Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer.

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

In Silico Ultrafast Nonlinear Spectroscopy Meets Experiments: The Case of Perylene Bisimide Dye.

Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.

Multidimensional Potential Energy Surfaces Resolved at the RASPT2 Level for Accurate Photoinduced Isomerization Dynamics of Azobenzene.

We have used state-of-the-art ab initio restricted active RASPT2 computations using a 16 orbitals, 18 electrons active space to produce an extended three-dimensional map of the potential energy surfaces (PESs) of the ground and first nπ* excited states of azobenzene along CNNC torsion and the two CNN bending angles, which are the most relevant coordinates for the trans-cis photoisomerization process. Through comparison with fully unconstrained optimizations performed at the same level of theory, we show that the three selected coordinates suffice to correctly describe the photoisomerization mechanism and the S1-S0 crossing seam. We also provide a map of the nonadiabatic coupling between the two states in the region where they get closer in energy. Eventually, we show that treating the two CNN bending angles as independent coordinates is fundamental to break the symmetry and couple the two electronic states. The accuracy of the S0 and S1 PESs and couplings was validated with semiclassical dynamics simulations in the reduced space of the scanned coordinates, showing results in good agreement with published full-coordinate dynamics.

Exploring the capabilities of optical pump X-ray probe NEXAFS spectroscopy to track photo-induced dynamics mediated by conical intersections.

X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck-Condon point, towards the conical intersection(s).

Order and dynamics inside H-PDLC nanodroplets: an ESR spin probe study.

We have performed a detailed study of the order and dynamics of the commercially available BL038 liquid crystal (LC) inside nanosized (50-300 nm) droplets of a reflection-mode holographic-polymer dispersed liquid crystal (H-PDLC) device where LC nanodroplet layers and polymer layers are alternately arranged, forming a diffraction grating. We have determined the configuration of the LC local director and derived a model of the nanodroplet organization inside the layers. To achieve this, we have taken advantage of the high sensitivity of the ESR spin probe technique to study a series of temperatures ranging from the nematic to the isotropic phase of the LC. Using also additional information on the nanodroplet size and shape distribution provided by SEM images of the H-PDLC cross section, the observed director configuration has been modeled as a bidimensional distribution of elongated nanodroplets whose long axis is, on the average, parallel to the layers and whose internal director configuration is a uniaxial quasi-monodomain aligned along the nanodroplet long axis. Interestingly, at room temperature the molecules tend to keep their average orientation even when the layers are perpendicular to the magnetic field, suggesting that the molecular organization is dictated mainly by the confinement. This result might explain, at least in part, (i) the need for switching voltages significantly higher and (ii) the observed faster turn-off times in H-PDLCs compared to standard PDLC devices.

Expected and unexpected behavior of the orientational order and dynamics induced by azobenzene solutes in a nematic.

We have explored the changes in the phase stability, orientational order, and dynamics of the nematic 4-cyano-4'-n-pentylbiphenyl (5CB) doped with either the trans or the cis form of different p-azobenzene derivatives using the ESR spin-probe technique. In particular, we have studied the effects induced by each of the seven nonmesogenic 4-R-phenylazobenzenes (R = H, F, Br, CH3, CF3, On-Bu, Ot-Bu) at 1% and 7% mole fraction on the order parameter and on the shift of the nematic-isotropic transition temperature (TNI), as reported by a nitroxide spin probe, and we have tried to relate them to the solute shape and charge distribution. In all the cases the presence of the azo-derivative causes a depression of T(NI), more pronounced for the cis isomers. The dependence of on the reduced temperature T* = T/T(NI) remains the same as that of pure 5CB in all trans-doped samples at 1% and 7% and decreases only slightly in the cis at 1%. However, we observe different and in some cases large variations (up to 25%) in for the cis at 7%, showing solute effects that go beyond the shift in T(NI). Surprisingly enough, even at the highest concentration, the probe dynamics appears to be essentially independent of the nature, the configuration, and the concentration of the different solutes and very similar to that observed in the pure 5CB.

Relaxation processes of the liquid crystal ME6N in the isotropic phase studied by Raman scattering experiments.

We have investigated the Raman profiles of the nu(C[Triple Bond]N) and nu(C=O) vibrational modes of the nematic liquid crystal ME6N (4-cyanophenyl-4(')-hexylbenzoate) in the isotropic phase at different temperatures and used them as probes of the dynamics and structural organization of this liquid. The vibrational time correlation functions of the nu(C[Triple Bond]N) mode, rather adequately interpreted within the assumption of exponential modulation function (the Kubo-Rothschild theory), indicate that the system experiences an intermediate dynamical regime that gets only slightly faster with increasing temperature. However, this theory fails in predicting the non-exponential behavior that the time correlation functions manifest in the long time range (t>3 ps). For this reason we have additionally approached the interpretation of vibrational correlation functions in terms of the theory formulated by Rothschild and co-workers for locally structured liquids. The application of this theory reveals that the molecular dynamics in this liquid crystal in the isotropic phase is that deriving from a distribution of differently sized clusters, which narrows as the temperature increases. Even at the highest temperature reached in this study (87 degrees C above the nematic-isotropic transition), the liquid has not yet achieved the structure of the simple liquid and the dynamics has not reached the limit of the single channel process. The vibrational and orientational relaxations occur in very different time scales. The temperature independence of the orientational dynamics in the whole range from 55 degrees C to 135 degrees C has been referred to the nonhydrodynamic behavior of the system, arising when local pseudonematic structures persist for times longer than the orientational relaxation. The occurrence of the process of resonant vibrational energy transfer between the C=O groups of adjacent molecules has been revealed in the isotropic phase by a slightly positive Raman noncoincidence effect in the band associated with the nu(C=O) mode. A qualitative interpretation is tentatively given in terms of partial cancellation of contributions deriving from structures having opposite orientations of their C=O groups.