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Understanding the interactions between molecules on surfaces is crucial for advancing technologies in sensing, catalysis, and energy harvesting. In this study we explore the complex surface chemistry resulting from the interaction of Co(II)octaethylporphyrin (CoOEP) and iodine, I2, both in solution and at the phenyloctane/HOPG interface. In pursuit of this goal, we report results from electrochemistry, NMR and UV-Vis spectroscopy, X-ray crystallography, scanning tunneling microscopy (STM), and density functional theory (DFT). Both spectroscopic methods of analysis confirmed that at and above the stoichiometric ratio of one CoOEP to one I2 the reaction product was metal centered CoIII(OEP)I. X-ray crystallography verified that a single iodine is bonded to each cobalt ion in the triclinic, P-1 system. The surface chemistry of CoOEP and I2 is complicated and remarkably dependent on the iodine concentration. STM images of CoOEP and I2 in phenyloctane on highly oriented pyrolytic graphite (HOPG) at low halogen concentrations (1:<2 Co:I ratios) presented random individual Co(OEP)I molecules weakly adsorbed onto a hexagonal (HEX) CoOEP monolayer. Images of 1:2 Co:I ratio solutions, showed phase segregated HEX CoOEP and pseudo-rectangular (REC) Co(OEP)I incorporating one solvent molecule per Co(OEP)I. The REC structure formed in long parallel rows with the number of rows increasing with increasing solution I2. In this case, the presence of CoOEP on the surface was attributed to the spontaneous reduction of Co(OEP)I by the graphite substrate. DFT calculations indicate that the REC Co(OEP)I:PhO form is energetically more stable than the HEX form of Co(OEP)I on HOPG. Experimental STM images and DFT calculated adsorption energies and STM images support our interpretation of the observed structures. 

A comprehensive Scanning Tunneling Microscopy (STM)-driven ab initio investigation was conducted to explore the effects of peripheral substitution and central metalation on the molecular self-assembly of phthalocyanines on highly oriented pyrolytic graphite (HOPG). This study reports, for the first time, the self-assembly behavior of phthalocyanines with phenoxy and ethoxy substitutions and Co and Mg as central metals. Through periodic boundary simulations, we demonstrate that the peripheral substitutions significantly influence the energetic stability and monolayer structure, while central metal variations play a minor role. Our findings suggest that phthalocyanines with identical peripheral substitutions exhibit similar unit cell structures on Highly Oriented Pyrolytic Graphite (HOPG), regardless of the central metal. Furthermore, while substituent positional isomerism does not significantly impact the adsorption energy, the orientation of the peripheral substituents critically affects intermolecular interactions, influencing the stability of the monolayers. The study also reveals that octa-substituted phthalocyanines, such as H₂Pc(OPh)₈, form more stable, well-packed monolayers compared to tetra-substituted derivatives, like H₂Pc(OEt)₄, which exhibit phase segregation and disorder. Additionally, solvent molecules such as phenyl octane (PhOct) stabilize the disordered H₂Pc(OEt)₄monolayers by filling cavities between molecules. These results offer valuable insights into the design principles for engineering stable phthalocyanine monolayers, contributing to advancements in surface chemistry and materials science. 

Density functional theory (DFT) is used to investigate the conversion from a solvent incorporated pseudo-polymorph into a single component monolayer. Calculations of thermodynamic properties both for the surfaces in contact with gas phase and with solvent are reported. In the case of wetted surfaces, a simple bond-additivity model, first proposed by Campbell and modified here, is used to augment the DFT calculations. The model predicts a dramatic reduction in desorption energies in solvent as compared to gas phase. Eyring’s reaction rate theory is used to predict limiting desorption rates for guest (solvent) molecules from the pockets in the pseudo-polymorph and for cobalt octaethylporphyrin (COEP) molecules in all structures. The pseudo-polymorph studied here is a nearly rectangular lattice (REC) composed of two CoOEP and 2 molecules of either 1,2,4-trichlorobenzene (TCB) or toluene (TOL) supported on 63 atoms of Au(111). At sufficiently high initial concentrations of CoOEP, only a hexagonal unit cell (HEX) with two molecules of CoOEP, supported on 50 atoms of gold is observed. Experimentally, the TCB-REC structure is more stable than the TOL-REC structure existing in solution at initial mM concentrations of CoOEP in TCB as opposed to initial M concentration of CoOEP in toluene. Calculations here show that the HEX structure is the thermodynamically stable structure at all practical concentrations of CoOEP. Once the REC structure forms kinetically at low concentration because of the vast excess of solvent on the surface, it is difficult to convert to the more stable HEX structure. The difference in stability is primarily due to the difference in electronic adsorption energy of the solvents (TOL or TCB) and to the very low desorption rate of CoOEP. The adsorption energy of TCB has two important contributors: the adsorption energy onto Au alone, and the intermolecular interactions between TCB and the CoOEP host lattice. Neither factor can be neglected. We also find that planar adsorption of both TOL and TCB on Au(111) is the energetically preferred orientation when space is available on the surface. Rates of desorption are very sensitive to the solvent free activation energy and to the thermodynamic parameters required to convert the solvent free activation energy to one for the solvated surface. Small changes in the computed energy (of the order of 5%) can lead to one order of magnitude change in rates. Further, the solvation model used does not provide the barrier to adsorption in solution needed to determine values for the desorption activation energy. Thus, the rates computed here for desorption into solvent are limiting values.