Chemical and Biological Engineering ETDs


Raid Haddad

Publication Date



Porphyrins and related compounds are ubiquitous in nature, performing diverse functions including solar energy transduction, electron transport, molecular transport and storage, and catalysis. Due to their unique photophysical and chemical properties, they are excellent candidates for application as photosensitizers, catalysts, photocatalysts, molecular electronics and opto-electronics. Several properties of porphyrins are sensitive to small variations in their structure, and this dissertation investigates the effects of out-of-plane distortions of the macrocycle on optical properties, reactivity to axial ligands, and substituent rotation. The structure-functions relationships are examined using molecular simulations, UV-visible absorption spectroscopy, resonance Raman spectroscopy, and normal-coordinate structural decomposition (NSD) analysis of simulated and X-ray crystal structures. Concerning the optical properties, the view that the large red shifts seen in the optical absorption bands of peripherally crowded nonplanar porphyrins are the result of nonplanar deformations of the macrocycle had been challenged in the literature by studies suggesting that the shifts arise from substituent-induced changes in the macrocycle bond lengths and bond angles, termed in-plane nuclear reorganization (IPNR). The origins of the red shifts were here studied computationally and spectroscopically in a series of nickel or zinc meso-tetraalkyl porphyrins with graded amounts of ruffling deformations, as well as a series of novel bridled nickel chiroporphyrins in which ruffling deformation is determined by bridle length while other substituent effects are minimal. Using various structural restraints, the computational studies demonstrated conclusively that the large Soret band red shifts (~ 40 nm) seen for very nonplanar tetra(tert-butyl) porphyrin compared to tetra(methyl) porphyrin are primarily the result of nonplanar deformations and not IPNR. Strikingly, nonplanar deformations along the high-frequency 2B1u and 3B1u normal coordinates of the macrocycle are shown to contribute significantly to the observed red shifts, even though these deformations are an order of magnitude smaller than the observed ruffling (1B1u) deformation. Other structural and electronic influences on the UV-visible band shifts are discussed and problems with the previous studies that lead to a mistaken attribution of the red shift to IPNR are examined. These results suggest that adjustment of nonplanarity may be used to tweak porphyrin properties for specific applications, and that UV-visible band shifts of tetrapyrroles in proteins are potentially useful indicators of changes in nonplanarity provided other structural and electronic factors can be eliminated. With the aim of investigating the utility of axial ligand binding to drive porphyrinic molecular devices, the effects of nonplanarity on the axial ligation properties of nickel porphyrins were studied using again a series of meso-tetraalkyl porphyrins. Increased porphyrin ruffling is spectroscopically found to cause a drastic decrease in the binding affinity for pyrrolidine and piperidine, such that the affinity is greatly lowered for the tetraalkyl porphyrins porphyrins with methyl or primary alkyl groups compared to nearly planar NiTPP, and ligand binding is nearly completely inhibited for those with secondary or tertiary alkyl groups (i.e., cyclohexyl, cyclopropyl, iso-propyl, or tert-butyl). Ligand binding energies obtained from molecular mechanics calculations were in agreement with the spectroscopic results, and MM calculations determined that the lowered affinity is the result of the cores of the sterically crowded porphyrins being unable to expand and flatten to accommodate the larger high-spin nickel(II) ion. The computational studies also show that the switch to high-spin nickel has a marked effect on the conformational energy landscape of the nickel tetraalkylporphyrins; an \uf061Β\uf061Β\uf020ruffled conformation is strongly favored for low-spin nickel, whereas different conformations of the macrocycle (e.g., \uf061\uf061\uf061\uf061 domed) are more energetically accessible for high-spin nickel. The possible uses of the small but energetically significant structural change at the nickel ion to drive larger structural changes in nickel porphyrin-based molecular devices are discussed. Specifically, the utility of axial ligation as a mechanism for producing a switchable molecular device (e.g., nanotweezers) was demonstrated by computational and spectroscopic studies of the bridled nickel chiroporphyrin NiBCP-8. Porphyrins are an also an ideal platform for molecular rotors due to the versatility provided by the multiple substituent positions combined with their unique electronic and chemical properties potentially allowing several driving and switching mechanisms for rotation. Computer simulations were here used to explain the unusual experimentally observed rotational behavior of aryl substituents on porphyrins. Meso aryl rotational barriers might be expected to be much higher in dodecaaryl porphyrins than in tetraaryl porphyrins due to the great difference in peripheral crowding, and those NMR studies had found this indeed to be the case for the porphyrin dication (having four protons at the core). Suprisingly, however, small increases were found for the equivalent porphyrins with either nickel or zinc ions at the core. Previous studies of TArPs attributed variance in rotational barrier with core substituent to differing macrocycle nonplanar distortions caused by these substituents. However, it was shown here that the rotational barrier variance could not be accounted for merely by structural differences as observed in the static picture from x-ray crystal structures. Rather, molecular simulations showed that nonplanar deformability of the macrocycle, allowing substituents to move farther out-of-plane than their equilibrium positions, is important in lowering the activation energy for aryl-porphyrin rotation. Furthermore, uni-directional rotation, which is of technological interest since it is often considered a prerequisite for molecular motors, was demonstrated in a dodecaaryl porphyrin dication. This is likely the case for many other aryl-porphyrin rotors, particularly in similarly saddled structures.


porphyrin, simulation, computational, optical, redshift, axial ligation, molecular rotor, spectroscopy, Raman, UV-vis, absorption, nanotweezer; Porphyrins--Structure-activity relationships., Porphyrins--Optical properties., Ligand binding., Porphyrins--Molecular rotation.


Sandia National Labs

Document Type




Degree Name

Chemical Engineering

Level of Degree


Department Name

Chemical and Biological Engineering

First Advisor

Atanassov, Plamen

Second Advisor

Shelnutt, John

First Committee Member (Chair)

Fan, Hongyo

Second Committee Member

Graves, Steven

Third Committee Member

Grey, John