Jógvan Magnus Haugaard Olsen

The Dalton quantum chemistry program system

Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic‐structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge‐origin‐invariant manner. Frequency‐dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one‐, two‐, and three‐photon processes. Environmental effects may be included using various dielectric‐medium and quantum‐mechanics/molecular‐mechanics models. Large molecules may be studied using linear‐scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

Molecular Properties through Polarizable Embedding

Abstract We review the theory related to the calculation of electric and magnetic molecular properties through polarizable embedding. In particular, we derive the expressions for the response functions up to the level of cubic response within the density functional theory-based polarizable embedding (PE-DFT) formalism. In addition, we discuss some illustrative applications related to the calculation of nuclear magnetic resonance parameters, nonlinear optical properties, and electronic excited states in solution.

A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein

We present for the first time a QM/MM study of the one- and two-photon absorption spectra of the GFP chromophore embedded in the full protein environment described by an advanced quantum mechanically derived polarizable force field. The calculations are performed on a crystal structure of the green fluorescent protein (GFP) using the polarizable embedding density functional theory (PE-DFT) scheme. The importance of treating the protein environment explicitly with a polarizable force field and higher-order multipoles is demonstrated, as well as the importance of including water molecules close to the chromophore in the protein barrel. For the most advanced description we achieve good agreement with experimental findings, with a peak at 405 nm for the neutral and a peak at 475 nm for the anionic form of the GFP chromophore. The presence of a dark OPA state, as suggested by other studies to explain the discrepancies between OPA and TPA spectra, is not supported by our calculations.

Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L‐tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L‐tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re‐optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L‐tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.

Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants

Optogenetics is by now a well-established field within neuroscience where neuro-response is controlled at the molecular level using the photochemical properties of channelrhodopsin (ChR). In this study the recently published X-ray structure of retinal inside the ChR binding pocket serves as the basis for conducting high-level polarizable embedding quantum mechanical/molecular mechanical (QM/MM) mutation studies with the aim of providing insight into the tuning mechanisms of this remarkable protein. The levels of theory applied are the recently developed PERI-CC2 and PE-DFT approaches. Their computational efficiency makes it possible to rapidly carry out a large number of spectral calculations. This is exploited to construct in silico mutated ChR variants which are characterized in terms of the location of the relevant excitation energy and the magnitude of the two-photon absorption cross section. In turn, this allows us to pinpoint the amino acids that have the largest electrostatic effect on the studied excited state properties. We show that a single/double site mutation strategy in ChR does not perturb the electronic properties of retinal to a degree that satisfies the experimental demand for a significant red-shift. With respect to non-linear absorption we conjecture that the recently synthesized ChETA variant possesses an even larger two-photon cross section than the C1C2 variant and it is thus an ideal candidate for further studies on the two-photon activation of ChR.

Excited states in large molecular systems through polarizable embedding

In this perspective, we provide an overview of recent work within the polarizable embedding scheme to describe properties of molecules in realistic environments of increasing complexity. After an outline of the theoretical basis for the polarizable embedding model, we discuss the importance of using an accurate embedding potential, and how this may be used to significantly reduce the size of the part of the system treated using quantum mechanics without compromising the accuracy of the final results. Furthermore, we discuss the calculation of local electronic excited states based on response theory. We finally discuss aspects related to two recent extensions of the model (i) effective external field and (ii) polarizable density embedding emphasizing their importance for efficient yet accurate description of excited-state properties in complex environments.

Relativistic Polarizable Embedding

Most chemistry, including chemistry where relativistic effects are important, occurs in an environment, and in many cases, this environment has a significant effect on the chemistry. In nonrelativistic quantum chemistry, a lot of progress has been achieved with respect to including environments such as a solvent or protein in the calculations, and now is the time to extend the possibilities for also doing this in relativistic quantum chemistry. The polarizable embedding (PE) model efficiently incorporates electrostatic effects of the environment by describing it as a collection of localized electric multipoles and polarizabilities obtained through quantum chemical calculations. In this article, we present the theory and implementation of four- and exact two-component Hamiltonians within a PE framework. We denote the methods the PE-4c-DFT and PE-X2C-DFT models. The models include a linear response formalism to calculate time-dependent (TD) properties: PE-TD-4c-DFT and PE-TD-X2C-DFT. With this first implementation, we calculate the PE-TD-4c-PBE0 excitation energies of the TcO4- and ReO4- ions in an explicit water solvent. This initial investigation focuses on the relative size of relativistic and solvent contributions to the excitation energies. The solvent effect is divided into an indirect solvent effect due to the structural perturbation of the XO4- ion and a direct electrostatic effect. The relativistic effects as well as both types of solvent effects are found to contribute to a shift in the excitation energies, but they do so to different extents depending on the ion and the electronic transition in question.

Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

Full-protein nuclear magnetic resonance (NMR) shielding constants based on ab initio calculations are desirable, because they can assist in elucidating protein structures from NMR experiments. In this work, we present NMR shielding constants computed using a new automated fragmentation (J. Phys. Chem. B 2009, 113, 10380-10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be to successfully compute 13C NMR shielding constants that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we can obtain a representative subset of snapshots that gives the smallest predicted error, compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3.

A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile

QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear birefringences Kerr, Cotton-Mouton, and Jones, as shown by acetonitrile in the gas and pure liquid phases. The relevant first-order properties as well as linear, quadratic, and cubic frequency-dependent response functions were computed using time-dependent Kohn-Sham density-functional theory with use of the standard CAM-B3LYP functional. In the liquid phase, a series of room temperature (293.15 K) molecular dynamics snapshots were selected, for which averaged values of the observables were obtained at an optical wavelength of 632.8 nm. The birefringences were computed for electric and magnetic induction fields corresponding to the laboratory setup previously employed by T. Roth and G. L. J. A. Rikken in Phys. Rev. Lett., 2000, 85, 4478. Under these conditions, acetonitrile is shown to exhibit a weak Jones response-in fact roughly 6.5 times smaller than the limit of detection of the apparatus employed in the measurements mentioned above. A comparison is made with the corresponding gas-phase results and an assessment is made of the index of measurability, estimating the degree of overlap of the three birefringences in actual measurements. For acetonitrile, it is shown that this index is a factor of 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively-two compounds reported in Phys. Rev. Lett., 2000, 85, 4478 to exhibit a strong Jones signal.

Parallelization of the polarizable embedding scheme for higher-order response functions

We present a parallel implementation of the Polarizable Embedding (PE) method, an advanced quantum mechanics/molecular mechanics (QM/MM) approach, for Hartree–Fock (PE-HF) and density functional theory (PE-DFT). The parallelization includes calculations of energies and linear, quadratic, and cubic response functions. The couplings to the QM system due to the polarizable embedding potential have been implemented using a master/slave approach. The implementation shows good scaling behaviour, demonstrated through calculations on a small (a water molecule in a bulk of water molecules) and a larger system (Green Fluorescent Protein (GFP)).