Journal of Theoretical and Computational Chemistry

Spermine synthase (SpmSyn) is an enzyme critical for maintaining the balance of spermine/spermidine in the cell. The amino acid sequence of SpmSyn is highly conserved among the species. Most of the mutations found in the human population are shown to be causing Snyder–Robinson syndrome, a severe mental disorder, while not so many are neutral. This is intriguing since SpmSyn is a relatively large protein and less than 10% of its amino acids are directly involved in the catalysis. Here, we demonstrated that a mutation (G191S) at a site far away from the active pocket affects the active site dynamics and thus the functionality of SpmSyn. This suggests that SpmSyn functionality is regulated by networks of interacting residues and thus expands the functional and structural importance beyond the amino acids directly involved in the catalysis. Comparing the calculated effects of G191S and a nine-residue deletion shown to decrease SpmSyn activity [Wu H, Min J, Zeng H, McCloskey DE, Ikeguchi Y, Loppnau P, Michael AJ, Pegg AE, Plotnikov AN, Crystal structure of human spermine synthase: Implications of substrate binding and catalytic mechanism, J Biol Chem 283:16135–16146, 2008], we predict that G191S mutation also decreases SpmSyn activity and may be causing disease.

This study employed first principles calculations to investigate Fe-doped Bi₄O₅Br₂ as a potential photocatalyst with high efficiency. Based on formation energy calculation, the Fe atoms prefer to replace the Bi atoms with coordination bond of 3, and the optimal concentration for Fe-doping is 6.06wt.%. From surface energy calculations, the $(10\bar{1})$ surface has the lowest surface energy, and therefore the easiest cleavage facet is $\{10\bar{1}\}$. The key factors for the improvement of photocatalytic efficiency after Fe-doped Bi₄O₅Br₂ are estimated as follows. First, the band gap decreases from 2.63eV in pristine case to 2.40eV in 4 Fe-doped Bi₄O₅Br₂ case, resulting in the photon absorption edge shift to lower energy range and the absorption coefficient increase. Secondly, the work functions decrease from 5.66 eV (pristine) to 4.92eV (4 Fe-doped Bi₄O₅Br₂), which facilitate the electrons escaping from the surface. Thirdly, the relative mass ratio of photo-induced electrons and holes increases with Fe concentration. Because the Fe 3$d$ impurity states in the forbidden band gap become wider, the relative ratio increased after Fe-doped Bi₄O₅Br₂. Finally, the Fe doping process introduces more active sites on the surface, which can effectively improve the capacity of target molecules adsorption. Therefore, it is reasonable to believe that Fe-doped Bi₄O₅Br₂ can effectively improve the photocatalytic efficiency because the abovementioned key factors have tremendously improved. Our work provides a reasonable reason for choosing Fe as a dopant, which can help our experimental work and provide explanation for photocatalytic efficiency improvement.

The adsorption interactions between ethylene oxide (EO) molecule and pristine and aluminum-doped coronene (Al-coronene) were studied in the presence and absence of perpendicular external electric fields (EFs) with strengths $1.0\times 10^{-2}$, $2.0\times 10^{-2}$ and $3.0\times 10^{-2}$ a.u. using density functional theory (DFT) calculations. The geometry optimizations and adsorption calculations were carried out by employing 6-31$++$G** basis set. The changes in geometric and electronic structures after the adsorption were investigated to characterize the sensitivity of pristine and Al-coronene toward EO molecules. For all the studied systems, adsorption energies ($E_{\mathrm{\text{ads}}})$, band gap energy ($E_g)$, Mulliken charge transfer, molecular electrostatic potential (MEP) and density of electron state (DOS) were calculated and discussed. According to the obtained results, the high impact of the applied EFs on the adsorption characteristics of EO molecules on the pristine and Al-doped coronenes showed that applying EF is a good strategy for enhancing the EO adsorption capability of the pristine and Al-doped coronenes, improving the potential application of coronene-based sensors for detection of EO in trace amounts.

In this paper, a series of cationic iridium complexes [(2-phenylpyridine)₂(2,2${}^{\prime }$-bipyridine)Ir]${}^{+}$ which substituted phenyl on different ligands position have been systematically investigated by density functional theory (DFT) method. Significantly, the first hyperpolarizability ${\beta }_{\mathrm{\text{tot}}}$ values can be enhanced by introducing phenyl on 2-phenylpyridine ligands R₁ or R₂, whereas substituting phenyl on 2,2${}^{\prime }$-bipyridine ligands R₃ result in a decreasing ${\beta }_{\mathrm{\text{tot}}}$ values. The ${\beta }_{\mathrm{\text{tot}}}$ values exhibit obvious connection with the corresponding HOMO and LUMO energy gap. Furthermore, the time-dependent (TD) DFT calculations suggest that the enhanced ${\beta }_{\mathrm{\text{tot}}}$ values are related to obvious charge transfer from 2-phenylpyridine ligands to 2,2${}^{\prime }$-bipyridine ligands. The investigation of frequency-dependent first hyperpolarizability $\beta$ ($-\omega$; $\omega$, 0) and $\beta$ ($-2\omega$; $\omega$, $\omega$) shown less dispersion effect at the low-frequency region for all of the studied complexes. Overall, tuning phenyl on the different ligands position can be seen as an effective strategy to modulate the second-order nonlinear optical response for these iridium complexes, which is benefit to theoretical and experimental further investigation.

Bisphenol-A (BPA) is considered as one of the most suspicious disruptors. Exposure to BPA may bring about possible human toxicities. BPA is an emerging contaminant widely used in manufacturing of epoxy, unsaturated polyester-styreneand polycarbonate resins. BPA is released into the environment through industrial and municipal wastewater discharges; its degradation products are probably more dangerous than BPA itself. The present study aims at a better insight into its ground state electronic and acid–base properties, and the mechanism of its thermal decomposition. Density functional theory (DFT) is utilized to study the geometry, electronic structure and electrostatic potential (ESP) for BPA. The molecule is noncoplanar with one of the phenolate moieties forced out of the plane by 57${}^{\circ }$. This might very well determine the dissociation reaction pathway and in the meantime facilitates strong conjugation and considerable delocalization along the rest of the molecule. Proton affinities and deprotonation enthalpies are computed and discussed. Bonding characteristics are investigated within the natural bond-orbital (NBO) and quantum theory of atom in molecule (QTAIM) frameworks.

In this paper, the experimental and theoretical vibrational frequencies of a potential bioactive pyrimidine derivative molecule named 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile has been investigated. The experimental FT-IR and Laser-Raman spectra of the studied molecule are in the region (4000–400cm${}^{-1})$ and (4000–100cm${}^{-1})$, respectively, in gas phase. The vibrational modes and optimized ideal structure parameters(bond lengths, bond angles and selected dihedral angles) were calculated by using DFT/B3LYP, DFT/BHandHLYP and DFT/PBE1PBE methods with 6-311$++$G(d,p) basis set. The theoretical mode assignments have been obtained by using potential energy distribution (PED) with the VEDA4 software program. Additionally, infrared and Raman intensities, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies and their clouds, and other related molecular properties were calculated and evaluated. The proton (¹H) and carbon-13 (${}^{13}$C) nuclear magnetic resonance (NMR) chemical shifts have been investigated for the title molecule, both experimentally (in DMSO-d${}_6)$ and theoretically (in vacuum and DMSO). The thermodynamic properties of the tile compound have been investigated using the mentioned theoretical computational methods. The results revealed that there isgood agreement between experimental and theoretical results and these results have supported the related literature.

Structure and energies of capsaicin and its probable transients formed in oxidation processes (single electron transfer and hydrogen atom transfer) have been investigated using theoretical calculations. Molecular geometries and energies of truncated and complete capsaicin structures have been optimized using density functional theory (DFT) with Becke three-parameter Lee-Yang-Parr (B3LYP) functional and 6–31$++$G(d) basis set. The stable geometries have been confirmed by vibrational analysis. The calculations suggest that single-electron transfer takes place at phenolic O-atom in the first step followed by delocalization of positive charge over the whole molecule. Further, the first step of hydrogen atom abstraction should take place at phenolic group due to lowest dissociation energy but post-optimization bond dissociation energy is least for benzylic group in the side chain as compared to other transients. Effect of water as a solvent on the energies has also been studied using self-consistent reaction field calculation. Similar results are obtained for truncated and complete capsaicin structures. The present study also includes Mulliken spin, charge, vibrational frequencies and assignments of frequencies of the transients. The present study provides explanation for the observation of phenoxyl radical in fast kinetic studies using pulse radiolysis study and, formation of breakdown and dimeric products in other studies.

Nuclear energy gradients for the incremental molecular fragmentation (IMF) method presented in our previous work [Meitei OR, Heßelmann A, Molecular energies from an incremental fragmentation method, J Chem Phys 144(8):084109, 2016] have been derived. Using the second-order Møller–Plesset perturbation theory method to describe the bonded and nonbonded energy and gradient contributions and the uncorrelated Hartree–Fock method to describe the correction increment, it is shown that the IMF gradient can be easily computed by a sum of the underlying individual derivatives of the energy contributions. The performance of the method has been compared against the supermolecular method by optimizing the structures of a range of polyglycine molecules with up to 36 glycine residues in the chain. It is shown that with a sensible set of parameters used in the fragmentation the supermolecular structures can be fairly well reproduced. In a few cases the optimization with the IMF method leads to structures that differ from the supermolecular ones. It was found, however, that these are more stable geometries also on the supermolecular potential energy surface.