Density functional theory calculations on the thermodynamic properties of polynitrosoprismanes

A series of polynitrosoprismanes, C(6)H(6 - n )(NO)( n ) (n?=?1-6), considered as high energy density compounds (HEDCs), have been designed computationally. We calculated the electronic structures, the heats of formation, the specific enthalpies of combustion, the bond dissociation energies, and the strain energies of the title compounds using density functional theory (DFT) with the 6-311G** basis set. It was found that the ΔE (LUMO-HOMO) values of the title compounds decrease as the number of nitroso groups increase, and the energy gaps of the prismane derivatives are much lower than that of TATB. Their high positive heats of formation indicate that polynitrosoprismanes can store a great deal of energy. Furthermore, the HOFs for the nitrosoprismane series were observed to decrease until three nitroso groups were connected to the prismane skeleton. For the polynitrosoprismanes, the trigger bond was confirmed to be the C-C bond in the skeleton. According to our calculations, all nitrosoprismanes appear to have large strain energies, and these calculations can provide basic information that may prove useful for the molecular design of novel high energy density materials.     

Looking for high energy density compounds among polynitraminecubanes

Based on fully optimized geometric structures at DFT-B3LYP/6-311G** level, we calculated electronic structures, heats of formation, strain energies, bond dissociation energies and detonation performance (detonation velocity and detonation pressure) for a series of polynitraminecubanes. Our results have shown that energy gaps of cubane derivatives are much higher than that of triaminotrinitrobenzene (TATB), which means that cubane derivatives may be more sensitive than TATB. Polynitraminecubanes have high and positive heats of formation, and a good linear relationship between heats of formation and nitramine group numbers was presented. As the number of nitramine groups in the molecule increases, the enthalpies of combustion values are increasingly negative, but the specific enthalpy of combustion values decreases. It is found that all cubane derivatives have high strain energies, which are affected by the number and position of nitramine group. The calculated bond dissociation energies of C-NHNO₂ and C-C bond show that the C-C bond should be the trigger bond in the pyrolysis process. It is found that detonation velocity (D), detonation pressure (P) and molecule density (ρ) have good linear relationship with substituented group numbers. Heptanitraminecubane and octanitraminecubane have good detonation performance over 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), and they can be regarded as potential candidates of high energy density compounds (HEDCs). The results have not only shown that these compounds may be used as HEDCs, but also provide some useful information for further investigation.     

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.     

Theoretical investigation on the heats of formation and detonation performance in polydinitroaminocubanes

A series of polydinitroaminocubanes have been designed computationally. We calculated the heats of formation, the detonation velocity (D) and detonation pressure (P) of the title compounds by density function theory (DFT) with 6-311?G** basis set. The relationship between the heats of formation and the molecular structures is discussed. The result shows that all cubane derivatives have high and positive heats of formation, which increase with increasing number of dinitroamino groups. The detonation performances of the title compound were estimated by Kamlet-Jacobs equation, and the result indicated that most cubane derivatives have good detonation performance over RDX (hexahydro-1,3,5-trinitro-1,3,5-trizine) and HMX (1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane). In addition, we also found that the heat of detonation (Q) is another very important impact in increasing detonation performance except density. The relative stabilities of the title compound are discussed in the terms of the calculated heats of formation, and the energy gaps between the frontier orbitals. The results have not only shown that these compounds may be used as high energy density compounds (HEDCs), but also provide some useful information for further investigation.     

Computational study of energetic nitrogen-rich derivatives of 1,4-bis(1-azo-2,4-dinitrobenzene)-iminotetrazole

The heats of formation (HOFs), electronic structure, energetic properties, and thermal stabilities for a series of 1,4-bis(1-azo-2,4-dinitrobenzene)-iminotetrazole derivatives with different substituents and substitution positions and numbers of nitrogen atoms in the nitrobenzene rings were studied using the DFT-B3LYP method. All the substituted compounds have higher HOFs than their parent compounds. As the number of nitrogen atoms in the nitrobenzene ring increases, the HOFs of the derivatives with the same substituent rise gradually. Replacing carbon atoms in the nitrobenzene with nitrogen atoms to form N–N bonds is very helpful in improving their HOFs. Most of the substituted compounds have higher HOMO–LUMO gaps than the corresponding unsubstituted compounds. Substitution of the –NO₂, –NF₂, or –ONO₂ group and an increase in the number of nitrogen atoms in the nitrobenzene rings are useful for enhancing their detonation performance. The substituents’ substitution is not favorable for improving thermal stability. Considering detonation performance and thermal stability, five compounds may be considered potential candidates for high energy density compounds (HEDCs).     

Dinitroamino benzene derivatives: a class new potential high energy density compounds

Dinitroamino benzene derivatives are designed and studied in detail with quantum chemistry method. The molecular theory density, heats of formation, bond dissociation energies, impact sensitive and detonation performance are investigated at DFT-B3LYP/6-311G** level. The results of detonation performance indicated most of the compounds have better detonation velocity and pressure than RDX and HMX. The N-N bond can be regard as the trigger bond in explosive reaction, and the bond dissociation energies of trigger bond are almost not affected by the position and number of substituent group. The impact sensitive are calculated by two different theory methods. It is found that the compounds, which can become candidates of high energy materials, have smaller H₅₀ values than RDX and HMX. It is hoped that this work can provide some basis information for further theory and experiment studies of benzene derivatives.     

Conjugation in multi-tetrazole derivatives: a new design direction for energetic materials

Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO–LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these molecules with conjugated structures showed low energies of their crystal structures, molecular layering in their crystals, high average ESPs, high multicenter bond order values, and enhanced detonation properties. The derivative 1,2-di(1H-tetrazol-5-yl)diazene (N2) was predicted to have the best density (1.87 g/cm³), detonation velocity (9006 m/s), and detonation pressure (36.8 GPa) of the designed molecules, while its total crystal energy was low, suggesting that it is relatively stable. Its sensitivity was also low, as the molecular stacking that occurs in its crystal allows external forces to be dissipated into movements of crystal layers. Finally, its multicenter bond order was high, indicating a highly conjugated structure.     

Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization

Low energy conformations have been generated for melittin, pancreatic polypeptide, and ribonuclease S-peptide, both in the vicinity of x-ray structures by energy refinement and by an unconstrained search over the entire conformational space. Since the structural polymorphism of these medium-sized peptides in crystal and solution is moderate, comparing the calculated conformations to x-ray and nmr data provides information on local and global behavior of potential functions. Local analysis includes standardization calculations, which show that models with standard geometry can approximate good resolution x-ray data with less than 0.5 Å rms deviation (RMSD). However, the atomic coordinates are shifted up to 2 Å RMSD by local energy minimization, and thus 2 Å is generally the smallest RMSD value one can target in a conformational search using the same energy evaluation models. The unconstrained search was performed by a buildup-type method based on dynamic programming. To accelerate the generation of structures in the conformational search, we used the ECEPP potential, defined in terms of standard polypeptide geometry. A number of low energy conformations were further refined by relaxing the assumption of standard bond lengths and bond angles through the use of the CHARMM potential, and the hydrophobic folding energies of Eisenberg and McLachlan were calculated. Each conformation is described in terms of the RMSD from the native, hydrogen-bonding structure, solvent-acessible surface area, and the ratio of surfaces corresponding to nonpolar and polar residues. The unconstrained search finds conformations that are different from the native, sometimes substantially, and in addition, have lower conformational energies than the native. The origin of deviations is different for each of the three peptides, but in all examples the refined x-ray structures have lower energies than the calculated incorrect folds when (1) the assumption of standard bond lengths and bond angles is relaxed; (2) a small and constant effective dielectric permittivity (ε < 10) is used; and (3) the hydrophobic folding energy is incorporated into the potential. © 1993 John Wiley & Sons, Inc.     

Thermodynamic cycle analysis and inhibitor design against beta-lactamase

Beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics, such as the penicillins and cephalosporins. Transition-state analogues that bind to the enzymes with nanomolar affinities have been introduced in an effort to reverse the resistance conferred by these enzymes. To understand the origins of this affinity, and to guide design of future inhibitors, double-mutant thermodynamic cycle experiments were undertaken. An unexpected hydrogen bond between the nonconserved Asn289 and a key inhibitor carboxylate was observed in the X-ray crystal structure of a 1 nM inhibitor (compound 1) in complex with AmpC beta-lactamase. To investigate the energy of this hydrogen bond, the mutant enzyme N289A was made, as was an analogue of 1 that lacked the carboxylate (compound 2). The differential affinity of the four different protein and analogue complexes indicates that the carboxylate-amide hydrogen bond contributes 1.7 kcal/mol to overall binding affinity. Synthesis of an analogue of 1 where the carboxylate was replaced with an aldehyde led to an inhibitor that lost all this hydrogen bond energy, consistent with the importance of the ionic nature of this hydrogen bond. To investigate the structural bases of these energies, X-ray crystal structures of N289A/1 and N289A/2 were determined to 1.49 and 1.39 A, respectively. These structures suggest that no significant rearrangement occurs in the mutant versus the wild-type complexes with both compounds. The mutant enzymes L119A and L293A were made to investigate the interaction between a phenyl ring in 1 and these residues. Whereas deletion of the phenyl itself diminishes affinity by 5-fold, the double-mutant cycles suggest that this energy does not come through interaction with the leucines, despite the close contact in the structure. The energies of these interactions provide key information for the design of improved inhibitors against beta-lactamases. The high magnitude of the ion-dipole interaction between Asn289 and the carboxylate of 1 is consistent with the idea that ionic interactions can provide significant net affinity in inhibitor complexes.     

On the role of strain in blue copper proteins

Theoretical investigations of the structure and function of the blue copper proteins are described. We have studied the optimum vacuum geometry of oxidised and reduced copper sites, the relative stability of trigonal and tetragonal Cu(II) structures, the relation between the structure and electronic spectra, the reorganisation energy, and reduction potentials. Our calculations give no support to the suggestion that strain plays a significant role in the function of these proteins; on the contrary, our results show that the structures encountered in the proteins are close to their optimal vacuum geometries (within 7 kJ/mol). We stress the importance of defining what is meant by strain and of quantifying strain energies or forces in order to make strain hypotheses testable.     

Comparative theoretical studies of energetic pyrazole-pyridine derivatives

The pyrazole-pyridine derivatives were optimized to obtain their molecular geometries and electronic structures at the DFT-B3LYP/6-31G(d,p) and DFT-B3P86/6-31G(d,p) levels. Molecular mechanics (MM) calculations were performed for the title compounds. Heats of formation (HOFs) were predicted through designed isodesmic reactions. Detonation performance was evaluated by using the Kamlet-Jacobs equations based on the calculated densities and heats of formation. The thermal stability of the title compounds was investigated via the bond dissociation energies (BDEs). The simulation results reveal that the compound with one pyrazole ring that is fully nitro-substituted performs similarly to the famous explosive HMX, and the compound with two pyrazole rings that are fully nitro-substituted outperforms HMX. According to the quantitative standard of energetics and stability as high energy density materials (HEDMs), the compound with two pyrazole rings that are fully nitro-substituted essentially satisfies this requirement.     

Bond-optimized ring closure for proline: comparison of conformations and semiempirical energies with small molecule X-ray structures

A method is described for generating proline ring structures by successive addition of atoms, wherein ring closure is achieved by optimizing the fit to known ring bond-angles and one closing bond-length ("bond-optimized ring closure"). Two ring torsion angles are fixed independently within broad, allowed ranges, and the remaining torsion angles are determined uniquely in most cases. The independent torsion angles are chosen as phi and chi 2, and ring closure is achieved without prohibitive strain through most of the ranges -130 degrees less than phi less than -20 degrees and -60 degrees less than chi 2 less than 60 degrees. Comparisons of predicted ring structures to 191 X-ray diffraction structures from the literature, starting with the known values of phi and chi 2, yielded root-mean-square deviations of 4.8 degrees in chi 1, 4.7 degrees in chi 3, 8.3 degrees in chi 4, and 0.3-2% in the ring bond angles and the N-C delta distance. Semiempirical energies were calculated for the optimized structures using three sets of energy parameters from the literature. The energy surfaces show broad minima coinciding with the torsion angle regions in which the highest concentrations of observed structures are found. Two of the sets of energy parameters produce double minima corresponding to the "up" and "down" puckered conformations.     

Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study

Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into flavonoids. The activity of CHI is essential for the biosynthesis of flavonoids precursors of floral pigments and phenylpropanoid plant defense compounds. In the present study, we explored the detailed binding structures and binding free energies for two different active site conformations of CHI with s-cis/s-trans conformers of three chalcone compounds by performing molecular dynamics (MD) simulations and binding free energy calculations. The computational results indicate that s-cis/s-trans conformers of chalcone compounds are orientated in the similar binding position in the active site of CHI and stabilized by the different first hydrogen bond network and the same second hydrogen bond network. The first hydrogen bond network results in much lower binding affinity of s-trans conformer of chalcone compound with CHI than that of s-cis conformer. The conformational change of the active site residue T48 from indirectly interacting with the substrate via the second hydrogen bond network to directly forming the hydrogen bond with the substrates cannot affect the binding mode of both conformers of chalcone compounds, but remarkably improves the binding affinity. These results show that CHI has a strong stereoselectivity. The calculated binding free energies for three chalcone compounds with CHI are consistent with the experimental activity data. In addition, several valuable insights are suggested for future rational design and discovery of high-efficiency mutants of CHI.

The electronic properties of poly(p-phenylenevinylene) derivatives and their monomers and oligomers

The electronic structures of monomers, oligomers and polymers of poly(p-phenylenevinylene) (PPV) derivatives are calculated and analysed based on density functional theory (DFT) methods. The influences of different substituent groups on the band gaps are discussed. Strong relationships are found between band-gap and bond length alternation (BLA) of polymers, and between band-gap and Wiberg bond index (WBI). Analysis of nuclear independent chemical shift (NICS) reveals that oligomers with similar energy gaps have close values of NICS.     

Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors

Among the available methods for predicting free energies of binding of ligands to a protein, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA) approaches have been validated for a relatively limited number of targets and compounds in the training set. Here, we report the results of an extensive study on a series of 28 inhibitors of aldose reductase with experimentally determined crystal structures and inhibitory activities, in which we evaluate the ability of MM-PBSA and MM-GBSA methods in predicting binding free energies using a number of different simulation conditions. While none of the methods proved able to predict absolute free energies of binding in quantitative agreement with the experimental values, calculated and experimental free energies of binding were significantly correlated. Comparing the predicted and experimental ΔG of binding, MM-PBSA proved to perform better than MM-GBSA, and within the MM-PBSA methods, the PBSA of Amber performed similarly to Delphi. In particular, significant relationships between experimental and computed free energies of binding were obtained using Amber PBSA and structures minimized with a distance-dependent dielectric function. Importantly, while free energy predictions are usually made on large collections of equilibrated structures sampled during molecular dynamics in water, we have found that a single minimized structure is a reasonable approximation if relative free energies of binding are to be calculated. This finding is particularly relevant, considering that the generation of equilibrated MD ensembles and the subsequent free energy analysis on multiple snapshots is computationally intensive, while the generation and analysis of a single minimized structure of a protein–ligand complex is relatively fast, and therefore suited for high-throughput virtual screening studies. At this aim, we have developed an automated workflow that integrates all the necessary steps required to generate structures and calculate free energies of binding. The procedure is relatively fast and able to screen automatically and iteratively molecules contained in databases and libraries of compounds. Taken altogether, our results suggest that the workflow can be a valuable tool for ligand identification and optimization, being able to automatically and efficiently refine docking poses, which sometimes may not be accurate, and rank the compounds based on more accurate scoring functions.     

Theoretical study of the decomposition mechanisms and kinetics of the ingredients RDX in composition B

RDX as a component in composition B (TNT + RDX) was first studied by us on its mechanism and kinetics of decomposition reactions in this paper. We have pointed out three possible pathways and found a new low-energy process of its decomposition. The N-N bond cleavage in composition B has higher dissociation energies than the monomer, but it is also the initial step. The optimized structures and the frequencies of all the stationary points were calculated at the B3LYP/6-31G(d) level. The minimum-energy paths were obtained by using the intrinsic reaction coordinate (IRC) theory, and the reaction potential energy curve was corrected with zero-point energy. Finally, the rate constants were calculated in a wide temperature region from 200 to 2500 K using TST, TST/Eckart theories. The obtained results also indicate that the tunneling effects are remarkable at low temperature (200 K 相似文献   

Looking for high energy density compounds among polynitraminepurines

A series of purine derivatives with nitramine groups are calculated by using density functional theory (DFT). The molecular theory density, heats of formation, bond dissociation energies and detonation performance are investigated at DFT-B3LYP/6-311G** level. The isodesmic reaction method is employed to calculate the HOFs of the energies obtained from electronic structure calculations. Results show that the position of nitramine groups can influence the values of HOFs. The bond dissociation energies and the impact sensitivity are analyzed to investigate the thermal stability of the purine derivatives. The calculated bond dissociation energies of ring-NHNO₂ and NH-NO₂ bond show that the NH-NO₂ bond should be the trigger bond in pyrolysis processes. The H₅₀ of most compounds are larger than that of CL-20 and RDX.     

An important factor in relation to shock-induced chemistry: resonance energy

With density function theory BLYP/DNP method, together with homodesmotic reactions and isodesmic reactions, we calculated the resonance energies of some explosives, including eight nitro compounds which contains benzene rings, three nitro compounds which contains azaheterocycles (2,4-dinitroimidazole (2,4-DNI), 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) and 2,4,6-trinitro-1,3,5-triazine) and one nitrogen-rich energetic compound of 3,3’-azobis(6-amino-s-tetrazine) (DAAT). The results indicate that their resonance energies are in relation to their shock sensitivity which measuring their threshold pressures of initiation, that is, the lower the resonance energy is, the higher the shock sensitivity of the explosive behaves. And this measuring method according to resonance energy is based on the global property of the molecule instead of the local one, such as one nitro group in the molecule. It is meaningful to calculate resonance energies of these kind of compounds quickly and accurately because resonance structures exist widely in these organic compounds and resonance energies may play a significant role in determining their shock sensitivity, and it is helpful in the rational design or synthesis of high energy and insensitive materials.     

Computational studies on polynitropurines as potential high energy density materials

As part of a search for high energy density materials (HEDMs), a series of purine derivatives with nitro groups were designed computationally. The relationship between the structures and the performances of these polynitropurines was studied. Density functional theory (DFT) at the B3LYP/6-311G** level was employed to evaluate the heats of formation (HOFs) of the polynitropurines by designing an isodesmic reaction method. Results indicated that the HOFs were influenced by the number and positions of substituent groups. Detonation properties were evaluated using the Kamlet–Jacobs equations, based on the theoretical densities and heats of formation of the polynitropurines. The relative stabilities of the polynitropurines were studied via the pyrolysis mechanism and the UB3LYP/6-311G** method. Homolysis of the ring–NO₂ bond is predicted to be the initial step in the thermal decomposition of these purine derivatives. Considering their detonation properties and relative stabilities, the tetranitropurine (D1) derivatives may be regarded as potential candidates for practical HEDCs. These results may provide useful information for further investigations.     

A computational approach to the polymerizabilities of diallylamines

Some selected diallylamine monomers have been studied with the semiempirical PM3 method as model compounds for N,N-dialkyl-N-2-(alkoxycarbonyl)allylammonium salts, in order to build up a quantitative and qualitative relationship between the experimental cyclopolymerizabilities of the monomers and calculated parameters such as charge, energy, geometrical features, bond orders, local softness values and HOMO-LUMO gaps. The charges on nitrogen, vinyl and allyl carbons, the activation barriers, the local softness values and the HOMO-LUMO gaps are found to represent the polymerizability trend of the monomers in general. Three-dimensional structures have been proposed for the reactants and their transition states by geometry optimizations with PM3.