In collaboration with Alec Wodtke (Max Planck Göttingen) and Tom Miller (Caltech), this work describes scattering experiments supported by simulations, and is featured on the cover of Science. The research reveals an ultrafast energy dissipation mechanism for atoms hitting an on-top site, in which up to 1–2 eV of kinetic energy is lost from the nascent C–H bond in as little as 10 fs, primarily through in-plane motion of the graphene carbon atoms.
Embedded mean-field theory implemented in entos was used to run enough ab initio molecular dynamics to reliably parameterize a reactive empirical bond order potential, which was in turn used for the bulk of the simulation of scattering events for this study.
Imaging covalent bond formation by H atom scattering from graphene
There are about four or five distinct ingredients used in modern density functionals:
- integrals of functions of the density and its gradients (GGAs, etc)
- inclusion of the kinetic energy density in such expressions (meta-GGAs)
- a fraction of exact Hartree–Fock exchange (or a length-scale-screened variant)
- a contribution from a wavefunction-based correlation method like MP2 or RPA
Now there is another:
Tim Wiles and F R Manby, ‘Wavefunction-like Correlation Model for Use in Hybrid Density Functionals’, J. Chem. Theory Comput., Article ASAP, DOI: 10.1021/acs.jctc.8b00337.
In this paper we introduce the UW12 correlation functional:
- an explicit functional of occupied orbitals (i.e. a functional of the 1-RDM)
- an F12-like model of dynamic electron correlation
- can be self-consistently optimized in a straightforward way
- most of the complicated stuff handled through familiar DFT quadrature
- no double-summation over virtual orbitals, so fast basis-set convergence
This functional can be used as a viable (and hybrid) alternative to use of MP2 in double-hybrid functionals, as we demonstrate in this paper. Our hybrid XCH-BLYP-UW12 functional has only one parameter, and is competitive with more highly parameterised double hybrids for reaction barrier test sets.
If you don’t have access and want to read the paper, just email Fred.
Congratulations to Tim for publishing this work!
Felix’s work on Markovianity in photosynthetic energy transport has been published: Felix Vaughan, N Linden and F R Manby, J. Chem. Phys. 146, 124113 (2017); http://dx.doi.org/10.1063/1.4978568.
Modelling the interaction between excitons and the surrounding environment is a non-trivial problem. Many interesting insights about excitonic energy transfer have made use of a Markovian or “memoryless” approximation to this interaction. In this paper we assess the applicability of this approximation by employing a new metric of non-Markovianity.
We find that for smooth spectral densities the Markovian approximation works well provided that a precise change to the system Hamiltonian is made, which for the dimer system studied corresponds to an increase in the coupling strength between chromophores. We also find that discrete vibrational modes resonant with the eigenstates of the Hamiltonian induce the greatest degree of non-markovianity. Ultimately we conclude that to model exciton dynamics coupled to realistic spectral densities a Markovian approximation is not suitable.
Delocalization error in approximate DFT clearly manifests itself in homodimer cation systems (like H2+ or (H2O)2+), with GGA functionals typically leading to large energy errors and qualitatively incorrect structures. It also causes problems in a variety of other chemically important contexts.
Spurious delocalization of spin density in a small radical-cation water cluster.
We have found that the delocalization error in densities can cause major errors in WF-in-DFT embedding – these errors are not particular to the projector-based scheme we use,but simple expose a limitation of partitioning systems based on the electron density when that electron density is qualitatively flawed.
Following work from Kieron Burke, we have found the simple expedient of using Hartree-Fock densities in WF-in-DFT calculations really improves reliability in cases where there is a serious delocalization error, and doesn’t cause major problems (in the examples we have studied) when there is not a big delocalization error.
You can read about this work in a paper that has just appeared online: Pennifold et al., ‘Correcting density-driven errors in projection-based embedding’, J. Chem. Phys. 146, 084113 (2017); DOI: 10.1063/1.4974929.
Clem’s paper on the interpretation of pump-probe experiments on the purple-bacteria light-harvesting complex LHII is now in print in J Phys Chem B.
Through careful and extensive calculations involving molecular dynamics, time-dependent density functional theory, and quantum dynamics we have shown that the interpretation of anisotropy decay rates in terms of strength of coupling to a dissipative bath is not so easily justified. The reason is that static (or inhomogeneous) disorder itself produces anisotropy decay at about the experimentally observed rate.
The paper also contains an epic, paper-length appendix on how to compute such quantities for the circularly degenerate oscillator model.
C. Stross, M. W. Van der Kamp, T. A. A. Oliver, J. N. Harvey, N. Linden and F. R. Manby, “How Static Disorder Mimics Decoherence in Anisotropy Pump–Probe Experiments on Purple-Bacteria Light Harvesting Complexes”, J. Phys. Chem. B, 120, 11449-11463 (2016), DOI: 10.1021/acs.jpcb.6b09916
Interactions between Drude oscillators (two opposite charges, one fixed, one mobile, interacting by a spring) are almost always modelled in the dipole approximation. This is because the Hamiltonian for describing Drude oscillators in this way is quadratic in the creation/annihilation operators (or equivalently, is quadratic in position and momentum) and can therefore be diagonalized exactly through a normal-mode transformation.
Second-order perturbation theory for the interaction of two such oscillators produces the expected –C6 R–6 dispersion interaction. At short distances this diverges, and the exact interaction energy ceases to be defined at all.
Therefore people use screening functions to fix up the short range. How much are the screening functions fixing up the divergence, and how much are they just compensating for the use of the dipole interaction Hamiltonian? Now we can find out, because Mainak has calculated the (almost) exact binding energy between Drude oscillators with the full Coulomb interaction.
Quantum mechanics of Drude oscillators with full Coulomb interaction
M. Sadhukhan and F. R. Manby, Phys. Rev. B 94, 115106 (2016) 10.1103/PhysRevB.94.115106
Our paper A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase has appeared online in JCTC, and was one of the most highly downloaded papers soon after publication.
Citrate synthase active site and QM/MM reaction profiles computed with DFT and with CCSD(T)-in-DFT for various approximate exchange-correlation functionals.
The great thing about this is that by tuning in CCSD(T) for just a handful of reacting atoms, almost all of the dependence on the approximate exchange-correlation functional is eliminated.
The latest release of Molpro provides a range of new functionality, including methods developed in the Manby group
A key new addition is wavefunction-in-DFT embedding through the projector method with basis-set truncation. This enables straightforward embedding of practically any electronic structure method implemented in Molpro in a chemical environment modelled by DFT. Unlike many embedding methods of this kind
there are no issues with partitioning across covalent bonds.
We have performed many calculations using the combination CCSD(T)-in-DFT, with the expensive coupled-cluster calculation only on a few, chemically active atoms. The exciting opportunity here is that the method all but eliminates dependence on choice of exchange-correlation functional.
The research behind this functionality was carried out by Martina Stella, Simon Bennie and Rob Pennifold in the Manby group; and by Jason Goodpaster and Taylor Barnes in Tom Miller’s group at Caltech.
Distinguishable cluster theory
Distinguishable cluster theory with singles and doubles (DCSD) is a simple modification of CCSD, but with remarkable properties, including the ability to dissociate molecules correctly even with a closed-shell reference state.
The method was developed by Daniel Kats while he was a DFG-funded postdoc in the Manby group. There is much discussion about what exactly this approximation means (but see Daniel’s interesting paper about a screened Coulomb derivation). Whatever it turns out to mean, DCSD is already a useful tool and a powerful addition to the set of available methods. Now in Molpro running it is as simple as replacing ccsd with dcsd in the input (and the computational cost is the same as CCSD). Gradients as well as F12, orbital-optimized and Brueckner variants are available.
Thanks to the efforts of Dr James Womack, we now have Intception, an incredibly powerful framework for automatic implementation of Gaussian integrals from equations that define the recurrence relations.
More on this later – but feel free to look at the information online and use Intception to generate integrals for your project.
Intception is open source, but as with a compiler, you can generate inputs and outputs under any licensing model you like.