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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. 

Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented. 

One of the common practices in the literature of molecular desorption is the comparison of theoretically (mostly using DFT) calculated single molecule adsorption energies with experimental desorption energies from studies like temperature programmed desorption (TPD) etc. Comparisons like those do not consider that the experimental desorption energies are obtained via ensemble techniques while theoretical values are calculated at the single molecule level. Theoretical values are generally based upon desorption of a single molecule from a clean surface, or upon desorption of an entire monolayer. On the other hand, coverage dependent molecule–molecule interactions add to and modify molecule–substrate interactions that contribute to the experimentally determined desorption energies. In this work, we explore the suitability of an additive nearest neighbor model for determining general coverage dependent single molecule desorption energies in non-covalent self-assembled monolayers (SAMs). These coverage dependent values serve as essential input to any model attempting to reproduce coverage dependent desorption or for understanding the time dependent desorption from a partially covered surface. This method is tested using a case study of coronene adsorbed on Au(111) and HOPG substrates with periodic DFT calculations. Calculations show that coronene exhibits coverage and substrate dependence in molecular desorption. We found that intermolecular contact energies in the coronene monolayer are not strongly influenced by the HOPG substrate, while coronene desorption on Au(111) exhibits strong cooperativity where the additive model fails.