Structure Of Cis Research Articles

Development of a novel carboplatin like cytoplasmic trackable near infrared fluorophore conjugate via strain-promoted azide alkyne cycloaddition

The successful design and pre-clicked synthesis of a non-toxic and cytosol trackable carboplatin-like near infrared fluorophore conjugate via strain-promoted azide alkyne cycloaddition (SPAAC) is reported. Reaction of cis-[Pt(2-azidopropane-1,3-diamine)(cbdca)] (cbdca = cyclobutane-1,1-dicarboxylato) and a bicyclo[6.1.0]non-4-yne near-infrared (NIR) azadipyrromethene fluorophore gave the corresponding clicked Pt-Fluorophore conjugate. The X-ray crystal structure of cis-[Pt(2-azidopropane-1,3-diamine)(cbdca)] was determined featuring the azide on the bidentate 1,3-diaminopropane ligand. The Pt-fluorophore conjugate is the first example of a Pt conjugate clicked via strain-promoted azide alkyne cycloaddition (SPAAC) where the reactive azide handle is on the amine carrier ligand. The in vitro cytotoxicity and widefield fluorescence imaging of the Pt-Fluorophore conjugate in A2780P and A2780cisR cells are described.

Powder X-ray diffraction structural characterization of the coordination complex cis-[Co(κ2N,N′-1,10-phenanthroline-5,6-dione)2Cl2

The reduction of cis-[CoIII(κ2N,N′-1,10-phenanthroline-5,6-dione)2Cl2]Cl into the neutral compound cis-[CoII(κ2N,N′-1,10-phenanthroline-5,6-dione)2Cl2] was observed during developmental studies of new antimalarial drugs. The crystal structure of cis-[CoII(κ2N,N′-1,10-phenanthroline-5,6-dione)2Cl2] was unveiled by powder X-ray diffraction studies (PXRD). PXRD details, unit cell parameters, and space group for cis-[CoII(κ2N,N′-1,10-phenanthroline-5,6-dione)2Cl2], C24H12Cl2CoN4O4, are reported [a = 41.4951 (13) Å, b = 8.2768 (2) Å, c = 12.4994 (3) Å, unit cell volume V = 4292.9 (2) Å3, Z = 8, and space group Fdd2]. Infrared spectroscopy features are also discussed.

The Molecular Structure of gauche‐1,3‐Butadiene: Experimental Establishment of Non‐planarity

AbstractThe planarity of the second stable conformer of 1,3‐butadiene, the archetypal diene for the Diels–Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis‐1,3‐butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche‐ and trans‐butadiene provides an opportunity to examine the effects of conjugation and steric interactions.

The Molecular Structure of gauche-1,3-Butadiene: Experimental Establishment of Non-planarity.

The planarity of the second stable conformer of 1,3-butadiene, the archetypal diene for the Diels-Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis-1,3-butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche- and trans-butadiene provides an opportunity to examine the effects of conjugation and steric interactions.

New transition metal complexes of 2,4-dihydroxybenzaldehyde benzoylhydrazone Schiff base (H2dhbh): Synthesis, spectroscopic characterization, DNA binding/cleavage and antioxidant activity

New complexes [VO2(Hdhbh)] (1), [VO(phen)(dhbh)].1.5H2O (2), [Zn(Hdhbh)2] (3), [MoO2(dhbh)(D)] (D = H2O (4) or MeOH (5)), [Ru(PPh3)(dhbh)Cl(H2O)] (6), and [Pd(Hdhbh)Cl]·H2O (7) (H2dhbh = Schiff base derived from 2,4-dihydroxybenzaldehyde and benzoylhydrazone) have been isolated and characterized by IR, 1H NMR, Mass, UV–Visible and ESR spectroscopy. They were also investigated by cyclic voltammetry, thermal and magnetic measurements and the structure of complex cis-[MoO2(dhbh)(H2O)] (4) was solved by X-ray crystallography. Analytical data showed that H2dhbh behaves as monobasic/or dibasic tridentate ligand via phenolate O, azomethine N and amide O/or deprotonated amide O atoms. Antioxidant activity of the complexes has been evaluated against DPPH (2,2-diphenyl-1-picrylhydrazyl) radical and it has been found that oxovandium (IV) complex (2) displays the highest radical scavenging potency comparable to ascorbic acid as a standard antioxidant. The DNA binding properties of the ligand and its complexes have been investigated by electronic spectroscopy together with DNA cleavage by gel electrophoresis whose results showed also that vanadium (IV) complex (2) has a significant oxidative cleavage among other complexes.

Solid-state structure of cyclic dipeptides: an X-ray and computational study of cis- and trans-diketopiperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines

Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the β, γ or δ position) or thia-proline (with sulfur in the β or γ position) and N-methyl phenylalanine [(NMe)Phe]: cyclo[(β-S)Pip-(NMe)Phe], cyclo[(γ-S)Pip-(NMe)Phe], cyclo[(δ-S)Pip-(NMe)Phe], cyclo[(β-S)Pro-(NMe)Phe] and cyclo[(γ-S)Pro-(NMe)Phe] were determined with X-ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H...O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non-planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell (Z′ > 1), though in some cases a correlation is observed.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

Synthesis, X-ray structure, spectroscopic, DFT study and catalytic activity of cis-[RuCl2(L)(EPh3)] complexes (E = P, As, Sb; L = NN′N″ tridentate azoimine-quinoline ligands)

Abstract New of complexes of formula cis-[RuCl2(L)(PPh3)] (C1–C5) where L = XC6H4N NC(COCH3) NC9H6N, X = H, L1 (C1); CH3, L2 (C2); Br, L3 (C3); CN, L4 (C4), F, L5 (C5)} and cis-[RuCl2(L1)(EPh3)] where E = As (C6); E = Sb (C7) have been synthesized by refluxing [RuCl2(EPh3)3 ] and L in a mixture of (5:1) chloroform/ethanol solution. The complexes have been characterized by the spectroscopic techniques (IR, NMR and UV–Vis) and geometries have been confirmed by X-ray crystal structures of cis-[RuCl2(L3)(PPh3)] (C3). The electronic structure, redox and absorption properties of the complexes have been explained based on DFT and TDDFT results. Cyclic voltammetric studies show one reversible Ru(III)/Ru(II) oxidation couple and two successive one electron reductions leading to the formation of L(0/−1) and L(−1/−2), respectively. The complexes cis-[RuCl2(L)(EPh3)](C1–C7) catalyze the transfer hydrogenation of acetophenone in 2-propanol at 86 °C and in the presence NaOCH3.

Infrared-Vacuum Ultraviolet Spectroscopic and Theoretical Study of Neutral Methylamine Dimer.

The methylamine dimer, (CH3NH2)2, is a model system to study the CH3 and NH2 spectral patterns in the neutral microsolvated systems relevant to chemical biology, atmospheric chemistry, and catalysis. We report infrared-vacuum ultraviolet spectroscopic measurements to probe the neutral (CH3NH2)2. Quantum chemical calculations and ab initio molecular dynamics simulations were performed to understand the observed spectral features. Experimental and theoretical results indicate the likely coexistence of both cis and trans structures. A salient feature of this work is that the peak widths are not significantly affected by the structural transformation and the fluctuation of hydrogen bond distance, allowing the stretching modes to be clearly resolved.

A theoretical study of the structural and electronic properties of trans and cis structures of chlorprothixene as a nano-drug

Geometrical structure, electronic and optical properties, electronic absorption spectra, thermodynamic properties, natural charge distribution, MEP analysis, and charge transfer analysis of trans and cis structures of chlorprothixene drug have been investigated with DFT and TDDFT methods. The results of the computations show that the calculated quantum quantities of the cis isomer of chlorprothixene are in agreement with the activity of cis-chlorprothixene as a drug. Cis structure of chlorprothixene has slightly better absorption properties than the trans structure on the basis of TDDFT calculations. The NLO quantities of the cis structure are higher than the trans structure, and the chemical hardness of the cis isomer, is smaller than the trans isomer which specifies that the reactivity and charge transfer of the cis structure of chlorprothixene is higher than the trans structure. The MEP maps of both conformations of chlorprothixene show that the top of the N atom and the around of the S and Cl atoms of the molecule are proper regions for electrophilic reactions. The calculated thermodynamic parameters illustrate that these parameters are improving with increasing temperature because of the enhancement of molecular vibrational intensities with temperature.

Polymorphism in cis–trans Muconic Acid Crystals and the Role of C–H···O Hydrogen Bonds

Cis–trans isomerization of muconic acid is an important component of various chemical syntheses. Despite the existence of three geometric muconic acid isomers, little atomically precise information is actually known of their structures. In this work, the complete crystal structures of cis–cis, cis–trans, and trans–trans muconic acid were determined via single-crystal X-ray diffraction and then further analyzed using terahertz vibrational spectroscopy and solid-state density functional theory. In addition to being the first reported crystal structure for cis–trans muconic acid, two polymorphs of this species were discovered, with one exhibiting a two-dimensional hydrogen-bonding pattern stabilized through C–H···O interactions. Terahertz spectroscopy aided in polymorph characterization and also provided clear evidence of a hydrated crystalline species that grows only from one of the cis–trans muconic acid polymorphs. Ab initio simulations showed that while the typical end-to-end hydrogen-bonding motif found...

Versatile Reactivity of Cyclic 1,2-Dimethylhydrazinodiphosphines

A versatile reactivity from the cage compound P(NMeNMe)3P is presented. The Staudinger reaction with Me3SiN3 is carried out. The crystal structure of the compound issued from the reaction on both sides (Me3SiN=P(NMeNMe)3P=NSiMe3) is reported. When the reaction occurs on only one side, the remaining free phosphorus atom is complexed with RuCl2(p-cymene). P(NMeNMe)3P reacts with PCl3, leading to the heterocyclic compound ClP(NMeNMe)2PCl. This heterocycle also displays a versatile reactivity. Substitution reaction with HNiPr2 leads to iPr2NP(NMeNMe)2PNiPr2. Very complex 1H and 13C NMR spectra suggest that the cis isomer is the largely major isomer of this compound. The cis structure is confirmed by X-ray diffraction. Besides the reaction on the P–Cl functions, the reaction on the lone pair of ClP(NMeNMe)2PCl is carried out, leading to the complex (p-cymene)Cl2RuPCl(NMeNMe)2ClPRuCl2(p-cymene). Characterization of this compound by X-ray diffraction displays a cis isomer for this compound also.

Computational investigation of structural and electronic properties of cis and trans structures of fluvoxamine as a nano-drug

In this study, geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, thermodynamic properties, natural charge distribution and MEP analysis of trans and cis structure of fluvoxamine medicine have been studied by quantum chemical calculations using density functional theory (DFT) and time-dependent DFT (TDDFT) method with the B3LYP hybrid functional and 6-311+G∗∗ basis set. The results of the calculations show that trans structure of fluvoxamine has convenient quantum chemical properties to verify that this structure of the molecule is marked as a medicine. The relative energies of trans and cis structures of fluvoxamine shows that the trans structure is more stable than the cis form with a small energy difference. TDDFT calculations display that trans structure of fluvoxamine has the best absorption properties. The calculated NLO properties confirm that the NLO properties of trans structure of fluvoxamine are higher than the cis structure, and the chemical hardness of the trans structure, is lower than the cis structure that shows that the reactivity and charge transfer of trans-fluvoxamine is higher than cis-fluvoxamine. The MEP maps of trans and cis structures of fluvoxamine illustrate that there are some possible region for electrophilic and nucleophilic reactivity. The calculated thermodynamic parameters are increasing with enhancing temperature. The vibrational frequencies of the two configurations of fluvoxamine demonstrate that both structures of fluvoxamine have practically comparable modes of vibrations, but the trans conformation of fluvoxamine is better in agreement with the experiment.

Survey of content of trans-fatty acids in meat

Trans-fatty acids are a type of unsaturated fatty acid in which the double bonds have a trans structure, as opposed to the cis structure often found in nature. Natural types of trans-fatty acids are produced in the first stomach (rumen) of ruminant animals and are known to accumulate in the milk and meat of these animals. A large-scale epidemiological survey in Europe and the U.S.A. has suggested that excessive intake of trans-fatty acids increases the risk of coronary heart disease. We have performed a comprehensive study of the amount of trans-fatty acids present in meat circulating throughout Japan to assess the current amounts of trans -fatty acids. The results reveal that the amount of trans-fatty acids in the type of beef (lean and fat) regularly consumed in Japan ranges from 0.33 to 1.87 g per 100 g. In addition, in beef fat, the amount of trans-fatty acids ranges from 1.43 to 9.83 g per 100 g. Among offal, rumen showed 1.70 g/100 g, the highest level. The results of this study indicate that, even between the same cuts, trans-fatty acid levels vary depending on the type of feed and duration of the grain-feeding period. In addition, in a study of pork and chicken, the amount of trans-fatty acids did not exceed 0.3 g/100 g in any part of the animal.

Quantum chemical investigation of structural and electronic properties of trans- and cis-structures of some azo dyes for dye-sensitized solar cells

Trans and cis isomers of a series of azobenzene dyes: dyes 1–3 with the carboxylic acid anchoring group in the ortho-position; dyes 4–6 with an anchoring group in the para-position and dye 7 with a carboxylic acid in the meta-position, are studied with DFT and TDDFT approaches. The donating group of dyes 1, 4 and 7 is dimethylamino. The donating group of dyes 2 and 5 is diethylamino and the donating group of dyes 3 and 6 is dipropylamino. Computational studies let us investigate geometrical structures, UV–Vis absorption spectra, electronic properties, light harvesting efficiency (LHE), chemical hardness (η), the weight of LUMO orbital of the dyes on the carboxylic acid group (QLUMO), exciton binding energy (EBE) and charge transfer of two configurations of these dyes. According to the results, we could justify that how the different donating groups and trans and cis structures of the seven dyes with three positions of anchoring group (ortho-, meta-, and para-) influence the parameters affecting the Jsc and the Voc of DSSCs.

Structural Basis of cis- and trans-Combretastatin Binding to Tubulin

Summary Combretastatin A4 (CA-4) derivatives are microtubule-destabilizing agents, some of which are in advanced clinical trials for cancer therapy. The active cis conformation of CA-4 can readily isomerize into a thermodynamically more stable but significantly less active trans form. Here, we solved the high-resolution crystal structure of cis -CA-4 in complex with tubulin. The compound binds to the colchicine site of tubulin and displays both common and distinct interaction points with colchicine. Using metadynamics simulations, we generated the trans form of the ligand within its binding site and computed the relative binding free energy of the cis -CA-4 and trans -CA-4 isomers via a thermodynamic cycle. The calculations suggest structural distortions of the bound trans -CA-4 molecule as the likely cause of its reduced activity in comparison with that of its cis isomer. Our findings could open up unique possibilities for structure-guided drug engineering with the aim of discovering combretastatin variants with improved chemical properties and pharmacological profiles.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging.

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Stereoselective synthesis of chlorido–phosphine ruthenium complexes bearing a pyrazole-based protic tripodal amine ligand

Octahedral ruthenium(II) complexes bearing a tripodal amine ligand featuring three ionizable pyrazole NH groups, tris((5-mesitylpyrazol-3-yl)methyl)amine (LH3), have been synthesized in a stereoselective manner. Treatment of the chlorido complex [{RuCl(LH3)}2(μ2-Cl)]Cl (1) with triphenylphosphine in methanol and subsequent anion exchange with potassium hexafluorophosphate resulted in the clean formation of the phosphine complex cis(P,Namine)-[RuCl(PPh3)(LH3)]PF6 (cis(P,Namine)-2), in which the phosphine ligand lies in the position cis to the amine nitrogen atom. Similarly, diphosphines Ph2P(CH2)nPPh2 reacted with 1 under the same conditions to give the diphosphine-bridged dinuclear ruthenium complexes cis(P,Namine)-[{RuCl(LH3)}2{μ2-Ph2P(CH2)nPPh2}](PF6)2 (3a: n=4; 3b: n=3; 3c: n=2). The cis-selectivity is in marked contrast with the reaction in toluene, which affords the trans isomer exclusively (Yamagishi et al., Inorg. Chem. 54 (2015) 11584.). On the other hand, a related chlorido–(dimethyl sulfoxide) complex trans(S,Namine)-[RuCl(Me2SO-S)(LH3)]Cl (4) was synthesized by the reaction of cis-[RuCl2(Me2SO)4] with LH3. Detailed structures of cis(P,Namine)-2, 3a, and 4 have been determined by X-ray crystallography.

Structural and Conformational Aspects of Equatorial and Axial Trifluoromethyl, Difluoromethyl, and Monofluoromethyl Groups.

The X-ray crystal structures of cis- and trans-1-(indol-3-yl)-4-methyl cyclohexane and its congeners with stepwise fluorination of the methyl group are reported. The trans-configured compounds adopted diequatorial conformations, whereas the cis analogues adopted regular cyclohexane chair conformations with the methyl group preferentially assuming the axial position, even in the case of the CF3 group. Surprisingly, although the axial CF3 derivative displayed distinct valence deformations in the cyclohexane moiety, the observed structural changes were relatively modest. The cis derivatives with axial mono- and difluorinated methyl groups exhibited conformational disorder in the crystals with significant population levels for the staggered conformations that had one fluorine atom in the endo position; their respective trans counterparts adopted unique conformations, but again with one fluorine atom in the endo position. Theoretical calculations for a series of cis- and trans-1,4-dimethyl cyclohexane model compounds with stepwise fluorination of one equatorial or axial methyl group reproduced the experimentally observed structural response patterns very well, reproduced the experimentally determined nonlinear correlation of the axial-equatorial energy difference with the degree of methyl fluorination in a satisfactory manner, and provided further insights into important conformational aspects of partially fluorinated methyl groups.

Synthesis, characterization and in vitro cytotoxicity of three types of platinum(II) complexes containing 5,7-diethyl-1,2,4-triazolo[1,5-a]pyrimidine

Three structurally different mononuclear dichlorido platinum(II) complexes with 5,7-diethyl-1,2,4-triazolo[1,5-a]pyrimidine (detp) were synthesized and characterized through multinuclear magnetic resonance (1H, 13C, 15N, 195Pt) and infrared spectroscopy. The X-ray structure of cis-[PtCl2(detp)(dmso)] (2) was determined using the single-crystal X-ray diffraction technique. The molecular structure of (2) exhibits a square planar geometry surrounding the Pt(II) ion with a unique placement of two chlorido ligands in the cis position in the presence of a S-dmso molecule in the coordination sphere.All NMR data obtained in solution unambiguously confirmed the square planar geometry of Pt(II) with monodentate N3-bonded detp, a monodentate second ligand (detp or NH3 or dmso) and two chlorido ligands in the cis geometry.Cytotoxicity tests using human carcinoma cell lines, specifically the T47D (breast cancer), A549 (non-small cell lung carcinoma), and LoVo (colon cancer) cell lines, and the healthy cell line BALB/3T3 (mouse embryonic fibroblast), indicated that only cis-[PtCl2(detp)2] (1) possesses similar in vitro cytotoxicity against T47D and sevenfold lower toxicity than cisplatin.