Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite

Restructuring of Porphyrin Networks Driven by Self-Assembled Octanoic Acid Monolayer on Au(111)

We report time-dependent surface restructuring of bicomponent domain structures of 2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine (H₂OEP) and cobalt(II) 2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine (CoOEP) (H₂/Co OEP) driven by self-assembled octanoic acid on the surface of Au(111). Scanning tunneling microscopy (STM) visualized molecular adsorption/desorption and rearrangement of supramolecular architectures in real-time in a solution of octanoic acid. We found that unique domain structures emerged at an initial state guided by adsorbed octanoic acid on the Au surface. Moreover, the desorption of octanoic acid occurred in solution, leading to the surface restructuring of porphyrin molecular networks. This molecular evidence is well-manifested in the time-dependent phase transitions, monitored by in situ STM.

Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations

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.

Cooperativity and coverage dependent molecular desorption in self-assembled monolayers: computational case study with coronene on Au(111) and HOPG

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.

In Situ Observations of UV-Induced Restructuring of Self-Assembled Porphyrin Monolayer on Liquid/Au(111) Interface at Molecular Level

Porphyrin-derived molecules have received much attention for use in solar energy conversion devices, such as artificial leaves and dye-sensitized solar cells. Because of their technological importance, a molecular-level understanding of the mechanism for supramolecular structure formation in a liquid, as well as their stability under ultraviolet (UV) irradiation, is important. Here, we observed the self-assembled structure of free-base, copper(II), and nickel(II) octaethylporphyrin formed on Au(111) in a dodecane solution using scanning tunneling microscopy (STM). As evident in the STM images, the self-assembled monolayers (SAMs) of these three porphyrins on the Au(111) surface showed hexagonal close-packed structures when in dodecane solution. Under UV irradiation (λ = 365 nm), the porphyrin molecules in the SAM or the dodecane solution move extensively and form new porphyrin clusters on the Au sites that have a high degree of freedom. Consequently, the Au(111) surface was covered with disordered porphyrin clusters. However, we found that the porphyrin molecules decomposed under UV irradiation at 254 nm. Molecular-scale observation of the morphological evolution of the porphyrin SAM under UV irradiation can provide a fundamental understanding of the degradation processes of porphyrin-based energy conversion devices.

How Equilibrium Gets Mimicked During Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers

The recent review of Hipps and Mazur is extended to consider the origins and significance of their conclusion that "surface structures vary with relative component concentration in a way that may mimic equilibria but is not". How this situation can arise during self-assembly is discussed, as well as a range of qualitative and quantitative observations and high-level free-energy calculations that document the effect for meso-tetraalkylporphyrins self-assembled monolayer (SAM) polymorphs. This leads to a discussion of modern challenges facing quantification of the effects caused by kinetic control, as well as to the usefulness of equilibrium mimicking in the design and synthesis of SAMs.

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

S-Shaped Conformation of the Quaterthiophene Molecular Backbone in Two-Dimensional Bisterpyridine-Derivative Self-Assembled Nanoarchitecture

The conformation and the two-dimensional self-assembly of 4'-(3',4″-dihexyloxy-5,2':5',2″:5″,2‴-quaterthien-2,5‴-diyl)-bis(2,2':6',2″-terpyridine) molecules are theoretically and experimentally investigated. This molecular building block forms a hydrogen-bonded chiral supramolecular nanoarchitecture on graphite at the solid/liquid interface. Scanning tunneling microscopy (STM) shows that the molecule adopts an S-shaped conformation in this structure. DFTB+ calculations reveal that this conformation is not the lowest-energy conformation. The molecular nanoarchitecture appears to be stabilized by hydrogen bonding as well as van der Waals interactions. I-, L-, and D-shaped molecular conformations are, however, locally observed at the domain boundary, but these conformations do not self-assemble into organized 2D structures.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Engineering porous and compact two-dimensional nanoarchitectures on surfaces taking advantage of bisterpyridine-derivatives self-assembly

The self-assembly of bis-terpyridine molecules is investigated using STM. Images reveal that close-packed as well as porous two-dimensional nanoarchitectures can be engineered by changing the molecular backbone separating the terpyridine groups.

Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation

Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(II) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules.

Effect of dispersion on surface interactions of cobalt(ii) octaethylporphyrin monolayer on Au(111) and HOPG(0001) substrates: a comparative first principles study

Implication of dispersion interactions on geometric, adsorption and electronic properties of porphyrin monolayer on conductive surfaces using density functional theory.

Little exchange at the liquid/solid interface: defect-mediated equilibration of physisorbed porphyrin monolayers

The transition from low to high density 2D surface structures of copper porphyrins at a liquid/solid interface requires specific defects at which nearly all exchange of physisorbed molecules with those dissolved in the supernatant occurs.