Modeling the spontaneous initiation of the polymerization of methyl methacrylate

The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically. The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional and 6-31G* basis set. The Diels-Alder initiation mechanism (path (I) and path (II)) with remarkably high energy barriers is not applicable to MMA. Four favorable paths were found (path (III), path (IV), path (V) and path (VI)), which are supporting the Flory mechanism. Path (V) has the lowest active energy. Therefore this path is considered as the main path for the spontaneous polymerization of MMA. Figure The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically. The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional and 6-31G* basis set.     

Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking,molecular dynamics,and charge density analysis

Acetylcholinesterase (AChE) is an important enzyme responsible for Alzheimer’s disease, as per report, keto-enol form of curcumin inhibits this enzyme. The present study aims to understand the binding mechanism of keto-enol curcumin with the recombinant human Acetylcholinesterase (rhAChE) from its conformational flexibility, intermolecular interactions, charge density distribution, and the electrostatic properties at the active site of rhAChE. To accomplish this, a molecular docking analysis of curcumin with the rhAChE was performed, which gives the structure and conformation of curcumin in the active site of rhAChE. Further, the charge density distribution and the electrostatic properties of curcumin molecule (lifted from the active site of rhAChE) were determined from the high level density functional theory (DFT) calculations coupled with the charge density analysis. On the other hand, the curcumin molecule was optimized (gas phase) using DFT method and further, the structure and charge density analysis were also carried out. On comparing the conformation, charge density distribution and the electrostatic potential of the active site form of curcumin with the corresponding gas phase form reveals that the above said properties are significantly altered when curcumin is present in the active site of rhAChE. The conformational stability and the interaction of curcumin in the active site are also studied using molecular dynamics simulation, which shows a large variation in the conformational geometry of curcumin as well as the intermolecular interactions.     

Photophysics, photochemistry, and reactivity: molecular aspects of perylenequinone reactions.

Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to elucidate the photochemistry and photophysics of eight different perylenequinones (PQ). The objective of this work has been to quantitatively investigate the photodynamic therapeutic potential of this family of compounds and give an overview of their photoreactivity. The effects of solvation were evaluated through single-point calculations using the integral equation formalism of the polarised continuum model. It is concluded that the eight studied perylenequinones can generate singlet oxygen (in aqueous solution) and superoxide radical anions, and that the autoionisation of two nearby PQ molecules is possible.     

Computational study of conformational and chiroptical properties of (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol

Conformational analysis of (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol, a flavonoid compound displaying both antioxidant and pro-oxidant properties, is performed by molecular mechanics and density functional theory calculations both in the gas phase and in methanol solution by using the Polarizable Continuum Model. Nine different conformations are identified. Absorption (UV) and circular dichroism (CD) spectra and optical rotations are calculated by means of time dependent density functional theory (TDDFT) and compared with experiments. The effects of a complex environment formed by water and proline-rich peptide molecules on the conformational characteristics of (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol and therefore on its UV and CD spectra are investigated by atomistic molecular dynamics simulations.     

Synthesis and density functional theoretical study of steroidal spiro-triazolidinone

The reaction of 3beta-chloro-5alpha-cholestan-6-one semicarbazone 1 with hydrogen peroxide at 0 degrees C gives 3beta-chloro-5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2 as a product. The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral data. The ab initio calculations were performed by using density functional theory (DFT) at B3LYP/6-31G* basis set in order to describe a free radical reaction mechanism. The reaction proceeds through two radical intermediates formation. The mechanism of the reaction was explained by using frontier molecular orbital (FMO), spin electronic density map, encoded electrostatic potential map and atomic charges. It was found that the localization of frontier orbitals and the flow of atomic charges of all the calculated structures support the present reaction mechanism. The molecular properties like total energy, dipole moment and hardness of each optimized structure, were also explained. Stability of all the optimized structures in this study was supported by their respective fundamental frequencies and energy minima.     

First-principles study of electric field effects on the structure,decomposition mechanism,and stability of crystalline lead styphnate

The electric field effects on the structure, decomposition mechanism, and stability of crystalline lead styphnate have been studied using density functional theory. The results indicate that the influence of external electric field on the crystal structure is anisotropic. The electric field effects on the distance of the Pb–O ionic interactions are stronger than those on the covalent interactions. However, the changes of most structural parameters are not monotonically dependent on the increased electric field. This reveals that lead styphnate can undergo a phase transition upon the external electric field. When the applied field is increased to 0.003 a.u., the effective band gap and total density of states vary evidently. And the Franz-Keldysh effect yields larger influence on the band gap than the structural change induced by external electric field. Furthermore, lead styphnate has different initial decomposition reactions in the presence and absence of the electric field. Finally, we find that its sensitivity becomes more and more sensitive with the increasing electric field.     

Spectroscopic investigations and hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine: a theoretical study

The structure, spectral properties and the hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine have been studied by using quantum chemical methods. The time-dependent density functional theory (TD-DFT) and the singly excited configuration interaction (CIS) methods are employed to optimize the excited state geometries of isolated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine in both the gas and solvent phases. The solvent phase calculations are performed using the polarizable continuum model (PCM). The absorption and emission spectra are calculated using the time-dependent density functional theory (TD-DFT) method. The results from the TD-DFT calculations reveal that the excitation spectra are red shifted relative to absorption in aqueous medium. These changes in the transition energies are qualitatively comparable to the experimental data. The examination of molecular orbital reveals that the molecules with a small H→L energy gap possess maximum absorption and emission wavelength. The relative stability and hydrogen bonded interactions of mono and heptahydrated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine have been studied using the density functional theory (DFT) and Møller Plesset perturbation theory (MP2) implementing the 6-311++G(d,p) basis set. The formation of strong N-H…O bond has resulted in the highest interaction energy among the monohydrates. Hydration does not show any significant impact on the stability of heptahydrated complexes. The atoms in molecule (AIM) and natural bonding orbital (NBO) analyses have been performed to elucidate the nature of the hydrogen bond interactions in these complexes.

First-principles study of the structural,elastic and electronic properties of SbXI (X=S,Se, Te) crystals

The structural, elastic, elastic anisotropy and electronic properties of ferroelectric SbSI and paraelectric SbSI, SbSeI and SbTeI crystals were computed using the local density approximation with first-principle calculations, based on density functional theory. The independent elastic constants of SbXI compounds were computed and the results reveal that they are mechanically stable. Some polycrystalline quantities such as bulk modulus, shear modulus, acoustic velocities, Young’s modulus, Poisson’s ratio, elastic anisotropy and elastic Debye temperatures of these compounds were derived from computed elastic constants. Energy band structures show that these compounds have an indirect band gap. The electronic charge distribution and partial density of states of SbXI compounds indicate that the Sb-X bond is typically covalent with a strong hybridization as well as Sb-I compounds that have strong ionic character. The results obtained were compared with experimentally measured values and other theoretical data.     

Triethanolammonium acetate as a multifunctional ionic liquid in the palladium-catalyzed green Heck reaction

An efficient green Heck reaction protocol was performed using a triethanolammonium acetate ionic liquid–palladium(II) catalytic system. The ionic liquid used acts as a reaction medium, base, precatalyst-precursor, and mobile support for the active Pd species. Our experimental investigation indicates that performing the Heck reaction in ionic liquid is superior to the same procedure carried out in triethanolamine. The mechanism of the reaction of triethanolammonium acetate with PdCl₂ was examined using density functional theory (M06 method). It was found that two Pd(II) complexes are formed, one of which acts further as a precatalyst yielding catalytically active Pd(0) complex. The calculated activation energies are in agreement with our experimental findings.     

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.     

Revealing the Intercalation Mechanisms of Lithium,Sodium, and Potassium in Hard Carbon

Hard carbon is the most promising anode material for sodium‐ion batteries and potassium‐ion batteries owing to its high stability, widespread availability, low‐cost, and excellent performance. Understanding the carrier‐ion storage mechanism is a prerequisite for developing high‐performance electrode materials; however, the underlying ion storage mechanism in hard carbon has been a topic of debate because of its complex structure. Herein, it is demonstrated that the Li⁺‐, Na⁺‐, and K⁺‐ion storage mechanisms in hard carbon are based on the adsorption of ions on the surface of active sites (e.g., defects, edges, and residual heteroatoms) in the sloping voltage region, followed by intercalation into the graphitic layers in the low‐voltage plateau region. At a low current density of 3 mA g^–1, the graphitic layers of hard carbon are unlocked to permit Li⁺‐ion intercalation, resulting in a plateau region in the lithium‐ion batteries. To gain insights into the ion storage mechanism, experimental observations including various ex situ techniques, a constant‐current constant‐voltage method, and diffusivity measurements are correlated with the theoretical estimation of changes in carbon structures and insertion voltages during ion insertion obtained using the density functional theory.     

Interaction Between Equally Charged Membrane Surfaces Mediated by Positively and Negatively Charged Macro-Ions

In biological systems, charged membrane surfaces are surrounded by charged molecules such as electrolyte ions and proteins. Our recent experiments in the systems of giant phospholipid vesicles indicated that some of the blood plasma proteins (macro-ions) may promote adhesion between equally charged membrane surfaces. In this work, theory was put forward to describe an IgG antibody-mediated attractive interaction between negatively charged membrane surfaces which was observed in experiments on giant phospholipid vesicles with cardiolipin-containing membranes. The attractive interactions between negatively charged membrane surfaces in the presence of negatively and positively charged spherical macro-ions are explained using functional density theory and Monte Carlo simulations. Both, the rigorous solution of the variational problem within the functional density theory and the Monte Carlo simulations show that spatial and orientational ordering of macro-ions may give rise to an attractive interaction between negatively charged membrane surfaces. It is also shown that the distinctive spatial distribution of the charge within the macro-ions (proteins) is essential in this process.     

Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12

The mechanism of C-H bond activation of ethane was catalyzed by palladium halide cations (PdX+ (X = F, Cl, Br, H, and CH3)), which was investigated using density functional theory (DFT) at B3LYP level. The reaction mechanism was taken into account in triplet and singlet spin state potential energy surfaces. For PdF+, PdCl+, and PdBr+, the high spin states were the ground states, whereas the ground states were the low spin states in PdH+ and PdCH3+. The reaction of PdF+, PdCl+, and PdBr+ with ethane occurred via a typical “two-state reactivity” mechanism. In contrast, for PdH+ and PdCH3+, the overall reaction performed on the ground state PESs in a spin-conserving manner. The crossing points between two potential energy surfaces were observed and effectively decreased the activation barrier in PdX+/C2H6 (X = F, Cl, and Br). The minimum energy crossing points (MECP) were obtained used the algorithm in Harvey method. The natural valence electron configuration calculations were analyzed by natural bond orbital. The distribution and contribution of the front molecular orbital of the initial complexes could be further understand by the density of states. The feature of the bonding evolution in the main pathways was studied using topological analysis including localized orbital locator and atoms in molecules.     

DFT study of linear and nonlinear optical properties of donor-acceptor substituted stilbenes, azobenzenes and benzilideneanilines

A theoretical analysis of the linear and nonlinear optical properties of six push–pull π-conjugated molecules with stilbene, azobenzene and benzilideneaniline as a backbone is presented. The photophysical properties of the investigated systems were determined by using response functions combined with density functional theory (DFT). Several different exchange-correlation potentials were applied in order to determine parameters describing the one- and two-photon spectra of the studied molecules. In particular, the recently proposed Coulomb-attenuated model (CAM-B3LYP) was used to describe charge-transfer (CT) excited states. In order to compare theoretical predictions with available experimental data, calculations with inclusion of solvent effects were performed. The BLYP and the CAM-B3LYP functionals were found to yield values of two-photon absorption (TPA) probabilities closer to experimental values than the B3LYP functional or the HF wavefunction. Moreover, molecular static hyperpolarisabilities were determined using both DFT and second-order Møller-Plesset perturbation (MP2) theory. Likewise, the CAM-B3LYP functional was found to outperform other applied exchange-correlation potentials in determining first hyperpolarisability (β). Moreover, it was confirmed on a purely theoretical basis that the presence of a –C=C– bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a –N=N– bridge.     

Spectroscopic investigation and hydrogen-bonding analysis of triazinones

NIR FT-Raman, FTIR and UV-vis spectra of the herbicide metamitron were recorded and analyzed. The aromaticities, equilibrium geometries, bonding features, electrostatic potentials, and harmonic vibrational wavenumbers of the monomers and dimers of triazinone derivatives were also investigated with the aid of BLYP/6-311 G(df, p) density functional theory. Features in the vibrational spectra were assigned with the aid of the VEDA.4 program. The calculated results were a good match to the experimental data obtained from FTIR, Raman, and electronic absorption spectra. Mulliken population analysis was performed on the atomic charges and the HOMO-LUMO energies were also calculated. NBO analysis highlighted the intra- and intermolecular N-H…O and C-H…O hydrogen bonds in the crystal structures of the triazinones. The solvent effect was calculated using time-dependent density functional theory in combination with the polarizable continuum model.     

NO inhibitory constituents as potential anti-neuroinflammatory agents for AD from Blumea balsamifera

Our continuous search for new nitric oxide (NO) inhibitory substances as anti-neuroinflammatory agents for AD resulted in the isolation of one new labdane diterpenoid and three new guaiane sesquiterpenoids, as well as ten known compounds from Blumea balsamifera. Their structures were elucidated by NMR spectroscopic data analysis and the time-dependent density functional theory (TDDFT) electronic circular dichroism (ECD) calculations. The anti-neuroinflammatory effects were examined by inhibiting NO release in LPS-induced murine microglial BV-2 cells. The possible mechanism of NO inhibition of some bioactive compounds was also investigated using molecular docking, which revealed the interactions of bioactive compounds with the iNOS protein.     

QSAR,DFT and quantum chemical studies on the inhibition potentials of some carbozones for the corrosion of mild steel in HCl

Experimental aspects of the inhibition of the corrosion of mild steel in HCl solutions by some carbozones were studied using gravimetric, thermometric and gasometric methods, while a theoretical study was carried out using density functional theory, a quantitative structure–activity relation, and quantum chemical principles. The results obtained indicated that the studied carbozones are good adsorption inhibitors for the corrosion of mild steel in HCl. The inhibition efficiencies of the studied carbozones were found to increase with increasing concentration of the respective inhibitor. A strong correlation was found between the average inhibition efficiency and some quantum chemical parameters, and also between the experimental and theoretical inhibition efficiencies (obtained from the quantitative structure–activity relation).     

On the Mechanism of HOONO to HONO2Conversion

We have conducted an examination (using density functional theory) of possible transition states that could lead to HNO₃from peroxynitrous acid (HOONO) and one or two water molecules. We find no transition states with free energies in the range of 20 kcal/mol, i.e., near the experimental value in solution. The implications for the mechanism of conversion of HOONO to nitrate are discussed.     

Crystal structure, detonation performance, and thermal stability of a new polynitro cage compound: 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptacyclo [5.5.1.13, 11. 15, 9] pentadecane

A new polynitro cage compound 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptcyclo [5.5.1.1(3,11).1(5,9)] pentadecane (NNNAHP) was designed in the present work. Its molecular structure was optimized at the B3LYP/6-31 G(d,p) level of density functional theory (DFT) and crystal structure was predicted using the Compass and Dreiding force fields and refined by DFT GGA-RPBE method. The obtained crystal structure of NNNAHP belongs to the P-1 space group and the lattice parameters are a = 9.99 ?, b = 10.78 ?, c = 9.99 ?, α = 90.01°, β = 120.01°, γ = 90.00°, and Z = 2, respectively. Based on the optimized crystal structure, the band gap, density of state, thermodynamic properties, infrared spectrum, strain energy, detonation characteristics, and thermal stability were predicted. Calculation results show that NNNAHP has detonation properties close to those of CL-20 and is a high energy density compound with moderate stability.