Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian's De Stijl

Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties. We, as chemists, are comfortable with pictorial representations of structure, in which some nuance is lost-investigating molecular shape numerically by looking at how closely it fits a reference, such as a plane, or a set of vectors or coordinates, is informative, though far from engaging. Often relationships between chemical structure and derived values are obscured. Taking our inspiration from Piet Mondrian's Compositions, we have depicted the symmetry information encoded within 3D data as blocks of color, to show clearly how chemical arguments and resultant molecular distortion may contribute to symmetry. Great art gives us a new perspective on the world; as a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, understanding how their shape and properties are intertwined.

Bicyclo[1.1.1]pentane Embedded in Porphyrinoids

We report a two-step approach to obtain synthetically versatile bicyclo[1.1.1]pentane (BCP) derivatives using Grignard reagents. This method allows the incorporation of BCP units in tetrapyrrolic macrocycles and the synthesis of a new class of calix[4]pyrrole analogues by replacing two bridging methylene groups with two BCP units. In addition, a doubly N-confused system was also formed in the presence of electron-withdrawing substituents at the BCP bridgeheads. The pyrrole rings in BCP containing macrocycles exist in 1,3-alternate or abab conformation, as observed from single-crystal X-ray diffraction analyses and 2D NMR spectroscopy.

Nonplanar porphyrins: synthesis, properties, and unique functionalities

Porphyrins are variously substituted tetrapyrrolic macrocycles, with wide-ranging biological and chemical applications derived from metal chelation in the core and the 18π aromatic surface. Under suitable conditions, the porphyrin framework can deform significantly from regular planar shape, owing to steric overload on the porphyrin periphery or steric repulsion in the core, among other structure modulation strategies. Adopting this nonplanar porphyrin architecture allows guest molecules to interact directly with an exposed core, with guest-responsive and photoactive electronic states of the porphyrin allowing energy, information, atom and electron transfer within and between these species. This functionality can be incorporated and tuned by decoration of functional groups and electronic modifications, with individual deformation profiles adapted to specific key sensing and catalysis applications. Nonplanar porphyrins are assisting breakthroughs in molecular recognition, organo- and photoredox catalysis; simultaneously bio-inspired and distinctly synthetic, these molecules offer a new dimension in shape-responsive host-guest chemistry. In this review, we have summarized the synthetic methods and design aspects of nonplanar porphyrin formation, key properties, structure and functionality of the nonplanar aromatic framework, and the scope and utility of this emerging class towards outstanding scientific, industrial and environmental issues.

Unraveling the Pivotal Role of Atropisomerism for Cellular Internalization

The intrinsic challenge of large molecules to cross the cell membrane and reach intracellular targets is a major obstacle for the development of new medicines. We report how rotation along a single C-C bond, between atropisomers of a drug in clinical trials, improves cell uptake and therapeutic efficacy. The atropisomers of redaporfin (a fluorinated sulfonamide bacteriochlorin photosensitizer of 1135 Da) are separable and display orders of magnitude differences in photodynamic efficacy that are directly related to their differential cellular uptake. We show that redaporfin atropisomer uptake is passive and only marginally affected by ATP depletion, plasma proteins, or formulation in micelles. The α₄ atropisomer, where meso-phenyl sulfonamide substituents are on the same side of the tetrapyrrole macrocycle, exhibits the highest cellular uptake and phototoxicity. This is the most amphipathic atropisomer with a conformation that optimizes hydrogen bonding (H-bonding) with polar head groups of membrane phospholipids. Consequently, α₄ binds to the phospholipids on the surface of the membrane, flips into the membrane to adopt the orientation of a surfactant, and eventually diffuses to the interior of the cell (bind-flip mechanism). We observed increased α₄ internalization by cells of the tumor microenvironment in vivo and correlated this to the response of photodynamic therapy when tumor illumination was performed 24 h after α₄ administration. These results show that properly orientated aryl sulfonamide groups can be incorporated into drug design as efficient cell-penetrating motifs in vivo and reveal the unexpected biological consequences of atropisomerism.

Quantitative Structure-Property Relationship Modelling for the Prediction of Singlet Oxygen Generation by Heavy-Atom-Free BODIPY Photosensitizers*

Heavy-atom-free sensitizers forming long-living triplet excited states via the spin-orbit charge transfer intersystem crossing (SOCT-ISC) process have recently attracted attention due to their potential to replace costly transition metal complexes in photonic applications. The efficiency of SOCT-ISC in BODIPY donor-acceptor dyads, so far the most thoroughly investigated class of such sensitizers, can be finely tuned by structural modification. However, predicting the triplet state yields and reactive oxygen species (ROS) generation quantum yields for such compounds in a particular solvent is still very challenging due to a lack of established quantitative structure-property relationship (QSPR) models. In this work, the available data on singlet oxygen generation quantum yields (ΦΔ ) for a dataset containing >70 heavy-atom-free BODIPY in three different solvents (toluene, acetonitrile, and tetrahydrofuran) were analyzed. In order to build reliable QSPR model, a series of new BODIPYs were synthesized that bear different electron donating aryl groups in the meso position, their optical and structural properties were studied along with the solvent dependence of singlet oxygen generation, which confirmed the formation of triplet states via the SOCT-ISC mechanism. For the combined dataset of BODIPY structures, a total of more than 5000 quantum-chemical descriptors was calculated including quantum-chemical descriptors using density functional theory (DFT), namely M06-2X functional. QSPR models predicting ΦΔ values were developed using multiple linear regression (MLR), which perform significantly better than other machine learning methods and show sufficient statistical parameters (R=0.88-0.91 and q2 =0.62-0.69) for all three solvents. A small root mean squared error of 8.2 % was obtained for ΦΔ values predicted using MLR model in toluene. As a result, we proved that QSPR and machine learning techniques can be useful for predicting ΦΔ values in different media and virtual screening of new heavy-atom-free BODIPYs with improved photosensitizing ability.

Dipyrrinato-Iridium(III) Complexes for Application in Photodynamic Therapy and Antimicrobial Photodynamic Inactivation

The generation of bio-targetable photosensitizers is of utmost importance to the emerging field of photodynamic therapy and antimicrobial (photo-)therapy. A synthetic strategy is presented in which chelating dipyrrin moieties are used to enhance the known photoactivity of iridium(III) metal complexes. Formed complexes can thus be functionalized in a facile manner with a range of targeting groups at their chemically active reaction sites. Dipyrrins with N- and O-substituents afforded (dipy)iridium(III) complexes via complexation with the respective Cp*-iridium(III) and ppy-iridium(III) precursors (dipy=dipyrrinato, Cp*=pentamethyl-η5 -cyclopentadienyl, ppy=2-phenylpyridyl). Similarly, electron-deficient [IrIII (dipy)(ppy)2 ] complexes could be used for post-functionalization, forming alkenyl, alkynyl and glyco-appended iridium(III) complexes. The phototoxic activity of these complexes has been assessed in cellular and bacterial assays with and without light; the [IrIII (Cl)(Cp*)(dipy)] complexes and the glyco-substituted iridium(III) complexes showing particular promise as photomedicine candidates. Representative crystal structures of the complexes are also presented.

Crystal structures of 4-bromo-2-formyl-1-tosyl-1H-pyrrole, (E)-4-bromo-2-(2-nitro-vin-yl)-1-tosyl-1H-pyrrole and 6-(4-bromo-1-tosyl-pyrrol-2-yl)-4,4-dimethyl-5-nitro-hexan-2-one

Crystal structures of three substituted N-tosyl­pyrrole compounds are reported; these compounds show a variety of ‘weak’ inter­molecular inter­actions owing to different substitution patterns and supra­molecular arrangements. The benefits of collecting crystal structure data to extreme resolution (0.5 Å) are discussed.

The crystal structures of three inter­mediate compounds in the synthesis of 8-bromo-2,3,4,5-tetra­hydro-1,3,3-tri­methyl­dipyrrin are reported; 4-bromo-2-formyl-1-tosyl-1H-pyrrole, C₁₂H₁₀BrNO₃S, (E)-4-bromo-2-(2-nitro­vin­yl)-1-tosyl-1H-pyrrole, C₁₃H₁₁BrN₂O₄S, and 6-(4-bromo-1-tosyl­pyrrol-2-yl)-4,4-dimethyl-5-nitro­hexan-2-one, C₁₉H₂₃BrN₂O₅S. The compounds show multitudinous inter­molecular C—H⋯O inter­actions, with bond distances and angle consistent in the series and within expectations, as well as varied packing types. The merits of collecting data beyond the standard resolution usually reported for small mol­ecules are discussed.

An Insight into Non-Covalent Interactions on the Bicyclo[1.1.1]pentane Scaffold

Bicyclo[1.1.1]pentane (BCP) is studied extensively as a bioisosteric component of drugs. Not found in nature, this molecular unit approximates the distance of a para-disubstituted benzene which is replaced in medicines as a method of improving treatments. Predicting interactions of these drugs with specific active sites requires knowledge of the non-covalent interactions engaged by this subunit. Structure determinations and computational analysis (Hirshfeld analysis, 2D fingerprint plots, DFT) of seven BCP derivatives chosen to probe specific and directional interactions. X-ray analysis revealed the presence of various non-covalent interactions including I ⋅⋅⋅ I, I ⋅⋅⋅ N, N-H ⋅⋅⋅ O, C-H ⋅⋅⋅ O, and H-C ⋅⋅⋅ H-C contacts. The preference of halogen bonding (I ⋅⋅⋅ I or I ⋅⋅⋅ N) in BCP 1-4 strictly depends upon the electronic nature and angle between bridgehead substituents. The transannular distance in co-crystals 2 and 4 was longer as compared to monomers 1 and 3. Stronger N-H ⋅⋅⋅ O and weaker C-H ⋅⋅⋅ O contacts were observed for BCP 5 while the O ⋅⋅⋅ H interaction was a prominent contact for BCP 6. The presence of 3D BCP units prevented the π ⋅⋅⋅ π stacking between phenyl rings in 3, 4, and 7. The BCP skeleton was often rotationally averaged, indicating fewer interactions compared to bridgehead functional groups. Using DFT analysis, geometries were optimized and molecular electrostatic potentials were calculated on the BCP surfaces. These interaction profiles may be useful for designing BCP analogs of drugs.

Exploring the relationship between structure and activity in BODIPYs designed for antimicrobial phototherapy

A synthetic strategy to BODIPY dyes is presented giving access to a range of new compounds relevant in the context of antimicrobial photodynamic therapy (aPDT). BODIPYs with the 8-(4-fluoro-3-nitrophenyl) and the 8-pentafluorophenyl substituents were used for the synthesis of new mono- and dibrominated BODIPYs. The para-fluorine atoms in these electron-withdrawing groups facilitate functional modification via nucleophilic aromatic substitution (SNAr) with a number of amines and thio-carbohydrates. Subsequently, the antibacterial phototoxic activity of these BODIPYs has been assessed in bacterial assays against the Gram-positive germ S. aureus and also against the Gram-negative germ P. aeruginosa. The bacterial assays allowed to identify substitution patterns which ensured antibacterial activity not only in phosphate-buffered saline (PBS) but also in the presence of serum, hereby more realistically modelling the complex biological environment that is present in clinical applications.

Crystal structures of 2,3,7,8,12,13,17,18-octa-bromo-5,10,15,20-tetra-kis-(penta-fluoro-phen-yl)porphyrin as the chloro-form monosolvate and tetra-hydro-furan monosolvate

The crystal structures of the title compounds, two solvates (CHCl3 and THF) of a symmetric and highly substituted porphyrin, C44H2Br8F20N4 or OBrTPFPP, are described. These structures each feature a non-planar porphyrin ring, exhibiting a similar conformation of the strained ring independent of solvent identity. These distorted porphyrins are able to form hydrogen bonds and sub-van der Waals halogen inter-actions with enclathrated solvent; supra-molecular inter-actions of proximal macrocycles are additionally affected by solvent choice. The crystal studied for compound 1·CHCl3 was refined as an inversion twin. One penta-fluoro-phenyl group was modelled as disordered over two sites [occupancy ratio = 0.462 (7):0.538 (7)]. The chloro-form solvate was also modelled as disordered over two orientations [occupancy ratio = 0.882 (7): 0.118 (7).

Square Grid Metal-Chloranilate Networks as Robust Host Systems for Guest Sorption

Reaction of the chloranilate dianion with Y(NO₃ )₃ in the presence of Et₄ N⁺ in the appropriate proportions results in the formation of (Et₄ N)[Y(can)₂ ], which consists of anionic square-grid coordination polymer sheets with interleaved layers of counter-cations. These counter-cations, which serve as squat pillars between [Y(can)₂ ] sheets, lead to alignment of the square grid sheets and the subsequent generation of square channels running perpendicular to the sheets. The crystals are found to be porous and retain crystallinity following cycles of adsorption and desorption. This compound exhibits a high affinity for volatile guest molecules, which could be identified within the framework by crystallographic methods. In situ neutron powder diffraction indicates a size-shape complementarity leading to a strong interaction between host and guest for CO₂ and CH₄ . Single-crystal X-ray diffraction experiments indicate significant interactions between the host framework and discrete I₂ or Br₂ molecules. A series of isostructural compounds (cat)[M^III (X-an)₂ ] with M=Sc, Gd, Tb, Dy, Ho, Er, Yb, Lu, Bi or In, cat=Et₄ N, Me₄ N and X-an=chloranilate, bromanilate or cyanochloranilate bridging ligands have been generated. The magnetic properties of representative examples (Et₄ N)[Gd(can)₂ ] and (Et₄ N)[Dy(can)₂ ] are reported with normal DC susceptibility but unusual AC susceptibility data noted for (Et₄ N)[Gd(can)₂ ].

An indirect generation of 1D MII-2,5-dihydroxybenzoquinone coordination polymers, their structural rearrangements and generation of materials with a high affinity for H2, CO2 and CH4

1D coordination polymers undergo transformations upon desolvation to yield sorbent materials.

In vitro pulsatile flow evaluation of a stentless porcine aortic bioprosthesis

Suboptimal hemodynamic performance, tissue calcification, and limitation in long-term durability have been encountered clinically after aortic valve replacement with currently available bioprostheses. It is believed that some of these problems may be caused, directly or indirectly, by the stents of the bioprostheses. To address these deficiencies, the authors undertook the development of the Edwards Prima Stentless Bioprosthesis. This study was designed to evaluate the hemodynamic performance of the Edwards Prima Stentless Bioprosthesis in a pulse duplicator system. The stented Carpentier-Edwards Porcine Bioprosthesis (Baxter Healthcare Corp., Irvine, CA), which has been used in United States clinics for more than 10 years, was used as a control device. The flow fields in the vicinity of the test bioprostheses were inspected with color Doppler flow mapping. The transvalvular pressure gradients were measured invasively with a catheter and calculated with the Doppler determined velocity using a simplified Bernoulli equation. Additionally, the leakage volumes were determined with an electromagnetic flowmeter. In the Doppler flow mapping study, during systole, a central flow was observed distal to the stentless and stented bioprostheses. The central flow distal to the stentless bioprosthesis was broader than that observed distal to its stented counterpart. During diastole, no regurgitation was detected by color Doppler flow mapping in either the stentless or stented groups. The Doppler determined transvalvular pressure gradients correlated well with those measured by catheter (r = 0.990). Moreover, it was learned that the transvalvular pressure gradients of the stentless bioprosthesis were less than those of its stented counterpart, especially for the smaller sizes.(ABSTRACT TRUNCATED AT 250 WORDS)

A newly developed porcine heart valve bioprosthesis fixed with an epoxy compound. An experimental evaluation

Concerns with currently available bioprostheses are calcification, long-term durability, and functional and hemodynamic performance. It has been well known that these concerns are all more or less related to the fixatives, glutaraldehyde or formaldehyde, used in preserving bioprostheses. To address these concerns, we undertook the development of a porcine bioprosthesis fixed with an epoxy compound. It was discovered that the porcine leaflets fixed with the epoxy compound appeared more natural than those preserved with glutaraldehyde. The performance of this newly developed epoxy compound bioprosthesis (three samples) was evaluated in a juvenile sheep model. The results were compared to those of its glutaraldehyde counterpart (three samples). Two-dimensional echocardiographic inspection of the valvular leaflet motion indicated that the epoxy compound leaflets were more pliable than their glutaraldehyde counterparts. In addition, the epoxy compound valve appeared to open more widely than the glutaraldehyde valve. Color Doppler flow mapping demonstrated that the blood flow distal to the epoxy compound valve was slightly broader than that observed distal to the glutaraldehyde valve. Moreover, at retrieval, less calcium and pannus ingrowth were observed in the epoxy compound valve than its glutaraldehyde counterpart. The results of this preliminary evaluation indicated that the performance of this newly developed epoxy compound valve was at least equivalent to its glutaraldehyde counterpart, if not better.

In vitro evaluation of a stentless porcine aortic bioprosthesis. A preliminary study

Currently available aortic bioprosthetic heart valves are all relatively suboptimal due to the constraints placed on leaflets by stenting. The constraints on the stenting mechanism may directly or indirectly cause turbulence in the orifice neighborhood, be nidi of tissue calcification, and impart transleaflet stress differentials. To address all these deficiencies, we undertook the development of a stentless porcine aortic bioprosthesis (SPAB). This study evaluates the hemodynamic performance and durability of this design in special chambers with near physiologic compliance. The results are compared to those shown by a stented porcine aortic bioprosthesis. The pressure measurements under steady flow conditions showed that the hemodynamic performance (including pressure gradient and effective orifice area) of SPAB is superior to that of its stented counterpart, especially in the smaller sizes. In addition, it is expected that this stentless design should minimize the mechanical stress to which the leaflets are subjected throughout the cardiac cycle, thus enhancing the durability of the bioprosthesis. In our accelerated durability study for up to 2 equivalent years, no valve failure has been observed. More in vitro studies under pulsatile flow conditions, including color Doppler flow visualization, are currently being conducted.