Density functional theory (DFT) provides a formally exact framework for quantum embedding. The appearance of nonadditive kinetic energy contributions in this context poses significant challenges, but using optimized effective potential (OEP) methods, various groups have devised DFT-in-DFT methods that are equivalent to Kohn–Sham (KS) theory on the whole system. This being the case, we note that a very considerable simplification arises from doing KS theory instead. We then describe embedding schemes that enforce Pauli exclusion via a projection technique, completely avoiding numerically demanding OEP calculations. Illustrative applications are presented using DFT-in-DFT, wave-function-in-DFT, and wave-function-in-Hartree–Fock embedding, and using an embedded many-body expansion.

Projector-based embedding has recently emerged as a robust multiscale method for the calculation of various electronic molecular properties. We present the coupling of projector embedding with quantum mechanics/molecular mechanics modeling and apply it for the first time to an enzyme-catalyzed reaction. Using projector-based embedding, we combine coupled-cluster theory, density-functional theory (DFT), and molecular mechanics to compute energies for the proton abstraction from acetyl-coenzyme A by citrate synthase. By embedding correlated ab initio methods in DFT we eliminate functional sensitivity and obtain high-accuracy profiles in a procedure that is straightforward to apply.

The externally corrected coupled cluster approach with four-and five-body clusters from the CASSCF wave function J. Chem. Phys. 142, 094119 (2015) Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O(N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of S N 2 substitution of fluorine by chlorine in α-fluoroalkanes. C 2015 AIP Publishing LLC. [http://dx

The BigDFT project started in 2005 with the aim of testing the advantages of using a Daubechies wavelet basis set for Kohn-Sham density functional theory with pseudopotentials. This project led to the creation of the BigDFT code, which employs a computational approach with optimal features for exibility, performance and precision of the results. In particular, the employed formalism has enabled the implementation of an algorithm able to tackle DFT calculations of large systems, up to many thousands of atoms, with a computational eort which scales linearly with the number of atoms. In this work we recall some of the features that have been made possible by the peculiar properties of Daubechies wavelets. In particular, we focus our attention on the usage of DFT for large-scale systems. We show how the localised description of the KS problem, emerging from the features of the basis set, are helpful in providing a simplied description of large-scale electronic structure calculations. We provide some examples on how such simplied description can be employed, and we consider, among the case-studies, the SARS-CoV-2 main protease.

Using electrospray ion beam deposition, we collide a complex molecule Reichardt's Dye (C 41 H 30 NO + ) at low, hyperthermal translational energy (2 -50 eV) with a Cu(100) surface and image the outcome at single-molecule level by Scanning Tunneling Microscopy. We observe bond-selective reaction induced by the translational kinetic energy. The collision impulse compresses the molecule and bends specific bonds, prompting them to react selectively. This dynamics drives the system to seek thermally inaccessible reactive pathways, since the compression timescale (sub-ps) is much shorter than the thermalization timescale (ns), thereby yielding reaction products that are unobtainable thermally

Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine and serine and identify chemical state contributions to experimental spectra of crystalline amino acids. File list (3) download file view on ChemRxiv amino_paper.pdf (2.77 MiB) download file view on ChemRxiv amino_paper_SI.pdf (2.92 MiB) download file view on ChemRxiv amino_structures.zip (12.01 KiB)

In the past decade, developments of computational technology around density functional theory (DFT) calculations have considerably increased the system sizes which can be practically simulated. The advent of robust high performance computing algorithms which scale linearly with system size has unlocked numerous opportunities for researchers. This fact enables computational physicists and chemists to investigate systems of sizes which are comparable to systems routinely considered by experimentalists, leading to collaborations with a wide range of techniques and communities. This has important consequences for the investigation paradigms which should be applied to reduce the intrinsic complexity of quantum mechanical calculations of many thousand atoms. It becomes important to consider portions of the full system in the analysis, which have to be identified, analyzed, and employed as building‐blocks from which decomposed physico‐chemical observables can be derived. After introducing the state‐of‐the‐art in the large scale DFT community, we will illustrate the emerging research practices in this rapidly expanding field, and the knowledge gaps which need to be bridged to face the stimulating challenge of the simulation of increasingly realistic systems. This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Simulation Methods Structure and Mechanism > Computational Materials Science

We investigate the binding of the cobalt atom on small aromatic model systems as a proxy for interaction with graphene, using density functional theory, coupled-cluster theory, and combinations of them using projector-based quantum embedding. We set out in some detail the electronic structure of the cobalt atom alone, because some nuances of atomic structure appear to have been overlooked in previous studies. Two states of the complex in particular are studied: those formed from the a 4 F ground state of the atom; and from c 2 D, the lowest doublet state with configuration 3d 9 4s 0 . We highlight the difficulties in extracting reliable results from typical approximate density functionals, and demonstrate that embedding calculations using the coupled-cluster theory in an active subsystem greatly reduce functional dependence, and produce a picture more consistent with the available experimental information. Our results cast doubt on previous calculations that have predicted strong chemisorptive binding between graphene and the c 2 D state of cobalt.