To the question on radiationless transitions in electronically excited zones of molecular crystals

A model is proposed describing the dynamics of radiationless transitions in the energy zones corresponding to excited electronic states in molecular crystals. In this model, the migration effect is explicitly reflected, which initially appears under pulse excitation of the systems with a periodical structure of a density distribution of states in separate parts of molecular crystals.     

外电场对甲醛分子的结构与电子光谱的影响

采用密度泛函理论(DFT)在B3LYP/6-311++G(d,p)基组水平上,计算了不同外加电场(-8.22×10~9~8.22×10~9 V/m)下甲醛分子基态稳定构型、分子键长、电荷分布、能级分布、能隙、红外光谱、拉曼光谱和分子的总能量.在此基础上利用TDDFT/B3LYP/6-311++G(d,p)方法研究了甲醛分子由基态跃迁到前25个激发态的激发能E、谐振强度f、吸收波长λ受外电场的影响.结果表明:随着C=O连线方向外电场的增加,C=O键键长、氢原子电荷、偶极矩和能隙递增;C—H键键长、C,O原子电荷递减,总能量降低.振动频率与红外强度及拉曼强度由于不同振动有不同变化.甲醛分子UV-Vis光谱随外电场的增加,不同的吸收峰发生了不同程度的蓝移或者红移;外电场对甲醛分子的激发能、谐振强度和吸收波长的强度有一定影响,但随电场变化比较复杂.     

Influences of the molecule–electrode interface structure on the conducting characteristics of the gold-4,4 bipyridine-gold molecular junction

Two popular models of the gold-4,4 bipyridine (44BPD)-gold molecular junction, i.e., the direct contact of the 44BPD molecule with the Au(1 1 1) surface and the intermediary contact through one extra gold atom on each side, were studied using density functional theory calculations under periodic boundary conditions. The relative position of the Fermi level is changed by the extra gold atom from well below the LUMO (lowest unoccupied molecular orbital) of the 44BPD molecule in the direct contact model to within the energy range of the LUMO in the intermediary contact model, indicating that the local structure of the contact can significantly affect the conducting characteristics of the junction. The dependence of the molecule–electrode interaction on the interface structure was also investigated in details.     

The molecular structure of tetra-tert-butyldiphosphine: an extremely distorted, sterically crowded molecule

The molecular structure of tetra-tert-butyldiphosphine has been determined in the gas phase by electron diffraction using the new DYNAMITE method and in the crystalline phase by X-ray diffraction. Ab initio methods were employed to gain a greater understanding of the structural preferences of this molecule in the gas phase, and to determine the intrinsic P-P bond energy, using recently described methods. Although the P-P bond is relatively long [GED 226.4(8) pm; X-ray 223.4(1) pm] and the dissociation energy is computed to be correspondingly small (150.6 kJ mol(-1)), the intrinsic energy of this bond (258.2 kJ mol(-1)) is normal for a diphosphine. The gaseous data were refined using the new Edinburgh structure refinement program ed@ed, which is described in detail. The molecular structure of gaseous P(2)Bu(t)(4) is compared to that of the isoelectronic 1,1,2,2-tetra-tert-butyldisilane. The molecules adopt a conformation with C(2) symmetry. The P-P-C angles returned from the gas electron diffraction refinement are 118.8(6) and 98.9(6) degrees, a difference of 20 degrees, whilst the C-P-C angle is 110.3(8) degrees. The corresponding parameters in the crystal are 120.9(1), 99.5(1) and 109.5(1) degrees. There are also large deformations within the tert-butyl groups, making the DYNAMITE analysis for this molecule extremely important.     

Strong effects of molecular structure on electron transport in carbon/molecule/copper electronic junctions

Carbon/molecule/copper molecular electronic junctions were fabricated by metal deposition of copper onto films of various thicknesses of fluorene (FL), biphenyl (BP), and nitrobiphenyl (NBP) covalently bonded to flat, graphitic carbon. A "crossed-wire" junction configuration provided high device yield and good junction reproducibility. Current/voltage characteristics were investigated for 69 junctions with various molecular structures and thicknesses and at several temperatures. The current/voltage curves for all cases studied were nearly symmetric, scan rate independent, repeatable at least thousands of cycles and exhibited negligible hysteresis. Junction conductance was strongly dependent on the dihedral angle between phenyl rings and on the nature of the molecule/copper "contact". Junctions made with NBP showed a decrease in conductivity of a factor of 1300 when the molecular layer thickness increased from 1.6 to 4.5 nm. The slope of ln(i) vs layer thickness for both BP and NBP was weakly dependent on applied voltage and ranged from 0.16 to 0.24 A(-1). These attenuation factors are similar to those observed for similar molecular layers on modified electrodes used to study electrochemical kinetics. All junctions studied showed weak temperature dependence in the range of approximately 325 to 214 K, implying activation barriers in the range of 0.06 to 0.15 eV. The carbon/molecule/copper junction structure provides a robust, reproducible platform for investigations of the dependence of electron transport in molecular junctions on both molecular structure and temperature. Furthermore, the results indicate that junction conductance is a strong function of molecular structure, rather than some artifact resulting from junction fabrication.     

All-atom molecular simulation study of cellulose acetate: amorphous structure and the dissolution of small molecule

All-atom analysis was conducted for cellulose acetate (CA) using molecular dynamics simulation. The intermolecular interactions were elucidated at the amorphous state with degrees of acetyl substitution (DS) of 2, 2.5, and 3, and the energetics of dissolution was treated for H₂O, CO₂, and CH₄. It was observed for the CA amorphous that DS strongly affects the hydrogen bonding among the hydroxy groups of CA and that the short-range packing of pyranose rings becomes tighter with acetylation. The free energy of dissolution was computed by the energy-representation method of solvation. The dissolution into CA was more favorable in the order of H₂O?>?CO₂?>?CH₄, and the DS dependence of the dissolution free energy was evident only for H₂O between DS?=?2 and 2.5. The roles of the intermolecular interaction components were further addressed. It was seen that the electrostatic component brings the DS dependence of the dissolution free energy for H₂O as well as the difference in the affinity to CA between CO₂ and CH₄. The van der Waals component was still dominant for the nonpolar CO₂ and CH₄, and the summed contribution to it from the acetyl and main-chain groups of CA was weakly dependent on DS. The connection of the dissolution energetics with the underlying structures is also discussed.

Graphical abstract

     

The question of the chemical structure of amber

Summary 1. The identity of the IR spectra of the main types of amber (transparent, semitransparent, opaque and bone ambers) in the 700–2000 cm^–1 region has been confirmed. At the same time, differences between them have been shown by elemental analysis.2. In order to isolate the fraction of amber soluble in alcohol, extraction with boiling alcohol instead of by prolonged extraction at room temperature has been proposed.3. The amber fraction soluble in alcohol and petroleum ether can be separated into acid and ester (lactone) fractions by successive treatment of its ethereal solution with 1% and 15% aqueous alkalis.4. The acid fraction isolated from the alcohol-soluble and the petroleum ether-insoluble fractions of amber have similar IR spectra but differ in elemental composition.5. Succinin contains lactone (or ester) groupings whose hydrolysis forms hydroxyacids.Khimiya Prirodnykh Soedinenii, Vol. 2, No. 6, pp. 429–436, 1966     

Effect of the type of molecular nonplanar structure on the chemical reactivity of NH bonds in the coordination center of porphyrin molecule

Russian Journal of General Chemistry - Effect of out-of-plane screwing of the porphyrin macrocycle (H2P) by means of tetra-meso-substitution and intracyclic N-substitution on the state of NH bonds...     

Theoretical electronic structure of the molecule ScBr

The potential energy curves have been investigated for the 23 lowest electronic states in the ^2s+1Λ^± representation of the molecule ScBr via CASSCF and MRCI (single and double excitations with Davidson correction) calculations. Seventeen electronic states have been studied theoretically for the first time. The harmonic frequency ω_e, the internuclear distance r_e, and the electronic energy with respect to the ground state T_e have been calculated. By using the canonical functions approach, the eigenvalues E_v, the rotational constant B_v, and the abscissas of the turning points (R_min, R_max) have been calculated for electronic states up to the vibrational level v = 32. The comparison of these values to the theoretical and experimental results available in the literature shows a good agreement. © 2007 Wiley Periodicalsm Inc. Int J Quantum Chem, 2008     

Theoretical electronic structure of the molecule ScI

Theoretical investigation of the 18 lowest electronic states of the molecule ScI in the representation ^2S+1Λ^(±) has been performed via CASSCF and MRCI (single and double excitation with Davidson correction) calculations. To the best of our knowledge these calculated electronic states are the first ones from ab initio methods. Thirteen electronic states between 4,500 cm^?1 and 21,000 cm^?1 have been studied for the first time and have not yet been observed experimentally. The harmonic frequency ω_e, the internuclear distance R_e, the electronic transition energy with respect to the ground state T_e, and the rotational constant B_e have been calculated for the considered electronic states. By using the canonical functions approach the eigenvalues E_υ and the rotational constants B_υ have also been calculated for the six lowest‐lying electronic states. The comparison of these results with the theoretical and the experimental data available in the literature shows a good agreement. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Equilibrium structure of the GeI4 molecule

Ivanovo Chemical Engineering Institute. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 2, pp. 50–54, March–April, 1988.     

On the structure of the FeF3 molecule

With increasing computational possibilities the question of critical comparison of computed results with experimental data gains importance. Differences in the physical meaning of parameters determined by different techniques and the uncertainties of both experimental and computed parameters need to be scrutinized in such comparisons. In view of a recent computational study [V. G. Solomonik, J. F. Stanton, and J. E. Boggs, J. Chem. Phys.122, 094322 (2005)] of the FeF(3) molecule, its earlier electron-diffraction data were reanalyzed and compared with the theoretical results. Based on this reanalysis we can rule out the suggested source of the slight discrepancy between the computed and measured bond lengths.     

Automated molecule editing in molecular design

The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins.