Вкратце, о том как это было в ныншнем году:
А также список докладчиков, если никого не забыл. В зависимости от области ваших интересов список будет выглядеть менее или более представительным. Про себя скажу что многих их доклачиков я знаю лично и достаточно хорошо знаком с объектами их работы, но тем не менее получил удовольствие от многих прослушанных лекций.Virtual Winterschool on Computational Chemistry
It is a great tradition to share information among scientists. Since we strongly believe in this principle, in 2015, we started the winter school of Computational Chemistry initiative. The last edition (2016) brought us over 600 visitors, with an audience originating from 72 countries.
With the internet as basic tool, sharing information is today easier than ever. Already in the 90’s, Steven Bachrach had the idea of running a virtual computational chemistry conference (ECCC, electronic conference on computational chemistry) and Henry Rzepa followed it up with ECTOC (electronic conference on trends in organic chemistry, all of which are still online at http://www.ch.ic.ac.uk/ectoc/). These were made to share information among (computational and theoretical) chemists using media apart from regular conferences.
This year’s ‘Virtual Winterschool on Computational Chemistry’ organizes virtual lectures, with a special focus on educational training sessions. Our excellent speakers (see confirmed speakers) will provide background theoretical information for young scientists (PhD/post-doc). The format of the lectures include an online, live virtual conference, where participants can attend the talk and even ask questions. Participants need to register in order to get a login granting access to the secured website, forum and the E-presentations. Registration was free but mandatory. Furthermore, participants are encouraged to upload their work as a Single Figure Presentation (SFP) on the secured forum.
- Paul Ayers, Department of Chemistry & Chemical Biology, McMaster University, Canada
- Benoît Braïda, Pierre and Marie Curie university, Paris, France
- Kieron Burke, University of California, Irvine, USA
- Rachel Crespo-Otero, Queen Mary Universty of London, UK
- Catharine Esterhuysen, University of Stellenbosch, South-Africa
- David Glowacki, School of Chemistry, University of Bristol, UK
- Philippe Hiberty, Université de Paris-Sud, France
- Junming Ho, Institute of High Performance Computing, Singapore
- Hannes Loeffler, Scientific Computing Department, Science and Technology Facilities Council, UK
- John Perdew, College of Science and Technology, Temple University, USA
- Elisa Rebolini: Centre for Theoretical and Computational Chemistry (CTCC), Universities of Tromsø and Oslo, Norway
- Dennis R. Salahub, Inst. for Quantum Science and Technology, Centre for Molecular Simulation, University of Calgary, Canada
- Alex Simperler, UK National service for Computational Chemistry Software
- Danny Vanpoucke, Center for Molecular Modeling, Ghent University, Belgium
- Henryk Witek, Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
- Chris Woods, Centre for Computational Chemistry, School of Chemistry, University of Bristol, UK
- 1. Junming Ho: Calculating pKas and redox potentials. (pdf)
Abstract писал(а):The solution phase pKas and reduction potentials provide a direct measure of the thermodynamic driving force for proton and electron transfer. These processes are fundamentally important in many biological reactions, as well as in chemical synthesis and drug design. In this talk, I will introduce some of the methods available for calculating these properties, and highlight some of the strategies towards reliable first principles prediction. The focus will be on protocols based on implicit solvation models, and I will discuss some of the recent developments in the field. I will also present recent examples of how theoretical calculations are applied in areas such as chemical synthesis, drug and materials design.
Abstract писал(а):My talk will focus on reactions catalyzed by transition-metal-containing nanoparticles. I will show that, under working conditions (in the context of oil sands upgrading), it is necessary to go beyond the concept of structure, minima on a potential energy surface, to include dynamics, entropy and free-energy surfaces. I will describe a multiscale modelling approach to study benzene hydrogenation on molybdenum carbide nanoparticles (MCNPs) [1]. The QM DFTB method is coupled with an MM force field to yield a quantum mechanical/molecular mechanical (QM/MM) model describing the reactants, the nanoparticles and the surroundings. Umbrella sampling (US) is employed to calculate the free energy profiles for benzene hydrogenation in a model aromatic solvent under realistic conditions. Comparisons are made with traditional methodologies; the results reveal new features of the metallic MCNPs. Under working conditions, rather than being rigid, they are very flexible due to the entropic contributions of the MCNPs and the solvent, which greatly affect the free energy profiles.
[1] X.Liu and D. R. Salahub, Molybdenum Carbide Nanocatalysts at work in the In-situ Environment: a DFTB and QM(DFTB)/MM Study, J. Am. Chem. Soc, 137, 4249 -4259 (2015)
- 3. A. Simperler: Concepts of Molecular Excited States Calculations. (webm)
Abstract писал(а):We will cover how an electronic excited state can be computed within the orbital based methods used in ground state chemistry. We cover symmetry, spin and orthogonality constraints. An overview of CIS methods (TD-DFT, etc.) and CASSCF methods is given. Dynamical correlation are introduced and we can explore the need of multi-reference theories. The last part leads us beyond the Jablonski Diagram – potential energy surfaces for excited states.
- 4. A. Simperler: Intro to CASSCF calculations. (webm)
Abstract писал(а):CASSCF - Complete Active Space Self-Consistent Field: The concept of an active space and the full CI expansion in that space will be introduced. Practical Things will be introduced using the software Gaussian 09 to discuss workflows. We try keep this talks however software agnostic and will make suggestions what to look out for in general. For example, software like Molpro or Molcas will have the same underlying concepts but have different input syntaxes.
RASSCF - Restricted Active Space SCF: This is a method to limit what may happen in an active space, and widen thus the number of active orbitals that may be considered. A couple of applications to excited states will be introduced.
Abstract писал(а):Modern materials research has evolved to the point where it is now common practice to manipulate materials at nanometer scale or even at the atomic scale (e.g. Intel’s skylake architecture with 14nm features, atomic layer deposition and surface structure manipulations with an STM-tip). At these scales, quantum mechanical effects become ever more relevant, making their prediction important for the field of materials science.
In this session, we will discuss how advanced quantum mechanical calculations can be performed for solids and indicate some differences with standard quantum chemical approaches. We will touch upon the relevant concepts for performing such calculations (plane-wave basis-sets, pseudo-potentials, periodic boundary conditions,...) and show how the basic calculations are performed with the VASP-code. You will familiarize yourself with the required input files and we will discuss several of the most important output-files and the data they contain.
At the end of this session you should be able to set up a single-point calculation, a structure optimization, a density of states and band structure calculation.
Abstract писал(а):This is an introductory lecture on some very basic principles of density functional theory, and some basic properties of density functional approximations.
- 7. B. Braida: Basics of Valence Bond theory. (pdf, webm) & P. Hiberty: An overview of modern ab initio valence bond methods. (webm)
Abstract писал(а):Valence Bond (VB) theory, formulated in the turn of the 1930s, has evolved in parallel with the molecular orbital theory (OM). Both theories led to fundamental developments in chemistry, with VB-based models of reactivity being at the origin of two recent Nobel laureates. VB theory has the advantage of being close to the natural language of chemists, and views the electron pairs of a molecule as located in local bonds or lone pairs. As such, it offers a direct connection between quantum mechanics and usual concepts of molecular chemistry (Lewis structures, resonance, arrow-pushing language, and so on...). This is why it remains a tool of choice for the study of problems of electronic structure and reactivity. Moreover, modern VB ab initio computational methods are now reliable and can provide bonding energies and reaction barriers that are at par with the best standard ab initio computational methods. These two courses will aim at briefly laying the fundations of VB theory, introduce modern ab initio Valence Bond methods, and illustrate their applications in the study of chemical reactivity with a few notable recent applications.
- 8. C. Esterhuysen: Gold as a Lewis base. (webm)
Abstract писал(а):Although hydrogen bonds are the most common and well-known intermolecular interactions, a wide variety of other, fascinating interactions that play a role in stabilising crystal structure packing have been identified. For instance, Au(I) complexes are well-known for forming aurophilic interactions, which are inter- or intramolecular Au···Au interactions of a similar strength to hydrogen bonds, with Au···Au distances similar to those found in gold metal [1]. In the intervening thirty years since these interactions were identified they have been extensively studied, and are known to have their origin in relativistic effects [2]. They are also of interest since they are often luminescent and exhibit unusual electronic properties.
It has recently been shown that the auride ion, Au–, can also act as a hydrogen bond acceptor.[3] However there appears to be a lack of experimental evidence for a hydrogen bonding to Au(I) acceptors, since identification of these interactions in crystal structures is complicated by the simultaneous presence of other hydrogen bonding interactions.[4] Here we present quantum mechanical evidence confirming that a number of different hydrogen bond donors do form interactions with a variety of Au(I) complexes, which can therefore be classified as Lewis bases.[5] Furthermore, we show that the Lewis-base nature of these complexes means that they are also able to act as halogen bond acceptors.
Figure 1: Au(CH3)2– forming a hydrogen bond with water
The nature of these interactions will be described utilising results obtained with the Atoms in Molecules and Noncovalent Interactions (NCI) methodologies, while the role that relativistic effects play in stabilising such interactions will be explored.
[1] H. Schmidbaur, F. Scherbaum, B. Hubert, G. Müller, Angew. Chem. Int. Ed. Engl., 1988, 27, 419. (b) S. S. Pathaneni, G. R. Desiraju J. Chem. Soc., Dalton Trans., 1993, 319-322.
[2] (a) Pyykkö, P., Chem. Rev., 1997, 97, 597-636; Pyykkö, P., Angew. Chem. Int. Ed. Engl., 2004, 43, 4412-4456.
[3] E. S. Kryachko, J Mol. Struct., 2008, 880, 23-30.
[4] H. Schmidbaur, H. G. Raubenheimer, L. Dobraska, Chem. Soc. Rev. 2014, 43, 345 – 380.
[5] F. Groenewald, J. Dillen, H. G. Raubenheimer, C. Esterhuysen, Angew. Chem. Int. Ed. 2016, DOI: 10.1002/anie.201508358.
Abstract писал(а):The simplest and most computationally efficient density functionals for the exchange-correlation energy are semilocal. The local spin density approximation and the generalized gradient approximation (GGA) are semilocal in the electron density. The meta-GGA is fully nonlocal in the electron density, but still computationally semilocal in any Kohn-Sham calculation, since it can be expressed as a single integral over 3D space of a function of ingredients that are available at each point r of space: the electron density, its gradient, and the positive orbital kinetic energy density. Since the exact exchange-correlation energy can be regarded as the electrostatic interaction between the electron density at r and the density at r’ of the exchange-correlation hole around an electron at r, semilocal approximations are expected to work when the exact exchange-correlation hole is well localized around its electron. This is the case in the electron gas of uniform or slowly-varying density, and also in an atom or other single-center system, where semi-local approximation can be accurate for exchange alone and for correlation alone. Since the exact exchange-correlation hole is typically deeper and more short-ranged than the separate exchange hole and correlation hole, semilocal approximations can still work by error cancellation between exchange and correlation in many molecules and solids near equilibrium geometries. But semilocal approximations necessarily fail when the exact exchange-correlation hole is delocalized over two or more centers, as when electrons are shared over stretched bonds (e.g., in stretched H2+). In that case, fully nonlocal functions (hybrids, self-interaction-corrected functionals, etc.) are needed, at considerably higher computational cost. We review the construction and performance of the SCAN (strongly constrained and appropriately normed) meta-GGA [1], which is designed to be accurate when the exact exchange-correlation hole is indeed well-localized around its electron, and is constructed without fitting to any bonded system.
[1] J. Sun, A. Ruzsinszky, and J.P. Perdew, Phys. Rev. Lett. 115, 036402 (2015).
- 10. H. Witek: Mathematics in quantum chemistry: selected topics. (webm)
Abstract писал(а):The main objective of this presentation is to introduce to you some mathematical tools and concepts helpful to understand the foundations of quantum chemistry. We will start with a somewhat unusual approach to the hydrogen atom, resulting in the obvious quantization conditions for angular momentum and energy. Later we try to extend this approach to a few-electron systems with particular focus on the analytical approach and on the algebraization techniques. The ultimate goal of the presentation will be to review the existing wave-function based quantum chemical techniques from the mathematical perspective.
Abstract писал(а):Since the electronic Schrödinger equation is too complicated to be soluble for most interesting chemical systems, the task of the quantum chemist is to develop practical approximations that provide accurate models for the behavior of electrons in molecules. The difficulty of the underlying problem implies that these models are necessarily limited to certain special cases For example, it is relatively easy to describe cases where the electrons in a molecule move nearly independently, so that the motion of one electron does not affect others very much. When this is not true, many of our conceptual precepts lose their utility (e.g., the notion of an electron configuration, and even the mere concept of orbitals) and many popular computational quantum chemistry methods become unreliable. In this lecture, I will discuss quantum chemical models for strongly correlated molecules, including multireference orbital-based approaches and alternatives to orbital-based models.
Abstract писал(а):Linear-response time-dependent density-functional theory (TDDFT)[1] is nowadays one of the most widely used method to compute molecular excitation energies thanks to its good cost versus accuracy ratio. The key object in TDDFT is the Hartree-exchange-correlation kernel which must describe the effects of the electron-electron interaction on the excitation energies of the system. Unfortunately the form of this kernel is unknown and the design of approximations remains a major challenge. Within the usual adiabatic semi-local approximations, although it reproduces correctly valence excitations, TDDFT is not able to describe properly Rydberg, charge-transfer or multiple excitations. Range separation of the electron-electron interaction [2] allows one to mix rigorously density-functional methods at short range and wave-function or Green’s function methods at long range. When applied to the exchange kernel, the inclusion of the long-range Hartree-Fock exchange kernel already corrects most of TDDFT deficiencies [3] as in particular the correct asymptotic behavior of the potential at long range is recovered. However multiple excitations are still missed by such a kernel as they need a frequency-dependent kernel in order to be captured which is prevented by the adiabatic approximation. In this talk, I will present several developments in range-separated time-dependent and time-independent density-functional theory to improve the treatment of such excitations. The effects of range separation are first assessed on the excitation energies of a partially-interacting system in an analytic and numerical study in order to provide guidelines for future developments of range-separated methods for excitation energy calculations [4]. It is then applied on the exchange and correlation TDDFT kernels in a single-determinant approximation in which the long-range part of the correlation kernel vanishes [5]. A long-range frequency-dependent second-order correlation kernel is then derived from the Bethe-Salpeter equation and added perturbatively to the range-separated TDDFT kernel in order to take into account the effects of double excitations.
[1] M. Casida. “Time-Depent Density-functional response theory for molecules”. In: Recent Adv. Density Funct. Methods, Part I. Ed. by D. P. Chong. Singapore: World Scientific, 1995, p. 155.
[2] A. Savin. “On degeneracy, near-degeneracy and density functional theory”. In: Recent Dev. Appl. Mod. Density Funct. Theory. Ed. by J.M. Seminario. Amsterdam: Elsevier, 1996, p. 327.
[3] Y. Tawada, T. Tsuneda, S. Yanagisawa, et al. 2004. J. Chem. Phys. 120. P. 8425.
[4] E. Rebolini, J. Toulouse, A. M. Teale, et al. 2014. J. Chem. Phys. 141. P. 044123.
[5] E. Rebolini, A. Savin, and J. Toulouse. 2013. Mol. Phys. 111. Pp. 1219–1234.
Abstract писал(а):Tully’s Surface hopping (SH) method has become very popular for the study of non-adiabatic dynamics in the excited states.[1] In this talk, I will showcase several applications of SH in the area of photochemistry considering two mechanisms in the excited states: photo-dissociation and proton transfer.[2-4] Practical aspects of these simulations and their implementation in the Newton-X platform[5] will be discussed with particular focus on the appropriate selection of the electronic structure method.
[1] J. C. Tully, J. Chem. Phys., 1990, 93, 1061.
[2] R. Crespo-Otero, N. Kungwan and M. Barbatti, Chem. Sci., 2015, 6, 5762–5767.
[3] R. Crespo-Otero, A. Mardykov, E. Sanchez-Garcia, W. Sander and M. Barbatti, Phys. Chem. Chem. Phys., 2014, 16, 18877.
[4] R. Crespo-Otero, A. Mardyukov, E. Sanchez-Garcia, M. Barbatti and W. Sander, ChemPhysChem, 2013, 14, 827–36.
[5] M. Barbatti, G. Granucci, M. Ruckenbauer, F. Plasser, R. Crespo-Otero, J. Pittner, M. Persico and H. Lischka, NEWTON-X: a package for Newtonian dynamics close to the crossing seam, 2013, http://www.newtonx.org
- 14. D. Glowacki: Cheap & Accurate Reactive Molecular Dynamics: A Guided Demonstration. (webm)
Abstract писал(а):Over the past few years, we have been developing efficient software frameworks designed to simulate non-equilibrium chemical reaction dynamics. These methods utilize an MPI-parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within commonly used molecular dynamics packages, including both CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to electronic structure theory results (including explicitly correlated coupled cluster theory), we are able to build reactive potential energy surfaces whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. These methods have found application in atomistic studies of fundamental chemical reaction dynamics occurring in liquids, and have shed light on a number of interesting chemical phenomena, including: (a) vibrational energy deposition in typical organic solvents; (b) ultrafast energy flow and transient spectroscopy in the immediate aftermath of a chemical reaction, and © the interplay between microsolvation dynamics and chemical reaction dynamics. [1-5]
In this talk, I will briefly outline some of the recent applications that we have tackled using this framework. I will also provide a guided demonstration of how to use the MS-EVB enabled version of TINKER which we have been developing. I will walk the audience through a short example, showing how to compile the MPI-parallelized version of TINKER, and then set up and simulate a simple chemical reaction.
[1] Dunning et al., Science, 347, 530 (2015).
[2] Glowacki et al., J Chem. Phys., 143, 044120 (2015)
[3] Carpenter et al., Phys. Chem. Chem. Phys., 17, 8372 (2015).
[4] Glowacki et al., Nature Chemistry, 3, 850 (2011).
[5] Glowacki et al., J Chem. Phys., 134, 214508 (2011)
- 15. H. Loeffler: Automating workflows: FESetup for Alchemical Free Energy Simulations. (odp, webm1, webm2)
Abstract писал(а):The Free Energy is certainly one of the most important physical quantities because it can help to understand fundamental processes in nature. Various methods have been devised to estimate this quantity by means of computational techniques. Among those is the pertubative or “alchemical” free energy method. The method is based on a rigorous physical model and thus promises, in principle, accurate results. In practice, however, the method can be difficult to use and manual setup rather tedious.
In this lecture, I will talk about automating workflows, in general, and how this can be used to set up relative alchemical free energy simulations for a large number of small organic ligand molecules. FESetup[1] is a tool that assists in automating these steps as much as possible through a simple input file. The aim of the software is to minimise the human bottleneck by helping the researcher to focus more on scientific problems and much less on the intricacies of a particular software. The lecture will explain the concepts behind the software.
FESetup currently supports relative free energy simulations with AMBER, Gromacs and Sire[2]. Supported force fields are all modern AMBER type force fields including GAFF for the ligand. The ligand charge model is currently AM1/BCC. Beyond alchemical free energy simulations, FESetup also implements an abstract MD engine to ease the setup (“equilibration”) of general MD simulations. Supported MD engines are Amber, Gromacs, NAMD and DL–POLY. A complete, ready–to–run package of the FESetup code is available via [1]. FESetup is developed as part of the software support project effort within the Collaborative Computational Project for Biomolecular
Simulation (CCPBioSim) [3].
[1] http://www.hecbiosim.ac.uk/fesetup
[2] http://www.siremol.org
[3] http://www.ccpbiosim.ac.uk
- 16. C. Woods: How Who is the What, Where and Why of Scientific Software Development. (webm)
Приятного просмотра.Abstract писал(а):Developing successful scientific software is a challenging but extremely important task for many computational modellers. Successful scientific software has to satisfy four opposing requirements;
it has to be trustably correct, calculating the right result without error;
it has to be very flexible, in recognition that it is to be used as part of an ongoing research project, and so its requirements and underlying equations and assumptions are subject to change;
it has to be have high performance, and be able to efficiently compute the result on a wide variety of computer hardware, and
most importantly, the software has to be sustainable, i.e. the software can be sustained by a team of developers over many years, and does not die or disappear when the original developer moves on to another research or industrial position.
Balancing correctness, flexibility and performance while delivering sustainable, well-engineered scientific software is extremely difficult, particularly as scientific software developers rarely have formal training in programming or computer science. More significantly, the academic rewards for developing such software are small, and the time available to researchers for software development is negligible compared to that devoted to active research, or grant/paper writing.
In this talk I will present techniques that can help overcome these challenges. I will talk about how sustainability can be added to your workflow, how software can be designed to balance correctness, flexibility and performance, and how new initiatives, such as Research Software Engineering, are providing the personnel and career pathways to support scientific software development.
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PPS
Материалы предыдущего года в "свободном плавании":Зимняя школа конференция 2015. Материалы.