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.

Predicting the Second-Order Nonlinear Optical Responses of Organic Materials: The Role of Dynamics.

The last 30 years have witnessed an ever-growing application of computational chemistry for rationalizing the nonlinear optical (NLO) responses of organic chromophores. More specifically, quantum chemical calculations proved highly helpful in gaining fundamental insights into the factors governing the magnitude and character of molecular first hyperpolarizabilities (ß), be they either intrinsic to the chromophore molecular structure and arising from symmetry, chemical substitution, or π-electron delocalization, or induced by external contributions such as the laser probe or solvation and polarization effects. Most theoretical reports assumed a rigid picture of the investigated systems, the NLO responses being computed solely at the most stable geometry of the chromophores. Yet, recent developments combining classical molecular dynamics (MD) simulations and DFT calculations have evidenced the significant role of structural fluctuations, which may induce broad distributions of NLO responses, and even generate them in some instances.This Account presents recent case studies in which theoretical simulations have highlighted these effects. The discussion specifically focuses on the simulation of the second-order NLO properties that can be measured experimentally either from Hyper-Rayleigh Scattering (HRS) or Electric-Field Induced Second Harmonic Generation (EFISHG). More general but technical topics concerning several aspects of the calculations of hyperpolarizabilities are instead discussed in the Supporting Information.Selected examples include organic chromophores, photochromic systems, and ionic complexes in the liquid phase, for which the effects of explicit solvation, concentration, and chromophore aggregation are emphasized, as well as large flexible systems such as peptide chains and pyrimidine-based helical polymers, in which the relative variations of the responses were shown to be several times larger than their average values. The impact of geometrical fluctuations is also illustrated for supramolecular architectures with the examples of nanoparticles formed by organic dipolar dyes in water solution, whose soft nature allows for large shape variations translating into huge fluctuations in time of their NLO response, and of self-assembled monolayers (SAMs) based on indolino-oxazolidine or azobenzene switches, in which the geometrical distortions of the photochromic molecules, as well as their orientational and positional disorder within the SAMs, highly impact their NLO response and contrast upon switching. Finally, the effects of the rigidity and fluidity of the surrounding are evidenced for NLO dyes inserted in phospholipid bilayers.

Characterizing Counterion-Dependent Aggregation of Rhodamine B by Classical Molecular Dynamics Simulations.

The aggregation in a solution of charged dyes such as Rhodamine B (RB) is significantly affected by the type of counterion, which can determine the self-assembled structure that in turn modulates the optical properties. RB aggregation can be boosted by hydrophobic and bulky fluorinated tetraphenylborate counterions, such as F5TPB, with the formation of nanoparticles whose fluorescence quantum yield (FQY) is affected by the degree of fluorination. Here, we developed a classical force field (FF) based on the standard generalized Amber parameters that allows modeling the self-assembling process of RB/F5TPB systems in water, consistent with experimental evidence. Namely, the classical MD simulations employing the re-parametrized FF reproduce the formation of nanoparticles in the RB/F5TPB system, while in the presence of iodide counterions, only RB dimeric species can be formed. Within the large, self-assembled RB/F5TPB aggregates, the occurrence of an H-type RB-RB dimer can be observed, a species that is expected to quench RB fluorescence, in agreement with the experimental data of FQY. The outcome provides atomistic details on the role of the bulky F5TPB counterion as a spacer, with the developed classical FF representing a step towards reliable modeling of dye aggregation in RB-based materials.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.

Self-assembling, structure and nonlinear optical properties of fluorescent organic nanoparticles in water.

Owing to their intense emission, low toxicity and solubility in aqueous medium, fluorescent organic nanoparticles (FONs) have emerged as promising alternatives to inorganic ones for the realization of exogenous probes for bioimaging applications. However, the intimate structure of FONs in solution, as well as the role played by intermolecular interactions on their optical properties, remains challenging to study. Following a recent Second-Harmonic Scattering (SHS) investigation led by two of us [Daniel et al., ACS Photonics, 2015, 2, 1209], we report herein a computational study of the structural organization and second-order nonlinear optical (NLO) properties of FONs based on dipolar chromophores incorporating a hydrophobic triphenylamine electron-donating unit and a slightly hydrophilic aldehyde electron-withdrawing unit at their extremities. Molecular dynamics simulations of the FON formation in water are associated with quantum chemical calculations, to provide insight into the molecular aggregation process, the molecular orientation of the dipolar dyes within the nanoparticles, and the dynamical behavior of their NLO properties. Moreover, the impact of intermolecular interactions on the NLO responses of the FONs is investigated by employing the tight-binding version of the recently developed simplified time-dependent density functional theory (sTD-DFT) approach, allowing the all-atom quantum mechanics treatment of nanoparticles.

Second-order nonlinear optical properties of Stenhouse photoswitches: insights from density functional theory.

We report the first investigation of the second-order nonlinear optical (NLO) properties of donor-acceptor Stenhouse adducts (DASAs), an emerging class of colored photochromes that undergo photoswitching with visible light to a colorless form. By using time-dependent density functional theory, we provide insights into the relationships linking the nature of the chemical substituents to the amplitude and contrasts of the NLO response. Solvent and frequency dispersion effects are also analyzed. The calculations predict that DASAs behave as high contrast NLO switches, a finding that extends their potential applications to photo-responsive NLO materials and devices.

Nonlinear optical responses of self-assembled monolayers functionalized with indolino-oxazolidine photoswitches.

A computational approach combining molecular dynamic simulations and density functional theory (DFT) calculations is implemented to evaluate the second-order nonlinear optical (NLO) responses of photoresponsive self-assembled monolayers (SAMs) based on indolino-oxazolidine molecular switches. These numerical simulations provide a complete atomistic picture of the morphology of the SAMs, revealing a high degree of positional disorder and an almost isotropic orientation of the chromophores. Subsequent DFT calculations, carried out to evaluate the average first hyperpolarizability of indolino-oxazolidine switches within the SAM, predict that the structural disorder does not significantly reduce the NLO contrast compared to that of the isolated molecules. Chromophores in the SAM can assume a limited number of specific conformations, due to the high rotational barrier that characterize the conjugated bonds along the indolino/oxazolidine-dyene-thiophene sequence. A notable exception is the rotation about the thiophene-thioalkyl bond, which is not only almost free, but also strongly correlated with the magnitude of the first hyperpolarizability. Controlling this rotation by chemical design could thus be a viable strategy to optimize the SAMs NLO response and the performance of photoresponsive devices based on indolino/oxazolidine switches.

Energetic fluctuations in amorphous semiconducting polymers: Impact on charge-carrier mobility.

We present a computational approach to model hole transport in an amorphous semiconducting fluorene-triphenylamine copolymer (TFB), which is based on the combination of molecular dynamics to predict the morphology of the oligomeric system and Kinetic Monte Carlo (KMC), parameterized with quantum chemistry calculations, to simulate hole transport. Carrying out a systematic comparison with available experimental results, we discuss the role that different transport parameters play in the KMC simulation and in particular the dynamic nature of positional and energetic disorder on the temperature and electric field dependence of charge mobility. It emerges that a semi-quantitative agreement with experiments is found only when the dynamic nature of the disorder is taken into account. This study establishes a clear link between microscopic quantities and macroscopic hole mobility for TFB and provides substantial evidence of the importance of incorporating fluctuations, at the molecular level, to obtain results that are in good agreement with temperature and electric field-dependent experimental mobilities. Our work makes a step forward towards the application of nanoscale theoretical schemes as a tool for predictive material screening.

Molecular organization in freely suspended nano-thick 8CB smectic films. An atomistic simulation.

We present an atomistic molecular dynamics simulation of freely suspended films of the smectic liquid crystal 8CB formed by nl = 2, 3,…,10, 20 theoretical monolayers, determining their orientational and positional order as a function of the film thickness. We find that films are always composed by bilayers of antiparallel molecules, and that in the case of odd nl, the system prefers to self-assemble in (nl + 1)/2 bilayers, with an increase of surface tension with respect to even nl samples. We also show that external layers have higher positional and orientational order, and that upon heating the disordering of the system proceeds from the inside, with the central layers progressively losing their smectic character, while the external ones are more resistant to temperature changes and keep the film from breaking.

Communication: molecular dynamics and (1)H NMR of n-hexane in liquid crystals.

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

Charge dissociation at interfaces between discotic liquid crystals: the surprising role of column mismatch.

The semiconducting and self-assembling properties of columnar discotic liquid crystals have stimulated intense research toward their application in organic solar cells, although with a rather disappointing outcome to date in terms of efficiencies. These failures call for a rational strategy to choose those molecular design features (e.g., lattice parameter, length and nature of peripheral chains) that could optimize solar cell performance. With this purpose, in this work we address for the first time the construction of a realistic planar heterojunction between a columnar donor and acceptor as well as a quantitative measurement of charge separation and recombination rates using state of the art computational techniques. In particular, choosing as a case study the interface between a perylene donor and a benzoperylene diimide acceptor, we attempt to answer the largely overlooked question of whether having well-matching donor and acceptor columns at the interface is really beneficial for optimal charge separation. Surprisingly, it turns out that achieving a system with contiguous columns is detrimental to the solar cell efficiency and that engineering the mismatch is the key to optimal performance.

Supramolecular organization of functional organic materials in the bulk and at organic/organic interfaces: a modeling and computer simulation approach.

The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational "engine" (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions. Recent literature dealing with the simulation of organic semiconductors is critically reviewed in order of increasing complexity of the system studied, from low molecular weight molecules to semiflexible polymers, including the challenging problem of determining the morphology of heterojunctions between two different materials.

Quinquephenyl: the simplest rigid-rod-like nematic liquid crystal, or is it? An atomistic simulation.

We have performed an atomistic molecular-dynamics study on the molecular organization and liquid-crystalline properties of quinquephenyl (P5), a prototypical mesogen that is of interest for organic electronics. The thermotropic behavior reveals different mesophases. When cooling down from the isotropic phase, a transition to nematic (≈715 K) is found, then a smectic SA (≈657 K) and another smectic, SXA (≈642 K), before a crystalline phase is recovered (≈617 K). This phase sequence is compared with experimental findings. The different phases are described in terms of their molecular organization, orientational and positional order parameters, and pair distribution functions, as well as of their dynamics properties. In particular, the smectic phases that have not yet been characterized experimentally are discussed. By analyzing the effective shape of P5, it is concluded that its internal torsions and bending make it less rigid than could be expected.

Order and conformation of biphenyl in cyanobiphenyl liquid crystals: a combined atomistic molecular dynamics and 1H NMR study.

The alignment of biphenyl (2P) in the liquid-crystal phases of 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4-n-octyl-4'-cyanobiphenyl (8CB) is investigated by using a combination of predictive atomistic molecular dynamics (MD) simulations and (1)H liquid-crystal nuclear magnetic resonance (LXNMR) residual dipolar coupling measurements. A detailed comparison and validation of the MD results with LXNMR is provided, showing a good agreement between the simulated and experimental dipolar couplings at the same reduced temperature. MD is then used to examine the location of 2P in the smectic phase, which is unavailable to LXNMR, and 2P is found to be rather uniformly distributed. The combination of MD and NMR spectroscopy provides detailed information about the order, interconnection between orientation and conformation, local positional order, and interactions with the liquid-crystalline solvent.

Charge separation energetics at organic heterojunctions: on the role of structural and electrostatic disorder.

Improving the performance of organic photovoltaic cells requires the individuation of the specific factors limiting their efficiency, by rationalizing the relationship between the chemical nature of the materials, their morphology, and the electronic processes taking place at their interface. In this contribution, we present recent theoretical advances regarding the determination of the energetics and dynamics of charge carriers at organic-organic interfaces, highlighting the role of structural and electrostatic disorder in the separation of electron-hole pairs. The influence of interfacial electrostatic interactions on charge carrier energetics is first illustrated in model aggregates. Then, we review some of our recent theoretical studies in which we combined molecular dynamics, quantum-chemical and classical micro-electrostatic methods to evaluate the energy landscape explored by the mobile charges in the vicinity of donor-acceptor interfaces with realistic morphologies. Finally, we describe the theoretical challenges that still need to be overcome in order to gain a complete overview of the charge separation processes at the molecular level.

Molecularly induced order promotes charge separation through delocalized charge-transfer states at donor-acceptor heterojunctions.

The energetic landscape at the interface between electron donating and accepting molecular materials favors efficient conversion of intermolecular charge-transfer (CT) states into free charge carriers (FCC) in high-performance organic solar cells. Here, we elucidate how interfacial energetics, charge generation and radiative recombination are affected by molecular arrangement. We experimentally determine the CT dissociation properties of a series of model, small molecule donor-acceptor blends, where the used acceptors (B2PYMPM, B3PYMPM and B4PYMPM) differ only in the nitrogen position of their lateral pyridine rings. We find that the formation of an ordered, face-on molecular packing in B4PYMPM is beneficial to efficient, field-independent charge separation, leading to fill factors above 70% in photovoltaic devices. This is rationalized by a comprehensive computational protocol showing that, compared to the more amorphous and isotropically oriented B2PYMPM, the higher structural order of B4PYMPM molecules leads to more delocalized CT states. Furthermore, we find no correlation between the quantum efficiency of FCC radiative recombination and the bound or unbound nature of the CT states. This work highlights the importance of structural ordering at donor-acceptor interfaces for efficient FCC generation and shows that less bound CT states do not preclude efficient radiative recombination.

Predicting the anchoring of liquid crystals at a solid surface: 5-cyanobiphenyl on cristobalite and glassy silica surfaces of increasing roughness.

We employ atomistic molecular dynamics simulations to predict the alignment and anchoring strength of a typical nematic liquid crystal, 4-n-pentyl-4'-cyano biphenyl (5CB), on different forms of silica. In particular, we study a thin (~20 nm) film of 5CB supported on surfaces of crystalline (cristobalite) and amorphous silica of different roughness. We find that the orientational order at the surface and the anchoring strength depend on the morphology of the silica surface and its roughness. Cristobalite yields a uniform planar orientation and increases the order at the surface with respect to the bulk whereas amorphous glass has a disordering effect. Despite the low order at the amorphous surfaces, a planar orientation is established with a persistence length into the film higher than the one obtained for cristobalite.

An atomistic description of the nematic and smectic phases of 4-n-octyl-4' cyanobiphenyl (8CB).

We report the results of atomistic molecular dynamics simulations of 4-n-octyl-4' cyanobiphenyl (8CB) on samples of 750 and 3000 molecules showing the spontaneous formation of the nematic phase and then of smectic layers by gradually cooling down from the isotropic phase. Orientational, positional, and mixed order parameters, layer spacing, translational diffusion tensor components and their temperature dependence are reported. A detailed comparison with available experimental data validates the model and force field employed and clarifies the molecular organization of this important liquid crystal often used as reference smectic material.

Temperature dependence of charge mobility in model discotic liquid crystals.

We address the calculation of charge carrier mobility of liquid-crystalline columnar semiconductors, a very promising class of materials in the field of organic electronics. We employ a simple coarse-grained theoretical approach and study in particular the temperature dependence of the mobility of the well-known triphenylene family of compounds, combining a molecular-level simulation for reproducing the structural changes and the Miller-Abrahams model for the evaluation of the transfer rates within the hopping regime. The effects of electric field, positional and energetic disorder are also considered. Simulations predict a low energetic disorder (~0.05 eV), slightly decreasing with temperature within the crystal, columnar and isotropic phases, and fluctuations of the square transfer integral of the order of 0.003 eV(2). The shape of the temperature-dependent mobility curve is however dominated by the variation of the transfer integral and barely affected by the disorder. Overall, this model reproduces semi-quantitatively all the features of experimentally measured mobilities, on one hand reinforcing the correctness of the hopping transport picture and of its interplay with system morphology, and on the other suggesting future applications for off-lattice modeling of organic electronics devices.

Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics.

The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems.