Cis-trans Conformation Research Articles

Synthesis and Structure Determination of S,S′-(Naphthalen-2-ylmethyl sulfanyl (1-p-tolyl-ethylidene) Hydrazine

AbstractS,S′-(Naphthalen-2-ylmethyl sulfanyl (1-p-tolyl-ethylidene) hydrazine (SNM4MA) was prepared by the condensation of S-napthalen-2-ylmethyldithiocarbazate (SNMDTC) and 4-methylacetophenone. Yellow needles of SNM4MA were obtained upon slow evaporation of a 50:50 mixture of acetonitrile and DMSO over a period of weeks. The compound crystallizes in the monoclinic system with the space group C 2/c and Z = 4. The unit cell parameters are a = 7.0221(2) A, b = 22.8428(6) A, c = 23.5127(6) A with β = 94.0222(13)°. Single crystal X-ray analysis shows that the molecule has crystallographic two-fold rotational symmetry coincident with the S-S bond. The title compound exists as a trans-cis conformer in which the naphthalene group is trans with respect to the thione sulfur while the benzyl group adopts a cis geometry. 13 C and 1 H spectra confirm that the dimeric nature is retained in DMSO solution.Graphical AbstractSingle crystal X-ray analysis of S,S′-(naphthalen-2-ylmethyl sulfanyl (1-p-tolyl-ethylidene) hydrazine shows that the molecule is dimeric with a two-fold rotational symmetry coincident with the S-S bond via both the thione sulfur atoms. The molecule was found to retain its dimeric structure in dimethylsulfoxide solution.[IMAGE]

Spectroscopic detection of isolated carbonic acid

Carbonic acid (cis-trans H(2)CO(3)) in the gas phase has been successfully produced in a supersonic jet using a pulsed discharge nozzle, and pure rotational transitions of this molecule have been observed by Fourier-transform microwave spectroscopy. Although the observed cis-trans conformer is not the global minimum structure, it is an important conformer as a starting point of its dissociation to CO(2) and H(2)O. Three deuterated isotopologues of the cis-trans conformer (cis-trans HDCO(3), cis-trans DHCO(3), and cis-trans D(2)CO(3)) have also been observed, yielding the r(0) structure of cis-trans H(2)CO(3). The present result is accurate enough to be used in radio astronomical observations.

Acryloyl Chloride and Acryloyl Isocyanate (CH2═CHC(O)X, X = Cl, NCO): A HeI Photoelectron Spectroscopy and Theoretical Study

Acryloyl isocyanate CH(2)=CHC(O)NCO is quantitatively prepared by the metathesis reaction between CH(2)=CHC(O)Cl and AgNCO. Also, jointly with acryloyl chloride, their molecular and electronic structures have been investigated by photoionization mass spectroscopy (PIMS), HeI photoelectron spectroscopy (PES), and theoretical calculations. CH(2)=CHC(O)NCO was theoretically predicted to prefer the trans-cis (tc) conformation as the most stable conformer, with the C=O bond trans to the C=C bond and cis to the NCO moiety. IR and Raman spectra also suggest the presence of the trans-cis (tc) conformation only. Calculations of the cationic-radical form were carried out in order to compare their properties with those of the neutral molecules. It is worthwhile mentioning that both compounds retain planar structures after ionization. After structural optimizations, a theoretical study involving the calculation of the ionization energies using orbital valence Green's functional (OVGF) was performed. The ionization energies of different bands in the photoelectron spectrum are in good agreement with the calculated values from the OVGF method. The first vertical ionization energies of CH(2)=CHC(O)Cl and CH(2)=CHC(O)NCO are determined to be 10.97 and 10.68 eV, respectively. The HOMOs correspond to the ionization of electrons mainly localized on the pi(C=C) or the pi(NCO) orbitals: {4a''(pi(C=C))}(-1) and {5a''(pi(NCO))}(-1), respectively.

Quantum Chemistry and Molecular Dynamics Simulation Study of Dimethyl Carbonate: Ethylene Carbonate Electrolytes Doped with LiPF6

Quantum chemistry studies of ethylene carbonate (EC) and dimethyl carbonate (DMC) complexes with Li+ and LiPF6 have been conducted. We found that Li+ complexation significantly stabilizes the highly polar cis-trans DMC conformation relative to the nearly nonpolar gas-phase low energy cis-cis conformer. As a consequence, the binding of Li+ to EC in the gas phase is not as favorable relative to binding to DMC as previously reported. Furthermore, quantum chemistry studies reveal that, when complexation of LiPF6 ion pairs is considered, the DMC/LiPF6 complex is about 1 kcal/mol more stable than the EC/LiPF6 complex. The EC3DMC(cis-cis)/Li+ complex was found to be the most energetically stable among ECnDMCm/Li+ (n+m=4) investigated complexes followed by EC4/Li+. Results of the quantum chemistry studies of these complexes were utilized in the development of a many-body polarizable force field for EC:DMC/LiPF6 electrolytes. Molecular dynamics (MD) simulations of EC/LiPF6, DMC/LiPF6, and mixed solvent EC:DMC/LiPF6 electrolytes utilizing this force field were performed at 1 M salt concentration for temperatures from 298 to 363 K. Good agreement was found between MD simulation predictions and experiments for thermodynamic and transport properties of both pure solvents and the electrolytes. We find increased ion pairing with increasing DMC content; however, both EC and DMC were found to participate in Li+ solvation in mixed EC:DMC electrolytes despite a huge difference in their dielectric constants. In contrast to previous NMR studies, where dominance of EC in cation solvation was reported, we find a slight preference for DMC in the cation solvation shell for EC:DMC (1 wt:1 wt) electrolytes and show that reanalyzed Raman spectroscopy experiments are in good agreement with results of MD simulations. Finally, analysis of solvent residence times reveals that cation transport is dominated by motion with solvating DMC and approximately equal contributions from vehicular motions with the first solvation shell and solvent exchange with respect to solvating EC.

Molecular and electronic structures of acryloyl isothiocyanate, CH2CHC(O)NCS: a joint experimental and theoretical study

Acryloyl isothiocyanate, CH2CHC(O)NCS, was prepared and studied by IR, Raman, photoelectron spectroscopy (PES), photoionization spectroscopy (PIMS) and theoretical calculations. This molecule was theoretically predicted to prefer the trans-cis (tc) conformation as the most stable conformer, with the CO bond trans to the CC bond and cis to the NCS group. IR and Raman spectra also suggest the presence of the tc conformation only. A theoretical study involving the calculation of the ionization energies using the orbital valence Green’s functional (OVGF/6-311+G(d)) was performed to aid the assignment of the PE spectrum. The first vertical ionization energy of CH2CHC(O)NCS was determined to be 9.89 eV, which is mainly the ionization of the out-of-plane bonding πNCS orbital. Natural population analysis (NPA and NBO) were also performed to investigate the reactivity of CH2CHC(O)NCS.

Synthesis and Anticancer Evaluation of Some New 4-Amino-3- (p-methoxybenzyl)-4,5-dihydro-1,2,4-triazole-5-one Derivatives

Abstract 4-Amino-3-p-methoxybenzyl-5-oxo-4,5-dihydro-1,2,4-triazol-1-yl-acetic acid ethyl ester (2) was prepared from 4-amino-4,5-dihydro-1H-1,2,4-triazole-5-one (1) and ethyl bromoacetate. Compound 3 was synthesized by the condensation of 2 with hydrazine hydrate. The treatment of compound 3 with various aromatic aldehydes resulted in the formation of arylidene hydrazides as cistrans conformers 4a - g. Thiosemicarbazide derivative 5 was prepared by the reaction of compound 3 with phenylisothiocyanate. Cyclization of 5 with sodium hydroxide resulted in the formation of compound 6. Treatment of 6 with benzyl bromide gave compound 7. Four of the newly synthesized compounds were screened for their anticancer activity against a panel of 60 cell lines derived from nine cancer types, namely, non-small cell lung, colon, breast, ovarian, leukemia, renal, melanoma, prostate and CNS cancers at a fixed dose of 10 μM.

Metal-Dependent Assembly of a Helical-[Co3L3] Cluster versus a Meso-[Cu2L2] Cluster with O,N,N′,O′-Schiff Base Ligand: Structures and Magnetic Properties

Self-assembly of a tetradentate ligand, N, N'-bi(salicylidene)-2,6-pyridinediamine (H 2L), with Cu(II) or Co(II), affords a dinuclear [Cu 2L 2] complex ( 1) or a trinuclear [Co 3L 3] complex ( 2), which were characterized by the single crystal X-ray diffraction study. The coordination geometry of the Cu (II) centers in 1 is between square planar and tetrahedral, with the ligand adopting a cis-cis conformation to give a centrally symmetric structure, which can be regarded as a mesocate. However, the coordination geometry of Co (II) centers in 2 is distortedly tetrahedral, and the ligand adopts a cis-trans conformation. The whole complex of 2 is of a pseudo- C 3 symmatrical, torus-like structure, which can be regarded as a circular helicate. Both the mesocate and the helicate exhibit expanded supramolecular structures due to elaborate intercomplex pi-stacking interactions. These two complexes were also characterized by element analysis, IR spectra, and TGA. To verify the stability of 2, ESI-MS was carried out on both the crystal and the powdered samples. Variable temperature magnetic susceptibility measurements reveal that both 1 and 2 display antiferromagnetic properties. DFT calculations were carried out on 1 to verify the antiferromagnetic coupling between intracluster metal centers.

Influence of the position of the double bond on the autoignition of linear alkenes at low temperature

The influence of the position of the double bond on the autoignition of linear alkenes has been investigated by modeling the behavior of the three isomers of linear hexene and those of linear heptene. Low-temperature kinetic mechanisms for the oxidation of these six alkenes have been obtained after some improvements made to the system EXGAS, for the automatic generation of mechanisms, which had been previously adapted to model the oxidation of 1-pentene and 1-hexene. Quantum mechanical calculations have shown that cis–trans conformations should be taken into account and that isomerizations of alkenyl and alkenyl peroxy radicals involving a transition state including a double bond could be neglected. The new mechanisms have been validated using experimental data obtained in two rapid compression machines between 600 and 900K with a good prediction of cool flame and ignition delay times. The model reproduces well the decreasing reactivity at low temperature when going from 1- to 3-alkene. While the profiles of products are well reproduced for 1-hexene in a jet-stirred reactor above 780K, more problems are encountered for the prediction of products in a rapid compression machine at 707K, showing persisting problems in the understanding of the chemistry of the low-temperature oxidation of alkenes. Reaction rates analysis have been used to explain the difference of reactivity between the isomers of hexene.

Conformational Stability from Variable Temperature FT-IR Spectra of Krypton Solutions, r0 Structural Parameters, Vibrational Assignment, and ab Initio Calculations of 4-Fluoro-1-butene

Variable temperature (-115 to -155 degrees C) studies of the infrared spectra (3200-400 cm-1) of 4-fluoro-1-butene, CH2=CHCH2CH2F, dissolved in liquid krypton have been carried out. The infrared spectra of the gas and solid as well as the Raman spectra of the gas, liquid, and solid have also been recorded from 3200 to 100 cm-1. From these data, an enthalpy difference of 72 +/- 5 cm-1 (0.86 +/- 0.06 kJ x mol-1) has been determined between the most stable skew-gauche II conformer (the first designation refers to the position of the CH2F group relative to the double bond, and the second designation refers to the relative positions of the fluorine atom to the C-C(=C) bond) and the second most stable skew-trans form. The third most stable conformer is the skew-gauche I with an enthalpy difference of 100 +/- 7 cm-1 (1.20 +/- 0.08 kJ x mol-1) to the most stable form. Larger enthalpy values of 251 +/- 12 cm-1 (3.00 +/- 0.14 kJ x mol-1) and 268 +/- 17 cm-1 (3.21 +/- 0.20 kJ x mol-1) were obtained for the cis-trans and cis-gauche conformers, respectively. From these data and the relative statistical weights of one for the cis-trans conformer and two for all other forms, the following conformer percentages are calculated at 298 K: 36.4 +/- 0.9% skew-gauche II, 25.7 +/- 0.1% skew-trans, 22.5 +/- 0.2% skew-gauche I, 10.0 +/- 0.6% cis-gauche, and 5.4 +/- 0.2% cis-trans. The potential surface describing the conformational interchange has been analyzed and the corresponding two-dimensional Fourier coefficients were obtained. Nearly complete vibrational assignments for the three most stable conformers are proposed and some fundamentals for the cis-trans and the cis-gauche conformers have been identified. The structural parameters, dipole moments, conformational stability, vibrational frequencies, infrared, and Raman intensities have been predicted from ab initio calculations and compared to the experimental values when applicable. The adjusted r0 structural parameters have been determined by combining the ab initio predicted parameters with previously reported rotational constants from the microwave data. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.

2-NaphthylmethylN-(3-pyridylmethylene)hydrazinecarbodithioate

The title mol­ecule, C18H15N3S2, is a trans–cis conformer. The thione S atom is in a trans configuration with respect to the pyridine ring but adopts a cis configuration with respect to the napthylmethyl substituent. In the crystal structure, mol­ecules are linked by inter­molecular N—H⋯N hydrogen bonds viaα-N donor atoms and pyridyl N acceptor atoms into one-dimensional chains along the a axis. In addition, pairs of inversion-related dithio­carbazate groups and the attached pyridine groups are arranged with an inter­planar distance 3.30 Å, leading to π–π stacking inter­actions. The crystal used for the structure determination was twinned.

S-Quinolin-2-ylmethyldithiocarbazate

In the title compound, C11H11N2S2, there is an intramolecular N-H...N [2.778 (2) A] hydrogen bond linking the quinoline N atom and the imino N atom. The planar quinoline ring system forms an angle of 67.7 (1)° with the dithiocarbazate group. Bond angles for both S-C-S [115.66 (8)°] and N-C-S [119.05 (11)°] are comparable with cis-trans S-methyldithiocarbazate but differ from those found in trans-cis S-methyldithiocarbazate and trans-cis S-benzyldithiocarbazate. This is due to the N-H...N hydrogen bond that exists only in the cis-trans conformation found for the title compound.

Dissociation of carbonic acid: Gas phase energetics and mechanism from ab initio metadynamics simulations

A comprehensive metadynamics study of the energetics, stability, conformational changes, and mechanism of dissociation of gas phase carbonic acid, H2CO3, yields significant new insight into these reactions. The equilibrium geometries, vibrational frequencies, and conformer energies calculated using the density functional theory are in good agreement with the previous theoretical predictions. At 315 K, the cis-cis conformer has a very short life time and transforms easily to the cis-trans conformer through a change in the O=C-O-H dihedral angle. The energy difference between the trans-trans and cis-trans conformers is very small (approximately 1 kcal/mol), but the trans-trans conformer is resistant to dissociation to carbon dioxide and water. The cis-trans conformer has a relatively short path for one of its hydroxyl groups to accept the proton from the other end of the molecule, resulting in a lower activation barrier for dissociation. Comparison of the free and potential energies of dissociation shows that the entropic contribution to the dissociation energy is less than 10%. The potential energy barrier for dissociation of H2CO3 to CO2 and H2O from the metadynamics calculations is 5-6 kcal/mol lower than in previous 0 K studies, possibly due to a combination of a finite temperature and more efficient sampling of the energy landscape in the metadynamics calculations. Gas phase carbonic acid dissociation is triggered by the dehydroxylation of one of the hydroxyl groups, which reorients as it approaches the proton on the other end of the molecule, thus facilitating a favorable H-O-H angle for the formation of a product H2O molecule. The major atomic reorganization of the other part of the molecule is a gradual straightening of the O=C=O bond. The metadynamics results provide a basis for future simulation of the more challenging carbonic acid-water system.

BenzylN′-[1-(3-pyridyl)ethylidene]hydrazinecarbodithioate

The title compound, C15H5N2S2, crystallizes as a trans–cis conformer. The thione sulfur is in a trans position with the methyl pyridyl fragment with respect to the C—N bond but adopts a cis position with the benzyl ring across the C—S bond. The dihedral angle between the planar quinoline ring and the dithio­carbazate unit is 103.70 (1)°. The inclination of the dithio­carbazate unit with the benzyl group is 17.20 (1)°. There are strong π–π stacking inter­actions between pairs of dithio­carbazate units and also pairs of pyridine rings [3.27 (5) and 3.28 (5) Å, respectively]. A long-distance inter­molecular N—H⋯N hydrogen bond [3.171 (2) Å] also stabilizes the structure.

2-QuinolylmethylN′-[1-(m-tolyl)ethylidene]hydrazinecarbodithioate

The title compound, C20H19N3S2, crystallized as a cis–trans conformer in which the quinoline ring system is cis across the C—S bond but adopts a trans geometry with respect to the C—N bond. The compound exists in the thione form with the presence of a C=S bond.

Conformational Studies of Cyclopropylmethyl Isothiocyanate from Temperature-Dependent FT-IR Spectra of Rare Gas Solutions and Ab Initio Calculations

Variable temperature (-55 to -150 degrees C) studies of the infrared spectra (3200-100 cm(-1)) of cyclopropylmethyl isothiocyanate, c-C(3)H(5)CH(2)NCS, dissolved in liquefied rare gases (Xe and Kr), have been carried out. The infrared spectra of the gas and solid, as well as the Raman spectrum of the liquid, have also been recorded from 3200 to 100 cm(-1). By analyzing six conformer pairs in xenon solutions, a standard enthalpy difference of 228 +/- 23 cm(-1) (2.73 +/- 0.27 kJ.mol(-1)) was obtained with the gauche-cis (the first designation indicates the orientation of the CNCS group with respect to the three-membered ring, the second designation indicates the relative orientation of the NCS group with respect to the bridging C-C bond) rotamer the more stable form, and it is also the only form present in polycrystalline solid. Given statistical weights of 2:1 for the gauche-cis and cis-trans forms (the only stable conformers predicted); the abundance of cis-trans conformer present at ambient temperature is 14 +/- 2%. The potential surface describing the conformational interchange has been analyzed, and the corresponding two-dimensional Fourier coefficients were obtained. From MP2 ab initio calculations utilizing various basis sets with diffuse functions, the gauche-cis conformer is predicted to be more stable by 159-302 cm(-1), which is consistent with the experimental results. However, without diffuse functions, the conformational energy differences are nearly zero even with large basis sets. For calculations with density functional theory by the B3LYP method, basis sets without diffuse functions also predict smaller energy differences between the conformers, although not nearly as small as the MP2 results. A complete vibrational assignment for the gauche-cis conformer is proposed, and several fundamentals for the cis-trans conformer have been identified. The structural parameters, dipole moments, conformational stability, vibrational frequencies, and infrared and Raman intensities have been predicted from ab initio calculations and compared to the experimental values when applicable; the r(0) structural parameters are also estimated. The energies for the linear CNCS moiety were calculated. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.

Conformational studies of cyclopropylmethyl isocyanate from temperature dependent FT-IR spectra of xenon solutions and ab initio calculations

Variable temperature (−55 to −100 °C) studies of the infrared spectra (3200 to 100 cm −1) of cyclopropylmethyl isocyanate, c-C 3H 5CH 2NCO, dissolved in liquefied xenon, have been carried out. The infrared spectra (gas and solid) as well as the Raman spectrum of the liquid have been recorded from 3200 to 100 cm −1. By analyzing six conformer pairs in xenon solutions, an enthalpy difference of 193 ± 19 cm −1 (2.31 ± 0.23 kJ/mol) was obtained with the gauche–cis rotamer (the first designation indicates the orientation of the CNCO group with respect to the three-membered ring, the second designation indicates the relative orientation of the NCO group with respect to the bridging C C bond) the more stable form and the only form present in polycrystalline solid. The abundance of the cis–trans conformer present at ambient temperature is 16 ± 1%. The potential function governing the conformational interchange has been obtained from B3LYP/6-31G(d) calculations and the two-dimensional potential has been obtained. From MP2 ab initio calculations utilizing various basis sets with diffuse functions, the gauche–cis conformer is predicted to be more stable by 223 to 269 cm −1, which is consistent with the experimental results. However, without diffuse functions the predicted conformational energy differences are much smaller (77–166 cm −1). Similar diffuse function dependency affects density functional theory calculations by the B3LYP method to a lesser extent. A complete vibrational assignment for the gauche–cis conformer is proposed and several fundamentals for the cis–trans conformer have been identified. The structural parameters, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and r 0 structural parameters are estimated. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.

2,2′:6′,2′′-Terpyridinium perrhenate

In the title compound, (C15H12N3)[ReO4], the cations exhibit a cis–trans conformation of the pyridine rings. The crystal structure is stabilized by a three-dimensional network of C—H⋯O hydrogen-bond inter­actions.

Bis(thiocarbohydrazide)dithiocyanatoiron(II)

In the title compound, [FeII(NCS)2(CH6N4S)2], the Fe(II) cation is surrounded by two S atoms and two N atoms from thiocarbohydrazide groups and by two N atoms from thiocyanate groups. The geometry around the FeII cation, which is located on a center of inversion, is distorted octahedral. The thiocarbohydrazide molecule assumes a cis-trans conformation, which is reinforced by an N-H...N hydrogen bond. Molecules of the title compound are connected via intermolecular N-H...S and N-H...N hydrogen bonds to form a three-dimensional network structure.

Internal rotation in peroxynitrous acid (ONOOH)

Using higher levels of wave-function-based electronic structure theory than previously applied, as well as density functional theory (B-LYP and B3-LYP functionals), all theoretical models conclude that three ONOOH conformers are stationary point minima, in disagreement with some of the previous studies that we survey. In order of increasing energy, these are the cis-cis, cis-perp, and trans-perp conformers. Basis sets including diffuse functions seem to be needed to obtain a qualitatively correct representation of the internal rotation potential energy surface at higher levels of theory. Internal rotation about the peroxide bond involving the cis-cis, cis-gauche transition structure (TS), cis-perp, and cis-trans TS conformers is studied in detail. To help ascertain the relative stability of the cis-perp conformer, multireference configuration interaction energy calculations are carried out, and rule of thumb estimates of multireference character in the ground-state wave functions of the ONOOH conformers are considered. CCSD(T)/aug-cc-pVTZ physical properties (geometries, rotational constants, electric dipole moments, harmonic vibrational frequencies, and infrared intensities) are compared with the analogous experimental data wherever possible, and also with density functional theory. Where such experimental data are nonexistent, the CCSD(T) and B3-LYP results are useful representations. For example, the electric dipole moment |mu(e)| of the cis-cis conformer is predicted to be 0.97+/-0.03 D. CCSD(T) energies, extrapolated to the aug-cc-pVNZ limit, are employed in isodesmic reaction schemes to derive zero Kelvin heats of formation and bond dissociation energies of the ONOOH stationary point minima. In agreement with recent gas-phase experiments, the peroxide bond dissociation energies of the cis-cis and trans-perp conformers are calculated as 19.3+/-0.4 and 16.0+/-0.4 kcalmol, respectively. The lowest energy cis-cis conformer is less stable than nitric acid by 28.1+/-0.4 kcalmol at 0 K.

Synthesis and Antimicrobial Activities of Some New 1‐(5‐Phenylamino‐[1,3,4]thiadiazol‐2‐yl)methyl‐5‐oxo‐[1,2,4]triazole and 1‐(4‐Phenyl‐5‐thioxo‐[1,2,4]triazol‐3‐yl)methyl‐5‐oxo‐[1,2,4]triazole Derivatives.

AbstractFor Abstract see ChemInform Abstract in Full Text.