Increasing protein stability by engineering the n → π* interaction at the β-turn

Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction.

Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.     

DNAzyme- and light-induced dissipative and gated DNA networks

Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb²⁺-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to “waste” products. Applying the Pb²⁺-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks. Blocking the competitively operating networks with selective inhibitors leads, however, to gated transient operation of dictated networks, yielding gated catalytic operations. A second system introduces a “non-waste” generating out-of-equilibrium, dissipative network driven by light. The system consists of a trans-azobenzene-functionalized photoactive module that is reconfigured by light to an intermediary state consisting of cis-azobenzene units that are thermally recovered to the original trans-azobenzene-modified module. The cyclic transient photoinduced operation of the device is demonstrated. The kinetic simulation of the systems allows the prediction of the transient behavior of the networks under different auxiliary conditions.

Functional DNA modules are triggered in the presence of appropriate inhibitors to yield transient gated catalytic functions, and a photoresponsive DNA module leads to “waste-free” operation of transient, dissipative dynamic transitions.     

Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

Automatic discovery of photoisomerization mechanisms with nanosecond machine learning photodynamics simulations

Photochemical reactions are widely used by academic and industrial researchers to construct complex molecular architectures via mechanisms that often require harsh reaction conditions. Photodynamics simulations provide time-resolved snapshots of molecular excited-state structures required to understand and predict reactivities and chemoselectivities. Molecular excited-states are often nearly degenerate and require computationally intensive multiconfigurational quantum mechanical methods, especially at conical intersections. Non-adiabatic molecular dynamics require thousands of these computations per trajectory, which limits simulations to ∼1 picosecond for most organic photochemical reactions. Westermayr et al. recently introduced a neural-network-based method to accelerate the predictions of electronic properties and pushed the simulation limit to 1 ns for the model system, methylenimmonium cation (CH₂NH₂⁺). We have adapted this methodology to develop the Python-based, Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics (PyRAI²MD) software for the cis–trans isomerization of trans-hexafluoro-2-butene and the 4π-electrocyclic ring-closing of a norbornyl hexacyclodiene. We performed a 10 ns simulation for trans-hexafluoro-2-butene in just 2 days. The same simulation would take approximately 58 years with traditional multiconfigurational photodynamics simulations. We generated training data by combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to adaptively sample sparse data regions along reaction coordinates. The final data set of the cis–trans isomerization and the 4π-electrocyclic ring-closing model has 6207 and 6267 data points, respectively. The training errors in energy using feedforward neural networks achieved chemical accuracy (0.023–0.032 eV). The neural network photodynamics simulations of trans-hexafluoro-2-butene agree with the quantum chemical calculations showing the formation of the cis-product and reactive carbene intermediate. The neural network trajectories of the norbornyl cyclohexadiene corroborate the low-yielding syn-product, which was absent in the quantum chemical trajectories, and revealed subsequent thermal reactions in 1 ns.

Photochemical reactions are widely used by academia and industry to construct complex molecular architectures via mechanisms that are often inaccessible by other means.     

Tuning π-Acceptor/σ-Donor Ratio of the 2-Isocyanoazulene Ligand: Non-Fluorinated Rival of Pentafluorophenyl Isocyanide and Trifluorovinyl Isocyanide Discovered

Isocyanoazulenes (CNAz) constitute a relatively new class of isocyanoarenes that offers rich structural and electronic diversification of the organic isocyanide ligand platform. This article considers a series of 2-isocyano-1,3-X₂-azulene ligands (X = H, Me, CO₂Et, Br, and CN) and the corresponding zero-valent complexes thereof, [(OC)₅Cr(2-isocyano-1,3-X₂-azulene)]. Air- and thermally stable, X-ray structurally characterized 2-isocyano-1,3-dimethylazulene may be viewed as a non-benzenoid aromatic congener of 2,6-dimethyphenyl isocyanide (2,6-xylyl isocyanide), a longtime “workhorse” aryl isocyanide ligand in coordination chemistry. Single crystal X-ray crystallographic {Cr–CNAz bond distances}, cyclic voltametric {E_1/2(Cr^0/1+)}, ¹³C NMR {δ(¹³CN), δ(¹³CO)}, UV-vis {dπ(Cr) → pπ*(CNAz) Metal-to-Ligand Charge Transfer}, and FTIR {ν_N≡C, ν_C≡O, k_C≡O} analyses of the [(OC)₅Cr(2-isocyano-1,3-X₂-azulene)] complexes provided a multifaceted, quantitative assessment of the π-acceptor/σ-donor characteristics of the above five 2-isocyanoazulenes. In particular, the following inverse linear relationships were documented: δ(¹³CO_trans) vs. δ(¹³CN), δ(¹³CO_cis) vs. δ(¹³CN), and δ(¹³CO_trans) vs. k_C≡O,trans force constant. Remarkably, the net electron withdrawing capability of the 2-isocyano-1,3-dicyanoazulene ligand rivals those of perfluorinated isocyanides CNC₆F₅ and CNC₂F₃.     

Non-empirical calculations on the conformational structure of azobenzene and benzylideneaniline

The conformational structures of cis- and trans-azobenzene and benzylideneaniline have been investigated by means of ab initio SCF calculations. Contrary to semiempirical results, the equilibrium molecular geometries are correctly accounted for in the non-empirical SCF-formalism. Trans-azobenzene is found to be planar, or at least peri-planar, while the phenyl rings of the cis-isomer are twisted by 56° out-of-plane. Both isomers of benzylideneaniline are non-planar, with rotational angles θ₁ (C-N) = 48°, θ₂(C-C) = 0° and θ₁ = θ₂ = 75° for the trans and cis form, respectively. Trans-azobenzene is calculated to be more stable by 10.4 kcal mol^?1 than the cis isomer, which is in good accord with the experimental value of 10 kcal mol^?1. The energy of isomerization of benzylideneaniline amounts to 13.0 kcal mol^?1.     

An ab initio study of electronic spectra and excited-state properties of 7-azaindole in vapour phase and aqueous solution

The geometries of 7-azaindole (7AI), its tautomer (7AT), and 7AI–H₂O and 7AT–H₂O complexes were optimised in the ground state and some low-lying singlet excited states using the 3-21G basis set. Differences of total energies of the optimised ground and excited states and the vertical excitation energies of these systems were used to explain the observed electronic spectra. Effect of solvation of these systems in bulk water was studied using the polarized continuum model (PCM). The mode of binding of a water molecule in the S₂(n–π^*) excited state of 7AI was found to be quite different from those in its ground and π–π^* excited states. It is shown that crossing of the lowest two singlet excited-state potential surfaces S₁(π–π^*) and S₂(n–π^*) of 7AI occurs in the vapour phase under geometry relaxation while on interaction with water, the S₂(n–π^*) excited state is raised up appreciably going even above the S₃(π–π^*) excited state. Ground- and excited-state molecular electrostatic potential mapping was carried out, which led to valuable information regarding the nature of excited states of the above-mentioned systems.     

Direct observation of a 220 cm structure in the lowest π–π* absorption band in the vapour phase of trans-azobenzene

In this work we present the first direct observation of a 220 cm⁻¹ progression in the absorption spectrum of trans-azobenzene in the vapour phase. The mode at 220 cm⁻¹ is essential to explain both the electronic absorption spectrum and the Raman excitation profiles of the most intense Raman bands of trans-azobenzene in the 1000–1600 cm⁻¹ shift range. Our data in the vapour phase assure that this frequency pertains to an internal molecular mode.     

Is solvated trans-azobenzene twisted or planar?

To arbitrate between previous conflicting theoretical and experimental results, a quantum-mechanical investigation of the ground-state geometry and UV spectrum of trans-azobenzene has been performed by using the Møller–Plesset approach and time-dependent density functional theory. It turns out that gas-phase trans-azobenzene is consistently predicted to be planar by the most accurate approaches. In solvent, the energy difference between planar and twisted trans-azobenzene is also negligible, although the twisted form tends to be favoured by a polar surrounding medium. These predictions are supported by comparisons between measured and predicted excitation energies.     

Synthesis and characterization of dendrons and dendrimers skeleton-constructed with azobenzene moiety

A series of dendrons and dendrimers skeleton-constructed with azobenzene moiety based upon 4-carboxy-4′-(1,2-propanediolether)-azobenzene as an AB₂ monomer, via a convergent approach, proceeding in a repeated stepwise growth manner starting from 4-carboxy-4′-(n-butylether)-azobenzene as a peripheral monomer, were synthesized, and characterized by NMR, FTIR, and MALDI-TOF-MS analysis. Their regular molecular architecture and thus monodispersed molecular weights were confirmed by GPC. The UV-Vis absorbance and ¹H NMR spectrum study indicated that the azobenzene moieties in CHCl₃ solution took fully trans-cis isomerization under UV irradiation, and reversely isomerization back to the trans by visible light irradiation or by heat.     

Photoinduced charge shift as the driving force for the excited-state relaxation of analogues of the Photoactive Yellow Protein chromophore in solution

Transient absorption spectroscopy with subpicosecond laser excitation is used to probe the primary photoinduced processes in two ester analogues (linear and cyclic) of the Photoactive Yellow Protein (PYP) chromophore in solution. The PYP chromophore is the thioester derivative of the deprotonated trans-4-hydroxycinnamic acid. The results found for the ester analogues are compared to those previously obtained for the deprotonated trans-4-hydroxycinnamic acid and its amide and thioester derivatives. Special attention is paid to the role of the electron donor–acceptor character of the chromophore substituents and of the molecular flexibility on the excited-state relaxation pathway and kinetics. Solvent viscosity and polarity effects on the kinetics are also analyzed. Two hypothetical relaxation pathways involving a one-bond flip mechanism are proposed to explain the observation of a transient species in the course of the excited-state relaxation of the analogues bearing the stronger electron-acceptor substituents. In the first one, the intermediate is described as a perp ground state, whereas the second one involves a twisted excited state where the conformation of the ethylenic bond deviates from 90°. In both cases, the relaxation of the transient state may lead or not to the cis isomer.     

Comparative study of azobenzene and stilbene bridged crown ether p-tert-butylcalix[4]arene

Photo-switchable calixarenes consisting of a stilbene or azobenzene bridge, spanning the narrow rim as a switching unit, were synthesized through reductive coupling of o-, m- and p-bis-benzaldehyde and bis-nitrobenzene-substituted calix[4]arenes. Both cis- and trans-stilbenes were produced from the reductive coupling of the o- and m-bis-benzaldehyde with the cis isomer being predominant for both regioisomers, whilst the coupling of p-bis-benzaldehyde gave only cis product. On the other hand, the only isolable product obtained from the reductive coupling of bis-o- and bis-m-nitrobenzene was the corresponding trans-azobenzene and the coupling product from bis-p-nitrobenzene was not stable. Each of the synthesized compounds showed a photostationary state in their cis-trans isomerization. The complexation of alkali metal ions was observed for only the o-azobenzene derivative suggesting that the lone pair of N-atom in the azo bridge participates in this process.     

Charge-transfer biexciton annihilation in a donor–acceptor co-crystal yields high-energy long-lived charge carriers

Organic donor–acceptor (D–A) co-crystals have attracted much interest due to their important optical and electronic properties. Co-crystals having ⋯DADA⋯ π-stacked morphologies are especially interesting because photoexcitation produces a charge-transfer (CT) exciton, D˙⁺–A˙⁻, between adjacent D–A molecules. Although several studies have reported on the steady-state optical properties of this type of CT exciton, very few have measured the dynamics of its formation and decay in a single D–A co-crystal. We have co-crystallized a peri-xanthenoxanthene (PXX) donor with a N,N-bis(3-pentyl)-2,5,8,11-tetraphenylperylene-3,4:9,10-bis(dicarboximide) (Ph4PDI) acceptor to give an orthorhombic PXX–Ph4PDI ⋯DADA⋯ π-stacked co-crystal with a CT transition dipole moment that is perpendicular to the transition moments for S_n ← S₀ excitation of PXX and Ph4PDI. Using polarized, broadband, femtosecond pump–probe microscopy, we have determined that selective photoexcitation of Ph4PDI in the single co-crystal results in CT exciton formation within the 300 fs instrument response time. At early times (0.3 ≤ t ≤ 500 ps), the CT excitons decay with a t^−1/2 dependence, which is attributed to CT biexciton annihilation within the one-dimensional ⋯DADA⋯ π-stacks producing high-energy, long-lived (>8 ns) electron–hole pairs in the crystal. These energetic charge carriers may prove useful in applications ranging from photovoltaics and opto-electronics to photocatalysis.

Femtosecond transient absorption microscopy of donor–acceptor single co-crystals shows that photogenerated charge transfer excitons in one-dimensional donor–acceptor π stacks annihilate to produce high-energy, long-lived electrons and holes.     

Isolation,Physicochemical Properties,and Structural Characteristics of Arabinoxylan from Hull-Less Barley

Arabinoxylan (HBAX-60) was fractioned from alkaline-extracted arabinoxylan (HBAX) in the whole grain of hull-less barley (Hordeum vulgare L. var. nudum Hook. f. Poaceae) by 60% ethanol precipitation, which was studied for physicochemical properties and structure elucidation. Highly purified HBAX-60 mainly composed of arabinose (40.7%) and xylose (59.3%) was created. The methylation and NMR analysis of HBAX-60 indicated that a low-branched β-(1→4)-linked xylan backbone possessed un-substituted (1,4-linked β-Xylp, 36.2%), mono-substituted (β-1,3,4-linked Xylp, 5.9%), and di-substituted (1,2,3,4-linked β-Xylp, 12.1%) xylose units as the main chains, though other residues (α-Araf-(1→, β-Xylp-(1→, α-Araf-(1→3)-α-Araf-(1→ or β-Xylp-(1→3)-α-Araf-(1→) were also determined. Additionally, HBAX-60 exhibited random coil conformation in a 0.1 M NaNO₃ solution. This work provides the properties and structural basis of the hull-less barley-derived arabinoxylan, which facilitates further research for exploring the structure–function relationship and application of arabinoxylan from hull-less barley.     

X-ray guided H NMR analysis of pinched cone calix[4]arenes

The analysis of structural parameters of azobenzene- and stilbene-bridged calix[4]arene obtained from AM1 calculation are in good agreement with those obtained from X-ray crystallography. The bridge longer than 9.0 Å such as p,p-trans-azobenzene and p,p-trans-stilbene cannot be constructed over the narrow rim of calix[4]arene through two ethylene oxide linkers. The m,m-stilbene bridge is the most promising photo switch because its shorter cis stereoisomer (5.85 Å) allows calix[4]arene to assume the perfect cone conformation, whilst its longer trans stereoisomer (8.00 Å) forces calix[4]arene to adapt a pinched cone conformation. The pinched cone conformation has longer distances between the neighbouring phenoxyl groups causing the weaker intramolecular hydrogen bonding and the upfield shifts of the phenolic proton signals to below 7.00 ppm. This upfield shift is useful for quick identification of pinched cone conformation of new calix[4]arene compounds.     

Chiral cis-iron(ii) complexes with metal- and ligand-centered chirality for highly regio- and enantioselective alkylation of N-heteroaromatics

Iron-catalyzed highly regio- and enantioselective organic transformations with generality and broad substrate scope have profound applications in modern synthetic chemistry; an example is herein described based on cis-Fe^II complexes having metal- and ligand-centered chirality. The cis-β Fe^II(N₄) complex [Fe^II(L)(OTf)₂] (L = N,N′-bis(2,3-dihydro-1H-cyclopenta-[b]quinoline-5-yl)-N,N′-dimethylcyclohexane-1,2-diamine) is an effective chiral catalyst for highly regio- and enantioselective alkylation of N-heteroaromatics with α,β-unsaturated 2-acyl imidazoles, including asymmetric N1, C2, C3 alkylations of a broad range of indoles (34 examples) and alkylation of pyrroles and anilines (14 examples), all with high product yields (up to 98%), high enantioselectivity (up to >99% ee) and high regioselectivity. DFT calculations revealed that the “chiral-at-metal” cis-β configuration of the iron complex and a secondary π–π interaction are responsible for the high enantioselectivity.

A cis-β Fe^II complex having metal- and ligand-centered chirality catalyzes highly regio- and enantioselective alkylation of indoles (at the N1, C2, or C3 position), pyrroles and anilines with α,β-unsaturated 2-acyl imidazoles (48 examples, up to 99% ee).     

Theoretical study of 2,5-diphenyl-1,4-distyrylbenzene (A model compound of PPV): A comparison of the electronic structure and photophysical properties of cis- and trans-isomers

2,5-Diphenyl-1,4-distyrylbenzene (DPDSB), a model compound of PPV, have been synthesized with two isomers: cis- and trans-DPDSB in our lab. We have found three distinguishing features of photophysical properties between these two isomers. To explain these three special spectral behaviors, the quantum-chemical computations were performed to investigate the ground-state and excited-state molecular geometries, electronic structure, absorption and emission properties, potential–energy curve of the ground-state and excited-state, and so on. According to our calculated results, the nature causing above distinguishing photophysical properties is larger configuration displacement of cis-DPDSB than trans-DPDSB from the ground-state to the excited-state, especially for the changes in torsion angle along vinyl double bonds in cis-DPDSB.     

Prebiotic Potential of Oligosaccharides Obtained by Acid Hydrolysis of α-(1→3)-Glucan from Laetiporus sulphureus: A Pilot Study

Increasing knowledge of the role of the intestinal microbiome in human health and well-being has resulted in increased interest in prebiotics, mainly oligosaccharides of various origins. To date, there are no reports in the literature on the prebiotic properties of oligosaccharides produced by the hydrolysis of pure fungal α-(1→3)-glucan. The aim of this study was to prepare α-(1→3)-glucooligosaccharides (α-(1→3)-GOS) and to perform initial evaluation of their prebiotic potential. The oligosaccharides were obtained by acid hydrolysis of α-(1→3)-glucan isolated from the fruiting bodies of Laetiporus sulphureus and then, characterized by HPLC. Fermentation of α-(1→3)-GOS and reference prebiotics was compared in in vitro pure cultures of Lactobacillus, Bifidobacterium, and enteric bacterial strains. A mixture of α-(1→3)-GOS, notably with a degree of polymerization of 2 to 9, was obtained. The hydrolysate was utilized for growth by most of the Lactobacillus strains tested and showed a strong bifidogenic effect, but did not promote the growth of Escherichia coli and Enterococcus faecalis. α-(1→3)-GOS proved to be effective in the selective stimulation of beneficial bacteria and can be further tested to determine their prebiotic functionality.     

Effects of high pressure on optical activity induced by chiral solvents

A technique for measuring CD spectra of solutions under pressure has been developed. The positive induced CD of the n-π^* band of trans-azobenzene in (?)-bornyl acetate solution was blue-shifted by 1.7 kK and enhanced by a factor of 2.7 at 700 bar.     

Au3-to-Ag3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength

An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(μ-Pz-(i-C₃H₇)₂)]₃·[Ag(μ-Tz-(n-C₃F₇)₂)]₃ (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1^st crystallographically-verified stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M′ (Au → Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol⁻¹ between the two trimer moieties – a large value for intermolecular interactions between adjacent d¹⁰ centres (nearly doubling the value for a recently-claimed Au(i) → Cu(i) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol⁻¹ with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M′ frontier molecular orbitals in such polar-covalent M–M′ bonds in this family of molecules. The Au → Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H₃N: → Ag in [Ag(NH₃)₂]⁺, as demonstrated herein quantitatively. Solid-state and molecular modeling illustrate electron flow from the π-basic gold trimer to the π-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL′CT) and metal-to-ligand (MLCT) charge transfer.

A stacked Ag₃–Au₃ bonded (66 kcal mol⁻¹) complex obtained crystallographically exhibits charge-transfer characteristics arising from multiple cooperative supramolecular interactions.