Structural characteristics of some mercaptoacetic acid hydrazides

NMR and molecular modeling were used to analyze the conformational states of a series of mercaptoacetic acid hydrazides. A chemical exchange phenomenon was observed in the phase-sensitive NOESY spectrum of all derivatives in both CDCl₃ and DMSO-d6 solvents. Chemical shifts, temperature and solvent dependence as well as MonteCarlo conformational search suggest that two rotamers exist around the amide bond in solution in a slow, for the NMR time scale, interconversion at room temperature. The trans conformer is predominant in CDCl₃ and seems to be stabilized by the presence of hydrophobic interactions between the two aliphatic ends of the molecule. The relative population of the cis conformer increases tenfold in DMSO-d6 stabilized through the formation of hydrogen bonds.     

Water wafers: structure and melting of a hydrate inclusion compound of a neutral Pt(IV) complex with 1-methylcytosinato ligands

The characterization by X-ray analysis of the trans,trans,trans-[bis(1-methylcytosinate,N4)bis(ammine)bis(hydroxo)platinum(IV)] octahydrate complex (I) reveals an unexpected crystal packing. The neutral complex molecule is hosted by layers, totally built up by water molecules which do not exhibit a direct coordination to metal ions. These corrugated layers are made by puckered eight- and planar four-membered rings of water molecules, held together by hydrogen bonds with an ordered proton arrangement.     

Vibrational study of tamoxifen citrate polymorphism

The trans isomer of (Z)-2-[p-(1,2-diphenyl-butenyl)phenoxy]-N,N-dimethyletylamine (tamoxifen) is well known for its endocrine activity as an antiestrogenic agent. Its citrate salt, a widely used pharmaceutical agent, appears in three main polymorphic forms, two of which are well known (I and II) and another form not yet well evidenced.

A vibrational study has been conducted for identifying the two known polymorphic forms of tamoxifen citrate (I and II) and for characterising the other form (form III) examined in this study.

Other techniques for the characterization of the different polymorphs, such as XRDP, have been used.     

Fragment chemistry of the hydrogen thioperoxide molecule; energy, chemical potential and hardness

In this paper we present a complete theoretical study of the hydrogen thioperoxide molecule (HSOH). We characterize the internal rotation by studying the evolution of the energy, chemical potential and hardness along the torsional angle. We have found that hydrogen thioperoxide in its electronic singlet state is a gauche molecule. Barrier heights, activation chemical potential and activation hardness have been obtained, and it has been found that the trans barrier is lower than the cis one. Good agreement of rotation barriers is obtained on the basis of comparisons with the available literature experimental data for the HOOH and HSSH parent molecules. Another important result is that the maximum hardness principle is verified for the torsional motion. On the other hand, we characterize the thermochemistry of chemical reactions leading to formation of HSOH from the electronic properties associated with the free constituent fragments. The procedure, which involves the use of Sanderson's rule to estimate chemical potentials and hardnesses, is shown to be promising and opens the possibility of rationalizing the behavior of other series of reactions.     

Vibrational assignment and rotational isomerism of 2-chloro-1-butene and 2-bromo-1-butene

Infrared spectra were obtained for 2-chloro-l-butene and 2-bromo-l-butene that show the presence of trans and gauche rotamers in both compounds. Vibrational assignments were made with the aid of normal coordinate calculations that utilized a thirty-eight parameter valence force field.     

An ab initio SCF study of conformational isomerism in HNO2

The structures and complete force fields of cis and trans nitrous acid have been calculated with a (7, 3) basis set. The differences between the two stable isomers are reproduced well. The dipole moments, centrifugal distortion constants, vibrational frequencies and isotope shifts also agree satisfactorily with observed values. The fully optimized structures of rotamers corresponding to intermediate values of internal rotation around the N-O bond have been calculated to investigate structural changes during internal rotation. The considerable changes show the strong influence of π electron delocalization in the planar forms. The barrier is calculated to be 8.7 kcal mol⁻¹ in reasonable agreement with experimental values. Both the cis and trans barriers are calculated to be attractive dominant in contradiction to earlier work.     

Conformations and barriers to internal rotation in trans-diarylethylenes: Theoretical investigation using a new INDO-type method (C-INDO)

C-INDO, a new INDO-based technique specially devised for conformational studies of conjugated systems, is used to investigate conformational equilibria in ground state trans-diarylethylenes, as revealed by a number of emission spectroscopic observations (both steady-state and time resolved). Conformations, ΔE and barriers to internal rotation are provided for all the possible rotamers of 1-StN (1-styrilnaphthalene), 2-StN, 2,2′-DNE (2,2′-dinaphthylethylene) and 1,2′-DNE. Energetic parameters are used to predict the relative abundances of the distinct rotameric species at equilibrium as well as to estimate the rate at which equilibria are established (at different T). The results prove to be a consistent basis on which experimentally observed behaviour can be rationalized.     

Computer simulation of chiral liquid crystal phases. IV. Intermolecular chirality transfer to rotamers in a cholesteric phase

Intermolecular chirality transfer was studied by investigating the conformational distribution of rotamers in a cholesteric guest-host phase using Monte Carlo (MC) simulations in the NVT ensemble. The guest-host system under investigation was given by N_c = 238 rigid, chiral Gay-Berne atropisomers as host molecules and N_a = 18 flexible Gay-Berne rotamers as guest molecules. The rigid, chiral Gay-Berne atropisomers of point symmetry group D₂ were defined by joining two Gay-Berne particles through a bond with a suitable fixed dihedral angle. The possibility of internal rotation about the bond axis without a rotational barrier was introduced as an internal degree of freedom for the guest molecules, for convenience denoted as Gay-Berne rotamers. Starting from an isotropic configuration, cholesteric phases were obtained on equilibrating the guest-host systems, whereby left-handed and right-handed cholesterics were formed depending on the M- and P-helicity of the atropisomers, respectively. Analysing the conformational distribution of the guest molecules in the cholesteric phase, we found an enantiomeric excess of rotamers of the guest molecules with the same helicity as the host molecules which is favoured on account of the intermolecular interactions in the cholesteric phase.     

Molecular orientation of azobenzene chromophores in ultrathin polymer nanosheets studied by attenuated total reflection spectroscopy

This paper describes characterization of molecular orientation for azobenzene moieties in a polymer nanosheet. Copolymers of N-[4-(phenylazo)phenyl] acrylamide (PAZoA) with tert-pentyl acrylamide (tPA) were synthesized and the monolayers deposited on tapered quartz waveguides by Langmuir–Blodgett (LB) technique. Spectroscopic properties of the copolymer (p(tPA/PAZoA)) monolayers were monitored by integrated optical waveguide technique on the molecular level. Molecular orientation of the azobenzene was precisely determined by polarized absorption spectra. It was found that the azobenzene groups took a horizontal orientation and distributed uniformly in the p(tPA/PAZoA) monolayer without significant PAZoA aggregation. Photoisomerization process from trans to cis form was also investigated. More than half of the trans form (60–70%) was photoisomerized under unpolarized light irradiation, and the photoisomerization rate was independent on the PAZoA contents. This implies that the microenvironment of PAZoA moieties was almost the same in three different p(tPA/PAZoA) monolayers.     

Atomic charges for molecular dynamics calculations

Atomic charges obtained with the fit of the ab initio electrostatic potential suffers of several defects, for instance, chemical meaning is not insured. We have employed a method recently put forward for deriving atomic charges which addresses the issue of chemical meaning and conformational transferability to N,N-dibutylacetamide and ethylenediaminetetraacetate. The charges have been used in molecular dynamics calculations where the interaction with a metallic cation is considered. We found structural parameters for the complexes in good agreement with the available experimental results.     

Syntheses, crystal structures and electronic properties of a series of copper(II) complexes with 3,5-halogen-substituted Schiff base ligands and their solutions

We have systematically investigated the structural features, electronic properties, thermally-induced structural phase transitions and absorption spectra depending on the solvent for ten Cu(II) complexes with 3,5-halogen-substituted Schiff base ligands. Structural characterization of two new complexes, bis(N-R-1-phenylethyl- and N-R,S-2-butyl-5-bromosalicydenaminato-κ²N,O)copper(II), reveals that they afford a compressed tetrahedral trans-[CuN₂O₂] coordination geometry with trans-N–Cu–N = 159.4(2)° and trans-O–Cu–O = 151.7(3)° for the 1-phenylethyl complex and trans-N–Cu–N = 157.9(3)° and trans-O–Cu–O = 151.0(3)° for the 2-butyl one. All the complexes exhibit a structural phase transition by heating in the solid state regardless of their structures at room temperature. The absorption spectra of a series of ten complexes exhibit a slight shift of the d–d band at 16 000–20 000 cm⁻¹ and remarkable shift of the π–π* band at 24 000–28 000 cm⁻¹, which suggests that the dipole moment of the solvents presumably affects the conformation of the π-conjugated moieties of the ligands rather than the coordination environment. We have also attempted ‘photochromic solute-induced solvatochromism’ by a system of bis(N-R-1-phenylethyl-3,5-dichlorosalicydenaminato-κ²N,O)copper(II) and photochromic 4-hydroxyazobenzene in chloroform solution. We successfully observed a change of the d–d and π–π* bands of the complex in the absorption spectra caused by cis–trans photoisomerization of 4-hydroxyazobenzene.     

Vibrational spectrum and structure of dimethylamino-dichloroarsine

The infrared spectra of solid and gaseous dimethylaminodichloroarsine have been recorded from 4000 to 33 cm⁻¹. The Raman spectra of the liquid and solid phases have also been recorded. A comparison of the Raman spectra of the liquid and solid indicates that there is a change in conformational composition between the two phases. The isomer present at room temperature in the liquid and gas phases is assigned to the trans form. A study of the temperature dependence of the intensities of the Raman spectrum indicates that the trans form is converted to a second isomer which is believed to be the gauche isomer as the temperature is decreased. At −190°C, the Raman intensities indicate that the molecule still exists as a mixture of these two isomers. A vibrational assignment is presented and discussed in detail.     

Cis- and trans-3-hexene: infrared spectrum in liquid argon solution, ab initio calculations of equilibrium geometry, normal coordinate analysis, and vibrational assignments

The infrared spectra of cis-3-hexene and trans-3-hexene dissolved in liquid argon have been obtained at temperatures from 93 to 120 K. The absorptions were observed with a low-temperature cell and a Fourier transform infrared spectrophotometer. Ab initio molecular orbital calculations were performed to obtain the equilibrium geometry, vibrational frequencies, force fields, and infrared intensities. The calculations were done at the Hartree-Fock level using 6-31G basis set. The Cartesian force fields from ab initio calculations have been converted to the force field in symmetry coordinates. The scale factors of ab initio calculated force fields were determined. Normal coordinate calculations were performed using a scaled quantum mechanical (SQM) force field. Vibrational normal modes calculated for the lowest energy rotamers of cis- and trans-3-hexene have been assigned to infrared absorption bands observed in liquid argon solution. The assignments were based on calculated frequencies and potential energy distributions. The equilibrium geometries of the two lowest energy rotamers (symmetry C₂ and C_s) of cis-3-hexene and of the three lowest energy rotamers (symmetry C_i, C₂, and C₁) of trans-3-hexene were calculated. Variable temperature studies of the infrared spectrum of cis- and trans-3-hexenes dissolved in liquid argon were done to obtain the ΔH of conversion between the rotamers C₂ and C_s of cis-3-hexene and between the rotamers C_i, C₂, and C₁ of trans-3-hexene.     

Effect of “topotactic” reduction product of molybdenum disulfide on catalytic activity of metallocene catalyst for olefin polymerization

N,N-Dimethylanilinium salt of molybdenum disulfide (MoS₂) was developed as a novel cocatalyst for metallocene catalysts. The cocatalyst is composed of N,N-dimethylanilinium ion as a cationic part and “topotactic” reduction product of MoS₂, obtained by acquisition of an electron by neutral host lattice of MoS₂ without structural alteration, as an anionic part. In ethylene polymerization, addition of the N,N-dimethylanilinium salt of MoS₂ to the bis(indenyl)zirconium dichloride (Ind₂ZrCl₂)/triethylaluminum (Et₃Al) catalyst improved the catalytic activity per mmol of Ind₂ZrCl₂. The catalytic activity of this system activated by addition of the cocatalyst depended significantly on the amount of the cocatalyst and the N,N-dimethylanilinium ion content in the cocatalyst. Poly(ethylene) and poly(ethylene-co-1-hexene) obtained with the metallocene catalyst activated by addition of the cocatalyst have typical features such as narrow molecular weight distribution and narrow composition distribution like polymers obtained with conventional metallocene catalysts.     

Ab initio analysis of the conformational changes of the prolyl-proline model peptide

For- -Pro- -Pro-NH₂ is an ab initio model of the prolyl-proline sequence unit present in numerous peptides and proteins. Cis–trans isomerization of the peptide linkage is a crucial step in accessing the active conformation of several proline containing macromolecules.

The present study focuses on the flexibility of the five-membered pyrrolidine ring, which is considered to help other conformational changes as well as cis–trans isomerization. Ring flexibility is characterized by the pseudorotational amplitude, A, and the phase angle, P. Calculations are carried out at the RHF/6-31+G(d) level of theory. The choice of method and level of theory is further supported by single point DFT calculations.

In the course of NMR structure determination of peptides or proteins, proline residues present in the sequences need special attention. Because of the lack of an amide hydrogen, sequential assignment of proline is rather complicated. Furthermore, in solution state, peptide cis–trans isomers are almost always present. Ab initio study on the For- -Pro- -Pro-NH₂ model is a useful tool to discover the structural characteristics of the prolyl-proline sequence unit.     

Conformational study of CH3OP(O)Cl2 and CD3OP(O)Cl2 : Part 2. Gas phase spectra and profile sinulation

The gas phase infrared- and far infrared spectra of the normal and totally deuterated molecules have been recorded and are briefly discussed.

Rigid-rotor asymmetric top profiles for gauche and trans conformers were used to simulate the experimental gas phase infrared absorption profiles of four conformational doublets of CH₃OP(O)Cl₂. From this, a consistent assignment of the more intense component of each doublet to the gauche, and the less intense component to the trans conformer, is deduced.     

Raman and infrared spectra, conformational stability, ab initio calculations and vibrational assignments for 2-chloroethyl silane

The infrared (3500–30 cm⁻¹) spectra of gaseous and solid and the Raman (3500–10 cm⁻¹) spectra of liquid with quantitative depolarization ratios and solid 2-chloroethyl silane, ClCH₂CH₂SiH₃, have been recorded. Similar data have been recorded for the Si–d₃ isotopomer. These data indicate that two conformers, trans and gauche, are present in the fluid states but only one conformer, trans, is present in the solid. The mid-infrared spectra of the sample dissolved in liquified xenon as a function of temperature (−55 to −100°C) has been recorded. The enthalpy difference between the conformers has been determined to be 181±12 cm⁻¹ (2.17±0.14 kJ/mol) with the trans rotamer the more stable form. From the isolated Si–H frequencies from the Si–d₂ isotopomer the r_o Si–H distances of 1.484 and 1.483 Å for the trans and 1.481 for the gauche conformers have been obtained. Ab initio calculations have been carried out with several different basis sets up to MP2/6-311+G** from which structural parameters and conformational stabilities have been determined. With all the basis sets the trans form is predicted to be the more stable conformer which is consistent with the experimental results. These results are compared to the corresponding quantities for the carbon analogue.     

Base induced C-5 epimerisation of 4-methyl-5-phenyl oxazolidinones: Chiral auxiliaries derived from norephedrine and norpseudoephedrine.

Treatment of cis- and trans-4-methyl-5-phenyl oxazolidinones 2 and 3 with excess butyllithium at 0°C results in C-5 epimerisation, via a common intermediate N,C-5-dianion, generating after protonation a 1:4 mixture of 2:3.     

Interaction in trans-2-halocyclohexanols — an infrared and theoretical study

The O–H and C–O stretching frequencies of trans-2-halocyclohexanols in CCl₄ solutions have been measured and theoretical calculations have been performed to elucidate the main interactions, which are responsible for the conformational equilibria in these systems. It can be concluded that hydrogen bonding is predominant for trans-2-fluorocyclohexanol, leading to a stabilization of the eq–eq conformation, while for the chlorine, bromine and iodine derivatives, besides hydrogen bonding, gauche and steric interactions are also present.     

X-ray diffraction studies on cis- and trans-4'-cyanobiphenyl-4-yl 3-n-propylcyclobutane-1-carboxylate

X-ray diffraction has been used to study the nematic phases of the cis and trans isomers of an elongated molecule containing the cyclobutane group. It has been shown that these nematic phases consist of a mixture of single molecules and overlapping core dimers. It has been found that increasing the temperature of the cis isomer rapidly reduces the dimer population, whereas increasing the temperature of the trans isomer enhances the dimer population. This provides an explanation of the relatively high clearing temperature of the trans isomer. The different temperature dependences of the dimer population in the cis and trans isomers has been explained by a model involving inversion of the cylobutane group.