Generalized polarization and time-resolved fluorescence provide evidence for different populations of Laurdan in lipid vesicles.

The solvatochromic dye Laurdan is widely used in sensing the lipid packing of both model and biological membranes. The fluorescence emission maximum shifts from about 440 nm (blue channel) in condensed membranes (So) to about 490 nm (green channel) in the liquid-crystalline phase (Lα). Although the fluorescence intensity based generalized polarization (GP) is widely used to characterize lipid membranes, the fluorescence lifetime of Laurdan, in the blue and the green channel, is less used for that purpose. Here we explore the correlation between GP and fluorescence lifetimes by spectroscopic measurements on the So and Lα phases of large unilamellar vesicles of DMPC and DPPC. A positive correlation between GP and the lifetimes is observed in each of the optical channels for the two lipid phases. Microfluorimetric determinations on giant unilamellar vesicles of DPPC and DOPC at room temperature are performed under linearly polarized two-photon excitation to disentangle possible subpopulations of Laurdan at a scale below the optical resolution. Fluorescence intensities, GP and fluorescence lifetimes depend on the angle between the orientation of the linear polarization of the excitation light and the local normal to the membrane of the optical cross-section. This angular variation depends on the lipid phase and the emission channel. GP and fluorescence intensities in the blue and green channel in So and in the blue channel in Lα exhibit a minimum near 90o. Surprisingly, the intensity in the green channel in Lα reaches a maximum near 90o. The fluorescence lifetimes in the two optical channels also reach a pronounced minimum near 90o in So and Lα, apart from the lifetime in the blue channel in Lα where the lifetime is short with minimal angular variation. To our knowledge, these experimental observations are the first to demonstrate the existence of a bent conformation of Laurdan in lipid membranes, as previously suggested by molecular dynamics calculations.

Dual photoisomerization mechanism of azobenzene embedded in a lipid membrane.

The photoisomerization of chromophores embedded in biological environments is of high importance for biomedical applications, but it is still challenging to define the photoisomerization mechanism both experimentally and computationally. We present here a computational study of the azobenzene molecule embedded in a DPPC lipid membrane, and assess the photoisomerization mechanism by means of the quantum mechanics/molecular mechanics surface hopping (QM/MM-SH) method. We observe that while the trans-to-cis isomerization is a slow process governed by a torsional mechanism due to the strong interaction with the environment, the cis-to-trans mechanism is completed in sub-ps time scale and is governed by a pedal-like mechanism in which both weaker interactions with the environment and a different geometry of the potential energy surface play a key role.

Multiscale Modeling Unravels the Influence of Biomembranes on the Photochemical Properties of Embedded Anti-Oxidative Polyphenolic and Phenanthroline Chelating Dyes.

The embedding of caffeate methyl ester, the flavonoids luteolin and quercetin, and the o-phenanthroline and neocuproine in a liquid disordered lipid bilayer has been studied through extensive atomistic calculations. The location and the orientation of these bio-active antioxidants are explained and analyzed. While the two phenanthrolines strongly associate with the lipid tail region, the other three compounds are rather found among the head groups. The simulations showcase conformational changes of the flavonoids. Through the use of a hybrid quantum mechanics-molecular mechanics scheme and supported by a profound benchmarking of the electronic excited-state method for these compounds, the influence of the anisotropic environment on the compounds' optical properties is analyzed. Influences of surrounding water molecules and of the polar parts of the lipids on the transition dipole moments and excited-state dipole moments are weighted with respect to a change in conformation. The current study highlights the importance of the mapping of molecular interactions in model membranes and pinpoints properties, which can be biomedically used to discriminate and detect different lipid environments.

Multiscale simulations of polyzwitterions in aqueous bulk solutions and brush array configurations.

Zwitterionic polymers are very promising candidates for antifouling materials that exhibit high chemical stability as compared to polyethylene glycol-based systems. A number of simulation and experimental studies have emerged over recent years for the investigation of sulfobetaine-based zwitterionic polymers. Investigating the structural and thermodynamic properties of such polymers requires access to broad time and length regimes, thus necessitating the development of multiscale simulation strategies. The present article advocates a mesoscopic dissipative particle dynamics (DPD) model capable of addressing a wide range of time and length scales. The mesoscopic force field was developed hand-in-hand with atomistic simulations based on the OPLS force field through a bottom-up parameterization procedure that matches the atomistically calculated strand-length, strand-angle and pair distribution functions. The DPD model is validated against atomistic simulations conducted in this work, and against relevant atomistic simulation studies, theoretical predictions and experimental correlations from the literature. Properties examined include the conformations of SPE polymers in dilute bulk aqueous solution, the density profile and thickness of brush arrays as functions of the grafting density and chain length. In addition, we compute the potential of mean force of an approaching hydrophilic or hydrophobic foulant via umbrella sampling as a function of its position relative to the poly-zwitterion-covered surface. The aforementioned observables lead to important insights regarding the conformational tendencies of grafted polyzwitterions and their antifouling properties.

The influence of lipid membranes on fluorescent probes' optical properties.

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.

Influence of Membrane Phase on the Optical Properties of DPH.

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.

Cyanine dyes with tail length asymmetry enhance photoselection: A multiscale study on DiD probes in a liquid disordered membrane.

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.

Conformational Changes as Driving Force for Phase Recognition: The Case of Laurdan.

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 dipalmitoylphosphatidylcholine (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 ß-position of the naphthalene core (Conf-I) or to the α-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.

Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments.

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 (Ld), liquid ordered (Lo), and solid ordered (So) composed of phosphatidylcholines (Ld and So) or a sphingomyelin/cholesterol (SM/Chol) mixture (Lo). To the best of our knowledge, this is the first simulation of DPH in Lo SM/Chol and So DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the Lo 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 P2 and P4 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 P4. We suggest a rescaling of the recovered P4 yielding an orientation distribution of DPH close to the one observed in our MD simulations.

Laurdan as a Molecular Rotor in Biological Environments.

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.

Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition.

The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as one-photon absorption (OPA), two-photon absorption (TPA), and second harmonic generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (dioleoyl- sn-glycero-3-phosphocholine, room temperature) and DPPC (1,2-dipalmitoyl- sn-glycero-3-phosphocholine, 323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of sphingomyelin and cholesterol. By means of extensive hybrid quantum mechanics-molecular mechanics calculations and based upon the (non)linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as a versatile probe for phase recognition. In particular, the SHG data obtained by means of hyper-Rayleigh scattering and by electric field induced second harmonic generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar headgroup region of the 2:1 SM:Chol mixture in the liquid ordered phase.

Triggering On/Off States of Photoswitchable Probes in Biological Environments.

The use of hybrid systems for which the change in properties of one component triggers the change in properties of the other is of outmost importance when "on/off" states are needed. For such a reason, azobenzene compounds are one of the most used probes due to their high photoswitching efficiency. In this study, we consider a new derivative of azobenzene interacting with different lipid membrane phases as a versatile fluorescent probe for phase recognition. By means of a multiscale approach, we found that the cis and trans conformers have different positions and orientations in the different lipid membranes (DOPC for the liquid disordered phase and DPPC for the gel phase), and these have a profound effect on the optical properties of the system, for both one and two photon absorption. In fact, we found that the cis state is the "on" state when the probe is inserted into the DOPC membrane, while it is in the "off" state in the DPPC membrane. This behavior enhances the selectivity of this probe for phase recognition, since the different environments will generate different responses on the same conformer of the probe. The same effect is found for the fluorescence anisotropy analysis, for which the trans (cis) isomer in DOPC (DPPC) presents a fast decay time. Due to the "on/off" effect it is possible to screen the different membrane phases via fluorescence decay time analysis, making this new probe versatile for phase detection.

Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives.

The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50° between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70-80° with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition.

Benchmarking Post-Hartree-Fock Methods To Describe the Nonlinear Optical Properties of Polymethines: An Investigation of the Accuracy of Algebraic Diagrammatic Construction (ADC) Approaches.

Third-order nonlinear optical (NLO) properties of polymethine dyes have been widely studied for applications such as all-optical switching. However, the limited accuracy of the current computational methodologies has prevented a comprehensive understanding of the nature of the lowest excited states and their influence on the molecular optical and NLO properties. Here, attention is paid to the lowest excited-state energies and their energetic ratio, as these characteristics impact the figure-of-merit for all-optical switching. For a series of model polymethines, we compare several algebraic diagrammatic construction (ADC) schemes for the polarization propagator with approximate second-order coupled cluster (CC2) theory, the widely used INDO/MRDCI approach and the symmetry-adapted cluster configuration interaction (SAC-CI) algorithm incorporating singles and doubles linked excitation operators (SAC-CI SD-R). We focus in particular on the ground-to-excited state transition dipole moments and the corresponding state dipole moments, since these quantities are found to be of utmost importance for an effective description of the third-order polarizability γ and two-photon absorption spectra. A sum-overstates expression has been used, which is found to quickly converge. While ADC(3/2) has been found to be the most appropriate method to calculate these properties, CC2 performs poorly.

A Blue-Light-Emitting BODIPY Probe for Lipid Membranes.

Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C18, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5-positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single-exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C18. The directions of the absorption and emission transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70°, which is comparable with the value reported for DiI-C18.

Self-assembly and hybridization mechanisms of DNA with cationic polythiophene.

The combination of DNA and π-conjugated polyelectrolytes (CPEs) represents a promising approach to develop DNA hybridization biosensors, with potential applications for instance in the detection of DNA lesions and single-nucleotide polymorphisms. Here we exploit the remarkable optical properties of a cationic poly[3-(6'-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] (CPT) to decipher the self-assembly of DNA and CPT. The ssDNA/CPT complexes have chiroptical signatures in the CPT absorption region that are strongly dependent on the DNA sequence, which we relate to differences in supramolecular interactions between the thiophene monomers and the various nucleobases. By studying DNA-DNA hybridization and melting processes on preformed ssDNA/CPT complexes, we observe sequence-dependent mechanisms that can yield DNA-condensed aggregates. Heating-cooling cycles show that non-equilibrium mixtures can form, noticeably depending on the working sequence of the hybridization experiment. These results are of high importance for the use of π-conjugated polyelectrolytes in DNA hybridization biosensors and in polyplexes.

Synthesis and optical properties of pyrrolo[3,2-b]pyrrole-2,5(1H,4H)-dione (iDPP)-based molecules.

We describe the synthesis and photophysical properties of a series of derivatives of pyrrolo[3,2-b]pyrrole-2,5(1H,4H)-dione-3,6-diyl (iDPP) linked to two oligothiophenes of variable length (nT). The iso-DPP-oligothiophenes (iDPPnTs) differ from the common pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione-3,6-diyl-oligothiophene analogues (DPPnTs) by a different orientation of the two lactam rings in the bicyclic iDPP unit compared to DPP. In contrast to the highly fluorescent DPPnTs, the new isomeric iDPPnTs exhibit only very weak fluorescence. We demonstrate with the help of quantum-chemical calculations that this can be attributed to a different symmetry of the lowest excited state in iDPPnT (A in C2 symmetry) compared to DPPnTs (B) and the corresponding loss in oscillator strength of the lowest energy transition. Upon extending the oligothiophene moiety in the iDPPnTs molecules, the charge transfer character of the lowest A excited state becomes more pronounced. This tends to preclude high fluorescence quantum yields even in extended iDPPnTs systems.

Computational design of improved two-photon active caging compounds based on nitrodibenzofuran.

Nitrodibenzofuran (NDBF) has recently been established as photolabile protecting group and efficiently used as two-photon active cage. In this work, a computational approach is exploited to rationally design improved two-photon active caging groups based on this NDBF chromophore. For this objective, first the two-photon absorption (TPA) properties of NDBF are investigated in detail and a suitable theoretical approach for the reliable simulation of TPA spectra of this class of compounds is identified. Then, virtual chemical modifications are performed by introduction of substituents at the chromophore and replacement of the central furan ring by pyrolle, thiophene, and borrole heterocycles. Subsequently, the TPA properties of the resulting compounds are computed, and the influences of the chemical modifications on TPA properties investigated in detail. The most promising candidates with largely increased two-photon uncaging efficiencies are dimethylamino-substituted derivatives of NDBF, nitrodibenzopyrrol, and nitrodibenzothiophene.

Simulation of photoelectron spectra using the reflection principle in combination with unrestricted excitation ADC2 to assess the accuracy of excited-state calculations.

The gas-phase photoelectron spectra of ethene, formaldehyde, formic acid and difluoromethane are simulated using the reflection principle and the unrestricted second-order algebraic diagrammatic construction [UADC(2)] scheme of the polarization propagator for the computation of the vertical-excited states of the cations at the equilibrium geometry of the parent neutral molecule. Comparison is made with experimental spectra and the established highly accurate ionization IP-ADC(3) theory to gain insight into the accuracy and applicability of recently developed excitation UADC schemes. Within UADC(2), we distinguish between the strict and extended schemes UADC(2)-s and UADC(2)-x. While the latter approach is found to slightly underestimate the experimental photoelectron spectra by 0.3 eV and can thus be regarded as a reliable scheme within the limits of the applied reflection principle and the underlying approximations, the UADC(2)-s scheme tends to overestimate the excitation energies by about 0.5 eV. Time-dependent density functional theory is also applied in combination with the standard B3LYP xc functional and turns out to be a useful computational tool for the simulation of the photoelectron spectra of the studied species.

Ring-puckering motion in cyclopentene studied by time-resolved rotational coherence spectroscopy and ab initio calculations.

The ring-puckering vibration in cyclopentene was studied by rotational time-resolved femtosecond degenerate four-wave mixing (fs DFWM) spectroscopy. The fs DFWM spectra of cyclopentene were measured both in a supersonic expansion and in a gas cell at room temperature. The room temperature fs DFWM spectrum has been satisfactorily reproduced by a fitted simulation based on a one-dimensional model for the ring-puckering vibration. This has allowed for the determination of energetic parameters of the ring-puckering motion such as the energy barrier to ring inversion of 274(+12/-20) cm(-1) and the equilibrium ring-puckering angle of 24.3 degrees . The derived dependences of the rotational constants A and B on the puckering angle resemble very closely those obtained by microwave spectroscopy. In addition, previous theoretical estimates of the ring inversion barrier of cyclopentene were improved by performing high level ab initio calculations. Zero-point vibrational energy correction was found to be essential for an accurate evaluation of the puckering potential. Altogether, this study provides a proof-of-principle of the applicability of the fs DFWM technique for investigating large amplitude intramolecular motions.