Theoretical study of the structure and stability of oxo heme derivatives

The geometric and electronic structures, energy stability, and normal mode frequencies of molecules and ions of oxo heme derivatives Heme=O^0,±, Heme-O-Heme^0,±, Heme-OO^0,±, and Heme-OO-Heme^0,± (Heme=FeC₃₄H₃₂N₄O₄) in the states of different multiplicity have been calculated by the density functional theory B3LYP method with several basis sets. Energetically preferred states have been determined, and the energies of different channels of their decomposition with dissociation of the Fe-O and O-O bonds have been estimated. The relative energies of superoxide and peroxide isomers of the dioxygenyl complexes Heme-OO^0,± and Heme-OO-Heme^0,± have been estimated. For the double-decker Heme-OO-Heme^0,± complexes, local minima (intermediates) have been found, which correspond to the structures containing rhombic Fe(μ-O)₂Fe moieties with the iron atoms linked by two covalent oxygen bridges Fe-O-Fe. The trends in the behavior of the equilibrium geometric parameters, vibrational frequencies, and spin density distribution between the Fe and O atoms and the porphyrin ring of oxohemes have been analyzed as a function of the electronic state multiplicity and the external charge of the complex.     

Theoretical study of the stability of multiply charged C70 fullerenes

We have calculated the electronic energies and optimum geometries of C(70) (q+) and C(68) (q+) fullerenes (q=0-14) by means of density functional theory. The ionization energies for C(70) and C(68) fullerenes increase more or less linearly as functions of charge, consistent with the previously reported behavior for C(60) and C(58) [S. Diaz-Tendero et al., J. Chem. Phys. 123, 184306 (2005)]. The dissociation energies corresponding to the C(70) (q+)-->C(68) (q+)+C(2), C(70) (q+)-->C(68) ((q-1)+)+C(2) (+), C(70) (q+)-->C(68) ((q-2)+)+C(+)+C(+), C(70) (q+)-->C(68) ((q-3)+)+C(2+)+C(+), and C(70) (q+)-->C(68) ((q-4)+)+C(2+)+C(2+) decay channels show that C(70) (q+) (like C(60) (q+)) is thermodynamically unstable for q>or=6. However, the slope of the dissociation energy as a function of charge for a given decay channel is different from that of C(60) (q+) fullerenes. On the basis of these results, we predict q=17 to be the highest charge state for which a fission barrier exists for C(70) (q+).     

Theoretical study on the stability and the structure

The structure of H⁺_n(n = 3, 5, 7, 9, 11) is determined from ab initio MO calculations. The result for H⁺_n(n = 5, 7, 9) obtained by energy optimization in the 4-31G and 4-31G + p bais sets is reasonably explained in terms of a charge-transfer interaction from H₂ to H⁺_n?2 site. The orientation of H₂ toward the H⁺₉ cluster (D_3H) is found to be critically influenced by the basis set adopted.     

Theoretical study of stability, structures, and aromaticity of multiply N-confused porphyrins.

The total electronic energy and nucleus-independent chemical shift (NICS) of 95 isomers of N-confused porphyrin (NCP: normal porphyrin (N(0)CP), singly N-confused porphyrin (N(1)CP), doubly N-confused porphyrin (N(2)CP), triply N-confused porphyrin (N(3)CP), and fully N-confused porphyrin (N(4)CP)) have been calculated by the density functional theory (DFT) method. The stability of NCP decreased by increasing the number of confused pyrrole rings. Namely, the relative energies of the most stable isomers in each confusion level increased in a stepwise manner approximately by +18 kcal/mol: 0 (N(0)CP1), +17.147 (N(1)CP2), +37.461 (N(2)CPb3), +54.031 (N(3)CPd6), and +65.636 kcal/mol (N(4)CPc8). In this order, the mean plane deviation of these isomers increased from 0.000 to 0.123, 0.170, 0.215, and 0.251 A, respectively. The unusual tautomeric forms of pyrrole ring with an sp(3)-carbon were found in the stable forms of N(3)CP and N(4)CP. The NICS values at the mean position of the 24 core atoms were nearly the same for the most aromatic isomers regardless of the confusion level: -15.1280 (N(0)CP1), -13.8493 (N(1)CP2), -13.7267 (N(2)CPd1), -11.7723 (N(3)CPb5), and -13.6224 ppm (N(4)CPa6). The positive correlation between aromaticity and stability was inferred from the plots of NICS and the relative energy of NCP for N(0)CP, N(1)CP, and trans-N(2)CP. On the other hand, the correlation was negative for cis-N(2)CP, N(3)CP, and N(4)CP isomers.     

Theoretical study on the structure and stability of some unusual boron-nitrogen helices

Ab initio self-consistent field molecular orbital and density functional theory calculations have been performed on a series of helical structures comprised of boron-nitrogen analogues of extended helicenes, with helically arranged N fused benzene rings, and alternating N benzene units fused to N - 1 cyclobutadiene rings as reference structures. The electronic structure and stability of boron-nitrogen analogues of angular [N]helicenes, [N]phenylenes (N = 5, 6, 7, 12), and [N]methylenylnaphthalenes (N = 6) were investigated at the HF/6-31G(d) and the B3LYP/6-31G(d) levels of theory. The presence of an even number N of rings in the boron-nitrogen [N]helicenes leads to the possibility of angular isomers. Electron density contours were calculated in order to interpret the existing bonding patterns. These structures may provide supramolecular building blocks and macromolecular "springs" with unusual electronic properties.     

Thermodynamic stability of 2,4,6-tris(nitromethyl)-1,3,5-triazine: an experimental and theoretical study

The molecular geometries and electronic structures of 2,4,6-tris(nitromethyl)-1,3,5-triazine isomers were investigated by the density functional method DFT/B3LYP/6-311++G** to elucidate the structural factors responsible for the stability of these systems. It was shown that a characteristic feature of the nitromethyl tautomer (1) of 2,4,6-tris (nitromethyl)-1,3,5-triazine consists in nonvalence interactions between an oxygen atom of nitro group and a carbon atom of triazine ring, which are probably due to Coulomb attraction between them. The tautomer with the 2,4,6-tris (nitromethylene)-hexahyrdo-1,3,5-triazine structure (2) is stabilized trough direct polar conjugation between the amino and nitro groups at the double bond. Structural strain of the molecule with the 2,4,6-tris(aci-nitromethyl)-1,3,5-triazine structure (3) is the reason for its thermodynamic instability. X-ray data indicate that the compound under study exists in the triazine tautomeric form 1 and the distances between oxygen atoms of nitro group and carbon atom of the triazine ring are shortened. NMR data suggest the existence of triazine in the nitromethyl form 1 in acetonitrile and acetone and a tautomeric equilibrium between the nitromethyl and nitromethylene forms in a more polar solvent (DMSO). The results obtained suggest a Coulomb-type stabilization of the 2,4,6-tris(nitromethyl)-1,3,5-triazine molecule in the gas phase, in the crystal, and in nonpolar solvents.     

Theoretical study of structure and stability of fullerene derivative: C50O

A total of eight possible isomers of C₅₀O, an oxide of fullerene C₅₀ (D_5h), have been investigated by B3LYP/3‐21G calculations. The isomer, which has an annulene‐like structure with oxygen bridging across a [5,6] type C? C bond at the site between the pole and the equatorial belt, is found being the ground state of C₅₀O. Four isomers are relatively more stable and the energy differences between them are not large. This result indicates that more than one C₅₀O isomer will coexist once C₅₀O is synthesized. The relative stabilities of the C₅₀O isomers may be determined mainly by the strain release and by the formation of the cyclic phenylene substructure at the equatorial belt of the cage. The calculated nucleus independent chemical shifts (NICS) of the C₅₀O isomers will be useful because from them one can expect outstanding NMR properties that can lead to their identification and characterization. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical and experimental study of the structure and vibration spectra of 4,4′-carbonyl-di-morpholine

4,4′-Carbonyl-di-morpholine was synthesized and characterized by X-ray diffraction, the FTIR and NMR spectra. The extended MO calculations using density functional theory (DFT) and self-consistent field molecular orbital Hartree-Fock theory were carried out. The results of the calculations were compared with experimental data. The experimental and calculated results were supported each other. The performance of a hybrid B3LYP density functional was compared with the ab initio restricted Hartree-Fock method. With the basis sets of the 6-311G** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.     

TBHQ及其衍生物结构和热力学性质的理论研究

采用Materials Studio软件中的DMol3程序对特丁基对苯二酚(TBHQ)及衍生物二特丁基对苯二酚(DTBHQ)的几何结构和性质(振动频率、反应活性及热力学性质)进行了理论研究,得到了分子的稳定几何构型、各原子上的电荷分布、热力学性质、Fukui指数和前线分子轨道.计算结果表明:TBHQ与DTBHQ分子结构中的2个—OH是影响其抗氧化活性的主要部位和亲电反应发生的活性位点,整体表现为比较理想的稳定抗氧化性能.     

Theoretical study of electronic structure of rhodium mononitride and interpretation of experimental spectra

Potential energy curves of 22 electronic states of RhN have been calculated by the complete active space second‐order perturbation theory method. The X¹Σ₀⁺ is assigned as the ground state, and the first excited state a³Π₀+ is 978 cm^?1 higher. The ¹Δ(I) and B¹Σ⁺ states are located at 9521 and 13,046 cm^?1 above the ground state, respectively. The B¹Σ⁺ state should be the excited state located 12,300 cm^?1 above the ground state in the experimental study. Moreover, two excited states, C¹Π and b³Σ⁺, are found 14,963 and 15,082 cm^?1 above the X¹Σ⁺ state, respectively. The transition C¹Π₁–X¹Σ₀⁺ may contribute to the experimentally observed bands headed at 15,071 cm^?1. There are two excited states, D¹Δ and E¹Σ⁺, situate at 20,715 and 23,145 cm^?1 above the X¹Σ⁺ state. The visible bands near 20,000 cm^?1 could be generated by the electronic transitions D¹Δ₂–a³Π₁ and E¹Σ⁺₀–X¹Σ⁺₀ because of the spin–orbit coupling effect. © 2013 Wiley Periodicals, Inc.     

A theoretical study of the structure and vibrations of 2,4,6-trinitrotolune

Theoretical calculations of the structure, internal rotations and vibrations of 2,4,6-trinitrotolune, TNT, in the gas phase were performed at the B3LYP/6-31G* and B3LYP/6-311+G** levels of theory. Two genuine energy minimum structures were found. In both structures the 4-nitro group is planar to the phenyl ring, while the 2,6-nitro groups are slightly out of plane with the phenyl ring due to steric interaction with the methyl group. The two structures are related by internal rotations of the methyl and 2, or 6-nitro group. The lowest energy route for interconversion between them is a concerted motion of the methyl group and 2 or 6 nitro group in a ‘cog wheel’ type of mechanism. The geometry of the low energy structure A is closest to that observed in the crystal structures of TNT, where all three nitro groups are out of plane with the phenyl ring. FTIR and Raman spectra of solid TNT and ¹³C, ¹⁵N enriched TNT are presented and assigned with the help of the B3LYP/6-311+G** calculations on A. The lower level B3LYP/6-31G* calculation fails to predict the correct vibrational coupling between the nitro and phenyl groups. The B3LYP/6-311+G** calculation gives a good prediction of the nitro vibrations and the isotopic shifts observed for TNT isotopomers.     

Theoretical study of the structure and stability of cage-substituted octahedral boranes,alanes, and gallanes

The equilibrium geometric parameters and energetic and spectroscopic characteristics of low-lying isomers for a series of successively cage-substituted octahedral closo-borane, alane, and gallane dianions Al_{6 − i} B _i H₆²⁻ and Ga_{6 − i} Al _i H₆²⁻ (i = 0−6) and mono- and disubstituted anions and neutral molecules of boranes, XB₅H₆⁻ and XYB₄H₆ and alanes, XAl₅H₆⁻ and XYAl₄H₆, with the same or different cage heteroatoms of Group IV elements (X and Y = C, Si, Ge, Ti) were calculated at the B3LYP level of the density functional theory using the 6-31G* and 6-311+G** basis sets. Differences in structure and stability between borane and alane clusters of like composition are revealed. The mutual influence of the X and Y heteroatoms in the trans and cis isomers and its manifestations in the behavior of molecular characteristics are considered for the disubstituted octahedral clusters XYB₄H₆ and XYAl₄H₆.     

Synthesis and stability of 2,4,6-trinitrobenzylamine

2,4,6-Trinitrobenzylamine was synthesized via 2,4,6-trinitrophenylacetic acid and 2,4,6-trinitrobenzyl isocyanate. The title compound decomposes at room temperature but forms a stable hydrochloride and acetyl derivative.     

Theoretical and experimental study of nonlinear electrophoresis

Linear and nonlinear electrophoresis of conducting and nonconducting spherical disperse particles is studied. A comparative analysis is performed for the regularities of nonlinear electrophoresis in the stationary and pulsed modes at small and large Peclet numbers.     

Lead‐enhanced gas‐phase stability of multiply charged EDTA anions: a combined experimental and theoretical study

Besides their fundamental importance, multiply charged anions (MCAs) are considered as promising molecular capacitors for which their intrinsic stabilities are of great significance. Herein, the gas‐phase stabilities of ethylenediaminetetraacetic acid (EDTA) anions (i.e. [EDTA‐nH]^n?, n = 1–4) and their Pb(II) complexes (i.e. [EDTA + Pb‐nH]^(2‐n)?, n = 3, 4) have been investigated using an approach that combines extractive electrospray ionization mass spectrometry (EESI‐MS) measurements, Car–Parrinello molecular dynamics simulations and density functional theory/Tao–Perdew–Staroverov–Scuseria calculations. The EESI‐MS data showed that the doubly charged EDTA anions in the form of [EDTA‐2H]^2? and [EDTA + Pb‐4H]^2? were much more abundantly observed than the singly charged species such as [EDTA‐H]^? and [EDTA + Pb‐3H]^?, respectively. The calculation results indicated that [EDTA‐2H]^2? and [EDTA + Pb‐4H]^2? anions were thermodynamically more stable than the [EDTA‐H]^? and [EDTA + Pb‐3H]^? species in the gas phase, respectively. The [EDTA + Pb‐3H]^? anions preferred five‐coordinated structure, whereas [EDTA + Pb‐4H]^2? anions formed either five‐coordinated or six‐coordinated structures. The calculations further revealed that significant electron clouds drifting from the ligand EDTA to the metal Pb(II) ions and the large distances between the carboxylic groups reduced the Coulomb repulsion among the excess electrons of these MCAs. Our data demonstrated that EESI‐MS combined with theoretic calculations were able to provide a deep insight into the fundamental behavior of stability of MCAs in the gas phase and, thus, might be useful tools for studying MCAs for potential molecular capacitors. Copyright © 2012 John Wiley & Sons, Ltd.     

Theoretical study of mono- and dithiocarbazic acid derivatives

The patterns of charge distribution in a series of derivatives of thiocarbazic acid are studied by means of several theoretical LCAO-MO methods: ab initio minimal basis-set, CNDO/2, INDO and EHT. Correlations are made between the electronic structures obtained from the calculations, the nature of the different substituents and some experimental IR, X-ray and XPS results.