Insight into shock-induced chemical reaction from the perspective of ring strain and rotation of chemical bonds

Density functional theory BLYP/DNP and hyperhomodesmotic equations were employed to calculate ring strain energy, the bond dissociation energy of X–NO₂ (X=C, N) and the charges on the nitro groups of several four-membered and six-membered heterocycle compounds. BLYP/DNP and LST/QST + CG method were also applied to calculate bond rotational energy of X–NO₂ (X=C, N) of above mentioned compounds. It indicated that ring strain energy of four-membered heterocycle nitro compounds is apparently higher than that of six-membered heterocycle nitro compounds. Predictably, ring-opening reactions may preferentially occur for those compounds containing higher ring strain energy under shock. In addition, C–NO₂ bonds in these compounds may rotate easier than N–NO₂ bonds in response to the external shock. As for N–NO₂ bonds in these compounds, they also respond to the external shock by the rotation of N–NO₂ bonds, once to the saddle point of the rotational energy barrier, the whole molecule will become relaxed, N–NO₂ bond becomes weaker and eventually leads to the breakage. When one ?C=O, ?C=NH or ?NH₂ group is introduced to the six-membered heterocycle, the charges on the nitro groups of the new compound decrease drastically, and ring strains increase remarkably. It can be predicted that the new compounds will be more sensitive to shock, and the viewpoint is confirmed by the experimental results of shock sensitivity (small scale gap test) of several explosives.     

Theoretical studies on the structures and detonation properties of nitramine explosives containing benzene ring

The nitramine compounds containing benzene ring were optimized to obtain their molecular geometries and electronic structures at DFT-B3LYP/6-31+G(d) level. The theoretical molecular density (ρ), heat of formation (HOF), energy gap (ΔE(LUMO-HOMO)), charge on the nitro group (-Q(NO2)), detonation velocity (D) and detonation pressure (P), estimated using Kamlet-Jacobs equations, showed that the detonation properties of these compounds were excellent. It is found that there are good linear relationships between density, heat of formation, detonation velocity, detonation pressure and the number of nitro group. The simulation results reveal that molecule G performs similarly to famous explosive HMX, and molecule H outperforms HMX. According to the quantitative standard of energetics as an HEDC (high energy density compound), molecule H essentially satisfies this requirement. These results provide basic information for molecular design of novel high energetic density compounds.     

Table of contents - volume 30

The preparation of 2,4-dihydroxyestrone, 2,4-dihydroxyestradiol-17β and their methyl ethers (14 compounds) is described. The structures were established by nuclear magnetic resonance, infrared and mass spectra as well as by elemental analyses, microchemical reactions, alternative synthetic routes and by their Chromatographic properties.     

Density functional calculations for a high energy density compound of formula C6H6?n (NO2) n

A series of polynitroprismanes, C(6)H(6-n )(NO(2))(n) (n?=?1-6) intended for use as high energy density compounds (HEDCs) were designed computationally. Their electronic structures, heats of formation, interactions between nitro groups, specific enthalpies of combustion, bond dissociation energies, and explosive performances (detonation velocities and detonation pressures) were calculated using density functional theory (DFT) with the 6-311 G** basis set. The results showed that all of the polynitroprismanes had high positive heats of formation that increased with the number of substitutions for the prismane derivatives, while the specific enthalpy of combustion decreased as the number of nitro groups increased. In addition, the range of enthalpy of combustion reducing is getting smaller. Interactions between ortho (vicinal) groups deviate from the group additivity rule and decrease as the number of nitro groups increases. In terms of thermodynamic stability, all of the polynitroprismanes had higher bond dissociation energies (BDEs) than RDX and HMX. Detonation velocities and detonation pressures were estimated using modified Kamlet-Jacobs equations based on the heat of detonation (Q) and the theoretical density of the molecule (ρ). It was found that ρ, D, and P are strongly linearly related to the number of nitro groups. Taking both their energetic properties and thermal stabilities into account, pentanitroprismane and hexanitroprismane are potential candidate HEDCs.     

Bioconjugation of CdTe quantum dot for the detection of 2,4-dichlorophenoxyacetic acid by competitive fluoroimmunoassay based biosensor

Quantum dots (QD) are semiconductor fluorescent nanoparticles, which can be made use of for environmental monitoring with high sensitivity. In view of the alarming levels of pesticides and herbicides being used in agriculture practices, there is a need for their rapid, sensitive and specific detection in food and environmental samples, as pesticides and herbicides are harmful to living beings even at trace levels. Present study was carried out to develop a reliable and rapid method for analysis and detection of 2,4-D (herbicide) using cadmium telluride quantum dot nanoparticle (CdTe QD). Fluoroimmunoassay based on the fluorescent property of quantum dot was used along with immunoassay to detect 2,4-D. CdTe capped with mercaptopropionic acid, was conjugated using N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride (EDC) and a coupling reagent like N-hydroxysuccinimide (NHS) to alkaline phosphatase (ALP) which was in turn conjugated to 2,4-D molecule. Anti 2,4-D-IgG antibodies were immobilized in an immunoreactor column using Sepharose CL-4B as an inert matrix. The detection of 2,4-D was carried out by fluoroimmunoassay-based biosensor using competitive binding between conjugated 2,4-D-ALP-CdTe and free 2,4-D with immobilized anti 2,4-D antibodies in an immunoreactor column. It was possible to detect 2,4-D upto 250pgmL(-1). Present study also emphasizes on the resonance energy transfer between ALP and CdTe QD as a result of bioconjugation, which can be used for future biosensor development based on quantum dot-biomolecular interactions.     

Inhibitory effects of phenolic ecotoxicants on photobacteria at various pH values

Kinetic characteristics of light emission by intact cells of the photobacteria Photobacterium phosphoreum and Vibrio harveyi at pH 5.5, 7.0, and 8.0 were studied as well as specific features of inhibitory effects of 2,4-di- and 2,4,5-triphenoxyacetic acids (2,4-D and 2,4,5-T), pentachlorophenol (PCP), and 2,6-dimethylphenol (2,6-DMP) at the same pH values. Nonstationarity of emission kinetics was observed at all the pH values studied. Exponential luminescence decay in a 60-sec range was observed at pH 5.5; a 5-min luminescence activation, at pH 7.0 and 8.0. The cell respiratory activity drops by over one order of magnitude at pH 5.5 compared with the activities at pH 7.0 and 8.0. The inhibitory effects of 2,4-D, 2,4,5-T, and PCP differ by one-two orders of magnitude depending on pH. The maximal cell sensitivity to these compounds appears at pH 5.5; the minimal, at pH 8.0. The effect of 2,6-DMP is independent of pH. As is demonstrated, it is hydrophobicity of the molecule and pK values of the toxicants that determine the inhibitory effect. Characteristic of the substrate-starved photobacterial cells are higher sensitivity to chlorophenolic compounds compared with the cells provided with high energy supply at all the pH values.     

3-Nitroadipate, a Metabolic Intermediate for Mineralization of 2,4-Dinitrophenol by a New Strain of a Rhodococcus Species

The bacterial strain RB1 has been isolated by enrichment cultivation with 2,4-dinitrophenol as the sole nitrogen, carbon, and energy source and characterized, on the basis of 16S rRNA gene sequence comparison, as a Rhodococcus species closely related to Rhodococcus opacus. Rhodococcus sp. strain RB1 degrades 2,4-dinitrophenol, releasing the two nitro groups from the compound as nitrite. The release of nitro groups from 2,4-dinitrophenol occurs in two steps. First, the 2-nitro group is removed as nitrite, with the production of an aliphatic nitro compound identified by ¹H nuclear magnetic resonance and mass spectrometry as 3-nitroadipate. Then, this metabolic derivative is further metabolized, releasing its nitro group as nitrite. Full nitrite assimilation upon reduction to ammonia requires that an additional carbon source be supplied to the medium.     

Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp.

Previous studies of the biodegradation of nonpolar nitroaromatic compounds have suggested that microorganisms can reduce the nitro groups but cannot cleave the aromatic ring. We report here the initial steps in a pathway for complete biodegradation of 2,4-dinitrotoluene (DNT) by a Pseudomonas sp. isolated from a four-member consortium enriched with DNT. The Pseudomonas sp. degraded DNT as the sole source of carbon and energy under aerobic conditions with stoichiometric release of nitrite. During induction of the enzymes required for growth on DNT, 4-methyl-5-nitrocatechol (MNC) accumulated transiently in the culture fluid when cells grown on acetate were transferred to medium containing DNT as the sole carbon and energy source. Conversion of DNT to MNC in the presence of 18O2 revealed the simultaneous incorporation of two atoms of molecular oxygen, which demonstrated that the reaction was catalyzed by a dioxygenase. Fully induced cells degraded MNC rapidly with stoichiometric release of nitrite. The results indicate an initial dioxygenase attack at the 4,5 position of DNT with the concomitant release of nitrite. Subsequent reactions lead to complete biodegradation and removal of the second nitro group as nitrite.     

Harmonic force field for nitro compounds

Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).     

Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp.

Previous studies of the biodegradation of nonpolar nitroaromatic compounds have suggested that microorganisms can reduce the nitro groups but cannot cleave the aromatic ring. We report here the initial steps in a pathway for complete biodegradation of 2,4-dinitrotoluene (DNT) by a Pseudomonas sp. isolated from a four-member consortium enriched with DNT. The Pseudomonas sp. degraded DNT as the sole source of carbon and energy under aerobic conditions with stoichiometric release of nitrite. During induction of the enzymes required for growth on DNT, 4-methyl-5-nitrocatechol (MNC) accumulated transiently in the culture fluid when cells grown on acetate were transferred to medium containing DNT as the sole carbon and energy source. Conversion of DNT to MNC in the presence of 18O2 revealed the simultaneous incorporation of two atoms of molecular oxygen, which demonstrated that the reaction was catalyzed by a dioxygenase. Fully induced cells degraded MNC rapidly with stoichiometric release of nitrite. The results indicate an initial dioxygenase attack at the 4,5 position of DNT with the concomitant release of nitrite. Subsequent reactions lead to complete biodegradation and removal of the second nitro group as nitrite.     

Inhibitory Effects of Phenolic Ecotoxicants on Photobacteria at Various pH Values

Kinetic characteristics of light emission by intact cells of photobacteria Photobacterium phosphoreum and Vibrio harveyi were studied (at pH 5.5, 7.0, and 8.0), as well as inhibitory effects of 2,4-di- and 2,4,5-triphenoxyacetic acids (2,4-D and 2,4,5-T), pentachlorophenol (PCP), and 2,6-dimethylphenol (2,6-DMP) (at the same pH values). The emission kinetics lacked a steady state, irrespective of pH. At pH 5.5, luminescence decayed exponentially in the 60-s range; at pH 7.0 and 8.0, a 5-min luminescence activation was observed. The respiratory activity of the cells decreased by more than an order of magnitude at pH 5.5 (compared to the levels observed at pH 7.0 and 8.0). The inhibitory effects of 2,4-D, 2,4,5-T, and PCP differed by one to two orders of magnitude, depending on pH. Maximum cell sensitivity to these compounds appeared at pH 5.5; minimum sensitivity, at pH 8.0. The effect of 2,6-DMP was pH-independent. The inhibitory effect was determined by the hydrophobicity of the molecule and pK values of the toxicants. At all pH values, substrate-depleted cells of photobacteria were more sensitive to chlorophenolic compounds than cells supplied with energy.     

A B3LYP and MP2(full) theoretical investigation into the strength of the C–NO2 bond upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C–NO₂ bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C–NO₂ bond upon complex formation, leading to the strengthened C–NO₂ bond and the possibly reduced explosive sensitivity.

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.     

Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase

Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability of the benzene ring. However, the bacterium Comamonas sp. strain JS765 can grow with nitrobenzene as a sole source of carbon, nitrogen and energy. Biodegradation is initiated by the nitrobenzene dioxygenase (NBDO) system. We have determined the structure of NBDO, which has a hetero-hexameric structure similar to that of several other Rieske non-heme iron dioxygenases. The catalytic subunit contains a Rieske iron-sulfur center and an active-site mononuclear iron atom. The structures of complexes with substrates nitrobenzene and 3-nitrotoluene reveal the structural basis for its activity with nitroarenes. The substrate pocket contains an asparagine residue that forms a hydrogen bond to the nitro-group of the substrate, and orients the substrate in relation to the active-site mononuclear iron atom, positioning the molecule for oxidation at the nitro-substituted carbon.     

Computational active site analysis of molecular pathways to improve functional classification of enzymes

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis.     

Theoretical investigation on detonation performances and thermodynamic stabilities of the prismane derivatives

Based on DFT-B3LYP/6-311G** method, the molecular geometric structures of polynitramineprismanes are fully optimized. The detonation performances, energy gaps, strain energies, as well as their stability were investigated to look for high energy density compounds (HEDCs). Our results show that all polynitramineprismanes have high and positive heat of formation. To construct the relationship between stabilities and structures, energy gaps and bond dissociation energies are calculated, and these results show that the energy gaps of prismane derivatives are much higher than that of TATB (0.1630). In addition, the C-C bonds on cage are confirmed as trigger bond in explosive reaction. All polynitramineprismanes have large strain energies, and the strain energies of all compounds are slightly smaller than prismane, which indicated that the strain energies were somewhat released compared to prismane. Considering the quantitative criteria of HEDCs, hexanitramineprismane is a good candidate of high energy compounds.     

Mechanism of nonphotochemical quenching in green plants: energies of the lowest excited singlet states of violaxanthin and zeaxanthin

The xanthophyll cycle is an enzymatic, reversible process through which the carotenoids violaxanthin, antheraxanthin, and zeaxanthin are interconverted in response to the need to balance light absorption with the capacity to use the energy to drive the reactions of photosynthesis. The cycle is thought to be one of the main avenues for safely dissipating excitation energy absorbed by plants in excess of that needed for photosynthesis. One of the key factors needed to elucidate the molecular mechanism by which the potentially damaging excess energy is dissipated is the energy of the lowest excited singlet (S(1)) state of the xanthophyll pigments. Absorption from the ground state (S(0)) to S(1) is forbidden by symmetry, making a determination of the S(1) state energies of these molecules by absorption spectroscopy very difficult. Fluorescence spectroscopy is potentially the most direct method for obtaining the S(1) state energies. However, because of problems with sample purity, low emission quantum yields, and detection sensitivity, fluorescence spectra from these molecules, until now, have never been reported. In this work these technical obstacles have been overcome, and S(1) --> S(0) fluorescence spectra of violaxanthin and zeaxanthin are presented. The energies of the S(1) states deduced from the fluorescence spectra are 14 880 +/- 90 cm(-)(1) for violaxanthin and 14 550 +/- 90 cm(-)(1) for zeaxanthin. The results provide important insights into the mechanism of nonphotochemical dissipation of excess energy in plants.     

Nitrite elimination and hydrolytic ring cleavage in 2,4,6-trinitrophenol (picric acid) degradation

Two hydrogenation reactions in the initial steps of degradation of 2,4,6-trinitrophenol produce the dihydride Meisenheimer complex of 2,4,6-trinitrophenol. The npdH gene (contained in the npd gene cluster of the 2,4,6-trinitrophenol-degrading strain Rhodococcus opacus HL PM-1) was shown here to encode a tautomerase, catalyzing a proton shift between the aci-nitro and the nitro forms of the dihydride Meisenheimer complex of 2,4,6-trinitrophenol. An enzyme (which eliminated nitrite from the aci-nitro form but not the nitro form of the dihydride complex of 2,4,6-trinitrophenol) was purified from the 2,4,6-trinitrophenol-degrading strain Nocardioides simplex FJ2-1A. The product of nitrite release was the hydride Meisenheimer complex of 2,4-dinitrophenol, which was hydrogenated to the dihydride Meisenheimer complex of 2,4-dinitrophenol by the hydride transferase I and the NADPH-dependent F(420) reductase from strain HL PM-1. At pH 7.5, the dihydride complex of 2,4-dinitrophenol is protonated to 2,4-dinitrocyclohexanone. A hydrolase was purified from strain FJ2-1A and shown to cleave 2,4-dinitrocyclohexanone hydrolytically to 4,6-dinitrohexanoate.     

Halogen bonding in substituted cobaloximes

Aquabis(dimethylglyoximato)nitrocobalt(III) reacts with halogen-substituted pyridines to give nitro complexes in which the pyridine donors substitute the aqua ligand; reaction with halogen-substituted pyridinium chlorides directly displaces both the coordinated water molecule and the nitro ligand in a one-pot reaction and affords the analogous chloro complexes. Ten crystal structures of eight new compounds are reported: among these, the nitro complex bis(dimethylglyoximato)nitro(4-chloropyridine)cobalt(III) is characterized by a remarkably long bond between the metal and the nitro ligand whereas the analogous chloro complex chlorobis(dimethylglyoximato)(4-chloropyridine)cobalt(III) features a very long Co-Cl distance. The structures communicated comprise three isomorphous pairs which are particularly suited for the comparative study of chloro and bromo derivatives. The most relevant intermolecular interactions in these compounds are due to very short oxygen?halogen contacts of ca. 2.9 Å whereas shortest interhalogen distances are slightly longer than the sum of the van der Waals radii. For both types of interactions, contact distances involving bromine are shorter than those associated with chlorine.     

High-performance liquid chromatographic assays for free and phosphorylated derivatives of the creatine analogues beta-guanidopropionic acid and 1-carboxy-methyl-2-iminoimidazolidine (cyclocreatine).

Creatine and phosphocreatine are substrates for creatine kinase which is a key enzyme involved in energy transfer within the cell. Analogues of creatine have been fed to animals to determine the role this enzyme plays in energy metabolism, but progress in interpretation has been hampered by the lack of quantitative techniques to determine tissue content of these compounds. We describe the separation and quantitation of substituted guanidino compounds and their phosphorylated forms by high-performance liquid chromatography. First, a cation-exchange column is used to assay free creatine and its unphosphorylated analogues, and then phosphocreatine and its phosphorylated analogues as well as adenylate content (AMP, ADP, ATP) are assayed on an anion-exchange column. These methods have proven successful in measuring the chemical contents of these compounds in neutralized perchloric acid extracts of mammalian skeletal muscles. The sensitivity of this method ranges from 50 to 200 pmol, which is adequate to provide information from tissue extracts of 5- to 10-mg samples.