Arnfinn Hykkerud Steindal

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.

Excitation Energies in Solution: The Fully Polarizable QM/MM/PCM Method

We present the theory and an implementation of the combined quantum mechanics/molecular mechanics/polarizable dielectric continuum (QM/MM/PCM) method. This is a fully polarizable layered model designed for effective inclusion of a medium in a quantum-mechanical calculation. The short-range part of the solvent electrostatic potential is described by an atomistic model while the long-range part of this potential is described by a dielectric continuum. The QM/MM/PCM method has been implemented in combination with QM linear response techniques allowing for the assessment of, e.g., vertical electronic excitation energies and linear dipole-dipole polarizabilities, in all cases using a nonequilibrium formulation of the environmental response. The model is general, but is here implemented for the case of density functional theory. Numerical examples are given for solvatochromic shifts relating to a set of organic molecules in aqueous solution. We find in general the QM/MM/PCM interface to exhibit a faster convergence with respect to the system size as compared to the use of QM/MM only.

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.

Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore.

We present a detailed study of the protein environmental effects on the one- and two-photon absorption (1PA and 2PA, respectively) properties of the S0-S1 transition in the DsRed protein using the polarizable embedding density functional theory formalism. We find that steric factors and chromophore-protein interactions act in concert to enhance the 2PA activity inside the protein while adversely blue-shifting the 1PA maximum. A two-state model reveals that the 2PA intensity gain is primarily governed by the increased change in the permanent dipole moment between the ground and the excited states acquired inside the protein. Our results indicate that this mainly is attributable to counter-directional contributions stemming from Lys163 and the conserved Arg95 with the former additionally identified as a key residue in the color tuning mechanism. The results provide new insight into the tuning mechanism of DsRed and suggest a possible strategy for simultaneous improvement of its 1PA and 2PA properties.

Development of different human skin colors: A review highlighting photobiological and photobiophysical aspects

Skin color has changed during human evolution. These changes may result from adaptations to solar ultraviolet radiation (protection of sweat glands, sunburn, skin cancer, vitamin D deficiency, defence against microorganisms, etc.), and/or sexual selection. Migration to areas with high levels of UV is associated with skin darkening, while migration to areas with low levels has led to skin lightening. However, other factors may have played roles. Temperature and food have probably been secondary determinants: heat exchange with the environment is dependent on ambient temperature, and a high intake of food rich in vitamin D allows a dark skin color to persist even at latitudes of low UV levels, as exemplified by Inuits living at high latitudes. Future studies of human migration will show if skin lightening is a faster process and has a higher evolutionary impact than skin darkening. Maybe due to that some American Indians have kept a relatively light skin although they live under the equator. The following hypotheses for skin darkening are reviewed: shielding of sweat glands and blood vessels in the skin, protection against skin cancer and overproduction of vitamin D, camouflage, adaptation to different ambient temperatures, defense against microorganisms, protection against folate photodestruction. Hypotheses for skin lightening are: sexual selection, adaptation to cold climates, enhancement of vitamin D photoproduction, and changing food habits leading to lower intake of vitamin D. The genetical processes behind some of the changes of skin color will be also briefly reviewed.

Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules

A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.

Density Functional Restricted-Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution

A density functional restricted-unrestricted approach, capable of evaluating hyperfine coupling constants with the inclusion of spin polarization effects in a spin-restricted Kohn-Sham method, has been extended to incorporate environmental effects. This is accomplished by means of a hybrid quantum mechanics/molecular mechanics formalism which allows for a granular representation of the polarization and electrostatic interactions with the classically described medium. By this technique, it is possible to trace the physical origin of hyperfine coupling constants in terms of spin polarization and spin density contributions and disentangle the dependence of these contributions on molecular geometry and solvent environment, something that increases the prospects for optimal design of spin labels for particular applications. A demonstration is given for the nitrogen isotropic hyperfine coupling constant in di-tert-butyl nitroxide solvated in water. The results indicate that the direct spin density contribution is about 5 times smaller than the spin polarization contribution to the nitrogen isotropic hyperfine coupling constant and that the latter contribution is solely responsible for the solvent shift of the constant. The developed approach is found capable of achieving satisfactory accuracy in prediction of the hyperfine coupling constants of solvated di-tert-butyl nitroxide and other similar nitroxides without the inclusion of solvent molecules in the quantum region provided polarizable force fields are used for the description of these molecules.

Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties

We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use of averaged parameters reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. The results are promising for the development of general embedding parameters for biomolecules, where the reduction in computational cost can be considerable.

Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems.

We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA) properties can be studied by evaluating single residues of the response functions. The PE approach includes mutual polarization effects between the quantum and classical parts of the system through induced dipoles that are determined self-consistently with respect to the electronic density. The applicability of our approach is demonstrated by calculating MPA strengths up to four-photon absorption for the green fluorescent protein. We show how the size of the quantum region, as well as the treatment of the border between the quantum and classical regions, is crucial in order to obtain reliable MPA predictions.

Electronic circular dichroism of fluorescent proteins: a computational study.

The electronic circular dichroism (ECD) properties of the green fluorescent protein and other fluorescent proteins have been calculated with density functional theory. The influence of different embedding models on the ECD signal of the chromophore has been investigated by modeling the protein environment by the polarizable continuum model (QM/PCM), by the polarizable embedding model (PE-QM/MM), by treating the minimal environment quantum mechanically at the same footing as the chromophore (QM/QM), and by adding the remaining part of the protein by means of PCM (QM/QM/PCM). The rotatory strength is found to be more sensitive than the oscillatory strength to changes in the geometry of the chromophore and its surroundings and to the type of embedding model used. In general, explicit embedding of the surrounding protein (PE-QM/MM or QM/QM) induces an increase in the rotatory strength of the chromophore. Explicit inclusion of the whole protein through polarizable embedding is found to be an affordable embedding model that gives the correct sign of the rotatory strength for all fluorescent proteins. PCM is useful as a first approximation to protein environment effects, but as a rule seems to underestimate the rotatory strength.