Molecular Insight into Long‐Wavelength Fluorogenic Dye Design: Hydrogen Bond Induces Activation of a Dormant Acceptor

The detection of chemical or biological analytes in response to molecular changes relies increasingly on fluorescence methods. Therefore, there is a substantial need for the development of improved fluorogenic dyes. In this study, we demonstrated how an intramolecular hydrogen bond activates a dormant acceptor through a charge induction between phenolic hydrogen and a heteroaryl nitrogen moiety. As a result, a new fluorochrome is produced, and the molecule exhibits a strong fluorescent emission. When the strength of the hydrogen bonding was increased by conformational locking, the obtained dye emitted at longer wavelengths and fluoresced under physiological conditions. The dye was implemented in a turn‐ON system responsive to hydrogen peroxide. The molecular insight provided by this study should assist in the design of fluorescent dyes that are suitable for in vitro and in vivo applications.     

Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes

Azo-hydrazone tautomerism in azo dyes has been modeled by using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The most stable tautomer was determined both for model compounds and for azo dyes Acid Orange 7 and Solvent Yellow 14. The effects of the sulfonate group substitution and the replacement of the phenyl group with naphthyl on the tautomer stability and on the behavior in solvent have been discussed. Intramolecular hydrogen bond energies have been estimated for the azo and hydrazone tautomers to derive a relationship between the tautomer stability and the hydrogen bond strength. The transition structures for proton transfer displayed resonance assisted strong hydrogen bonding properties within the framework of the electrostatic-covalent hydrogen bond model (ECHBM). Evolution of the intramolecular hydrogen bond with changing structural and environmental factors during the tautomeric conversion process has been studied extensively by means of the atoms-in-molecules (AIM) analysis of the electron density. The bulk solvent effect was examined using the self-consistent reaction field model. Special solute-solvent interactions were further investigated by means of quantum mechanical calculations after defining the first-solvation shell by molecular dynamics simulations. The effect of cooperative hydrogen bonding with solvent molecules on the tautomer stability has been discussed.     

Isotopic splitting patterns in the 13C NMR spectra of some partially deuterated 1‐aryl‐2‐(phenyldiazenyl)butane‐1,3‐dione and 4‐hydroxy‐3‐(phenyldiazenyl)‐2H‐chromen‐2‐one: evidence for elucidation of tautomeric forms

Nuclear magnetic resonance spectra of synthesized azo dyes derived from aniline derivatives in reaction with benzoylacetone and 4‐hydroxycoumarin were studied in both CDCl₃ and (CD₃)₂SO (two drops of D₂O were added into solutions of dyes). All dyes showed intramolecular hydrogen bonding. Dyes derived from o‐nitro aniline in the reaction with benzoylacetone, and 4‐hydroxycoumarin showed bifurcated intramolecular hydrogen bonds. The solvent‐substrate proton exchange of dyes derived from benzoylacetone and 4‐hydroxycoumarin was examined in the presence of two drops of D₂O. Among ten dye samples, two dyes derived from benzoylacetone did not show deuteration, three dyes showed partial deuteration and five dyes showed full deuteration under similar conditions. For the partially deuterated dyes the β‐isotope effect in ¹³C splitting was investigated and was used for the determination of the predominant tautomeric form. Copyright © 2016 John Wiley & Sons, Ltd.     

Hydrogen‐Bonding Effect on Spin‐Center Transfer of Tetrathiafulvalene‐Linked 6‐Oxophenalenoxyl Evaluated Using Temperature‐Dependent Cyclic Voltammetry and Theoretical Calculations

The stable tetrathiafulvalene (TTF)‐linked 6‐oxophenalenoxyl neutral radical exhibits a spin‐center transfer with a continuous color change in solution caused by an intramolecular electron transfer, which is dependent on solvent and temperature. Cyclic voltammetry measurements showed that addition of 2,2,2‐trifluoroethanol (TFE) to a benzonitrile solution of the neutral radical induces a redox potential shift that is favorable for the spin‐center transfer. Temperature‐dependent cyclic voltammetry of the neutral radical using a novel low‐temperature electrochemical cell demonstrated that the redox potentials change with decreasing temperature in a 199:1 CH₂Cl₂/TFE mixed solvent. Furthermore, theoretical calculation revealed that the energy levels of the frontier molecular orbitals involved in the spin‐center transfer are lowered by the hydrogen‐bonding interaction of TFE with the neutral radical. These results indicate that the hydrogen‐bonding effect is a key factor for the occurrence of the spin‐center transfer of TTF‐linked 6‐oxophenalenoxyl.     

Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers

Little is known about the effect of conformation on passive membrane diffusion rates in small molecules. Evidence suggests that intramolecular hydrogen bonding may play a role by reducing the energetic cost of desolvating hydrogen bond donors, especially amide N-H groups. We set out to test this hypothesis by investigating the passive membrane diffusion characteristics of a series of cyclic peptide diastereomers based on the sequence cyclo[Leu-Leu-Leu-Leu-Pro-Tyr]. We identified two cyclic hexapeptide diastereomers based on this sequence, whose membrane diffusion rates differed by nearly two log units. Results of solution NMR studies and hydrogen/deuterium (H/D) exchange experiments showed that membrane diffusion rates correlated with the degree of intramolecular hydrogen bonding and H/D exchange rates. The most permeable diastereomer, cyclo[d-Leu-d-Leu-Leu-d-Leu-Pro-Tyr] (1), exhibited a passive membrane diffusion rate comparable to that of the orally available drug cyclosporine A.     

Relative predominance of azo and hydrazone tautomers of 4-carboxyl-2,6-dinitrophenylazohydroxynaphthalenes in binary solvent mixtures

Azo-hydrazone tautomerism is a phenomenon that occurs in azo dyes possessing substituents conjugated to the azo linkage which has labile proton that can be exchanged intramolecularly. Thus the predominance of one tautomer over another is a function of many factors among which are solvent polarity, solvent type, solute-solvent interactions and the structure of the dye molecule itself. The 4-carboxyl-2,6-dinitrophenylazohydroxynaphthalenes, previously shown to exhibit azo-hydrazone tautomerism, were studied for the relative predominance of one form over another based on interaction at the microenvironment of binary solvent mixtures containing DMF and non-hydrogen bonding (CCl(4)), hydrogen bond donor (toluene, chloroform), hydrogen bond acceptor (acetonitrile, acetone) and the alcohols; ethanol and methanol as solvent pairs. The three dyes gave two main bands in the 50:50 mixture of DMF with these solvents consisting of a high energy band at 250-382 nm while the low energy bands for the dyes occurred at 415-485 nm. Spectral shifts in the binary solvent mixtures were related to the solvent dipolarity, basicity of the less polar component relative to DMF, substituent type, molar transition energy, formation constant for the hydrogen-bonding solvated complexes and the standard free energy change for hydrogen bonding with DMF. The relative predominance of the hydrazone tautomer bears a direct relationship to the basicity of the solvent, presence of hydrogen bond donor substituent and was associated with high molar transition energies and low formation constant. The microenvironment surrounding the dye molecules played a major role in the stability of one tautomer relative to the other.     

Solvent- and guest-responsive self-assembly of Hamilton receptor tethered bis(merocyanine) dyes

A novel supramolecular building block (8) that consists of a Hamilton receptor and two merocyanine dyes has been synthesized, and the self-assembly based on orthogonal hydrogen bonding and dipolar interactions has been studied in detail. Different self-assembled species, including oligomers, polymers, and inverted micelles could be observed upon variation of the solvent polarity and the concentration. Moreover, this system is highly responsive toward molecular stimuli such as merocyanine molecules with the barbituric acid motif that are bound by the Hamilton receptors. Detailed UV/Vis absorption studies provided insight into isodesmic or cooperative steps during the self-assembly of 8 into different species. The size of the aggregates in solution and the morphology on substrates have been explored by a combination of dynamic light scattering (DLS), atomic force microscopy (AFM), and TEM investigations.     

Density functional theory and atoms-in-molecules investigation of intramolecular hydrogen bonding in derivatives of malonaldehyde and implications for resonance-assisted hydrogen bonding

A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.     

Structure and dynamics of pyrimidine-based macrocycles in solution

The conformational structure of macrocycles obtained from two thiopyrimidine and uracil nucleic acids linked by polymethylene spacers is determined by the length of the spacers, intramolecular NH bonding, pH and solvent. In CDCl₃, NH-OC hydrogen bonding can impact the overall stabilization of the folded conformation, however spatial preorganization to such hydrogen bonding is a prerequisite. Protonation leads to disruption of intramolecular hydrogen bonds, destabilization of the folded conformation and to strong counterion assisted self-aggregation of macrocyles which can be destroyed in polar solvents.     

Design of Weak‐Donor Alkyl‐Functionalized Push–Pull Pyrene Dyes Exhibiting Enhanced Fluorescence Quantum Yields and Unique On/Off Switching Properties

We designed, synthesized, and evaluated environmentally responsive solvatochromic fluorescent dyes by incorporating weak push–pull moieties. The quantum yields of the push (alkyl)–pull (formyl) pyrene dyes were dramatically enhanced by the introduction of alkyl groups into formylpyrene (1‐formylpyrene: Φ_F=0.10; 3,6,8‐tri‐n‐butyl‐1‐formylpyrene: Φ_F=0.90; in MeOH). The new dyes exhibited unique sensitivity to solvent polarity and hydrogen‐bond donor ability, and specific fluorescence turn‐on/off properties (e.g., 3,6,8‐tri‐n‐butyl‐1‐formylpyrene: Φ_F=0.004, 0.80, 0.37, and 0.90 in hexane, chloroform, DMSO, and MeOH, respectively). Here, the alkyl groups act as weak donors to suppress intersystem crossing by destabilizing the HOMOs of 1‐formylpyrene while maintaining weak intramolecular charge‐transfer properties. By using alkyl groups as weak donors, environmentally responsive, and in particular, pH‐responsive fluorescent materials may be developed in the future.     

Study of intramolecular interactions in aspirin

A detailed quantum chemical study of the solvent effects in the intramolecular hydrogen bonding, conformational stability, and reactivity of aspirin has been performed using density functional theory (DFT) at the B3LYP/6‐31G(d) theory level. Seven conformational isomers, three of them presenting intramolecular hydrogen bonds, have been located. Thermochemical functions have been computed, and relative energies and free enthalpies have been determined in gas and aqueous phases. Several molecular properties have been calculated to predict the ability of aspirin to acylate cyclooxygenase (COX) enzymes. A six‐membered‐ring hydrogen‐bonded conformer was found to be the most reactive species. The solvation in aqueous phase increases the reactivity and strengthens intramolecular hydrogen bonding.     

Photoinduced electron transfer between various coumarin analogues and N,N-dimethylaniline inside niosome, a nonionic innocuous polyethylene glycol-based surfactant assembly

Photoinduced electron transfer (ET) reactions between coumarin dyes and N,N-dimethylaniline have been investigated inside niosome, a nonionic innocuous polyethylene glycol (PEG)-based surfactant assembly using steady state and time-resolved fluorescence measurements. The location of coumarin dyes inside the bilayer headgroup region of niosome has been reported and it was verified by determination of the high distribution coefficient of all the dyes inside niosome compared to bulk water. Fluorescence anisotropy parameters of the dyes inside niosome are also in good correlation with the above inference about their location. Bimolecular diffusion guided rates inside niosome were determined by comparing the microviscosities inside niosome and in acetonitrile and butanol solutions and it was found that diffusion of the donor and the acceptor is much slower than the ET rates, implying insignificant role of reactant diffusion in ET reaction inside niosome. We have observed a Marcus inversion region in our restricted media, which shows maxima at lower exergonicity. Such behavior has been demonstrated by the presence of nonequilibrium solvent excited state using two dimensional ET (2DET) theory. Unusually high quenching rates of two coumarins C-152 and C-152A inside niosome were explained by the presence of a stable non-fluorescent twisted intramolecular charge transfer (TICT) state along with an emissive intramolecular charge transfer (ICT) state. Moreover, intermolecular hydrogen bonding between carbonyl oxygens of these two dyes and water in their non-emissive and emissive charge transfer states also plays a key role in their dynamical exchange with each other [G.-J. Zhao and K.-L. Han, Acc. Chem. Res., 2011].     

Conformer-independent ureidoimidazole motifs--tools to probe conformational and tautomeric effects on the molecular recognition of triply hydrogen-bonded heterodimers

Linear arrays of hydrogen bonds are useful for the reversible assembly of “stimuli‐responsive” supramolecular materials. There is thus an ongoing requirement for easy‐to‐synthesise motifs that are capable of presenting hydrogen‐bonding functionality in a predictable manner, such that high‐affinity and high‐fidelity recognition occurs. The design of linear arrays is made challenging as a consequence of their ability to adopt multiple conformational and tautomeric configurations; with each additional hydrogen‐bonding heteroatom added to an array, the available tautomeric and conformational space increases and it can be difficult to anticipate where unproductive conformers/tautomers will arise. This paper describes a detailed study on the complementary ureidoimidazole donor–donor–acceptor (DDA) array ( 1 ) and amidoisocytosine donor–acceptor–acceptor (DAA) array ( 2 ). A specific feature of 1 is that two degenerate, intramolecular hydrogen‐bonded conformations are postulated, both of which present a DDA array that is complementary to appropriate DAA partners. 1D and 2D ¹H NMR spectroscopy, isothermal titration calorimetry, and ab initio structure calculations confirm 1 interacts with 2 (K_a≈33000 M ^?1 in CDCl₃) in a conformer‐independent fashion driven by enthalpy. Comparison of the binding behaviour of 1 with hexylamidocytosine ( 4 ) and amidonaphthyridine ( 5 ) provides insight on the role that intramolecular hydrogen‐bonding plays in mediating affinity towards DAA partners.     

Hydrogen bonding properties of Coumarin 151, 500, and 35: the effect of substitution at the 7-amino position

The steady-state spectral properties (absorption and emission) of three structurally similar Coumarin dyes, C151, C500, and C35 were investigated in 13 different solvents. A Kamlet-Taft (KT) analysis of the spectral peak frequencies reveals that, in addition to polarity, hydrogen bonding between the carbonyl oxygen and a protic solvent in the excited state imparts maximum stabilization for C151 and minimum for C35, while that for C500 lies in between. The spectral properties of the three dyes in two solvents, chloroform and THF, which have similar polarity in the KT scale but have only hydrogen-bond donor (chloroform) and hydrogen-bond acceptor (THF) properties, are seen to be sensitive to the substitution pattern at the 7-amino position. In addition, a slow emission spectral relaxation is observed for C151 and C500 having a time constant of approximately 500 ps in chloroform. For C35 this was too fast to be detected by the time resolution of our setup. The exact reason for this slow spectral relaxation in chloroform is unclear at present, and further studies are needed to understand clearly the structural effects on the hydrogen bonding dynamics of these dyes.     

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

The influence of intramolecular hydrogen bonding on the structure and E ↔ Z photoisomerization of urocanic acid derivatives

The molecular structures and E ? Z photoisomerization reactions of methyl urocanate and several urocanamides were investigated. All of the Z isomers possess intramolecular hydrogen bonds. The intramolecular hydrogen bonds may influence the efficiency of photoisomerization but do not totally inhibit its occurrence. The relative energies of the electronic absorption of the E and Z isomers depends on the mode of hydrogen bonding and are accurately predicted in the case of methyl urocanate using INDO/S-CI calculations. The solvent dependence of the absorption spectra of methyl urocanate can be related to the effects of inter- and intramolecular hydrogen bonding.     

The role of hydrogen bonding in excited state intramolecular charge transfer

Intramolecular charge transfer (ICT) that occurs upon photoexcitation of molecules is a vital process in nature and it has ample applications in chemistry and biology. The ICT process of the excited molecules is affected by several environmental factors including polarity, viscosity and hydrogen bonding. The effect of polarity and viscosity on the ICT processes is well understood. But, despite the fact that hydrogen bonding significantly influences the ICT process, the specific role of hydrogen bonding in the formation and stabilization of the ICT state is not unambiguously established. Some literature reports predicted that the hydrogen bonding of the solvent with a donor promotes the formation of a twisted intramolecular charge transfer (TICT) state. Some other reports stated that it inhibits the formation of the TICT state. Alternatively, it was proposed that the hydrogen bonding of the solvent with an acceptor favors the TICT state. It is also observed that a dynamic equilibrium is established between the free and the hydrogen bonded ICT states. This perspective focuses on the specific role played by hydrogen bonding of the solvent with the donor and the acceptor, and by proton transfer in the ICT process. The utility of such influence in molecular recognition and anion sensing is discussed with a few recent literature examples in the end.     

Evidence for a Bulky Unit of a Pillar[5]arene Flipping in the Solid State

It is well known that pillar[5]arenes have two most stable conformations (pS and pR) in their crystal structures. Because of the intramolecular H‐bonding interactions, substituents, temperature, solvent and so on, the rotational behaviors of the phenolic units on pillararenes are also common. This paper showed some other kinds of conformations in the functionalized pillar[5]arenes and gave evidence for a bulky unit (1,4‐methoxycarbonylmethoxybenzene unit) flipping in the solid state. The presence of hydrogen bonding facilitated the intermolecular self‐assembly in terms of energy‐minimized packing in the crystals. Thus, the main driving force for the flipping of this bulky unit might be both the intramolecular hydrogen bonding between the phenolic units on pillararenes and quadrupolar hydrogen bonding between the host and water. This paper helps us to have a better understanding on the conformations of pillar[5]arenes.     

Energy Dissipation Processes of singlet‐excited 1‐Hydroxyfluorenone and its Hydrogen‐bonded Complex with N‐methylimidazole¶

Effects of solvent, pH and hydrogen bonding with N‐methylimidazole (MIm) on the photophysical properties of 1‐hydroxyfluorenone (1HOF) have been studied. Fluorescence lifetime, fluorescence quantum yield and triplet yield measurements demonstrated that intersystem crossing was the dominant process in apolar media and its rate constant significantly diminished with increasing solvent polarity. The acceleration of internal conversion in alcohols paralleled the strength of intermolecular hydrogen bonding. The faster energy dissipation from the singlet‐excited state in cyclohexane was attributed to intramolecular hydrogen bonding. The pK_a of 1HOF decreased from 10.06 to 5.0 on light absorption, and H₃O⁺ quenched the singletexcited molecules in a practically diffusion‐controlled reaction. On addition of MIm in toluene, dual fluorescence was observed, which was attributed to reversible formation of excited hydrogen‐bonded ion pair. Rate constants for the various deactivation pathways were derived from the combined analysis of the steady‐state and the time‐resolved fluorescence results.     

Coupling of intramolecular hydrogen bonding to the cis-to-trans isomerization of a proline imide bond of small model peptides

A relationship between intramolecular hydrogen bonding and the cis-trans isomerization of a proline imide bond for proline-containing short peptides were studied by proton NMR and infrared spectroscopy using DMSO-d6/CDCl3 mixed solvents. The percentage of the trans form increases with increasing fraction of CDCl3 in the mixed solvents except for compounds without possibility of intramolecular hydrogen bonding. Chemical shift variations of amide protons with solvent mixing ratios were found to be useful for judging whether the amide protons take part in the intramolecular hydrogen bonding to a considerable degree or not. These results and infrared spectra were used to specify intramolecularly hydrogen bonded structures of the peptides. Formation of the 10-membered or 13-membered hydrogen bonded ring which includes the carbonyl group precedent to the prolyl residue facilitates the cis-to-trans isomerization and these hydrogen bonded rings are strong enough to restrict the proline imide bond to the trans form in CDCl3 solution. On the other hand, a 7-membered hydrogen bonded ring is not so effective in restricting the proline imide bond.