Characterization of excited states in time-dependent density functional theory using localized molecular orbitals.

Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an adequate basis for the treatment of excited states, a chemically meaningful identification of the different excited-state processes is difficult within such a delocalized orbital basis. In this work, starting from an initial set of supermolecular canonical molecular orbitals, we provide a simple one-step top-down embedding procedure for generating a set of orbitals, which are localized in terms of the supermolecule but delocalized over each subsystem composing the supermolecule. Using an orbital partitioning scheme based on such sets of localized orbitals, we further present a procedure for the construction of local excitations and charge-transfer states within the linear response framework of time-dependent density functional theory (TDDFT). This procedure provides direct access to approximate diabatic excitation energies and, under the Tamm-Dancoff approximation, also their corresponding electronic couplings-quantities that are of primary importance in modeling energy transfer processes in complex biological systems. Our approach is compared with a recently developed diabatization procedure based on subsystem TDDFT using projection operators, which leads to a similar set of working equations. Although both of these methods differ in the general localization strategies adopted and the type of basis functions (Slaters vs Gaussians) employed, an overall decent agreement is obtained.

Towards the description of charge transfer states in solubilised LHCII using subsystem DFT.

Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.

Comparing the nature of quantum plasmonic excitations for closely spaced silver and gold dimers.

In the new field of quantum plasmonics, plasmonic excitations of silver and gold nanoparticles are utilized to manipulate and control light-matter interactions at the nanoscale. While quantum plasmons can be described with atomistic detail using Time-Dependent Density Functional Theory (DFT), such studies are computationally challenging due to the size of the nanoparticles. An efficient alternative is to employ DFT without approximations only for the relatively fast ground state calculations and use tight-binding approximations in the demanding linear response calculations. In this work, we use this approach to investigate the nature of plasmonic excitations under the variation of the separation distance between two nanoparticles. We thereby provide complementary characterizations of these excitations in terms of Kohn-Sham single-orbital transitions, intrinsic localized molecular fragment orbitals, scaling of the electron-electron interactions, and probability of electron tunneling between monomers.

Understanding the Relation between Structural and Spectral Properties of Light-Harvesting Complex II.

Light-harvesting complex II (LHCII) is a pigment-protein complex present in higher plants and green algae. LHCII represents the main site of light absorption, and its role is to transfer the excitation energy toward the photosynthetic reaction centers, where primary energy conversion reactions take place. The optical properties of LHCII are known to depend on protein conformation. However, the relation between the structural and spectroscopic properties of the pigments is not fully understood yet. In this respect, previous classical molecular dynamics simulations of LHCII in a model membrane [Sci. Rep. 2015, 5, 1-10] have shown that the configuration and excitonic coupling of a chlorophyll (Chl) dimer functioning as the main terminal emitter of the complex are particularly sensitive to conformational changes. Here, we use quantum chemistry calculations to investigate in greater detail the effect of pigment-pigment interactions on the excited-state landscape. While most previous studies have used a local picture in which electrons are localized on single pigments, here we achieve a more accurate description of the Chl dimer by adopting a supramolecular picture where time-dependent density functional theory is applied to the whole system at once. Our results show that specific dimer configurations characterized by shorter inter-pigment distances can result in a sizable intensity decrease (up to 36%) of the Chl absorption bands in the visible spectral region. Such a decrease can be predicted only when accounting for Chl-Chl charge-transfer excitations, which is possible using the above-mentioned supramolecular approach. The charge-transfer character of the excitations is quantified by two types of analyses: one focusing on the composition of the excitations and the other directly on the observable total absorption intensities.

Generalization of Intrinsic Orbitals to Kramers-Paired Quaternion Spinors, Molecular Fragments, and Valence Virtual Spinors.

Localization of molecular orbitals finds its importance in the representation of chemical bonding (and antibonding) and in the local correlation treatments beyond mean-field approximation. In this paper, we generalize the intrinsic atomic and bonding orbitals [G. Knizia, J. Chem. Theory Comput. 2013, 9, 11, 4834-4843] to relativistic applications using complex and quaternion spinors, as well as to molecular fragments instead of atomic fragments only. By performing a singular value decomposition, we show how localized valence virtual orbitals can be expressed on this intrinsic minimal basis. We demonstrate our method on systems of increasing complexity, starting from simple cases such as benzene, acrylic acid, and ferrocene molecules, and then demonstrate the use of molecular fragments and inclusion of relativistic effects for complexes containing heavy elements such as tellurium, iridium, and astatine. The aforementioned scheme is implemented into a standalone program interfaced with several different quantum chemistry packages.

Theoretical Investigations on the Mechanistic Aspects of O2 Activation by a Biomimetic Dinitrosyl Iron Complex.

Though dinitrosyl-iron complexes (DNICs) are largely believed to act as NO carriers, several experiments on model DNICs have suggested that they can also act as nitrating agents in presence of dioxygen. Oxygen activation by DNICs has been implicated as a possible route for protein tyrosine nitration (PTN), which leads to neurodegenerative disorders. Herein using static and dynamic theoretical techniques we unravel a previously unknown dual state mechanistic paradigm for dioxygen activation of a biomimetic nitrating DNIC complex leading to phenolic nitration. Our computations reveal that the model DNIC, the ground electronic state of which is singlet, has a low-lying triplet state and an inherent singlet-triplet spin-crossover of DNICs can be triggered by fluxional changes in the bite angle of the two NO ligands. The presence of a low-lying triplet state in the DNIC affords an avenue for O2 activation other than a direct O2 activation by O2 -induced spin-crossover of the singlet ground state. These two low-lying channels facilitate the formation of a peroxynitrite species. Nitration of phenolic substrates is facilitated by the release of NO2 . The corresponding minimum energy crossing points (MECP) have been located. Along the reaction path, the changes in the electronic structure scenarios have been studied and interpreted. Our report also sheds light on the plausible mechanistic pathway of PTN by reactive species formed once O2 activation by DNICs have been achieved.