Vibrational spectra of an RDX film over an aluminum substrate from molecular dynamics simulations and density functional theory

We report calculated vibrational spectra in the range of 0–3,500 cm^?1 of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) molecules adsorbed on a model aluminum surface. A molecular film was modeled using two approaches: (1) density functional theory (DFT) was used to optimize a single RDX molecule interacting with its periodic images, and (2) a group of nine molecules extracted from the crystal structure was deposited on the surface and interacted with its periodic images via molecular dynamics (MD) simulations. In both cases, the molecule was initialized in the AAA conformer geometry having the three nitro groups in axial positions, and kept that conformation in the DFT examination, but some molecules were found to change to the AAE conformer (two nitro groups in axial and one in equatorial position) in the MD analysis. The vibrational spectra obtained from both methods are similar to each other, except in the regions where collective RDX intermolecular interactions (captured by MD simulations) are important, and compare fairly well with experimental findings.

Spectroscopic Studies on the Binding of Cobalt(II) 1,10-Phenanthroline Complex to Bovine Serum Albumin

The binding interaction of the cobalt(II) 1,10-phenanthroline complex (Co(phen) ₃ ²⁺ , phen = 1,10-phenanthroline) with bovine serum albumin (BSA) was investigated by fluorescence spectroscopy combined with UV–Vis absorption and circular dichroism measurements under simulative physiological conditions. The experiment results showed that the fluorescence intensity of BSA was dramatically decreased owing to the formation of Co(phen) ₃ ²⁺ –BSA complex. The corresponding association constants (K _a) between Co(phen) ₃ ²⁺ and BSA at four different temperatures were calculated according to the modified Stern–Volmer equation. The enthalpy change (ΔH°) and entropy change (ΔS°) were calculated to be ?2.73 kJ mol^?1 and 82.27 J mol^?1?K^?1, respectively, which suggested that electrostatic interaction and hydrophobic force played major roles in stabilizing the Co(phen) ₃ ²⁺ –BSA complex. Site marker competitive experiments indicated that the binding of Co(phen) ₃ ²⁺ to BSA primarily took place in site I of BSA. A value of 4.11 nm for the average distance r between Co(phen) ₃ ²⁺ (acceptor) and tryptophan residues of BSA (donor) was derived from Förster’s energy transfer theory. The conformational investigation showed that the presence of Co(phen) ₃ ²⁺ resulted in the change of BSA secondary structure and induced the slight unfolding of the polypeptides of protein, which confirmed the microenvironment and conformational changes of BSA molecules.     

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.

Excited-state relaxation paths of oxo/hydroxy and N9H/N7H tautomers of guanine: a CC2 theoretical study

We performed a theoretical investigation, at the CC2/aug-cc-pVDZ level, of the ring-deformation mechanisms of four guanine tautomers (oxo, hydroxy, N9H, and N7H). The study showed that the optimized conical intersections S₀/S₁ are accessible through the ¹ππ* excited states of tautomers. The optimized conical intersections S₀/S₁, which show deformation at the pyrimidine ring, have high energies. This means that the relaxations of the ¹ππ* excited states via internal conversion are disfavored. For two tautomers we found crossing points ¹ππ*/¹πσ* of the excited-state reaction paths, revealing the possibility of a population of the ¹πσ* excited state by the ¹ππ* excited state.

Calixarene building block bis(2-hydroxyphenyl)methane (2HDPM) and hydrogen-bonded 2HDPM-H2O complex in electronic excited state

Intramolecular and intermolecular hydrogen bonding in electronic excited states of calixarene building blocks bis(2-hydroxyphenyl)methane (2HDPM) monomer and hydrogen-bonded 2HDPM-H₂O complex were studied theoretically using the time-dependent density functional theory (TDDFT). Twenty-four stable conformations (12 pairs of enantiomers) of 2HDPM monomer have been found in the ground state. From the calculation results, the conformations 1a and 1b which both have an intramolecular hydrogen bond are the most stable ones. The infrared spectra of 2HDPM monomer and 2HDPM-H₂O complex in ground state and S₁ state were calculated. The stretching vibrational absorption band of O₂???H₃ group in the monomer and complex disappeared in the S₁ state. At the same time, a new strong absorption band appeared at the C=O stretching region. From the calculation of bond lengths, it indicates that the O₂???H₃ bond is significantly lengthened in the S₁ state. However, the C₁???O₂ bond is drastically shortened upon electronic excitation to the S₁ state and has the characteristics of C=O band. Furthermore, the intramolecular hydrogen bond O₂???H₃?·?·?·?O₄ of the 2HDPM monomer and the intermolecular hydrogen bonds O₂???H₃?·?·?·?O₇ and O₇???H₉?·?·?·?O₄ of 2HDPM-H₂O complex are all shortened and strengthened in the S₁ state.

DFT study on the reactions of ClO–/BrO– with RCl (R = CH3, C2H5, and C3H7) in gas phase

Gas-phase reactions of ClO^–/BrO^– with RCl (R = CH₃, C₂H₅, and C₃H₇) have been investigated in detail using the popular DFT functional BHandHLYP/aug-cc-pVDZ level of theory. As a result, our findings strongly suggest that the type of reaction is firstly initiated by a typical S_N2 fashion. Subsequently, two competitive substitution steps, named as S_N2-induced substitution and S_N2-induced elimination, respectively, would proceed before the initial S_N2 product ion-dipole complex separates, in which the former exhibits less reactivity than the latter. Those are consistent with relevant experimental results. Moreover, we have also explored reactivity difference for the title reactions in term of some factors derived from methyl group, p-π electronic conjugation, ionization energy (IE), as well as molecular orbital (MO) analysis.

Relating normal vibrational modes to local vibrational modes: benzene and naphthalene

Local vibrational modes can be directly derived from normal vibrational modes using the method of Konkoli and Cremer (Int J Quant Chem 67:29, 1998). This implies the calculation of the harmonic force constant matrix F ^q (expressed in internal coordinates q) from the corresponding Cartesian force constant matrix f ^x with the help of the transformation matrix U?=?WB ^?(BWB ^?)^?1 (B: Wilson’s B-matrix). It is proven that the local vibrational modes are independent of the choice of the matrix W. However, the choice W?=?M ^?1 (M: mass matrix) has numerical advantages with regard to the choice W?=?I (I: identity matrix), where the latter is frequently used in spectroscopy. The local vibrational modes can be related to the normal vibrational modes in the form of an adiabatic connection scheme (ACS) after rewriting the Wilson equation with the help of the compliance matrix. The ACSs of benzene and naphthalene based on experimental vibrational frequencies are discussed as nontrivial examples. It is demonstrated that the local-mode stretching force constants provide a quantitative measure for the C–H and C–C bond strength.     

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ 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 molecule-cation interaction between Na⁺ 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 in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis 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.

Theoretical study about the 5-azido-1H-tetrazole and its ion salts

Periodic DFT method has been firstly used to calculate the bulk structure, electronic structure, electrical transferring and thermodynamic properties of crystalline 5-azido-1H-tetrazole (HCN₇) and its four different salts. The anion CN₇ ^? was included in all of the salts such as ammonium 5-azidotetrazolate ([NH₄]⁺[CN₇]^?), hydrazinium 5-azidotetrazolate ([N₂H₅]⁺[CN₇]^?), guanidinium 5-azidotetrazolate ([CH₆N₃]⁺[CN₇]^??·?H₂O) and 1-aminoguanidinium 5- azidotetrazolate ([CH₇N₄]⁺[CN₇]^?). The simulation is in reasonable agreement with the experimental results. It is found the salts of HCN₇ are more stable than itself because the band gap of the salts is larger. The density of state shows the p states of them (including HCN₇ and its four salts) have played a very significant role in the reaction.

Theoretical studies of the interaction between enflurane and water

Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6–311++G(d,p) level. In these complexes the CH…O_w hydrogen bonds are formed, with the H…O_w distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the H_w…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between ?5.89 and ?4.66 kcal?mol^?1, while the enthalpies of formation are between ?4.35 and ?3.22 kcal?mol^?1. The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about ?2 kcal?mol^?1.

Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach

Density functional theory (DFT) calculations at B3LYP/6-31 G (d,p) and B3LYP/6-311?+?G(d,p) levels for the substituted pyridine-catalyzed isomerization of monomethyl maleate revealed that isomerization proceeds via four steps, with the rate-limiting step being proton transfer from the substituted pyridinium ion to the C=C double bond in INT1. In addition, it was found that the isomerization rate (maleate to fumarate) is solvent dependent. Polar solvents, such as water, tend to accelerate the isomerization rate, whereas apolar solvents, such as chloroform, act to slow down the reaction. A linear correlation was obtained between the isomerization activation energy and the dielectric constant of the solvent. Furthermore, linearity was achieved when the activation energy was plotted against the pK _a value of the catalyst. Substituted-pyridine derivatives with high pK _a values were able to catalyze isomerization more efficiently than those with low pK _a values. The calculated relative rates for prodrugs 1–6 were: 1 (406.7), 2 (7.6?×?10⁶), 3 (1.0), 4 (20.7), 5 (13.5) and 6 (2.2?×?10³). This result indicates that isomerizations of prodrugs 1 and 3–5 are expected to be slow and that of prodrugs 2 and 6 are expected to be relatively fast. Hence, prodrugs 2 and 3–5 have the potential to be utilized as prodrugs for the slow release of monomethylfumarate in the treatment of psoriasis and multiple sclerosis.

A comparative study on carbon, boron-nitride, boron-phosphide and silicon-carbide nanotubes based on surface electrostatic potentials and average local ionization energies

A density functional theory study was carried out to predict the electrostatic potentials as well as average local ionization energies on both the outer and the inner surfaces of carbon, boron-nitride (BN), boron-phosphide (BP) and silicon-carbide (SiC) single-walled nanotubes. For each nanotube, the effect of tube radius on the surface potentials and calculated average local ionization energies was investigated. It is found that SiC and BN nanotubes have much stronger and more variable surface potentials than do carbon and BP nanotubes. For the SiC, BN and BP nanotubes, there are characteristic patterns of positive and negative sites on the outer lateral surfaces. On the other hand, a general feature of all of the systems studied is that stronger potentials are associated with regions of higher curvature. According to the evaluated surface electrostatic potentials, it is concluded that, for the narrowest tubes, the water solubility of BN tubes is slightly greater than that of SiC followed by carbon and BP nanotubes.

Structure and spectral characteristics of diquat-cucurbituril complexes from density functional theory

Electronic structure, ¹H NMR and infrared spectra of diquat (6,7-dihydrodipyrido[1,2-b:1′,2′-e] pyrazine-5,8-diium or DQ²⁺) encapsulated by cucurbit[n]uril (n?=?7,8) hosts are obtained using the density functional theory. Theoretical calculations have shown that both CB[7] or CB[8] host possesses strong affinity toward DQ²⁺ compared to its reduced cation or neutral species. Calculated ¹H NMR spectra reveal that H_α protons on bi-pyridinium rings of DQ²⁺@CB[8] complex are de-shielded owing to C=O?H interactions. On the other hand aromatic (H_β and H_δ) of DQ²⁺ within the CB[8] cavity exhibit significant shielding. The complexation of CB[8] with DQ²⁺ splits the carbonyl stretching vibration (1788 cm^?1) into two distinct vibrations which correspond to 1765 cm^?1 arising from hydrogen bonded carbonyls and the 1792 cm^?1 band from non-interacting ones. Further, the CN stretching vibration in DQ²⁺ exhibits a frequency blue-shift of 6 cm^?1 on its encapsulation within the CB[8] cavity. The direction of frequency shift has been explained on the basis of natural bond orbital analyses.

Dynamic motion of La atom inside the C74 (D 3h) cage: a relativistic DFT study

The interaction between lanthanum atom (La) and C₇₄ (D _3h) was investigated by all-electron relativistic density function theory (DFT). With the aid of the representative patch of C₇₄ (D _3h), we studied the interaction between C₇₄ (D _3h) and La and obtained the interaction potential. Optimized structures show that there are three equivalent stable isomers, with La located about 1.7 Å off center. There is one transition state between every two stable isomers. According to the minimum energy pathway, the possible movement trajectory of La atoms in the C₇₄ (D _3h) cage was explored. The calculated energy barrier for La atoms moving from the stable isomer to the transition state is 18.4 kcal mol^?1. In addition, the dynamic NMR spectra of La@C₇₄ according to the trajectory was calculated.

Dissociation quenching using exceptional points

We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na₂ molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. The resonances are due to the field-induced coupling with the continuum of a repulsive potential. We also draw attention to a new kind of exceptional point involving a resonance originating from a vibrational state coalescing with a shape-type resonance of the repulsive potential. A laser control scenario, aiming at the adiabatic transport from this field-free decaying state to a stable field-free vibrational state, is discussed in terms of field-induced dissociation quenching.

DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg2+ and Ca2+ ions

The interactions of L-aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg²⁺, Ca²⁺, and H⁺) were studied by a quantum mechanical method that utilized DFT with B3LYP/6-311G**. Docking studies were also carried out in order to explore the surface recognition properties of L-aminoglucoside with respect to Mg²⁺ and Ca²⁺ ions under solvated and nonsolvated conditions. Although both of the stereoisomers possess similar physicochemical/antibiotic properties against Helicobacter pylori, the thermochemical values for these complexes showed that its high affinity for Mg²⁺ cations caused the hydration of Rho B. According to the results of the calculations, for Rho A–Ca²⁺(H₂O)₆, ΔH = ?72.21 kcal?mol^?1; for Rho B–Ca²⁺(H₂O)₆, ΔH = ?72.53 kcal?mol^?1; for Rho A–Mg²⁺(H₂O)₆, ΔH = ?72.99  kcal?mol^?1 and for Rho B–Mg²⁺(H₂O)₆, ΔH = ?95.00  kcal?mol^?1, confirming that Rho B binds most strongly with hydrated Mg²⁺, considering the energy associated with this binding process. This result suggests that Rho B forms a more stable complex than its isomer does with magnesium ion. Docking results show that both of these rhodostreptomycin molecules bind to solvated Ca²⁺ or Mg²⁺ through hydrogen bonding. Finally, Rho B is more stable than Rho A when protonation occurs.

Effects of NO 3 − -N on the growth and salinity tolerance of Tamarix laxa Willd

The influence of NO ₃ ^? -N on growth and osmotic adjustment was studied in Tamarix laxa Willd., a halophyte with salt glands on its twigs. Seedlings of T. laxa Willd. were exposed to 1 mM (control) or 300 mM NaCl, with 0.05, 1 or 10 mM NO ₃ ^? -N for 24 days. The relative growth rate of seedlings at 300 mM NaCl was lower than that of control plants at all NO ₃ ^? -N levels, but the concentrations of organic N and total N in the twigs did not differ between the two NaCl treatments. Increasing NO ₃ ^? supply under 300 mM NaCl improved the growth of T. laxa, indicating that NO ₃ ^? played positive roles in improving salt resistance of the plant. The twigs of T. laxa Willd. accumulated mainly inorganic ions, especially Na⁺ and Cl^?, to lower osmotic potential (Ψs): the contributions of Na⁺ and Cl^? to Ψs were estimated at 31% and 27% respectively, at the highest levels of supply of both NaCl and NO ₃ ^? -N. The estimated contribution of NO ₃ ^? -N to Ψs was as high as 20% in the twigs in these conditions, indicating that NO ₃ ^? was also involved in osmotic adjustment in the twigs. Furthermore, increases in tissue NO ₃ ^? were accompanied by decreases in tissue Cl^? and proline under 300 mM NaCl. The estimated contribution of proline to Ψs declined as with NO ₃ ^? -N supply increased from 1 to 10 mM, while the contributions of nitrate to Ψs were enhanced under 300 mM NaCl. This suggested that higher accumulation of nitrate in the vacuole alleviated the effects of salinity stress on the plant by balancing the osmotic potential. In conclusion, NO ₃ ^? -N played both nutritional and osmotic roles in T. laxa Willd. in saline conditions.     

A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline

In this work, computations of density functional theory (DFT) were carried out to investigate the nature of interactions in solid 2,6-dibromo-4-nitroaniline (DBNA). This system was selected to mimic the hydrogen/halogen bonding found within crystal structures as well as within biological molecules. DFT (M06-2X/6-311++G**) calculations indicated that the binding energies for different of interactions lie in the range between ?1.66 and ?9.77 kcal mol^?1. The quantum theory of atoms in molecules (QTAIM) was applied to provide more insight into the nature of these interactions. Symmetry-adapted perturbation theory (SAPT) analysis indicated that stability of the Br···Br halogen bonds is predicted to be attributable mainly to dispersion, while electrostatic forces, which have been widely believed to be responsible for these types of interactions, play a smaller role. Our results indicate that, for those nuclei participating in hydrogen/halogen bonding interactions, nuclear quadrupole resonance parameters exhibit considerable changes on going from the isolated molecule model to crystalline DBNA.