We have developed automatic methods to calculate multipoles and anisotropic polarizabilities for all atoms and bond centers in a protein and to include such a model in the calculation of electronic properties at any level of quantum mechanical theory. This approach is applied for the calculation of the electronic spectra of retinal in rhodopsin at the CASPT2//CASSCF level (second-order multiconfigurational perturbation theory) for the wild-type protein, as well as two mutants and isorhodopsin in QM/MM structures based on two crystal structures. We also perform a detailed investigation of the importance and distance dependence of the multipoles and the polarizabilities for both the absolute and the relative absorption energies. It is shown that the model of the surrounding protein strongly influences the spectrum and that different models give widely different results. For example, the Amber 1994 and 2003 force fields give excitation energies that differ by up to 16 kJ/mol. For accurate excitation energies, multipoles up to quadrupoles and anisotropic polarizabilities are needed. However, interactions with residues more than 10 Å from the chromophore can be treated with a standard polarizable force field without any dipoles or quadrupoles.

How are hydrogen bonds modified by metal binding?Husberg, Charlotte; Ryde, Ulf General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. AbstractWe have used density-functional theory calculations to investigate how the hydrogenbond strength is modified when a ligand is bound to a metal, using over 60 model systems involving six metals and eight ligands frequently encountered in metalloproteins. We study how the hydrogen-bond geometry and energy vary with the nature of metal, the oxidation state, the coordination number, the ligand involved in the hydrogen bond, other first-sphere ligands, and different hydrogen-bond probe molecules. The results show that in general, the hydrogen-bond strength is increased for neutral ligands and decreased for negatively charged ligands. The size of the effect is mainly determined by the net charge of the metal complex and all effects are typically decreased when the model is solvated. In water solution, the hydrogen-bond strength can increase by up to 37 kJ/mol for neutral ligands, and that of negatively charged ligands can both increase (for complexes with a negative net charge) or decrease (for positively charged complexes). If the net charge of the complex does not change, there is normally little difference between different metals or different types of complexes. The only exception is observed for sulphur-containing ligands (Met and Cys) and if the ligand is redox active (e.g. high-valent Fe-O complexes).Key Words: hydrogen bonds, metalloproteins, quantum-mechanical calculations, densityfunctional theory, dispersion correction, solvation. 2 IntroductionHydrogen bonds play an important role in all types of biochemical systems, strongly affecting catalysis, ligand binding, and enzyme function, for example [1]. They have been thoroughly studied by a variety of experimental and theoretical methods [2,3,4,5,6,7,8,9,10,11,12,13,14,15] so that the strengths of the common hydrogen bonds in biological systems are accurately known.However, it is well-known that metal sites affect the properties of bound ligands. For example, the pK a value of water in aqueous metal complexes is reduced from 15.7 for bulk water, to 12.8 for Ca 2+ and to 2.2 for Fe 3+ [16]. Therefore, it is also likely that metal ions also change the strength and structure of hydrogen bonds inv...