Reaction of CO₂ with Atomic Transition Metal M^+/0/– Ions: A Theoretical Study

The activation of carbon dioxide mediated by the first row 3d transition metal (TM) M^+/0/– atomic ions was studied theoretically. Theoretical calculations show left-hand transition-metal ions Sc⁺, Sc, Ti⁺, Ti, and V can mediate oxygen atom transfer (OAT) from carbon dioxide. In the anionic system, for early transition metal ions (Sc to Cr), [OM–CO]⁻ are more stable than [M–OCO]⁻, while the others favor binding formation, [M–OCO]⁻. TSR was observed in O atom transfer. The OAT reaction is exothermic only for the first three transition metal cations and atoms (Sc^+/0, Ti^+/0, and V^+/0), Fe⁰ and all the anions except Cu^– and Zn^–. Furthermore, in most case, reaction enthalpy, and energy barrier of OAT for the cationic system is the highest, and the anionic system is the lowest. We discuss the performances of 18 methods on the energies and structures

Comparative Insight into Electronic Properties and Reactivities toward C–H Bond Activation by Iron(IV)–Nitrido, Iron(IV)–Oxo, and Iron(IV)–Sulfido Complexes: A Theoretical Investigation

A range of novel octahedral iron­(IV)–nitrido complexes with the TMC ligand (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) in the equatorial plane and one axial ligand trans to the nitrido have been designed theoretically, and a systematic comparative study of their geometries, electronic properties, and reactivities in hydrogen atom abstraction reactions regarding the iron­(IV)–oxo and −sulfido counterparts has been performed using density-functional theory methods. Further, the relative importance of the axial ligands on the reactivity of the iron­(IV)–nitrido systems is probed by sampling the reactions of CH₄ with [Fe^IVN­(TMC)­(L_ax)]^<i>n</i>+, (L_ax = none, CH₃CN, CF₃CO₂^–, N₃^–, Cl^–, NC^–, and SR^–). As we find, one hydrogen atom is abstracted from the methane by the iron­(IV)–nitrido species, leading to an Fe^III(N)–H moiety together with a carbon radical, similar to the cases by the iron­(IV)–oxo and −sulfido compounds. DFT calculations show that, unlike the well-known iron­(IV)–oxo species with the <i>S</i> = 1 ground state where two-state reactivity (TSR) was postulated to involve, the iron­(IV)–nitrido and −sulfido complexes stabilize in a high-spin (<i>S</i> = 2) quintet ground state, and they appear to proceed on the single-state reactivity <i>via</i> a dominantly and energetically favorable low-lying quintet spin surface in the H-abstraction reaction that enjoys the exchange-enhanced reactivity. It is further demonstrated that the iron­(IV)–nitrido complexes are capable of hydroxylating C–H bond of methane, and potential reactivities as good as the iron­(IV)–oxo and −sulfido species have been observed. Additionally, analysis of the axial ligand effect reveals that the reactivity of iron­(IV)–nitrido oxidants in the quintet state toward C–H bond activation enhances as the electron-donating ability of the axial ligand weakens

Insight into the impact of environments on structure of chimera C3 of human β-defensins 2 and 3 from molecular dynamics simulations

<div><p>C3 is a chimera from human β-defensins 2 and 3 and possesses higher antimicrobial activity compared with its parental molecules, so it is an attractive candidate for clinical application of antimicrobial peptides. In continuation with the previous studies, molecular dynamics (MD) simulations were carried out for further investigating the effect of ambient environments (temperature and bacterial membrane) on C3 dynamics. Our results reveal that C3 has higher flexibility, larger intensity of motion, and more relevant secondary structural changes at 363 K to adapt the high temperature and maintain its antimicrobial activity, comparison with it at 293 K; when C3 molecule associates with the bacterial membrane, it slightly fluctuates and undergoes local conformational changes; in summary, C3 molecule demonstrates stable conformations under these environments. Furthermore, MD results analysis show that the hydrophobic contacts, the hydrogen bonds, and disulfide bonds in the peptide are responsible for maintaining its stable conformation. In addition, our simulation shows that C3 peptides can make anionic lipids clustered in the bacterial membrane; it means that positive charges and pronounced regional cationic charge density of C3 are most key factors for its antimicrobial activity.</p></div

Correction to Comparative Insight into Electronic Properties and Reactivities toward C–H Bond Activation by Iron(IV)–Nitrido, Iron(IV)–Oxo and Iron(IV)–Sulfido Complexes: A Theoretical Investigation

Correction to Comparative Insight into Electronic Properties and Reactivities toward C–H Bond Activation by Iron(IV)–Nitrido, Iron(IV)–Oxo and Iron(IV)–Sulfido Complexes: A Theoretical Investigatio

Elucidating proton-mediated conformational changes in an acid-sensing ion channel 1a through molecular dynamics simulation

Elucidating proton-mediated conformational changes in an acid-sensing ion channel 1a through molecular dynamics simulatio

Inhibition mechanism understanding from molecular dynamics simulation of the interactions between several flavonoids and proton-dependent glucose transporter

Proton-dependent glucose transporters as important drug targets can have different protonation states and adjust their conformational state under different pHs. So based on this character, research on its inhibition mechanism is a significant work. In this article, to study its inhibitory mechanism, we performed the molecular dynamics of several classical flavonoid molecules (Three inhibitors Phloretin, Naringenin, Resveratrol. Two non-inhibitors Isoliquiritigenin, Butein) with glucose transporters under two distinct environmental pHs. The results show inhibitors occupy glucose binding sites (GLN137, ILE255, ASN256) and have strong hydrophobic interactions with proteins through core moiety (C6-Cn-C6). In addition, inhibitors had better inhibitory effects in protonation state. In contrast, non-inhibitors can not occupy glucose binding sites (GLN137, ILE255, ASN256), thus they do not have intense interactions with the protein. It is suggested that favorable inhibitors should effectively take up the glucose-binding site (GLN137, ILE255, ASN256) and limit the protein conformational changes. Communicated by Ramaswamy H. Sarma</p

Investigations of Takeout proteins’ ligand binding and release mechanism using molecular dynamics simulation

<p>Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.</p

Doping the Alkali Atom: An Effective Strategy to Improve the Electronic and Nonlinear Optical Properties of the Inorganic Al₁₂N₁₂ Nanocage

Under ab initio computations, several new inorganic electride compounds with high stability, M@<i>x</i>-Al₁₂N₁₂ (M = Li, Na, and K; <i>x</i> = <i>b</i>₆₆, <i>b</i>₆₄, and <i>r</i>₆), were achieved for the first time by doping the alkali metal atom M on the fullerene-like Al₁₂N₁₂ nanocage, where the alkali atom is located over the Al–N bond (<i>b</i>₆₆/<i>b</i>₆₄ site) or six-membered ring (<i>r</i>₆ site). It is revealed that independent of the doping position and atomic number, doping the alkali atom can significantly narrow the wide gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) (<i>E</i>_H‑L = 6.12 eV) of the pure Al₁₂N₁₂ nanocage in the range of 0.49–0.71 eV, and these doped AlN nanocages can exhibit the intriguing <i>n</i>-type characteristic, where a high energy level containing the excess electron is introduced as the new HOMO orbital in the original gap of pure Al₁₂N₁₂. Further, the diffuse excess electron also brings these doped AlN nanostructures the considerable first hyperpolarizabilities (β₀), which are 1.09 × 10⁴ au for Li@<i>b</i>₆₆-Al₁₂N₁₂, 1.10 × 10⁴, 1.62 × 10⁴, 7.58 × 10⁴ au for M@<i>b</i>₆₄-Al₁₂N₁₂ (M = Li, Na, and K), and 8.89 × 10⁵, 1.36 × 10⁵, 5.48 × 10⁴ au for M@<i>r</i>₆-Al₁₂N₁₂ (M = Li, Na, and K), respectively. Clearly, doping the heavier Na/K atom over the Al–N bond can get the larger β₀ value, while the reverse trend can be observed for the series with the alkali atom over the six-membered ring, where doping the lighter Li atom can achieve the larger β₀ value. These fascinating findings will be advantageous for promoting the potential applications of the inorganic AlN-based nanosystems in the new type of electronic nanodevices and high-performance nonlinear optical (NLO) materials

Theoretical investigation on the mechanism of FeCl₃-catalysed cross-coupling reaction of alcohols with alkenes

<div><p>The mechanism of the FeCl₃-catalysed cross-coupling reaction of alcohols with alkenes has been investigated using the density functional theory. All calculations were performed in liquid phase. The structures of intermediates and transition states are computed and analysed in detail. The calculations show that the entire catalytic cycle consists in three steps: (1) H-abstraction, (2) free-radical addition, and (3) hydrogen transfer. The rate-limiting step in the whole catalytic cycle is the hydrogen-abstraction step. Only the quartet potential surface is likely to play an essential role in this cross-coupling reaction. The alpha-C(sp³)–H bond of the phenylpropanol is cleaved in a homolytic fashion. Moreover, we justify the change of the oxidation state of iron along the overall reaction pathway on the basis of the computed natural population atomic charges and spin densities. Our calculated results are consistent with and provide a reliable interpretation for the experimental observations that suggest the cross-coupling reaction occurs through a radical mechanism.</p></div

Aromatic Residues Regulating Electron Relay Ability of S‑Containing Amino Acids by Formations of S∴π Multicenter Three-Electron Bonds in Proteins

The ab initio calculations predict that the side chains of four aromatic amino acids (Phe, His, Tyr, and Trp residues) may promote methionine and cystine residues to participate in the protein electron hole transport by the formation of special multicenter, three-electron bonds (S∴π) between the S-atoms and the aromatic rings. The formations of S∴π bonds can efficiently lower the local ionization energies, which drive the electron hole moving to the close side chains of S-containing and aromatic residues in proteins. Additionally, the proper binding energies for the S∴π bonds imply that the self-movement of proteins can dissociate these three-electron bonds and promote electron hole relay