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. Further, a module to run molecular dynamics simulations is added and two surface hopping algorithms are included to enable nonadiabatic calculations. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

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Ab initio CASPT2//CASSCF relaxation path computations are employed to determine the intrinsic (e.g., in vacuo) mechanism underlying the rise and decay of the luminescence of the anionic form of the green fluorescent protein (GFP) fluorophore. Production and decay of the fluorescent state occur via a two-mode reaction coordinate. Relaxation along the first (totally symmetric) mode leads to production of the fluorescent state that corresponds to a planar species. The second (out-of-plane) mode controls the fluorescent state decay and mainly corresponds to a barrierless twisting of the fluorophore phenyl moiety. While a "space-saving" hula-twist conical intersection decay channel is found to lie only 5 kcal mol(-1) above the fluorescent state, the direct involvement of a hula-twist deformation in the decay is not supported by our data. The above results indicate that the ultrafast fluorescence decay observed for the GFP chromophore in solution is likely to have an intrinsic origin. The possible effects of the GFP protein cavity on the fluorescence lifetime of the investigated chromophore model are discussed.

The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at Ϸ60-fs delay, initiates a space saving ''asynchronous bicycle-pedal or crankshaft'' motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy.photoisomerization ͉ rhodopsin ͉ vision T he visual pigment rhodopsin (Rh) (1, 2) is a G protein-coupled receptor containing a 11-cis retinal chromophore (PSB11) bounded to a lysine residue (Lys-296) via a protonated Schiff base linkage (see Fig. 1). While the biological activity of Rh is triggered by the light-induced 11-cis all-trans isomerization of PSB11, this reaction owes its efficiency (e.g., short time scale and high quantum yields) to the protein cavity (1). Recently, the mechanism of the isomerization of retinal in Rh has been investigated by using femtosecond-stimulated Raman spectroscopy (FSRS) (3). Kukura et al. (3) have reported on experimentally derived structures of photoRh and bathoRh, namely the first and second ground-state intermediates of the Rh photocycle.While such progress has provided information on the structural changes achieved 200 fs after light absorption, the faster structural changes prompting the excited-state decay of PSB11 (i.e., the central event of the isomerization mechanism) remain to be established. Indeed, it has been suggested that such decay may occur on a 60-fs time scale through fast hydrogen out-ofplane (HOOP) motion (3), whereas the traditional view points to a slower Ϸ150-fs decay driven by cis-trans isomerization motion (4). In principle, molecular dynamics simulations featuring a quantum chemical description of the chromophore can be used to address such issues. This fact was shown by Warshel (5) using semiempirical quantum chemistry to describe PSB11 and geometrical constraints to account for the protein environment. Later, Birge and Hubbard (6) reported a different semiempirical study of an explicit chromophore-counterion pair evolving along a single coordinate. While the first simulation of the retinal photoisomerization using a full atomic-level protein model (7) was reported for the related receptor bacterio-Rh (bR), attempts to simulate the PSB11 excited-state motion in a complete Rh model are more recent (8-10). On the other hand, a quantitative evaluation of the isomerization coordinate and time scale requires, as a prerequisite, an accurate excited-st...

Singlet fluorescence lifetimes of adenosine, cytidine, guanosine, and thymidine, determined by femtosecond pump-probe spectroscopy (Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2000, 122, 9348. Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370), show that the excited states produced by 263 nm light in these nucleosides decay in the subpicosecond range (290-720 fs). Ultrafast radiationless decay to the ground state greatly reduces the probability of photochemical damage. In this work we present a theoretical study of isolated cytosine, the chromophore of cytidine. The experimental lifetime of 720 fs indicates that there must be an ultrafast decay channel for this species. We have documented the possible decay channels and approximate energetics, using a valence-bond derived analysis to rationalize the structural details of the paths. The mechanism favored by our calculations and the experimental data involves (1) a two-mode decay coordinate composed of initial bond length inversion followed by internal vibrational energy redistribution (IVR) to populate a carbon pyramidalization mode, (2) a state switch between the pi,pi* and nO,pi* (excitation from oxygen lone pair) excited states, and (3) decay to the ground state through a conical intersention. A second decay path through the nN,pi* state (excitation from the nitrogen lone pair), with a higher barrier, involves out-of-plane bending of the amino substituent.

The minimum energy path for photoisomerization of the minimal retinal protonated Shiff base model tZt-penta-3,5-dieniminium cation (cis-C5H6NH2 +) is computed using MC−SCF and multireference Møller−Plesset methods. The results show that, upon excitation to the spectroscopic state, this molecule undergoes a barrierless relaxation toward a configuration where the excited and ground states are conically intersecting. The intersection point has a ∼80° twisted central double bond which provides a route for fully efficient nonadiabatic cis → trans isomerization. This mechanism suggests that cis-C5H6NH2 + provides a suitable “ab initio” model for rationalizing the observed “ultrafast” (sub-picosecond) isomerization dynamics of the retinal chromophore in rhodopsin. The detailed analysis of the computed reaction coordinate provides information on the changes in molecular structure and charge distribution along the isomerization path. It is shown that the initial excited state motion is dominated by stretching modes which result in an elongation of the central double bond of the molecule associated with the change in bond order in the excited state. Thus, the actual cis → trans isomerization motion is induced only after the bond stretching has been completed. It is also demonstrated that, along the excited state isomerization coordinate, the positive charge is progressively transferred from the -CHCHNH2 to the CH2CHCH- molecular fragment. Thus, at the intersection point, the charge is completely localized on the CH2CHCH- fragment. This result suggests that strategically placed counterions can greatly affect the rate, specificity, and quantum yield of the photoisomerization.

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

In this article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational