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.

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.

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 S-S crossing seam. We also provide a map of the nonadiabatic coupling between the two states in the region where they get closer in energy.

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.

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.

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.

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).