Structure Of Cis Research Articles

Tuning Intermolecular Interactions for Chiral Analysis: The Microwave Spectra and Molecular Structures of the Chiral Tag Candidates cis- and trans-2-Fluoro-3-(trifluoromethyl)oxirane and Their Gas-Phase Heterodimers with the Argon Atom.

The cis and trans isomers of the chiral tagging candidate molecule, 2-fluoro-3-(trifluoromethyl)oxirane, as well as the lowest energy gas-phase heterodimer of each with the argon atom, are characterized via quantum chemistry calculations and microwave rotational spectroscopy from 5 to 18 GHz and their ground state, vibrationally averaged structures, are determined. Apart from the cis/trans nature of the ring substitution and small differences in the dihedral angle specifying the rotation of the trifluoromethyl group, the two oxirane molecules and their respective argon complexes each have remarkable structural similarity. In contrast, the binding mode of argon to the oxirane, while similar for the two complexes here, is distinct from those modes observed in previous argon-fluorooxirane species. The ability to tune the preferred mode of binding with differing levels of fluorine substitution may prove advantageous in applications of chiral tagging to a wide variety of analytes.

Na[GeF5]·2HF: the first quarternary phase in the H-Na-Ge-F system.

The structure of cis- or trans-bridged [GeF5]- anionic chains have been investigated [Mallouk et al. (1984). Inorg. Chem. 23, 3160-3166] showing the first crystal structures of μ-F-bridged pentafluorogermanates. Herein, we report the second crystal structure of trans-pentafluorogermanate anions present in the crystal structure of sodium trans-pentafluorogermanate(IV) bis(hydrogen fluoride), Na[GeF5]·2HF. The crystal structure [orthorhombic Pca21, a= 12.3786 (3), b= 7.2189 (2), c= 11.4969 (3) Å and Z= 8] is built up from infinite chains of trans-linked [GeF6]2- octahedra, extending along the b axis and spanning a network of pentagonal bipyramidal distorted Na-centred polyhedra. These [NaF7] polyhedra are linked in a trans-edge fashion via hydrogen fluoride molecules, in analogy to already known sodium hydrogen fluorides and potassium hydrogen fluorides.

Ring-chain tautomerism of vicinal hydroxyimines bearing sulfolane moiety

Cyclic sulfones and their derivatives have vast applications in biological, pharmaceutical, medicinal and in many other fields. Herein, we report synthesis of ten new hydroxyimines bearing sulfolane moiety by reaction of cis- and trans-amino alcohols with aromatic aldehydes. An extensive spectroscopic characterization of the products, using 1D and 2D NMR techniques (1H, 13C, NOE, NOESY, COSY, HSQC, HMBC) showed ring-chain tautomerism in deuterochloroform solution for cis-hydroxyimines. The content of the cyclic (1,3-oxazolidine) form increases with increasing electron-withdrawing strength of the substituent in the para position of the benzene ring of the imine. The structure of cis-(3S,4R)-3-hydroxy-4-((E)-(2-hydroxybenzylidene)amino)tetrahydrothiophene 1,1-dioxide was confirmed using XRD analysis. In addition, ADMET properties of products were evaluated in silico and showed high drug similarity.

The Temperature Dependence of Hydrogen Bonds Is More Uniform in Stable Proteins: An Analysis of NMR h3JNC' Couplings in Four Different Protein Structures.

Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC', 2JNC', 3JNCγ, and h3JNC' couplings. The h3JNC' couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC' couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases.

Phosphorylation Mechanism Switching in Histidine Kinases Is a Tool for Fast Protein Evolution: Insights From AlphaFold Models.

Histidine kinases (HKs) are a central part of bacterial environmental-sensing two-component systems. They provide their hosts with the ability to respond to a wide range of physical and chemical signals. HKs are multidomain proteins consisting of at least a sensor domain, dimerization and phosphorylation domain (DHp), and a catalytic domain. They work as homodimers and the existence of two different autophosphorylation mechanisms (cis and trans) has been proposed as relevant for pathway specificity. Although several HKs have been intensively studied, a precise sequence-to-structure explanation of why and how either cis or trans phosphorylation occurs is still unavailable nor is there any evolutionary analysis on the subject. In this work, we show that AlphaFold can accurately determine whether an HK dimerizes in a cis or trans structure. By modeling multiple HKs we show that both cis- and trans-acting HKs are common in nature and the switch between mechanisms has happened multiple times in the evolutionary history of the family. We then use AlphaFold modeling to explore the molecular determinants of the phosphorylation mechanism. We conclude that it is the difference in lengths of the helices surrounding the DHp loop that determines the mechanism. We also show that very small changes in these helices can cause a mechanism switch. Despite this, previous evidence shows that for a particular HK the phosphorylation mechanism is conserved. This suggests that the phosphorylation mechanism participates in system specificity and mechanism switching provides these systems with a way to diverge.

Cis and trans isomers of Ru(III)-based complexes with lapachol: X-ray diffractions and DFT theoretical insights

Lapachol (lap) is widely studied due to its biological application, as well as its importance in the coordination chemistry field. The structure of cis and trans isomers of new ruthenium(III) complex [RuCl2(PPh3)2(lap)] is reported here. The complexes present one molecule of the natural product lapachol, coordinated as bidentate by oxygen atoms, two monodentate triphenylphosphines and two chlorido ligands in a cis or trans configurations. All neutral complexes were characterized by single-crystal X-ray diffraction and these data were compared with Density Functional Theory (DFT) data results. This study highlights the stereochemistry and structural versatility of metal complexes containing lapachol as ligand.

Pb2H2 +: convergent quantum mechanical study of seven lead hydride cation structures. Toward laboratory identification

ABSTRACT Lead is heavily utilised in industry, but it bears potential harm due to its toxic nature. Identifying lead is important in diagnosing and preventing lead poisoning. Hydride generation via inductively-coupled plasma mass spectrometer (HG-ICP-MS) can detect small amounts of lead with high accuracy. Here we investigate seven structures of Pb 2 H 2 + . The geometries of each structure were optimised using coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] method with the cc-pwCVQZ-PP basis set for lead and the cc-pVQZ basis set for hydrogen. Likewise, harmonic vibrational frequencies were obtained using the same method. Anharmonic frequencies were determined using CCSD(T) with cc-pwCVTZ-PP and cc-pVTZ basis sets for lead and hydrogen, respectively. The focal point approach (FPA), including CCSDT and CCSDT(Q) computations, was applied to the seven structures to find the relative energies with respect to the global minimum butterfly structure. Relative to the global minimum butterfly structure, the energies for the planar transition state, monobridged, vinylidene-like, trans, cis, and linear structures are: 1.1, 18.3, 26.5, 27.8, 28.8, and 93.7 kcal mol − 1 , respectively. Natural bond orders and dipole moments are reported as well. The predicted vibrational frequencies should be helpful in guiding the laboratory observation of Pb 2 H 2 + .

Structures and Energetics of E2H3+ (E = As, Sb, and Bi) Cations.

E2H2 (E = As, Sb, Bi) structures involving multiple bonds have attracted much attention recently. The E2H3+ cations (protonated E2H2) are predicted to be viable with substantial proton affinities (>180 kcal/mol). Herein, the bonding characters and energetics of a number of E2H3+ isomers are explored through CCSD(T) and DFT methods. For the As2H3+ system, the CCSD(T)/cc-pVQZ-PP method predicts that the vinylidene-like structure lies lowest in energy, with the trans and cis isomers higher by 6.7 and 9.3 kcal/mol, respectively. However, for Sb2H3+ and Bi2H3+ systems, the trans isomer is the global minimum, while the energies of the cis and vinylidene-like structures are higher, respectively, by 2.0 and 2.4 kcal/mol for Sb2H3+ and 1.6 and 15.0 kcal/mol for Bi2H3+. Thus, the vinyledene-like structure is the lowest energy for the arsenic system but only a transition state of the bismuth system. With permanent dipole moments, all minima may be observable in microwave experiments. Besides, we have also obtained transition states and planar-cis structures with higher energies. The current results should provide new insights into the various isomers and provide a number of predictions for future experiments.

Emerging functions of lycopene in the management of digestive premalignant lesions.

Common digestive precancerous lesions, including oral potentially malignant disorders (OPMDs), gastric ulcers and colorectal adenoma, harbor high risk of cancerous transformation. Early intervention of these lesions is significant to prevent carcinogenesis and improve patients' prognosis. Lycopene, a carotenoid predominantly accumulated in tomatoes, is clinically recommended with its cis structure; as lycopene harbors the most potent antioxidative effects among carotenoids, its chemopreventive effects on the premalignant lesions is noted. Despite several reviews have assessed lycopene's efficacy for OPMDs, emerging studies have reported varying efficacy for digestive precancerous lesion with no comprehensive summary. Therefore, this review initially evaluates the efficacy and underlying mechanisms of lycopene for management of digestive precancerous lesions. According to the included studies, lycopene may show high promise in the management of digestive precancerous lesions, such as relieving mouth opening and burning sensation of oral submucous fibrosis (OSF), presenting potentially equivalent efficacy on managing oral lichen planus (OLP) as steroids and alleviating gastrointestinal precancers' symptoms, meanwhile lowering colon cancer risk. Moreover, its mechanisms for managing digestive precancerous lesions are concretely summarized, including anti-oxidative stress effects, anti-inflammatory response and regulation of cell proliferation and apoptosis, especially its modifications on TLR4/TRIF/NF-κB signaling pathway and p53-dependent cell cycle control and apoptosis. More studies are warranted to confirm its long-term efficacy and preventive role against malignant transformation of digestive precancerous lesions as evidence is insufficient.

Emergence of CuInS2 derived photocatalyst for environmental remediation and energy conversion

Hydrogen production, catalytic organic synthesis, carbon dioxide reduction, environmental purification, and other major fields have all adopted photocatalytic technologies due to their eco-friendliness, ease of use, and reliance on sunlight as the driving force. Photocatalyst is the key component of photocatalytic technology. Thus, it is of utmost importance to produce highly efficient, stable, visible-light-responsive photocatalysts. CIS stands out among other visible-light-response photocatalysts for its advantageous combination of easy synthesis, non-toxicity, high stability, and suitable band structure. In this study, we took a brief glance at the synthesis techniques for CIS after providing a quick introduction to the fundamental semiconductor features, including the crystal and band structures of CIS. Then, we discussed the ways doping, heterojunction creation, p-n heterojunction, type-II heterojunction, and Z-scheme may be used to modify CIS's performance. Subsequently, the applications of CIS towards pollutant degradation, CO2 reduction, water splitting, and other toxic pollutants remediation are reviewed in detail. Finally, several remaining problems with CIS-based photocatalysts are highlighted, along with future potential for constructing more superior photocatalysts.

Conformational analysis of carboxylic acid anhydrides: A microwave and computational study

The microwave spectra of four carboxylic acid anhydrides, RCOOCOR′, (R,R′) = (CH3,CF3), (C(CH3)3,CF3), (C6H5, CF3) and (CH3, C(CH3)3), have been observed in a supersonic jet. Calculations at the M06-2X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory predict the lowest energy conformations for all four species to be nonplanar cis structures, i.e., conformations in which the C=O groups point in approximately the same direction, but are twisted out of a coplanar orientation. The observed spectra are consistent with these predictions. In addition, for all but the (R,R′) = (CH3, C(CH3)3) species, higher energy nonplanar trans conformers are also predicted, typically within 1–2 kcal/mole the nonplanar cis form. For (R,R′)= (C(CH3)3, CF3), extensive isotopic substitution has enabled a determination of most of the (non-fluorine) heavy atom structural parameters. Excellent agreement with the DFT and MP2 structures was obtained, thus validating the theoretical methods used. A strong correlation is found between the calculated O=C⋯C=O dihedral angle and the average of the vapor phase C=O stretching frequencies of RCOOH and R′COOH.

Solvent-Dependent Conformational Switching of N-Methyl-N,N'-diarylsquaramide.

N,N'-Diarylsquaramide and N,N'-dialkylsquaramide are conformationally stable linkers with extended (trans, trans) and folded (cis, cis) structures, respectively, independently of external conditions. Here, we show that N-monomethylated N,N'-diarylsquaramides generally take a (trans, cis) structure in the crystal but show a solvent-dependent conformational equilibrium in solution. In particular, the stable conformer of N-methyl-N,N'-bis(1-naphthyl)squaramide (1f) changes depending upon the solvent. Thus, aromatic N-monomethylated squaramides could find application as components of environment-responsive molecular switches.

Synthesis of oriented J type ZnIn2S4@CdIn2S4 heterojunction by controllable cation exchange for enhancing photocatalytic hydrogen evolution

Construction of semiconductor heterojunctions which promote the separation and transport of photogenerated carriers is an effective strategy for improving photocatalytic reaction efficiency. Based on the anisotropic electrical conductivity of layered ZnIn2S4 (ZIS) photocatalyst, an efficient heterojunction should be constructed along the layer plane of ZIS, that is, a J type heterojunction. However, achieving controllable synthesis of the oriented heterojunction of ZIS faces challenges. Herein, we develop a facile, cost-effective and spatially-selective cation exchange synthesis approach to construct J type ZnIn2S4@CdIn2S4 (J-ZIS@CIS) heterojunction using a flower-like hexagonal ZIS as the parent material. The developed synthesis approach can also control crystal structure of the heterojunction component CIS. This work presents a facile and controllable synthesis strategy to construct oriented anisotropic heterojunctions that are otherwise inaccessible. The as-prepared J-ZIS@CIS heterojunction displays a greatly enhanced photocatalytic hydrogen evolution activity with a rate of 183 μmol h−1, 2.77 times higher than that of pristine ZIS. Furthermore, the possible photocatalytic reaction mechanism is presented for the heterojunction.

Development of visible-light driven photo-switching copolymers with pH indicating performance

Visible-light-driven azobenzene had been reported by theoretical calculation, but could not be detected by any characterization method due to unstable cis structure. Herein, copolymerization was applied to solve the problem based on a time-dependent characteristic of macromolecular motion. Therefore, two copolymers, namely, MRAA-PEG20 copolymer and MRAA-NIPAM copolymer, were synthesized with a definite segment ratio. Both copolymers had photosensitive groups, which were confirmed by UV-vis spectra. Furthermore, copolymer concentration had a linear relationship with absorbance value at 425 nm. Firstly, blue light as an excitation source to induce the isomerization of copolymers. At the same time, repeated interval irradiation was used to evaluate the fatigue performance of the copolymer. Consequently, both copolymers could quickly transform to their cis isomers upon irradiation, which could be reversible recovered to their trans isomers in operable recovery time after removing irradiation. However, the MRAA-PEG20 copolymer had an obvious photobleaching phenomenon along with the circle index, which did not exist in the MRAA-NIPAM copolymer. Secondly, the effects of excitation light source on isomerization were investigated. It was found that blue light was the most efficient excitation source for both copolymers though other light could also induce trans-to-cis transition. Thirdly, the influence of light intensity and temperature was respectively studied. With increasing of light intensity, the absorbance ratio before and after irradiation monotonously decreased, the irradiation response time shortened and the recovery response time prolonged. Moreover, higher temperature resulted in a higher absorbance ratio, shorter irradiation response time, and shorter recovery response time. Finally, synthesized copolymers had characteristic of pH indicator with a critical point of pH 5.0.

Hydrosilylation-Promoted Group Transfer Polymerization of Ethyl Sorbate: A Controlled/Living System Applied to the Synthesis of an α-End Functionalized Polymer and a Triblock Copolymer with a (Meth)acrylate Polymer

The polymerization method, preparation of well-defined (co)polymers, and controlled/living property of ethyl sorbate (ES) have been investigated using hydrosilylation-promoted group transfer polymerization (GTP). The GTP of ES with hydrosilane (R3SiH) was performed in a living manner to produce well-defined poly(ethyl sorbate) (PES) via two methods: single catalyst and catalyst switch. For the single catalyst method, B(C6F5)3 served as the catalyst for the hydrosilylation of ES and R3SiH, yielding silyl ketene acetal (SKA), as well as the polymerization of ES and PES with the trans structure. SKA was prepared using the catalyst switch method via equimolar hydrosilylation with B(C6F5)3, and the phosphazene base of t-Bu-P4 catalyzed the polymerization of ES, yielding PES with cis and trans structures. The kinetic experiments demonstrated that the propagation rate kp for t-Bu-P4-catalyzed GTP is significantly higher than that for B(C6F5)3. The α-end-functionalized PES was synthesized via the hydrosilylation-promoted GTP of ES using a sorbate ester with a functional group as the moisture-stable latent initiator via the catalyst switch method. Furthermore, the controlled/living property has enabled the hydrosilylation-promoted GTP of ES with MMA and n-butyl acrylate (nBA) to produce the AB-diblock copolymer and ABA- and ABC-triblock copolymers composed of PES, PMMA, and PnBA.

Determination of the molecular structure and spectroscopic properties of capsaicin

In this study, the ground state molecular structure and spectroscopic features of cis- and trans-forms of capsaicin were investigated using DFT (B3LYP) invoking 6–311++G(d,p) basis set. The optimized geometry of capsaicin was determined for the isolated molecule in a vacuum, and then the vibrational spectra –IR and Raman-were obtained, and the assignments of fundamental vibrational modes were done. By applying the GIAO method, proton and carbon chemical shifts were computed for the gas and solvated phases. Besides using the TD-DFT, the Hirshfeld surface and Molecular Electrostatic Potential surfaces were obtained and evaluated to understand the electronic properties. The Total and partial density of state (TDOS and PDOS) spectra were also examined. All obtained computational results were compared with the previously reported experimental data. A high accuracy was obtained for the ground state geometrical structure, and thus, the vibrational frequencies especially lie on the finger print region are predicted also with a high correlation. Similarly, the optimization of chemical shift values calculated by considering solvent effects with experimental data were found as high R2 values of 0.9953 and 0.9455 for C and H atoms, respectively. This comparison shows that the DFT method precisely predicts capsaicin's molecular and spectroscopic characteristics.

α-Methylstilbene Isomers: Relationship of Structure to Photophysics and Photochemistry.

Significant differences in the photochemical and photophysical behavior of trans-α-methylstilbene and trans-stilbene have been attributed to structural changes caused by the steric requirements of the methyl group. We present here the X-ray structures of cis- and trans-α-methylstilbene (c- and t-MeSt). This is the first X-ray structure of a cis-stilbene. Despite the pronounced departure from phenyl group coplanarity, the solid-state packing of t-MeSt resembles that of trans-stilbene in that both exhibit disorder with a bicycle pedal structural relationship, dynamic in t-St but static in t-MeSt. We compare the X-ray structures with calculated structures. We also compare our steady state and transient photochemical and spectroscopic results with predictions in a recent theoretical paper that anticipated some of our experiments. Deviations from planarity imposed by the methyl substitution account for the shorter lifetimes of the trans excited states. The rapid torsional relaxation of 1t-MeSt* to the twisted intermediate 1p*, ktp = 2.9 × 1012 s-1, observed using fs transient absorption spectroscopy, explains the sharp decrease in the fluorescence quantum yield of t-MeSt. We correct misconceptions that have appeared in the literature concerning the shape of the stilbene potential energy surface in S1. The nonplanarity due to methyl substitution leads to chirality issues that are relevant in biological molecules such as the protonated Schiff bases of retinal in the opsins.

GPGPU MCII for high-energy implantation

In this paper, we develop a GPGPU acceleration methodology for the Binary-Collision-Approximation based Monte Carlo ion implantation simulation (MCII). Our proposed method avoids the branch-divergence issue which comes from the difference of material crystallinity for the structure with multiple materials. We also introduce an efficient scheme to mitigate the side effect for damage accumulation due to massive parallelization of simulation. Our demonstration of high energy implantation into CIS structure shows almost 40x speed-up compared to CPU implementation of MCII. We conclude that GPU-MCII is effective for acceleration of Monte Carlo simulations with high energy implantation e.g. deep photodiode or well isolation formation.

“On Water” Effect for Green Click Reaction: Spontaneous Polymerization of Activated Alkyne with “Inert” Aromatic Amine in Aqueous Media

“On Water” Effect for Green Click Reaction: Spontaneous Polymerization of Activated Alkyne with “Inert” Aromatic Amine in Aqueous Media

Toward the Observation of the Tin and Lead Analogs of Formaldehyde

Heavy aldehyde and ketone analogues, R2X═O (X = Si, Ge, Sn, or Pb), differ from their R2C═O counterparts due to their greater tendency to oligeramize as the X═O bond polarity increases as one goes down the periodic table. To date, H2Sn═O and H2Pb═O have eluded experimental detection. Herein we present the most rigorous theoretical study to date on these structures, providing CCSD(T)/pwCVTZ fundamental frequencies computed on CCSD(T)/CBS optimized structures for the H2X═O (X = Sn, Pb) potential energy surface. The focal point approach is employed to produce the CCSDTQ/CBS relative energies. For the Sn and Pb structures, the carbene-like cis-HXOH was the global minima, with the trans species being less than 0.6 and 1.1 kcal mol-1 above the cis structures, respectively. The formaldehyde-like H2X═O structure is in an energy well of at least 34.8 and 25.4 kcal mol-1 for Sn and Pb, respectively. Our results provide guidance for future work that may detect H2Sn═O or H2Pb═O for the first time.