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Indenofluorenes are non-benzenoid conjugated hydrocarbons that have received great interest owing to their unusual electronic structure and potential applications in non-linear optics and photovoltaics. Here, we report the generation of unsubstituted indeno[1,2-a]fluorene, the final and yet unreported parent indenofluorene regioisomer, on various surfaces by cleavage of two C-H bonds in 7,12-dihydro indeno[1,2-a]fluorene through voltage pulses applied by the tip of a combined scanning tunneling microscope and atomic force microscope. On bilayer NaCl on Au(111), indeno[1,2-a]fluorene is in the neutral charge state, while it exhibits charge bistability between neutral and anionic states on the lower work function surfaces of bilayer NaCl on Ag(111) and Cu(111). In the neutral state, indeno[1,2-a]fluorene exhibits either of two ground states: an open-shell {\pi}-diradical state, predicted to be a triplet by density functional and multireference many-body perturbation theory calculations, or a closed-shell state with a para-quinodimethane moiety in the as-indacene core. Switching between open- and closed-shell states of a single molecule is observed by changing its adsorption site on NaCl., Comment: 12 pages, 3 figures and supplementary information containing additional data

Nobelovu nagradu iz kemije za 2018. godinu podijelilo je troje znanstvenika, što se ustalilo kao uobičajena praksa u posljednjih desetak godina. Polovicu nagrade dobila je Frances H. Arnold s Caltecha za usmjerenu evoluciju enzima, a drugu polovicu 9 milijuna švedskih kruna podijelili su George P. Smith (University of Missoury Columbia) i Sir Gregory P. Winter (Cambridge), za tehniku prikaza peptida na površini faga (phage display).

Using the dimerization-dissociation of aromatic C-nitroso compounds as a molecular model (Scheme) we have opened the discussion about the possible conceptualization of the reaction mechanisms in the molecular crystals. By detailed studies of the thermodynamics and kinetics of these thermally induced reactions occurring in crystalline solids we have found that the most important parameter which modify the chemical reactivity is activation entropy. Variation in activation entropy that could be caused by softening of the reactive zone within the crystal can in most cases compensate the changes in the enthalpy of activation, keeping the rate coefficient (and the free energy of activation) within the same range of values under different conditions. Since similar idea appeared also in studying thermodynamics and kinetics of the enzyme catalysis, investigations of the solid-state reaction mechanisms by using convenient models could be of more general importance in physical organic chemistry.

Aromatic C-nitroso compounds can appear as nitroso monomers, and Z- and E-azodioxy dimers. In solution, there is an equilibrium between monomers and dimers which is usually shifted towards the monomers at ambient conditions. However, lowering of solution temperature or crystallization favor dimerization. We studied possible dimerization and/or oligomerization of several new aromatic dinitroso derivatives differing in the spacer group between the aromatic rings. Compounds with multiple aromatic nitroso groups are interesting because thay can form oligomeric and polymeric azodioxides. Solution-state structures and nitroso monomer-azodioxide equilibria of aromatic dinitroso compounds were investigated by one- and two-dimensional variable temperature 1H NMR spectroscopy and quantum chemical calculations.1 Inspection of NMR spectra revealed that aromatic dinitroso compounds dimerize at low temperatures yielding the mixture of monomers and Z- and/or E- azodioxides. The proton chemical shifts of nitroso monomer-azodioxide mixtures were assigned and validated by DFT calculations. In most cases, a preference towards the formation of Z-dimer was observed. The ability of aromatic C-nitroso compounds to dimerize could be used for design of self-assembled bilayers on metal surfaces (Figure 1). Our studies suggested that adsorption of nitrosobenzene derivatives, functionalized with sulfur headgroups, on an Au(111) surface results with the formation of ordered self-assembled monolayers and bilayers with molecules arranged into hexagonal structures.2 More recently, we investigated the possibility of self-assembly and dimerization of sulfur-containing aromatic dinitroso compounds, with nitroso groups in mutual meta-position, on gold surface.3 The results demonstrated that aromatic dinitroso compounds dimerize on an Au(111) surface by forming bilayers through E-azodioxide bonds. However, adlayers of dinitroso compounds are less ordered when compared to those of mononitroso compounds probably due to the steric hindrance of meta-situated nitroso groups.

Dimerizacija aromatskih nitrozo spojeva koristan je modelni sustav za praćenje kemijskih reakcija u čvrstom stanju.

Using the dimerization-dissociation of aromatic C-nitroso compounds as a molecular model (Scheme) we have developed the method for studying the reaction mechanisms in the molecular crystals. By detailed studies of the thermodynamics and kinetics of these thermally induced reactions we have found that the most important parameter, which modify the chemical reactivity is activation entropy. Variation in activation entropy could be explained by softening of the reactive zone around the transition state within the crystal. Since the analogous entropic effect of the variable rigidity has been found also for the transition state encapsulated in the enzyme cavity, our investigations of the solid-state reaction mechanisms by using convenient models could be of more general importance in physical organic chemistry.

Aromatic C-nitroso compounds can exist as monomers or Z- and E-azodioxides (dimers). The preferred form in solution at ambient temperature is monomeric while lowering of temperature or crystallization favors dimerization. Azodioxides undergo solid-state photodissociation to corresponding monomers under cryogenic conditions, which again dimerize by warming. Aromatic C- nitroso compounds with two or more nitroso groups could be used as building blocks for supramolecular structures that could be disassembled or reassembled by external stimuli such as UV radiation or heat. In the present work, we studied solution-state monomer-dimer equilibrium of several new aromatic dinitroso compounds that differ in spacer between two aromatic rings (Scheme 1). In order to observe formation of dimers, we recorded 1H and COSY NMR spectra in chloroform-d5 at ambient and low temperatures. Inspection of NMR spectra revealed that by lowering of temperature new signals appear in the spectra that could be assigned to dimers. Signals of dimers disappear after warming the solution to room temperature. The NMR spectra of monomers and dimers were also modelled using density functional theory. Solution-phase (SMD) optimizations, followed by GIAO calculations, were done at the ωB97-XD/6-311G(d, p) level of theory. In case of dimers, multiple conformers had to be considered in order to obtain a good agreement (MUE < 0.1 ppm) between calculated and experimental spectra.

Aromatic C-nitroso compounds can exist in three different forms, as monomers, Z- or E- dimers (azodioxides). Nitroso compounds also exhibit photochromic and thermochromic behavior in solid state. Azodioxides dissociate under UV irradiation at low temperatures and again dimerize at elevated temperatures. Aromatic nitroso compounds with two or more nitroso groups could be used as supramolecular building blocks. Wuest et al. utilized tetranitroso bocks for construction of covalent organic networks (COFs) by polymerization. Supramolecular structures with azodioxides groups could be disassembled or reassembled by applying external stimuli such as UV radiation or heat. Our goal was to prepare aromatic dinitroso compounds with various spacers between two aromatic rings and to investigate their polymerization properties in solid state. Most of the examined dinitroso compounds form oligomers in the solid state which are mainly in E- configuration. Diphenyl-ether derivative doesn’t form dimers because of the quinoid resonance structure, while diphenylmethane derivative forms Z- oligomers. In the case of diphenylmethane derivative, Z- conformers are stabilized by favorable aromatic ring π-π stacking. Monomers are generated upon UV irradiation at cryogenic temperatures. Monomers dimerize by heating the samples to ~150 K. Methane, ethane, biphenyl and benzophenone derivatives form Eoligomers upon redimerization. In the case of diphenylmethane, E- dimers isomerize to thermodynamically more stable Z- conformation upon further heating.

U radu je testirana nova klaster-kontinuum metoda modeliranja solvatacije. U sklopu rada optimiziran je prvi korak metode - stohastičko raspršenje molekula vode oko funkcijskih skupina i generiranje mnoštva različitih i fizikalno smislenih klastera kratkom optimizacijom. To je postignuto variranjem parametara basin hopping Monte Carlo procedure u programu GAMESS, pri čemu je povećana učinkovitost metode. Na temelju početnih klastera napravljene su funkcije radijalne gustoće vjerojatnosti nalaženja atoma kisika molekula vode oko funkcionalnih skupina. Na temelju toga solutima su određeni solvatacijski bazeni funkcionalnih skupina, koji sadrže sve potencijalno bitne molekule otapala za mikrosolvataciju soluta. Nakon toga, odabir najčvršće vezanih molekula vode proveden je NCU analizom.

U ovoj disertaciji predstavljena je i primijenjena nova klaster-kontinuum metoda za opis solvatacije. U odnosu na postojeće, ova metoda uvodi novi pristup generiranju klastera na način da se solutu dodaju najvažnije molekule otapala. Pristup se temelji na konceptu solvatacijskih sfera funkcionalnih skupina. Radijusi solvatacijskih sfera dobivaju se analizom radijalnih funkcija raspodjele molekula otapala oko funkcionalnih skupina soluta, što omogućuje eliminaciju molekula otapala koje nisu potrebne za točan opis solvatacije. Nakon toga, daljnja analiza vrši se usporedbom interakcijskih energija preostalih molekula otapala. Predstavljena metoda omogućuje jednostavno, efikasno i nepristrano dobivanje geometrija s određenim brojem molekula otapala. Testiranje metode provedeno je na dva modelna sustava u vodi. Analizom dobivenih geometrija identificirani su obrasci vezanja nabijenih i neutralnih vrsta s molekulama vode, dok su dobivene energije, utežene Boltzmannovom raspodjelom, dale vrijednosti termodinamičkih veličina u odstupanju od 1 kcal/mol od eksperimentalnih. Nakon toga, metoda je iskorištena za istraživanje mogućih reakcijskih mehanizama hidrolize acetil-klorida. In this dissertation, a new cluster-continuum solvation modeling method is presented and applied. The most important feature of this method is a novel approach for the generation of clusters, in which only important solvent molecules are added to the solute. This approach is based on the concept of functional group solvation spheres. Solvation sphere radii are defined by analyzing radial distribution functions of solvent molecules around solute functional groups, which enables the elimination of molecules unperturbed by the solute. Also, the presented method implements a procedure for simple, effective and unbiased generation of geometries with a selected number of solvent molecules. This is achieved by sorting the solvent molecules according to their interaction energy. The method was tested on two model systems, using water as the solvent. The patterns of solvent-solute bonding for neutral and charged molecules were identified by analysis of obtained geometries, while the calculated Boltzmann weighted Gibbs energies gave values of thermodynamic quantities with an average deviation of 1 kcal/mol when compared to experimental data. After that, the method was used for the investigation of acetyl-chloride hydrolysis reaction mechanisms.

Polymerization 1, 4-dinitrosobenzene was examined to gain a deeper understanding of solid-state reactions. The experimental part included the study of depolymerization and low temperature polymerization of 1, 4-dinitrosobenzene in the solid state by IR spectroscopy. The dissociation of azodioxide bonds was induced either by 254 nm UV irradiation at cryogenic temperatures or by sublimation. Monomers started to form azodioxy bonds at around 150 K. While E-polymers were obtained from monomers prepared by UV photodissociation, Z-forms were detected in samples prepared by sublimation and subsequent deposition on a CsI surface. Because Z-forms isomerized to more stable E polymers above 150 K, these isomers are probably kinetically stabilized by interactions with alkali halide surface. Since polymerization is accompanied by phase transition, a non-linear Avrami-Erofeev kinetic analysis was utilized to determine kinetic parameters. The results suggested a one-dimensional phase growth, as was expected for a linear polymer. The structure of oligomers was also studied computationally. DFT methods were used for shorter polymers, while longer ones were calculated by Fragment Molecular Orbitals method. Both methods suggest helical E-conformations to be the most stable, with a full helix turn after 38 Å. Lower stability of Z-isomers is explained by electrostatic repulsions between oxygen atoms which are spaced much more closely than in E- isomers. Since FMO method showed good correlation with the DFT results and was much faster, we find it suitable for theoretical study of similar polymers and further investigation.