Aromatic stacking interactions in flavin model systems

Identification and Characterization of Thiamine Diphosphate-Dependent Lyases with an Unusual CDG Motif

The thiamine diphosphate (ThDP)-binding motif, characterized by the canonical GDG(X)24-27N sequence, is highly conserved among ThDP-dependent enzymes. We investigated a ThDP-dependent lyase (JanthE from Janthinobacterium sp. HH01) with an unusual cysteine (C458) replacing the first glycine of this motif. JanthE exhibits a high substrate promiscuity and accepts long aliphatic α-keto acids as donors. Sterically hindered aromatic aldehydes or non-activated ketones are acceptor substrates, giving access to a variety of secondary and tertiary alcohols as carboligation products. The crystal structure solved at a resolution of 1.9 Å reveals that C458 is not primarily involved in cofactor binding as previously thought for the canonical glycine. Instead, it coordinates methionine 406, thus ensuring the integrity of the active site and the enzyme activity. In addition, we have determined the long-sought genuine tetrahedral intermediates formed with pyruvate and 2-oxobutyrate in the pre-decarboxylation states and deciphered the atomic details for their stabilization in the active site. Collectively, we unravel an unexpected role for the first residue of the ThDP-binding motif and unlock a family of lyases that can perform valuable carboligation reactions.

Chiral Supramolecular Organogel Constructed Using Riboflavin and Melamine: Its Application in Photo-Catalyzed Colorimetric Chiral Sensing and Enantioselective Adsorption

The synthesis of a chiral supramolecular organogel via the hierarchical helical self-assembly of optically active riboflavin and melamine derivatives is described herein. Owing to the photocatalysis of riboflavin and the supramolecular chirality induced in the helically stacked riboflavin/melamine complex, the gel is observed to act as a light-stimulated chiral sensor of optically active alcohols by detecting the change in color from yellow to green. The gel also served as an efficient chiral adsorbent, enabling optical resolution of a racemic compound with high chiral recognition ability.

Tuning the Photophysical Properties of Flavins by Attaching an Aryl Moiety via Direct C-C Bond Coupling

Palladium-catalyzed Suzuki reactions of brominated flavin derivatives (5-deazaflavins, alloxazines, and isoalloxazines) with boronic acids or boronic acid esters that occur readily under mild conditions were shown to be an effective tool for the synthesis of a broad range of 7/8-arylflavins. In general, the introduction of an aryl/heteroaryl group by means of a direct C-C bond has been shown to be a promising approach to tuning the photophysical properties of flavin derivatives. The aryl substituents caused a bathochromic shift in the absorption spectra of up to 52 nm and prolonged the fluorescence lifetime by up to 1 order of magnitude. Moreover, arylation of flavin derivatives decreased their ability to generate singlet oxygen.

A Self‐Assembling Flavin for Visible Photooxidation

A new flavin‐based gelator is reported which forms micellar structures at high pH and gels at low pH. This flavin can be used for the photooxidation of thiols under visible light, with the catalytic efficiency being linked to the self‐assembled structures present.

Designing Stacked Assembly of Type III Rubisco for CO2 Fixation with Higher Efficiency

The slow catalytic rate of the carboxylation enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major barrier to increasing the rate of carbon assimilation from the atmosphere into the biosphere. It is of great importance to establish a method to improve the carboxylation efficiency of Rubisco. Inspired by the assembly of Rubisco in carboxysomes, herein, we presented a rational protein engineering approach for the construction of one-dimensional (1D) protein arrays of type III Rubisco through designed π-π stacking interactions by using crystal structural information as a guide. In aqueous solutions, the dimensions of these 1D protein arrays collectively span nearly the entire nano- and micrometer scale (200 nm to 5.0 μm) by adjusting protein and NaCl concentrations. As a result, the stacked Rubisco assemblies increase by 40% in the carboxylase activity, while their turnover number (k_cat) is around twofold larger than that of wild-type III Rubisco. Notably, upon heat treatment at temperature up to 75 °C for 30 min, most of the assembled nanostructures and the enzyme activity are retained. More importantly, the initial relative activity of stacked assemblies retained 91% after 10 cycles of reuse. This work provides a simple, effective solution for the improvement of the CO₂ carboxylation efficiency of Rubisco.

Tunable Properties of Nature-Inspired N,N'-Alkylated Riboflavin Semiconductors

A series of novel soluble nature-inspired flavin derivatives substituted with short butyl and bulky ethyl-adamantyl alkyl groups was prepared via simple and straightforward synthetic approach with moderate to good yields. The comprehensive characterization of the materials, to assess their application potential, has demonstrated that the modification of the conjugated flavin core enables delicate tuning of the absorption and emission properties, optical bandgap, frontier molecular orbital energies, melting points, and thermal stability. Moreover, the thin films prepared thereof exhibit smooth and homogeneous morphology with generally high stability over time.

Benzo-Dipteridine Derivatives as Organic Cathodes for Li- and Na-ion Batteries

Organic-based electrodes for Li- and Na-ion batteries present attractive alternatives to commonly applied inorganic counterparts which can often carry with them supply-chain risks, safety concerns with thermal runaway, and adverse environmental impact. The ability to chemically direct the structure of organic electrodes through control over functional groups is of particular importance, as this provides a route to fine-tune electrochemical performance parameters. Here, we report two benzo-dipteridine derivatives, BF-Me₂ and BF-H₂ , as high-capacity electrodes for use in Li- and Na-ion batteries. These moieties permit binding of multiple Li-ions per molecule while simultaneously ensuring low solubility in the supporting electrolyte, often a precluding issue with organic electrodes. Both display excellent electrochemical stability, with discharge capacities of 142 and 182 mAh g^-1 after 100 cycles at a C/10 rate and Coulombic efficiencies of 96% and ∼ 100% demonstrated for BF-Me₂ and BF-H₂ , respectively. The application of a Na-ion cell has also been demonstrated, showing discharge capacities of 88.8 and 137 mAh g^-1 after 100 cycles at a C/2 rate for BF-Me₂ and BF-H₂ , respectively. This work provides an encouraging precedent for these and related structures to provide versatile, high-energy density, and long cycle-life electrochemical energy storage materials.

Characterization in aqueous medium of an FMN semiquinone radical stabilized by the enzyme-like microenvironment of a modified polyethyleneimine

The elusive flavin semiquinone intermediate found in flavoproteins such as cryptochromes has been obtained in aqueous solution by single electron reduction of the natural FMN cofactor using sodium ascorbate. This species was formed in the local hydrophobic microenvironment of a modified polyethyleneimine and characterized by UV-Visible, fluorescence and EPR spectroscopies.

Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO

Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.

Competing Allosteric Mechanisms for Coordination-Directed Conformational Changes of Chiral Stacking Structures with Aromatic Rings

This work revealed that significant asymmetric nonlinear effects can be found in a coordination-directed conformational alteration through competing allosteric mechanisms. Toward this aim, we have prepared new chiral bridging ligands [( S, S)- and ( R, R)-Im₂An] containing an anthracene ring as a spacer with two ethynyl-linked chiral imidazole groups at the 9,10-positions. The ( S, S)- and ( R, R)-Im₂An ligands (L) spontaneously form the assemblies with Zn²⁺ ions (M) in solution phase, giving L₄M₂-type assemblies with a general formula [( S, S)- or ( R, R)-Im₂An]₄(Zn²⁺)₂. NMR studies revealed that the [( S, S)-Im₂An]₄(Zn²⁺)₂ assembly has an anthracene dimer structure with a parallel-displaced geometry, leading to relatively small circular dichroism (CD) signals, as expected for nonchiral objects. Conversely, subsequent addition of chiral coligands [( R)- or ( S)-Ph-box] to [( S, S)-Im₂An]₄(Zn²⁺)₂ afforded an alternative Zn²⁺ assembly with general formula [( R)- or ( S)-Ph-box]₂[( S, S)-Im₂An]₂(Zn²⁺)₂, where the chiral coligands expel two of the ( S, S)-Im₂An ligands that were singly bound to the Zn²⁺ ions in the original [( S, S)-Im₂An]₄(Zn²⁺)₂ assembly. This ligand-exchange reaction causes conformational alteration from a parallel-displaced structure to a twisted stacking between the anthracene rings inside the Zn²⁺ assembly, which results in a significant enhancement of CD signals due to excitonic interactions of the chiral anthracene dimer. Dissymmetry factor ( g_CD) for CD due to chiral stacking structures shows a significant inverse sigmoidal response to the enantiomeric excess of the chiral coligands. The observed nonlinear phenomena are results of the two conflicting mechanisms, homochiral cooperative association (homochiral self-sorting) to form CD-active assemblies [( S)- or ( R)-Ph-box]₂[( S, S)-Im₂An]₂(Zn²⁺)₂ versus heterochiral cooperative dissociation of [( S, S)-Im₂An]₄(Zn²⁺)₂ by sequestering of Zn²⁺ inside the assembly through formation of a heterochiral 2:1 Zn²⁺ complex ([( R)-Ph-box][( S)-Ph-box]Zn²⁺). The presented mechanisms provide a new strategy for generating switch-like OFF/ON states in chiral systems.

Investigation of Different Prototropic Forms of Biologically Active Flavin Lumichrome in the Presence of Liposome

Herein, we reported the photophysical behavior of lumichrome (LC), one of the biologically active flavin molecules, in the presence of small unilamellar vesicle of anionic lipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). With the help of different spectroscopic techniques, we have proposed that anionic DMPC liposome interacts with the cationic form LC in ground state and in excited state and modulate the spectral properties of LC. Photophysical study reveals that different prototropic forms of LC are present in DMPC liposome medium. In the presence of DMPC liposome, fluorescence emission properties of LC vary with change in excitation and emission wavelengths. This indicates switch over between different structural forms of LC. From fluorescence lifetime measurements and fluorescence lifetime imaging (FLIM) study, it was revealed that emission decay profile of LC was fitted biexponentially in the presence of liposome. It suggests that in the presence of liposome, more than one form of LC is present. We have constructed the time-resolved area-normalized emission spectra (TRANES) of LC in the liposome and found one isoemissive point. This confirmed that two emissive species of LC are present in liposome. FLIM study and FE-SEM study give an idea about the structural feature of the complex between LC and liposome.

Functionalized gold nanostructures: promising gene delivery vehicles in cancer treatment

Surface-modified gold nanoparticles are recognized as promising gene delivery vehicles in the treatment of cancer owing to their excellent biocompatibility with biomolecules (like DNA or RNA) and their unique optical and structural properties. In this context, this review article focuses on the diverse transfection abilities of the gene to the targeted cell on the basis of different shapes and sizes of gold nanoparticles in order to promote its effective expression for cancer treatment. In addition, recent trends in gold nanoparticle mediated gene silencing, gene delivery, detection and combinatory therapies are highlighted considering their cytotoxic effects on healthy human cells.

Various functions of gold nanoparticles in conjugation with nucleic acids.

Novel Riboflavin-Inspired Conjugated Bio-Organic Semiconductors

Flavins are known to be extremely versatile, thus enabling routes to innumerable modifications in order to obtain desired properties. Thus, in the present paper, the group of bio-inspired conjugated materials based on the alloxazine core is synthetized using two efficient novel synthetic approaches providing relatively high reaction yields. The comprehensive characterization of the materials, in order to evaluate the properties and application potential, has shown that the modification of the initial alloxazine core with aromatic substituents allows fine tuning of the optical bandgap, position of electronic orbitals, absorption and emission properties. Interestingly, the compounds possess multichromophoric behavior, which is assumed to be the results of an intramolecular proton transfer.

Triptycene as a Supramolecular Additive in PTB7:PCBM Blends and Its Influence on Photovoltaic Properties

Additives play an important role in modifying the morphology and phase separation of donor and acceptor molecules in bulk heterojunction (BHJ) solar cells. Here, we report triptycene (TPC) as a small-molecule additive for supramolecular control of phase separation and concomitant improvement of the power conversion efficiency (PCE) of PTB7 donor and fullerene acceptor-based BHJ polymer solar cells. An overall 60% improvement in PCE is observed for both PTB7:PC₆₁BM and PTB7:PC₇₁BM blends. The improved photovoltaic (PV) performance can be attributed to three factors: (a) TPC-induced supramolecular interactions with donor:acceptor components in the blends to realize a nanoscale phase-separated morphology; (b) an increase in the charge transfer state energy that lowers the driving force for electron transfer from donor to acceptor molecules; and (c) an increase in the charge carrier mobility. An improvement in efficiency using TPC as a supramolecular additive has also been demonstrated for other BHJ blends such as PBDB-T:PC₇₁BM and P3HT:PCBM, implying the wide applicability of this new additive molecule. A comparison of the photostability of TPC as an additive for PTB7:PCBM solar cells to that of the widely used 1,8-diiodooctane additive shows ∼30% higher retention of PV performance for the TPC-added solar cells after 34 h of AM 1.5G illumination. The results obtained suggest that the approach of using additives that can promote supramolecular interactions to modify the length scale of phase separation between donor and acceptor is very promising and can lead to the development of highly efficient and stable organic photovoltaics.

DNA Damage and Apoptosis Induction in Cancer Cells by Chemically Engineered Thiolated Riboflavin Gold Nanoassembly

Herein we have engineered a smart nuclear targeting thiol-modified riboflavin-gold nano assembly, RfS@AuNPs, which accumulates selectively in the nucleus without any nuclear-targeting peptides (NLS/RGD) and shows photophysically in vitro DNA intercalation. A theoretical model using Molecular Dynamics has been developed to probe the mechanism of formation and stability as well as dynamics of the RfS@AuNPs in aqueous solution and within the DNA microenvironment. The RfS@AuNPs facilitate the binucleated cell formation that is reflected in the significant increase of DNA damage marker, γ-H2AX as well as the arrest of most of the HeLa cells at the pre-G1 phase indicating cell death. Moreover, a significant upregulation of apoptotic markers confirms that the cell death occurs through the apoptotic pathway. Analyses of the microarray gene expression of RfS@AuNPs treated HeLa cells show significant alterations in vital biological processes necessary for cell survival. Taken together, our study reports a unique nuclear targeting mechanism through targeting the riboflavin receptors, which are upregulated in cancer cells and induce apoptosis in the targeted cells.

Effects of Noncovalent Interactions on the Catalytic Activity of Unsupported Colloidal Palladium Nanoparticles Stabilized with Thiolate Ligands

This article presents the systematic evaluation of colloidal palladium nanoparticles functionalized with well-defined small organic ligands that provide spatial control of the geometric and electronic surface properties of nanoparticle catalysts. Palladium nanoparticles stabilized with thiolate ligands of different structures and functionalities (linear alkyl vs cyclohexyl vs phenyl) are synthesized using the thiosulfate protocol in a two-phase system. The structure and composition of palladium nanoparticles are characterized using transmission electron microscopy, thermogravimetric analysis, NMR, and UV-vis spectroscopies. The catalysis studies show that the chemical and structural compositions of monolayers surrounding the nanoparticle core greatly influence the overall activity and selectivity of colloidal palladium nanoparticle catalysts for the hydrogenation, isomerization, and hydrogenolysis of allylic alcohols. Especially, noncovalent interactions between surface phenyl ligands and incoming aromatic substrates are found to have a profound influence on the selectivity of colloidal palladium nanoparticles.

Synthesis and characterisation of push–pull flavin dyes with efficient second harmonic generation (SHG) properties

We report push–pull flavins bearing different donor groups that exhibit high hyperpolarisabilities (β = 355–9550 × 10⁻³⁰ esu) and decomposition temperatures thereby indicating their potential application as non-linear optical device materials.

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

The atom-by-atom control provided by synthetic organic chemistry presents a means of generating new functional nanomaterials with great precision. Bringing together these two very disparate skill sets is, however, quite uncommon. This autobiographical review provides some insight into how my program evolved, as well as giving some idea of where we are going.

Synthesis and properties of pteridine-2,4-dione-functionalised oligothiophenes

The synthesis of symmetrical acceptor-functionalised oligothiophenes is described and their electrochemical and optical properties are reported.

A Click Chemistry Approach towards Flavin-Cyclodextrin Conjugates-Bioinspired Sulfoxidation Catalysts

A click chemistry approach based on the reaction between alkynylflavins and mono(6-azido-6-deoxy)-β-cyclodextrin has proven to be a useful tool for the synthesis of flavin-cyclodextrin conjugates studied as monooxygenase mimics in enantioselective sulfoxidations.

Synthesis and electronic properties of π-extended flavins

Flavin derivatives with an extended π-conjugation were synthesized in moderate to good yields from aryl bromides via a Buchwald-Hartwig palladium catalyzed amination protocol, followed by condensation of the corresponding aromatic amines with violuric acid. The electronic properties of the new compounds were investigated by absorption and emission spectroscopy, cyclic voltammetry, density functional theory (DFT) and time dependent density functional theory (TDDFT). The compounds absorb up to 550 nm and show strong luminescence. The photoluminescence quantum yields ϕPL measured in dichloromethane reach 80% and in PMMA (poly(methyl methacrylate)) 77%, respectively, at ambient temperature. The electrochemical redox behaviour of π-extended flavins follows the mechanism previously described for the parent flavin.

Effects of Low to Intermediate Water Concentrations on Proton-Coupled Electron Transfer (PCET) Reactions of Flavins in Aprotic Solvents and a Comparison with the PCET Reactions of Quinones

The electrochemical reduction mechanisms of 2 synthesized flavins (Flox) were examined in detail in deoxygenated solutions of DMSO containing varying amounts of water, utilizing variable scan rate cyclic voltammetry (ν = 0.1-20 V s(-1)), controlled-potential bulk electrolysis, and UV-vis spectroscopy. Flavin 1, which contains a hydrogen atom at N(3), is capable of donating its proton to other reduced flavin species. After 1e(-) reduction, the initially formed Fl(•-) receives a proton from another Flox to form FlH(•) (and concomitantly produce the deprotonated flavin, Fl(-)), although the equilibrium constant for this process favors the back reaction. Any FlH(•) formed at the electrode surface immediately undergoes another 1e(-) reduction to form FlH(-), which reacts with Fl(-) to form 2 molecules of Fl(•-). Further 1e(-) reduction of Fl(•-) at more negative potentials produces the dianion, Fl(2-), which can also be protonated by another Flox to form FlH(-) and Fl(-). Flavin 2, which is methylated at N(3) (and therefore has no acidic proton), undergoes a simple chemically reversible 1e(-) reduction process in DMSO provided the water content is low (<100 mM). Further 1e(-) reduction of Fl(•-) (from flavin 2) at more negative potentials leads to the dianion, Fl(2-), which is protonated by trace water in solution to form FlH(-), similar to the mechanism of flavin 1 at high scan rates. Addition of sufficient amounts of water to nonaqueous solvents results in protonation of the anion radical species, Fl(•-), for both flavins, causing an increase in the amount of FlH(-) in solution. This behavior contrasts with what is observed for quinones, which are also reduced in two 1e(-) steps in aprotic organic solvents to form the radical anions and dianions, but are able to exist in hydrogen-bonded forms (with trace or added water) without undergoing protonation.

Colorful surface architectures with three different types of dynamic covalent bonds: integration of anthocyanins, tritylium ions and flavins

Although they combine the best of covalent and non-covalent bonds, dynamic covalent bonds are usually not used together. Building on pioneering examples for functional systems with two orthogonal dynamic covalent bonds, we herein elaborate on multicomponent surface architectures that operate with three different types of dynamic covalent bonds. Disulfide exchange under basic conditions is used to grow single π stacks directly on oxide surfaces, hydrazone exchange under acidic conditions to add a second string or stack, and boronic-ester exchange under neutral conditions to build the third one. In this study, we show that this synthetic approach to complex systems provides access to emergent properties, as exemplified with ordered stacks of anthocyanins, pyrocatchol violet and riboflavins. The integration of anthocyanins, the central component of the pigments of plant flowers, is interesting to protect the blue flavylium cation against deprotonation, deplanarization and degradation. The integration of pyrocatchol violet is of interest to stabilize the blue, disfavored tritylium cation. The red riboflavin stacks are attractive because they generate high photocurrent. These colorful examples hint at the potential of synthetic methods that use three different types of dynamic covalent bonds in concert to build complex systems with emergent properties.

Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond

Enzyme-catalyzed reactions often rely on a noncovalently bound cofactor whose reactivity is tuned by its immediate environment. Flavin cofactors, the most versatile catalyst encountered in biology, are often maintained within the protein throughout numbers of complex ionic and aromatic interactions. Here, we have investigated the role of π-π stacking and hydrogen bond interactions between a tyrosine and the isoalloxazine moiety of the flavin adenine dinucleotide (FAD) in an FAD-dependent RNA methyltransferase. Combining several static and time-resolved spectroscopies as well as biochemical approaches, we showed that aromatic stacking is assisted by a hydrogen bond between the phenol group and the amide of an adjacent active site loop. A mechanism of recognition and binding of the redox cofactor is proposed.

Photophysics of lumichrome in anionic and cationic micellar media

The photophysics of lumichrome in the presence of cationic and anionic micellar environments was reported in this article.

Effect of stacking interactions on the thermodynamics and kinetics of lumiflavin: a study with improved density functionals and density functional tight-binding protocol

The π-π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation density functionals. Six known lumiflavin-aromatic adducts were used and the models were evaluated by comparing the geometry and energetics with experimental results. The study found that dispersion-corrected and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodynamic characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biologically relevant aromatic groups. Additionally, the reduction of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were observed in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking phenyl alanine, tryptophan, and tyrosine side chains, respectively, of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodynamics of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-methyl nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the density functional theory (DFT) and the computationally less expensive dispersion-corrected self-consistent density functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and additional DFT-computed perturbative corrections could significantly improve these results.

Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine

Aromatic stacking interactions between isoalloxazine (ISA) of flavin and three prototypical aromatics (benzene, pyridine, chlorobenzene) were investigated using electronic structure calculations with Monte Carlo simulated annealing. The Effective Fragment Potential (EFP) method was used to locate the low-energy equilibrium configurations for the three dimer systems. These structures were further characterized through DFT (M06-2X) and MP2 calculations. One equilibrium configuration exists for ISA-benzene; characterizing the stacked dimer surface revealed a steep, single-welled potential that funnels benzene directly between rings II and III, positioning a substituent hydrogen adjacent to the redox-active N5. ISA-pyridine and ISA-chlorobenzene minimum-energy structures contain the aromatic ring in very similar position to that in ISA-benzene. However, the added rotational degree of freedom leads to two distinct binding motifs, having approximately antiparallel or parallel dipole moment alignment with ISA. The existence of the latter binding configuration was unexpected but is explained by the shape of the ISA electrostatic potential. Dispersion is the primary noncovalent interaction driving the positioning of aromatic rings above ISA, while electrostatics determine the orientation in dipole-containing substituted benzenes. The interplay of these interactions can be used to tune molecular recognition properties of synthetic redox cofactors, including positioning desired functional groups adjacent to the redox-active N5.