Computer simulation of ordering and dynamics in liquid crystals in the bulk and close to the surface

The aim of this PhD thesis is to investigate the orientational and dynamical properties of liquid crystalline systems, at molecular level and using atomistic computer simulations, to reach a better understanding of material behavior from a microscopic point view. In perspective this should allow to clarify the relation between the micro and macroscopic properties with the objective of predicting or confirming experimental results on these systems. In this context, we developed four different lines of work in the thesis. The first one concerns the orientational order and alignment mechanism of rigid solutes of small dimensions dissolved in a nematic phase formed by the 4-pentyl,4 cyanobiphenyl (5CB) nematic liquid crystal. The orientational distribution of solutes have been obtained with Molecular Dynamics Simulation (MD) and have been compared with experimental data reported in literature. we have also verified the agreement between order parameters and dipolar coupling values measured in NMR experiments. The MD determined effective orientational potentials have been compared with the predictions of Maier­Saupe and Surface tensor models. The second line concerns the development of a correct parametrization able to reproduce the phase transition properties of a prototype of the oligothiophene semiconductor family: sexithiophene (T6). T6 forms two crystalline polymorphs largely studied, and possesses liquid crystalline phases still not well characterized, From simulations we detected a phase transition from crystal to liquid crystal at about 580 K, in agreement with available experiments, and in particular we found two LC phases, smectic and nematic. The crystal­smectic transition is associated to a relevant density variation and to strong conformational changes of T6, namely the molecules in the liquid crystal phase easily assume a bent shape, deviating from the planar structure typical of the crystal. The third line explores a new approach for calculating the viscosity in a nematic through a virtual exper- iment resembling the classical falling sphere experiment. The falling sphere is replaced by an hydrogenated silicon nanoparticle of spherical shape suspended in 5CB, and gravity effects are replaced by a constant force applied to the nanoparticle in a selected direction. Once the nanoparticle reaches a constant velocity, the viscosity of the medium can be evaluated using Stokes' law. With this method we successfully reproduced experimental viscosities and viscosity anisotropy for the solvent 5CB. The last line deals with the study of order induction on nematic molecules by an hydrogenated silicon surface. Gaining predicting power for the anchoring behavior of liquid crystals at surfaces will be a very desirable capability, as many properties related to devices depend on molecular organization close to surfaces. Here we studied, by means of atomistic MD simulations, the flat interface between an hydrogenated (001) silicon surface in contact with a sample of 5CB molecules. We found a planar anchoring of the first layers of 5CB where surface interactions are dominating with respect to the mesogen intermolecular interactions. We also analyzed the interface 5CB­vacuum, finding a homeotropic orientation of the nematic at this interface.

Atomistic simulations of liquid crystals in the bulk and at their interfaces

In this thesis, we have dealt with several problems concerning liquid crystals (LC) phases, either in the bulk or at their interfaces, by the use of atomistic molecular dynamics (MD) simulations. We first focused our attention on simulating and characterizing the bulk smectic phase of 4-n-octyl-4'-cyanobiphenyl (8CB), allowing us to investigate the antiparallel molecular arrangement typical of SmAd smectic phases. A second topic of study was the characterization of the 8CB interface with vacuum by simulating freely suspended thin films, which allowed us to determine the influence of the interface on the orientational and positional order. Then we investigated the LC-water and LC-electrolyte water solution interface. This interface has recently found application in the development of sensors for several compounds, including biological molecules, and here we tried to understand the re-orientation mechanism of LC molecules at the interface which is behind the functioning of these sensors. The characterization of this peculiar interface has incidentally led us to develop a polarizable force field for the pentyl-cyanobiphenyl mesogen, whose process of parametrization and validation is reported here in detail. We have shown that this force field is a significant improvement over its previous, static charge non polarizable version in terms of density, orientational order parameter and translational diffusion.

Sistemi liquido cristallini complessi: simulazioni al calcolatore e studi ESR

The aim of this PhD thesis was to study at a microscopic level different liquid crystal (LC) systems, in order to determine their physical properties, resorting to two distinct methodologies, one involving computer simulations, and the other spectroscopic techniques, in particular electron spin resonance (ESR) spectroscopy. By means of the computer simulation approach we tried to demonstrate this tool effectiveness for calculating anisotropic static properties of a LC material, as well as for predicting its behaviour and features. This required the development and adoption of suitable molecular models based on a convenient intermolecular potentials reflecting the essential molecular features of the investigated system. In particular, concerning the simulation approach, we have set up models for discotic liquid crystal dimers and we have studied, by means of Monte Carlo simulations, their phase behaviour and self­-assembling properties, with respect to the simple monomer case. Each discotic dimer is described by two oblate Gay­Berne ellipsoids connected by a flexible spacer, modelled by a harmonic "spring" of three different lengths. In particular we investigated the effects of dimerization on the transition temperatures, as well as on the characteristics of molecular aggregation displayed and the relative orientational order. Moving to the experimental results, among the many experimental techniques that are typically employed to evaluate LC system distinctive features, ESR has proved to be a powerful tool in microscopic scale investigation of the properties, structure, order and dynamics of these materials. We have taken advantage of the high sensitivity of the ESR spin probe technique to investigate increasingly complex LC systems ranging from devices constituted by a polymer matrix in which LC molecules are confined in shape of nano- droplets, as well as biaxial liquid crystalline elastomers, and dimers whose monomeric units or lateral groups are constituted by rod-like mesogens (11BCB). Reflection-mode holographic-polymer dispersed liquid crystals (H-PDLCs) are devices in which LCs are confined into nanosized (50­-300 nm) droplets, arranged in layers which alternate with polymer layers, forming a diffraction grating. We have determined the configuration of the LC local director and we have derived a model of the nanodroplet organization inside the layers. Resorting also to 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. The results suggest that the molecular organization is dictated mainly by the confinement, explaining, at least in part, the need for switching voltages significantly higher and the observed faster turn-off times in H-PDLCs compared to standard PDLC devices. Liquid crystal elastomers consist in cross-linked polymers, in which mesogens represent the monomers constituting the main chain or the laterally attached side groups. They bring together three important aspects: orientational order in amorphous soft materials, responsive molecular shape and quenched topological constraints. In biaxial nematic liquid crystalline elastomers (BLCEs), two orthogonal directions, rather than the one of normal uniaxial nematic, can be controlled, greatly enhancing their potential value for applications as novel actuators. Two versions of a side-chain BLCEs were characterized: side­-on and end­-on. Many tests have been carried out on both types of LCE, the main features detected being the lack of a significant dynamical behaviour, together with a strong permanent alignment along the principal director, and the confirmation of the transition temperatures already determined by DSC measurements. The end­-on sample demonstrates a less hindered rotation of the side group mesogenic units and a greater freedom of alignment to the magnetic field, as already shown by previous NMR studies. Biaxial nematic ESR static spectra were also obtained on the basis of Molecular Dynamics generated biaxial configurations, to be compared to the experimentally determined ones, as a mean to establish a possible relation between biaxiality and the spectral features. This provides a concrete example of the advantages of combining the computer simulation and spectroscopic approaches. Finally, the dimer α,ω-bis(4'-cyanobiphenyl-4-yl)undecane (11BCB), synthesized in the "quest" for the biaxial nematic phase has been analysed. Its importance lies in the dimer significance as building blocks in the development of new materials to be employed in innovative technological applications, such as faster switching displays, resorting to the easier aligning ability of the secondary director in biaxial phases. A preliminary series of tests were performed revealing the population of mesogenic molecules as divided into two groups: one of elongated straightened conformers sharing a common director, and one of bent molecules, which display no order, being equally distributed in the three dimensions. Employing this model, the calculated values show a consistent trend, confirming at the same time the transition temperatures indicated by the DSC measurements, together with rotational diffusion tensor values that follow closely those of the constituting monomer 5CB.

Theoretical studies of microfluidics: "walking" drops and "melting" snowflakes.

The present PhD thesis summarizes two examples of research in microfluidics. Both times water was the subject of interest, once in the liquid state (droplets adsorbed on chemically functionalized surfaces), the other time in the solid state (ice snowflakes and their fractal behaviour). The first problem deals with a slipping nano-droplet of water adsorbed on a surface with photo-switchable wettability characteristics. Main focus was on identifying the underlying driving forces and mechanical principles at the molecular level of detail. Molecular Dynamics simulation was employed as investigative tool owing to its record of successfully describing the microscopic behaviour of liquids at interfaces. To reproduce the specialized surface on which a water droplet can effectively “walk”, a new implicit surface potential was developed. Applying this new method the experimentally observed droplet slippage could be reproduced successfully. Next the movement of the droplet was analyzed at various conditions emphasizing on the behaviour of the water molecules in contact with the surface. The main objective was to identify driving forces and molecular mechanisms underlying the slippage process. The second part of this thesis is concerned with theoretical studies of snowflake melting. In the present work snowflakes are represented by filled von Koch-like fractals of mesoscopic beads. A new algorithm has been developed from scratch to simulate the thermal collapse of fractal structures based on Monte Carlo and Random Walk Simulations (MCRWS). The developed method was applied and compared to Molecular Dynamics simulations regarding the melting of ice snowflake crystals and new parameters were derived from this comparison. Bigger snow-fractals were then studied looking at the time evolution at different temperatures again making use of the developed MCRWS method. This was accompanied by an in-depth analysis of fractal properties (border length and gyration radius) in order to shed light on the dynamics of the melting process.

Computing the structural and vibrational properties of polymorphic organic molecular crystals through van der Waals corrected density functional theory and the electronic properties of organic thin films through microelectrostatic calculations.

The present Thesis reports on the various research projects to which I have contributed during my PhD period, working with several research groups, and whose results have been communicated in a number of scientific publications. The main focus of my research activity was to learn, test, exploit and extend the recently developed vdW-DFT (van der Waals corrected Density Functional Theory) methods for computing the structural, vibrational and electronic properties of ordered molecular crystals from first principles. A secondary, and more recent, research activity has been the analysis with microelectrostatic methods of Molecular Dynamics (MD) simulations of disordered molecular systems. While only very unreliable methods based on empirical models were practically usable until a few years ago, accurate calculations of the crystal energy are now possible, thanks to very fast modern computers and to the excellent performance of the best vdW-DFT methods. Accurate energies are particularly important for describing organic molecular solids, since they often exhibit several alternative crystal structures (polymorphs), with very different packing arrangements but very small energy differences. Standard DFT methods do not describe the long-range electron correlations which give rise to the vdW interactions. Although weak, these interactions are extremely sensitive to the packing arrangement, and neglecting them used to be a problem. The calculations of reliable crystal structures and vibrational frequencies has been made possible only recently, thanks to development of some good representations of the vdW contribution to the energy (known as “vdW corrections”).

Morphological transitions in molecular and polymeric materials: patterning, fabrication, devices

This thesis individuates and characterizes irreversible transformations occurring in specific organic and oligomeric/polymeric thin films. These transformations are dewetting in discotic liquid crystals thin films and dewetting and smoothing in oligomeric and polyemeric films. Irreversible transformations are extensively characterized by means of optical and atomic force microscopy. In the case of discotic liquid crystals films the morphological characterization is performed sinchronically with electrical measurements of current during dewetting.

Modeling and simulations of nanoparticles in liquid crystalline systems

The aim of this work is to investigate, using extensive Monte Carlo computer simulations, composite materials consisting of liquid crystals doped with nanoparticles. These systems are currently of great interest as they offer the possibility of tuning the properties of liquid crystals used in displays and other devices as well as providing a way of obtaining regularly organized systems of nanoparticles exploiting the molecular organization of the liquid crystal medium. Surprisingly enough, there is however a lack of fundamental knowledge on the properties and phase behavior of these hybrid materials, making the route to their application an essentially empirical one. Here we wish to contribute to the much needed rationalization of these systems studying some basic effects induced by different nanoparticles on a liquid crystal host. We investigate in particular the effects of nanoparticle shape, size and polarity as well as of their affinity to the liquid crystal solvent on the stability of the system, monitoring phase transitions, order and molecular organizations. To do this we have proposed a coarse grained approach where nanoparticles are modelled as a suitably shaped (spherical, rod and disk like) collection of spherical Lennard-Jones beads, while the mesogens are represented with Gay-Berne particles. We find that the addition of apolar nanoparticles of different shape typically lowers the nematic–isotropic transition of a non-polar nematic, with the destabilization being greater for spherical nanoparticles. For polar mesogens we have studied the effect of solvent affinity of the nanoparticles showing that aggregation takes places for low solvation values. Interestingly, if the nanoparticles are polar the aggregates contribute to stabilizing the system, compensating the shape effect. We thus find the overall effects on stability to be a delicate balance of often contrasting contributions pointing to the relevance of simulations studies for understanding these complex systems.

Simulation of Smart Materials

The aim of this thesis is the elucidation of structure-properties relationship of molecular semiconductors for electronic devices. This involves the use of a comprehensive set of simulation techniques, ranging from quantum-mechanical to numerical stochastic methods, and also the development of ad-hoc computational tools. In more detail, the research activity regarded two main topics: the study of electronic properties and structural behaviour of liquid crystalline (LC) materials based on functionalised oligo(p-phenyleneethynylene) (OPE), and the investigation on the electric field effect associated to OFET operation on pentacene thin film stability. In this dissertation, a novel family of substituted OPE liquid crystals with applications in stimuli-responsive materials is presented. In more detail, simulations can not only provide evidence for the characterization of the liquid crystalline phases of different OPEs, but elucidate the role of charge transfer states in donor-acceptor LCs containing an endohedral metallofullerene moiety. Such systems can be regarded as promising candidates for organic photovoltaics. Furthermore, exciton dynamics simulations are performed as a way to obtain additional information about the degree of order in OPE columnar phases. Finally, ab initio and molecular mechanics simulations are used to investigate the influence of an applied electric field on pentacene reactivity and stability. The reaction path of pentacene thermal dimerization in the presence of an external electric field is investigated; the results can be related to the fatigue effect observed in OFETs, that show significant performance degradation even in the absence of external agents. In addition to this, the effect of the gate voltage on a pentacene monolayer are simulated, and the results are then compared to X-ray diffraction measurements performed for the first time on operating OFETs.

Supramolecular hybrid organic-inorganic multicomponent architectures in solution and on surface

Supramolecular architectures can be built-up from a single molecular component (building block) to obtain a complex of organic or inorganic interactions creating a new emergent condensed phase of matter, such as gels, liquid crystals and solid crystal. Further the generation of multicomponent supramolecular hybrid architecture, a mix of organic and inorganic components, increases the complexity of the condensed aggregate with functional properties useful for important areas of research, like material science, medicine and nanotechnology. One may design a molecule storing a recognition pattern and programming a informed self-organization process enables to grow-up into a hierarchical architecture. From a molecular level to a supramolecular level, in a bottom-up fashion, it is possible to create a new emergent structure-function, where the system, as a whole, is open to its own environment to exchange energy, matter and information. “The emergent property of the whole assembly is superior to the sum of a singles parts”. In this thesis I present new architectures and functional materials built through the selfassembly of guanosine, in the absence or in the presence of a cation, in solution and on the surface. By appropriate manipulation of intermolecular non-covalent interactions the spatial (structural) and temporal (dynamic) features of these supramolecular architectures are controlled. Guanosine G7 (5',3'-di-decanoil-deoxi-guanosine) is able to interconvert reversibly between a supramolecular polymer and a discrete octameric species by dynamic cation binding and release. Guanosine G16 (2',3'-O-Isopropylidene-5'-O-decylguanosine) shows selectivity binding from a mix of different cation's nature. Remarkably, reversibility, selectivity, adaptability and serendipity are mutual features to appreciate the creativity of a molecular self-organization complex system into a multilevelscale hierarchical growth. The creativity - in general sense, the creation of a new thing, a new thinking, a new functionality or a new structure - emerges from a contamination process of different disciplines such as biology, chemistry, physics, architecture, design, philosophy and science of complexity.

Biomimetic Materials for Biomedical Applications

Objects with complex shape and functions have always attracted attention and interest. The morphological diversity and complexity of naturally occurring forms and patterns have been a motivation for humans to copy and adopt ideas from Nature to achieve functional, aesthetic and social value. Biomimetics is addressed to the design and development of new synthetic materials using strategies adopted by living organisms to produce biological materials. In particular, biomineralized tissues are often sophisticate composite materials, in which the components and the interfaces between them have been defined and optimized, and that present unusual and optimal chemical-physical, morphological and mechanical properties. Moreover, biominerals are generally produced by easily traceable raw materials, in aqueous media and at room pressure and temperature, that is through cheap process and materials. Thus, it is not surprising that the idea to mimic those strategies proper of Nature has been employed in several areas of applied sciences, such as for the preparation of liquid crystals, ceramic thin films computer switches and many other advanced materials. On this basis, this PhD thesis is focused on the investigation of the interaction of biologically active ions and molecules with calcium phosphates with the aim to develop new materials for the substitution and repair of skeletal tissue, according to the following lines: I. Modified calcium phosphates. A relevant part of this PhD thesis has been addressed to study the interaction of Strontium with calcium phosphates. It was demonstrated that strontium ion can substitute for calcium into hydroxyapatite, causing appreciable structural and morphological modifications. The detailed structural analysis carried out on the nanocrystals at different strontium content provided new insight into its interaction with the structure of hydroxyapatite. At variance with the behaviour of Sr towards HA, it was found that this ion inhibits the synthesis of octacalcium phosphate. However, it can substitute for calcium in this structure up to 15 atom %, in agreement with the increase of the cell parameters observed on increasing ion concentration. A similar behaviour was found for Magnesium ion, whereas Manganese inhibits the synthesis of octacalcium phosphate and it promotes the precipitation of dicalcium phosphate dehydrate. It was also found that Strontium affects the kinetics of the reaction of hydrolysis of α-TCP. It inhibits the conversion from α-TCP to hydroxyapatite. However, the resulting apatitic phase contains significant amounts of Sr2+ suggesting that the addition of Sr2+ to the composition of α-TCP bone cements could be successfully exploited for its local delivery in bone defects. The hydrolysis of α-TCP has been investigated also in the presence of increasing amounts of gelatin: the results indicated that this biopolymer accelerates the hydrolysis reaction and promotes the conversion of α-TCP into OCP, suggesting that its addition in the composition of calcium phosphate cements can be employed to modulate the OCP/HA ratio, and as a consequence the solubility, of the set cement. II. Deposition of modified calcium phosphates on metallic substrates. Coating with a thin film of calcium phosphates is frequently applied on the surface of metallic implants in order to combine the high mechanical strength of the metal with the excellent bioactivity of the calcium phosphates surface layers. During this PhD thesis, thank to the collaboration with prof. I.N. Mihailescu, head of the Laser-Surface-Plasma Interactions Laboratory (National Institute for Lasers, Plasma and Radiation Physics – Laser Department, Bucharest) Pulsed Laser Deposition has been successfully applied to deposit thin films of Sr substituted HA on Titanium substrates. The synthesized coatings displayed a uniform Sr distribution, a granular surface and a good degree of crystallinity which slightly decreased on increasing Sr content. The results of in vitro tests carried out on osteoblast-like and osteoclast cells suggested that the presence of Sr in HA thin films can enhance the positive effect of HA coatings on osteointegration and bone regeneration, and prevent undesirable bone resorption. The possibility to introduce an active molecule in the implant site was explored using Matrix Assisted Pulsed Laser Evaporation to deposit hydroxyapatite nanocrystals at different content of alendronate, a bisphosphonate widely employed in the treatments of pathological diseases associated to bone loss. The coatings displayed a good degree of crystallinity, and the results of in vitro tests indicated that alendronate promotes proliferation and differentiation of osteoblasts even when incorporated into hydroxyapatite. III. Synthesis of drug carriers with a delayed release modulated by a calcium phosphate coating. A core-shell system for modulated drug delivery and release has been developed through optimization of the experimental conditions to cover gelatin microspheres with a uniform layer of calcium phosphate. The kinetics of the release from uncoated and coated microspheres was investigated using aspirin as a model drug. It was shown that the presence of the calcium phosphate shell delays the release of aspirin and allows to modulate its action.

Structure-Property Relationships and Charge Transport Modeling of Organic Molecular Materials

From the perspective of a new-generation opto-electronic technology based on organic semiconductors, a major objective is to achieve a deep and detailed knowledge of the structure-property relationships, in order to optimize the electronic, optical, and charge transport properties by tuning the chemical-physical characteristics of the compounds. The purpose of this dissertation is to contribute to such understanding, through suitable theoretical and computational studies. Precisely, the structural, electronic, optical, and charge transport characteristics of several promising organic materials recently synthesized are investigated by means of an integrated approach encompassing quantum-chemical calculations, molecular dynamics and kinetic Monte Carlo simulations. Particular care is addressed to the rationalization of optical and charge transport properties in terms of both intra- and intermolecular features. Moreover, a considerable part of this project involves the development of a home-made set of procedures and parts of software code required to assist the modeling of charge transport properties in the framework of the non-adiabatic hopping mechanism applied to organic crystalline materials. As a first part of my investigations, I mainly discuss the optical, electronic, and structural properties of several core-extended rylene derivatives, which can be regarded to as model compounds for graphene nanoribbons. Two families have been studied, consisting in bay-linked perylene bisimide oligomers and N-annulated rylenes. Beside rylene derivatives, my studies also concerned electronic and spectroscopic properties of tetracene diimides, quinoidal oligothiophenes, and oxygen doped picene. As an example of device application, I studied the structural characteristics governing the efficiency of resistive molecular memories based on a derivative of benzoquinone. Finally, as a second part of my investigations, I concentrate on the charge transport properties of perylene bisimides derivatives. Precisely, a comprehensive study of the structural and thermal effects on the charge transport of several core-twisted chlorinated and fluoro-alkylated perylene bisimide n-type semiconductors is presented.

Modeling and simulations of some anisotropic soft-matter systems: from biaxial to chiral materials

We have modeled various soft-matter systems with molecular dynamics (MD) simulations. The first topic concerns liquid crystal (LC) biaxial nematic (Nb) phases, that can be possibly used in fast displays. We have investigated the phase organization of biaxial Gay-Berne (GB) mesogens, considering the effects of the orientation, strength and position of a molecular dipole. We have observed that for systems with a central dipole, nematic biaxial phases disappear when increasing dipole strength, while for systems characterized by an offset dipole, the Nb phase is stabilized at very low temperatures. In a second project, in view of their increasing importance as nanomaterials in LC phases, we are developing a DNA coarse-grained (CG) model, in which sugar and phosphate groups are represented with Lennard-Jones spheres, while bases with GB ellipsoids. We have obtained shape, position and orientation parameters for each bead, to best reproduce the atomistic structure of a B-DNA helix. Starting from atomistic simulations results, we have completed a first parametrization of the force field terms, accounting for bonded (bonds, angles and dihedrals) and non-bonded interactions (H-bond and stacking). We are currently validating the model, by investigating stability and melting temperature of various sequences. Finally, in a third project, we aim to explain the mechanism of enantiomeric discrimination due to the presence of a chiral helix of poly(gamma-benzyl L-glutamate) (PBLG), in solution of dimethylformamide (DMF), interacting with chiral or pro-chiral molecules (in our case heptyl butyrate, HEP), after tuning properly an atomistic force field (AMBER). We have observed that DMF and HEP molecules solvate uniformly the PBLG helix, but the pro-chiral solute is on average found closer to the helix with respect to the DMF. The solvent presents a faster isotropic diffusion, twice as HEP, also indicating a stronger interaction of the solute with the helix.

Molecular modelling of organic functional materials

The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials. In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules. Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description. This thesis presents an approach that combines QM calculations with a classical Molecular Dynamics (MD) approach by means of accurate QM-derived force fields. It is based on a careful selection of the most relevant molecular degrees of freedom, whose potential energy surface is calculated at QM level and reproduced by the analytic functions of the force field, as well as by an accurate tuning of the approximations introduced in the model of the process to be simulated. This is made possible by some tools developed purposely, that allow to obtain and test the FF parameters through comparison with the QM frequencies and normal modes. These tools were applied in the modelling of three processes: the npi* photoisomerisation of azobenzene, where the FF description was extended to the excited state too and the non-adiabatic events were treated stochastically with Tully fewest switching algorithm; the charge separation in donors-acceptors bulk heterojunction organic solar cells, where a tight-binding Hamiltonian was carefully parametrised and solved by means of a code, also written specifically; the effect of the protonation state on the photoisomerisation quantum yield of the aryl-azoimidazolium unit of the axle molecule of a rotaxane molecular shuttle. In each case, the QM-based MD models that were specifically developed gave noteworthy information about the investigated phenomena, proving to be a fundamental key for a deeper comprehension of several experimental evidences.