Aromaticity and photophysics of tetrasila- and tetragerma-annelated tetrathienylenes as new representatives of the hetero[8]circulene family

The electronic structure, absorption and emission spectra, aromaticity and photophysical behavior of the recently synthesized tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene compounds have been studied computationally.

Identification of tautomeric intermediates of a novel thiazolylazonaphthol dye - A density functional theory study

The recently synthesized thiazolylazo dye, 1-[5-benzyl-1,3-thiazol-2-yl)diazenyl]naphthalene-2-ol called shortly BnTAN, is studied by density functional theory (DFT) in three tautomeric forms in order to explain the available ¹H NMR, UV-Vis and FTIR spectra. An experimentally observed IR band at 1678 cm^-1, assigned to the CO bond stretching vibration, supports the notion that BnTAN retains in the less stable keto-form even in the solid state due to an ultrafast single-coordinate intramolecular proton transfer. This finding is also in a good agreement with an X-ray crystallography analysis which indicates an intermediate position of the proton between the -OH and -N=N- groups. Calculations also show that some experimentally observed ¹H NMR signals could be considered as being averaged values between theoretically calculated chemical shifts for the corresponding protons in the keto- and enol-tautomers. At the same time the UV-Vis spectra are almost insensitive to the tautomerization processes as the main single band absorption at 500 nm is present in all tautomers according to our TD DFT simulations. The minor differences in spectral features of the long-wavelength visible region are also noted and discussed with respect to the manifestation of the less stable tautomer form.

Fragmentation of the adenine and guanine molecules induced by electron collisions

Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.

The art of the possible: computational design of the 1D and 2D materials based on the tetraoxa[8]circulene monomer

Single-wall nanotube based on tetraoxa[8]circulene monomer.

Vibrational spectra of the steroid hormones, estradiol and estriol, calculated by density functional theory. The role of low-frequency vibrations

The structure of estrogen receptors and their interaction with 17beta-estradiol and estriol are of particular interest today because the treatment of breast cancer and the cause of the disease are intricately linked to the activity of the estrogen receptor and the normal blood serum level of these hormones. Molecular geometry and vibration frequencies of these steroid hormones are calculated by density functional theory with the B3LYP/ 6-31G** approximation. Intensities of infrared absorption and Raman spectra for estradiol are in an agreement with the experiment data. The assignments of all vibrational bands in the spectra of these hormones are presented on the basis of quantum chemical calculations of frequencies and normal modes. For the large number of bands such an assignment is made for the first time. The analysis of infrared spectra of both hormones indicates some nontrivial structure-spectra correlations. A series of specific vibrations is predicted in the low-frequency region of the IR spectra; their role in hormone-receptor interaction and in energy transfer processes are discussed. The search of the optimized geometrical structure by minimization of the total energy gradient is accompanied by the second derivatives calculation; diagonalization of the Hessian matrix leads finally to solution of vibration problem. The 17beta-estradiol molecule consists of 44 atoms and has 126 normal modes of internal vibrations. All these normal modes are presented together with their analysis and comparison with experimental data. From this comparison we have obtained an assignment of all absorption IR bands of 17beta-estradiol recorded earlier in KBr. For all stretching vibrations our assignment is in agreement with the previous one, obtained on the basis of the empirical rules. Direct DFT calculation of vibrational frequencies cannot provide a 100% agreement with the experimental IR spectra and scaling factors in the range of 0.95-0.97 are used in order to fit theoretical and experimental data.