Trans Form Research Articles

Crystal packing modes in the salts of ethane-1,2-diamine with acetic acid and its halogeno derivatives

In a series of salts of ethane-1,2-diamine with acetic (1), trifluoroacetic (2), trichloroacetic (3), and dichloroacetic (4) acids, the amine is doubly protonated so the cation:anion stoichiometry is 2:1. In 1 and 2, dications are lying across the center of symmetry (Z′ = 1/2), in 4 dication is nonsymmetric (Z′ = 1), while the structure of 3 contains both symmetric and nonsymmetric cations (Z′ = 3/2). All dications, either symmetric or not, are in extended (trans) form, by far the most popular among the salts of ethane-1,2-diamine. Strong hydrogen N–H···O bonds constitute the main specific, directional force determining the crystal packing. In 1, one of the N–H hydrogen atoms is involved in bifurcated hydrogen bonds, and in this case, four alresaacceptor oxygen atoms are almost equally involved in accepting the hydrogen bonds; in consequence, the C–O bond lengths are almost equal. In all other cases, the C–O bonds with oxygen atoms involved in more hydrogen bonds are systematically longer than those which accept less such interactions. Halogen C–Cl···O interactions are observed in two (out of five) symmetry-independent anions of 3 and 4, suggesting that at least in this series, the roles of these interactions are only secondary in nature. No significant involvement of fluorine atoms in directional interactions is detected, however. The hydrogen-bond networks are described by means of graph-set method. In addition, Hirshfeld surfaces are used to detect and visualize the differences between similar moieties, and fingerprint plots are presented in order to analyze the mutual importance of different kinds of interactions.

A Theoretical Study of the Binding of [Re₆Se₈(OH)₂(H₂O)₄] Rhenium Clusters to DNA Purine Base Guanine.

Hexanuclear rhenium complexes are promising candidates for use as antitumor drugs. However, to date, there has been no investigation into the nature of their binding to DNA. In this study, density functional theory (DFT) was used to examine the binding of [Re6Se8(OH)2(H2O)4] to the DNA purine base guanine. The geometrical structures of cluster-guanine adducts in water were modeled at the zero order regular approximation (ZORA)-PW91 level. Calculating the bond energies allowed us to compare the cis and trans forms of the cluster, and a possible manners of interaction between [Re6Se8(OH)2(H2O)3] clusters and DNA was obtained and explained.

COMPREHENSIVE ANALYSIS OF PREBIOTIC PROPENAL UP TO 660 GHz

Since interstellar detection of propenal is only based on two rotational transitions in the centimeter wave region, its high resolution rotational spectrum has been measured up to 660 GHz and fully characterized by assignment of more than 12,000 transitions to provide direct laboratory data to the astronomical community. Spectral assignments and analysis include transitions from the ground state of the trans and cis isomers, three trans-13C isotopologues, and ten excited vibrational states of the trans form. Combining new millimeter and submillimeter data with those from the far-infrared region has yielded the most precise set of spectroscopic constants of trans-propenal obtained to date. Newly determined rotational constants, centrifugal distortion constants, vibrational energies, and Coriolis and Fermi interaction constants are given with high accuracy and were used to predict transition frequencies and intensities over a wide frequency range. Results of this work should facilitate astronomers further observation of propenal in the interstellar medium.

Solvent-Induced Manipulation of Supramolecular Organic Frameworks

Supramolecular organic frameworks based on C-alkylresorcin[4]arenes (RsCn) and the conformationally flexible spacer 1,2-bis(4-pyridyl)ethane (bpea) are discussed here. The conformational flexibility of bpea was predetermined with the help of electronic structure calculations of bpea in the gas and solution phases. The architectures of these frameworks are primarily governed by O–H···O and O–H···N intermolecular hydrogen-bonding interactions between the components of the frameworks. The unique arrangement of the bpea spacer around RsCn yields continuous 1D wavelike and 1D lateral hydrogen-bonded frameworks. The cocrystals of RsCn with bpea show conformational variation as a function of a change in the solvent of crystallization. In acetonitrile, the bpea spacer exists in the trans form, whereas in ethanol it adopts both gauche and trans forms. RsCn, on the other hand, adopts a pinched-cone conformation in both solvents. The extended frameworks of RsCn–bpea in ethanol enclose continuous channels filled with...

Solid-State NMR Study of Paramagnetic Bis(alaninato-κ(2)N,O)copper(II) and Bis(1-amino(cyclo)alkane-1-carboxylato-κ(2)N,O)copper(II) Complexes: Reflection of Stereoisomerism and Molecular Mobility in (13)C and (2)H Fast Magic Angle Spinning Spectra.

Solid-state stereochemistry and mobility of paramagnetic copper(II) complexes formed by aliphatic amino acids (l-alanine, d,l-alanine, 1-amino-2-methyl-alanine) and 1-amino(cyclo)alkane-1-carboxylic acids (alkane = propane, butane, pentane, hexane) as bidentate ligands has been studied by (13)C and (2)H solid-state fast magic angle spinning (MAS) NMR spectroscopy. We examined the prospective method to characterize solid-state paramagnetic compounds in a routine way. Both (13)C and (2)H MAS spectra can distinguish d,l and l,l diastereomers of natural and polydeuterated bis([Dn]alaninato)copper(II) (n = 0, 2, 8) complexes with axial and/or equatorial methyl positions (conformations) primarily due to different Fermi-contact (FC) contributions. The three-bond hyperfine couplings clearly show Karplus-like dependence on the torsional angles which turned out to be a useful assignment aid. Density functional theory calculations of the FC term and crystal structures were also used to aid the final assignments. The correlations obtained for bis(alaninato-κ(2)N,O)copper(II) complexes were successfully used to characterize other complexes. The usefulness of the (2)H MAS spectra of the deuterated complexes was underlined. Even the spectra of the easily exchangeable amine protons contained essential stereochemical information. In the case of a dimer structure of bis(1-aminohexane-1-carboxylato-κ(2)N,O)copper(II) both the (13)C and (2)H resolutions were good enough to confirm the presence of the cis and trans forms in the asymmetric unit. With regard to the internal solid-state motions in the crystal lattice, the obtained quadrupolar tensor parameters were similar for the d,l- and l,l-alaninato isomers and also for the cis-trans forms suggesting similar crystal packing effects, static amine deuterons involved in hydrogen bonding, and fast rotating methyl groups.

(2E)-1-(5-Chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one: Synthesis, XRD, FT-IR, Raman and DFT studies

A novel (2E)-1-(5-chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one [C21H15ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of HF, MP2, BP86, BLYP, BMK, B3LYP, B3PW91, B3P86 and M06-2X functionals. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the triclinic space group P-1 with the cis–trans–trans form. There is a good agreement between the experimentally determined structural parameters and vibrational frequencies of the compound and those predicted theoretically using the density functional theory with the BLYP and BP86 functionals.

Microwave, structural, conformational, vibrational studies and ab initio calculations of fluoroacetyl chloride

The infrared and Raman spectra (3200–50cm−1) of the gas, liquid or solution, and solid of fluoroacetyl chloride, FCH2COCl have been recorded. FT-microwave studies have also been carried out and 22 transitions were recorded for the trans conformer. Variable temperature (−50 to −105°C) studies of the infrared and Raman spectra (3200–50cm−1) of xenon solutions have been carried out. From these data, the trans, cis and gauche conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 159±11cm−1 (1.90±0.14kJmol−1) with the trans conformer the more stable form than the cis. The energy difference between the cis and gauche form is 222±18cm−1 (2.66±0.21kJ/mol) and the energy difference between the trans and gauche forms is 386±13cm−1 (4.61±0.16kJ/mol). Vibrational assignments have been made for the observed bands for the three conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, and Raman activities for the three conformers. By utilizing the microwave rotational constants of two isotopomers for trans, combined with the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for the trans conformer. The results are discussed and compared to the corresponding properties of some related molecules.

Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar (1HN–1Hα) and amide-proton chemical shift anisotropy (1HN CSA) has been measured in a model tripeptide Piv-LPro-LPro-LPhe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA.

Synthesis and Evaluation of Novel Photoisomerizable Small Molecules as Chemical Tools

Tubulin, a central component of the cellular cytoskeleton is critical for the formation of the mitotic spindle in mitosis. Without this dynamic protein, a cell is unable to properly divide. As a result, a number of cancer drugs target tubulin, and prevent the cell from properly undergoing mitosis. A class of drugs known as mitotic inhibitors disrupt tubulin polymerization by acting to stabilize or destabilize tubulin polymer formation. While these drugs are often used to treat disease, they may also be used as biochemical tools to study tubulin polymerization. However, these molecules often lack precise spatial and temporal control, rendering them inadequate to fully study a dynamic process such as tubulin polymerization. Recently, photoisomerizable compounds have gained attention due to their increased spatial and temporal control. Azo‐stilbene compounds are well known to be photoisomerizable between the cis and the trans form at 400‐600nm. This photoisomerization gives azo‐stilbene compounds great power as biochemical tools. Certain mitotic inhibitors have a stilbene backbone, which make azo‐stilbene compounds the ideal starting point for the discovery of photoisomerizeable tubulin polymerization inhibitors. We have developed a library of azo‐stilbenes, which we have supplemented with rationally designed compounds, for the purpose of inhibiting tubulin polymerization. We will discuss the synthesis of these compounds and their activity as novel azo‐stilbene tubulin binders, as well as the implications of our findings for the synthesis of next‐generation compounds to inhibit tubulin polymerization.

Partitioning, Aqueous Solubility, and Dipole Moment Data for cis- and trans-(4-Methylcyclohexyl)methanol, Principal Contaminants of the West Virginia Chemical Spill

In 2014, the U.S. National Response Center recorded more than 30000 incidents of oil spills, chemical releases, or maritime security issues, including crude (4-methylcyclohexyl)methanol (MCHM) that contaminated river and drinking water in West Virginia. This research yielded physicochemical partitioning data for the two major compounds released in West Virginia, cis- and trans-(4-methylcyclohexyl)methanol. Octanol–water partition coefficients (KOW) were 225 for cis-4-MCHM and 291 for trans-4-MCHM. The aqueous solubility for total 4-MCHM was 2250 mg/L at 23 °C; solubilities of individual isomers were dependent on their mole fractions. The cis isomer was more soluble and less well sorbed to activated carbon than the trans isomer, consistent with its lower KOW. The partition behavior is supported by a larger computed solvated dipole moment for the cis form than for the trans form at the MP2 aug-cc-pwCVDZ SMD level of theory. Different partition properties would result in the differential fate and transport o...

Explicit versus implicit solvation effects on the first hyperpolarizability of an organic biphotochrome.

The first hyperpolarizability of the four trans forms of a dithienylethene indolinooxazolidine biphotochrome in acetonitrile solution has been evaluated by using two solvation models, an explicit and an implicit one. The implicit solvation model is the integral equation formalism of the polarizable continuum model (IEF-PCM), whereas in the explicit one, the solvent molecules are represented by point charges, of which the positions have been generated by Monte Carlo simulations whereas the solute is treated quantum mechanically. At optical frequencies, first hyperpolarizabilities calculated with the implicit solvation model are usually larger than those obtained with the multiscale approach. However, both approaches predict similar contrasts, indicating that implicit solvation models such as IEF-PCM are well-suited to describe the variations in the NLO responses of molecular switches. In addition, the analysis of the contrasts of first hyperpolarizabilities shows that the biphotochrome can act as a three-state NLO switch.

Photoinduced formation of an azobenzene-based CD-active supramolecular cyclic dimer.

A series of new photo-responsive amino acid-derived azobenzenedicarboxylic acid derivatives (S)-1 a-e were synthesized. Compound (S)-1 a in the trans form exhibited no circular dichroism (CD) signal in DMF under ambient conditions, whereas intense Cotton effects were observed upon UV irradiation, indicating the formation of a chiral supramolecular structure in the cis form. The CD signals disappeared when trifluoroacetic acid (TFA) was added to the solution. The ester counterpart [(S)-1 a'] showed no CD signal. Hydrogen bonding between the carboxy groups seemed necessary for constructing the supramolecular structure. The kinetic studies of cis to trans isomerization of (S)-1 a demonstrated that the formation of a chiral supramolecule enhances the stability of the cis-azobenzene structure. The ESI mass spectrum of stilbenedicarboxylic acid (S)-4, an analogue of (S)-1 b, confirmed the formation of a dimer. A theoretical CD study revealed that (S)-1 a in the cis form should be present as a cyclic chiral dimer.

Photoinduced isomerization-driven structural transformation between decanuclear and octadecanuclear gold(I) sulfido clusters.

Upon photoirradiation, isomerization of the ligands, 1,2-bis(diphenylphosphino)ethene (dppee) from the cis to the trans form in polynuclear gold(I) sulfido clusters, led to the structural transformation of the decagold(I) cluster to the octadecagold(I) cluster. Both polynuclear μ3-sulfido gold(I) clusters have been fully characterized by NMR, mass spectrometry, elemental analysis, and single crystal X-ray diffraction analysis. The transformation process could be readily detected and monitored by UV-vis absorption, emission, and (31)P NMR spectroscopy in solution. Supported and driven by Au(I)···Au(I) bonding interactions, the nuclearity and symmetry of these clusters were largely different from each other, resulting in completely distinct photophysical features.

Visible‐Light‐Triggered Molecular Photoswitch Based on Reversible E/Z Isomerization of a 1,2‐Dicyanoethene Derivative

AbstractA designed bis(dithienyl) dicyanoethene‐based, strictly E/Z photoswitch (4TCE) operates through state‐selective (E and Z isomer) photoactivation with visible light. The E and Z isomers of 4TCE exhibit remarkably different spectroscopic characteristics, including a large separation (70 nm) in their absorption maxima (λmax) and a 2.5‐fold increase in molar extinction coefficient from cis to trans. The energetically stable trans form can be completely converted to the cis form within minutes when exposed to white light, whereas the reverse isomerization occurs readily upon irradiation by blue light (λ<480 nm) or completely by thermal conversion at elevated temperatures. These features together with excellent thermal stability and photostability of both isomers make this new E/Z photoswitch a promising building block for photoswitchable materials that operate without the need for UV light.

Visible-light-triggered molecular photoswitch based on reversible E/Z isomerization of a 1,2-dicyanoethene derivative.

A designed bis(dithienyl) dicyanoethene-based, strictly E/Z photoswitch (4TCE) operates through state-selective (E and Z isomer) photoactivation with visible light. The E and Z isomers of 4TCE exhibit remarkably different spectroscopic characteristics, including a large separation (70 nm) in their absorption maxima (λ(max)) and a 2.5-fold increase in molar extinction coefficient from cis to trans. The energetically stable trans form can be completely converted to the cis form within minutes when exposed to white light, whereas the reverse isomerization occurs readily upon irradiation by blue light (λ<480 nm) or completely by thermal conversion at elevated temperatures. These features together with excellent thermal stability and photostability of both isomers make this new E/Z photoswitch a promising building block for photoswitchable materials that operate without the need for UV light.

The conformational stability, solvation and the assignments of the experimental infrared, Raman, 1H and 13C NMR spectra of the local anesthetic drug lidocaine

The structure, vibrational and 1H and 13C NMR spectra of the local anesthetic drug lidocaine were investigated by the B3LYP/6-311G∗∗ calculations. The molecule was predicted to have the non-planar cis (NCCN∼0°) structures being about 2–6kcal/mol lower in energy than the corresponding trans (NCCN∼180°) forms. The calculated NCCN (9.6°) and CNCC (−132.2°) torsional angles were in a good qualitative agreement with the reported X-ray angles (3.1 and 13.0°, −102.67 and −77.9°, respectively, for H-bonded dimers). The Gibbs energy of solution of lidocaine in formamide, water, dimethylsulfoxide, acetonitrile, methanol, ethanol and chloroform solutions was estimated at the B3LYP level. The predicted affinity of lidocaine toward the alcohols, acetonitrile and chloroform solutions was in excellent agreement with the reported experimental solubility of the drug in organic solvents. The analysis of the observed vibrational spectra is consistent with the presence of lidocaine in only one conformation at room temperature. The 1H and 13C NMR spectra of lidocaine were interpreted by experimental and DFT calculated chemical shifts of the drug. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine is 0.47 and 8.26ppm, respectively.

Infrared photoisomerization of 1-propanol CD3 and OD trapped in four cryogenic matrices: Ne, N2, Ar, and Xe.

The conformational equilibria and isomerization processes of 1-propanol -OD and -CD3 have been studied by vibrational spectroscopy at low temperatures in four cryogenic matrices to investigate the effect of deuteration on their photochemistry. These isotopic species were selectively irradiated in the νOH and νOD domains, resulting in the identification of several conformers that are able to interconvert upon selective IR irradiation. The experimental results were compared with theoretical geometries obtained at the B3LYP/6-311+G(d) level of theory. Alkyl chain isomerization can be induced in rare gas and nitrogen cryogenic matrices by suitable selective irradiation. Selective excitation of the OH and OD stretches of two Gauche isomers transfers the alkyl chain from the gauche to the trans form. The competition between intramolecular vibrational energy relaxation and the matrix-dopant interaction determines the torsional subspace dynamics of the vibrationally excited propanol molecules.

Host–guest interaction between fluoro-substituted azobenzene derivative and cyclodextrins

This system is completely opposite to the conventional azobenzene/β-CD system in that cis-F-azo-COOH fits β-CD more tightly than its trans form.

Photoswitching the mechanical properties in Langmuir layers of semifluorinated alkyl-azobenzenes at the air-water interface.

Semifluorinated alkyl-azobenzene derivatives (SFAB) can form stable Langmuir layers at the air-water interface. These systems combine the amphiphobic character of semifluorinated alkyl units as structure-directing motifs with photochromic behavior based on the well-known reversible cis-trans isomerization upon irradiation with UV and visible light. Herein, we report our investigations of the structural and dynamic tunability of these SFAB layers at the air-water interface in response to an external light stimulus. The monolayer structures and properties of [4-(heptadecafluorooctyl)phenyl](4-octylphenyl)diazene (F8-azo-H8) and bis(4-octylphenyl)diazene (H8-azo-H8) were studied by neutron reflectivity, surface pressure-area isotherms with compression-expansion cycles, and interfacial rheology. We find that UV irradiation reversibly influences the packing behavior of the azobenzene molecules and interpret this as a transition from organized layer structures with the main axis of the molecule vertically oriented in the trans form to random packing of the cis isomer. Interestingly, this trans-cis isomerization leads to an increase in surface pressure, which is accompanied by a decrease in viscoelastic moduli. These results suggest ways of tailoring the properties of responsive fluid interfaces.

A DFT study on Diels-Alder cycloadditions oftrans-1,3-butadiene to C60and C70

Investigation of the relative reactivity of bonds in fullerenes will provide fundamental theory for the design of fullerene-based materials. We have theoretically investigated the reactivity of the Diels–Alder (DA) cycloaddition of cis-1,3-butadiene to all types of bonds in C60 and C70 using the M06-2X hybrid density functional theory (DFT) calculations (J. Phys. Org. Chem. 2012, 25 850–855) and have pointed out that the DA cycloadditions of cis and trans forms of 1,3-butadiene to ethylene have a specially intimate relationship (J. Phys. Org. Chem. 2014, 27 652–660). For the aim of telling a whole story of the DA cycloaddition concerning C60 and C70, the DA cycloadditions of trans-1,3-butadiene to all types of bonds in C60 and C70 were explored at the same theoretical level as those of the cis-1,3-butadiene. The calculated results related with the trans- and cis-1,3-butadienes were compared. The potential energy curves of DA cycloadditions of trans- and cis-1,3-butadiene to C60 and C70 were discussed. The distortion–interaction energy model was employed to elucidate the origin of different reactivity of all kinds of CC bonds. The solvent effects were examined using the continuum solvent model. These current results, along with our previous research, will help to obtain an overall view of the DA cycloadditions of 1,3-butadiene to C60 and C70. Copyright © 2014 John Wiley & Sons, Ltd.