222 research outputs found
Environment influences on the aromatic character of nucleobases and amino acids
Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues
Effect of base–acid properties of the mixtures of water with methanol on the solution enthalpy of selected cyclic ethers in this mixture at 298.15 K
The enthalpies of solution of cyclic ethers: 1,4-
dioxane, 12-crown-4 and 18-crown-6 in the mixture of
water and methanol have been measured within the whole
mole fraction range at T = 298.15 K. Based on the obtained
data, the effect of base–acid properties of water–
methanol mixtures on the solution enthalpy of cyclic ethers
in these mixtures has been analyzed. The solution enthalpy
of cyclic ethers depends on acid properties of water–
methanol mixtures in the range of high and medium water
contents in the mixture. Based on the analysis performed, it
can be assumed that in the mixtures of high methanol
contents, cyclic ethe
Quantification of thermal ring flexibilities of aromatic and heteroaromatic compounds
The consequences of thermal fluctuations occurring at room temperatures on the aromatic character of a broad group of compounds were analyzed in three distinct ways. First of all, the ring deformations were modeled along normal coordinates coming from quantum thermo-chemistry computations. The amplitudes of vibrations were estimated according to absorbed energies at room temperature. Alternatively, in-plane and out-of-plane ring deformations were modeled via scanning procedure with partial relaxation of the molecular geometry. The influence of ring deformations on π–electron delocalization was expressed in terms of HOMA values. Besides, the ring deformability was defined as the averaged change of bond angles or dihedral angles constituting the ring that was associated with 1.5 kcal mol-1 increase of the system energy. The molecules structures adopted during vibrations at room temperature can lead to significant heterogeneity of structural index of aromaticity. The broad span of HOMA values was obtained for analyzed five- or six-membered aromatic and heteroaromatic rings. However, the averaged values obtained for such fluctuations almost perfectly match HOMA values of molecule in the ground state. It has been demonstrated that the ring deformability imposed by bond angle changes is much smaller than for dihedral angles with the same rise of system energy. Interestingly in the case of out-of-plane vibrations modeled by scanning procedure there is observed linear correlation between ring deformability and HOMA values. Proposed method for inclusion of thermal vibrations in the framework of π–electron delocalization provides natural shift of the way of thinking about aromaticity from a static quantity to a dynamic and heterogeneous one due to inclusion of a more realistic object of analysis – thermally deformed structures. From this perspective the thermal fluctuations are supposed to be non-negligible contributions to aromaticity phenomenon
Continuous symmetry of C60 fullerene and its derivatives
Conventionally, the Ih symmetry of fullerene C60 is accepted which is
supported by numerous calculations. However, this conclusion results from the
consideration of the molecule electron system, of its odd electrons in
particular, in a close-shell approximation without taking the electron spin
into account. Passing to the open-shell approximation has lead to both the
energy and the symmetry lowering up to Ci. Seemingly contradicting to a
high-symmetry pattern of experimental recording, particularly concerning the
molecule electronic spectra, the finding is considered in the current paper
from the continuous symmetry viewpoint. Exploiting both continuous symmetry
measure and continuous symmetry content, was shown that formal Ci symmetry of
the molecule is by 99.99% Ih. A similar continuous symmetry analysis of the
fullerene monoderivatives gives a reasonable explanation of a large variety of
their optical spectra patterns within the framework of the same C1 formal
symmetry exhibiting a strong stability of the C60 skeleton.Comment: 11 pages. 5 figures. 6 table
Clar's Theory, STM Images, and Geometry of Graphene Nanoribbons
We show that Clar's theory of the aromatic sextet is a simple and powerful
tool to predict the stability, the \pi-electron distribution, the geometry, the
electronic/magnetic structure of graphene nanoribbons with different hydrogen
edge terminations. We use density functional theory to obtain the equilibrium
atomic positions, simulated scanning tunneling microscopy (STM) images, edge
energies, band gaps, and edge-induced strains of graphene ribbons that we
analyze in terms of Clar formulas. Based on their Clar representation, we
propose a classification scheme for graphene ribbons that groups configurations
with similar bond length alternations, STM patterns, and Raman spectra. Our
simulations show how STM images and Raman spectra can be used to identify the
type of edge termination
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