Experimental and theoretical electron density study of estrone

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.     

Experimental and theoretical electron momentum spectroscopic study of the valence electronic structure of tetrahydrofuran under pseudorotation

The most populated structure of tetrahydrofuran (THF) has been investigated in our previous study using electron momentum spectroscopy (EMS). Because of the relatively low impact energy (600 eV) and low energy resolution (DeltaE = 1.20 eV) in the previous experiment, only the highest occupied molecular orbital (HOMO) of THF was investigated. The present study reports the most recent high-resolution EMS of THF in the valence space for the first time. The binding energy spectra of THF are measured at 1200 and 2400 eV plus the binding energies, respectively, for a series of azimuthal angles. The experimentally obtained binding energy spectra and orbital momentum distributions (MDs) are employed to study the orbital responses of the pseudorotation motion of THF. The outer valence Greens function (OVGF), the OVGF/6-311++G** model, and density function theory (DFT)-based SAOP/et-pVQZ model are employed to simulate the binding energy spectra. The orbital momentum distributions (MDs) are produced using the DFT-based B3LYP/aug-cc-pVTZ model, incorporating thermodynamic population analysis. Good agreement between theory and experiment is achieved. Orbital MDs of valence orbitals exhibit only slight differences with respect to the impact energies at 1200 and 2400 eV, indicating validation of the plane wave impulse approximation (PWIA). The present study has further discovered that the orbital MDs of the HOMO in the low-momentum region (p < 0.70 a.u) change significantly with the pseudorotation angle, phi, giving a v-shaped cross section, whereas the innermost valence orbital of THF does not vary with pseudorotation, revealing a very different bonding mechanism from the HOMO. The present study explores an innovative approach to study pseudorotation of sugar puckering, which sheds a light to study other biological systems with low energy barriers among ring-puckering conformations.     

Relationship between retention behavior and molecular structure in HPLC. Correlation between solubility parameter and molecular properties

Chromatographia - The application and significance of the solubility parameter are detailed for chromatographic systems. A critical review of the general concept and several empirical and...     

Experimental and theoretical investigation of the molecular and electronic structure of anticancer drug camptothecin

The Fourier Transform Infrared spectrum of (S)-4 ethyl-4-hydroxy-1H-pyrano [3',4':6,7]-indolizino-[1,2-b-quinoline-3,14-(4H,12H)-dione] [camptothecin] was recorded in the region 4000-400 cm(-1). The Fourier Transform Raman spectrum of camptothecin (CPT) was also recorded in the region 3500-50 cm(-1). Quantum chemical calculations of geometrical structural parameters and vibrational frequencies of CPT were carried out by MP2/6-31G(d,p) and density functional theory DFT/B3LYP/6-311++G(d,p) methods. The assignment of each normal mode has been made using the observed and calculated frequencies, their IR and Raman intensities. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. Most of the computed frequencies were found to be in good agreement with the experimental observations. The isotropic chemical shifts computed by (13)C and (1)H NMR analysis also show good agreement with experimental observations. Comparison of calculated spectra with the experimental spectra provides important information about the ability of computational method to describe the vibrational modes of large sized organic molecule.     

An electron diffraction study of the molecular structure of hexamethyldisiloxane

An electron diffraction determination of the molecular geometry of hexamethyldisiloxane has removed much of the uncertainty concerning this structure. The length of the SiO bond and the SiOSi bond angle were determined to be 1.631 ± 0.003 Å and 148 ± 3°, respectively. The experimental data are consistent with a staggered conformation (C_2v symmetry) while a model with twist angles around the SiO bonds of about 30° cannot be excluded. The molecule is probably performing large amplitude intramolecular motion.     

An electron diffraction study of the molecular structure of meta-difluorobenzene

The molecular structure of meta-difluorobenzene in the gas phase has been determined by electron diffraction at room temperature. The carbon ring deviates slightly from D_6h symmetry. The four C-C distances adjacent to the F atoms are 1.384 Å, the two other C-C distances are slightly longer, i.e. 1.405 Å. The C-F and C-H distances are 1.324 and 1.107 Å. The C-C-F valency angle is 119.5°.     

Relationship between retention and molecular structure of pyrimidine bases

Summary The influence of the type and position of CH₃, NH₂ and OH groups in the pyrimidine ring, the eluent composition and the surface chemistry of the stationary phase on the retention of pyrimidine bases in reversed-phase liquid chromatography was investigated. On the basis of the hypothesis about the additivity of the adsorption energy the contribution of various structural groups on retention has been established.     

A theoretical study of photoinduced electron transfer between tetracyanoethylene and arene

 Ab initio calculations have been performed to investigate the state transition in photoinduced electron transfer reactions between tetracyanoethylene and biphenyl as well as naphthalene. Face-to-face conformations of electron donor–acceptor (EDA) complexes were selected for this purpose. The geometries of the EDA complexes were determined by using the isolated optimized geometries of the donor and the acceptor to search for the maximum stabilization energy along the center-to-center distance. The correction of interaction energies for basis set superposition error was considered by using counterpoise methods. The ground and excited states of the EDA complexes were optimized with complete-active-space self-consistent-field calculations. The theoretical study of the ground state and excited states of the EDA complex in this work reveals that the S₁ and S₂ states of the EDA complexes are charge–transfer (CT) excited states, and CT absorption which corresponds to the S₀→S₁ and S₀→S₂ transitions arise from π−π^* excitation. On the basis of an Onsager model, CT absorption in dichloromethane was investigated by considering the solvent reorganization energy. Detailed discussions on the excited state and on the CT absorptions were made. Received: 30 April 2001 / Accepted: 18 October 2001 / Published online: 9 January 2002     

Gas electron diffraction study of the molecular structure of NbCl4

The structure of the NbCl₄ molecule is studied experimentally by the synchronous electron diffraction and mass spectrometry methods. The model molecular geometries of C_2v, C_3v, D_2d, and T_d symmetries are verified. The advantages of the tetrahedral model over the other models are established. The thermally averaged parameters of the effective configuration of the NbCl₄ molecule are as follows: r_g(Nb?Cl)=2.279(5) Å, l(Nb?Cl)=0.073(2) Å, r_g(Cl?Cl)=3.692(17) Å, l(Cl?Cl)=0.275(11) Å, ∠_g(Cl-Nb-Cl)=108.2(5)°, and δ(Cl?Cl)=0.030(19) Å.     

A gas-phase electron diffraction study of the molecular structure of tetravinylsilane

The molecular structure of tetravinylsilane has been studied by gas-phase electron diffraction. The radial distribution curve suggests the absence of conformers having vinyl double bonds staggered with respect to the SiC₄ skeleton. Of the eclipsed or approximately-eclipsed conformers, the one with S₄ symmetry gives the best fit with experiment, although a small admixture of a C₁ conformation cannot be ruled out. Least-squares refinement gave the following values for the independent structural parameters (lengths, r_a basis; angles, r_α basis): C-H = 1.118 ± 0.003 Å, CC = 1.355 ± 0.002 Å, Si-C = 1.855 ±0.002 Å, ∠SiCC = 124.0 ± 0.3°, ∠SiCH = 118.4 ± 1.0°, torsion angles CSiCC are 17.5 ± 0.6° from the eclipsed conformation. During the refinement the vibrational amplitudes u and perpendicular amplitude corrections K were held constant at calculated values. The CC bond length provides evidence of interaction between the vinyl π-bonds and the vacant d-orbitals of silicon.     

A gas electron diffraction study of the molecular structure of trans-stilbene

The molecular structure of trans-stilbene has been studied by the gas electron diffraction method. Unlike the approximately planar structure with C_i symmetry found for the solid state, the molecule in the gas phase was found to be non-planar and to possess C₂ symmetry. The phenyl groups were found to be rotated ca. 30° about the C-φ bonds. The non-planarity of the molecule is, however, not so large as to seriously influence the resonance energy.     

An electron diffraction study of the molecular structure of gaseous cyclobutylgermane

The molecular structure and conformation of cyclobutylgermane have been determined by gas-phase electron diffraction. Like its counterpart cyclobutylsilane (CBS) it possesses quasi-equatorial and quasi-axial conformers. The most interesting aspect of the structure of CBG is the influence of the germyl group on the ratio of equatorial to axial conformers. The predominance of the quasi-equatorial conformer (ΔG = 3.1(1) kJ mol⁻¹), the near equality of the skeleton C---C bond lengths (C---C = 1.557(3)A) (r_a value) and the values of the puckering angles for the equatorial angles form and the axial one of 25.3(3.1)° and −20.4(3.6)° respectively, all support the predictions made by Jonvik and Boggs concerning the correlation between electronegativity and structural parameters in four-membered rings. From a consideration of these predictions, a comparison of the most prominent structural factors in CBG and cyclobutylsilane indicates that the germanium atom is more electronegative than silicon. This result could be considered as the first structural evidence for the previously postulated inversion of the electronegativity order within group IV.     

A gas electron diffraction study of the molecular structure of cis-stilbene

The cis-Stilbene molecule is found to possess C₂ symmetry and may be described as having a propeller-like conformation with the phenyl groups rotated ca. 43° about the C-φ bonds. The deviation from planarity is found to be more extensive than predicted by most theoretical calculations. The steric strain in the molecule is also revealed by large valence angles at the central carbon-carbon double bond (∠CC-C: 129.5°).     

An electron diffraction study of the molecular structure of 1,2-difluoroethane

The molecular structure of 1,2-difluoroethane in the gas phase has been determined by electron diffraction at room temperature. Only the gauche conformation was found, the dihedral angle F-C-C-F is 74.5°. The bond lengths r_g(1) are: r(C-C) = 1.535 Å, r(C-F) = 1.394 Å, r(C-H) = 1.13 Å. The valency angles are: α(C-C-F) = 108.3, α(C-C-H) = 108.3. The dihedral angle between the C-C-F and C-C-H planes is 113.6°.     

The molecular structure and conformation of trichloronitromethane as determined by gas-phase electron diffraction and theoretical calculations

The molecular structure of trichloronitromethane has been studied in the gas phase using electron diffraction data. The molecules are found to undergo low barrier rotation about the CN bond with a planar CNO₂ moiety in agreement with HF/MP2/B3LYP/6-311G(d,p) calculations. The experimental data are consistent with a dynamic model using a potential function for the torsion of V = (V₆/2)(1 − cos 6τ). The major geometrical parameters (r_g and ) for the eclipsed form, obtained from least squares analysis of the data are as follows: r(NO₃) = r(NO₄) = 1.213(2) Å, r(CN) = 1.592(6) Å, r(CCl)_av = 1.749(1) Å, Cl₅CN/Cl₆CN = 109. 6°/106.3°(2), O₃NC/O₄NC = 117. 6°/114.1°(4), τCl₅C₁N₂O₃ = 0.0°, and V₆ = 0.20(25) kcal/mol.     

Experimental and theoretical study of the electronic structure of methyl chloroformate and methyl cyanoformate

The HeI photoelectron spectra of methyl chloroformate (CH₃OC(O)Cl) and methyl cyanoformate (CH₃OC(O)CN) in the gas phase have been obtained for the first time. A complete theoretical study involving the calculation of the ionization energies using outer valence Green’s functional (OVGF) was performed, based on the calculated and previously reported energetically favorable cis-conformer (the carbonyl group eclipses the methyl group). Calculations of cationic-radical forms were carried out in order to interpret the main characters of the first six highest occupied molecular orbitals (HOMOs). The first vertical ionization potentials are 11.36 eV for CH₃OC(O)Cl and 11.65 eV for CH₃OC(O)CN, each attributed to {19a′(n_O(CO), n_Cl)}⁻¹ and {18a′(n_O(CO))}⁻¹, respectively.     

Effects of molecular structure on the stability of a thermotropic liquid crystal. Gas electron diffraction study of the molecular structure of phenyl benzoate.

As a model of the core of molecules forming liquid crystals, the molecular structure of phenyl benzoate (Ph-C(=O)-O-Ph) at 409 K was determined by gas electron diffraction, and the relationship between the gas-phase structures of model compounds and the nematic-to-liquid transition temperatures was studied. Structural constraints were obtained from RHF/6-31G ab initio calculations. Vibrational mean amplitudes and shrinkage corrections were calculated from the harmonic force constants given by normal coordinate analysis. Thermal vibrations were treated as small-amplitude motions, except for the phenyl torsion, which was treated as a large-amplitude motion. The potential function for torsion was assumed to be V(phi(1),phi(2)) = V(12)(1 - cos 2phi(1))/2 + V(14)(1 - cos 4phi(1))/2 + V(22)(1 - cos 2phi(2))/2, where phi(1) and phi(2) denote the torsional angles around the C-Ph and O-Ph bonds, respectively. The potential constants (V(ij)()/kcal mol(-)(1)) and the principal structure parameters (r(g)/A, angle(alpha)/deg) with the estimated limits of error (3sigma) are as follows: V(12) = -1.3 (assumed); V(14) = -0.5(9); V(22) = 3.5(15); r(C=O) = 1.208(4); r(C(=O)-O) = 1.362(6); r(C(=O)-O) - r(O-C) = -0.044 (assumed); r(C(=O)-C) = 1.478(10); = 1.396(1); angleOCO = 124.2(13); angleO=CC = 127.3(12); angleCOC = 121.4(22); ( angleOCC(cis) - angleOCC(trans))/2 = 3.0(15); ( angleC(=O)CC(cis) - angleC(=O)CC(trans))/2 = 4.8(17), where < > means an average value and C-C(cis) and C-C(trans) bonds are cis and trans to the C(=O)-O bond, respectively. The torsional angle around the O-Ph bond was determined to be 64(+26,-12) degrees. An apparent correlation was found between the contributions of the cores to the clearing point of liquid crystals and the gas-phase structures of model compounds of the cores of mesogens, i.e., phenyl benzoate, trans-azobenzene (t-AB), N-benzylideneaniline, N-benzylideneaniline N-oxide (NBANO), trans-azoxybenzene (t-AXB), and trans-stilbene. The structures of t-AB, NBANO, and t-AXB have been obtained by our research group.     

Experimental and theoretical study on the structure and reactions of 1-methoxypropane radical cations

Structure and mechanism of thermal and photochemical reactions of radical cations of methyl n-propyl ether (MPE) were studied in irradiated freonic matrices CFCl₃, CF₂ClCFCl₂, and CF₃CCl₃ at 77 K. The quantum chemical calculations of the structure of radical cations and products of their transformations were carried out with methods based on the density functional theory (DFT). Experimental and calculation results show that the MPE radical cations are characterized by substantial delocalization of spin density to the propyl group. The action of light on the MPE radical cations in a CF₃CCl₃ matrix at 77 K results in intramolecular rearrangement yielding the distonic radical cation ^.CH₂CH₂CH₂(OH⁺)CH₃. It was found that the primary MPE radical cations underwent irreversible transformation to CH₃CH₂CH₂OCH ₂ ^. radical as a result of an ion-molecule reaction that occurred in a CF₂ClCFCl₂ matrix upon heating the sample to 110–120 K or in a CFCl₃ matrix upon increasing the solute concentration.Translated from Khimiya Vysokikh Energii, Vol. 39, No. 2, 2005, pp. 105–113.Original Russian Text Copyright © 2005 by Belevskii, Feldman, Tyurin.This revised version was published online in April 2005 with a corrected cover date.     

Tuning the electron structure enables the NiZn alloy for CO2 electroreduction to formate

Formate is an important liquid chemical,which can be produced by electrocatalytic carbon dioxide reduction reaction (CO2RR).Most of the metal catalysts for CO2R...