Cis-trans Conformation Research Articles

Conformational isomerism breaks the electrolyte solubility limit and stabilizes 4.9 V Ni-rich layered cathodes

By simply increasing the concentration of electrolytes, both aqueous and non-aqueous batteries deliver technical superiority in various properties such as high-voltage operation, electrode stability and safety performance. However, the development of this strategy has encountered a bottleneck due to the limitation of the intrinsic solubility, and its comprehensive performance has reached its limit. Here we demonstrate that the conformational isomerism of the solvent would significantly affect the solubility of electrolytes. By transforming the configuration of solvent from cis-cis to cis-trans upon thermal triggering, we successfully break the solubility limit, and a beyond concentrated electrolyte with the lowest solvent-to-salt molar ratio of 0.70 is constructed. Transitions between cis-cis and cis-trans conformers are observed through Nuclear Magnetic Resonance (NMR) testing. The electrolyte consists entirely of anion-mediated solvation structures and promotes the formation of robust inorganic-dominated cathode electrolyte interphase. As a result, it enables stable cycling of 4.9 V-class LiNi0.8Co0.1Mn0.1O2 positive electrodes. Moreover, a high capacity of 151.2 mAh g−1 can be maintained after 1000 cycles at cut-off voltage of 4.8 V. This work provides a chemical pathway to build new concept electrolytes working under harsh conditions.

Stimulus-Induced Dynamic Behavior Regulation of Flexible Crystals through the Tuning of Module Rigidity.

Introducing dynamic behavior into periodic frameworks has borne fruit in the form of flexible porous crystals. The detailed molecular design of frameworks in order to control their collective dynamics is of particular interest, for example, to achieve stimulus-induced behavior. Herein, by varying the degree of rigidity of ditopic pillar linkers, two isostructural flexible metal-organic frameworks (MOFs) with common rigid supermolecular building bilayers were constructed. The subtle substitution of single (in bibenzyl-4,4'-dicarboxylic acid; H2BBDC) with double (in 4,4'-stilbenedicarboxylic acid; H2SDC) C-C bonds in pillared linkers led to markedly different flexible behavior of these two MOFs. Upon the removal of guest molecules, both frameworks clearly show reversible single-crystal-to-single-crystal transformations involving the cis-trans conformation change and a resulting swing of the corresponding pillar linkers, which gives rise to Flex-Cd-MOF-1a and Flex-Cd-MOF-2a, respectively. Strikingly, a more favorable gas-induced dynamic behavior in Flex-Cd-MOF-2a was verified in detail by stepwise C3H6/C3H8 sorption isotherms and the corresponding in situ powder X-ray diffraction experiments. These insights are strongly supported by molecular modeling studies on the sorption mechanism that explores the sorption landscape. Furthermore, a consistency between the macroscopic elasticity and microscopic flexibility of Flex-Cd-MOF-2 was observed. This work fuels a growing interest in developing MOFs with desired chemomechanical functions and presents detailed insights into the origins of flexible MOFs.

A hit expansion of 3-benzamidopyrazine-2-carboxamide: Towardinhibitors of prolyl-tRNA synthetase with antimycobacterial activity.

This study presents an exploration of the chemical space around derivatives of 3-benzamidopyrazine-2-carboxamides, previously identified as potent antimycobacterial compounds with predicted binding to mycobacterial prolyl-transfer RNA synthetase. New urea derivatives (Series-1) were generally inactive, probably due to their preference for cis-trans conformation (confirmed by density functional theory calculations and experimentally by nuclear overhauser effect spectroscopy NMR). Series-2 (3-benzamidopyrazine-2-carboxamides with disubstituted benzene ring) demonstrated that substituents larger than fluorine are not tolerated in the ortho position of the benzene ring. This series brought two new compounds (21: R = 2-F, 4-Cl and 22: R = 2-F, 4-Br) with in vitro activity against Mycobacterium tuberculosis H37Rv as well as multidrug-resistant clinical isolates, with minimum inhibitory concentration ranging from 6.25 to 25 μg/mL. The lactone-type derivatives 4H-pyrazino[2,3-d][1,3]oxazin-4-ones (Series-3) were inactive, but solvent stability studies of compound 29 indicated that they might be developed to usable lactone prodrugs of inhibitors of mycobacterial aspartate decarboxylase (PanD).

Photoresponsive Viscoelasticity of the Granular Materials of Azobenzene-Bearing Molecular Nanoparticles.

The large sizes of granular particles lead to their slow diffusive dynamics and significant interparticle friction, bringing enormous difficulty to tune the mechanical properties and processability of the granular materials (GMs). Herein, 1 nm polyhedral oligomeric silsesquioxane (POSS) particles functionalized with azobenzene are designed as structural units, and the obtained GMs show unique photoswitchable viscoelasticity. The azobenzene group can undergo a reversible trans-cis conformation switch while the π-π stacking among the azobenzene fragments is only favored by the trans-conformation due to molecular geometrical requirements. The POSS units from neighboring assemblies close pack to form microdomains, and the POSS is under confinement by both the supramolecular bonding and the other POSS in the microdomains. The simultaneous breaking of the two types of confinement is difficult and, therefore, the free diffusion of POSS is hindered, leading to the elasticity of the GMs of trans-POSS. For cis-POSS, the interparticle supramolecular interaction is weak and the POSS unit can undergo free diffusion, contributing to their high flowability at room temperature. The photoswitching viscoelasticity of GMs is further used for self-healing and photoswitchable adhesion. This work paves new pathways for the regulation of material viscoelasticity and the design of GM-based smart materials.

Conformer-Specific Photoelectron Spectroscopy of Carbonic Acid: H2CO3.

Carbonic acid (H2CO3) is a fundamental species in biological, ecological, and astronomical systems. However, its spectroscopic characterization is incomplete because of its reactive nature. The photoionization (PI) and the photoion mass-selected threshold photoelectron (ms-TPE) spectra of H2CO3 were obtained by utilizing vacuum ultraviolet (VUV) synchrotron radiation and double imaging photoelectron photoion coincidence spectroscopy. Two carbonic acid conformers, namely, cis-cis and cis-trans, were identified. Experimental adiabatic ionization energies (AIEs) of cis-cis and cis-trans H2CO3 were determined to be 11.27 ± 0.02 and 11.18 ± 0.03 eV, and the cation enthalpies of formation could be derived as ΔfH°0K = 485 ± 2 and 482 ± 3 kJ mol-1, respectively. The cis-cis conformer shows intense peaks in the ms-TPES that are assigned to the C=O/C-OH stretching mode, while the cis-trans conformer exhibits a long progression to which two C=O/C-OH stretching modes contribute. The TPE spectra allow for the sensitive and conformer-selective detection of carbonic acid in terrestrial experiments to better understand astrochemical reactions.

Elucidating photocycle in large Stokes shift red fluorescent proteins: Focus on mKeima.

Large Stokes shift red fluorescent proteins (LSS-RFPs) are genetically encoded and exhibit a significant difference of a few hundreds of nanometers between their excitation and emission peak maxima (i.e., the Stokes shift). These LSS-RFPs (absorbing blue light and emitting red light) feature a unique photocycle responsible for their significant Stokes shift. The photocycle associated with this LSS characteristic in certain RFPs is quite perplexing, hinting at the complex nature of excited-state photophysics. This article provides a brief review on the fundamental mechanisms governing the photocycle of various LSS-RFPs, followed by a discussion on experimental results on mKeima emphasizing its relaxation pathways which garnered attention due to its >200 nm Stokes shift. Corroborating steady-state spectroscopy with computational studies, four different forms of chromophore of mKeima contributing to the cis-trans conformers of the neutral and anionic forms were identified in a recent study. Furthering these findings, in this account a detailed discussion on the photocycle of mKeima, which encompasses sequential excited-state isomerization, proton transfer, and subsequent structural reorganization involving three isomers, leading to an intriguing temperature and pH-dependent dual fluorescence, is explored using broadband femtosecond transient absorption spectroscopy.

Manipulating Cis-Trans Copolymer Chain Conformation to Simultaneously Improve Permittivity and DC Breakdown Strength in Polythiourea.

Polythioureas (PTUs) show great potentials for applications in the new generation of film capacitors due to their excellent dielectric properties. Herein, the cis-trans copolymer chain of PTU is successfully tailored by employing cis and trans cyclohexyl spacers. The relationship between the copolymer chain conformation, microstructure, and dielectric properties is carefully explored by a series of analysis. Compared with cis conformation, the trans with less steric hindrance can promote the formation of H-bonds. The enhanced H-bonding interactions not only reduce the molecular inter-chain spacing, but also drive the self-assembly of molecular chains to form cylindrical and droplet nano-morphologies. The phase separation between cis and trans PTUs is confirmed by combining the experimental results of TEM and DSC, and the CT64-PTU with the most two-phase interface thus obtains the highest permittivity of 5.5 (@10Hz). The reduced molecular inter-chain spacing is accompanied by a decreased hopping distance of charges, which improves breakdown strength by 17% from 498 MV/m to 580 MV/m. Therefore, the cis-trans copolymer chain conformation in PTU provides a simultaneous high permittivity and breakdown strength. This research offers a strategy to further design high-performance dielectrics via regulation of copolymer chain conformation.

New line intensities for the far infrared bands of the Trans- and Cis-conformer of nitrous acid (HONO), new determination of the Trans-Cis conformer barrier and its impact on the astrophysical detection of nitrous acid in protostellar clouds

The first goal of this work is to improve the determination of the energy difference (ΔECis-Trans) between the ground vibrational state of the Cis- and Trans-HONO conformers of nitrous acid. For this, high resolution spectra were recorded in the 50–200 cm−1 spectral region at three different temperatures, 240, 270 and 296 K. The relative line intensities for the B-type transitions of pure rotational bands of Trans-HONO and Cis-HONO achieved from our measurements were combined in least squares fit computations to those measured previously by Sironneau et al. [Sironneau V, Flaud JM, Orphal J, Kleiner I, Chelin P. Absolute line intensities of HONO and DONO in the far-infrared and re-determination of the Energy Difference between the trans- and cis-species of nitrous acid. J Mol Spectrosc 2010;259:100–104]. In this way, we can significantly improve the accuracy on the HONO conformer energy difference, with a value for ΔECis-Trans = 95.8 ± 9.2 cm−1 compared to SIRΔECis-Trans = 99 ± 25 cm−1 in the previous study of Sironneau et al. The second goal is to generate a line list with “absolute” line intensities for the pure rotational bands in the far infrared region of Trans-HONO and Cis-HONO, with both A- and B-type transitions. This new line list proved to be more robust for an improved detection of HONO in astrophysical objects [Coutens A, Ligterink NFW, Loison JC, Wakelam V, Calcutt H, Drozdovskaya MN, Jørgensen JK, Müller HSP, Van Dishoeck EF, Wampfler SF. The ALMA-PILS survey: First detection of nitrous acid (HONO) in the interstellar medium. Astronomy & Astrophysics 2019;623:L13].

Conformational study into N-alkyl-N′-aryl ureas to inform drug discovery

Ureas are an important functional group in small molecule drugs as well as having wider applications in organic chemistry. Understanding of their conformation is of critical importance for rational design of urea-containing bioactive compounds. Whilst the conformational preferences of biaryl ureas have been extensively studied, very little attention has been paid to alkylated analogues. We carried out a systematic study of N-aryl (phenyl and pyridyl)-N′-cyclopentyl ureas with differing N-methylation patterns using Well Tempered Metadynamics at a semi-empirical level in implicit water (GBSA) using Well-Tempered Metadynamics to generate their conformational free-energy landscapes. Geometries and energetics of the most relevant configurations are further refined using DFT level of theory. Validation for the computation was obtained by synthesis of all 8 analogues followed by conformational studies by X-ray crystallography and NMR. These findings reveal that the methylation pattern significantly affects the conformational preference of the system. Most notably, N-phenyl-N′-cyclopentyl urea is shown to adopt both the trans–trans, and cis–trans conformations with equal energy and that the cis–trans conformation can be significantly stabilised by the presence of an internal hydrogen bond to the N′-hydrogen. This study will be of utility for the design of N-alkyl-N′-aryl ureas as drug candidates.

Solution structures and thermodynamics of cis-trans X-Pro conformers of a novel single disulfide conopeptide

Solution structures and thermodynamics of cis-trans X-Pro conformers of a novel single disulfide conopeptide

Molecular-Level Control over Oxygen Transport and Catalyst–Ionomer Interaction by Designing Cis–Trans Isomeric Ionomers

We here demonstrate a monographic study to investigate the effects of cis–trans conformation on the properties of anion exchange ionomers for the first time. Twisted cis-conformation possessed of abundant subnanoscale free volume cavities facilitates oxygen permeability and water adsorption. Moreover, its nonplanar conformation can alleviate the undesirable absorption of ionomer on Pt and Pt–Ru surfaces, thus improving the electrochemical performance of the catalyst layers. Theoretical and electrochemical investigations are mutual corroborations, demonstrating our proof-of-concept. The catalyst layer equips cis-ionomer showing 51% and 54% increases in limiting current density and electrochemically active surface area. The H2/O2 single-cell peak power density of the cis-membrane electrode assembly (c-MEA) is increased by 56% (1.0 vs 0.64 W cm–2) compared with that of the t-MEA at 100% relative humidity (RH). Moreover, the performance of c-MEA is particularly prominent at low humidity (increased by 114% and 113% at 80% and 60% RH, respectively).

Matrix Isolation Study of Fumaric and Maleic Acids in Solid Nitrogen.

Fumaric and maleic acids ((E)- and (Z)-HOOC-CH═CH-COOH, FA and MA) were studied experimentally by infrared spectroscopy in nitrogen matrixes and theoretically by quantum chemical calculations. The calculations, carried out at the DFT(B3LYP) and MP2 levels of theory, predicted the existence of at least 5 conformers of maleic acid and 10 conformers of fumaric acid. After the deposition of the matrixes, two conformers of maleic acid (I and II) and three conformers (I-III) of fumaric acid were observed and characterized vibrationally. Selective narrowband near-infrared (NIR) excitation of the first OH stretching overtones of the different conformers of maleic and fumaric acids initially present in the matrixes allowed the generation of higher-energy forms, never before observed experimentally. In the case of maleic acid, conformers I (a cis-trans form, where cis and trans designate the conformation of the carboxylic groups of the molecule) and II (cis-cis) were found to generate the novel conformers VI (trans-trans) and VII (cis-trans), respectively. The conversion of conformer II into the most stable conformer I was also observed. For fumaric acid, the cis-cis conformers I-III were found to give rise to the new cis-trans conformers IV-VII, respectively. The tunneling decay of the new conformers produced upon NIR excitation of the lowest-energy conformers initially trapped in the matrixes was observed, and their lifetimes in solid N2 were determined. The increased stability of all of the observed high-energy conformers of the studied acids in the N2 matrix, compared to the argon matrix, where they could not be observed experimentally, demonstrates the stabilizing effect of the interaction between the OH groups of the acids with the matrix N2 molecules, in line with previous observations for other carboxylic acids. In addition, the photochemistry of matrix-isolated maleic and fumaric acids upon broad-band UV irradiation (λ > 235 nm) was also investigated. UV-induced isomerization of both acids around the C═C double bond was observed, together with their decarboxylation to acrylic acid.

Rhodium(0) nano particles within an organic cage with better durability and gated activity for hydrogen generation reaction

Stable and catalytically active nano particles with small sizes are of paramount importance in catalysis, but the preparation of such particles has been a great challenge due to their propensity to aggregate into large and less active particles. Herein, we would like to report the formation of ultra-small and uncommon RhO2 particles within an organic cage in the homogeneous solution, and the soluble assembly showed both better durability and high activity towards ammonia borane methanolysis to generate hydrogen gas. A volcanic plot of the turnover frequencies (TOFs) over the molar amount of Rh per cage was demonstrated, and RhO2-30@COP1-T showed a TOF of around 286 min−1 at room temperature. Our assembly also showed better durability during the catalysis in contrast to NPs made from pure rhodium acetate, and there was no aggregation formed after five runs. We further demonstrated the Michaelis-Menten model through the kinetic study, an indication that the catalytic reaction happened within the organic cage. The actual active sites of the catalyst was zero-valent metal Rh. Interestingly the installation of azobenzene groups at the opening of the cage led to gated activity through the trans-cis conformation interchange, due to the different steric hindrances affecting the diffusion rates of reactants.

Evaluation of oxygen partial pressure, temperature and stripping of antioxidants for accelerated shelf-life testing of oil blends using 1H NMR

Lipid oxidation compromises the shelf-life of lipid-containing foods, leading to the generation of unpleasant off-flavours. Monitoring lipid oxidation under normal shelf-life conditions can be time-consuming (i.e. weeks or months) and therefore accelerated shelf-life conditions are often applied. However, little is known on their impact on the lipid oxidation mechanisms. In this study, different oxygen partial pressures (PO2; 10 and 21%), temperatures (20, 30 and 40 °C), and the removal of antioxidants through stripping of the oil were tested to accelerate lipid oxidation. Increasing the incubation temperature of stripped oil blends from 30 to 40 °C reduced the onset of lipid oxidation from 4 to 2 weeks, whereas the PO2 had no impact. Surprisingly, at room temperature, an increase in PO2 resulted in a longer onset time (10 weeks under 10% oxygen, 15 weeks under 21% oxygen). We hypothesize that this is due to a shift in (initiation) mechanism. In non-stripped oil, an increase in PO2 from 10 to 21% decreased the onset time from 16 to 10 weeks (40 °C). Temperature elevations and stripping led to a shift towards more trans–trans diene hydroperoxides, as compared to the cis–trans conformation. Additionally, oil stripping led to an increase in oxidized PUFAs with three or more double bonds in which the hydroperoxide group is located between the double bond pattern, instead of on the edge of it. Lastly, it was shown that small additions of LC-PUFAs (0, 0.3, 0.6, 1.2 and 2.3%, w/w) accelerate lipid oxidation, even in relatively stable stripped oils. In conclusion, increased PO2 and slightly elevated temperatures hold fair potential for accelerated shelf-life testing of non-stripped oils with a limited impact on the lipid oxidation mechanisms, whereas stripping significantly changes propagation mechanisms.

Theoretical investigation of the structural and electronic features of SLC-0111, a novel inhibitor of human carbonic anhydrase IX, and its anion

The various tautomers and conformers of SLC-0111, a well-known biologically potent compound, have been investigated using density functional theory (DFT) calculations in the gas phase and aqueous solution. The amide form is found to be the only stable tautomeric form in both the phases, with the trans-cis conformer as the most stable structure in the gas phase and the trans-trans conformer in aqueous solution. The deprotonation of the sulfonamide nitrogen leading to the formation of the SLC-0111 anion occurs at pH > 10. The various intramolecular interactions and reactivity of the molecule have been characterized using natural bond orbital (NBO) analysis and calculation of global reactivity parameters. The effect of the solvent polarity on the energies and nature of the frontier molecular orbitals has been investigated for both the neutral and anionic forms. Further, the electronic spectra and vibrational spectra of both the states have also been computed and the effect of changing solvents on the electronic spectra has been investigated. The calculated nonlinear optical (NLO) properties of the molecule show that the molecule has potential to be featured as an NLO material.

Fabrication of Soft-Oxometalates {Mo132} Clusters With Novel Azobenzene Surfactants: Size Control by Micelles and Light.

Soft-oxometalates (SOMs) are colloid suspensions of superstructured assemblies of polyoxometalates (POMs) and are found to be very effective photo-catalysts in a number of chemical reactions. The stabilization of SOMs generally requires legends or stabilizers, e.g., polymers and surfactants. In this paper, a light responsive azobenzene surfactant, C10AZOC2N3, was developed and used to stable {Mo132} SOMs. Various techniques such as Dynamic light scattering, TEM, UV-Vis spectra and cyclic voltammetry were employed to characterize the experimental results. The outstanding structure-directing effect of surfactant self-assembly micelles in solution on inorganic counter-anions was demonstrated. Different amount of cyclohexane was solubilized into C10AZOC2N3 micelles to successfully control the size of {Mo132} SOMs cluster. Furthermore, the clusters exposed to UV light for a certain time can be served as a second trigger to control the size of SOMs due to the trans-cis conformation transition of surfactant molecules. The redox potentials of C10AZOC2N3-{Mo132} SOMs were investigated as the cluster size varied. Interestingly, the redox potential of {Mo132} was not affected by the cluster size, indicating that the presence of surfactant did not change the main function of {Mo132} as an electrochemical catalyst, but merely assisted in the size control of SOM aggregation.

Why Does Dimethyl Carbonate Dissociate Li Salt Better Than Other Linear Carbonates? Critical Role of Polar Conformers.

The marked difference in the ionic conductivities of linear carbonate (LC) electrolyte solutions despite their similar viscosities and permittivities is a long-standing puzzle. This study unraveled the critical impact of solvent conformational isomerism on salt dissociation in 0.1-3.0 M LiPF6 dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC) solutions using Raman and dielectric relaxation spectroscopies. The extent of salt dissociation in the LC solutions, which decreased in the order DMC > EMC > DEC, is closely related to the fraction of polar cis-trans LC conformers, as this conformer participates in Li ion solvation more readily than the nonpolar cis-cis counterpart. Our first-principles calculations corroborated that the cis-trans conformer facilitates free ion formation more than the cis-cis conformer, and the extent of this effect decreased in the order DMC > EMC > DEC. This study provides an avenue for the design of highly conductive electrolytes by exploiting the conformational isomerism of solvent molecules.

Why Dimethyl Carbonate Is Better Co-Solvent Than Other Linear Carbonates: Important Role of Polar Conformer Formation

The underlying nature of the ion conduction in concentrated battery electrolytes still remains elusive. An archetypal example is a long-standing puzzle why a dimethyl carbonate (DMC) solution exhibit higher ionic conductivity than other linear carbonate (LC) solutions despite the similar physicochemical properties of the LC solvents. To address this, we investigate the correlation between the conformation isomer formation and salt dissociation behavior in 0.1 M–3.0 M LiPF6 DMC, ethyl methyl carbonate, and diethyl carbonate solutions using Raman spectroscopy, dielectric relaxation spectroscopy, and pfg-NMR. Importantly, we corroborate that compared to the other two LCs, DMC more readily dissociates Li-salt into free, conducting ions. The higher salt-dissociation ability of DMC was attributed to the extensive formation of polar cis-trans conformer participating in Li-ion solvation compared to non-polar cis-cis conformer. This study unveils the critical role of the solvent isomerism in the ion-solvation chemistry, suggesting an avenue to achieve highly conductive electrolytes for rechargeable batteries.

DFT Investigation on the Electronic Properties and Intramolecular Hydrogen Bond of Trans-Cisand Cis-TransMethyl Substituted N-Benzoyl-N’-(2-pyridyl)thiourea

Five single molecule methyl substituted Benzoyl pyridinylthiourea compounds namely N-benzoyl-N’-(2-pyridyl)thiourea, N-benzoyl-N’-(6-methyl-2-pyridyl)thiourea, N-benzoyl-N’-(5-methyl-2-pyridyl)thiourea, N-benzoyl-N’-(4-methyl-2-pyridyl) thiourea and N-benzoyl-N’-(3-methyl-2-pyridyl)thiourea are investigate theoretically for trans-cis and cis-trans conformation at B3LYP 6-31G(d,p) level of theory. Electronic properties have been analyzed by Gaussian 09W package and AIMAll code. Methyl substituent and its position give noticeable effect to reactivity, stabilization, and hydrogen bond interaction strength. AIM prove that 6-methyl substituted on pyridyl ring has significant effect to preferent conformation.

Effects of cis-trans Conformation between Thiophene Rings on Conductance of Oligothiophenes.

Oligothiophenes have been established as important π-conjugated frameworks in organic electronics and molecular electronics. Although oligothiophenes possess the rotational flexibility of thiophene rings, the effects of cis-trans conformations on their electrical conductance have not been investigated yet. To investigate the effects of cis-trans conformations between thiophene rings on the conductance of oligothiophenes, we performed first-principles transport calculations. The conductance of the cis-oligothiophene was calculated to be higher than that of trans-oligothiophene, because the highest occupied molecular orbital was closer to the Fermi level of the gold electrode in the cis isomer than the trans isomer. This prediction was confirmed through mechanically controllable break junction measurements and fitting of the current-voltage characteristics for the newly synthesized, insulated oligothiophenes with controlled cis-trans conformations. This study demonstrates that cis- and trans-conformations can affect the electrical properties of oligothiophene frameworks and can potentially be used to control the electronic structure of long oligothiophene molecular wires.