Coordination Chemistry Reviews: Christopher J. Kingsbury, Mathias O. Senge

Coordination Chemistry Reviews 431 (2021) 213760
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Coordination Chemistry Reviews

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Review
The shape of porphyrins

Christopher J. Kingsbury a, Mathias O. Senge a,b,⇑
a
School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
b
Institute for Advanced Study (TUM-IAS), Technical University of Munich, Focus Group – Molecular and Interfacial Engineering of Organic Nanosystems, Lichtenberg-Str. 2a,
85748 Garching, Germany
a r t i c l e i n f o a b s t r a c t
Article history: Porphyrin molecules are a widely exploited biochemical moiety, with uses in medicinal chemistry, sens-
Received 18 November 2020 ing and materials science. The shape of porphyrins, as an aromatic unit, is reductively imagined to be
Accepted 20 December 2020 approximately flat, with regular, rigid shape, owing to the popular depiction as a simplified skeletal
Available online 22 January 2021
model. While this regular conformation does exist, the array of substitution patterns in synthetic por-
Dedicated to the memory of Prof. John A. phyrins or interactions with the apoprotein in biochemical moieties often induce distortions both in-
Shelnutt plane and out-of-plane. Structural deviation reduces symmetry from the ideal D4h and can introduce
changes in the physical and electronic structure; physical changes can introduce pockets for favorable
Keywords: intermolecular interactions, and electronic distortion can introduce new electronic transitions and prop-
Porphyrins erties. A quantification of porphyrin distortion is presented based on the Normal-coordinate Structural
X-ray crystallography Decomposition method (NSD) pioneered by Shelnutt. NSD transforms crystallographically-determined
Normal-coordinate analysis atomic positions of each porphyrin into a summation of common concerted atom vectors, allowing for
Structure-property relationship quantification of porphyrin anisotropy by symmetry. This method has been used previously for compar-
Macrocyclic ligands
ison of small data sets of synthetic and biological porphyrins. In the twenty-five years since the method
Principal component analysis
was pioneered, the volume and variety of available crystal structure data has ballooned, and data analysis
tools available have become more sophisticated, while the method has languished. Using modern data-
science methods, clusters of porphyrin distortions are grouped to show the average effect that a substi-
tution pattern has on porphyrin shape. Aiming to provide an overview on the shape and conformation of
these key macrocycles we here provide context to the strategies employed for introducing porphyrin dis-
tortion and to provide a quantitative comparative basis for analysis of novel structures. This is achieved
by demonstrating that porphyrin molecules often have a predictable NSD pattern, and therefore solid-
state conformation, based on chemical arguments. This quantification allows for assessment of predicted
structures and forms the basis of a symmetry-by-design motif for a range of porphyrinoids. A modernized
computer program used in this structural determination is provided for analysis, with this treatise acting
as a guide to the interpretation of results in new structure determinations. New features include simple
report generation, prediction of symmetry and assessment of cluster behavior for a range of porphyrin
moieties, as well as convenient plotting functions and data reductions.
Ó 2020 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).
Contents
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2. Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1. Normal-coordinate structural decomposition (NSD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2. Basic description of the NSD analysis program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Abbreviations: CCDC, Cambridge Crystallographic Data Centre; CSD, Crystal Structure Database; Hb, hemoglobin; HOMO, highest-occupied molecular orbital; KDE, Kernel
Density Estimation; OEP, 2,3,7,8,12,13,17,18-octaethylporphyrinato; OETPP, 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetraphenylporphyrinato; NSD, Normal-coordinate
structural decomposition; TPP, 5,10,15,20-tetraporphyrinato; Pc, Phthalocyaninato; PDB, Protein Data Bank.
⇑ Corresponding author at: School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, The
University of Dublin, Dublin 2, Ireland.
E-mail address: sengem@tcd.ie (M.O. Senge).
https://doi.org/10.1016/j.ccr.2020.213760
0010-8545/Ó 2020 The Author(s). Published by Elsevier B.V.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
C.J. Kingsbury and M.O. Senge Coordination Chemistry Reviews 431 (2021) 213760
3. Brief overview of the normal-coordinate analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

4. Analysis of porphyrin structures by cluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.1. B2u . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.1.1. Core modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4.1.2. Peripheral modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4.2. B2g . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
4.3. B1u . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4.4. B1g . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.5. A1g . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.6. A2u . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.7. Eg(x) and Eg(y) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
5. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
5.1. Relation between NSD parameters and techniques for chirality conformer generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
5.2. Some comments on the present analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
6. Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Declaration of Competing Interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Appendix A. Supplementary data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1. Introduction
Tetrapyrrole molecules such as porphyrins (1), chlorins, bacteri-

ochlorins and corrinoids are the colors of life – arguably the most
widely known and exploited biochemical and synthetic macro-
cyclic chelate [1–3]. Porphyrins and chlorins are essential for plant
and animal life, playing essential roles in respiration [4], photosyn-
thesis [5], and electron transport [6]. Porphyrin materials are char-
acterized by strong and tunable light absorption and allow for
modulation of their excited state and catalytic properties. Readily
accessible through stepwise and synchronous condensation routes
[7–9], synthetic porphyrins are used as sensor components [10],
photodynamic therapy medicines [11,12], photocatalysts [13],
and solar energy conversion dyes [14,15], to name only a few.
Well-developed synthetic modification techniques allow for
introduction of a wide variety of modifications to the core and
periphery of the macrocyclic systems (Fig. 1) [7,8,16–22].
Simple synthetic porphyrins, such as (5,10,15,20-tetraphenyl
porphyrinato)zinc(II) (1, M = Zn(II), [23]) or (2,3,7,8,12,13,17,18-
octaethylporphyrinato)zinc(II) (2, M = Zn(II) [24]), are highly
symmetrical and approximately planar, as observed from crystal
structure analysis. The shape of porphyrin molecules is reductively
imagined to be similarly symmetrical and invariant and, while
many have approximately regular structure, the combination of
steric, bonding, and electronic effects can induce variations on this
core pattern. The simplest variation is the modification of the core
– metal centers which have an optimal coordination environment
smaller or larger than that provided by the planar macrocycle
induce distortion in the macrocycle to elicit the preferred coordi-
nation environment. The classic case here are the Ni(II) porphyrins
(e.g., 2, M = Ni(II) [25]) which predominantly adopt the ruffled
out-of-plane geometry, as shown in Fig. 2 [26].
Biogenic tetrapyrroles, chief among them the variants of the
heme and phytochlorin subunits, show a range of distortions from
planar, regular structure [27–29]. These molecular shapes alter the
properties of pyrrolic molecules to perform a range of functions
within the natural world, including photosynthesis, reversible Fig. 1. Standard substituent pattern in core and/or peripherally substituted
binding of oxygen and electron transfer [30–34]. The alteration of porphyrins and numbering scheme used herein.
shape of a ligand by protein environment, a form of allostery, is a
method of fine-tuning reactivity [35,36]. For example, the shape
change from domed to planar in hemoglobin (Hb) upon coopera- Stone and Fleischer, in their groundbreaking paper on the dis-
tive oxygen-binding having been an extensively studied case of tortional profiles of non-planar porphyrins, such as the porphyrin
this effect [37,38]. A comparison of the conformation of the heme diacids (see later in Fig. 10), noted that out of plane distortion were
unit in the two crystal structures of this classic is shown in Fig. 3 significantly more accessible than in-plane distortion for these aro-
[39,40]. matic units [41]. Descriptive terms such as saddle, ruffled, twisted,
2
redox reactions, as well as exocyclic bridging or strapping, and

interfacial manipulation. More detail on the synthetic and struc-
tural aspects of nonplanar porphyrins and the concomitant alter-
ations in chemical reactivity, electrochemistry and
(photo)physical properties [45] can be found in respective reviews
[46,47]. For example, the out-of-plane shape of a porphyrin mole-
cule has a strong effect on porphyrin electronic structure
[45,48,49]. Using the four-orbit model of porphyrin electronic
HOMO/LUMO states presented by Gouterman [50], the molecular
orbitals responsible for the absorption spectra of the porphyrin
chromophore derivative exist on the ligand surface of the por-
phyrinoid molecule, i.e. localized to the macrocycle. In the simplest
representation, out of plane distorted porphyrins show red-shifted
Q- and Soret bands, in line with destabilization of the HOMO a1u
and a2u orbitals, especially for ruffled and saddled porphyrins
[49–53]. Additionally, satellite peaks are observed when molecular
distortion and orbital symmetry correspond, such as for the domed
porphyrin series (A2u distortion) with the a2u HOMO. To highlight,
overcrowding of the porphyrin periphery, such as in the classic chi-
mera of TPP and OEP skeletons 2,3,7,8,12,13,17,18-octaethyl-5,10,
15,20-tetraphenylporphyrin (4, M = 2H; H2OETPP), yields a por-
phyrin molecule distorted significantly from planar structure, usu-
ally in a saddle shape, as demonstrated in Fig. 5 [54]. Later we will
describe in detail means how to assign numerical values to these
distortional profiles.
Next to their relevance as biomimetic compounds out-of-plane
distorted porphyrins such as OETPP and other saddle-distorted
porphyrinoids have recently found renewed interest as organocat-
alysts [55,56] due to their ability to facilitate N–H X interactions
and to use the porphyrin macrocycle as a ligand [57]. Non-planar
Fig. 2. Top and side view of the ruffled porphyrin core in the crystal structure of
porphyrins are especially interesting as sensor components, due
(5,10,15,20-tetraphenylporphyrinato)nickel(II) [1, M = Ni(II)]. Images generated to the conformational and prototropic changes on the binding of
from CCDC No. 1,320,805 CSD code ZZZUUC01 [25]. analytes resulting in measurable photophysical change [10,58,59]
and have also been used as scaffolds for accessing specific por-
phyrin atropisomers [60].
etc. were used to describe the various conformations over the years Out-of-plane distortion of the porphyrin macrocycle has been
and first systematically applied by Scheidt in his fundamental characterized well, the more subtle shifts in atom positions which
studies on metalloporphyrin stereochemistry [42,43]. The out-of- occur parallel to the mean plane of the macrocycle (in-plane dis-
plane distortions of porphyrin macrocycles were observed to be tortions) have been less interrogated. The substitution patterns
broadly correlated with the lowest frequency calculated vibra- around a porphyrin can access lower symmetry of a macrocycle
tional modes of each irreducible representation of the D4h idealized in a complimentary fashion to the out-of-plane structure, which
symmetric group, and are given trivial names such as saddle (B2u), allows for fine-tuning of electronic structure, and access to chiral
ruffle (B1u), dome (A2u) and wave (Eg) [29,43,44], Illustrative exam- aromatics. Substitution patterns such as 5,15-diarylporphyrin ser-
ples of these main distortion modes are shown in Fig. 4. ies stretch the 5,15-axis of the porphyrin and compress the 10,20-
Strategies to yield porphyrins with significant deviations from axis, rectangularizing the square porphyrin moiety [61–67]. This
planarity include core, peripheral and electronic manipulation, structural distortion is complementary to an equivalent electronic
Fig. 3. The conformation of the heme core of human hemoglobin (Hb) as Hb (left) and oxyHb (right). Images generated from structures in references [39,40] (pdb codes
2 W72 and 2DN1, respectively).
3
Fig. 4. The four principal modes of porphyrin 24-atom out-of-plane deformation – the saddle (B2u, blue), ruffle (B1u, yellow), dome (A2u, green) and wave (Eg(x) or Eg(y), red).
effect a particular porphyrin substitution will have on the macro-

cycle shape, and to what magnitude. Individual crystal structures
are susceptible to effects of crystalline solvate, intermolecular
interactions and symmetry constraints of the solid state, which
may affect the measured porphyrin shape. As such, one crystal
structure is not necessarily representative of the same molecule’s
solution-phase symmetry.
This review describes an approach to assessing specific por-
phyrin distortional profiles, using crystallographic data mining
[73] in combination with data pretreatment by Normal-
coordinate Structural Decomposition (NSD) [29], to quantify dis-
tortion in reported porphyrin molecules in the CCDC CSD 2020.1
[74]. This method of assessing the complete literature for the
design of molecules is a powerful tool to inform synthetic investi-
gations, and necessary for the design of chiral porphyrins. Addi-
tionally, this dataset allows for crystallographers to fully
contextualize the structure of novel molecules with reference to
previously published structures. A program for assessment of novel
Fig. 5. View of the molecular structure in the crystal of (5,10,15,20-tetraphenyl- crystal structures in relation to this data set is similarly described,
2,3,7,8,12,13,17,18-octaethylporphyrinato)zinc(II) methanol solvate [42MeOH,
and the set of tools which was used in this analysis is presented as
M = Zn(II)] demonstrating the saddle-shape out-of-plane distortion of the porphyrin
core. Solvate and H-atoms are omitted from view. Image generated from CCDC No. well.
1185828, CSD code JICNIS [54]. The method of deconvolution of structural effects in chro-
mophores along symmetry-based normal coordinates is, we
believe, an especially powerful tool for chemical understanding,
distortion patterning, such as in the push-pull-type porphyrins as well as machine learning data pre-treatment. While this review
[68]. is specifically restricted to porphyrin molecules, the potential
Designing molecules with complimentary in-plane and out-of- applications of a wider application of the methods herein will be
plane structure allows for distorted macrocycles with ideal sym- discussed later in Section 5.
metry being substantially altered from the ideal D4h. Examples of The individual modes presented in Section 4 are intended to
design of chiral porphyrins have used a saddle shape (B2u) and dif- give an overview of the most accessible and prevalent distortional
ferential substitution at the 5,15 and 10,20 position (B2g) in either a modes in porphyrin macrocycles, the substitution patterns
porphyrin [64,65] or porphodimethene [70,71] to elicit a D2- required to attain them, and the factors affecting the extent of
symmetric macrocyclic conformation. Chirality in supramolecular the mode as measured. Porphyrin compounds with similar substi-
porphyrin complexes has been reviewed previously [72]. tution patterns cluster together in NSD terms, indicating that they
A strong bidirectional relationship between chemical substitu- adopt similar conformations. A list of these clusters, which often
tion pattern and macrocyclic conformation can be used both to identify a bidirectional substitution pattern-conformational rela-
reliably design systems and to predict both structure and proper- tionship, is provided in Tables 1 and 2, with justifications and dis-
ties in systems for which direct structural information may not cussion in Section 4. By no means an exhaustive list, this overview
be available. Symmetry-by-design access to chiral porphyrin mole- of the distortional profile invites others to attempt to break these
cules – highly desirable compounds for use in catalysis and sensing soft rules, to furnish the literature with results outside the
– is somewhat stymied by lack of quantitative information of what expected. In many cases, however, the mean structure of even
4
Table 1
The fitted structural deviation in NSD terms due to porphyrin core modifications.
Chemical substitution pattern NSD modes affected (induced shape) Value (NSD magnitude) Standard deviation Number of structures
Core modification
M = 2H (free base), 6, R21,23 = H A1g1 0.164 0.027 709
B1g2 0.07 0.01 709
21-24
M = 4H (diacid), 6, R =H B2u1 3.082 0.885 82
B2u2 0.703 0.135 82
mono and cis-dialkyl, 6, R21 = C / R21,22 = C B2u1 1.313 0.787 33
B2u2 0.375 0.223 33
trans-dialkyl, tri- and tetra-alkyl, B2u1 3.796 0.604 25
6, R21,23 / R21-23 /R21-24 = C B2u2 1.106 0.174 25
N-C-N Bridging motif, 6, R21 = R22 = C Eg(x)1 & Eg(y)1 0.530 0.131 9
0.521 0.192
N-N at pyrrole, 6, R21 = N, R22-24 = M or H B2u1 1.304 0.509, 21
B2u2 0.435 0.091, 21
B1g1 0.157 0.094 22
5, M = Mg* A1g1 0.246 0.053 51
5, M = Mn* A1g1 0.077 0.102 167
5, M = Fe* A1g1 0.061 0.084 567
5, M = Co* A1g1 0.040 0.096 144
5, M = Ni* A1g1 0.104 0.136 314
5, M = Ni ** A1g1 0.371 0.210 528
B1u1 1.368 0.622 528
5, M = Cu* A1g1 0.032 0.071 140
5, M = Zn* A1g1 0.171 0.038 870
5, M = P, Si B1u1 1.909 0.989 36
A1g1 0.358 0.312 36
Core bis-chelate i.e. 6, R21 = R22 = MR23 = R24 = M0 Eg(x) + Eg(y)* 1.022 0.271 12
Core bis-metallation, 6, R21 = M, R23 = M0 Eg(x) + Eg(y)* 0.57 0.369 99
5, M = Lnà-L2, L2 = Phthalocyanine A2u1 0.795 0.087 66
A2u2 0.054 0.026 66
5, M = Lnà-L2, L2 = Porphyrin A2u1 0.9 0.155 44
A2u2 0.039 0.027 44
5, M = Lnà-L2, L2 = non-pyrrolic A2u1 0.49 0.149 156
A2u2 0.02 0.035 156
All Ln-porphyrin A2u1 0.615 0.243 274
A2u2 0.005 0.046 274
A1g1 0.129 0.086 274
* à
Due to the significant effects of nonplanar distortion induced by peripheral substitution, only those porphyrins with Doop < 1 are listed. ** Porphyrins with Doop > 1.
Ln = lanthanoid metal ions, Sc, Y + La:Lu and the larger metals Bi,Th,Pb,Zr,U,Hf in all oxidation states.
highly nonplanar porphyrins can be routinely predicted by know- information which directly allows for assessment of the symmetry
ing only the substitution pattern in an empirical manner. A guide of the porphyrin macrocycle (Fig. 6).
to potentially overlooked pathways to chirality in porphyrins is NSD relies on the generation of matrices which represent the
presented. It is hoped that structural comparison in normal- calculated vibrational distortion modes of an idealized macrocycle,
coordinate terms becomes commonplace – a method is currently in this case (5,10,15,20-tetraphenylporphyrinato)copper(II) [2,
being developed by the authors to perform normal-coordinate M = Cu(II)] [76], which is used as a reference structure. Query
structural decomposition on any collection of points, and visualiza- atoms, such as those from a crystallographic structure solution,
tions of the same. This review is additionally intended to provide are then fitted to the reference structure via a least squares mini-
an example of the demonstrating quantitative structural analysis mization [77], to remove the rotation and translational elements
of immense numbers of crystal structures beyond the comparison of the resultant matrix, and assigned to their corresponding atom
of choice bond distances, angles or qualitative descriptors, and into in the reference structure [78]. The crystallographically
comparative analysis of molecular conformation, even when mole- determined atom positions are fitted, using a linear algebra least-
cules adopt a varied array of shape-combinations. squares method, to a linear combination of the optimized
vibrational modes. In the implementation reported here, this fit-
ting occurs at four levels of approximation: the minimum (lowest
2. Methods frequency mode per symmetric group) extended (lowest 2 modes)
total (comparison of all calculated modes) and complete (square-
2.1. Normal-coordinate structural decomposition (NSD) root of the sum of squares of total modes) basis sets. Due to the
modes being divided by symmetry elements, the in-plane and
The quantification of structural effects of substitution is a natu- out-of-plane distortions can be treated independently.
ral evolution of the Normal-coordinate Structural Decomposition A pair of overall distortion parameters (Doop and Dip) are
(NSD) method as originally developed by Shelnutt and coworkers assigned as the square root of the sum of squares of out-of-plane
[28,29,75]. NSD is the quantification of porphyrin atom positions and in-plane distortions, respectively. The accrued error margins
by transform of cartesian atom positions as into magnitudes of (doop and dip) are the sum of residual matrix elements – in the total
concerted deviation of all atoms along symmetry-banded case, this should equal zero, indicating a perfect fit to 66 parame-
normal-coordinate modes, allowing these quantified distortions ters and no residual translational or rotational elements.
to be compared. These normal modes additionally carry symmetry
5
Table 2
The fitted structural deviation in NSD terms due to peripheral porphyrin modifications.
Periphery modification NSD modes affected (induced shape) Value (NSD Standard Number of structures
magnitude) deviation
5, R5,15 – H, R10,20 = H, R2,3,7,8,12,13,17,18 = H B2g1 0.082 0.032 55
B2g2 0.026 0.023 55
5,15 10,20 2,3,7,8,12,13,17,18 21 23
6, R – H, R = H, R = H, R ,R =H B2g1 0.210 0.068 93
B2g2 0.110 0.033 93
5, R5,15 – H, R10,20 = H, R2,3,7,8,12,13,17,18 – H B2g1 0.270 0.090 35
B2g2 0.058 0.023 35
6, R5,15 – H, R10,20 = H, R2,3,7,8,12,13,17,18 – H, R21, R23 = H B2g1 0.607 0.100 54
B2g2 0.136 0.035 54
5-monosubstituted, R5 – H, R10,15,20 = H B2g1 0.209 0.139 80
B2g2 0.055 0.039 80
5,10,15-trisubstituted, R5,10,15 – H, R20 = H B2g1 0.070 0.072 66
B2g2 0.015 0.026 66
5,15-Diexo-enylporphyrin B2g1 0.117 0.076 36
B2g2 0.007 0.249 36
A2u1 0.682 0.237 36
A2u2 0.311 0.069 36
Picenoporphyrin B1g1 0.172 0.088 5
B1u1 0.057 0.044 5
trans-beta substitution 5, R2,3,12,13 – H, R7,8,17,18 = H B1g1 0.135 0.092 78
Eg(x) + Eg(y)y 0.214 0.161 78
Dodecasubstitution, R2,3,5,7,8,10,12,13,15,17,18,20 – H B2u1 2.701 1.136 379
B2u2 0.322 0.248 379
Undecasubstitution, R2 or R5 = H B2u1 1.661 1.298 8
B2u2 0.109 0.113 8
Decasubstitution Any two R2-20 = H B2u1 0.498 0.684 196
B2u2 0.032 0.075 196
Supramolecular interaction
with fullerene 5C60 A2u1 0.198 0.047 99
A2u2 0.039 0.013 99
y
Calculated as the sum of Eg(x) and Eg(y) modes, due to degeneracy of these modes.
mation (S.I. 6.5). A database of CCDC (version 2020.1) crystal

structures in NSD terms is attached to this report as Supplemen-
tary Information (see S.I. 6.3). The introduction of a ‘total’ matrix
report is the complete decomposition of coordinates into normal
modes, without the uncertainty associated with approximation of
the fewer degrees of freedom. This additional parameterization is
intended to reduce uncertainty in structures derived retroactively
from the NSD matrices, by tools provided in the program package
(S.I. 6.5) for producing accurate coordinates of structure predic-
tions. Where the NSD program was originally designed for analysis
of individual crystallographic determinations, this new program
allows for the unattended, reliable analysis and comparison of large
databases of structures. This opens the door to cluster analysis,
machine learning and a host of other methods of structural
interrogation.
When querying a new crystal structure, the results of NSD
analysis are presented in tabular and graphical form as indicated
Fig. 6. The NSD program (Shelnutt, 1993) for individual molecular structure
in Fig. 7. In the tables provided, each number is representative of
evaluation.
the extent of distortion along the normal coordinate modes,
which are presented in the S.I. sections S1 and S6.2. A graphical
representation allows for immediate validation of results and
Despite the elegance of this method, the use of this technique structure assignment, to reduce results derived from incorrect
has fallen out of favor as a characterization method, partly due to structural fitting. Our intention is that this table and graphic
the unavailability of the original porphyrin-NSD program after could be included as SI information easily for papers which
the passing of Prof. Shelnutt in 2014 [79] and the complexity of include porphyrin crystal structures, and that the further tables
the method discouraging reverse engineering. Additionally, inter- could assist the author in contextualizing structures and writing
preting this obfuscated data is difficult for non-specialists, espe- of the manuscript. The shift in research papers to have all
cially without access to source code. research data available (‘open data’) in a concise manner is
To revitalize NSD, we have written a new program which faith- important when considering the new approach in publishing
fully replicates and extends the original methodology in a modern [80], with a machine-focus and data science (i.e. the quantitative
programming language, Python 3.8, to assist with analysis of mul- approach) rightly taking precedence over the comparison of a
tiple structures, report generation and idealized structure genera- handful of cherry-picked examples. Having data available in a for-
tion. An interface to this program can be accessed online at mat amenable to machine interrogation is an exceptional advan-
https://www.sengegroup.eu/nsd, and the source code for this pro- tage, in the case for the Cambridge Crystallographic Data Centre
gram is freely available from the authors as Supplementary Infor- Crystal Structure Database [74].
6
Fig. 7. The short-form results of an individual structure query to the new NSD web interface, for Zn(II)OETPP (Fig. 5); a longer form output is available, shown in
Figs. S2.1-S2.4.
7
We believe strongly that a shift in scientific publishing toward cerned with the output each of the modes separately, as the total
availability of data, open presentation and interactive visualization matrix. A subsequent matrix was generated (total-f) which was
as instructive and investigative tools are of paramount importance. sign-normalized in each case to the first mode of the symmetry
To that end, we have provided the catalogued research data group, intended to correct for the sign-agnostic orientation of the
involved in the generation of the plots presented here, as a conve- fitted macrocycle.
nient Pandas DataFrame package. A convenient web portal for Database analysis was performed by identification and extrac-
structure analysis and literature survey is available at https:// tion of the porphyrinoid molecular substructure by CCDC-
www.sengegroup.eu/nsd. Additionally, interactive versions of the Mercury (using the CSD-Materials package) [74,86] or Protein Data
main distortional plots are provided online at https://www.senge- Bank online interface [87,88] into a ‘‘.sd” file, and application of the
group.eu/nsd_plots.html, intended to allow for researchers with- above procedure. The calculated databases are included as Sup-
out computational specialization to gain a more complete porting Information, and available at www.kingsbury.id.au/data.
understanding of the distortional landscape, or to investigate indi- The testing for structural clustering behavior was based on
vidual structures. A full toolkit, including the means to run the identification of clusters of high distortion from plots of NSD
equivalent webserver is available as supplementary information parameters derived from database structures [89]. Structures were
(S.I. 6.5); with these tools, the entire database can be reconstructed highlighted based on chemical substructures, from identifier lists
from any large collection of porphyrin crystal structures. extracted using CCDC-ConQuest [90]. Kernel Density Estimation
This method was designed to be used in the routine reporting of (KDE, scipy.stats.gaussian_kde) [82,91] was used to visually iden-
crystal structures with a porphyrin core and has therefore been tify bimodality in clusters. Two-dimensional bounds of identified
expanded from the original NSD methodology. A single page report structural distortion behavior were based on the ellipse defined
suitable for S.I. (shown in Fig. 7) provides important characteriza- by Pearson Chi-squared tensor at r < 2, as indicated in the interac-
tion information; however, more information can be gleaned from tive versions of these plots (included as supplementary informa-
the atom positions to assist with manuscript preparation. Tests tion, see S.I. S6.1). Cluster parameters are presented in S.I.
applied to the NSD parameters can compare experimental values Section S5.
to clusters of structures based on chemical motifs, which are
described in this paper, allowing for interrogation of specific chem-
ical substitution-crystallographic structure relationships in small 3. Brief overview of the normal-coordinate analysis results
datasets. Additionally, this program reports symmetry point
groups which can be conferred on the porphyrin subunit at prede- As stated above, NSD is a method of reductively and numeri-
termined levels and identifies the most similar structure by confor- cally describing the overall shape of a crystallographically identi-
mation in the CCDC and PDB databases, useful for structural fied porphyrin molecule using only a few parameters. The NSD
comparison. method provides a numeric value of macrocyclic distortion, in Å,
This contribution outlines the new NSD methodology and from the reference structure along each of the precomputed nor-
describes the most prominent distorted porphyrin types and rela- mal modes. As such, each of the data points in each of the plots
tionships of chemical structure to crystal structure from analysis of in this review is an individual crystal structure with all extraneous
the CSD data. A numerical basis for porphyrin shape can be structural minutiae stripped away, and each position on these axes
described by the new web accessible NSD method; the statistical represents a particular conformation of a reduced-symmetry
reduction of structural characteristics allows for novel structures macrocycle. Thus, the clustering of points due to an individual
to be contextualized simply in reference to all known structures. chemical moiety demonstrates mathematically that chemically
The method described here is published as a web-accessible pro- similar molecules adopt the similar shapes, and with magnitudes
gram, allowing for researchers to submit .pdb format files of chem- approximated by a probability distribution.
ical or biogenic porphyrins and receive a thorough analysis of the The numerical value is, by convention, the sum movement of an
porphyrin distortion (Fig. 7). This paper is intended to provide a individual pyrrole unit, or ¼ of the sum displacement of the macro-
referenceable guide of the porphyrin types, what they mean and cycle’s atoms along the normal coordinate vector. The precom-
how to design molecules to exploit these structural motifs. puted modes are the vibrational normal modes, as calculated by
Shelnutt [75], shown below to be approximations of the eigenvec-
2.2. Basic description of the NSD analysis program tors of the macrocyclic distortion in each symmetry operation
class. Normal modes are depicted in the Supplementary informa-
A full description of how the program functions is provided in tion (S.I. Figs. S1.1 – S1.5) and tabulated in the attached source
the comments of the attached source code. This NSD online pro- code, divided into those which occur in the plane of the ligand,
gram is written in python (version 3.8) with the libraries numpy and those resulting from out-of-plane movement, i.e. retention
[81], scipy [82], matplotlib [83], pandas [84], flask [85] and depen- and rejection of rh symmetry. Normal modes are further divided
dencies therein. The use of quaternion rotational minimization into the symmetry classes attributable to the D4h point group,
[77] and the Hungarian method [78] were keystone technologies the in-plane and out-of-plane distortions, respectively. The distor-
in the fitting of an arbitrary structure to the model. In order to pro- tion modes, in general terms, align with specific chemical modifi-
vide NSD results comparable to those in the literature currently, cations of the porphyrin macrocycle which can be quantified and
our program used distortion mode matrices provided by Jentzen discussed.
et al. (S.I., S1 and S6.2) [29]. The general form of a porphyrin macrocycle is presented in
The NSD technique is based around a least-squares matrix Fig. 1, with the R-groups representing the IUPAC-prescribed num-
reduction (implemented with numpy.linalg.lstsq) of porphyrin ber of the porphyrin atom to which the group is attached. This
atom positions for which rotational and translational elements numerical system is used throughout this paper. M represents
have been removed. The in-plane (x,y coordinates) and out-of- either a metal center or another core moiety; for clarity, the groups
plane (z coordinates) structure can be treated separately, given R21-24 are included in Fig. 1.
the bifurcation of relevant symmetry modes. Each set of n vibra- Certain types of core or peripheral modification can result in the
tional modes (n = 6 (‘‘min.”), 12 (‘‘ext.”) or 21/45 (‘‘comp.” & ‘‘to- presumed planar and aromatic porphyrin structure adopting a
tal”), represented as a 24 n (oop) or 48 n (ip) mode three-dimensional, nonplanar structure. Macrocycle atoms can, at
coefficient matrix. Each of the analyses presented here are con- extremes, deviate from the mean plane by more than 1 Å in
8
Fig. 8. A periodic table of porphyrin distortions, with log of the mean macrocyclic distortion represented as the size of each pie, divided into sections which represent the
ratio of lowest frequency mode magnitude.
solution and the solid state [92,93] and even more at interfaces generalizes multiple interactions (e.g., grouping free base and acid
[94]. An altered conformation can induce a profound color change, porphyrins together, as both involve N–H bonds) or differing bond
and can lead to altered reactivity, especially at the Cm positions and character (e.g., oxidation states), this gives a general overview of
with core protons. The methods and to produce varied types of the results of core modification.
non-planar porphyrins have become increasingly sophisticated Less dramatic, and often overlooked, are the in-plane distor-
due to the availability of techniques for formation of highly- tions of the porphyrin macrocycle. The in-plane modifications of
substituted porphyrins and core and peripheral post-synthetic the macrocycle are regularly induced by core or peripheral substi-
modifications, through organometallic and metal catalyzed tech- tution with a compatible symmetry to the distortional mode. An
niques [46,47]. As a general overview we performed a statistical example of a core distortion is the B1g(2) mode, predominantly
analysis of the CCDC entries with the most prominent substituent accessed by H2 ‘‘free base” porphyrins. This molecular distortion
patterns. Table 1 summarizes the statistical result of the impact of can be rationalized as an angular change from the core protons
core modifications on the macrocyclic conformation. Likewise, altering the angle Ca-N-Ca in protonated (110°) vs. non-
Table 2 comprises the statistical result of diverse peripheral substi- protonated (105°) pyrrole subunits.
tution patterns. Both tables show that these structures are often The in-plane distortions which are most encountered in crystal
predictable in both a qualitative and quantitative sense. structures are similarly correlated with the lowest frequency
The out-of-plane modes which are most frequently encoun- vibrational modes, as well as the totally symmetrical A1g modes
tered in crystal structures are correlated with the lowest fre- of isotropic expansion and contraction. The porphyrin can undergo
quency, or lowest energy vibrational modes; these are shown in isotropic expansion to accommodate a metal center or can be
Fig. 4. The saddle B2u(1) mode (Fig. 4a, blue) involves the tilting skewed by differential substitution around the macrocycle. Con-
of individual pyrrole units in an up-down-up-down manner. The ceptually simplest might be the 5,15-disubstituted porphyrins
ruffle B1u(1) (Fig. 4b, yellow) involves the twisting of individual which demonstrate a C5 M C15 core elongation or meso-stretch
pyrrole units around the centroid-N axis, in a concertinaed +// across the core of the macrocycle – compare the equivalent
+/ fashion. A dome A2u(1) (Fig. 4c, green) is the tilting of all pyr- C5 C15 at 6.88 Å in Zn(II)TPP [23], to 6.96 Å (C5 M C15) vs
role units in a concerted fashion towards one face, such as when 6.78 Å (C10 M C20) in (5,15-bis(4-tolyl)porphyrinato)zinc(II)
chelating a large metal ion. A combination of the wave Eg(x) and [118]. In NSD terms, this stretch correlates with the first mode of
Eg(y) 1st (Fig. 4d, red) and 2nd (Fig. S1.1) modes occurs as two B2g symmetry and, when quantified, can be compared, as in
dipyrrin halves tilt towards opposite faces, such that the individual Section 4.2 below.
pyrrole units tilt in in an up/up/down/down manner. In most of the In-plane distortion of the porphyrin moiety, while less dra-
other cases, other parameters have magnitude below the uncer- matic, is essential to consider in the generation of chiral porphyrin
tainty of the crystallographic determination and have been tradi- cores. The A1u mode, as the only chiral irreducible representation,
tionally ignored. is vanishingly rare, therefore multi-modal distortions are the best
The formation of non-planar porphyrins can result from core or method of accessing chiral point-groups. The combination of one
peripheral modification. A periodic table of porphyrin distortions is out-of-plane and a corresponding in-plane distortion has already
presented in Fig. 8 and shows the ratio and magnitude of the med- been shown to form porphyrins with non-superimposable solid-
ian distortion that results from binding core nitrogen atoms to state conformation [64] and used for chiral sensors [69–71]. In
specific atoms. Readily observed are that ruffling distortions result each case, the combination of a B2u (saddle) and B2g (meso-
primarily from Ni(II) [95], but also from Si(IV) [96–98], P(V) [99– stretch) was used to achieve this chiral conformation. It is hoped
101], Cr(III) [102–104], As(V) [105,106] and Au(III) [107]. Introduc- by analyzing the data, other potential paths may be illuminated
tion of lanthanoid or other large metal ions introduces a domed towards the generation of chiral porphyrins. The aim is that these
shape resulting from the sitting-atop type complex [108–112], compounds act as idealized receptors for photoactive chirality
and core-modification with pyrrole N-alkylation [22,113], or with transfer, a method by which a chiral analyte will force the statisti-
the formation of an N-N [114] or N-O [115,116] bond initiates a cal adoption of a preferred chiral conformation [118]. This chiral
dramatic increase in the B2u (saddle) parameter. While this graphic enrichment can then be measured by absorption or fluorescence
9
methods, providing an easy and general method of chiral sensing

based on porphyrin reporting units [69].
4. Analysis of porphyrin structures by cluster
The introduction of specific chemical motifs is, of course, gener-

ally known to induce structural distortion (e.g., with a ‘H4’ core for
saddle shape) in a qualitative sense. The redevelopment of the NSD
algorithm, allowing for analysis of the large dataset of 6811 por-
phyrin molecules found in the CCDC CSD (2020.1) allow for a quan-
titative discussion on the effect of chemical substitution on
structural distortion. Each porphyrin molecular core which has
been structurally characterized can be reduced to a summation
of symmetry-restricted vectors, and as such compared with other
molecules; a similar NSD value represents a similar macrocyclic
conformation.
Fig. 9. The porphyrin saddle shape of [H4TPP]2+ in [H4TPP][FeIIICl4](Cl), which
In an ideal sense, derived values for multiple crystal structures shows 3.1 Å B2u(1) distortion magnitude. The mean plane of the molecule is
can be analyzed as a collection of points, which cluster around a presented in translucent red as a guide to the eye; C-bound H atoms have been
given value, and therefore a particular macrocyclic conformation omitted. Image generated from CCDC No. 1275452, CSD code TPPFEC [41].
[119,120]. Owing to similar molecules being responsive to similar
forces controlling the macrocyclic conformation, one could expect
sary simplification which is only confounded by the presence of
that a similar shape would result. A cluster of NSD values deriving
minor ‘‘compensatory” modes, discussed further in Section S4. This
from a particular chemical modification shows a chemical
symmetry-stratification proves to be fortuitous in the quest for
structure/solid-state conformation relationship. When these are
chiral porphyrins, as the necessary information for the providence
related to a probability function, this represents a probability dis-
of a point-group is provided directly in terms of the irreducible
tribution in 3D space, similar to a thermal ellipsoid. Demonstrated
representations. Point groups are discussed further in Section 4.10.
here is that certain types of porphyrin molecules show an NSD pro-
Indications are given for each cluster to the mean distortion attri-
file, and therefore solid-state conformation, consistent with other,
butable to the chemical structure, and covariance of in NSD terms.
similarly patterned molecules. Often, by introducing additional
This can be thought of as a structural variance ellipsoid, relating
parameters which modulate the solid-state conformation, some
many distinct structures to a probability attributable to the
individual chemical motifs will show a unique signature, allowing
assigned substructure with the omission of small numbers of clear
for structural verification. Of course, even identical porphyrin
outliers. The structure codes related to each classification are listed
molecules vary slightly in solid state conformation, and therefore
in Section S3.
NSD profile, dependent on solvate or counter-ion, and we can
In many of the NSD scatterplots demonstrated in this section,
now account for this in statistical terms.
each parameter is plotted as the absolute value of the first mode,
The NSD parameters pertaining to individual chemical motifs
and the relative value of the second mode (e.g. B2u(2) sign
can be isolated from one another given a sufficient sample size,
(B2u(1)) in each case, as these modes (with the exception of A1g)
forming clusters of similar structural conformation and chemical
are conformationally identical whether moving in the positive or
properties. That these clusters are so often tightly constrained indi-
negative direction, with sign depending on the orientation of the
cates that the design regime employed for porphyrin molecules is
macrocycle with respect to the model compound. For this analysis,
similarly reliable, allowing for prediction of the structure of the
where each mode is treated independently, this is a valid mode of
identified porphyrin molecules by cluster analysis alone. For por-
data pretreatment, however the relative sign of NSD modes in
phyrins of significant biological and materials science relevance,
novel structures will be important in assigning a chiral
highly accurate structural data may not be available, and NSD anal-
conformation.
ysis provides a useful tool for empirically grounded structure pre-
diction and sanity-checking of results obtained through ab initio
methods. We have taken such an approach in the past to elucidate
the subtle changes in the bacterial photosynthetic reaction center 4.1. B2u
[30] and light-harvesting complexes [121]. Additionally, the tools
provided can yield structures for representative calculations. The saddle shape, the first mode of B2u distortional symmetry
These plots, representing the macrocyclic conformation, are from porphyrin macrocycles is shown in Fig. 9. Characterized by
possibly confusing at first inspection. It is important to remember the tilting of pyrrole units in an up-down-up-down manner, the
that each point on each of the axes below represents simply a par- saddle shape is commonly found in porphyrin diacid structures
ticular conformation of a macrocycle and a degree to which this and in dodecasubstituted porphyrins. This conformation was the
occurs; that two points proximity in normal-coordinate space is first structurally characterized, from pioneering work by Stone
equivalent to proximity of all atoms in real space, when the two and Fleischer; distortion was introduced by acidification of the
structures are overlaid. Two compounds with the same parameters core to yield a ‘H4’ porphyrin dication [41]. Similarly, nonplanarity
would necessarily be superimposable. In this sense, this can be has been classically introduced by steric conflict in macrocycles
described as a multi-atom equivalent of the common Ramachan- which are peripherally crowded, the so-called highly substituted
dran plot for macromolecular comparison [122,123]. porphyrins [46,124]. The series of dodecasubstituted porphyrins
The distinction of structural distortions into terms of the irre- (i.e. all meso and beta positions non-H, e.g. 4, OETPP, or 6
ducible representations is due to the initial modes being derived (R2,3,7,8,12,13,17,18 = Br) OBrTPP) provides a clear structural type of
from vibrational states. Similarly here, each irreducible representa- porphyrin molecule which display some of the most egregious
tion is treated individually and these substitution effects, known to nonplanarity among porphyrins [54]. These effects have been
be orthogonal are implied to be similarly non-interfering, a neces- demonstrated to act in concert [51].
10
Fig. 10. Derived NSD parameters for core-modified and peripherally modified structures attributable to certain chemical motifs, along concerted vectors of the B2u irreducible
representation. The interactive version of this plot is available at https://www.sengegroup.eu/nsd_plots.html and in supplementary information [128].
The nonplanarity of macrocycles distorted in this fashion can be single clearly defined cluster of conformations, with few outliers
used for activation of the porphyrin core, allowing for interaction [64]. This conformational cluster is identified by the ellipsoid pre-
of core N–H donors with pocketed guests [57]. Distortion is simi- sented in Fig. 10, with the population of various conformations
larly present in core-modified porphyrins in which steric conflicts analogous to a thermal ellipsoid of an individual crystal structure.
are introduced between adjacent or opposite pyrrole nitrogen Fig. 10 similarly displays N–‘‘C” [22,125,126] and N–‘‘N” [114,127]
atoms; either though acidification to form H4-porphyrin diacids, – highly B2u-distorted structures resulting from core modification.
or by covalent formation of N–C and N–N bonds from the core. The measured saddling parameter broadly forms two clusters –
The absence of a metal center in the core, such as in free base por- those involving one N-alkyl, or two at N21 and N22 yield a mean
phyrins, is a secondary factor in modelling the extent of distortion sum distortion of 1.7 Å, and those with denser substitution pat-
of peripherally modified porphyrins. While not causing distortion terns, at a mean of 4.7 Å. Structures with a N21-C-N22 bridge show
along B2u-symmetric modes alone, the free base porphyrins adopt an Eg distortion pattern in place of this saddling and are discussed
a more distorted arrangement than their metallated counterparts, further in Section 4.6.
perhaps owing to additional flexibility. This ‘‘H4 diacid” shape results from tilting of pyrrole units away
from each other, and not towards a shared center, as would be the
case in a metal complex or free base. These individual macrocyclic
4.1.1. Core modification deformations have been fitted, with the relevant parameters
Fleischer and coworkers’ pioneering work in the structural shown in Table 1; an example of the two-dimensional calculation
identification of porphyrin acids first demonstrated that por- and the cluster-fitting result is shown in S4.2 and visualized in
phyrins adopt a starkly nonplanar structure due to steric con- the interactive versions of these plots, available as supplementary
straints. An alternating up-down-up-down orientation of pyrrole information [128]. This same procedure of data fitting and gaussian
subunits around the porphyrin ring, a conformation which relates approximation is followed for all other clusters mentioned in this
to the saddle mode presented in Fig. 9, is shared by the over- review.
whelming majority of porphyrin diacids.
The B2u NSD parameters for ‘H4’ porphyrin diacids are shown in
Fig. 10 in green filled circles. The core protonated porphyrins are a 4.1.2. Peripheral modification
good example of a clear structural delineation; They are struc- The primary method of introduction of large degrees of non-
turally distinct from most other porphyrins, and mostly exist in a planarity is the use of peri-interactions, e.g. in dodecasubstituted
Fig. 11. The magnitude of B2u(1) and (2) parameters, with marker color representing the number of H-atoms around the porphyrin periphery. As can be seen, a higher degree
of non-H substitution leads to more distortion along the B2u modes. H-number refers to number of Cb and Cm hydrogen atoms.
11
porphyrins – the formation of a porphyrin such as 4, with all Cb and 4.2. B2g
Cm positions filled by non-H atoms. The steric effects of dodecasub-
stitution to promote a saddle-distortion non-planarity are well B2g, as distinct from the above B2u, acts within the plane of the
known and, as seen in Fig. 11, is reflected in the correlation macrocycle. The B2g distortion, or meso-stretch, is shown as in
between B2u parameter and fewer H-atoms around the porphyrin inset in Fig. 12(b & c), and can be imagined as the stretching of
periphery [46,52]. the C5 and C15 containing axis of an otherwise symmetrical por-
The mean distortion along this mode for the 410 dodecasubsti- phyrin core. Unsurprisingly, this distortion has been identified in
tuted examples is 2.6(11) Å. The porphyrins with the greatest steric compounds which have differential substitution at the meso posi-
demand, such as 2,3,7,8,12,13,17,18-octaisopropyl-5,10,15,20-tet tions of the porphyrin macrocycle. The simplest of these macrocy-
raphenylporphyrin (and oxidized derivatives), show the largest cle types, such as 5,15-diphenylporphyrin (6, R5,15 = Ph, R10,20 = H,
NSD parameters [129]. Some dodecasubstituted porphyrins, such M = 2H), show an elongation of the substituted axis of around
as 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (5, 0.3 Å. A scatterplot of the two predominant concerted coordinate
R2,3,5,7,8,10,12,13,15,17,18,20 = Ph [130]) or 2,3,7,8,12,13,17,18-octae vectors with B2g representation are shown in Fig. 12. An interactive
thyl-5,10,15,20-tetrakis(triisopropylsilylethynyl)porphyrin [131] version (available at https://www.sengegroup.eu/nsd_plots.html)
are not necessarily saddle-shaped, though are often non-planar of this plot allows for the overlay of cluster information and inter-
through ruffle or other distortion pathways; these porphyrins are rogation of individual points.
discussed further in Sections 4.3 and 4.7. Some, such as The additional influence of the substitution at the Cb positions
2,3,7,8,12,13,17,18-octa(phenylethynyl)-5,10,15,20-tetraphenyl magnifies this distortional aspect, approximately tripling the
porphyrin (5, M = 2H, R2,3,7,8,12,13,17,18 = C„CPh, R5,10,15,20 = Ph) are observed distortion in the B2g(1) mode and adding positive distor-
almost entirely planar due to lower steric demand [132]. Those tion of around 0.12 Å along the B2g(2) mode; e.g., in 2,8,12,18-tetra
structures with some b- and all four meso substituents show some ethyl-3,7,13,17-tetramethyl-5,15-diphenylporphyrin [62]. The
structural distortion, generally less than the dodecasubstituted presence of a metal center at the core has a dampening effect,
examples [52,133,134]. approximately halving the observed distortion when compared
Those porphyrins with both a core and peripheral pattern (e.g., to free base porphyrins, irrespective of metal center. For example,
dodecasubstituted porphyrin diacids [93] or N-substituted deriva- (5,15-bis(p-tolyl)porphyrinato)zinc(II) [117] has a B2u(1) value of
tives [125]) promoting a saddle structure are among the most dis- 0.11 Å vs 0.42 Å for the free base 5,15-diphenylporphyrin [64].
torted structures, i.e. that multiple modifications to structure to While these distortional magnitudes are significantly less than
engender specific distortion are additive. Comparing the dodeca- those for out-of-plane modes, preliminary investigations have
substituted ‘H4‘-diacid subset (|B2u1| = 3.8(4) Å, n = 36) with the indicated that a distortion of 0.2 Å is sufficient to induce measur-
nondodeca ‘H4‘-diacids (|B2u1| = 2.5(7) Å, n = 46) shows both that able chiral effects in ideal systems. The few examples of com-
multiple strategies towards distortion can work synergistically, pounds with a 5,15-dialkyl substitution pattern are among the
and that more intricate analyses of multiparametric distortional most distorted [135].
affect, such as those offered by machine learning studies, can nar- Both meso mono- and trisubstituted porphyrins show generally
row down specific structural magnitudes. less axial distortion than the 5,15-diarylporphyrin series, with
Fig. 12. The disposition of porphyrins along the B2g-symmetric mode, with the 5,15-substitution pattern containing structures highlighted alongside other identified groups.
The four most prominent groups are identified by ellipses, representing the 2(r) boundary, indicated by the covariance matrix outlined in Section S4.3. Some examples fall
outside of this plotting area, these are shown in the expanded interactive plot (S.I. 6.1) Parts b,c show the first and second fitted modes (x and y axes) of porphyrin B2g
distortion; arrows represent a 1.0 Å NSD parameter distortion along this mode.
12
Fig. 13. Measured B1u-symmetric distortion in the first and second modes of the macrocycle deformation.
mean values in B2g(1) of 0.21 and 0.07 Å, respectively. As with the a concertina-type folding of the porphyrin macrocycle, usually
5,15- series, the most distorted are those examples with additional paired with an overall contraction. A scatterplot of the ruffling
groups at Cb positions or alkyl substituents. Strong B2g modes are parameters observed for selected structural sublists is shown in
also observed for compounds with a porphyrindione substructure, Fig. 13. As hinted at in Fig. 5, and clearly seen here is the effect
which has been used to elicit chirality previously [71]. The most of nickel coordination; owing obviously to the large number of
strongly in-plane distorted structures are those structures which Ni(II)-porphyrin structures reported [95,136]. Traditionally, ruf-
have a bis-chelating structure, with multiple boron or transition fling distortion has been correlated with the coordination of Ni
metal atoms bound to the core [157]. This bis-chelation can addi- (II) metal centers in the core – the small size of the Ni(II) ion draws
tionally result in significant and simultaneous Eg(x) and Eg(y) out-of- pyrrole units closer to one another [26], as shown in A1g Section 4.5.
plane distortion; the B2g distortion measured can be compared to The induced steric demand placed upon the macrocycle by con-
the isotropic contraction ‘shadow’ which is concomitant with traction is relieved by out-of-plane movement, as ruffling distor-
out-of-plane distortion, discussed further in S4.3. tion [137–139]. As noted in Section 3, Ni(II) (ionic radius rionic =
0.83 Å)[177], Si(IV) (rionic = 0.54 Å), P(V) (rionic = 0.52 Å)], Cr(III)
4.3. B1u (0.755 Å), As(V) (0.60 Å) and Au(III) (0.99 Å) provide similar levels
of ruffled distortion. Additionally, there are a significant number of
The primary distortion of B1u symmetric representation, termed Ni-containing porphyrins with little-to-no ruffling distortion. Ni(II)
ruffling of the macrocycle, is shown in Figs. 1 and 2b), and involves coordination is therefore not a sure-fire method of introduction of
Fig. 14. A normalized violin plot of the relative B1u distortion parameters of porphyrins coordinating late first-row d-block metals.
13
this modal distortion or dissymmetry [95,140]. As can be seen in

Fig. 14, the ruffling distortion of Ni is still significant when com-
pared to that observed for the metalloporphyrins with the other
two most-reported metal centers; M = Fe and Zn.
Peripheral modification can similarly introduce a significant
ruffled distortion, as is the case for the {5,10,15,20-tetrakis(tert-
butyl)porphyrinato}zinc(II) [141]. A cluster of similarly distorted
structures can be observed with Rmeso = tBu and iPr, Rmeso = alkyl
generally, as well as those with Rb = non-H and Rm = C„CAR0 . Sim-
ilarly, the formation of exocyclic C@C double bonds (in the 5,15-
diexo-enyl porphyrins discussed in Section 4.6) induces a profound
non-planar distortion, usually including a ruffling component.
Generally, the success of each of these strategies is highly variable,
with each class showing non-ruffled examples. More parameters
may be required to ascertain the primary motivators for this speci-
fic distortional aspect.
4.4. B1g
The B1g mode of macrocyclic distortion involves the in-plane

movement of two pyrrole units away from one another, and the
remaining two towards one another. A plot of the magnitudes of
this distortion is shown in Fig. 15. Each of the distortional modes
is correlated with some difference in these pyrrole units. Free base
porphyrins are distorted by the second B1g mode, owing to proto-
nation of N21 and N23 and concomitant change in angle of the
CANAC bond [142]. Compounds with substitution at the 2,3,12
and 13 positions (R2,3,12,13 – H, R7,8,17,18 = H) show more prominent
distortion [143]. Similarly, those with alkylation of N21 and N23, or
those binding to different metals (N21-M, N23-M0 ) demonstrate
very strong B1g distortion in some cases [144]. Strapping from Cb
positions and additional exocyclic ring fusion from Cb to Cm has Fig. 16. Multiple-kernel density estimation plot relating first-row transition metal
identity with the isotropic expansion and contraction of the metallated porphyrin.
many different effects due to a multitude of related but distinct The kernel density estimation can be thought of as a continuous histogram; the
examples, dependent on strap length and bond order [145]. These normalized summation of Gaussian distributions using Silverman’s distribution
examples show both the largest magnitudes of distortion and no approximation [91].
clear clustering behavior.
4.5. A1g individual metal chelation. An indicator of this is shown in

Fig. 16, which relates the general isotropic size of planar (Doop <
The A1g distortion of the macrocycle, obviously not indicative of 0.5 Å) porphyrins with the first-row transition metals.
any symmetry breaking movement of the porphyrin macrocycle, is As expected, the identity of the metal center at the core of the
nonetheless usually the largest in-plane distortional aspect porphyrin dominates the contraction or expansion of planar por-
observed for porphyrin molecules. Owing to the symmetric nature phyrins. Similarly, free base porphyrins have an isotropic expan-
of this isotropic modality, A1g distortion both acts as a compen- sive signature, as shown in Fig. 17.
satory mechanism for out of plane distortion (discussed further This isotropic expansion and contraction is, however, far more
in S4) as well as a general measure of the symmetric impetus of widely variable when non-planar porphyrins are taken into
Fig. 15. The magnitudes of distortion along the B1g-symmetry modes of porphyrin.
14
N-displacement matrix ([0.200, 0.024, 0.375, 0.030, 0.204, 0.071])

by the A1g distortional terms. The plot of isotropic expansion of
the N-atoms when including nonplanar porphyrins is approxi-
mately equal to the distribution of the planar porphyrins, indicat-
ing that the M-N4 substructure is seemingly altered only slightly
by peripheral substitution patterns (Fig. 18).
4.6. A2u
The A2u mode represents movement of all four pyrrole units out
of plane in concert – in the simplest representation, rotation
towards the same face, directing the N-atoms to a point above
the plane of the molecule. This dome-like formation can occur in
several types of porphyrin, most simply in ‘sit-atop’ complexes of
large metal centers. The magnitudes of A2u distortion for several
identified groups are shown in Fig. 19. The sit-atop complex is gen-
erally a structural feature of coordinated lanthanoid and similar
metal centers with a large ionic radius and propensity for higher
coordination numbers (i.e. 7).
Fig. 17. A comparison of the histograms and fitted (least-squares) gaussian
approximations of the isotropic expansion of core modified porphyrins with The lanthanoid chelation at the core of the porphyrin offers
M = Zn (blue) M = Cu (green) and M = 2H (pink). three related shape-clusters, broadly dependent on the coordina-
tion environment of the metal center, but broadly similar between
all lanthanoid (La:Yb) and related (Sc, Y, Th, Pb, Zr, U, Hf) large
metal centers. Compounds with a single porphyrin chelating each
metal centre are less distorted than those forming a sandwich-
like bis-tetradentate structure, an example of which is shown in
Fig. 20 [147]. A structural dimorphism exists within these sand-
wich compounds; clusters are broadly those of the form (OEP)Ln
(Pc), with A2u(1) A2u(2) < 0, (upper (blue) ellipsoid in Fig. 19),
and (TPP)Ln(Pc) sandwich compounds (A2u(1) A2u(2) > 0), with
those of porphyrin-porphyrin dimer structures intermediate and
intermingled with the two clusters. The parameters of the distor-
tional motifs of lanthanoid compounds are plotted in Fig. 21, with
this clustering behavior evident by kernel density estimation.
Another class of porphyrinoids with significant A2u distortion
are the porphyrindi-exo-enyl compounds, oxidized forms of the
porphyrin moiety involving quinone and semiquinone moieties
appended to the porphyrin ring. The porphyrindi-exo-enyl mole-
cules discussed here are formally derivatives of 5,15-
dioxoporphyrinogens and involve an exocyclic double bond from
the 5- and 15-Cm positions of the porphyrin [148,149]. These mole-
cules are important chemical intermediates in the formation of
polycyclic porphyrin derivatives and are formally a 2e oxidation
of the porphyrin core. This electronic modification induces a strong
non-planar distortion, and molecules show vastly different absorp-
tion characteristics from porphyrins themselves. These compounds
are strongly ruffle and-dome distorted simultaneously, as indi-
cated in Section 4.3, in a similar manner to reduced porphyrin
derivatives such as the porphodimethens (‘calixdipyrrins’)
[150,151].
Fullerene-porphyrin assemblies are an example of a
supramolecular interaction influencing the conformation of a por-
phyrin core and show a marked distortion towards non-planarity
[152,153]. This conformational relief can be explained as the por-
phyrin conforming to the curved surface of the fullerene [154] –
as such, this mode is seemingly absent in similar dyads with flat
Fig. 18. Stacked violin plot of the N-displacement value with metal center identity, polycyclic aromatic hydrocarbons. Fullerenes introduce a modest
formed by multiplying the N-displacement matrix by the parameters (A1g(1:6)). distortion, of around 0.2 Å, along this conformational pathway. A
Additional nonsymmetric or out-of-plane distortion on N-atoms was not factored typical example is shown in Fig. 22 [155].
in.
4.7. Eg(x) and Eg(y)

account. A large out-of-plane distortion often results in contraction
within the plane, just as a rod will cast a shorter shadow from an The porphyrin distortion modes Eg(x) and Eg(y) are activated by
overhead lamp when raised at an angle [146]. The positioning of interaction of either an individual pyrrole, or two adjacent pyrrole
N-atoms should be a far more reliable indicator, and this can be units (i.e. N21 and N22) with a metal complex which does not inter-
provided directly from the NSD matrix by multiplying the act with N23 and N24. In this way, the macrocycle is deformed along
15
Fig. 19. The distortional profile of porphyrins in A2u symmetry, with lanthanoid-coordinating porphyrins highlighted alongside porphyrindiquinones and those with a
fullerene supramolecular interaction. Lanthanoid sandwich compounds are divided into two apparent clusters, with a positive and negative relative second A2u parameter.
unit [55], combined with a pre-arranged chirality induced by a chi-

ral partner, may allow these units to function as chiral organocat-
alysts or photocatalysts without permanent chirality, reducing the
cost and complexity of these transformative agents significantly.
Each of these potential applications is reliant on the generally
highly symmetrical porphyrin core becoming asymmetric with
respect to the inversion, rh, 2rv and 2rv0 symmetry operations
in D4h, and reducing to representation in D4, C4, D2, C2, or C1 sub-
groups of D4h.
Each individual mode of porphyrin distortion (except for the
rarely present A1u) results in a molecule with at least one mirror
plane. The resultant symmetry groups from these distortions are
tabulated in Table 3. Thus, the reliable introduction of chirality
Fig. 20. A typical lanthanoid octaethylporphyrin-(na)phthalocyanine [Ce(IV)(2) to a porphyrin relies on the simultaneous introduction of
(naphthalocyanine)] sandwich complex. Ethyl groups and hydrogen atoms on the
multiple distortional modes, such as those described in the
porphyrin, and the extended terminal benzo-rings on the naphthalocyanine
omitted. Image generated from CCDC No. 223659, CSD code ALIZOK [147].
previous section.
The combination of multiple modes resulting in the formation
of a porphyrin with chiral point group is a process demonstrated
one of the two equivalent wave-shaped modes shown in Fig. 4, or previously [64,69–71,159–161] In each of these cases, the use of
along a combination of the two modes, as shown in an example of a a B2g-inducing substitution pattern (5,15-disubstitution) and a
bis-Rh(I) porphyrin given in Fig. 23 [156]. The Eg distortional land- B2u-inducing core modification (core acidification) resulted in
scape is illustrated in Fig. 24. molecules with D2 symmetry. The introduction of two modes, as
The peripheral deformation strategies, such as differential and shown here, has a greater ability to introduce a wider range of
sterically demanding substitution at the 2,3,12,13-position of the symmetry groups. Table 4 shows the point group resulting from
porphyrin core (5, R2,3,5,10,12,13,15,20 – H, R7,8,17,18 = H) are not the introduction of two distortional modes simultaneously on a
observed to be particularly effective at promoting a wave-shaped molecule of D4h symmetry.
porphyrin outside of a few highly distorted examples, representing The demonstrated most-accessible chiral groups are therefore
a poor graph-conformational bidirectional relationship. Core- those in which a choice subset of the distortional modes are pre-
modification strategies, particularly the formation of bis-chelates sent, such as those enumerated as Type 1 to Type 4 below. Those
such as those with boron [157], or (RhI(CO)2)2 [156,158] as shown which have an in-plane mode which is static and an out of plane
in Fig. 23 are effective, though only a few examples have been mode which has some atropisomeric barrier to inversion provide
reported. the best chance of realizing chirality transfer, from an analyte, in
a sensor capacity, or to a substrate for chiral catalysis [162].
As described above, the peripheral and core substitution strate-
5. Discussion gies can work together for the generation of a chiral porphyrin
core. A few examples of potential methods to engender chiral con-
5.1. Relation between NSD parameters and techniques for chirality formation, including the previously explored B2g + B2u combina-
conformer generation tion, are enumerated in the following:
As stated in the introduction, the formation, however transient, Type 1: Saddle and Cm-stretch (B2g + B2u); e.g., saddled 5,15-
of a chiral porphyrin substructure is essential to the use of por- disubstituted porphyrins [64,71,159].
phyrins as reporting units for chiral sensing. Different interactions Type 2: Ruffle and N-stretching (B1g + B1u); e.g., ruffled trans-
with circularly polarized light, as expected by the energetic split- dibenzoporphyrins [163] or ruffled chlorins/bacteriochlorins
ting of the a1u orbital of Gouterman’s model [50], offers a method and similar [164,165].
to promote visible-light circular dichroism to measure chiral pollu- Type 3: Domed and pyrrole rotation (A2g + A2u); e.g., lanthanoid
tants [72]. Additionally, the organocatalytic activity of a porphyrin tetraindolyl porphyrins [166].
16
Fig. 21. Scatterplot of A2u parameters of monoporphyrin-lanthanoid coordination compounds (blue) and bis-porphyrinoids (green and orange), overlaid on a kernel density
estimation plot. The increased density and clustering of similar compounds indicates that there are three distinct conformational clusters for lanthanoid porphyrin
coordination compounds.
Fig. 22. Two views of a typical porphyrin-fullerene supramolecular complex (ZnOEPC60) showing the dome-like distortion of the macrocycle. A DABCO co-ligand has been
omitted from view. Image generated from CCDC No. 682233, CSD code COXMIM [155].
Type 4: Domed, ruffled, and saddled porphyrins (B2u + B1u + A2u), eschewed here by design; a multiparametric modelling is a
e.g., dodecasubstituted receptor porphyrins [59]. promising and computationally efficient manner of determining
whether deeper relationships exist. Some non-isoelectronic deriva-
5.2. Some comments on the present analysis tives of porphyrins, such as Lash’s tropioporphyrin series [167] and
the pyrrole-modified ‘chlorins’ obtained through Brückner’s ele-
Inherent in a database analysis of this type is that these data gant ‘breaking and mending strategy’ [164,168] are not included
may hold an inherent bias, i.e. may not be representative samples in this analysis due to absence of a C20N4 porphyrin core; however,
of the total set of crystallizable molecules. Necessarily, the sample they offer a tantalizing route to symmetry-broken porphyrins. Sim-
set for this analysis skews towards compounds which are synthet- ilarly, the expansion of the above symmetry arguments to nonpla-
ically achievable and crystallizable under standard conditions, and nar phthalocyanines could lead to highly stable variants of the
in the molecules which we and our colleagues choose to study and above [169].
report. The effect of these multiple demands is impossible to ascer- The principal benefit of this publication is, we believe, that
tain, as no comparable total-set exists; however, by using statisti- these extracted parameters provide a rapid means to contextualize
cal methods the influence of any individual data point is asymmetry within porphyrins. Either by using the data set pro-
diminished. Necessarily, the focus in this review is on molecules vided in Tables 1 and 2, or in the two-dimensional fits to the
which adopt different conformations and adopt certain specific parameter space provided in Section S4, new structures can be
structural ‘types’, i.e. a direct, 1:1 relationship between chemical contextualized as being within these named clusters, provided with
structure and molecular conformation. Obviously, some nuance is a t-statistic, and shape can therefore be reduced to comparison of
17
motifs indicates that the design regime is persistent and should

extrapolate to systems where atomic crystallographic data cannot
be gained, in enzymes, on surfaces, and in solution. The stark con-
formational differences resulting from substitution patterning
embolden the prospect and potentials of designing a range of por-
phyrins with responsive aromatic chirality.
The clear demonstration of a link between normal-coordinate
structure and chemical modification is one which can be extrapo-
lated in a similar manner to other chemical systems. The clear indi-
cation of a single predominant mode of distortion per symmetry
argument leads one to believe that the precomputed tables, while
computationally efficient, are an unnecessary computational com-
ponent of NSD analysis. On this basis, we are developing an empir-
ical system to perform symmetry-gated normal-coordinate
analysis on arbitrary chemical systems, particularly for chro-
mophore subunits. We believe new tools will allow similar
Fig. 23. View of the molecular structure in the crystal of [RhI2(2)(CO)4)], showing normal-coordinate based analyses to be performed with ease,
strong Eg-symmetry distortion along the (x + y) direction, modelled as a combination and for this type of quantitative structure comparison to become
of Eg(x) and Eg(y) distortions (REg(x) = 0.62 Å, REg(y) = 0.58 Å). Image generated from commonplace in crystallography. The link between the available
CCDC No. 1225717, CSC code OEPRHC10 [156].
structural data and the symmetry underpinning could perhaps
inform similar distortion-seeking chemical modification and
designed synthesis with other simple aromatic structures, such
a few numerical values. While the paper here is written entirely in
as the BODIPY series [172–174]. Normal-coordinate studies are
reference to the small-molecule dataset, the full multiparametric
an elegant method of quantifying and contextualizing measured
dataset for protein porphyrins has been computed and is available
dissymmetric structural distortion and could be equally applied
from the authors [128]. A similar approach to using NSD parame-
to other structure-property relationships.
ters for protein data bank (PDB) analysis has been published
A clear structural delineation and definable structural behavior,
recently, based on the lowest frequency modes [170,171]. The
as evidenced by close clusters of similarly patterned molecules,
NSD program reported here can be used to extract values for novel
could be rationalized for the A1g, B1u, B2u, B2g and A2u parameter
protein crystal structure coordinates of isolated porphyrin ligands
sets. The muddied and variable behavior in context of each of the
to compare with the values in the PyDISH database. Furthermore,
other parameters under study is implicative of a multiparametric
clustering of the porphyrin distortions with multiple normal
relationship between chemical structure and molecular conforma-
modes per symmetry operation, similar to the analysis performed
tion. This form of large conformational comparison analysis is not
here, could be potentially useful to parameterize allosteric effects
common, and as such, the simplest version was intended to be pre-
across the large protein data set.
sented here.
We have demonstrated that a molecular frame, from analysis of
6. Conclusions a very large number of examples, has perhaps many fewer degrees
of freedom than would be imagined, implying that a rational
The structural variance attributable to a simple, versatile chem- parameter-reduction can be made on symmetric grounds. This
ical unit, the porphyrin, is demonstrated to be both empirically type of dimension reduction analysis could assist algorithms in
predictable and strongly indicative of chemical substitution pat- the assignment of correct structure from low-data diffraction tech-
tern, oxidation state and exocyclic linkages. The comparison niques; for example, by reducing the parameter space. The param-
between multiple structures and the demonstration of consistent eter reduction and clear line from molecular conformation
Fig. 24. A scatterplot of the ‘comp’ NSD values, or sum distortion of porphyrins along the Eg distortional modes, in both the x- and y-oriented forms. An interactive version of
this plot is available at https://www.sengegroup.eu/nsd_plots.html and in supplementary information [128].
18
Table 3
Symmetry resulting from singular distortions applied to any molecule of D4h symmetry, e.g., a porphyrin.
Distortion Mode B2g B1g Eu(x) Eu(y) A1g A2g B2u B1u A2u Eg(x) Eg(y) A1u
Resulting point group D2h D2h C2v C2v D4h C4h D2d D2d C4v C2h C2h D4
Table 4
Symmetry resulting from two distortions applied to a porphyrin. *The E-modes, when both present are considered to have equal magnitude here, e.g., |Eg(x)(n)| = |Eg(y)(n)| such
that the resulting mode also has Eg or Eu symmetry.
B2g B1g Eu(x) Eu(y) A1g A2g B2u B1u A2u Eg(x) Eg(y) A1u
B2g D2h C2h Cs Cs D2h C2h D2 C2v C2v Ci Ci D2
B1g C2h D2h C2v C2v D2h C2h C2v D2 C2v C2h C2h D2
Eu(x) Cs C2v C2v C2h* C2v Cs Cs C2 Cs C2 Cs C2
Eu(y) Cs C2v C2h* C2v C2v Cs Cs C2 C2 Cs C2 C2
A1g D2h D2h C2v C2v D4h C4h D2d D2d C4v C2h C2h D4
A2g C2h C2h C2 Cs C4h C4h S4 S4 C4 Ci Ci C4
B2u D2 C5v Cs Cs D2d S4 D2d S4 C2v Cs Cs D2
B1u C2v D2 C2 C2 D2d S4 S4 D2d C2v C2 C2 D2
A2u C2v C2v Cs Cs C4v C4 C2v C2v C4v Cs Cs C4
Eg(x) Ci C2h C2 Cs C2h Ci Cs C2 Cs C2h C2v* C2
Eg(y) Ci C2h Cs C2 C2h Ci Cs C2 Cs C2v* C2h C2
A1u D2 D2 C2 C2 D4 C4 D2 D2 C4 C2 C2 D4
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Coordination Chemistry Reviews

The shape of porphyrins

3. Brief overview of the normal-coordinate analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Tetrapyrrole molecules such as porphyrins (1), chlorins, bacteri-

redox reactions, as well as exocyclic bridging or strapping, and

effect a particular porphyrin substitution will have on the macro-

mation (S.I. 6.5). A database of CCDC (version 2020.1) crystal

methods, providing an easy and general method of chiral sensing

4. Analysis of porphyrin structures by cluster

The introduction of specific chemical motifs is, of course, gener-

this modal distortion or dissymmetry [95,140]. As can be seen in

The B1g mode of macrocyclic distortion involves the in-plane

4.5. A1g individual metal chelation. An indicator of this is shown in

N-displacement matrix ([0.200, 0.024, 0.375, 0.030, 0.204, 0.071])

4.7. Eg(x) and Eg(y)

unit [55], combined with a pre-arranged chirality induced by a chi-

motifs indicates that the design regime is persistent and should

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