pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin.

A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH. It relies on the existence of a protein structure, the prediction of titratable amino-acid pK values and a very limited set of parameters. Applied to the case of the photochromic Anabaena sensory rhodopsin protein, the model succeeds in reproducing qualitatively the reported experimental data, confirming the importance of aspartic acid 217 in the observed blue shift in the λ of ASR at neutral pH.

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm.

Influence of Alkoxy Groups on the Photoinduced Dynamics of Organic Molecules Exemplified on Alkyl Vinyl Ethers.

A series of different alkyl vinyl ethers is investigated to decipher the possible reaction channels upon photoexcitation to the π3s-Rydberg and the ππ*-valence state at 200 nm using time-resolved photoelectron spectroscopy and on-the-fly time-dependent density functional theory dynamics simulations. The results indicate two possible relaxation pathways: (1) a radiationless decay through the ππ*-state back to the ground state via torsion of the C═C double bond, in accordance with the dynamics found in ethylene; and (2) a fast dissociation of the C-O bond between the alkyl and the vinoxy group in the πσ*-state. The latter state can be accessed only after excitation to the π3s-Rydberg state (quantum yield of ∼50% according to the dynamics simulations).

Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation.

A method is proposed to easily reduce the number of energy evaluations required to compute numerical gradients when constraints are imposed on the system, especially in connection with rigid fragment optimization. The method is based on the separation of the coordinate space into a constrained and an unconstrained space, and the numerical differentiation is done exclusively in the unconstrained space. The decrease in the number of energy calculations can be very important if the system is significantly constrained.