Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH₂(CH₂)_nCH₂NH₂ (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH₂(CH₂)_nCH₂NH₂ (n = 0–3) interact with BeF₂. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.     

Highly enantioselective sulfa-Michael addition reactions using N-heterocyclic carbene as a non-covalent organocatalyst

We report the first asymmetric sulfa-Michael addition (SMA) reactions using a chiral N-heterocyclic carbene (NHC) as a non-covalent organocatalyst. We demonstrate that a triazolium salt derived NHC functions as an excellent Brønsted base to promote enantioselective carbon–sulfur bond formation. The reaction is applicable to a wide range of thiols and electrophilic olefins. Notably, quaternary chiral centers bearing both an S atom and a CF₃ group were synthesized with excellent asymmetric control. Mechanistic studies suggest that the facial discrimination is likely to be guided by non-covalent interactions: hydrogen bonding and π–π stacking.     

Well-defined silica supported aluminum hydride: another step towards the utopian single site dream?

Reaction of triisobutylaluminum with SBA15₇₀₀ at room temperature occurs by two parallel pathways involving either silanol or siloxane bridges. It leads to the formation of a well-defined bipodal [(SiO)₂Al–CH₂CH(CH₃)₂] 1a, silicon isobutyl [Si–CH₂CH(CH₃)₂] 1b and a silicon hydride [Si–H] 1c. Their structural identity was characterized by FT-IR and advanced solid-state NMR spectroscopies (¹H, ¹³C, ²⁹Si, ²⁷Al and 2D multiple quantum), elemental and gas phase analysis, and DFT calculations. The reaction involves the formation of a highly reactive monopodal intermediate: [SiO–Al–[CH₂CH(CH₃)₂]₂], with evolution of isobutane. This intermediate undergoes two parallel routes: transfer of either one isobutyl fragment or of one hydride to an adjacent silicon atom. Both processes occur by opening of a strained siloxane bridge, Si–O–Si but with two different mechanisms, showing that the reality of “single site” catalyst may be an utopia: DFT calculations indicate that isobutyl transfer occurs via a simple metathesis between the Al-isobutyl and O–Si bonds, while hydride transfer occurs via a two steps mechanism, the first one is a β-H elimination to Al with elimination of isobutene, whereas the second is a metathesis step between the formed Al–H bond and a O–Si bond. Thermal treatment of 1a (at 250 °C) under high vacuum (10^–5 mbar) generates Al–H through a β-H elimination of isobutyl fragment. These supported well-defined Al–H which are highly stable with time, are tetra, penta and octa coordinated as demonstrated by IR and ²⁷Al–¹H J-HMQC NMR spectroscopy. All these observations indicate that surfaces atoms around the site of grafting play a considerable role in the reactivity of a single site system.     

Characterizing affinity epitopes between prion protein and β-amyloid using an epitope mapping immunoassay

Cellular prion protein, a membrane protein, is expressed in all mammals. Prion protein is also found in human blood as an anchorless protein, and this protein form is one of the many potential sources of misfolded prion protein replication during transmission. Many studies have suggested that β-amyloid_1–42 oligomer causes neurotoxicity associated with Alzheimer''s disease, which is mediated by the prion protein that acts as a receptor and regulates the hippocampal potentiation. The prevention of the binding of these proteins has been proposed as a possible preventative treatment for Alzheimer''s disease; therefore, a greater understanding of the binding hot-spots between the two molecules is necessary. In this study, the epitope mapping immunoassay was employed to characterize binding epitopes within the prion protein and complementary epitopes in β-amyloid. Residues 23–39 and 93–119 in the prion protein were involved in binding to β-amyloid_1–40 and _1–42, and monomers of this protein interacted with prion protein residues 93–113 and 123–166. Furthermore, β-amyloid antibodies against the C-terminus detected bound β-amyloid_1–42 at residues 23–40, 104–122 and 159–175. β-Amyloid epitopes necessary for the interaction with prion protein were not determined. In conclusion, charged clusters and hydrophobic regions of the prion protein were involved in binding to β-amyloid_1–40 and _1–42. The 3D structure appears to be necessary for β-amyloid to interact with prion protein. In the future, these binding sites may be utilized for 3D structure modeling, as well as for the pharmaceutical intervention of Alzheimer''s disease.     

Trifluoromethyl substitution enhances photoinduced activity against breast cancer cells but reduces ligand exchange in Ru(ii) complex

A series of five ruthenium complexes containing triphenyl phosphine groups known to enhance both cellular penetration and photoinduced ligand exchange, cis-[Ru(bpy)₂(P(p-R-Ph)₃)(CH₃CN)]²⁺, where bpy = 2,2′-bipyridine and P(p-R-Ph)₃ represent para-substituted triphenylphosphine ligands with R = –OCH₃ (1), –CH₃ (2) –H (3), –F (4), and –CF₃ (5), were synthesized and characterized. The photolysis of 1–5 in water with visible light (λ_irr ≥ 395 nm) results in the substitution of the coordinated acetonitrile with a solvent molecule, generating the corresponding aqua complex as the single photoproduct. A 3-fold variation in quantum yield was measured with 400 nm irradiation, Φ₄₀₀, where 1 is the most efficient with a Φ₄₀₀ = 0.076(2), and 5 the least photoactive complex, with Φ₄₀₀ = 0.026(2). This trend is unexpected based on the red-shifted metal-to-ligand charge transfer (MLCT) absorption of 1 as compared to that of 5, but can be correlated to the substituent Hammett para parameters and pK_a values of the ancillary phosphine ligands. Complexes 1–5 are not toxic towards the triple negative breast cancer cell line MDA-MB-231 in the dark, but 3 and 5 are >4.2 and >19-fold more cytotoxic upon irradiation with blue light, respectively. A number of experiments point to apoptosis, and not to necrosis or necroptosis, as the mechanism of cell death by 5 upon irradiation. These findings provide a foundation for understanding the role of phosphine ligands on photoinduced ligand substitution and show the enhancement afforded by –CF₃ groups on photochemotherapy, which will aid the future design of photocages for photochemotherapeutic drug delivery.

Ru(ii) complexes exhibit photoinduced exchange of coordinated CH₃CN and photocytotoxicity against breast cancer cells highly dependent on the substituents of the ancillary triphenylphospine ligand.     

Synthesis and Systematic Study on the Effect of Different PEG Units on Stability of PEGylated,Integrin-αvβ6-Specific A20FMDV2 Analogues in Rat Serum and Human Plasma

A20FMDV2 is a 20-mer peptide that exhibits high selectivity and affinity for the tumour-related αvβ6 integrin that can compete with extracellular ligands for the crucial RGD binding site, playing a role as a promising αvβ6-specific inhibitor for anti-cancer therapies. Unfortunately, the clinical value of A20FMDV2 is limited by its poor half-life in blood caused by rapid renal excretion and its reported high susceptibility to serum proteases. The incorporation of poly (ethylene glycol) chains, coined PEGylation, is a well-established approach to improve the pharmacokinetic properties of drug molecules. Here, we report a systematic study on the incorporation of a varying number of ethylene glycol units (1–20) into the A20FMDV2 peptide to establish the effects of PEGylation size on the peptide stability in both rat serum and human plasma. In addition, the effect of acetyl and propionyl PEGylation handles on peptide stability is also described. Selected peptide analogues were assessed for integrin-αvβ6-targeted binding, showing good specificity and activity in vitro. Stability studies in rat serum established that all of the PEGylated peptides displayed good stability, and an A20FMDV2 peptide containing twenty ethylene glycol units (PEG₂₀) was the most stable. Surprisingly, the stability testing in human plasma identified shorter PEGs (PEG₂ and PEG₅) as more resistant to degradation than longer PEGs, a trend which was also observed with affinity binding to integrin αvβ6.     

Structural Diversity of Silver Fluorinated β-Diketonates: Effect of the Terminal Substituent and Solvent

In order to demonstrate the role of the fluorination and some solvents in the structural organization of the Ag(I) coordination polymers with β-diketonate ligands (R¹C(O)C_αHC(O)R²)⁻ we synthesized a series of the compounds containing tfac- (R₁ = CH₃, R² = CF₃) and pfpac- (R₁ = CH₃, R² = C₂F₅) anions. Solvent-free [Ag(L)]_∞ (L = tfac 1, pfpac 2) compounds and the corresponding acetonitrile and toluene adducts have been characterized by elemental analysis and/or NMR, IR and single-crystal XRD. This series includes five new coordination polymers. Compound 1 is a 3D coordination framework based on Ag–O_{chelate/bridge}, Ag–C_α bonds, and argentophilic interactions. An increase in the fluorinated group leads to a chain coordination polymer 2 of an unusual structural organization. These chains can be represented as a “DNA-type”, where two intertwined helices based on Ag–O_chelate and Ag–C_α bonds are connected through Ag–O_bridge ones. Two structural types of chain coordination polymers, [Ag(tfac)(CH₃CN)] and [Ag₂(L)₂(solvent)], have been revealed for the adducts. The latter structural type differs significantly from the previously studied toluene and acetonitrile adducts of fluorinated Ag(I) β-diketonates of the same stoichiometry. Thermal analysis in helium showed that both 1 and 2 decompose to metallic silver with the compound of pfpac-ligand being slightly more stable.     

Quantum dynamical study of heavy-light-heavy reactions: application to the (Cl + CH<Subscript>4</Subscript> → HCl + CH<Subscript>3</Subscript>) reaction

A time dependent quantum-mechanical QM study is performed on the Cl + CH₄ → HCl + CH₃ reaction, using a pseudotriatomic ab initio based surface. Probabilities present some clear peaks versus t, which we assign to transition state resonances where the light H atom oscillates between heavy Cl and CH₃ groups. For ground-state reactants, the reactivity is of quantum origin. The reaction occurs through an abstraction mechanism, following both direct and an indirect mechanisms. The calculations show the participation of a short-lived collision complex in the microscopic reaction mechanism. This theoretical result and other oscillating properties found here could, however, be related to the existence of resonance for the production of HCl, as suggested by experimentalists.     

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

An Exploration of the Effect of the Kleier Model and Carrier-Mediated Theory to Design Phloem-Mobile Pesticides Based on Researching the N-Alkylated Derivatives of Phenazine-1-Carboxylic Acid-Glycine

The Kleier model and Carrier-mediated theory are effective for molecularly designing pesticides with phloem mobility. However, the single Kleier model or Carrier-mediated theory cannot achieve a reliable explanation of the phloem mobility of all exogenous substances. A detailed investigation of the two models and the scope of their applications can provide a more accurate and highly efficient basis for the guidance of the design and development of phloem-mobile pesticides. In the present paper, a strategy using active ingredient-amino acid conjugates as mode compounds is developed based on Carrier-mediated theory. An N-alkylated amino acid is used to improve the pesticide’s physicochemical properties following the Kleier model, thus allowing the conjugates to fall on the predicted and more accessible transportation region of phloem. Moreover, the influence of this movement on phloem is inspected by the Kleier model and Carrier-mediated theory. To verify this strategy, a series of N-alkylated phenazine-1-carboxylic acid-glycine compounds (PCA-Gly) were designed and synthesized. The results related to the castor bean seeds (R. communis L.) indicated that all the target compounds (4a–4f) had phloem mobility. The capacity for phloem mobility shows that N-alkylated glycine containing small substituents can significantly improve PCA phloem mobility, such as 4c(i-C₃H₇-N) > 4a(CH₃-N) ≈ 4b(C₂H₅-N) > 4d (t-C₄H₉-N) > PCA-Gly > 4e(C₆H₅-N) > 4f(CH₂COOH-N), with an oil–water partition coefficient between 1.2~2.5. In particular, compounds 4a(CH₃-N), 4b(C₂H₅-N), and 4c(i-C₃H₇-N) present better phloem mobility, with the average concentrations in phloem sap of 14.62 μΜ, 13.98 μΜ, and 17.63 μΜ in the first 5 h, which are 8 to 10 times higher than PCA-Gly (1.71 μΜ). The results reveal that the Kleier model and Carrier-mediated theory play a guiding role in the design of phloem-mobile pesticides. However, the single Kleier model or Carrier-mediated theory are not entirely accurate. Still, there is a synergism between Carrier-mediated theory and the Kleier model for promoting the phloem transport of exogenous compounds. Therefore, we suggest the introduction of endogenous plant compounds as a promoiety to improve the phloem mobility of pesticides through Carrier-mediated theory. It is necessary to consider the improvement of physicochemical properties according to the Kleier model, which can contribute to a scientific theory for developing phloem-mobile pesticides.     

Donor–acceptor–acceptor-type near-infrared fluorophores that contain dithienophosphole oxide and boryl groups: effect of the boryl group on the nonradiative decay

The use of donor–π–acceptor (D–π–A) skeletons is an effective strategy for the design of fluorophores with red-shifted emission. In particular, the use of amino and boryl moieties as the electron-donating and -accepting groups, respectively, can produce dyes that exhibit high fluorescence and solvatochromism. Herein, we introduce a dithienophosphole P-oxide scaffold as an acceptor–spacer to produce a boryl- and amino-substituted donor–acceptor–acceptor (D–A–A) π-system. The thus obtained fluorophores exhibit emission in the near-infrared (NIR) region, while maintaining high fluorescence quantum yields even in polar solvents (e.g. λ_em = 704 nm and Φ_F = 0.69 in CH₃CN). A comparison of these compounds with their formyl- or cyano-substituted counterparts demonstrated the importance of the boryl group for generating intense emission. The differences among these electron-accepting substituents were examined in detail using theoretical calculations, which revealed the crucial role of the boryl group in lowering the nonradiative decay rate constant by decreasing the non-adiabatic coupling in the internal conversion process. The D–A–A framework was further fine-tuned to improve the photostability. One of these D–A–A dyes was successfully used in bioimaging to visualize the blood vessels of Japanese medaka larvae and mouse brain.

Combination of electron-accepting diarylboryl terminal groups and dithienophosphole oxide spacers with electron-donating triarylamine moieties produces donor–acceptor–acceptor type π-systems, which exhibit emissions in the near-infrared region.     

Covalent flexible peptide docking in Rosetta

Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present Rosetta CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides. It produced a top-five scoring, near-native model, in 89% and 100% of the cases when docking from the native conformation, and 20% and 90% when docking from an extended peptide conformation, respectively. In addition, we developed a protocol for designing electrophilic peptide binders based on known non-covalent binders or protein–protein interfaces. We identified 7154 peptide candidates in the PDB for application of this protocol. As a proof-of-concept we validated the protocol on the non-covalent complex of 14-3-3σ and YAP1 phosphopeptide. The protocol identified seven highly potent and selective irreversible peptide binders. The predicted binding mode of one of the peptides was validated using X-ray crystallography. This case-study demonstrates the utility and impact of CovPepDock. It suggests that many new electrophilic peptide binders can be rapidly discovered, with significant potential as therapeutic molecules and chemical probes.

We developed Rosetta CovPepDock, a computational pipeline for covalent peptide docking. We showed it is highly accurate in retrospective benchmarks, and applied it prospectively to design potent and selective covalent binders of 14-3-3σ.     

2,2′-Bipyridyl formation from 2-arylpyridines through bimetallic diyttrium intermediate

An alkylyttrium complex supported by an N,N′-bis(2,6-diisopropylphenyl)ethylenediamido ligand, (ArNCH₂CH₂NAr)Y(CH₂SiMe₃)(THF)₂ (1, Ar = 2,6-ⁱPr₂C₆H₃), activated an ortho-phenyl C–H bond of 2-phenylpyridine (2a) to form a (2-pyridylphenyl)yttrium complex (3a) containing a five-membered metallacycle. Subsequently, a unique C(sp²)–C(sp²) coupling of 2-phenylpyridine proceeded through a bimetallic yttrium intermediate, derived from an intramolecular shift of the yttrium center to an ortho-position of the pyridine ring in 3a, to yield a bimetallic yttrium complex (4a) bridged by two-electron reduced 6,6′-diphenyl-2,2′-bipyridyl. Aryl substituents at the ortho-position of the pyridine ring were key in order to destabilize the μ,κ²-(C,N)-pyridyldiyttrium intermediate prior to the C(sp²)–C(sp²) bond formation.     

Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors

Numerous experiments have revealed that fullerene (C₆₀) and its derivatives can bind to proteins and affect their biological functions. In this study, we explored the interaction between fullerine and the β₂-adrenergic receptor (β₂AR). The MD simulation results show that fullerene binds with the extracellular loop 2 (ECL2) and intracellular loop 2 (ICL2) of β₂AR through hydrophobic interactions and π–π stacking interactions. In the C₆₀_in1 trajectory, due to the π–π stacking interactions of fullerene molecules with PHE and PRO residues on ICL2, ICL2 completely flipped towards the fullerene direction and the fullerene moved slowly into the lipid membrane. When five fullerene molecules were placed on the extracellular side, they preferred to stack into a stable fullerene cluster (a deformed tetrahedral aggregate), and had almost no effect on the structure of β₂AR. The hydroxyl groups of fullerene derivatives (C₆₀(OH)_X, X represents the number of hydroxyl groups, X = 4, 8) can form strong hydrogen bonds with the ECL2, helix6, and helix7 of β₂AR. The hydroxyl groups firmly grasp the β₂AR receptor like several claws, blocking the binding entry of ligands. The simulation results show that fullerene and fullerene derivatives may have a significant effect on the local structure of β₂AR, especially the distortion of helix4, but bring about no great changes within the overall structure. It was found that C₆₀ did not compete with ligands for binding sites, but blocked the ligands’ entry into the pocket channel. All the above observations suggest that fullerene and its derivatives exhibit certain cytotoxicity.     

Amphiphilic stilbene derivatives attenuate the neurotoxicity of soluble Aβ42 oligomers by controlling their interactions with cell membranes

The misfolded proteins or polypeptides commonly observed in neurodegenerative diseases, including Alzheimer''s disease (AD), are promising drug targets for developing therapeutic agents. To target the amyloid-β (Aβ) peptide plaques and oligomers, the hallmarks of AD, we have developed twelve amphiphilic small molecules with different hydrophobic and hydrophilic fragments. In vitro fluorescence binding assays demonstrate that these amphiphilic compounds show high binding affinity to both Aβ plaques and oligomers, and six of them exhibit selective binding toward Aβ oligomers. These amphiphilic compounds can also label the Aβ species in the brain sections of transgenic AD mice, as shown by immunostaining with an Aβ antibody. Molecular docking studies were performed to obtain structure–affinity relationships. To our delight, four amphiphilic compounds can alleviate the Cu²⁺–Aβ induced toxicity in cell viability assays. In addition, confocal fluorescence imaging studies provide evidence that two compounds, ZY-15-MT and ZY-15-OMe, can disrupt the interactions between Aβ oligomers and human neuroblastoma SH-SY5Y cell membranes. Overall, these studies strongly suggest that developing compounds with amphiphilic properties that target Aβ oligomers and modulate the Aβ oligomer–cell membrane interactions can be an effective strategy for the development of small molecule AD therapeutics.

Amphiphilic compounds with selectivity towards soluble Aβ₄₂ oligomers were developed. Cell imaging studies show the compounds can reduce the interactions between Aβ₄₂ oligomers and SH-SY5Y cell membranes, both in the presence and absence of Cu.     

Computational Studies of Coinage Metal Anion M− + CH3X (X = F,Cl, Br,I) Reactions in Gas Phase

We characterized the stationary points along the nucleophilic substitution (S_N2), oxidative insertion (OI), halogen abstraction (XA), and proton transfer (PT) product channels of M⁻ + CH₃X (M = Cu, Ag, Au; X = F, Cl, Br, I) reactions using the CCSD(T)/aug-cc-pVTZ level of theory. In general, the reaction energies follow the order of PT > XA > S_N2 > OI. The OI channel that results in oxidative insertion complex [CH₃–M–X]⁻ is most exothermic, and can be formed through a front-side attack of M on the C-X bond via a high transition state OxTS or through a S_N2-mediated halogen rearrangement path via a much lower transition state invTS. The order of OxTS > invTS is inverted when changing M⁻ to Pd, a d¹⁰ metal, because the symmetry of their HOMO orbital is different. The back-side attack S_N2 pathway proceeds via typical Walden-inversion transition state that connects to pre- and post-reaction complexes. For X = Cl/Br/I, the invS_N2-TS’s are, in general, submerged. The shape of this M⁻ + CH₃X S_N2 PES is flatter as compared to that of a main-group base like F⁻ + CH₃X, whose PES has a double-well shape. When X = Br/I, a linear halogen-bonded complex [CH₃−X∙··M]⁻ can be formed as an intermediate upon the front-side attachment of M on the halogen atom X, and it either dissociates to CH₃ + MX⁻ through halogen abstraction or bends the C-X-M angle to continue the back-side S_N2 path. Natural bond orbital analysis shows a polar covalent M−X bond is formed within oxidative insertion complex [CH₃–M–X]⁻, whereas a noncovalent M–X halogen-bond interaction exists for the [CH₃–X∙··M]⁻ complex. This work explores competing channels of the M⁻ + CH₃X reaction in the gas phase and the potential energy surface is useful in understanding the dynamic behavior of the title and analogous reactions.     

Long-lived charge carrier generation in ordered films of a covalent perylenediimide–diketopyrrolopyrrole–perylenediimide molecule

The photophysics of a covalently linked perylenediimide–diketopyrrolopyrrole–perylenediimide acceptor–donor–acceptor molecule (PDI–DPP–PDI, 1) were investigated and found to be markedly different in solution versus in unannealed and solvent annealed films. Photoexcitation of 1 in toluene results in quantitative charge separation in τ = 3.1 ± 0.2 ps, with charge recombination in τ = 340 ± 10 ps, while in unannealed/disordered films of 1, charge separation occurs in τ < 250 fs, while charge recombination displays a multiexponential decay in ∼6 ns. The absence of long-lived, charge separation in the disordered film suggests that few free charge carriers are generated. In contrast, upon CH₂Cl₂ vapor annealing films of 1, grazing-incidence X-ray scattering shows that the molecules form a more ordered structure. Photoexcitation of the ordered films results in initial formation of a spin-correlated radical ion pair (electron–hole pair) as indicated by magnetic field effects on the formation of free charge carriers which live for ∼4 μs. This result has significant implications for the design of organic solar cells based on covalent donor–acceptor systems and shows that long-lived, charge-separated states can be achieved by controlling intramolecular charge separation dynamics in well-ordered systems.     

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future.