DFT study on crystalline 1,1-diamino-2,2-dintroethylene under high pressures

DFT calculations have been performed to study the structural, electronic, absorption, and thermodynamic properties of crystalline 1,1-diamino-2,2-dintroethylene (α-FOX-7) in the pressure range of 0–40 GPa. A comprehensive analysis of the variation trends of the lattice constants, bond lengths, bond angles, and twist angles under compression shows that six structural transformations occur in α-FOX-7 at 2, 5, 11, 19, 29, and 35 GPa, respectively. The C1-N1 and C1-N2 bond lengths decrease much faster than any other bonds under compression, indicating that the C-NO₂ cleavage is possible to trigger the decomposition of α-FOX-7. The intra-molecular H-bonding interaction weakens at 2 and 5 GPa, which may be caused by the structural transformations, but it then strengthens with the increasing pressure up to 40 GPa. The inter-molecular H-bonding interaction strengthens with the increasing pressure. The band gap of α-FOX-7 increases at 11 GPa suddenly and decreases obviously at 19, 29, and 35 GPa, which are caused by the structural transformations. α-FOX-7 has relatively high optical activity at high pressure. All the structural transformations are endothermic and not spontaneous at room temperature.     

Periodic density functional theory study of the high-pressure behavior of energetic crystalline 1,4-dinitrofurazano[3, 4-b]piperazine

A detailed study of the structural, electronic, and optical absorption properties of crystalline 1,4-dinitrofurazano[3,4-b]piperazine (DNFP) under hydrostatic pressures of 0–100 GPa was performed using periodic density functional theory. As the pressure increases, the lattice constants and cell volumes calculated by LDA gradually approach those obtained by GGA-PW91. It was found that the structure of DNFP is much stiffer in the b direction than along the a and c axes, indicating that the compressibility of the crystal is anisotropic. As the pressure increases, the band gap gradually decreases, and this decrease is more pronounced in the low-pressure range than in the high-pressure region. An analysis of the density of states showed that the electronic delocalization in DNFP gradually increases under the influence of pressure. DNFP exhibits relatively high optical activity at high pressure. As the pressure increases, the bands in the fundamental absorption region of the absorption spectrum of DNFP become more numerous and intense.     

Pressure dependence on electronic structures,charge distribution and bond orders of solid nitromethane using nonlocal DFT functional

The electronic properties of solid nitromethane are studied using nonlocal exchange-correlation functional (optPBE–vdW) under hydrostatic compression up to 40?GPa. We found that the optPBE–vdW functional can reproduce well the crystalline structures compared with the experiments, and an isomorphic phase transition has been verified by their P–V curve. Bader’s charge analysis shows the electron flows from CH₃ group to NO₂ group with the pressure. Moreover, the calculated bond orders show that the pressure only strengthens the intermolecular C–N bond and intermolecular C–H···O hydrogen bonds though it shortens all bond lengths. Furthermore, the electronic structure and its pressure dependence have also been discussed in detail.     

Pressure-induced improvement in symmetry and change in electronic properties of SnSe

To explore the structural and electronic properties of SnSe under pressure, we applied hydrostatic pressure from 0 to 8 GPa to a fully relaxed SnSe cell sample based on plane-wave pseudopotential density functional theory. The calculated results indicate that the structure of SnSe changes gradually from an irregular zigzag structure with low symmetry to a B1-like structure with regular arrangement and high symmetry under pressure. The lattice parameters and cell volume of SnSe decrease monotonically as the applied pressure increases. The energy band gap of SnSe becomes narrow under pressure and is finally closed at 6.1 GPa. Moreover, we found that SnSe exhibits non-magnetic and semi-metallic features based on analyzing its electronic state density and spin state density. This can be attributed to the decrease in the lattices constants and the enhancement of the Sn–Se bond interaction under pressure, which causes the density of electronic states to increase near the Fermi surface. Finally, the charge distribution between Se–Sn–Se along the c-axis changes gradually from asymmetric to symmetric as the pressure is increased to 6.1 GPa and beyond. This implies that enhancement of the structure symmetry of SnSe can lead to a symmetrical distribution of charges, which further affects the bonding characteristics of the Sn–Se bond.     

Theoretical studies on the thermodynamic properties, densities, detonation properties, and pyrolysis mechanisms of trinitromethyl-substituted aminotetrazole compounds

Trinitromethyl-substituted aminotetrazoles with –NH₂, –NO₂, –N₃, and –NHC(NO₂)₃ groups were investigated at the B3LYP/6-31G(d) level of density functional theory. Their sublimation enthalpies, thermodynamic properties, and heats of formation were calculated. The thermodynamic properties of these compounds increase with temperature as well as with the number of nitro groups attached to the tetrazole ring. In addition, the detonation velocities and detonation pressures of these compounds were successfully predicted using the Kamlet–Jacobs equations. It was found that these compounds exhibit good detonation properties, and that compound G (D = 9.2 km/s, P = 38.8 GPa) has the most powerful detonation properties, which are similar to those of the well-known explosive HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocine). Finally, the electronic structures and bond dissociation energies of these compounds were calculated. The BDEs of their C–NO₂ bonds were found to range from 101.9 to 125.8 kJ/mol^-1. All of these results should provide useful fundamental information for the design of novel HEDMs.     

Correlated Variations of Bond Lengths in Pseudorotating Furanose Rings

Abstract

Correlated variations of bond lengths in pseudorotating furanose rings are investigated by a theoretical method. At first, matrix equations are proposed to determine the spatial coordinates of the ring atoms from the bond lengths, the bond angles, and the pseudorotation parameters. Secondly, a necessary functional form of the variations of the bond lengths of five-membered rings is derived from a consideration of symmetry. Finally, demonstrations are performed on a furanose ring whose bond angle variations have been precisely determined by experimental analyses. The resulting bond length variations are:

δR_i = β_iCos(8/5π · (i-2)+2P)

where δR_i is the variation of the bond length between atoms i and i+1, P is the pseudorotation phase, and β_iis a negative constant about ?0.01 Å. These bond length variations are balanced on the apparent strains of the bond lengths and the bond angles.     

Solid-state geometry and conformation of linear,diastereoisomeric oligoprolines

We have carried out a systematic analysis of the solid-state conformational preferences of a number of linear homo-oligoprolines (to the tetramer) by ir absorption and x-ray diffraction. The peptides present different chiral sequences (tacticities), various types (urethane and amide) of N-protecting groups, and free and blocked C-termini (which imply different capabilities of forming H-bonds). The following conclusions can be drawn: (i) values for the geometry of the prolyl residue and the peptide bond in the cis and in the trans conformations are proposed; (ii) in general the conformational angles φ and ψ in the linear homo-oligoprolines have values appropriate for the polyproline II structure (conformation F); (iii) the pyrrolidine ring shows various types of puckering with no apparent relation to the backbone conformation; (iv) Pro-Pro peptide bonds generally take the trans conformation, the few cases of cis conformation being formed by Pro residues of different chirality; (v) the single H-bond donor — OH, when present, is always bonded to H-acceptors, which can be either the urethane or the amide or the peptide carbonyl but never the carbonyl group of the — COOH moiety.     

Structural Implications of Hydrogen-Bond Energetics in Membrane Proteins Revealed by High-Pressure Spectroscopy

The light-harvesting 1 (LH1) integral membrane complex of Rhodobacter sphaeroides provides a convenient model system in which to examine the poorly understood role of hydrogen bonds (H-bonds) as stabilizing factors in membrane protein complexes. We used noncovalently bound arrays of bacteriochlorophyll chromophores within native and genetically modified variants of LH1 complexes to monitor local changes in the chromophore binding sites induced by externally applied hydrostatic pressure. Whereas membrane-bound complexes demonstrated very high resilience to pressures reaching 2.1 GPa, characteristic discontinuous shifts and broadenings of the absorption spectra were observed around 1 GPa for detergent-solubilized proteins, in similarity to those observed when specific (α or β) H-bonds between the chromophores and the surrounding protein were selectively removed by mutagenesis. These pressure effects, which were reversible upon decompression, allowed us to estimate the rupture energies of H-bonds to the chromophores in LH1 complexes. A quasi-independent, additive role of H-bonds in the α- and β-sublattices in reinforcing the wild-type LH1 complex was established. A comparison of a reaction-center-deficient LH1 complex with complexes containing reaction centers also demonstrated a stabilizing effect of the reaction center. This study thus provides important insights into the design principles of natural photosynthetic complexes.     

Theoretical investigation of a novel high density cage compound 4,8,11,14,15–pentanitro-2,6,9,13–tetraoxa-4,8,11,14,15-pentaazaheptacyclo[5.5.1.13,11. 15,9] pentadecane

A novel polynitro cage compound 4,8,11,14,15-pentanitro-2,6,9,13-tetraoxa-4,8,11,14,15–pentaazaheptacyclo [5.5.1.1^3,11.1^5,9]pentadecane(PNTOPAHP) has been designed and investigated at the DFT-B3LYP/6-31(d) level. Properties, such as electronic structure, IR spectrum, heat of formation, thermodynamic properties and crystal structure have been predicted. This compound is most likely to crystallize in C2/c space group, and the corresponding cell parameters are Z?=?8, a?=?29.78 Å, b?=?6.42 Å, c?=?32.69 Å, α?=?90.00°, β?=?151.05°, γ?=?90.00°and ρ?=?1.94 g/cm³. In addition, the detonation velocity and pressure have also been calculated by the empirical Kamlet-Jacobs equation. As a result, the detonation velocity and pressure of this compound are 9.82 km/s, 44.67 GPa, respectively, a little higher than those of 4,10-dinitro-2,6,8,12–tetraoxa?4,10-diazaisowurtzitane(TEX, 9.28 km/s, 40.72 GPa). This compound has a comparable chemical stability to TEX, based on the N-NO₂ trigger bond length analysis. The bond dissociation energy ranges from 153.09 kJ mol^–1 to 186.04 kJ mol^–1, which indicates that this compound meets the thermal stability requirement as an exploitable HEDM.     

Structural, mechanical and electronic properties of nano-fibriform silica and its organic functionalization by dimethyl silane: a SCC-DFTB approach

Self-consistent-charge density-functional tight-binding (SCC-DFTB) approximated method was employed to investigate the structural, mechanical and electronic properties of the zigzag and armchair nano-fibriform silica (SNTs) and their outer surface organic modified derivatives (MSNTs) with internal radii in the range of 8 to 36 Å. The strain energy curves showed that the nanotubes structures are energetically more stable compared to the respective sheet structures. External hydroxyl dihedral angles in silica nanotubes have small influence, about 0.5 meV.atom^?1, in the strain energy curve tendency of those materials favoring the zigzag chirality. The chemical modification of outer surface of SNTs by dimethyl silane group affects their relative stability favoring the armchair chirality in approximately 2 meV.atom^?1. MSNTs have axial elastic constants, Young’s moduli, determined at the harmonic approximation, around 100 GPa smaller than the respective SNTs. The Young’s moduli of zigzag and armchair SNTs are in the range of 150–195 GPa and 232–260 GPa, respectively. And for the zigzag and armchair MSNTs these values are in the range of 77–89 and 110–140 GPa, respectively. The SNTs and MSNTs were characterized as insulators with band gaps around 8–10 eV.

Modelling hydrogen bonds in NN-dimethylformamide

N, N-dimethylformamide (DMF) is a ‘universal’ solvent with the simplest amide structure. DMF has different interactions with many polymers and biomolecules. It is therefore necessary to study systematically the interactions in DMF itself first. In this study, both FT-IR and two molecular theoretical methods (MP2 and DFT/B3LYP) were used to study various hydrogen bonding interactions in DMF molecules based on its weak H-bonding donors CH/CH₃ and strong H-bonding acceptor C = O. The possible H-bonding donors and acceptors in DMF molecules were first analysed followed by modelling the effect of different structural environments on vC = O bands in infrared spectra. Finally, H-bonding properties including distance, angles and the energy as well as the probability of H-bonding patterns were obtained. The results showed that there exist five possible different weak types of H-bonding dimers; among them, three dimers consist of a pair of weak H-bonds, whereas two other dimers have two pairs of H-bonds, leading to 14 (including eight different) H-bonds. Two types of dimers were dominant, whereas three others can be omitted.     

Correlated variations of bond lengths in pseudorotating furanose rings

Correlated variations of bond lengths in pseudorotating furanose rings are investigated by a theoretical method. At first, matrix equations are proposed to determine the spatial coordinates of the ring atoms from the bond lengths, the bond angles, and the pseudorotation parameters. Secondly, a necessary functional form of the variations of the bond lengths of five-membered rings is derived from a consideration of symmetry. Finally, demonstrations are performed on a furanose ring whose bond angle variations have been precisely determined by experimental analyses. The resulting bond length variations are: delta Ri = beta icos(8/5 pi.(i-2)+2P) where delta Ri is the variation of the bond length between atoms i and i+1, P is the pseudorotation phase, and beta i is a negative constant about -0.01 A. These bond length variations are balanced on the apparent strains of the bond lengths and the bond angles.     

Theoretical studies on the crystal structure, thermodynamic properties, detonation performance and thermal stability of cage-tetranitrotetraazabicyclooctane as a novel high energy density compound

The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet–Jacobs equations. Thermal stability of 3,5,7,10,12,14,15,16-octanitro- 3,5,7,10,12,14,15,16-octaaza-heptacyclo[7.5.1.1^2,8.0^1,11.0^2,6.0^4,13.0^6,11]hexadecane (cage-tetranitrotetraazabicyclooctane) was investigated by calculating the bond dissociation energy (BDE) at unrestricted B3LYP/6-31G (d) level. The calculated results show that the N–NO₂ bond is a trigger bond during thermolysis initiation process. The crystal structure obtained by molecular mechanics (MM) methods belongs to Pna2₁ space group, with cell parameters a?=?12.840 Å, b?=?9.129 Å, c?=?14.346 Å, Z?=?6 and ρ?=?2.292 g·cm^?3. Both the detonation velocity of 9.96 km·s^?1 and the detonation pressure of 47.47 GPa are better than those of CL-20. According to the quantitative standard of energetics and stability, as a high energy density compound (HEDC), cage-tetranitrotetraazabicyclooctane essentially satisfies this requirement.     

Ab initio and molecular dynamics studies of solid β-HMX: effects of hydrostatic pressure and high temperature

Using first-principles density functional theory and classical molecular dynamics (MD), the structural, electronic and mechanical properties of the energetic material β-HMX have been studied. The crystal structure optimised by the local density approximation calculations compares reasonably with the experimental data. Electronic band structure and density of states indicate that β-HMX is an insulator with a band gap of 3.059 eV. The pressure effect on the crystal structure and physical properties has been investigated in the range of 0–40 GPa. The crystal structure and electronic properties change slightly as the pressure increases from 0 to 2.5 GPa; when the pressure is above 2.5 GPa, further increment of the pressure results in significant changes in crystal structure. There is a larger compression along the b-axis than along the a- and c-axes. Isothermal–isobaric MD simulations on β-HMX were performed in the temperature range of 5–400 K. Phase transition at 360 K, corresponding to a volume interrupt, was found. The computed thermal expansion coefficients show anisotropic behaviour with a slightly larger expansion along the b- and c-axes than along the a-axis. In the temperature range of 5–360 K, β-HMX possesses good plasticity and its stiffness decreases with increasing the temperature.     

Thermodynamics of pyrope–majorite,Mg3Al2Si3O12–Mg4Si4O12, solid solution from atomistic model calculations

Static lattice energy calculations, based on empirical pair potentials have been performed for a large set of different structures with compositions between pyrope and majorite, and with different states of order of octahedral cations. The energies have been cluster expanded using pair and quaternary terms. The derived ordering constants have been used to constrain Monte–Carlo simulations of temperature-dependent properties in the ranges of 1073–3673 K and 0–20 GPa. The free energies of mixing have been calculated using the method of thermodynamic integration. At zero pressure the cubic/tetragonal transition is predicted for pure majorite at 3300 K. The transition temperature decreases with the increase of the pyrope mole fraction. A miscibility gap associated with the transition starts to develop at about 2000 K and x _maj = 0.8, and widens with the decrease in temperature and the increase in pressure. Activity–composition relations in the range of 0–20 GPa and 1073–2673 K are described with the help of a high-order Redlich–Kister polynomial.     

Geometry of the five-membered ring mathematical demonstration of the pseudorotation formulae

The geometrical relations between the 15 typical parameters (bond lengths and angles, torsion angles) of a five-membered ring are derived for any ring then for a regular one. It is demonstrated that for the case of the 20 symmetrical C ₂ and C _sconformations, only geometrical considerations are needed to obtain the pseudorotation formulae for the torsion angles. However, the puckering intensity as well as the bond angle values cannot be expressed from geometrical constraints alone but would require energetical considerations.     

Spectroscopic investigation on glutamic acid by Coulomb-attenuating and double hybrid density functional theory methods

This study deals with the identification of glutamic acid by means of quantum chemical approach. FT-IR, FT-Raman and UV–vis spectra were recorded in the region 4000–400, 4000–50 cm^? 1 and 200–600 nm, respectively. CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p) calculations were performed to obtain the optimised molecular structures, vibrational frequencies and corresponding vibrational assignment, thermodynamic properties and natural bonding orbital (NBO) analysis. The results show that the obtained optimised geometric parameters (bond lengths, bond angles and bond dihedrals) and vibrational frequencies were found to be in good agreement with the experimental results. The calculations of the electronic spectra were compared with the experimental ones. Furthermore, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses and UV–vis spectral analysis were also performed to determine the energy band gaps and transition states. NBO analysis, calculated using density functional theory methods (CAM-B3LYP/6-31G(d,p) and B2PLYP/6-31G(d,p)), was induced to find inter-molecular atoms. ¹³C and ¹H NMR isotropic chemical shifts were calculated and the assignments made were compared with the ChemDraw Ultra values.     

Calculation of the molecular parameters of the alpha-helix-coil and beta-structure-coil transitions.

Monte-Carlo calculations of geometric and thermodynamic characteristics of the α-helix and the β-structure of polypeptides have been carried out. To describe a hydrogen bond both the Lippincott–Schroeder and Morse potentials were used. The internal rotation angles φ and ψ in the α-helix have been shown to fluctuate in the range of ±7°. The distribution functions on angles φ and ψ and on hydrogen bond lengths and angles in the α-helix have been computed and compared with those in myoglobin and lysozyme. Thermodynamic characteristics of the α-helix calculated in different approximations with the two forms of the hydrogen bond potentials have also been compared. The data obtained are close to the experimental values for polypeptides in neutral solution. Some geometric and thermodynamic characteristics of the regular parallel and antiparallel and irregular antiparallel β-structure have been found. In the β-structure the internal rotation angles vary within the interval ±15–20°. An increase in the cross and longitudinal dimensions of the β-structure only slightly influence both the geometric and thermodynamic characteristics.     

The McClure and Weiss models of Fe–O2 bonding for oxyhemes, and the HbO2 + NO reaction

For the Fe–O₂(S = 0) linkages of oxyhemes, valence bond (VB) structures are re-presented for the McClure [Fe^II(S = 1) + O₂(S = 1)], Pauling–Coryell [Fe^II(S = 0) + O₂*(S = 0)], and Weiss [Fe^III(S = ½) + O₂ ^?(S = ½)] models of bonding. The VB structures for the McClure and Weiss models are of the increased-valence type, with more electrons participating in bonding than occur in their component Lewis structures. The Fe–O bond number and O–O bond order for the McClure structure are correlated with measured Fe–O and O–O bond lengths for oxymyoglobin. Back-bonding from O ₂ ^? to Fe^III of the Weiss structure gives a restricted form of the McClure structure. The McClure and Weiss increased-valence structures are used to provide VB formulations of mechanisms for the oxyhemoglobin + NO reaction. The products of these two formulations are Hb⁺ and NO₃ ^? (where Hb is hemoglobin) and Hb⁺ and OONO^?, respectively. Because Hb⁺ and NO₃ ^? are the observed products, they provide an experimental procedure for distinguishing the McClure and Weiss models. It is also shown that the same type of agreement between McClure-type theory and experiment occurs for oxycoboglobin + NO, cytochrome P450 monooxygenases, and related hydrogen atom transfer reactions. In the appendices, the results of density functional theory and multireference molecular orbital calculations for oxyhemes are related to one formulation of the increased-valence wavefunction for the McClure model, and theory is presented for the calculation of approximate weights for the Lewis structures that are components of the McClure increased-valence structure.