Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization

A recent work [Ye et al. Mon. Not. R. Astron. Soc. 2023, 525, 1158] on the gas-phase formation of t-HC(O)SH, already detected in the interstellar medium, pointed out that the trans form of HC(S)OH is a potential candidate for astronomical observations. Prompted by these results, theCH 2 SO family of isomers has been investigated from an energetic point of view using a double-hybrid density functional in combination with a partially augmented triple-zeta basis set. This preliminary study showed that the most stable species of the family are the cis and trans forms of HC(O)SH and HC(S)OH. For their structural and spectroscopic characterization, a composite scheme based on coupled cluster (CC) calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects has been employed. This approach opens to the prediction of rotational constants with an accuracy of 0.1%. A hybrid scheme, based on harmonic frequencies computed using the CC singles, doubles and a perturbative treatment of triples method (CCSD(T)) in conjunction with a quadruple-zeta basis set, allowed us to obtain fundamental vibrational frequencies with a mean absolute error of about 1%.

Unraveling the Dynamic Molecular Motions of a Twin-Cavity Cage with Slow Configurational but Rapid Conformational Interconversions

Featuring diverse structural motions/changes, dynamic molecular systems hold promise for executing complex tasks. However, their structural complexity presents formidable challenge in elucidating their kinetics, especially when multiple structural motions are intercorrelated. We herein introduce a twin-cavity cage that features interconvertible C3- and C1-configurations, each configuration exhibiting interchangeable P- and M-conformations. This molecule is therefore composed of four interconnected chiral species (P)-C3, (M)-C3, (P)-C1, (M)-C1. We showcase an effective methodology to decouple these sophisticated structural changes into two kinetically distinct pathways. Utilizing time-dependent 1H NMR spectroscopy at various temperatures, which disregards the transition between mirror-image conformations, we first determine the rate constant (kc) for C3- to C1-configuration interconversion; while time-dependent circular dichroism spectroscopy at different temperatures quantifies the observed rate constant (kobs) of ensemble of all structural changes. As kobs >> kc, it allows us to decouple the overall molecular motions into a slow configurational transformation and rapid conformational interconversions, the latter further dissected into two independent conformational interchanges, namely (P)-C3 ⇄ (M)-C3 and (P)-C1 ⇄ (M)-C1. This work therefore sheds light on comprehensive kinetic study of complex molecular dynamics, offering valuable insights for the rational design of smart dynamic materials for applications of sensing, separation, catalysis, molecular machinery, etc.

Positional Thiophene Isomerization: A Geometric Strategy for Precisely Regulating the Electronic State of Covalent Organic Frameworks to Boost Oxygen Reduction

With the oxygen conversion efficiency of metal-free carbon-based fuel cells dramatically improved, the building blocks of covalent organic frameworks (COFs) raised principal concerns on the catalytic active sites with indistinct electronic states. Herein, to address this issue, we demonstrate COFs for oxygen reduction reaction (ORR) by regulating the edge-hanging thiophene units, and the molecular geometries are further modulated via positional thiophene isomerization strategy, affording isomeric COF-α with 2-substitution and COF-β with 3-substitution on the frameworks. The electronic states and intermediate adsorption ability are well-regulated through geometric modification, resulting in controllable chemical activity and local density of π-electrons. Notably, the introduction of thiophene units with different substitution positions into a pristine pure carbon-based COF model COF-Ph achieves excellent activity with a half-wave potential of 0.76 V versus the reversible hydrogen electrode, which is higher than most of those metal-free or metal-based electrocatalysts. Utilizing the combination of theoretical prediction and in situ Raman spectra, we show that the isomeric thiophene skeleton (COF-α and COF-β) can induce the dangling unit activation, accurately identifying the pentacyclic-carbon (thiophene α-position) adjacent to sulfur atom as active sites. The results suggest that the isomeric dangling groups in COFs are suitable for the ORR with promising geometry construction.

Metalloid-Organic Intermolecular Complexes with Charge State-Controlled Conformations

Shape alterations of molecular systems, induced by their (electric) charging/discharging, could facilitate useful electronic and/or mechanical functions in molecular-scale devices and machines. The present study reports structures, stabilities, charge distributions, and IR spectra for a group of complexes of a main-group metalloid (boron) atom with hydrocarbon molecules. The considered systems include the smallest species demonstrating the basic principle of operation, as well as their size-extended analogues, generalizing it to larger counterparts based on such units. The system geometries vary considerably between neutral and ionic counterparts and exhibit two-three typical conformations related to twisting by up to about 90 degrees. The predicted structures correlate with specific infrared spectra, which can enable their experimental identification and transformation tracking. The above-mentioned characteristics suggest the potential utility of such systems for intermolecular switches, with the possible spectral monitoring of their functioning.

Continuous isomerisation of 2,5-dimethylfuran to 2,4-dimethylfuran over Ga-silicate

2,4-dimethylfuran has a rare disubstitution pattern in the five-membered heterocyclic furan ring that is highly interesting chemically but challenging to access synthetically. We present a heterogeneously catalysed route to synthesise 2,4-dimethylfuran from commonly available 2,5-dimethylfuran using a zeolite packed-bed flow reactor. As supported by DFT calculations, the reaction occurs inside the zeolite channels, where the acid sites catalyse proton transfer followed by migration of a methyl group. The zeotype Ga-silicate (MFI type) appears superior to an aluminium-containing ZSM-5 by demonstrating higher selectivities and slower catalyst deactivation. This work provides new opportunities for the continuous valorisation of bio-feedstock molecules in the perspective of the emerging biorefinery era.

Regio- and Stereo-Selective Isomerization of Borylated 1,3-Dienes Enabled by Selective Energy Transfer Catalysis

Configurationally-defined dienes are pervasive across the bioactive natural product spectrum, where they typically manifest themselves as sorbic acid-based fragments. These C5 motifs reflect the biosynthesis algorithms that facilitate their construction. To complement established biosynthetic paradigms, a chemical platform to facilitate the construction of stereochemically defined, functionalizable dienes by light-enabled isomerization has been devised. Enabled by selective energy transfer catalysis, a variety of substituted β-boryl sorbic acid derivatives can be isomerized in a regio- and stereo-selective manner (up to 97 : 3). Directionality is guided by a stabilizing nO→pB interaction in the product: this constitutes a formal anti-hydroboration of the starting alkyne. This operationally simple reaction employs low catalyst loadings (1 mol %) and is complete in 1 h. X-ray analysis supports the hypothesis that the nO→pB interaction leads to chromophore bifurcation: this provides a structural foundation for selective energy transfer.

Stereodivergent, Kinetically Controlled Isomerization of Terminal Alkenes via Nickel Catalysis

Because internal alkenes are more challenging synthetic targets than terminal alkenes, metal-catalyzed olefin mono-transposition (i.e., positional isomerization) approaches have emerged to afford valuable E- or Z- internal alkenes from their complementary terminal alkene feedstocks. However, the applicability of these methods has been hampered by lack of generality, commercial availability of precatalysts, and scalability. Here, we report a nickel-catalyzed platform for the stereodivergent E/Z-selective synthesis of internal alkenes at room temperature. Commercial reagents enable this one-carbon transposition of terminal alkenes to valuable E- or Z-internal alkenes via a Ni-H-mediated insertion/elimination mechanism. Though the mechanistic regime is the same in both systems, the underlying pathways that lead to each of the active catalysts are distinct, with the Z-selective catalyst forming from comproportionation of an oxidative addition complex followed by oxidative addition with substrate and the E-selective catalyst forming from protonation of the metal by the trialkylphosphonium salt additive. In each case, ligand sterics and denticity control stereochemistry and prevent over-isomerization.

A Torquoselective Thermal 6π-Electrocyclization Approach to 1,4-Cyclohexadienes via Solvent-Aided Proton Transfer: Experimental and Theoretical Studies

The thermal 6π-electrocyclization of hexatriene typically delivers 1,3-cyclohexadiene (1,3-CHD). However, there is only limited success in directly synthesizing 1,4-cyclohexadiene (1,4-CHD) using such an approach, probably due to the difficulty in realizing thermally-forbidden 1,3-hydride shift after electrocyclic ring closure. The present study shows that by heating (2E,4E,6E)-hexatrienes bearing ester or ketone substituents at the C1-position in a mixture of toluene/MeOH or EtOH (2 : 1) solvents at 90-100 °C, 1,4-CHDs can be selectively synthesized. This is achieved through a torquoselective disrotatory 6π-electrocyclic ring closure followed by a proton-transfer process. The success of this method depends on the polar protic solvent-assisted intramolecular proton transfer from 1,3-CHD to 1,4-CHD, which has been confirmed by deuterium-labeling experiments. There are no reports to date for such a solvent-assisted isomerization. Density functional theory (DFT) studies have suggested that forming 1,3-CHD and subsequent isomerization is a thermodynamically feasible process, regardless of the functional groups involved. Two possible successive polar solvent-assisted proton-transfer pathways have been identified for isomerization.

NHC-Au-Catalyzed Isomerization of Propargylic B(MIDA)s to Allenes and Double Isomerization of Alkynes to 1,3-Dienes

The synthesis of allenyl boronates is an important yet challenging topic in organic synthesis. Reported herein is an NHC-gold-catalyzed 1,3-H shift toward allenyl boronates synthesis from simple propargylic B(MIDA)s. Mechanistic studies suggest dual roles of the boryl moiety in the reaction: to activate the substrate for isomerization and at the same time, to prevent the allene product from further isomerization. These effects should be a result of α-anion stabilization and α-cation destabilization conferred by the B(MIDA) moiety, respectively. The NHC-Au catalyst, which is commercially available, is also found to be reactive in alkyne-to-1,3-diene isomerization reactions in an atom-economic and base-free manner.

FASN negatively regulates p65 expression by reducing its stability via Thr254 phosphorylation and isomerization by Pin1

FASN, the sole cytosolic enzyme responsible for de novo palmitate synthesis in mammalian cells, has been associated with poor prognosis in cancer and shown to cause drug and radiation resistance by upregulating DNA damage repair via suppression of p65 expression. Targeting FASN by repurposing proton pump inhibitors has generated impressive outcomes in triple-negative breast cancer patients. While p65 regulation of DNA damage repair was thought to be due to its suppression of poly(ADP-ribose) polymerase 1 gene transcription, the mechanism of FASN regulation of p65 expression was unknown. In this study, we show that FASN regulates p65 stability by controlling its phosphorylation at Thr254, which recruits the peptidyl-prolyl cis/trans isomerase Pin1 that is known to stabilize many proteins in the nucleus. This regulation is mediated by palmitate, the FASN catalytic product, not by FASN protein per se. This finding of FASN regulation of p65 stability via phosphorylation of Thr254 and isomerization by Pin1 implicates that FASN and its catalytic product palmitate may play an important role in regulating protein stability in general and p65 more specifically.

Overcoming NMR line broadening of nitrogen containing compounds: A simple solution

This study presents a straightforward solution to the challenge of elucidating the structures of nitrogen containing compounds undergoing isomerization. When spectral line broadening occurs related to isomerization, be it prototropic tautomerism or bond rotations, this poses a significant obstacle to structural elucidation. By adding acids, we demonstrate a simple approach to overcome this issue and effectively sharpen NMR signals for acid stable prototropic tautomers as well as the conformational isomers containing a morpholine or piperazine ring.

(E,Z)-1,1,1,4,4,4-Hexafluorobut-2-enes: hydrofluoroolefins halogenation/dehydrohalogenation cascade to reach new fluorinated allene

A series of 2,3-dihalo-1,1,1,4,4,4-hexafluorobutanes and 2-halo-1,1,1,4,4,4-hexafluorobut-2-enes were prepared from commercially available hydrofluoroolefins 1,1,1,4,4,4-hexafluorobut-2-enes and their 1H, 19F and 13C chemical shifts measured. Some reactions of synthesized 2-halo-1,1,1,4,4,4-hexafluorobut-2-enes have been investigated. A simple, one-pot procedure for the preparation of a new allene (1,1,4,4,4-pentafluorobuta-1,2-diene) and some of its transformations is presented.

Biological Evaluation of Isosteric Applicability of 1,3-Substituted Cuneanes as m-Substituted Benzenes Enabled by Selective Isomerization of 1,4-Substituted Cubanes

We herein evaluate a biological applicability of 1,3-substituted cuneanes as an isostere of m-substituted benzenes based on its structural similarity. An investigation of a method to obtain 1,3-substituted cuneanes by selective isomerization of 1,4-substituted cubanes enables this attempt by giving a key synthetic step to obtain a cuneane analogs of pharmaceuticals having m-substituted benzene moiety. Biological evaluation of the synthesized analogs and in silico study of the obtained result revealed a potential usage of cuneane skeleton in medicinal chemistry.

Synthesis and Characterization of Carbon-Based Heterogeneous Catalysts for Energy Release of Molecular Solar Thermal Energy Storage Materials

Molecular solar thermal energy storage (MOST) systems are rapidly becoming a feasible alternative to energy storage and net-zero carbon emission heating. MOST systems involve a single photoisomerization pair that incorporates light absorption, storage, and heat release processes in one recurring cycle. Despite significant recent advancements in the field, the catalytic back-reaction from MOST systems remains relatively unexplored. A wide range of applications is possible, contingent on the energy densities of the specific photoisomers. Here, we report platinum-, copper-, and nickel-based heterogeneous catalysts screened in batch conditions for the back-conversion reaction on the cyano-3-(4-methoxyphenyl)-norbornadiene/quadricyclane pair. Catalyst reactivities are investigated using structural characterization, imaging techniques, and spectroscopic analysis. Finally, the thermal stability is also explored for our best-performing catalysts.

Photoinduced Solid-Liquid Phase Transition and Energy Storage Enabled by the Design of Linked Double Photoswitches

We demonstrate an effective design strategy of photoswitchable phase change materials based on the bis-azobenzene scaffold. These compounds display a solid phase in the E,E state and a liquid phase in the Z,Z state, in contrast to their monoazobenzene counterparts that exhibit less controlled phase transition behaviors that are largely influenced by their functional groups.

A Proof-of-Principle Design for Through-Space Transmission of Unidirectional Rotary Motion by Molecular Photogears

The construction of molecular photogears that can achieve through-space transmission of the unidirectional double-bond rotary motion of light-driven molecular motors onto a remote single-bond axis is a formidable challenge in the field of artificial molecular machines. Here, we present a proof-of-principle design of such photogears that is based on the possibility of using stereogenic substituents to control both the relative stabilities of two helical forms of the photogear and the double-bond photoisomerization reaction that connects them. The potential of the design was verified by quantum-chemical modeling through which photogearing was found to be a favorable process compared to free-standing single-bond rotation ("slippage"). Overall, our study unveils a surprisingly simple approach to realizing unidirectional photogearing.

Revealing the Origin of Fast Delayed Fluorescence in a Donor Functionalized Bisterpyridine

A new carbazole-substituted bisterpyridine with pronounced delayed fluorescence is presented. While the molecular donor-acceptor-donor design suggests the origin of this to be thermally activated delayed fluorescence (TADF), results from various photophysical characterizations, OLED characteristics, temperature-dependent NMR spectroscopy, and DFT calculations all point against the involvement of triplet states. The molecule exhibits blue emission at about 440 nm with two or more fast decay channels in the lower nanosecond range in both solution and thin films. The delayed emission is proposed to be caused by rotational vibrational modes. We suggest that these results are generally applicable, especially for more complex molecules, and should be considered as alternative or competitive emissive relaxation pathways in the field of organic light emitting materials.

Isomeric Effect of a π Bridge in an IDT-Based Nonfused Electron Photovoltaic Acceptor

A pair of isomers, IDT-BOF containing S⋅⋅⋅O/F⋅⋅⋅H noncovalently configurational locks and IDT-BFO containing F⋅⋅⋅H/O⋅⋅⋅H noncovalently configurational locks, with an acceptor-π-donor-π-acceptor (A-π-D-π-A) structure have been designed and synthesized by choosing 4,9-dihydro-s-indaceno[1,2-b : 5,6-b']dithiophene (IDT) as the D unit, an F/n-hexyloxy substituted phenyl ring as π bridge, and 3-(dicyanomethylidene)indan-1-one as the A unit. Owing to the S⋅⋅⋅O/F⋅⋅⋅H or F⋅⋅⋅H/O⋅⋅⋅H noncovalently configurational locks, both IDT-BOF and IDT-BFO have a completely planar structure. IDT-BOF exhibits a similar LUMO to IDT-BFO, but higher HOMO energy levels, leading to a smaller optical bandgap and red-shifted absorption. However, IDT-BOF-based bulk-heterojunction organic solar cells (BHJ-OSCs) coupled with PBDB-T, and PCE-10 as donor materials both exhibited a lower PCE than that of IDT-BFO (PBDB-T: 5.2 vs. 6.1 %; PCE-10: 1.7 vs. 3.2 %). Comprehensively comparing and investigating IDT-BOF : PBDB-T and IDT-BFO : PBDB-T OSCs suggested that the large phase separation and serious charge recombination of IDT-BOF-based OSCs contributed to its lower power conversion efficiency. Importantly, ternary solar cells based on PBDB-T : Y5 as control devices with an additional 10 % IDT-BFO exhibited a 5 % enhancement in the PCE compared to the control device (14.3 vs. 13.46 %).

Predicting deamidation and isomerization sites in therapeutic antibodies using structure-based in silico approaches

Asparagine (Asn) deamidation and aspartic acid (Asp) isomerization are common degradation pathways that affect the stability of therapeutic antibodies. These modifications can pose a significant challenge in the development of biopharmaceuticals. As such, the early engineering and selection of chemically stable monoclonal antibodies (mAbs) can substantially mitigate the risk of subsequent failure. In this study, we introduce a novel in silico approach for predicting deamidation and isomerization sites in therapeutic antibodies by analyzing the structural environment surrounding asparagine and aspartate residues. The resulting quantitative structure-activity relationship (QSAR) model was trained using previously published forced degradation data from 57 clinical-stage mAbs. The predictive accuracy of the model was evaluated for four different states of the protein structure: (1) static homology models, (2) enhancing low-frequency vibrational modes during short molecular dynamics (MD) runs, (3) a combination of (2) with a protonation state reassignment, and (4) conventional full-atomistic MD simulations. The most effective QSAR model considered the accessible surface area (ASA) of the residue, the pKa value of the backbone amide, and the root mean square deviations of both the alpha carbon and the side chain. The accuracy was further enhanced by incorporating the QSAR model into a decision tree, which also includes empirical information about the sequential successor and the position in the protein. The resulting model has been implemented as a plugin named "Forecasting Reactivity of Isomerization and Deamidation in Antibodies" in MOE software, completed with a user-friendly graphical interface to facilitate its use.

Naphtho[1,8-de][1,2]Oxazin-4-ol: Precursor to 1,2,8-Trisubstituted Naphthalenes and 1-Unsubstituted Naphtho[1,2-d]isoxazole 2-Oxide: A Novel Isomerization of the N-Oxide to Nitrile Oxide en Route to Isoxazol(in)es

Naphtho[1,8-de][1,2]oxazin-4-ol and its acyl or benzyl derivatives ring open to various 2,8-dihydroxy-1-naphthonitriles, which, through (de)protection protocols and reduction, afford the target (E)-2-hydroxy-8-methoxy-1-naphthaldehyde. This was converted to its corresponding oxime, which was oxidatively o-cyclized with phenyliodine(III) diacetate (PIDA) to 9-methoxynaphtho[1,2-d]isoxazole 2-oxide. The latter, in deuterated DMSO at room temperature, was rearranged to its isomer 2-hydroxy-8-methoxy(naphthalen-1-yl)nitrile oxide. The isomerization was detected by time-course plot 1H NMR spectroscopy and further identified from its 13C NMR and HRMS spectra. The nitrile oxide was stable in (non)deuterated DMSO for at least 18 h. A 3,4-bis(2-hydroxy-8-methoxynaphthalen-1-yl)-1,2,5-oxadiazole 2-oxide, as a dimerization product or an isocyanate as a rearrangement isomer, was ruled out, the former by its HRMS spectrum and the latter by its 1,3-dipolar cycloaddition reactions to substituted isoxazoles.

LC-MS Approach to Decipher a Light Chain Chromatographic Peak Splitting of a Monoclonal Antibody

PURPOSE

Monoclonal antibodies (mAbs), like other protein therapeutics, are prone to various forms of degradation, some of which are difficult to distinguish from the native form yet may alter potency. A generalizable LC-MS approach was developed to enable quantitative analysis of isoAsp. In-depth understanding of product quality attributes (PQAs) enables optimization of the manufacturing process, better formulation selection, and decreases risk associated with product handling in the clinic or during shipment.

METHODS

Reversed-phase chromatographic peak splitting was observed when a mAb was exposed to elevated temperatures. Multiple LC-MS based methods were applied to identify the reason for peak splitting. The approach involved the use of complementary HPLC columns, multiple enzymatic digestions and different MS/MS ion dissociation methods. In addition, mAb potency was measured by enzyme-linked immunosorbent assay (ELISA).

RESULTS

The split peaks had identical masses, and the root cause of the peak splitting was identified as isomerization of an aspartic acid located in the complementarity-determining region (CDR) of the light chain. And the early eluting and late eluting peaks were collected and performed enzymatic digestion to confirm the isoAsp enrichment in the early eluting peak. In addition, decreased potency was observed in the same heat-stressed sample, and the increased isoAsp levels in the CDR correlate well with a decrease of potency.

CONCLUSION

Liquid chromatography-mass spectrometry (LC-MS) has been utilized extensively to assess PQAs of biological therapeutics. In this study, a generalizable LC-MS-based approach was developed to enable identification and quantitation of the isoAsp-containing peptides.

Resolving D-Amino Acid Containing Peptides Using Ion Mobility-Mass Spectrometry: Challenges and Recent Developments

Peptides and proteins having D-amino acids in their sequences are now believed to be widespread among different living organisms. Their significance is attributed to the diverse functions of these molecules, such as having a certain pathological implication or enhancing biological activity. Indeed, some peptide molecules with D-amino acids in their structure have already found their way to clinical use such as the antibacterial gramicidin and the antidiabetic nateglinide. Ion mobility mass spectrometry (IM-MS) added an additional dimension of separation as it depends on ions mobility in the space, which is dependent on their shapes, and the shape depends on the orientation of atoms. Thus, D-amino acids containing peptides (DAACPs) will have different mobility and collision cross-section values than those with L-amino acids. Eventually, this will lead to baseline separation of the two peptides. Additionally, ion mobility can precisely locate the position of D-amino acids by analyzing the difference in the arrival times of the fragment ions. The importance of DAACPs, as well as the difficulties in discovering them, were addressed in this review. Similarly, we emphasized how recent developments in IM-MS have improved their detection and analysis. Consequently, the LC-IM-MS/MS platform appears to be promising in isomeric mixture analysis.

Diastereoselective Synthesis of Dispiro[Imidazothiazolotriazine-Pyrrolidin-Oxindoles] and Their Isomerization Pathways in Basic Medium

Highly diastereoselective methods for the synthesis of two series of regioisomeric polynuclear dispyroheterocyclic compounds with five or six chiral centers, comprising moieties of pyrrolidinyloxindole and imidazo[4,5-e]thiazolo[3,2-b]-1,2,4-triazine of linear structure or imidazo[4,5-e]thiazolo[2,3-c]-1,2,4-triazine of angular structure, have been developed on the basis of a [3+2] cycloaddition of azomethine ylides to functionalized imidazothiazolotriazines. Depending on the structure of the ethylenic component, cycloaddition proceeds as an anti-exo process for linear derivatives, while cycloaddition to angular ones resulted in a syn-endo diastereomer. Novel pathways of isomerization for the synthesized anti-exo products upon treatment with sodium alkoxides have been found, which resulted in two more series of diastereomeric dispiro[imidazothiazolotriazine-pyrrolidin-oxindoles] inaccessible with the direct cycloaddition reaction. For the first series, the inversion of the configuration of one stereocenter, i.e., C-4' atom of the pyrrolidine cycle, (epimerization) was established. For the second one, configuration of the obtained diastereomer formally corresponded to the syn-endo approach of the azomethine ylide in the case of cycloaddition to the ethylenic component.

Thermally Activated Geometrical Regioselective E→Z Isomerization-Enabled Cascade Sequences of Conjugated Dienals: Experimental and DFT Studies

The geometrical regioselective E→Z isomerization of a conjugated alkene under thermal activation pose a challenge due to microscopic reversibility. Herein we report that such reversibility issues can be circumvented by integrating E→Z isomerization with subsequent cyclization cascade, particularly in the absence of commonly employed light, acids, or metal-catalysts. Thus, linearly conjugated dienals in a mixture of toluene-alcohol (2 : 1) solvents or only with alcohol at 60-70 °C can be converted to γ-alkoxybutenolides in moderate to good yields. The intermediary 2Z,4E-isomer can be isolated, which includes the first example of isolating the regioselective isomerization product under thermal conditions. Density functional theory (DFT) studies have been employed to shed light on the feasibility of geometrical alkene isomerization and ensuing cascade sequences. It has been observed that the regioselective 2E,4E→2Z,4E isomerization of dienal is a thermodynamically facile (ΔG <0) process. Structural elucidation further reveals that the presence of a certain charge transfer and a non-covalent interaction may be the primary reasons for the enhanced stability of the 2Z,4E-isomer. The thermodynamic plausibility of the subsequent cascade reaction from the Z-isomer to the anticipated product in the presence of a polar protic solvent (here MeOH) is also explicated. Out of the two probable pathways, the "hemiacetal pathway" involving a relay proton transfer is kinetically more feasible due to the diminished activation barrier than the "conjugate addition pathway".

Photolysis of Phosphaketenyltetrylenes with a Carbazolyl Substituent

Phosphaketenes of divalent group 14 compounds can potentially serve as precursors for the synthesis of heavy multiple-bond systems. We have employed the dtbp Cbz substituent (dtbp Cbz=1,8-bis(3,5-ditertbutylphenyl)-3,6-ditertbutylcarbazolyl) to prepare such phosphaketenyltetrylenes [(dtbp Cbz)EPCO] (E=Ge, Sn, Pb). While the phosphaketenyltetrylenes are stable at ambient conditions, they can be readily decarbonylated photolytically. For the germylene and stannylene derivatives, dimeric diphosphene-type products [(dtbp Cbz)EP]2 (E=Ge, Sn) were obtained. In contrast, photolysis of the phosphaketenylplumbylene, via isomerisation of the [(dtbp Cbz)PbP] intermediate to [(dtbp Cbz)PPb], afforded an unsymmetric and incompletely decarbonylated product [(dtbp Cbz)2 Pb2 P2 CO] formally comprising a [(dtbp Cbz)PPb] and a [(dtbp Cbz)PbPCO] moiety.

Structural Fluctuation, Relaxation, and Folding of Protein: An Approach Based on the Combined Generalized Langevin and RISM/3D-RISM Theories

In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water's degrees of freedom onto the protein's degrees of freedom. Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix. The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.

Chemistry, Crystal Structure, and In Vitro Receptor Binding of Δ10-THC Isomers

Introduction: The psychoactive properties of Δ10-THC isomers (trans- and cis-Δ10-THC) are poorly understood. To shed more light on the biological effects of these compounds, we studied in vitro receptor binding of Δ10-THC isomers at cannabinoid CB1 and CB2 receptors. Materials and Methods: We first optimized and simplified catalytic synthesis of trans- and cis-Δ10-THC to allow their safe and cheap large-scale synthesis. In our synthesis, BuLi was replaced with KOtBu, and DMSO/anisole or NEt3/heptane solvent systems were used instead of HMPA/toluene. Single crystal X-ray analysis confirmed the structure of both isomers and the configuration of their chiral centers. Results: In the radioligand replacement assay, both isomers showed strong affinity toward the CB1 receptor, with IC50=29.1 nM for the trans isomer and IC50=294.2 nM for the cis counterpart. However, the IC50 values were significantly higher than that of Δ9-THC (2.1 nM), a naturally occurring psychoactive component of cannabis sativa, suggesting a lower affinity of Δ10-THCs toward this receptor. In function assays, in contrast to Δ9-THC, both isomers failed to show any agonist properties at concentrations up to 10 μM suggesting a lack of THC-like psychoactivity for trans- and cis-Δ10-THC. Conclusions: Our results established Δ10-THC isomers among antagonists of the CB1 receptor as both cis and trans isomers antagonized CP55,490 with IC50=460 nM for trans and IC50=1040 nM for cis. This functional property has not been previously observed for any other THC isomers.

A Doubly Dissipative System Driven by Chemical and Radiative Stimuli

The operation of a dissipative network composed of two or three different crown-ether receptors and an alkali metal cation can be temporally driven by the use (combined or not) of two orthogonal stimuli of a different nature. More specifically, irradiation with light at a proper wavelength and/or addition of an activated carboxylic acid, are used to modulate the binding capability of the above crown-ethers towards the metal ion, allowing to control over time the occupancy of the metal cation in the crown-ether moiety of a given ligand. Thus, application of either or both of the stimuli to an initially equilibrated system, where the metal cation is distributed among the crown-ether receptors depending on the different affinities, causes a programmable change in the receptor occupancies. Consequently, the system is induced to evolve to one or more out-of-equilibrium states with different distributions of the metal cation among the different receptors. When the fuel is exhausted or/and the irradiation interrupted, the system reversibly and autonomously goes back to the initial equilibrium state. Such results may contribute to the achievement of new dissipative systems that, taking advantage of multiple and orthogonal stimuli, are featured with more sophisticated operating mechanisms and time programmability.

Highly Selective Cyclization and Isomerization of Propargylamines to Access Functionalized Quinolines and 1-Azadienes

Developing new organic reactions with excellent atom economy and high selectivity is significant and urgent. Herein, by ingeniously regulating the reaction conditions, highly selective transformations of propargylamines have been successfully implemented. The palladium-catalyzed cyclization of propargylamines generates a series of functionalized quinoline heterocycles, while the base-promoted isomerization of propargylamines affords diverse 1-azadienes. Both reactions have good functional group tolerance, mild conditions, excellent atom economy and high yields of up to 93%. More importantly, these quinoline heterocycles and 1-azadienes could be flexibly transformed into valuable compounds, illustrating the validity and practicability of the propargylamine-based highly selective reactions.

Recent Progress in Understanding the Impact of Food Processing and Storage on the Structure-Activity Relationship of Fucoxanthin

Fucoxanthin, a brown algae carotenoid, has attracted great interest because of its numerous biological activities supported by in vitro and in vivo studies. However, its chemical structure is susceptible to alterations when subjected to food processing and storage conditions, such as heat, oxygen, light, and pH changes. Consequently, these conditions lead to the formation of fucoxanthin derivatives, including cis-isomers, apo-fucoxanthinone, apo-fucoxanthinal, fucoxanthinol, epoxides, and hydroxy compounds, collectively known as degradation products. Currently, little information is available regarding the stability and functionality of these fucoxanthin derivatives resulting from food processing and storage. Therefore, enhancing the understanding of the biological effect of fucoxanthin derivatives is crucial for optimizing the utilization of fucoxanthin in various applications and ensuring its efficacy in potential health benefits. To this aim, this review describes the main chemical reactions affecting the stability of fucoxanthin during food processing and storage, facilitating the identification of the major fucoxanthin derivatives. Moreover, recent advancements in the structure-activity relationship of fucoxanthin derivatives will be critically assessed, emphasizing their biological activity. Overall, this review provides a critical updated understanding of the effects of technological processes on fucoxanthin stability and activity that can be helpful for stakeholders when designing processes for food products containing fucoxanthin.

Low-Energy Transformation Pathways between Naphthalene Isomers

The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system and to evaluate the probability flows between them. The transition pathways between the different basins and the associated probabilities were investigated for several lid energies up to 11 eV, this value being close to the highest photon energy in the interstellar medium (13.6 eV). More than a hundred isomers were identified and a set of 23 minima was selected among them, on the basis of their energy and probability of occurrence. The return probabilities of these 23 minima and the transition probabilities between them were computed for several lid energies up to 11 eV. The first connection appeared at 3.5 eV while all minima were found to be connected at 9.5 eV. The local density of state was also sampled inside their respective basins. This work gives insight into both energy and entropic barriers separating the different basins, which also provides information about the transition regions of the energy landscape.

Isomerization and Stabilization of Amygdalin from Peach Kernels

In this study, isomerization conditions, cytotoxic activity, and stabilization of amygdalin from peach kernels were analyzed. Temperatures greater than 40 °C and pHs above 9.0 resulted in a quickly increasing isomer ratio (L-amygdalin/D-amygdalin). At acidic pHs, isomerization was significantly inhibited, even at high temperature. Ethanol inhibited isomerization; the isomer rate decreased with the ethanol concentration increasing. The growth-inhibitory effect on HepG2 cells of D-amygdalin was diminished as the isomer ratio increased, indicating that isomerization reduces the pharmacological activity of D-amygdalin. Extracting amygdalin from peach kernels by ultrasonic power at 432 W and 40 °C in 80% ethanol resulted in a 1.76% yield of amygdalin with a 0.04 isomer ratio. Hydrogel beads prepared by 2% sodium alginate successfully encapsulated the amygdalin, and its encapsulation efficiency and drug loading rate reached 85.93% and 19.21%, respectively. The thermal stability of amygdalin encapsulated in hydrogel beads was significantly improved and reached a slow-release effect in in vitro digestion. This study provides guidance for the processing and storage of amygdalin.

Discovery and Control of Succinimide Formation and Accumulation at Aspartic Acid Residues in The Complementarity-Determining Region of a Therapeutic Monoclonal Antibody

PURPOSE

Succinimide formation and isomerization alter the chemical and physical properties of aspartic acid residues in a protein. Modification of aspartic acid residues within complementarity-determining regions (CDRs) of therapeutic monoclonal antibodies (mAbs) can be particularly detrimental to the efficacy of the molecule. The goal of this study was to characterize the site of succinimide accumulation in the CDR of a therapeutic mAb and understand its effects on potency. Furthermore, we aimed to mitigate succinimide accumulation through changes in formulation.

METHODS

Accumulation of succinimide was identified through intact and reduced LC-MS mass measurements. A low pH peptide mapping method was used for relative quantitation and localization of succinimide formation in the CDR. Statistical modeling was used to correlate levels of succinimide with basic variants and potency measurements.

RESULTS

Succinimide accumulation in Formulation A was accelerated when stored at elevated temperatures. A strong correlation between succinimide accumulation in the CDR, an increase in basic charge variants, and a decrease in potency was observed. Statistical modeling suggest that a combination of ion exchange chromatography and potency measurements can be used to predict succinimide levels in a given sample. Reformulation of the mAb to Formulation B mitigates succinimide accumulation even after extended storage at elevated temperatures.

CONCLUSION

Succinimide formation in the CDR of a therapeutic mAb can have a strong negative impact on potency of the molecule. We demonstrate that thorough characterization of the molecule by LC-MS, ion exchange chromatography, and potency measurements can facilitate changes in formulation that mitigate succinimide formation and the corresponding detrimental changes in potency.

Hydration rearrangement in the 4-aminobenzonitrile-(H2O)2 cluster induced by photoionization: The effect of solvent-solvent interactions

The interplay between solute-solvent and solvent-solvent interactions plays an essential role in solvation dynamics that has important effects on the mechanism and dynamics of chemical reactions in solution. In this study, the rearrangement of the hydration shell induced by photoionization of a solute molecule is probed in a state- and isomer-specific manner by resonant multiphoton ionization detected IR spectroscopy of the prototypical 4-aminobenzonitrile-(H2O)2 cluster produced in a molecular beam. IR spectra reveal that the water molecules form a cyclic solvent network around the CN group in the initial neutral state (S0). Different from the singly-hydrated cluster, in which either the CN or the NH2 group is hydrated, hydration of the NH2 group is not observed in the dihydrated cluster. IR spectra obtained after ionizing the solute molecule into the cation ground state (D0) exhibit features ascribed to both NH-bound and CN-bound isomers, indicating that water molecules migrate from the CN to the NH site upon ionization with a yield depending on the ionization excess energy. Analysis of the IR spectra as a function of the excess energy shows that migration produces two different NH2 solvated structures, namely (i) the most stable structure in which both N-H bonds are singly hydrated.

Polarity-Driven Isomerization of a Hydroxynaphthalimide-Containing Spiropyran at Room Temperature

Design of spiropyrans showing spontaneous isomerization driven by the polarity of solvents is an important consideration for the synthesis of optical sensory materials. Although some spiropyrans undergo polarity-driven isomerization, they must be heated owing to the high activation energy required for isomerization. In this study, we describe that a spiropyran containing a hydroxynaphthalimide unit (1) exhibits a polarity-driven isomerization at room temperature. It exists as a colorless spirocyclic (SP) form in less polar solvents but is isomerized to a colored merocyanine (MC) form in polar solvents. The equilibrium amount of the MC form increases with an increase in the polarity of solvents. The MC form involves two resonance structures-the quinoidal and zwitterionic forms. In polar media, the zwitterionic form dominates mainly owing to solvation by polar molecules. Solvation stabilizes the negative charge of the zwitterionic form and decreases its ground state energy, thereby enhancing SP → MC isomerization. The SP ⇌ MC isomerization terminates within barely 30 s even at room temperature because the naphthol moiety with high π-electron density lowers the activation energy for the rate-determining rotational step.

Polarity Does Not Matter: Molecular Weight Reverses the Photoisomerization-Induced Phase Separation of an Azobenzene-Bearing Polymer

We find the non-canonical photoisomerization-induced phase separation of an azobenzene-bearing polymer. The polymer composed of acrylate-based azobenzene (AzoAA) and N,N-dimethylacrylamide (DMA), namely poly(AzoAA-r-DMA), phase separates under visible light-induced cis-to-trans isomerization at high molecular weight, whereas the phase separation is realized under ultraviolet light-induced trans-to-cis isomerization at low molecular weight. Conventionally, the origin of photoisomerization-induced phase separation is believed to arise from the difference in polarity between the apolar trans and polar cis states; thereby the direction of phase changes, either to separate or dissolute, is uniquely determined by the polarity changes during the isomerization of azobenzene. Contrary to this common perception, the poly(AzoAA-r-DMA) in this study phase separates through both trans and cis isomerization, depending on the molecular weight. The non-canonical phase separation of poly(AzoAA-r-DMA) reported herein suggest that molecular weight plays a significant role in determining the phase behavior of azobenzene-bearing polymers. This study provides a platform for the development of spatial temporally controlled delivery vehicles and microreactors. This article is protected by copyright. All rights reserved.

Counterion at an atypical position: Investigating the mechanism of photoisomerization in jellyfish rhodopsin

The position of the counterion in animal rhodopsins plays a crucial role in maintaining visible light sensitivity and facilitating the photoisomerization of their retinal chromophore. The counterion displacement is thought to be closely related to the evolution of rhodopsins, with different positions found in invertebrates and vertebrates. Interestingly, box jellyfish rhodopsin (JelRh) acquired the counterion in transmembrane 2 (TM2) independently. This is a unique feature, as in most animal rhodopsins, the counterion is found in a different location. In this study, we used Fourier Transform Infrared spectroscopy to examine the structural changes that occur in the early photointermediate state of JelRh. We aimed to determine whether the photochemistry of JelRh is similar to that of other animal rhodopsins by comparing its spectra to those of vertebrate bovine rhodopsin (BovRh) and invertebrate squid rhodopsin (SquRh). We observed that the N-D stretching band of the retinal Schiff base was similar to that of BovRh, indicating the interaction between the Schiff base and the counterion is similar in both rhodopsins, despite their different counterion positions. Furthermore, we found that the chemical structure of the retinal in JelRh is similar to that in BovRh, including the changes in the hydrogen-out-of-plane band that indicates a retinal distortion. Overall, the protein conformational changes induced by the photoisomerization of JelRh yielded spectra that resemble an intermediate between BovRh and SquRh, suggesting a unique spectral property of JelRh, and making it the only animal rhodopsin with a counterion in TM2 and an ability to activate G_s protein.

Isomerization and epimerization of glucose and galactose in arginine solution and phosphate buffer under subcritical fluid conditions

Reaction of glucose or galactose was performed in arginine solution or phosphate buffer (pH 7.0) using a batch reactor at 110 °C. The yields of products, pH, and absorbances at 280 nm and 420 nm were measured during the reaction. Fructose, mannose, and allulose were formed from glucose; tagatose, talose, and sorbose were done from galactose. The reaction proceeded more rapidly in arginine solution than in phosphate buffer. In arginine solution, yields of fructose and tagatose were 20% and 16%, respectively, after 30-min reaction; in phosphate buffer, they were 14% and 10%, respectively. However, in both reaction media, the pH drop and increase in absorbances continued even after the yield became almost constant. The absorbance increased particularly in the latter half of the reaction due to formation of browning products. Therefore, to avoid browning, the reaction should be stopped as soon as possible after the yield approaches its maximum value.

Fast Isomerization Before Isomerization-Hydroformylation: Probing the Neglected Period with A Novel Microfluidic Device

By combining the concept of flash chemistry and radial synthesis, a novel microreactor (Flashstop reactor) was designed to study isomerization process of hydroformylation by a Rh/tetraphosphite catalyst in a time scale of seconds. It was found that in the initial 313 seconds, 60~99% of 1-octene was isomerized to 2- and 3-octenes before the formation of aldehydes. Within this period, two different types of isomerization reactions were observed. It was proposed that a monohydride complex without CO ligand accounts for the ultrafast isomerization in the initial 30 seconds. The isomerization rate with such monohydride species was calculated much faster than that with the well-known H(CO)Rh(P-P) species. Both experimental and DFT computational studies were carried out to support this assumption. Fast transformations early on in catalytic cycles have been rarely studied due to the lack of proper tools. We believe that the Flashstop reactor is a powerful tool for analysis of kinetics in gas-liquid biphasic reactions within a time scale of seconds to minutes.

Isomerization of Galactose to Tagatose: Recent Advances in Non-enzymatic Isomerization

The valorization of galactose derived from acid whey to low-calorie tagatose has gained increasing attention. Enzymatic isomerization is of great interest but faces several challenges, such as poor thermal stability of enzymes and a long processing time. In this work, non-enzymatic (supercritical fluids, triethylamine, arginine, boronate affinity, hydrotalcite, Sn-β zeolite, and calcium hydroxide) pathways for galactose to tagatose isomerization were critically discussed. Unfortunately, most of these chemicals showed poor tagatose yields (<30%), except for calcium hydroxide (>70%). The latter is able to form a tagatose-calcium hydroxide-water complex, which stimulates the equilibrium toward tagatose and prevents sugar degradation. Nevertheless, the excessive use of calcium hydroxide may pose challenges in terms of economic and environmental feasibility. Moreover, the proposed mechanisms for the base (enediol intermediate) and Lewis acid (hydride shift between C-2 and C-1) catalysis of galactose were elucidated. Overall, it is crucial to explore novel and effective catalysts as well as integrated systems for isomerizing of galactose to tagatose.

Endogenous l- to d-amino acid residue isomerization modulates selectivity between distinct neuropeptide receptor family members

The l- to d-amino acid residue isomerization of neuropeptides is an understudied post-translational modification found in animals across several phyla. Despite its physiological importance, little information is available regarding the impact of endogenous peptide isomerization on receptor recognition and activation. As a result, the full roles peptide isomerization play in biology are not well understood. Here, we identify that the Aplysia allatotropin-related peptide (ATRP) signaling system utilizes l- to d-residue isomerization of one amino acid residue in the neuropeptide ligand to modulate selectivity between two distinct G protein-coupled receptors (GPCRs). We first identified a novel receptor for ATRP that is selective for the D2-ATRP form, which bears a single d-phenylalanine residue at position 2. Using cell-based receptor activation experiments, we then characterized the stereoselectivity of the two known ATRP receptors for both endogenous ATRP diastereomers, as well as for homologous toxin peptides from a carnivorous predator. We found that the ATRP system displayed dual signaling through both the Gαq and Gαs pathways, and each receptor was selectively activated by one naturally occurring ligand diastereomer over the other. Overall, our results provide insights into an unexplored mechanism by which nature regulates intercellular communication. Given the challenges in detecting l- to d-residue isomerization from complex mixtures de novo and in identifying receptors for novel neuropeptides, it is likely that other neuropeptide-receptor systems may also utilize changes in stereochemistry to modulate receptor selectivity in a manner similar to that discovered here.

Strain-Sensitive On-Surface Ladderization by Non-Dehydrogenative Heterocyclization

On-surface cyclodehydrogenation recently became an important reaction to planarize π-conjugated molecules and oligomers. However, the high-activation barrier to cleave the C-H bond often requires high-temperature annealing, consequently restricting structures of precursor molecules and/or leading to random fusion at their edges. Here, we present a synthesis of pyrrolopyrrole-bridged ladder oligomers from 11,11,12,12-tetrabromo-1,4,5,8-tetraaza-9,10-anthraquinodimethane molecules on Ag(111) with bond-resolved scanning tunnelling microscopy. This non-dehydrogenative cyclization between pyrazine and ethynylene/cumulene groups has a low-activation barrier for forming intermediary dimeric oligomer containing dipyrazinopyrrolopyrrolopyrazine units, thus giving new insight into the strain-sensitive in ladder-oligomer formation.

Mechanistic Insights into the Metal-Free Deoxygenative Borylation of Ketones and Aldehydes with Bis(catecholato)diborane

The mechanisms of direct deoxygenative borylation of acetone and benzaldehyde with bis(catecholato)diborane (B₂ cat₂ ) in the solvent N,N-dimethylacetamide (DMA) are investigated through detailed density functional theory calculations. These calculations show that the isomer 1,2-B₂ cat₂ in situ generated from 1,1-B₂ cat₂ induced by DMA is the reactive boron intermediate for the reactions. The addition of the B-B bond of 1,2-B₂ cat₂ to the C=O bond of acetone or benzaldehyde via a concerted [2σ+2π]-cycloaddition-like transition state is the rate-limiting step for both the triboration reaction of acetone and the monoboration reaction of benzaldehyde. DMA not only acts as the solvent but also promotes the structural isomerization of B₂ cat₂ , the deoxygenation of acetone to form the vinyl boronate intermediate and subsequent diboration of vinyl boronate with 1,2-B₂ cat₂ , as well as the protodeboronation of the gem-diboronate intermediate in the deoxygenative borylation of benzaldehyde. The presented computational results can explain the observed experimental facts and provide insight into the roles of the isomeric 1,2-B₂ cat₂ and the solvent DMA in related reactions.

Hydrogenolysis-Isomerization of Waste Polyolefin Plastics to Multibranched Liquid Alkanes

Upcycling of waste polyolefin plastics still meets with economic and technological challenges in practice. In this work, the catalytic hydrogenolysis-isomerization of nondegradable polyolefin plastic waste to high-value gasoline, diesel, and light lubricants with highly branched chain is achieved over a bifunctional Rh/Nb₂ O₅ catalyst under relatively mild conditions. Owing to the high efficiency of metallic Rh active sites, the dehydrogenation/hydrogenation of long carbon chains of polyolefins is enhanced. With the assistance of strong Brønsted acidity of Nb₂ O₅ , the cleavage of C-C bonds, skeletal rearrangements, as well as the β-scission of alkylcarbenium ions occurs, which boosts the one-step solvent-free catalytic hydrogenolysis and isomerization of polyolefins. In addition, the preliminary economic analysis shows that this technology is economical, feasible, and has great potential in accelerating the transition to a circular plastics economy for sustainable development.

Identification of a Functionally Efficient and Thermally Stable Outward Sodium-Pumping Rhodopsin (BeNaR) from a Thermophilic Bacterium

Rhodopsins are transmembrane proteins with retinal chromophores that are involved in photo-energy conversion and photo-signal transduction in diverse organisms. In this study, we newly identified and characterized a rhodopsin from a thermophilic bacterium, Bellilinea sp. Recombinant Escherichia coli cells expressing the rhodopsin showed light-induced alkalization of the medium only in the presence of sodium ions (Na⁺), and the alkalization signal was enhanced by addition of a protonophore, indicating an outward Na⁺ pump function across the cellular membrane. Thus, we named the protein Bellilinea Na⁺-pumping rhodopsin, BeNaR. Of note, its Na⁺-pumping activity is significantly greater than that of the known Na⁺-pumping rhodopsin, KR2. We further characterized its photochemical properties as follows: (i) Visible spectroscopy and HPLC revealed that BeNaR has an absorption maximum at 524 nm with predominantly (>96%) the all-trans retinal conformer. (ii) Time-dependent thermal denaturation experiments revealed that BeNaR showed high thermal stability. (iii) The time-resolved flash-photolysis in the nanosecond to millisecond time domains revealed the presence of four kinetically distinctive photointermediates, K, L, M and O. (iv) Mutational analysis revealed that Asp101, which acts as a counterion, and Asp230 around the retinal were essential for the Na⁺-pumping activity. From the results, we propose a model for the outward Na⁺-pumping mechanism of BeNaR. The efficient Na⁺-pumping activity of BeNaR and its high stability make it a useful model both for ion transporters and optogenetics tools.

Molecular Twisting Affects the Solid-State Photochemical Reactions of Unsaturated Ketones and the Photomechanical Effects of Molecular Crystals

Three groups of chalcone derivatives and their analogues involving halogen atoms (X=F, Cl, Br) have been synthesized. Firstly, the nearly planar acyclic chalcone derivatives were inclined to undergo photo-induced stereospecific [2+2] cycloaddition, which triggered the crystals to exhibit macroscopic motions of bending or cracking. In particular, the single-crystal-to-single-crystal transformation happened upon UV irradiation of the crystals, which was helpful for the understanding photomechanical effects. Cyclic 3,4-dihydronaphthalene-based chalcone analogues possess a more twisted conformation, and they tend to undergo trans-cis isomerization. No photomechanical effect was observed for the crystals of the cyclic chalcone analogues due to the lower isomerization rate. The twist degree of chroman-based molecules was in between of the first two, [2+2] cycloaddition and trans-cis isomerization simultaneously took place in crystals. Photo-induced bending and twisting were observed for the crystals of chroman-based chalcone analogues. Therefore, the differences in molecular dihedral angles in α,β-unsaturated ketones were responsible for their photochemical characters and in turn to tune the photomechanical effects. In this work, a bridge between the molecular structures and solid-state photochemical reactions triggered photomechanical crystals is built.

Lutein Isomers: Preparation, Separation, Structure Elucidation, and Occurrence in 20 Medicinal Plants

Lutein and its cis-isomers occur in a lot of plants, including a variety of flowers. In this study, lutein isomers were produced via iodine-catalyzed isomerization, and four cis-isomers (9Z-, 9'Z-, 13Z-, and 13Z') were isolated by means of column chromatography and semipreparative HPLC. The structures of the 9'Z- and 13'Z-isomers were elucidated via NMR measurements. These compounds were used as standards for the HPLC-DAD-MS determination of the carotenoid composition of the flowers of 20 plant species, in which lutein and its geometrical isomers are the main components. The flowers showed great variation in their cis- and trans-lutein content, and also in the presence or absence of other carotenoids, such as violaxanthin, neoxanthin, β-cryptoxanthin, and β-carotene. Some of the investigated flowers were found to be rich sources of lutein without zeaxanthin.

Assisted Tandem Pd Catalysis Enables Regiodivergent Heck Arylation of Transiently Generated Substituted Enol Ethers

Two complementary regiodivergent Pd-catalyzed assisted tandem [isomerization/Heck arylation] reactions are reported. They provide access to a broad array of acyclic trisubstituted vinyl ethers starting from readily available alkenyl ethers. In both cases, the isomerization is conducted with a [Pd-H] precatalyst supported by tris-tert-butyl phosphine ligands. When the catalyst is modified by the addition of a chelating bisphosphine ligand (dppp), an organic base (Cy₂NMe), sodium acetate, and aryl triflates are used as electrophiles, the α-arylation pathway is promoted preferentially. The β-arylation pathway is favored for electron-deficient and electron-neutral aryl halides when the catalyst is simply modified by the addition of an excess of an organic base (Et₃N) after completion of the isomerization reaction. Electron-rich aryl halides lead to reduced levels of regiocontrol. The moderate stereoselectivity obtained are proposed to reflect the absence of stereocontrol in the isomerization step. Computational analyses suggest that migratory insertion is selectivity-determining for both the arylations. For the β-selective arylation, an energy decomposition analysis underscored that electronic factors favor α-regioselectivity and steric effects favor β-regioselectivity. Preliminary investigations show that high levels of stereoselectivity can be achieved for the α-selective arylation by ligand control. Complementarily, reaction conditions for postcatalytic stereo-correction have also been identified for each catalytic system.

Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation-modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments.

Light Modulated Reversible "On-Off" Transformation of Arylazoheteroarene Based Discotics in Nematic Organization

Three benzene-1,3,5-tricarboxamide (BTA) core-based molecular systems appended with phenylazo-3,5-dimethylisoxazole photoswitches at the peripheral position through variable-length alkoxy chains have been designed and synthesized. The supramolecular interactions of the mesogens provided discotic nematic liquid crystalline assembly as confirmed by polarized optical microscopy (POM) and X-ray diffraction (XRD) studies. Spectroscopic studies confirmed the reversible photoswitching and excellent thermal stability of the photoswitched states in solution phase and thin film. Also, atomic force microscopic (AFM) and POM investigations demonstrated the morphological changes in the self-assembly induced by the photoirradiation as monitored by the changes in the height profiles and optical appearance of the textures, respectively. Remarkably, the liquid crystalline discotic molecules showed reversible "on and off states" controlled by light at ambient temperature.