Abstracts of the TCTC 2014
Slides available after the workshop
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Contributor's name
Affiliation
Title
Summary
[1] Popelier, P. L. A.; Brémond, É. A. G. Int.J.Quant.Chem. 2009, 109, 2542.
High accuracy methods /Relativistic corrections
Debashis Mukherjee
Affiliation
Title
Summary
Seiichiro Ten-no
Department of Computational Science, Graduate School of System Informatics, Kobe University
Recent advances in explicitly correlated electronic structure theory
In quantum chemistry, one of the main obstacles to accurate electronic structure calculations is the slow convergence of a CI expansion. F12 theory exploiting geminal basis functions with the Slater correlation factor leads to greatly improved convergence of correlation energies. Recent developments based on the rational generator approach from the cusp conditions is summarized. Four-component relativistic treatment and massively parallel implementation of F12 methods will be also presented.
Tron Saue
Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3 (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse, France
Parity violation in chiral molecules
The parity violation associated with the weak force implies that left- and right-hand forms of chiral molecules are diastereomers rather than enantiomers. A predominantly French collaboration of theoreticians and experimentalists, physicists and chemists, hunt for the signature of parity violation in the vibrational spectra of chiral molecules. The task of theory, using relativistic molecular quantum chemistry, is to guide experiment in the search for suitable candidate molecule.
In this talk I review recent progress with particular emphasis on the analysis and understanding of the mechanism of parity violation in molecules. A successful experiment will have a significant impact on our understanding of the stability and dynamics of chiral molecules as well as the origin of biochirality.
[1] Radovan Bast, Anton Koers, André Severo Pereira Gomes, Miroslav Ilia², Lucas Visscher, Peter Schwerdtfeger and Trond Saue, Analysis of parity violation in chiral molecules, Phys. Chem. Chem. Phys. 13 (2011) 854
[2] Benoit Darquié, Clara Stoeffer, Alexander Shelkovnikov, Christophe Daussy, Anne Amy-Klein, Christian Chardonnet, Samia Zrig, Laure Guy, Jeanne Crassous, Pascale Soulard, Pierre Asselin, Thérèse R. Huet, Peter Schwerdtfeger, Radovan Bast and Trond Saue, Progress toward the first observation of parity violation in chiral molecules by high-resolution laser spectroscopy, Chirality 22 (2010) 870
Toru Shiozaki
Department of Chemistry, Northwestern University
Modern Multireference Electron Correlation Methods
In this lecture, I will present the state of the art of multireference electron correlation theories for strongly correlated systems. The standard quantum chemistry methods, such as density functional theories and single-reference coupled-cluster theories, break down when wave functions are not approximated well by a single Slater determinant. Such situation includes (1) electronic structures of transition metal complexes that are important for catalytic reactions; (2) two-electron excited states that play a central role in next-generation solar energy conversion; and (3) state-crossing between the ground and excited states, relevant to photo-switches. First, I will describe the so-called completely active space self-consistent field (CASSCF) method that is a multi-determinant extension of the Hartree–Fock method. I will also discuss various approximate variants of CASSCF, including our recent development of an active space decomposition strategy and its connection to density matrix renormalization group. Second, I will present conventional electron correlation models that are based on multi-determinant reference states, such as second-order perturbation (CASPT2), configuration interaction (MRCI), and so on. Finally, I will present new approaches in this field, such as integration with explicit correlation methods, multireference coupled cluster methods, and beyond.
Density functional theory
Guanhua Chen
Affiliation
Title
Summary
John Perdew
Affiliation
Title
Summary
Adrienn Ruzsinszky
Affiliation
Title
Summary
Xin Xu
Affiliation
Title
Summary
Weitao Yang
Duke University, USA
Title
Summary
Thomas Frauenheim
Affiliation
Title
Summary
Mario Piris
Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU); Donostia International Physics Center (DIPC); IKERBASQUE, Basque Foundation for Science
NOF theory as an alternative to DFT
In 1974, Gilbert proved for the one-particle reduced density matrix (1-RDM) an analogous theorem to the Hohenberg-Kohn theorem for the density. Accordingly, one can employ the exact energy functional, with an approximate 2-RDM that is built from the 1-RDM using a reconstruction functional, to describe a molecule. The major advantage of a 1-RDM formulation is that the kinetic energy is explicitly constructed and does not require a functional. Like for the density, the ensemble N-representability conditions of the 1-RDM are well-known, but this does not overcome the N-representability problem of the energy functional.
The 1-RDM functional is called Natural Orbital Functional (NOF) when it is based upon the spectral expansion of the 1-RDM. An approximate reconstruction, in terms of the diagonal 1-RDM, has been achieved by imposing necessary N-representability conditions on the 2-RDM. Appropriate forms of the two-particle cumulant have led to different implementations, known in the literature as PNOFi (i=1,5) being the most successful the PNOF5, and its extended version PNOF5e. On the other hand, antisymmetrized product of strongly orthogonal geminals (APSG) with the expansion coefficients explicitly expressed by means of the occupation numbers have been used to generate these NOFs, which demonstrates strictly the N- representability, size-extensivity and size-consistency of the functionals. Moreover, it opens the possibility of using a perturbation theory to recover the missing dynamic correlation.
In this presentation, the theory behind these functionls is outlined, and some examples are presented to illustrate their potentiality. Special emphasis will be done on strong correlated problems. Our results are accurate values as compared to high level wavefunction methods and available experimental data.
Frontiers in computation
Robert Harrison and W. Scott Thornton
Institute for Advanced Computational Science, Stony Brook University
Evaluation of the GW method for applications in chemistry
The GW method is one of a hierarchy of many-body methods that forms an
analogue in the theory of solid-state-systems to coupled-cluster family of methods,though it is of necessity based upon the Green’s function rather than the wave
function. We examine the formulation and implementation of the GW and relatedmethods and evaluate their performance in comparison to standard quantum
chemical approaches.
Roland Lindh
Uppsala University
Title
Summary
Peter Taylor
University of Melbourne, Australia
Title
Summary
Kazuo Kitaura
Kobe University, Kobe Japan
The Fragment Molecular Orbital Method and Its Applications to Very Large Molecules
The fragment molecular orbital (FMO) method[1] is an approximate ab initio MO computational method for vary large molecules such as proteins. In the method a molecule is divided into fragments and ab initio MO calculations are performed on the fragments, their dimers and optionally trimers to obtain the total energy and other properties of the whole molecule. The method reproduces regular ab initio properties with good accuracy. Various FMO-based correlation methods have been developed including density functional theory (DFT), 2nd order Møller-Plesset perturbation theory (MP2), coupled cluster theory (CC), and MCSCF. Polarizable continuum model (PCM) was interfaced with FMO, allowing one to treat solvent effects of real size proteins. Recently, the analytical energy gradients and the second derivatives have been developed. In this presentation, I will talk about the FMO method and its applications to biomolecules.
[1] “The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems”, Dmitri.G..Fedorov, Kazuo Kitaura, Eds., CRC press, Boca Raton, 2009.
Takahito Nakajima
RIKEN Advanced Institute for Computational Science, Kobe, Japan
NTChem Program Package
An atomic- and molecular-level understanding of drug actions and the mechanisms of a variety of chemical reactions will provide insight for developing new drugs and materials. Although a number of diverse experimental methods have been developed, it still remains difficult to investigate the state of complex molecules and to follow chemical reactions in detail. Therefore, a theoretical molecular science that can predict the properties and functions of matter at the atomic and molecular levels by means of molecular theoretical calculations is keenly awaited as a replacement for experiment. Theoretical molecular science has recently made great strides due to progress in molecular theory and computer development. However, it is still unsatisfactory for practical applications. Consequently, our main goal is to realize an updated theoretical molecular science by developing a molecular theory and calculation methods to handle large complex molecules with high precision under a variety of conditions. To achieve our aim, we have so far developed several methods of calculation. Examples include a way for resolving a significant problem facing conventional methods of calculation, in which the calculation volume increases dramatically when dealing with larger molecules; a way for improving the precision of calculations in molecular simulations; and a way for high-precision calculation of the properties of molecules containing heavy atoms such as metal atoms. We have integrated these calculation methods into a software package named NTChem that we are developing, which can run on the K computer and which contains a variety of high-performance calculation methods and functions. By selecting and combining appropriate methods, researchers can perform calculations suitable for their purpose. For example, it is possible to obtain a rough prediction of the properties of a molecule in a short period of time, or obtain a precise prediction by selecting a longer simulation. In addition, NTChem is designed for high performance on a computer with many compute nodes (high concurrency), and so it makes optimum use of the K computer’s processing power. In this talk, I will introduce the current and future projects for the NTChem software.
Reducing complexity
Garnet Chan
Princeton University, USA
Quantum embeddings
I will give a brief overview of the relationship between dynamical mean-field theory, density matrix embedding, and density functional embedding theory, and describe some recent extensions of density matrix embedding theory to superconductivity, electron-phonon coupling, and quantum dynamics.
Thomas Miller
Caltech, USA
Accurate and systematically improvable density functional theory embedding for correlated wavefunctions
We will describe quantum embedding methods for performing accurate and scalable electronic structure theory calculations in large molecular systems, with application to clusters, liquids, transition metal complexes, and chemical reactions.
[1] "Exact non-additive kinetic potentials for embedded density functional theory." Goodpaster JD, Ananth N, Manby FR, and Miller TF, JCP, 133, 084103 (2010).
[2] "A simple, exact density-functional-theory embedding scheme." Manby FR, Stella M, Goodpaster JD, and Miller TF, JCTC, 8, 2564 (2012).
[3] "Accurate and systematically improvable density functional theory embedding for correlated wavefunctions." Goodpaster JD, Barnes TA, Manby FR, and Miller TF, JCP, 140, 18A507 (2014).
Dominika Zgid
University of Michigan, USA
Title
Summary
Gustavo Scuseria
Rice University, USA
Quantum embedding and hierarchical methods
This talk will address two topics currently developed in our research group: quantum embedding and hierarchical methods.
The first topic is based on the DMET proposal of Knizia and Chan (PRL 2013), which we have studied and tweaked [1] in myriad ways. We have recently implemented it for the ab initio Hamiltonian with several impurity solvers including coupled cluster and Projected Hartree-Fock (PHF) theories [2]. Originally designed for strong correlation, DMET works even better for weakly correlated systems. I will present proof-of-principle CC calculations on solids done at a fraction of the computational cost involved in a translationally invariant (k-point integration) calculation.
The second topic is hierarchical symmetry breaking and restoration [3], a natural extension of our PHF work where we treat correlated product states as references instead of single Slater determinants. In this context, the concept of quasi-symmetry appears naturally as a plaquette supersymmetry.
[1] Density matrix embedding theory from broken symmetry mean fields, I. W. Bulik, G. E. Scuseria, and J. Dukelsky, Phys. Rev. B 89, 035140 (2014).
[2] I. W. Bulik and G. E. Scuseria, to be published.
[3] C. A. Jiménez-Hoyos and G. E. Scuseria, to be published.
George Booth
Affiliation
Title
Summary
Theoretical spectroscopy / Magnetism
Jeppe Olsen
Affiliation
Title
Summary
Daniel Crawford
Affiliation
Title
Summary
Trygve Helgaker
Affiliation
Title
Summary
Dynamics
Florent Calvo
CNRS and University Joseph Fourier Grenoble, France
Modeling vibrational action spectroscopy: anharmonicities and quantum effects
Recent experimental progress in infrared spectroscopy has been driven by the development of free-electron lasers and the advent of infrared multiphoton dissociation (IRMPD) technique. With this method, a gas phase molecule is exposed to IR light and its dissociation is monitored by mass spectrometry, the measured signal being called an action (or depletion) spectrum. Interpretation of such spectra requires successful assignment by calculations of absorption spectra, usually carried out by density functional theory at the harmonic level. In this contribution we discuss and illustrate the fundamental differences between action and absorption spectra, and emphasize the crucial role played by anharmonicities and the way they are dynamically amplified by multiphoton processes. Our investigation relies on two separate but completary models that describe the interaction between the molecule and the laser field either classically through molecular dynamics at the atomistic level, or quantum mechanically through a Dunham expansion of the vibrational energy levels. For both models, specific spectral features such as additional redshifts or excessive broadenings are clearly identified.
Fabien Gatti, Hans-Dieter Meyer
CTMM Institut Charles Gerhardt UMR-CNRS 5253 University of Montpellier, France. Institute for Physical Chemistry, University of Heidelberg, Germany.
Full ab inito Molecular Quantum Dynamics with the Multi-Configuration Time-Dependent Hartree (MCTDH) method
We present the Multi-Configuration Time-Dependent Hartree (MCTDH) approach [1]. MCTDH is a general algorithm to solve the time-dependent Schr ̈odinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces. The possibilities offered by the Heidelberg MCTDH package [2] are also presented: calculation of photoabsorption spectra, cross sections, eigenstates and quantum resonances, dynamics around conical intersections, etc. Special emphasis is placed on the outlook for possible applications in chemistry in the context of coherent control with laser pulses.
[1] H.-D. Meyer, F. Gatti, and G. Worth, Multidimensional Quantum Dynamics: MCTDH Theory and Applications Wiley-VCH, 2009.
[2] See http://www.pci.uni-heidelberg.de/tc/usr/mctdh/
Aaron Kelly and Thomas E. Markland
Department of Chemistry, Stanford University, USA
Combining quantum-classical dynamics techniques with master equation methods: Exploiting complementary time-scales.
Quantum effects play a major role in a variety of condensed phase chemical processes such as electron and proton transfer reactions, proton-coupled electron transfer processes, and many other problems such as electronic excitation energy transfer. Developing an understanding of the underlying principles that govern mechanistic outcomes requires modeling of nonequilibrium relaxation from electronic excited states. To address this problem requires the development of accurate non-adiabatic quantum dynamics approaches that can be applied for long times starting from non- equilibrium initial configurations. Recently we have developed approaches that utilize the generalized quantum master equation in conjunction with quantum-classical dynamics techniques based on the quantum-classical Liouville (QCL) equation. By taking this combined approach we have been able to demonstrate that one can obtain highly accurate results for long times by circumventing the usual computational efficiency and accuracy problems which can plague solutions of the QCL.
In this talk I will show how this methodology allows accurate results to be achieved in an efficient and highly flexible manner. I will also illustrate its utility with applications to the dynamics of model systems involving charge and energy transfer in the condensed phase.
Benjamin Lasorne
Institut Charles Gerhardt, CNRS – Université Montpellier 2, 34095 Montpellier, France
and A. Perveaux[1,2] L. Joubert-Doriol[1] J. Jornet-Somoza[1] F. Gatti[1] D. Lauvergnat[2] H.-D. Meyer[3] D. Mendive-Tapia[4] M. A. Robb[4] M. J. Bearpark[4] G. A. Worth[5]
[1] Institut Charles Gerhardt, CNRS – Université Montpellier 2, 34095 Montpellier, France
[2] Laboratoire de Chimie Physique, CNRS – Université Paris-Sud, 91405 Orsay, France
[3] Ruprecht-Karls Universität, Physikalisch Chemisches Institut, 69120 Heidelberg, Germany
[4] Department of Chemistry, Imperial College London, SW7 2AZ London, UK
[5] School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
Diabatic Strategies for Photochemical Quantum Dynamics
Quantum dynamics simulations applied to ultrafast photoinduced processes often require an adiabatic-to-diabatic transformation (diabatisation) of the data produced from quantum chemistry calculations. The vibronic coupling Hamiltonian (VCH) quasidiabatic model developed by Köppel and coworkers is a fruitful strategy that has been used for calculating photoabsorption and photoelectron spectra with the multiconfiguration time-dependent Hartree (MCTDH) quantum dynamics approach. We present here a set of strategies to generalise the VCH model to the treatment of photochemical reactions whereby large-amplitude nuclear motions occur along complicated reaction pathways connecting several potential energy wells through transition barriers. This is illustrated on the photoisomerisation of ethylene [1] and the ring opening of benzopyran [2]. A global model based on local information at critical points is being developed for high-dimensional quantum dynamics simulations using the novel multilayer formulation of MCTDH termed ML-MCTDH. Alternatively, the direct dynamics variational multiconfiguration Gaussian (DD-vMCG) wavepacket method frees simulations from this preliminary step by calculating the potential energy and its derivatives on the fly [2]. The quasidiabatic Hamiltonian is currently generated from a regularisation method, and work is in progress to implement a local diabatisation procedure.
[1] J. Jornet Somoza, B. Lasorne, M. A. Robb, H.-D. Meyer, D. Lauvergnat, and F. Gatti, J. Chem. Phys. 137 (2012) 084304
[2] L. Joubert Doriol, B. Lasorne, D. Lauvergnat, H.-D. Meyer, and F. Gatti, “A generalised vibronic-coupling Hamiltonian model for benzopyran”, J. Chem. Phys. 140 (2014) 044301
[3] D. Mendive-Tapia, B. Lasorne, G. A. Worth, M. A. Robb, and M. J. Bearpark, J. Chem. Phys. 137 (2012) 22A548
Troy Van Voorhis
Massachusetts Institute of Technology
Title
Summary
Computational biochemistry / Solvation
Aurelien de la Lande
Paris-Sud University, France
COMPUTATIONAL INVESTIGATION OF THE HYDROXYLATION MECHANISM OF NON-COUPLED COPPER OXYGENASES
In Nature peptidylglycine alpha-hydroxylating monooxygenase (PHM), Dopamine beta-monooxygenase and Tyramine beta-monooxygenase are known to achieve the remarkable dioxygen-dependent hydroxylation of aliphatic C-H bonds using two uncoupled copper sites.1 In spite of many investigations, either biochemical, chemical or computational, the details of the C-H bond oxygenation mechanism remain elusive; conflicting proposals have been advanced in the recent literature for the enzymatic catalytic cycle.2 I will present an investigation of the hydroxylation mechanism of PHM using ab initio Molecular Dynamics simulations based on hybrid Density Functional Theory-classical potentials (ie. QM/MM). This computational scheme permits the inclusion of the intrinsic dynamics of the active site into the modeling strategy. The major result of this study has been an extremely fast (picoseconds timescale) rebound after the initial H-abstraction step promoted by the cupric-superoxide adduct. The H-abstraction/Rebound sequence leads to the formation of an alkylhydroperoxide intermediate. A long range electron transfer from the remote copper site subsequently triggers its reduction to the hydroxy lated substrate.3 The characteristic time scale of the rebound step (ps) suggests that it is very probably the fastest reactive pathway over the previously advanced proposals. Moreover, our proposal finds favorable echoes with recent experimental results obtained on biomimetic complexes.5 Overall our study sheds new lights on how PHM achieves hydroxylation of C-H bonds with two uncoupled copper sites.
1: a) Osborne R.L.; Klinman, J. P. "Copper Oxygen Chemistry", pp 1-22; 2011, Ed. Karlin, K. D.; Itoh, S. Pub. J. Wiley & Sons. b) Solomon, E. I. et al. Chem. Rev. ASAP. DOI: 10.1021/cr400327t 2: see for example scheme 2 of N. R. McIntyre, E. W. Lowe Jr., D. J. Merkler, J. Am. Chem. Soc. 2009, 131, 10308 –10319. 3: Melía C., Ferrer S., Řezáč J., Parisel O., Reinaud O., Moliner V., de la Lande A. Chem. Eur. J. 2013, 19, 17328 – 17337. 4: de la Lande A., Parisel O., Moliner V. J. Am. Chem. Soc. 2007, 129,11700-11707. 5: a) Izzet, G., Zeitouny, J., Akdas-Killig, H., Frapart, Y., Ménage, S., Douziech, B., Jabin, Y., Le Mest, Y, Reinaud,O. J. Am. Chem. Soc. 2008, 130, 9514 –9523. b) Thiabaud, G. Guillemot, G., Schmitz-Afonso, I., Colasson, B. Reinaud, Angew. Chem. Int. Ed. 2009, 48, 7383 –7386. c) Tano, T., Sugimoto, H., Fujieda, N., Itoh, S. Eur. J. Inorg. Chem. 2012, 4099–4103.
Lars G.M. Pettersson
FYSIKUM, AlbaNova University Center, Stockholm University, S-106 91 Stockholm
Water - Structure and origin of its anomalous properties
I will discuss recent experimental and simulation data from x-ray absorption (XAS), emission (XES) and scattering (XRD and SAXS) of liquid water and the picture of fluctuations between high-density (HDL) and low-density (LDL) liquid this has led to [1,2]. Such a two-liquid scenario would explain many anomalous properties, e.g., density maximum, heat capacity and isothermal compressibility minima, but no direct connection has been found to simulations of ambient water. Applying the local structure index (LSI) of Shiratani and Sasai [J. Chem. Phys. 104, 7671 (1996)] to the inherent structure of TIP4P/2005 water we find a strict bimodality in terms of spatially separated HDL- and LDL-like environments in the simulations at all temperatures and pressures with distributions in agreement with the conclusions from XAS and XES, i.e. 75% HDL and 25% LDL-like at ambient conditions [3]. The SAXS signal is connected to density fluctuations in the liquid which for water decrease (as measured by the isothermal compressibility) down to 46 ˚C, but then increase as the liquid is further cooled. Going into “No man’s land” to do experimental measurements has recently become possible through the Linac Coherent Light Source (LCLS) x-ray free-electron laser at SLAC by exploiting evaporative cooling in vacuum of micrometer-sized water droplets from which a full diffraction pattern of individual droplets is obtained through the 100 fs fully coherent x-ray pulses delivered by the LCLS showing a continuous and accelerated development towards an LDL liquid down to at least 227 K [4].
[1] A. Nilsson and L. G. M. Pettersson, Perspective on the Structure of Liquid Water, Chem. Phys. 389, 1-34 (2011)
[2] A. Nilsson, C. Huang and L.G.M .Pettersson, Fluctuations in Ambient Water, J. Mol. Liq. 176, 2-16 (2012)
[3] K. T. Wikfeldt, A. Nilsson and L. G. M. Pettersson, Spatially Inhomogeneous Bimodal Inherent Structure in Simulated Liquid Water, Phys. Chem. Chem. Phys. 13, 19918-19924 (2011)
[4] J. A. Sellberg et al., Experimental observation of bulk liquid water structure in “no-man’s land”, Nature, in press.
Ursula Roethlisberger
Affiliation
Title
Summary
G. Andres Cisneros
Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
Development of accurate force fields for classical simulations
We have developed a novel force field, called the Gaussian Electrostatic Model (GEM), that employs explicit molecular charge densities. These densities are employed to calculate each term in the Morokuma-style decompositon of the quantum mechanical intermolecular interaction, i.e., Coulomb, exchange-repulsion, polarization, charge-transfer and dispersion. GEM enables the evaluation of intermolecular interactions for molecular systems with errors below chemical accuracy for each component, and provides a novel procedure to obtain distributed multipoles (GEM-DM). We will discuss the details of our method, advances in the implementation of a GEM variant for molecular dynamics simulations, recent applications of this variant for liquid water simulations, and applications of GEM-DM for the development of AMOEBA for ionic liquids simulations.
Yingkai Zhang
Department of Chemistry, New York University, New York, NY 10003
Computational enzymology: from mechanistic study to inhibitor design
In this talk, I will present our recent progresses in developing and applying state-of-the-art computational methods to provide novel physical-chemical insights into important enzymes, and to facilitate the rational design of their modulators for probing important cellular pathways and for therapeutic use. Our computational approaches center on Born-Oppenheimer ab initio QM/MM molecular dynamics simulation (aiQM/MM-MD) with umbrella sampling, a computational tour-de-force to simulate enzyme reactions. In last few years, we have demonstrated the power of this state-of-the-art computational approach by solving important biochemical problems and making novel insightful suggestions for further experimental studies. One notable example is that we reported the first aiQM/MM study of zinc-dependent histone deacetylases (HDACs), which has been established as one of the most promising targets for the development of anti-tumor drugs. Our work disproved the previous mechanistic hypothesis, and determined a new mechanism which is more consistent with available experimental results. Subsequently, our discovered mechanism has guided the development of a novel class of HDAC inhibitors.
Guillaume Lamoureux
Affiliation
Title
Summary
Material science/ Catalysis
Michel A. Van Hove
Institute of Computational and Theoretical Studies & Department of Physics, Hong Kong Baptist University, Hong Kong SAR, China
Rotor molecules as machines
Molecular machines are gaining increasing interest, especially from a biological perspective. They promise to create and control mechanical motion at length scales down to the nanometer. Some molecular machines cause reciprocal motion, as in muscles and switches, while others cause rotational motion, as in flagellae: we focus here on rotor molecules.
Nature developed a variety of molecular machines to create and control motion. These natural machines tend to be complex and robust, due to the need to operate reliably for long times in variable biological environments.
In the last few decades, scientists have synthesized a wide range of new, relatively simpler molecular machines and learned to control and observe some of their important motions, mostly in solution. Increasingly, molecular motors have also been investigated at solid surfaces, allowing the use of surface science techniques for studying monolayers of well-oriented molecules. Nanoscience techniques have added further possibilities.
We shall discuss basic issues of the operation of molecular motors, including energy conversion steps, continuous energy supply, the role of thermal energy, intentional start and stop of motion, and unidirectionality of motion. Without intentional control of these aspects, motors create random motion and are largely useless.
This work was supported by grants from the Hong Kong Baptist University Strategic Development Fund, the Hong Kong RGC, the NBRPC and the NSFC, and by HKBU’s High Performance Cluster Computing Centre, which receives funding from the Hong Kong RGC, UGC and HKBU.
RuiQin Zhang
CiteU HongKong
Title
Summary
Alexis Markovits
Université Pierre et Marie Curie
Strong Metal Support Interaction: an electron count
Summary
Metal/Metal-oxide interface is an attractive topic in many aspects. It has been given considerable attention due to the various technological applications for electronic or photovoltaic devices, coating or sensor devices. The domain we are interested in is heterogeneous catalysis where the very special interaction between a support and a metal aggregate is known as Strong Metal Support Interaction (SMSI). The activation of the so-called SMSI catalyst is indispensable. Several explanations have been proposed since the discovery of SMSI as for instance metal dispersion allowing the formation of metal nanoparticules of various sizes and morphologies. Another explanation is the electronic effect. In this talk, we will mainly be focusing on this aspect. We take as an example CO dissociation that is important in many catalytic reactions. The first point is to evaluate and to rationalize the interaction strength between the metal M (M=K-Zn) and the reducible support TiO2. Then, CO dissociation on supported M is considered: is it assisted by hydrogenation? The influence of surface oxygen vacancy will be evaluated. The case of Iron supported on TiC support is developed: what is the influence of the support on CO dissociation? CO reactivity on bare and supported Fe clusters is compared.
Electron count and orbital analysis for understanding catalysts are supported by periodic DFT calculations. ↑ top of this page
Monica Calatayud
Univesité Pierre et Marie Curie
Title
Summary
Javier Fdez. Sanz
Universidad de Sevilla, Spain
Mechanism of the Water-Gas Shift Reaction: Insights from First Principles Calculations
The traditional approach to the optimization of metal/oxide catalysts has focused on the properties of the metal and the selection of the proper oxide for its dispersion. The importance of metal–oxide interfaces has long been recognized, but the molecular determination of their properties and role is only now emerging. In this talk we focus on the water gas shift reaction, WGSR, a chemical process that allows for obtaining clean molecular hydrogen: CO+H2O → CO2+H2. Bulk like phases or extended surfaces of coinage metals show low catalytic activity that improves when supported on a metal-oxide. Several reaction mechanisms have been proposed. In the redox mechanism, CO reacts with oxygen derived from the dissociation of H2O. In the associative process, the formation of a carboxyl intermediate must precede the production of H2 and CO2. The mechanism involves several steps that can take place at different sites of the catalyst: the metal, the support or the interface. Besides the dispersion effect, the role of the support is to increase the interaction with water and facilitate its dissociation. DF calculations show that supported CeOX nanoparticles are highly efficient in water splitting. Furthermore The M/CeOx /TiO2 (110) surfaces display outstanding activity for the WGS, in the sequence: Pt > Cu > Au. Such a high catalytic activity reflects the unique properties of the mixed-metal oxide at the nanometer level. STM and DF calculations show that Ce deposition on TiO2 (110) at low coverage gives rise to Ce2O3 dimers specifically aligned, indicating that the substrate imposes on the ceria NPs unusual coordination modes enhancing their chemical reactivity.
Frederik Tielens
Univesité Pierre et Marie Curie
Title
Summary
Chemical concepts
Paul Ayers
Using molecular properties to define similarity measures and predict chemical properties
Jerzy Cioslowski
Institute of Physics, University of Szczecin, Poland
A tale of natural orbitals
Natural orbitals (NOs) and their occupancies constitute a convenient and conceptually appealing representation of the one-electron reduced density matrix from which all one-electron properties (including the majority of indices of interest to chemists) follow. However, their importance notwithstanding, properties of NOs are not fully understood. In particular, the existence of NOs with vanishing occupancies has been the subject of several recent studies with contradictory conclusions.
In this talk, after a brief introduction to properties of natural orbitals and their occupancies, we discuss results of our recent work uncovering the existence of solitonic NOs that resolves the apparent contradictions encountered in the previously published research. Both numerical calculations and analytical derivations are presented.
Eduard Matito
Aromaticity
Patrick Bultinck
New insights on chemical reactivity descriptors from a matrix perspective
This lecture will focus on atoms in molecules, electrostatic potentials and chemical reactivity in the context of the breakdown of the conventional approaches due to the possibility of (near) degenerate states in molecules and crystals or inherent inadequacies in e.g., the Frontier Molecular Orbital picture. Can our trusted tools survive or do they need improving or must just be abandoned ? We show that in cases of (near) degeneracy, atomic charges become rather ill-defined as the electrostatic potential needs to be computed using degenerate perturbation theory (1). The effects are even more outspoken for the Fukui function (2), where in this case the Fukui matrix (3,4) is even more important.
1. Bultinck, P.; Cardenas, C.; Fuentealba, P.; Johnson, P.A.; Ayers, P.W. Atomic charges and the electrostatic potential are ill-defined in degenerate ground states. J. Chem. Theor. Comput., 2013, 9, 4779-4788.
2. Bultinck, P.; Cardenas, C.; Fuentealba, P.; Johnson, P.A.; Ayers, P.W. How to compute the Fukui matrix and function for (quasi-)degenerate states. J. Chem. Theory Comput., 2014, 10, 202–210.
3. Bultinck, P.; Clarisse, D.; Ayers, P.W., Carbo-Dorca, R. The Fukui matrix: a simple approach to the analysis of the Fukui function and its positive character. Phys. Chem. Chem. Phys., 2011, 13, 6110–6115.
4. Bultinck, P.; Van Neck, D.; Acke, G.; Ayers, P.W. Influence of electron correlation on the Fukui matrix and extension of frontier molecular orbital theory to correlated quantum chemical methods. Phys. Chem. Chem. Phys., 2012, 14, 2408 - 2416.
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Angel M Pendas
Learning (and teaching) chemical bonding from the statistics of electron populations in spatial domains
Electrons are countable particles, so asking how many of them will lie in a given region of space makes perfect sense. We will show in this didactic presentation how examining the possible distributions of the N electrons of a molecule in atomic regions leads to interesting descriptions of chemical bonding. This statistical scheme may be applied equally to naïve models or to high level computational descriptions, making it suitable for teaching purposes in frehsman courses. ↑ top of this page
Paul Geerlings
Conceptual DFT, Theoretical Models of Chemical Bonding
Posters
Alexey I. Baranov
Inorganic Chemistry II, Department of Chemistry and Food Chemistry, Dresden University of Technology, Max Planck Institute for Chemical Physics of Solids, Dresden, Germany.
Indicators for Quantitative Atomic Shell Structure Analysis from Fully Relativistic Calculations
One of the most fundamental concepts of chemistry is the concept of atomic shell structure. In the field of real space bonding analysis several bonding indicators have been proposed to reveal shell structure of chemical elements and thus visually represent key entities of chemical bonding like bonds or lone pairs. This type of analysis should be especially beneficial for relativistic 2c- or 4c-formalisms, eliminating the necessity of direct analysis of complicated multicomponent wavefunction.
This work presents an electron localizability indicator for spatially antisymmetrized electrons, which can be used to reveal an atomic shell structure at quantitative level in real space from the results of fully relativistic calculations. The indicator is universal and equally applicable for two-component and scalar-relativistic methods. Shell structures of heavy elements, calculated using this indicator from the results of fully relativistic, ZORA scalar relativistic and nonrelativistic numerical Kohn-Sham LDA calculations are reported and compared with each other.
[1] Baranov, A. I. J. Comp. Chem. 2014, 35, 565.
Sunghwan Choi
Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
Finding of Kinetic Energy Density Functional width Machine Learning
Density Functional Theory(DFT) calculations become more practical; however, the kinetic functional, computed with derivatives of Kohn-Sharm(KS) orbitals derives makes problem difficult. In order to get kinetic energy density accurately without KS orbitals, we tried to find out the hidden pattern through tons of data. we used semi-local information to get kinetic energy density. In one-dimensional soft-core model, kinetic energy densities are predicted not only qualitatively but also quantitatively, and it shows a high transferability. It can be applied with the elements and new geometrical structure, which is not belonging the dataset. It is possible to calculate the DFT level energy without the orbital picture.
Contributor's name
Affiliation
Title
Summary
[1] Popelier, P. L. A.; Brémond, É. A. G. Int.J.Quant.Chem. 2009, 109, 2542.