Energy extrapolation schemes for adaptive multi-scale molecular dynamics simulations

International audienceWe present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc

Bias-exchange metadynamics applied to the study of chemical reactivity

International audienceWe show how the combination of Bias Exchange metadynamics (BE) with Car-Parrinello molecular dynamics (CPMD) can lead to vast improvements in the study of chemical reactions. Bias Exchange metadynamics is a recently introduced methodology that combines replica exchange techniques with the metadynamics approach. It allows fast parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. The value of the method was previously demonstrated for the folding of a Triptophane cage miniprotein on the classical potential energy surface. As a test case for the DFT implementation, we investigated the competitive SN2 reaction of CH3Cl with Cl− and Br−. The results illustrate three important advantages of the method. (1) Fast and complete sampling of configuration space occurs in each replica. (2) A significant speed-up can be observed in the convergence of the free energy profiles, compared with regular metadynamics. (3) The best conformational distributions are successfully transferred from one replica to the others

Effect of temperature on the adsorption of short alkanes in the zeolite ssz-13-adapting adsorption isotherms to microporous materials

Understanding the diffusion and adsorption of hydrocarbons in zeolites is a highly important topic in the field of catalysis in micro-and mesoporous materials. Especially, the properties of alkanes in zeolites have been studied extensively. A theoretical description of these processes is challenging, because two interactions are involved: the alkane physisorbs to the zeolite wall and chemisorbs weakly to the active centers. At room temperature, the alkane remains physisorbed almost all the time, but the chemical bond to the active sites is regularly broken. In this work, we study this behavior using ab initio molecular dynamics simulations for the adsorption of methane, ethane, and propane in SSZ-13, the zeolite with the smallest unit cell, at temperatures of 250, 275, 325, and 350 K. We find a temperature dependence of the adsorption energy and the probability of the alkane to be close to the active site, which corresponds to chemisorption. We derive a temperature-dependent expression for these probabilities or active site coverages, which have the energy difference between physisorbed and chemisorbed state as the main variable. The methodology derived in this work will be highly useful in correlating static electronic structure calculations to finite temperature coverages, which, following the Sabatier principle, is a key step to understand the performance of catalysts under reaction conditions and a prerequisite to computationally design such materials

Multiscale Modeling of Chemistry in Water: Are We There Yet?

International audienceThis paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV–vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions

Proton transfer in aqueous solution: Exploring the boundaries of adaptive QM/MM

International audienceIn this chapter, we review the current state-of-the-art in quantum mechanical / molecular mechanical (QM/MM) simulations of reactions in aqueous solutions, and we dis- cuss how proton transfer poses new challenges for its successful application. In the QM/MM description of an aqueous reaction, solvent molecules in the QM region are diffusive and need to be either constrained within the region, or their description (QM versus MM) needs to be updated as they diffuse away. The latter approach is known as adaptive QM/MM. We review several constrained and adaptive QM/MM methods, and classify them in a consis- tent manner. Most of the adaptive methods employ a transition region, where every solvent molecule can continuously change their from QM to MM (and vice versa), temporarily becoming partially QM and partially MM. Where a conventional QM/MM scheme par- titions a system into a set of QM and a set of MM atoms, an adaptive method employs multiple QM/MM partitions, to describe the fractional QM character. We distinguish two classes of adaptive methods: Discontinuous and continuous. The former methods use at most two QM/MM partitions, and cannot completely avoid discontinuities in the energy and the forces. The more recent continuous adaptive methods employ a larger number of QM/MM partitions for a given configuration. Comparing the performance of the methods for the description of solution chemistry, we find that in certain cases the low-cost con- strained methods are sufficiently accurate. For more demanding purposes, the continuous adaptive schemes provide a good balance between dynamical and structural accuracy. Fi- nally, we challenge the adaptive approach by applying it to the difficult topic of proton transfer and diffusion. We present new results, using a well-behaved continuous adaptive method (DAS) to describe an alkaline aqueous solution of methanol. Comparison with fully QM and fully MM simulations shows that the main discrepancies are rooted in the presence of a QM/MM boundary, and not in the adaptive scheme. An anomalous confinement of the hydroxide ion to the QM part of the system stems from the mismatch between QM and MM potentials, which affects the free diffusion of the ion. We also observe an increased water density inside the QM region, which originates from the different chemical potentials of the QM and MM water molecules. The high density results in locally enhanced proton transfer rates

Protonated thiophene-based oligomers as formed within zeolites : understanding their electron delocalization and aromaticity

In an earlier work, protonated thiophene-based oligomers were identified inside ZSM-5 zeolites. The novel compounds exhibited π-π* absorption wavelengths deep within the visible region, earmarking them for possible use as chromophores in a variety of applications. In this computational study, we determine the factors that cause such low-energy transitions, and describe the electronic structure of these remarkable compounds. DFT calculations of conjugated thiophene-based oligomers with up to five monomer units reveal that the main absorption band of each protonated oligomer is strongly red-shifted compared to the unprotonated form. This effect is counterintuitive, since protonation is expected to diminish aromaticity, and thereby increase the HOMO-LUMO gap. We find that upon protonation the π-electrons remain delocalized over the entire π-conjugated molecule, but the positive charge is localized predominantly on the protonated side of the molecule. A possible explanation for this ground-state charge localization is the participation of the C-H bond in the π-system of the protonated ring, locally providing aromatic stabilization for the positive charge. The addition of the proton stabilizes all electronic orbitals, but due to the ground state π-electron distribution away from the added nucleus, the HOMO is stabilized less than the LUMO. The main absorption peak upon protonation corresponds to the charge transfer excitation involving the frontier orbitals, and the small band gap explains the observed red shift. Analogue calculations on thiophene within a ZSM-5 zeolite cluster model confirm the same trends upon protonation as observed in the non-interacting compounds. Understanding the electronic structure of these compounds is very relevant to correlate UV-Vis bands with acidic strength and possibly environment in zeolites and to improve their performance in catalytic and energy related applications

Insights into the activation of silica-supported metallocene olefin polymerization catalysts by methylaluminoxane

Metallocene-based olefin polymerization catalysts often require large excesses of co-catalyst for optimal catalyst activation. In this work, mechanistic insights into the activation of supported metallocenes by methylaluminoxane as co-catalyst are acquired. UV–vis diffuse reflectance (DR) spectroscopy of five metallocene catalysts with varying co-catalyst loading reveals the presence of different metallocene species on the surface of the catalyst particles. Deconvolution of the obtained spectra, in combination with an extensive TD–DFT study of UV–vis DR spectra of metallocene structures results in a proposed activation mechanism. We find that with increasing MAO loading, more AlMe2 +-bound metallocenes are observed with a shift towards the trimethylaluminum-stabilized cationic methylated metallocene compound. This shift can be directly correlated with a higher activity in the olefin polymerization reaction. Based on this finding, we propose a universal metallocene activation mechanism in which the cationic methylated metallocene is the active species. This species is formed through initial interaction with AlMe2 +, followed by ligand exchange with MAO and stabilized in complex with trimethylaluminum as a dormant species

Understanding Water-Zeolite Interactions: On the Accuracy of Density Functionals

Water is ubiquitous in zeolite catalysis, and electronic structure calculations play a crucial role in arriving at an atomistic understanding of water-zeolite interactions. However, a critical evaluation of the performance of different electronic structure methods in describing the interactions between water and zeolites is still missing. Here, we model the adsorption of one water molecule in all-silica chabazite (CHA) and of one and two water molecules in the acidic zeolite SSZ-13 using different electronic structure methods, which include 11 density functional theory (DFT)-based methods and two post Hartree-Fock (HF) methods, namely, the random phase approximation (RPA) and second-order Møller-Plesset (MP2) perturbation theory. We find that all DFT functionals lead to similar structures as long as water is strongly coordinated to the adsorption site, but adsorption energies vary in a range of 50 kJ/mol between the used methods. Subsequently, we use ab initio molecular dynamics calculations to show that all methods reproduce the experimentally observed hydrophobicity of purely siliceous zeolites. Comparing DFT energetics with RPA and MP2 calculations shows that PBE and revPBE-D3 adsorption energies show the best agreement with RPA, while BEEF-vdW agrees the best with MP2 results. At the same time, the performance of PBE functional without any dispersion correction is less consistent with respect to different adsorption sites (BAS, LAS, or the zeolite wall of all-silica CHA) and the BEEF-vdW functional fails to reproduce relative stabilities of the protonation sites. For the adsorption of two water molecules, most methods agree on the formation of a protonated water dimer, and only vdW-DF, vdW-DF2, and BEEF-vdW prefer the formation of a neutral complex. Based on these results, we suggest using the revPBE-D3 functional model water adsorption in purely siliceous or protonated zeolites since it can correctly capture covalent and dispersion interactions, is computationally efficient, correctly predicts the formation of a positively charged water dimer, and is able to closely reproduce adsorption energies calculated at the RPA or MP2 level of theory