8], which can be applied to a wide range of KEDFs using a flexible framework based on automatic differentiation techniques afforded by the XCFun library [9]. This approach provides a reasonably robust all electron approach to optimization using a variety of KEDFs. However, the nested nature of the optimization can lead to many steps to be required for convergence, see Fig 2.

To address this issue, we have developed a new trust-region image (TRIM) based optimization method for OF-DFT [10]. This second order approach simultaneously optimizes E and μ, leading to a significant reduction in the number of steps required for convergence and very precise quadratic convergence in the local region. Prospects for future use and development of this approach will be discussed. Presently, this approach provides a platform testing KEDFs in a fully self-consistent all electron context. Results demonstrating the essential requirement to consider self-consistency when designing new KEDFs will be discussed.

Figure 1: Ne atom, with ɣTFλW (ɣ = 0.697, λ = 0.599) and Dirac exchange. Convergence profiles for the Lopez-Acevedo approach (green), the Chan, Cohen, Handy method (blue), and the TRIM approach (orange). The change in the electronic energy, chemical potential and the particle number error are shown as a function of the number of iterations. Note that for the particle number variation the Lopez-Acevedo approach is normalized to the correct number of particles at each iteration by construction and the chemical potential in this scheme is determined by the lowest eigenvalue of the effective Hamiltonian.

Figure 2: N2 molecule with the E00 KEDF and PBE exchange and correlation. Convergence profiles for the Chan, Cohen, Handy method (blue), and the TRIM approach (orange). A superposition of atomic densities guess is used, calculated with the same functionals. The change in the electronic energy, chemical potential and the particle number error are shown as a function of the number of iterations.

References

[1] G. S. Ho, V. L. Lignères, and E. A. Carter, Comput. Phys. Commun. 179, 839 (2008)

[2] W. Mi, X. Shao, C. Su, Y. Zhou, S. Zhang, Q. Li, H. Wang, L. Zhang, M. Miao, Y. Wang, Y. Ma, Comput. Phys. Commun. 200, 87 (2016)

[3] J. Lehtomäki, I. Makkonen, M. A. Caro, A. Harju and O. Lopez-Acevedo, J. Chem. Phys. 141, 234102 (2014)

[4] L. A. Espinosa Leal, A. Karpenko, M. A. Caro and O. Lopez-Acevedo, Phys. Chem. Chem. Phys. 17, 31463 (2015)

[5] M. Levy, J. P. Perdew and V. Sahni, Phys. Rev. A 30, 2745 (1984)

[6] V. Karasiev and S. Trickey, Comput. Phys. Commun. 183, 2519 (2012)

[7] G. K.-L. Chan, A. J. Cohen and N. C. Handy, J. Chem. Phys. 114, 631 (2001)

[8] QUEST, a rapid development platform for QUantum Electronic Structure Techniques, http://quest.codes

[9] U. Ekström, L. Visscher, R. Bast, A. J. Thorvaldsen and K. Ruud, J. Chem. Theory Comput. 6, 1971 (2010)

[10] T. Helgaker, Chem. Phys. Lett. 182, 5, 503 (1991)

Marcos Mandado

Department of Physical Chemistry. Faculty of Chemistry. University of Vigo. 36310 Vigo. Galicia. Spain

Detecting plasmons at molecular scale by means of detachment/attachment electron density analysis

Marcos Mandado, Sara Gil-Guerrero, Ángeles Peña-Gallego: Department of Physical Chemistry. Faculty of Chemistry. University of Vigo. 36310 Vigo. Galicia. Spain

Collective electronic excitations in extended surfaces, also called plasmons, are represented by electron density oscillations using classical electromagnetic theory, nevertheless, a quantum definition for extended systems is obtained from linear response theory. Recent theoretical and experimental works have pointed out the presence of plasmon excitations at molecular scale as well, for instance, in metallic clusters, fullerenes or small and medium size nanotubes.[1-4] However, the definition of plasmon at molecular scale cannot be directly connected to that in extended systems as the key concept, the dielectric function, has not a straightforward analogy in molecules or clusters. Recently, using solid theoretical arguments, Bernadotte et al [1] have shown that plasmon character in finite systems can be attached to excitation modes strongly dependent on the response of the electron-electron operator, whereas those almost independent correspond to single-electron excitations. However, differentiation between single-electron and collective modes requires the introduction of an arbitrary multiplicative parameter in the electron-electron part of the Casida equation, which is varied gradually from 1 to 0 to connect the correct solutions with those obtained by the noninteracting electron picture. Unfortunately, this procedure entails a large number of calculations and is tricky when different excitation modes cross or collapse at an intermediate value of the parameter.

In this presentation, it is shown how an alternative differentiation between plasmons and single-electron excitations can be done at molecular scale by means of the attachment/detachment integrated density obtained from time-dependent linear response theory. This integrated density represents the electron population excited from the occupied to the virtual orbital band. Those excitations whose integrated density is close to the ideal value 1.0 correspond to single-electron excitations, whereas those whose integrated density is significantly higher than 1.0 are characterized as collective excitations or plasmons.[5] By the way, high values of the integrated density are linked to large weights of deexcitation terms, which are well-known to be key to representing the electron density oscillations associated to plasmon modes.[6]

References

[1] S. Bernadotte, F. Evers, C. R. Jacob, J. Phys. Chem. C 117, 1863, (2013)

[2] A. Crai, A. Pusch, D. E. Reiter, L. Román Castellanos, T. Kuhn, O. Hess, Phys. Rev. B 98, 165411, (2018)

[3] A. Manjavacas, F. Marchesin, S. Thongrattanasiri, P. Koval, P. Nordlander, D. Sánchez-Portal, F. J. García de Abajo, ACSNano 7, 3635, (2013)

[4] A. Lauchner, A. E. Schlather, A. Manjavacas, Y. Cui, M. J. McClain, G. J. Stec, F. J. García de Abajo, P. Nordlander, N. J. Halas, Nano Lett. 15, 6208, (2015)

[5] S. Gil-Guerrero, A. Peña-Gallego, M. Mandado, in preparation

[6] M. Grüning, A. Marini, X. Gonze, Nano Lett. 9, 2820, (2009)

Verònica Postils

Departamento de Ciencia y Tecnología de Polímeros, Kimika Fakultatea, Euskal Herriko Unibertsitatea (EHU). Paseo Manuel de Lardizabal 3, 20018 Donostia (Gipuzkoa, Spain)

Pro-oxidant activity of aluminium promoting radical-scavenging reactions. DPPH-QH2 pair as a test case.

José Manuel Lanuza, Xabi López and Verònica Postils

Aluminium is known to play an important role in biological systems altering the thermodynamics of a variety of proteins and biomolecules (e.g. specially those containing phosphate and carboxylate groups)[1] and affecting key redox reactions such the Fenton reaction of Fe3+/Fe2+ among others.[2] The formation of an Al-superoxide (O2·-) complex has been hypothesized to be central for this oxidant activity.[3]

Recently, experimental evidences have exhibited that the presence of aluminium promotes the scavenging reaction of dihydroquinone (QH2) with 2,2-diphenyl-1-picrylhydrazyl radical (DPPH·),[4] (Equation 1) being those reagents frequently used to model the reactivity between the antioxidant co-enzyme Q10 and reactive oxygen(nitrogen) species (ROS), respectively. The study concludes that Al3+, as a strong Lewis acid, acts as a radical scavenging promoter stabilizing the one-electron reduced species of the radical (i.e. DPPH·) rather than promoting the scavenging activity of QH2 against DPPH·.

QH2 + DPPH· --> QH· + DPPH-H (Equation 1)

We have performed a DFT computational study for the scavenging reaction of QH2 with DPPH·, both with and without the presence of Al3+. We have computed their effective redox potentials and identified the necessary conditions for the reaction to occur. Our computational study also reveals how the stabilization of anionic reactive oxygen/nitrogen species (i.e. the stabilization of DPPH-) is a key aspect in the influence of Al3+ in the scavenging reaction, finding a good agreement between theory and experiment. Moreover, it provides new insights about intermediate species involved in the redox reaction and the reaction mechanism, which may help to understand Al effects in the activity of the antioxidant co-enzyme Q10.

Favorable arrangement of [Al(EtOH)5(QH)]2+ and [Al(EtOH)5(DPPH·)]3+ towards the formation of radical-scavenging products.

References

[1] a) Luque, N. B.; Mujika, J. I.; Rezabal, E.; Ugalde, J. M.; López, X. Phys. Chem. Chem. Phys. 2014, 16, 20107-20119. (b) Mujika, J. I.; Ugalde, J. M.; López, X. J. Phys. Chem. B. 2014, 118, 6680-6686. [2] Ruipérez, F.; Mujika, J. I.; Ugalde, J. M.; Exley, C.; López, X. J. Inorg. Biochem. 2012, 117, 118-123. [3] Exley, C. Free Radic. Biol. Med. 2004, 36, 380-387. [4] Nakanishi, I.; Ohkubo, K.; Ogawa, Y.; Matsumoto, K.; Ozawa, T.; Fukuzumi, S. Org. Biomol. Chem. 2016, 14, 7956-7961.

Henryk Witek

Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan

Problems with multireference perturbation theory

Quantum chemical calculations of physical and chemical properties of molecular systems in their excited states are often performed using multireference perturbation theory (MRPT). MRPT comes in many flavors and is implemented in many various quantum chemistry packages. In the current talk I would like to review a number of serious methodological problems in MRPT, which make the method in many instances difficult or even impossible to apply for a non-specialist. I hope that the thorough discussion of the discovered problems might be of help for anybody planning to compute potential energy surfaces for excited states.

References

1. Y.-K. Choe, H. A. Witek, J. P. Finley, and K. Hirao, “Identifying and Removing Intruder States in Multireference Møller-Plesset Perturbation Theory”, J. Chem. Phys. 114, 3913 (2001)

2. H. A. Witek, Y.-K. Choe, J. P. Finley, and K. Hirao, “Intruder State Avoidance Møller-Plesset Perturbation Theory”, J. Comput. Chem. 23, 957 (2002)

3. H. A. Witek, N. Nakano, and K. Hirao, “Multireference Perturbation Theory with Optimized Partitioning. I. Theoretical and Numerical Aspects”, J. Chem. Phys. 118, 8197 (2003)

4. H. A. Witek, N. Nakano, and K. Hirao, “Multireference Perturbation Theory with Optimized Partitioning. II. Application to Molecular Systems”, J. Comput. Chem. 24, 1390 (2003)

5. C. Camacho, S. Yamamoto, and H. A. Witek, “Choosing a proper complete active space in calculations for transition metal dimers: Ground state of Mn2 revisited”, Phys. Chem. Chem. Phys. 10, 5128 (2008)

6. C. Camacho, S. Yamamoto, and H. A. Witek, “Intruder states in multireference perturbation theory: ground state of Mn2”, J. Comput. Chem. 30, 468–478 (2009)

7. C. Camacho, R. Cimiraglia, and H. A. Witek, “Multireference perturbation theory can predict a false ground state”, Phys. Chem. Chem. Phys. 12, 5058–5060 (2010)

8. C. Camacho, H. A. Witek, and R. Cimiraglia, “The low-lying states of the scandium dimer”, J. Chem. Phys. 132, 244306/1–9 (2010)

9. M. Andrzejak and H. A. Witek, “The elusive excited states of bithiophene: A detective CASPT2 story”, Theor. Chem. Acc. 129, 161–172 (2011)

10. S. W. Chang and H. A. Witek, “Choice of optimal shift parameter for the intruder state removal techniques in multireference perturbation theory”, J. Chem. Theory Comp. 8, 4053–4061 (2012)

11. M. Andrzejak, M. Kukułka, H.A. Witek, “Excited states manifold of 2,2’-bithiophene: basis set dependence study”, Mol. Phys. 115, 2823–2832 (2017)

Raúl Quintero-Monsebaiz

Alberto Vela and Raúl Quintero-Monsebaiz: Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV).México

Ion Mitxelena, Mauricio Mayorga and Mario Piris: Donostia International Physics Center (DIPC).España

Spin Polarized Natural Orbital Functional Theory

Within Natural Orbital Functional Theory, a spin-uncompensated formulation for the independent pair approach PNOF5[1][2] and the interacting pair model PNOF7[3][4] was proposed. Each one of these functionals fulfills certain N-representability necessary conditions of second-order reduced density matrices. The spin symmetry is also accomplished taking into account the conservation of total spin. A benchmarking was made using the one dimensional Hubbard model with periodic boundary conditions[5]. The spin-polarized functionals show the correct description of strong-correlation effects.

References

[1] M. Piris, X. Lopez, F. Ruipérez, J. M. Matxain, and J. M. Ugalde, J. Chem. Phys. 134, 164102 (2011).

[2] M. Piris, J. M. Matxain, and X. Lopez, J. Chem. Phys. 139, 234109 (2013).

[3] M. Piris, Phys. Rev. Lett. 119, 063002 (2017).

[4] I. Mitxelena, M. Rodríguez-Mayorga, and M. Piris, Eur. Phys. J. B91, 109 (2018).

[5] R Quintero, I. Mixtelena,M. Rodriguez,A. Vela, M. Piris, J. Phys: Condens Matter, (2019).

Eloy Ramos-Cordoba

Donostia International Physics Center (DIPC), Donostia, Euskadi, Spain

Molecular properties for orbital-optimized second order perturbation theory

Unrestricted Hartree-Fock (UHF) wavefunctions with spin contamination are usually poor zero-order approximations for second-order Moller-Plesset perturbation theory (MP2). Orbital-optimized secondorder perturbation theory (OOMP2) tackle this problem by using approximate Brueckner orbitals. In OOMP2 the orbitals are optimized in the presence of the meanfield energy plus the second-order manybody correlation energy. Since in OOMP2 the energy is fully minimized with respect to orbital rotations, a Hellman-Feynman condition is fulfilled and first-order properties do not present discontinuities. This method improves the description of geometries, vibrational frequencies, and relative energies. Additionally, in OOMP2 the response function does not show spurious second order poles, making it suitable for linear-response excited state properties. In this contribution, we present an extension of the OOMP2 method to excited states and we report test calculations for closed-shell systems and doublet radicals. The performance of method is compared with other secondorder methods for excitation energies such as the approximate coupled-cluster singles and doubles model (CC2), configuration interaction with doubles corrections (CIS(D)), and the algebraic diagrammatic construction through second order (ADC(2)).

Alberto Vela

Luis Soriano; Departamento de Química; Centro de Investigación y de Estudios Avanzados (Cinvestav-Zacatenco) Av. Instituto Politécnico Nacional 2508, 07360 Ciudad de México, México

Can we predict spin crossover in transition metal complexes?

Spin-crossover (SCO) in transition metal complexes is of great importance in the development of magnetic materials whose properties are used in visualization, memory and electrical devices, to mention a few. This phenomenon has been widely studied with Density Functional Theory (DFT) using a wide variety of exchange-correlation (XC) functionals with disappointing outcomes, pointing towards the incapability of current Density Functional Approximations (DFAs) in reliably predicting the energy differences between the high- and low-spin configurations in transition metal complexes. Recently, an approach based on density corrected DFT and called HF-DFT, consisting on evaluating the energy of a selected DFT functional with the Hartree-Fock (HF) density has been successfully applied to several problems, including SCO in some iron complexes with small ligands, yielding results that are close to coupled cluster (CC) and Diffusion Monte Carlo calculations, at a much lower computational cost. In this work we show that HF-DFT, using DFT optimized geometries, also offers an excellent alternative to describe SCO in manganocenes with ligands in the cyclopentadienyl rings going from hydrogen to tert-butyl, and again, providing results in excellent agreement with available CCSD calculations. By means of multiconfigurational-SCF calculations we show that these systems have an important contribution of static correlation. We also show that it is almost impossible to obtain gas-phase energy differences between the high and low spin configurations that can allow one a reliable prediction of SCO. In the case of neutral complexes, like manganocenes, the only approach that we have found to be robustly predictive for the existence of SCO is the periodic calculation, using the geometry of the complexes in the solid state. For charged complexes, like those containing iron, including the counterions seems to distort enough the crystal field of the transition metal, leading to high-low spin energy differences in agreement with the observation of SCO.

Mercedes Alonso

General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium

Towards the design of molecular conductance and bithermoelectric switches

Creating functional nanoscale devices using single molecules as active electronic components is the ultimate goal of the field of molecular electronics. Besides their potential to meet the growing demand for miniaturization of electronics, molecular electronics opens up the possibility of devices with novel, unforeseen functionalities beyond silicon-based technologies, such as molecular switches. Through a bottom-up quantum chemistry approach, we have shown that expanded porphyrins are flexible enough to switch between different π-conjugation topologies (Mobius, Hückel and twisted-Hückel) encoding distinct electronic properties and aromaticity.[1] Since these topology/aromaticity switches can be induced by different external stimuli,[2] these macrocycles represent a unique platform to develop a novel type of molecular switches for different nanoelectronic applications.

The first application involves the conductance switching in molecular junctions through aromaticity and topology changes. In this regard, the electron transport properties of the different states of the switches were carefully investigated with the non-equilibrium Green´s function formalism in combination with density functional theory for various configurations of the gold contacts.[3] Our findings reveal that the negative relationship between conductance and molecular aromaticity or polarizability does not hold for most of the configurations of the molecular junctions, so we devise new selection rules to predict the occurrence of quantum interference around the Fermi level for Hückel and Möbius systems.[4] A second application concerns the design of bithermoelectric switches, an entirely new class of switches that revert the direction of the heat and/or charge transport. Our in-house calculations reveal that the Hückel-Möbius switch in heptaphyrins causes the Seedbeck coefficient or thermopower to change considerably from +50 uV/K to -40 uV/K.[5] Chemical control over the thermoelectric properties can be achieved through substitution of the linker groups. Overall, our work demonstrates how the concept of aromaticity and molecular topology can be exploited to create efficient switching devices.

[Figure 1. Conductance switching and thermoelectric behaviour through aromaticity and topology switches in expanded porphyrins.]

References

[1] M. Alonso, P. Geerlings, F. De Proft, Chem. Eur. J. 2013, 19, 1617.

[2] M. Alonso, B. Pinter, P. Geerlings, F. De Proft, Chem. Eur. J 2015, 21, 17631; T. Woller, J. Contreras-García, P. Geerlings, F. De Proft, M. Alonso, Phys. Chem. Chem. Phys. 2016, 18, 11885.

[3] T. Stuyver, F. De Proft, P. Geerlings, M. Perrin, M. Alonso, J. Am. Chem. Soc. 2018, 140, 1313.

[4] T. Stuyver, S. Fias, P. Geerlings, F. De Proft, M. Alonso, J. Phys. Chem. C 2018, 122, 19482.

[5] T. Stuyver, P. Geerlings, F. De Proft, M. Alonso, J. Phys. Chem. C 2018, 122, 24436.

Carla Calvó-Tusell

Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, E-17003 Girona, Catalonia, Spain.

Unraveling the millisecond allosteric activation of Imidazole Glycerol Phosphate Synthase (IGPS) by means of Molecular Dynamics simulations

Carla Calvó-Tusell, Miguel A. Maria-Solano, Ferran Feixas, Sílvia Osuna

Allostery is an intrinsic property of proteins generally described as the process by which the effect of binding at one site is transmitted to another, often distal, functional site, allowing for activity or function regulation.[1] Exploring the mechanisms of allosteric regulation is important to understand biological processes such as enzyme catalysis, cell signaling or the molecular basis of disease. Allosteric transitions require the order of microsecond to second timescales. Imidazole Glycerol Phosphate Synthase (IGPS) is an heterodimeric enzyme complex widely used as a model to study allosteric regulation between subunits. Previous studies based on NMR experiments reported that the allosteric activation of IGPS, promoted by the binding of an effector, takes place in the millisecond timescale.[2] However, the active structure of IGPS has not been yet characterized.[2,3] Computational methods are used to study allostery, but obtaining enough conformational sampling to completely characterize allosteric events represents a challenge for current simulation techniques.[4]

In this work, the millisecond allosteric activation mechanism of IGPS is unraveled step by step by means of a combination of simulation techniques. First, nanosecond to microsecond motions that initiate the allosteric signal transmission are deciphered by means of conventional Molecular Dynamics (cMD). Second, accelerated Molecular Dynamics (aMD) is used to sample events that occur in the microsecond to millisecond timescale, including the complete characterization of IGPS allosteric activation and the active structure (characterized by the formation of an oxyanion hole). Third, the complete reconstruction of substrate binding process is performed to characterize the reactive complex of the allosterically activated enzyme. Then, the reaction mechanism of inactive and allosterically active IGPS are studied by means of density functional theory calculations. Finally, the allosteric communication pathway is traced through key residues for IGPS function and allostery using correlation-based tools.[5] In summary, we have been able to computationally characterize the activation mechanism of IGPS by applying a computational protocol designed to describe and characterize complex long timescale motions. This protocol can be generalized to study the activation mechanism of other allosterically regulated enzymes.

References:

[1] VanWart, A. T.; Eargle, J.; Luthey-Schulten, Z.; Amaro, R. E., J.Chem Theory Comput. 2012, 8, 2949-2961

[2] Lipchock, J. M. Loria, J. P., Structure, 2010, 18, 1596-1607

[3] Rivalta, I., Sultan, M. M.; Lee, N. S.; Manley, G. A.; Loria, J. P.; Batista, V. S., Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 1428-1436

[4] Wagner, J. R., Lee, C. T., Durrant, J. D., Malmstrom, R. D., Feher, V. A., Amaro, R. E., Chem. Rev., 2016, 116, 11, 6370-6390

[5] Romero-Rivera, A.; Garcia-Borràs, M.; Osuna, S., ACS Catalysis, 2017, 3, 949-960

Ferran Feixas

Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/ Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain

Understanding the role of non-covalent interactions in (bio)molecular recognition

(Bio)molecular recognition and assembly are key concepts in chemistry, biology and drug design. Chemical and life processes are critically dependent on the association and dissociation of (bio)molecules. A deep understanding of the mechanisms of these relevant processes is of utmost importance. Experimental methods can provide information on stable structures, binding affinities, or kinetics but cannot offer a complete description of binding and unbinding pathways at the required atomic detail. Molecular dynamics can provide an atomistic dynamic view of such relevant processes. However, a tremendous amount of conformational sampling is required to obtain accurate pathways and reliable stationary and kinetic properties. Current computational methods to study assembly, binding, and unbinding of (bio)molecules either require access to high-performance computing resources or the definition of a complex reaction coordinates to enhance conformational sampling.

Our goal is to develop a computational protocol to study, at the atomic level, the mechanisms of self-assembly, association and dissociation of (bio)molecules at a reasonable computational cost. This protocol relies on the basic ideas of accelerated molecular dynamics (aMD),[1,2] an unconstrained enhanced sampling technique that does not rely on the a priori definition of any reaction coordinate. The novel strategy consists in the redefinition of this methodology by selectively boosting non-bonded interactions between interacting molecules to enhance conformational sampling of associative and dissociative processes. This protocol is assessed for well-studied processes including protein folding, biomolecular recognition and protein-protein interactions. In particular, we focus on the potential of this novel technique as a tool to efficiently explore the rough free energy landscape of binding and unbinding in proteins and supramolecular systems. First, we focus on understanding enzyme-inhibitor binding process in a p38 protein kinase liver cancer drug target.[3] From MD simulations, we can reconstruct the free energy landscape of the binding process and identify relevant states of this process. Using, tools such as the non-covalent interaction index (NCI) and electron sharing indices we can rationalize the stability of the interactions established and improve the activity of the inhibitor. Second, we explore the dynamic role of non-covalent interactions in a series of host-guest systems including self-folding cavitands and supramolecular cages specifically designed for binding and release of fullerenes.

References

[1] Markwick, P. R. L.; McCammon, J. A. Phys. Chem. Chem. Phys. 2011, 13, 20053

[2] Miao, Y.; Feixas, F.; Eun, C.; McCammon, J. A. J. Comput. Chem. 2015, 36, 1536

[3] Tomás-Loba, A.; Manieri, E.; González-Terán, B.; Mora, A.; Leiva-Vega, L.; Santamans, A. M.; Rodríguez, E.; Feixas, F.; López, J. A.; Caballero, B.; Trakala, M.; Blanco, O.; Torres, J. L.; Roche-Molina, M.; Bernal, J. A.; Saavedra, D. M.; Ruiz-Cabello, J.; Brava-Sicilia, J.; Vázquez, J.; Marcos, M.; Malumbres, M.; Osuna, S.; Sabio, G. Nature 2019, 568, 557

Sommaire

Frederik Tielens

Sam Trickey

Adrienn Ruzsinszky

Luis Rincon

Ángel Martín Pendás

Dennis R. Salahub

Josep M. Luis

Joakim Halldin Stenlid

Juan E. Peralta

Emmanuel Fromager

Daniel Finkelstein-Shapiro

Thibault Terencio

Mark E. Tuckerman

Andy Teale

Marcos Mandado

Verònica Postils

Henryk Witek

Raúl Quintero-Monsebaiz

Eloy Ramos-Cordoba

Alberto Vela

Mercedes Alonso

Carla Calvó-Tusell

Ferran Feixas

José L. Gázquez

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