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The malononitrile group is considered one of the strongest natural electron-withdrawing groups in a chemist's arsenal. However, surprisingly little is known about how this group functions in push–pull fluorophores. In a recent computational study, we reported that replacing the ketone group of the traditional push–pull dye Laurdan with a malononitrile group significantly improves the optical properties while retaining the membrane behavior of the parent molecule Laurdan. Motivated by these results, we report here the synthesis and photophysical characterization of the said compound, 6-(1-undecyl-2,2-dicyanovinyl)-N,N-dimethyl-2-naphthylamine (CN-Laurdan). To our surprise, this new CN-Laurdan probe is found to be much less bright than the parent Laurdan due to a large drop in the fluorescence quantum yield. Using computational methods, we determine that the origin of this low quantum yield is related to the existence of a non-radiative decay pathway related to a rotation of the malononitrile moiety, suggesting that the molecule could nonetheless function very well as a molecular rotor. We confirm experimentally that CN-Laurdan functions as a molecular rotor by measuring the quantum yield in methanol/glycerol mixtures of increasing viscosity. Specifically, we found a consistent increase in the quantum yield across the entire range of tested viscosities. [ABSTRACT FROM AUTHOR]

In this paper we show a theoretical rational design approach on a series of intrinsically fluorescent analogues of cholesterol (FLACs), called polyene-sterols (P-sterols), followed by a step-by-step selection of potential candidates, employing, sequentially, state-of-the-art quantum mechanical (QM) computations of the optical properties (single- and multiphoton absorption electronic spectroscopies and emission), molecular dynamics (MD) simulations in model membranes, and multiscale approaches (polarizable embedding). This selection converged to a promising candidate that shows simultaneously interesting single- and multiphoton absorption properties as well as emitting properties and good abilities to mimic cholesterol order effects in model membranes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this perspective, we provide an overview of recent work within the polarizable embedding scheme to describe properties of molecules in realistic environments of increasing complexity. After an outline of the theoretical basis for the polarizable embedding model, we discuss the importance of using an accurate embedding potential, and how this may be used to significantly reduce the size of the part of the system treated using quantum mechanics without compromising the accuracy of the final results. Furthermore, we discuss the calculation of local electronic excited states based on response theory. We finally discuss aspects related to two recent extensions of the model (i) effective external field and (ii) polarizable density embedding emphasizing their importance for efficient yet accurate description of excited-state properties in complex environments. [ABSTRACT FROM AUTHOR]

In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN–methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration. [ABSTRACT FROM AUTHOR]

We investigate the performance of CC2 and TDDFT/CAM-B3LYP for the calculation of two-photon absorption (TPA) strengths and cross sections and contrast our results to a recent coupled cluster equation-of-motion (EOM-EE-CCSD) benchmark study [K. D. Nanda and A. I. Krylov, J. Chem. Phys., 2015, 142, 064118]. In particular, we investigate whether CC2 TPA strengths are significantly overestimated compared to higher-level coupled-cluster calculations for fluorescent protein chromophores. Our conclusion is that CC2 TPA strengths are only slightly overestimated compared to the reference EOM-EE-CCSD results and that previously published overestimated cross sections are a result of inconsistencies in the conversion of the TPA strengths to macroscopic units. TDDFT/CAM-B3LYP TPA strengths, on the other hand, are found to be 1.5 to 3 times smaller than the coupled-cluster reference for the molecular systems considered. The unsatisfactory performance of TDDFT/CAM-B3LYP can be linked to an underestimation of excited-state dipole moments predicted by TDDFT/CAM-B3LYP. [ABSTRACT FROM AUTHOR]

A combined experimental and computational study of solvent effects on one- and two-photon absorption spectra of three chlorinated harmine derivatives is presented. The systems studied were protonated forms of 6-chloroharmine, 8-chloroharmine and 6,8-dichloroharmine in two solvents, acetonitrile and water. For the computations, polarizable embedding density functional and coupled cluster response theory methods were used. The computations were able to model the solvent-dependent experimental data well. These results demonstrate that reasonably sophisticated computational methods can be successfully applied to accurately study linear and nonlinear spectroscopic properties of comparatively large organic molecules in solution. [ABSTRACT FROM AUTHOR]

Using the chromophore of the green fluorescent protein (GFP), the performance of a hybrid RI-CC2/polarizable embedding (PE) model is tested against a quantum chemical cluster approach. Moreover, the effect of the rest of the protein environment is studied by systematically increasing the size of the cluster and analyzing the convergence of the excitation energies. It is found that the influence of the environment of the chromophore can accurately be described using a polarizable embedding model with only a minor error compared to a full quantum chemical description. It is also shown that the treatment of only a small region around the chromophore is only by coincidence a good approximation. Therefore, such cluster approaches should be used with care. Based on our results, we suggest that polarizable embedding models, including a large part of the environment to describe its effect on biochromophores on top of an accurate way of describing the central subsystem, are both accurate and computationally favourable in many cases. [ABSTRACT FROM AUTHOR]

With the advent of molecular transistors, electrochemistry can now be studied at the single-molecule level. Experimentally, the redox chemistry of the molecule manifests itself as features in the observed Coulomb blockade diamonds. We present a simple theoretical method for explicit construction of the Coulomb blockade diamonds of a molecule. A combined quantum mechanical/molecular mechanical method is invoked to calculate redox energies and polarizabilities of the molecules, including the screening effect of the metal leads. This direct approach circumvents the need for explicit modelling of the gate electrode. From the calculated parameters the Coulomb blockade diamonds are constructed using simple theory. We offer a theoretical tool for assignment of Coulomb blockade diamonds to specific redox states in particular, and a study of chemical details in the diamonds in general. With the ongoing experimental developments in molecular transistor experiments, our tool could find use in molecular electronics, electrochemistry, and electrocatalysis. [ABSTRACT FROM AUTHOR]

Linear and nonlinear spectroscopic parameters of flavin mononucleotide, FMN, have been examined both experimentally and computationally under conditions in which FMN is (1) solvated in a buffered aqueous solution, and (2) encased in a protein that is likewise solvated in a buffered aqueous solution. The latter was achieved using “miniSOG” which is an FMN-containing protein engineered from Arabidopsis thaliana phototropin 2. Although it is reasonable to expect that the encasing protein could have an appreciable effect, certainly on the nonlinear two-photon absorption cross section, we find that replacing the dynamic aqueous environment with the more static protein environment does little to influence the spectroscopic properties of FMN. The experimental and computational studies are consistent in this regard, and this agreement indicates that comparatively high-level computational methods can indeed be used with success on large chromophores with a complicated local environment. The results of the present study facilitate the much-needed development of well-characterized and readily-controlled chromophores suitable for use as intracellular sensitizers and fluorophores. [ABSTRACT FROM AUTHOR]

Mössbauer spectroscopy is an indispensable spectroscopic technique and analytical tool in iron coordination chemistry. The linear correlation between the electron density at the nucleus (“contact density”) and experimental isomer shifts has been used to link calculated contact densities to experimental isomer shifts. Here we have investigated relativistic methods of systematically increasing sophistication, including the eXact 2-Component (X2C) Hamiltonian and a finite-nucleus model, for the calculation of isomer shifts of iron compounds. While being of similar accuracy as the full four-component treatment, X2C calculations are far more efficient. We find that effects of spin–orbit coupling can safely be neglected, leading to further speedup. Linear correlation plots using effective densities rather than contact densities versus experimental isomer shift lead to a correlation constant a = −0.294 a0−3 mm s−1 (PBE functional) which is close to an experimentally derived value. Isomer shifts of similar quality can thus be obtained both with and without fitting, which is not the case if one pursues a priori a non-relativistic model approach. As an application for a biologically relevant system, we have studied three recently proposed [Fe]-hydrogenase intermediates. The structures of these intermediates were extracted from QM/MM calculations using large QM regions surrounded by the full enzyme and a solvation shell of water molecules. We show that a comparison between calculated and experimentally observed isomer shifts can be used to discriminate between different intermediates, whereas calculated atomic charges do not necessarily correlate with Mössbauer isomer shifts. Detailed analysis reveals that the difference in isomer shifts between two intermediates is due to an overlap effect. [ABSTRACT FROM AUTHOR]

In this paper we demonstrate the importance of including polarization—especially in a fully self-consistent-field manner—when calculating excited states within linear response QM/MM methods based on correlated electronic structure methods. We perform a systematic investigation of solvent polarization effects by identifying lower order polarization reaction fields as compared to the full treatment. In the process we highlight the different nature of static and dynamic reaction fields and demonstrate—by method of example on both solvated systems as well as on biomolecules—that inclusion of both of these is mandatory for an accurate description of excited states. Ultimately, these findings reflect the importance of the change in the solvent reaction field upon electronic excitations. In light of the recent increasing interest in excited state QM/MM methods incorporating mutual polarization between subsystems as a method for treating large molecular systems, the reported investigation constitutes an important step towards dissecting the accuracy of such calculations. [ABSTRACT FROM AUTHOR]

The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e.in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium. [ABSTRACT FROM AUTHOR]

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA−) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA−inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP. [ABSTRACT FROM AUTHOR]

Based on hybrid QM/MM simulation techniques, we rationalize the spectacular solvatochromic reversal behavior observed for a stilbazolium merocyanine (SM) called Brooker's merocyanine dye. This solvatochromic reversal is attributed to a change in the solute π-electron distribution from zwitterionic to neutral following the change in solvents from polar to non polar. Based on our calculations, we suggest that a polar solvent, like water, with larger relative permittivity is influential enough to bring the change in molecular structure from neutral to zwitterionic. Our results clearly indicate that SM exists in a neutral molecular structure in non polar solvents like trichloromethane and thereby we suggest that self-aggregation of SM may not occur in this solvent. [ABSTRACT FROM AUTHOR]

Correction for ‘Analysis of computational models for an accurate study of electronic excitations in GFP’ by Tobias Schwabe et al., Phys. Chem. Chem. Phys., 2015, 17, 2582–2588. [ABSTRACT FROM AUTHOR]