A study of the aromaticity of heteroannelated cyclooctatetraene derivatives

The aromaticity of the rings of thiophene, pyrrole, furan, and benzene annelated cyclooctatetraene (COT) derivatives and of their double charged ions was studied using the graph-theoretical theory of aromaticity. On the basis of topological resonance energy, it was found that the global aromaticity is dependent upon on the arrangement of heteroatoms in the given molecule. Relative stability of these molecules when in different charged states can been explained in terms of the topological charge stabilization rule. We expect that fusing the COT ring with an increasing number of aromatic rings will lead to an increase in the aromaticity of the molecule. According to the bond resonance energy (BRE) and circuit resonance energy (CRE) indices, local antiaromaticity of the COT ring is weakened as the number of fused rings increases, and these changes play a significant role in the global aromaticity of the molecule. For some compounds, our BRE and CRE indices do not predict the same order of magnitude of the local aromatic character of certain rings that the nucleus independent chemical shift (NICS(0) and (NICS(1)) methods predict. Finally, for the available compounds, correlations between the diatropic and paratropic chemical shifts of the protons and our ring current results were analyzed and good agreement was found.     

The aromaticity of 5,6-dihydroborauracil, borauracil and benzoborauracil systems

The nucleus-independent chemical shift (NICS) indices of aromaticity, calculated for four boron compounds, 4-hydroxy-5,6-dihydroborauracil, 4-hydroxyborauracil, borazine and 4-hydroxybenzoborauracil, and parent uracil, were analyzed in parallel with the NMR properties, in order to learn more about the aromaticity of those heterocyclic systems. The existence of a unique solvent-dependent aromaticity of 4-hydroxyborauracil is indicated.     

A comparative study of the aromaticity of pyrrole, furan, thiophene, and their aza-derivatives

The relative aromaticity of pyrrole, furan, thiophene, and their aza-derivatives has been examined using TRE (topological resonance energy), MRE (magnetic resonance energy), ring current (RC), and ring current diamagnetic susceptibility (χ_G) methods. The results obtained were compared with results obtained by others who used the energetic method ASE (aromatic stabilization energy), the geometric method HOMA (harmonic oscillator model of aromaticity), and the magnetic method NICS(1) (nucleus-independent chemical shift). The impact of nitrogen atoms on the aromaticity of the aza-derivatives of pyrrole, furan, and thiophene is discussed. An excellent correlation was found between the energetic (TRE, MRE) and magnetic (RC and χ_G) criteria of aromaticity for all compounds. It was expected that inclusion of a heteroatom would decrease the aromaticity relative to the cyclopentadienyl anion. Our results show that the type of the first heteroatom, which donates two electrons to the system, as well as the number of nitrogen atoms and their positions in the molecule have a strong effect on aromaticity. In general, aromaticity is enhanced when the nitrogen atom is adjacent to the first heteroatom. The magnitude of aromaticity is related closely with the uniformity of distribution of π-electrons in the molecule.     

Solution of the time-dependent ionic diffusion equation

The ionic diffusion problem here solved is that of the voltage clamp experiment. In this, the total voltage across the membrane and double layers is held constant. Since the diffusion of the ions would normally result in a change in the membrane voltage with time, a part of the complexity of the solution of the problem is in the correction procedure required to so modify the electric field as to hold the voltage at a fixed value. The program could, however, be readily modified to conform to other requirements: e.g., current clamp, linearly rising voltages, etc.A significant improvement in speed of convergence is obtained by using the membrane parameters existing at the midpoint of the time step (Crank-Nicolson method), rather than, as has been more customarily done, at the end of the step (“implicit” method).Convergence is further speeded by estimating the new value of the electric field at each station by extrapolation; and convergence of iterations at each time level is aided by a backward-averaging of the computed electric field. So far as the author is aware, these procedures have not previously been described for use in this type of problem.     

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.     

Homodesmotic reactions in helicene and phenacene molecules

Helicene molecules were analysed on the basis of their intrinsic aromaticity, and compared with the corresponding phenacene. The analysis of aromaticity was performed by homodesmotic reactions, and by the nucleus independent chemical shifts (NICS) index in the centre of the aromatic rings as well as in the centre of the helix. The results are very interesting, because the NICS shows that there is a strong antiaromatic zone in the centre of the molecule, and a strong aromatic zone in the strip. Therefore, these molecules represent a medley of electronic effects.     

A MP2 and DFT study of the aromatic character of polyphosphaphospholes. Is the pyramidality the only factor to take into consideration?

A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, P _n (CH)_4-n PH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different magnetic properties (magnetic susceptibility anisotropy, χ_anis, and the nucleus-independent chemical shifts, NICS) were evaluated. For comparison, these magnetic properties were also calculated in the optimized structures with planarity constraints. We have also applied the ACID (anisotropy of the current-induced density) method in this analysis. The main conclusions are the aromatic character of these compounds, the relationship between aromaticity and planarity and the importance of other factors in this aromaticity.     

Ab initio and DFT study of the aromaticity of some Fulvalenes derived from Methylidenecyclopropabenzene

Methylidencyclopropabenzene (MCPB) 1 and Fulvalenes 2–4 are molecules of special interest due to the relation between structure and aromaticity. The aim of this work was to analyze this relation and to quantify the aromaticity in 1–4 using different methods. Magnetic properties are directly related with aromaticity; here we studied the magnetic susceptibility and the anisotropy of the magnetic susceptibility. Nucleus indepedent chemical shift (NICS) and the anisotropy of the induced current density (ACID) were also employed. Tools of very different nature, geometric indexes HOMA and Bird, were determinated too for 1–4. All of these measures were found to be in agreement. Figure Both spatial NICS and ACID plot allow to show the aromaticity/antiaromaticity of a ring     

Aromatic character of heptafulvene and its complexes with halogen atoms

Geometry optimization of heptafulvene-halogen complexes (halogens: F, Cl, Br, I, and At) carried out at the B3LYP/6-311+G(d,p) level of theory allowed us to estimate the geometry-based aromaticity index HOMA, the magnetism-based indices NICS, NICS(1), and NICS(1)(ZZ), as well as the energy of complex formation. Application of the NBO method allowed us to estimate the pEDA characteristics of the π-electron distribution in complexes (i.e., the electron excess/deficiency of the π-electron system in the ring). All of the characteristics of the complexes were found to be mutually interrelated, exhibiting good or at least acceptable correlation coefficients. It was also noted that halogen atoms with greater radii yielded weaker complexes and lower aromaticities, as shown by the HOMA, NICS, and pEDA indices. The energy of complex formation was observed to be linearly correlated with the degree of aromatization of the heptafulvene ring, as expressed by these indices.     

A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors

Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and (17)O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with alpha-helix initial structure. It was found that peptide loses its initial alpha-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate (17)O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31+G basis set. Calculated (17)O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, eta(Q). Difference between the calculated QCC and eta(Q) values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.     

TDPAC studies of the metal-binding sites in serum transferrin: comparison between 181Hf-labeled human- and rat-serum transferrin

The binding of hafnium to human serum transferrin was studied using the time differential perturbed angular correlation (TDPAC-) technique. The samples were prepared in vitro by adding 181Hf-NTA solution to human serum. Two specific electric quadrupole interactions were observed, which correspond to two well-defined binding configurations. Their relative intensities depend on the pH, salt- and hafnium-concentrations, and on the incubation time. The present data may be compared with the results of a previous rat serum study, where the hafnium binding to transferrin behaved rather similarly. Small but significant differences, however, can be deduced from the TDPAC-parameters for these human and rat transferrin species. For either binding configuration, the electric field gradient (EFG) is slightly higher in the case of rat transferrin. The most characteristic difference, however, concerns the asymmetry parameter eta 2 of the second binding configuration, which is about 10% smaller for rat serum transferrin. The TDPAC-technique might be used as a sensitive and reliable analytical method to study the metal-binding sites of different transferrin species.     

Theoretical study of borazine and its derivatives

The density functional theory is used to study the geometries, electronic structures, and aromaticity of borazine and its fused ring derivatives. Some new evidences for the ionic nature of B-N bond are found. Geometry studies show that the B-N bond lengths are equal. The lone pair VSCCs of the N atoms are found. As shown, the B-N bonds are of ionic nature based on their positive Laplacian. Magnatic shielding constants also are computed. The shielding and deshielding contributions are divided into Lewis and non-Lewis parts by the NCS-NBO method. It is demonstrated in the NICS studies that there are the ring current effects on borazine and its derivatives are very weak. The aromaticity of borazine is weakened with the fused ring number increasing.     

Sigma- and pi- electron structure of aza-azoles

The reasons behind changes of aromaticity in 10 unsubstituted aza-azoles were analysed by employing the natural bond orbital (NBO) approach at the MP2/6-311+G(d,p) level of theory. Sum of occupations of p _z orbitals at atoms in the ring correlates well with the magnetism based aromaticity index NICS as well as with the number of nitrogen atoms in the ring. Changes of NICS depend strongly in a linear way on the number of NN bonds. Classification of azoles based on the number of pyridine-type nitrogen atoms vicinal to NH is supported by plotting the relative occupation of π orbitals (π_occ) against the relative occupation of σ orbitals (σ_occ) for all individual atoms in rings.     

Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex

Theoretical calculations of structural parameters, 57Fe, 14N and 17 O electric field gradient (EFG) tensors for full size-hemin group have been carried out using density functional theory. These calculations are intended to shed light on the difference between the geometry parameters, nuclear quadrupole coupling constants (QCC), and asymmetry parameters (eta Q) found in three spin states of hemin; doublet, quartet and sextet. The optimization results reveal a significant change for propionic groups and porphyrin plane in different spin states. It is found that all principal components of EFG tensor at the iron site are sensitive to electronic and geometry structures. A relationship between the EFG tensor at the 14N and 17 O sites and the spin state of hemin complex is also detected.     

Aromaticity of graphene nanoflakes in a new way: fragment analysis by combination of the nucleus-independent chemical shifts and the anisotropy of current induced density

A graphene nanoflake (GNF) is a polycyclic aromatic hydrocarbon (PAH) with a huge two-dimensional π-conjugated carbon material in which a central benzene ring is surrounded by identical benzene-type rings through infinite alternant method. In this paper, we explore the structure-aromaticity relationship of the GNFs and the GNFs with hollow sites (GNFHs) by combining the nucleus-independent chemical shifts (NICS) with the anisotropy of the current induced density (ACID). Firstly, the benzene is a typical aromatic molecule (NICS = ?9.671 ppm), GNFs 1-6 is darned with benzene and the corresponding GNFHs 1′-6′. Secondly, the NICS values of GNFs 1-6 alternately vary: ?1.214 (1) > ?13.847 (2) < ?2.662 (3) > ?14.530 (4) < ?3.932 (5) > ?13.978 (6) ppm, the GNFs (2, 4, 6) with even fragments of annulene have larger aromaticity than that of GNFs (1, 3, 5) with odd fragments of annulene. Significantly, the NICS values of GNFs 1-6 can also be fragment analyzed by the NICS values and ACID of benzene and corresponding GNFHs 1′-6′. The NICS values for GNFs (2, 4, 6) can be roughly estimated by the NICS value of benzene minus the NICS value of the GNFHs (2′, 4′, 6′), respectively. The NICS values for GNFs (1, 3, 5) can be roughly estimated by the NICS value of the GNFHs (1′, 3′, 5′) minus the NICS value of benzene, respectively. We hope that the present work can provide a simple and reliable method for the rational design of the GNF with aromaticity, which may be used to understand the origin of the graphene nanoflake aromatic properties.     

Specificities of boron disubstituted sumanenes

In this article we focused on computational research of sumanenes disubstituted by boron where the two carbon atoms are substituted by two boron atoms. Disubstitution of rim carbon atoms with boron atoms significantly affected the geometry of the bowl. The main stability factors were used to determine the stability of isomers. The most stable, the shallowest and the deepest isomers were subjected to further study of NMR parameters, chemical shielding and NICS, aromaticity, bowl to bowl inversion barrier and NBO/NPA analysis. The introduction of boron atoms significantly affected the above parameters, changing the aromatic nature of rings, reducing bowl to bowl inversion barrier and produced charge transfer. The NICS are correlated with bowl depth having the result that the function of the fourth degree of bowl depth does not only correlate well to the bowl to bowl inversion barrier with bowl depth, but also finely correlates the change of the NICS and NICSzz with bowl depth.     

Contrast enhancement of x-ray images on layers exposed to a superimposed electric field

A method of raising the sensitivity of x-ray photomaterials using a pulsed electric field is considered. Methods for raising contrast of photo images by changing stages of x-ray film postexposure processing have been proposed. Processing in the proposed enhancing compounds makes it possible not only to raise sensitivity by one order or more but also to preserve a contrast coefficient value. Raising the contrast of photomaterials is important in medical radiography irrespective of electric fields imposing methods, therefore, it can be used in some radiodiagnostic procedures.     

Theoretical study of [ XN5 ]− (X=O, S, Se, Te) systems

A series of [XN₅]⁻ (X=O, S, Se, Te) compounds has been examined with ab initio and Density Functional Theory (DFT) methods. The five-membered nitrogen ring series of structures are global minima and may exist or be characterized due to their significant dissociation barriers (29.7–32.7 kcal mol⁻¹). Nucleus-independent chemical shifts (NICS) criteria and the presence of (4n+2) π-electrons confirmed that the five-membered nitrogen ring in their structures exhibits characteristics of aromaticity. Thus, the strong stability of the five-membered nitrogen ring structures may be attributed partially to their aromaticity.      

A density functional study of (17)O, (14)N and (2)H electric field gradient tensors in the real crystalline structure of alpha-glycine

A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.     

Numerical evaluation of currents induced in a worker by ELF non‐uniform electric fields in high voltage substations and comparison with experimental results

An ungrounded human, such as a substation worker, receives contact currents when touching a grounded object in electric fields. In this article, contact currents and internal electric fields induced in the human when exposed to non‐uniform electric fields at 50 Hz are numerically calculated. This is done using a realistic human model standing at a distance of 0.1–0.5 m from the grounded conductive object. We found that the relationship between the external electric field strength and the contact current obtained by calculation is in good agreement with previous measurements. Calculated results show that the contact currents largely depend on the distance, and that the induced electric fields in the tissues are proportional to the contact current regardless of the non‐uniformity of the external electric field. Therefore, it is concluded that the contact current, rather than the spatial average of the external electric field, is more suitable for evaluating electric field dosimetry of tissues. The maximum induced electric field appears in the spinal cord in the central nervous system tissues, with the induced electric field in the spinal cord approaching the basic restriction (100 mV/m) of the new 2010 International Commission on Non‐Ionizing Radiation Protection guidelines for occupational exposure, if the contact current is 0.5 mA. Bioelectromagnetics 34:61–73, 2013. © 2012 Wiley Periodicals, Inc.