To assess a tumor biomarker like the cyclooxygenase-2 enzyme (COX-2), non-invasive imaging techniques are powerful tools. The (non-) linear optical properties of activatable fluorescent probes which are selectively bound to the biomarker can therefore be exploited. The here presented molecular modelling results based on multi-scale modelling techniques highlight the importance of the conformational versatility and of changes in the electronic interactions of such probes when they are embedded in water or in the COX-2 homodimer enzyme. The ANQIMC-6 probe, which combines the binding domain/scaffold of indomethacin (IMC) on COX-2 with the optical properties of acenaphtho[1,2-b]quinoxaline (ANQ), is found to be folded in the solvent and unfolded in the enzyme. A concerted movement of the probe and the protein is seen, while the rotational autocorrelation function exhibits also the intrinsic properties of the probe. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations are used to simulate the one-photon and two-photon absorption spectra along with the first hyperpolarizability. The transition has a local character in vacuum, but changes to a charge transfer one in the presence of the microenvironment of the enzyme. This is also visible through a change of the shape of the absorption spectrum, while at the same time the simulated signals of second harmonic generation experiments are strongly enhanced. The results of this work prove that an environment sensitive probe with an anchoring group and an optical active part can be constructed for use in absorption spectroscopy, without the need to revert to fluorescence experiments.

Background: Organic fluorophores embedded in lipid bilayers can nowadays be described by a multiscale computational approach. Combining different length and time scales, a full characterization of the probe localization and optical properties led to novel insight into the effect of the environments. Scope of review: Following an introduction on computational advancements, three relevant probes are reviewed that delineate how a multiscale approach can lead to novel insight into the probes' (non) linear optical properties. Attention is paid to the quality of the theoretical description of the optical techniques. Major conclusions: Computation can assess a priori novel probes' optical properties and guide the analysis and interpretation of experimental data in novel studies. The properties can be used to gain information on the phase and condition of the surrounding biological environment. General significance: Computation showed that a canonical view on some of the probes should be revisited and adapted.

Visualization of membrane domains like lipid rafts in natural or artificial membranes is a crucial task for cell biology. For this purpose, fluorescence microscopy is often used. Since fluorescing probes in lipid membranes partition specifically in e.g. local liquid disordered or liquid ordered environments, the consequent changes in their orientation and location are both theoretically and experimentally of interest. Here we focused on a liquid disordered membrane phase and performed molecular dynamics (MD) simulations of the indocarbocyanine DiD probes by varying the length of the attached alkyl tails and also the length of the cyanine backbone. From the probed compounds in a DOPC lipid bilayer at ambient temperature, a varying orientation of the transition dipole moment was observed, which is crucial for fluorescence microscopy and which, through photoselection, was found to be surprisingly more effective for asymmetric probes than for the symmetric ones. Furthermore, we observed that the orientation of the probes was dependent on the tail length; with the methyls or propyls attached, DiD oriented with its tails facing the water, contrary to the ones with longer tails. With advanced hybrid QM/MM calculations we show that the different local environment for differently oriented probes affected the one-photon absorption spectra, that was blue-shifted for the short-tailed DiD with respect to the DiDs with longer tails. We show here that the presented probes can be successfully used for fluorescence microscopy and we believe that the described properties bring further insight for the experimental use of these probes.

The fluorescent molecule diphenylhexatriene (DPH) has been often used in combination with fluorescence anisotropy measurements, yet little is known regarding the non-linear optical properties. In the current work, we focus on them and extend the application to fluorescence, while paying attention to the conformational versatility of DPH when it is embedded in different membrane phases. Extensive hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the influence of the phase- and temperature-dependent lipid environment on the probe. Already, the transition dipole moments and one-photon absorption spectra obtained in the liquid ordered mixture of sphingomyelin (SM)-cholesterol (Chol) (2:1) differ largely from the ones calculated in the liquid disordered DOPC and solid gel DPPC membranes. Throughout the work, the molecular conformation in SM:Chol is found to differ from the other environments. The two-photon absorption spectra and the ones obtained by hyper-Rayleigh scattering depend strongly on the environment. Finally, a stringent comparison of the fluorescence anisotropy decay and the fluorescence lifetime confirm the use of DPH to gain information upon the surrounding lipids and lipid phases. DPH might thus open the possibility to detect and analyze different biological environments based on its absorption and emission properties.

The photoisomerization scheme of the cyanine-based 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe was investigated by means of molecular modeling techniques, accounting for differences between the potential energy surfaces in the ground and excited states. Starting from the trans conformation, the photoisomerization path to the cis conformation and its dependence on the acyl tail lengths of the probe were evaluated. Moreover, the ground-state conformational distribution was investigated and suitable topologies were built for the ground- and excited-state molecular dynamics (MD) calculations. A protocol for simulations in solvents and in liquid-disordered lipid bilayers was worked out. In a kinetic analysis, the decay of the excited singlet (S1) state via radiative and nonradiative decays and via dihedral twisting is discussed. The twisting of one of the dihedral angles in the S1 state is found to be faster than the direct decay rate, which explains the relatively low fluorescence quantum yield of the compound. The molecular dynamics simulations show that in lipid bilayers, the DiD probe with methyl groups as acyl tails from the headgroup brings the highest level of photoisomerization, while a compound with acyl tails of 18 carbon atoms does not isomerize at all.

The specific relationship between the alkyl tail lengths of four azobenzene probes embedded in DOPC liquid disorder membrane and their (non) linear optical (NLO) properties have been considered in the current study. Using extensive molecular dynamics calculations, the push/pull effect of the alkyl tails on the position and orientation of the probes in the model membrane are discussed. The simulations indicate that with increasing tail lengths the cis isomers are pushed closer to the membrane surface, while the trans ones are rather pulled toward the membrane center. Throughout hybrid quantum mechanics/molecular mechanics calculations, the linear and nonlinear optical properties of these compounds have been investigated. The pushing effect of the tails for cis azobenzene is translated in strong responses in the (non) linear I optical spectroscopies, while the opposite is seen for the trans isomers. The cis isomer can be seen as the active state of the azobenzene compound for membrane recognition. The current work highlights the correlation between the tails of photosensitive membrane probes and their NLO properties, and focuses on unexpected behaviors of azobenzene derivatives in biological environments which can be exploited in distinguishing between soft and stiff cellular compartments that are of utmost importance for ion carrier transport.

The development of a universal probe to assess the phase of a lipid membrane is one of the most ambitious goals for fluorescence spectroscopy. The ability of a well-known molecule as Laurdan to reach this aim is here exploited as the behavior of the probe is fully characterized in a dipalmitoyl-phosphatidylcholine (DPPC) solid gel (So) phase by means of molecular dynamics simulations. Laurdan can take two conformations, depending on whether the carbonyl oxygen points toward the beta-position of the naphthalene core (Conf-I) or to the alpha-position (Conf-II). We observe that Conf-I has an elongated form in this environment, whereas Conf-II takes an L-shape. Interestingly, our theoretical calculations show that these two conformations behave in an opposite way from what is reported in the literature for a DPPC membrane in a liquid disordered (Ld) phase, where Conf-I assumes an L-shape and Conf-II is elongated. Moreover, our results show that in DPPC (So) no intermixing between the conformations is present, whereas it has been seen in a fluid environment such as DOPC (Ld). Through a careful analysis of angle distributions and by means of the rotational autocorrelation function, we predict that the two conformers of Laurdan behave differently in different membrane environments.

Graphene quantum dots (GQD) are interesting materials due to the confined sizes which allow to exploit their optoelectronic properties, especially when they interface with organic molecules through physisorption. In particular, when interfaces are formed, charge transfer (CT) processes can occur, in which electrons can flow either from the GQD to the absorbed molecule, or vice versa. These processes are accessible by modeling and computational analysis. Yet, the presence of different environments can strongly affect the outcome of such simulations which, in turn, can lead to wrong results if not taken into account. In this multiscale study, we assess the sensibility of the computational approach and compute the CT, calculated at interfaces composed by GQD and amino-acene derivatives. The hole transfer is strongly affected by dynamic disorder and the nature of the environment, and imposes stringent descriptions of the modeled systems to ensure enhanced accuracy of the transfer of charges.

Laurdan is one of the most used fluorescent probes for lipid membrane phase recognition. Despite its wide use for optical techniques and its versatility as a solvatochromic probe, little is known regarding its use as molecular rotor, for which clear evidence is found in the current study. Although recent computational and experimental studies suggest the existence of two stable conformations of laurdan in different membrane phases, it is difficult to experimentally probe their prevalence. By means of multiscale computational approaches, we prove now that this information can be obtained through the optical properties of the two conformers, ranging from one-photon absorption over two-photon absorption to the first hyperpolarizability. Fluorescence decay and anisotropy analyses are performed as well and stress the importance of laurdan's conformational versatility. As a molecular rotor and with reference to the distinct properties of its conformers, laurdan can be used to probe biochemical processes that change the lipid orders in cell membranes.

Characterization of the membrane phases is a crucial task in cell biology. Cells differ in composition of the lipids and consequently in adopted phases. The phases can be discriminated based upon lipid ordering and molecular diffusion and their identification could be used for characterization of cell membranes. Here we used molecular dynamics (MD) simulations to study the behavior of the fluorescent reporter molecule diphenylhexatriene (DPH) in different lipid phases - liquid disordered (L-d), liquid ordered (L-o), and solid ordered (S-o) composed of phosphatidylcholines (L-d and S-o) or a sphingomyelin/cholesterol (SM/Chol) mixture (L-o). To the best of our knowledge, this is the first simulation of DPH in L-o SM/Chol and S-o DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the L-o phase we observed a significant fraction of DPH positioned in between membrane leaflets, which agrees with experimental findings, but which has not been observed in previous MD simulations of DPH in phosphatidylcholine membranes. Further, we calculated rotational autocorrelation functions (ROTACF) from our MD simulations in order to model the time-resolved fluorescence anisotropy decay. We observed that order parameters P-2 and P-4 are sufficient to fully describe the orientation distribution of DPH. We analyzed the ROTACFs by a so-called general model for the time-resolved fluorescence anisotropy [W. van der Meer et al., Biophys. J., 1984, 46, 515] and observed an overestimation of P-4. We suggest a rescaling of the recovered P-4 yielding an orientation distribution of DPH close to the one observed in our MD simulations.