This study focuses on elucidating the stable forms of a new energetic material that is a member of the class of insensitive munitions (IM), 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO), including its tautomers, and anions. The geometry and properties of all compounds were calculated using density functional theory (M06-2X) and MP2 quantum chemical approaches. Calculations were carried out in the gas phase and in aqueous solution. Chemical stability of these compounds was evaluated in terms of the Gibbs free energy change. Two different solvation models were applied (CPCM and PCM). Calculations showed that overall differences in the results obtained using these two solvation models are negligible for all compounds considered. All possible NTO tautomers were examined and the results are in good agreement with previous studies performed in the gas phase. The stability order was revealed to be slightly dependent on the method applied. In order to estimate acidic properties of NTO, anions of several NTO tautomers were analyzed. In addition, pK a values were calculated using different approaches. As compared with available experimental data it was found that the conductor-like screening model for real solvents approach leads to more accurate estimation of the pK a value than the CPCM and PCM approaches. The pK a value calculated using PCM and CPCM data showed large errors; however, it was proven that the pattern of deprotonation energy was correctly estimated.
We report a comprehensive quantum-chemical study on d(A) 5 •d(T) 5 and d(G) 5 •d(C) 5 DNA mini-helixes and the Dickerson dodecamer d[CGCGAATTCGCG].The research was performed to model the evolution of the spatial structure of d(A) 5 •d(T) 5 and d(G) 5 d(C) 5 DNA mini-helixes all the way from vacuum to water bulk. The influence of external factors such as the presence of counterions and the extent of hydration was included. Also, for comparison, limited calculations have been carried out on the Dickerson dodecamer. The study has been performed at the density functional theory level using B97D3 and ωB97XD exchange−correlation functionals augmented by the Def2SVP basis set. We found that the (dA) 5 •(dT) 5 anion when placed in vacuum forms a DNA duplex, which possesses an intermediate form between a helix and a ladder. The presence of compensating Na + counterions or explicit microhydration of minor and major grooves stabilizes a DNA mini-helix of B-shape. Factors such as water bulk play a minor role. Somewhat different behavior has been found in the case of the (dG) 5 •(dC) 5 duplex. In this case, we observe the formation of B-type mini-helixes even for the (dG) 5 •(dC) 5 anion placed in vacuum. This is due to an additional stabilization originated from the appearance of an extra hydrogen bond, compared to an AT base pair. To assess whether the obtained results are transferable to different sizes of mini-helixes, similar calculations have been performed for the duplex formed by the Dickerson dodecamer which contains a total of 12 dG•dC and dA•dT base pairs. It has been found that in vacuum, analogous to the d(A) 5 •d(T) 5 duplex, this system possesses a shape which is also quite close to a ladder. However, the presence of factors such as hydration restores the B-type geometry. Also, our results completely in line with the results of electrospray-ionization experiments suggest that uncompensated by counterions the DNA backbone preserves the duplex geometry in vacuum. We present arguments that this state is kinetically unstable.
Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account. The MD and the COSMOmic approaches were used to elucidate the ability of the energetic compounds to penetrate the living cell. Calculated free energy profiles and partitioning coefficients revealed distributions of the compounds in the lipid bilayer as well as an overall ability to enter the cell. MD in this case provides a better representation of the free energy profile, while the COSMOmic approach works better to predict log(K) values. The effect of the functional group was observed for the profiles that were obtained using the MD method.
The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol-water (log(Kow)) and liposome-water (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).
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