Ignacio Fdez. Galván

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

Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology

The ASEP/MD method has been employed for studying the solvent effect on the conformational equilibrium of the alanine dipeptide in water solution. MP2 and density functional theory (DFT) levels of theory were used and results were compared. While in gas phase cyclic structures showing intramolecular hydrogen bonds were found to be the most stable, the stability order is reversed in water solution. Intermolecular interaction with the solvent causes the predominance of extended structures as the stabilizing contacts dipeptide-water are favoured. Free-energy differences in solution were calculated and PPII, α(R), and C5 conformers were identified as the most stable at MP2 level. Experimental data from Raman and IR techniques show discrepancies about the relative abundance of α(R) y C5, our results support the Raman data. The DFT level of theory agrees with MP2 in the location and stability of PPII and α(R) forms but fails in the location of C5. MP2 results suggest the possibility of finding traces of C7eq conformer in water solution, in agreement with recent experiments.

Solvent Effects on the Radiative and Nonradiative Decay of a Model of the Rhodopsin Chromophore

The radiative and nonradiative decay of a model with five double bonds of the 11-cis-retinal protonated Schiff base was studied both in vacuum and in methanol solution using an extended version of the averaged solvent electrostatic potential from molecular dynamics data (ASEP/MD) method that allows the location of crossing points between free energy surfaces both in equilibrium and in frozen solvent conditions. The multireference quantum method CASSCF was used for the description of the states of interest, while the solvent structure was obtained from molecular dynamics simulations. Electron dynamic correlation corrections to the energy were included at CASPT2 level. Unlike in gas phase, where only two states seem to be implicated, in methanol solution, three states are necessary to describe the photoisomerization process. At the Franck-Condon point the S1 and S2 states are almost degenerate; consequently, the S1 surface has a region with an ionic character ((1)Bu-like) and another one with a covalent character ((2)Ag-like). Emission from the ionic minima is responsible for the low-frequency part of the fluorescence band, while emission from the covalent minima originates the high-frequency part. The ionic minimum is separated from the conical intersection yielding the all-trans isomer by an energy barrier that was estimated in 0.7 kcal/mol. The geometry of the optimized conical intersection was found at a torsion angle of the central double bond close to 90° both in vacuum and in methanol solution. This large torsion in addition to the accompanying charge displacements forces a strong solvent reorganization during the de-excitation process which slows down the photoisomerization kinetics in methanol with respect to the gas phase. Solvent fluctuations modulate the minima depth and the barrier height and could explain the multiexponential relaxation time observed in the experiments.

Retinal Models: Comparison of Electronic Absorption Spectra in the Gas Phase and in Methanol Solution

An accurate study on several models of the 11-cis-retinal protonated Schiff base (PSB) has been performed both in vacuo and in methanol solution. Condensed phase calculations have been carried out making use of the ASEP/MD method, which permits the employment of the same high-level ab initio calculations usually applied in gas phase studies as well as a detailed description of the solvent structure around the solute through molecular dynamics simulations of the complete system. The solute structure was completely optimized in vacuo and in solution at the CASSCF level and/or MP2 level, and the CASPT2 method was applied for the calculation of the vertical transition energies and solvent shift values. Our results reproduce and explain the main features of the experimental absorption spectra of the 11-cis-retinal PSB. Two well-resolved bands can be identified in vacuo (separated by roughly 1.0 eV), whereas only a single broad band is observed in solution. This fact is explained by the existence of two almost degenerate excited states in methanol. The inclusion of two methyl groups at the iminium end of the system permits the reproduction of the experimental solvent shift value.

Theoretical study of the preferential solvation effect on the solvatochromic shifts of para-nitroaniline.

The origin of the nonlinear solvatochromic shift of para-nitroaniline was investigated using a mean-field sequential QM/MM method, with electron transitions computed at the CASPT2/cc-pVDZ level. Experimental data shows that the solvatochromic shift has a strong nonlinear behavior in certain solvent mixtures. We studied the case of cyclohexane-triethylamine mixtures. The results are in good agreement with the experiments and correctly reproduce the nonlinear variation of the solvent shift. Preferential solvation is clearly observed, where the local solvent composition in the neighborhood of the solute is significantly different from the bulk. It is found that even at low triethylamine concentrations a strong hydrogen bond is formed between para-nitroaniline and triethylamine, and cyclohexane is practically absent from the first solvation layer already at a molar fraction of 0.6 in triethylamine. The hydrogen bond formed is sufficiently long-lived to determine an asymmetric environment around the solute molecule. The resulting nonlinear solvent effect is mainly due to this hydrogen bond influence, although there is also a small contribution from dielectric enrichment.

Simultaneous Solvent and Counterion Effects on the Absorption Properties of a Model of the Rhodopsin Chromophore.

The ASEP/MD (averaged solvent electrostatic potential from molecular dynamics) method was employed in studying the environment effects (solvent and counterion) on the absorption spectrum of a model of the 11-cis-retinal protonated Schiff base. Experimental studies of the absorption spectra of the rhodopsin chromophore show anomalously large solvent shifts in apolar solvents. In order to clarify their origin, we study the role of the counterion and of the solute-solvent interactions. We compare the absorption spectra in the gas phase, cyclohexane, dichloromethane, and methanol. The counterion effect was described from both a classical and quantum point of view. In the latter case, the contribution of the chromophore-counterion charge transfer to the solvent shift could be analyzed. To the best of our knowledge, this is the first time that counterion and solvent effects on the absorption properties of the 11-cis-retinal chromophore have been simultaneously examined. We conclude that the counterion-solute ionic pair in the gas phase is not a good model to represent the solvent shift in nonpolar solvents, as it does not account for the effect that the thermal agitation of the solvent has on the geometry of the ionic pair. In contrast to nonpolar solvents, the experimental solvent shift values in methanol can be exclusively explained by the polarity of the medium. In dichloromethane, the presence of the counterion does not modify the solvent shift of the first absorption band, but it affects the position of the second excited state. In the three solvents considered, the first two excited states become almost degenerate.

Framework‐based design of a new all‐purpose molecular simulation application: The Adun simulator

Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well‐defined structure. We present some examples on the use of Adun by performing simple free‐energy simulations for the adiabatic charging of a single ion, using both free‐energy perturbation and the Bennetts method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.

Theoretical Study of the Competition between Intramolecular Hydrogen Bonds and Solvation in the Cys-Asn-Ser Tripeptide

A study of the competition between intra- and intermolecular hydrogen bonds and its influence on the stability of the Cys-Asn-Ser tripeptide in aqueous solution was performed by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a DFT-B3LYP/6-311+G(d) quantum treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In gas phase, the most stable structure adopts a C5 conformation. Somewhat higher in energy are found the PP(II) and C7eq structures. In solution, the stability order of the different conformers is reversed: the PP(II) structure becomes the most stable, and the C5 structure is strongly destabilized. The conformational equilibrium is shifted toward conformations in which the intramolecular hydrogen bonds (IHB) have been substituted with intermolecular hydrogen bonds with the water molecules. The solvent stabilizes extended structures without IHBs that are not stable in vacuum. The effect of the protonation state on the conformational equilibrium was also analyzed.

Chemi- and Bioluminescence of Cyclic Peroxides

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model

The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.