Catalytic action of Mn‐superoxide dismutase in scavenging superoxide radical anion by double hydrogen abstraction from dihydrolipoic acid: A theoretical study

The mechanism of scavenging superoxide radical anion ( ) by dihydrolipoic acid (diLA) in absence and presence of the enzyme Manganese‐superoxide dismutase (Mn‐SOD) has been investigated using density functional theory. Mn‐SOD was modelled by a complex of a manganese cation (Mn²⁺) bonded to three similar molecules having a histidine ring each and a water molecule. It has been shown that the scavenging mechanism involves double hydrogen abstraction by from different pairs of neighboring sites of diLA. It has been found that diLA alone cannot scavenge superoxide radical anions efficiently as the barrier energies involved in the reactions are very high. However, in presence of Mn‐SOD, owing to its catalytic action, the corresponding reactions become barrierless due to which superoxide radical anions would be scavenged highly efficiently. H₂O₂ formed from superoxide radical anion due to double hydrogen abstraction from diLA is scavenged by diLA alone barrierlessly without involving Mn‐SOD or any other catalyst.     

Selective separation of strontium by multitopic ion‐pair receptor: A DFT exploration

Selective extraction of a radionuclide in the presence of other interfering ions is one of the vital steps in the back‐end‐of‐the‐nuclear fuel cycle. The presence of interfering cations (such as Ca²⁺) in the radioactive waste and involvement of multiple separation steps are known to be bottlenecks in the efficient Sr²⁺ extraction. Here, using free energy corrected density functional theory, we have proposed a two‐step Sr²⁺ extraction methodology in nitrate media in the presence of interfering Ca²⁺ ion using a multitopic ion‐pair receptor, which was earlier reported to be strongly selective for K⁺ (Kim et al. J. Am. Chem. Soc. 2012, 134 , 1782–1792). To depict the correct free energy trend in the proposed extraction processes, the most probable binding mode of the metal (Sr²⁺, Ca²⁺, and K⁺) nitrates in the host are identified. In excellent agreement with the previously reported experiment, Crown/Pyrrole (C/P) binding is noted to be the most preferable mode for KNO₃, where K⁺ and occupied the Crown (C) and Pyrrole (P) site, respectively. However, the divalent metal ions (Ca²⁺ and Sr²⁺) are noted to marginally prefer Crown/Crown‐Pyrrole (C/CP) mode, in which metal reside at the C site while two nitrates occupy the P site and also simultaneously bind at the outer sphere of C site to coordinate with the metal via monodentate motif. Based on the free energy of extraction, we predict that the selective separation of chemically alike Ca²⁺/Sr²⁺ pair is indeed achievable using this receptor. We propose that once [Sr(NO₃)₂] is extracted in organic media, the receptor's high affinity toward K⁺ in nitrate media can be used to back strip Sr²⁺ to the aqueous phase.     

Geometric and electronic structures of silicon fluorides (N = 4 – 6) and potential energy surfaces for dissociation reactions → SiF4 + F– and → + F–

The geometric and electronic structures of a series of silicon fluorides (n = 4 ? 6) were computationally studied with the aid of density functional theory (DFT) method with B3LYP and M06‐2X functionals and coupled cluster (CCSD and CCSD(T)) methods with 6‐311++G(d,p) basis set. The nature of the Si‐F bonds in these compounds was analyzed in the framework of the natural bond orbital theory and natural resonance theory. Energy characteristics (heats of reactions and energy barriers) of the dissociation reactions → SiF₄ + F^– and → + F^– were calculated using the DFT and CCSD methods. The potential energy surface of elimination of a fluoride anion from has a specific topology with valley‐ridge inflection points corresponding to bifurcations of the minimal energy reaction path. © 2016 Wiley Periodicals, Inc.     

Lanthanide metals in the boron cages: Computational prediction of M@Bn (M = Eu,Gd; n = 38, 40)

Endohedral metalloborofullerenes (EMBFs) are novel boron analogues of the famous endohedral metallofullerenes (EMFs). Many EMBFs have been proposed by theoretical calculations thus far. However, in sharp contrast to EMFs, which trap most of the lanthanides with f electrons inside the cages, the corresponding lanthanide‐based EMBFs have never been reported. In this work, the encapsulation of Eu and Gd in the B₃₈ and B₄₀ fullerenes was studied by means of density functional theory calculations. Our results revealed that Gd@B₃₈(⁹A), Eu@B₄₀(⁸B₂), and Gd@B₄₀(⁷A″) all favor the endohedral configuration, and the electronic structures can be described as Gd³⁺@ , Eu²⁺@ , and Gd³⁺@ with jailed f electron spins. The large binding energies and sizable HOMO–LUMO gaps suggest that they may be achieved experimentally. They feature σ and π double aromaticity, and their excellent stabilities were confirmed by the Born–Oppenheimer molecular dynamics simulations. Finally, the infrared and UV/vis spectra were simulated to assist experimental characterization.     

Carbon–sulfur chains: A high‐resolution infrared and quantum‐chemical study of C3S and SC7S

In the course of a 5 μm high‐resolution infrared study of laser ablation products from carbon–sulfur targets, the ν₁ vibrational mode region of linear C₃S has been studied continuously from 2046 to 2065 cm^?1. Besides the prominent vibrational fundamental, the region was found to feature the , and even hot bands, the latter two of which were observed for the first time. Owing to the high signal‐to‐noise ratio obtained, the ν₁ mode of S could also be observed in natural abundance for the first time at high spectral resolution in the infrared. At 2061 cm^?1, hidden inside the branch of the C₃S ν₁ fundamental mode, a weak new band is observed which exhibits very tight line spacing and stems from a heavy both carbon and sulfur containing carrier. On the basis of high‐level quantum‐chemical calculations of selected carbon–sulfur chains and other carbon‐rich cumulenes, this feature is attributed to the ν₅ vibrational fundamental of linear SC₇S, which stands for the first gas‐phase spectroscopic detection of this long cumulenic chain.     

Dealing with the shifted and inverted Tietz–Hua oscillator potential using the J‐matrix method

The tridiagonal J‐matrix approach has been used to calculate the low and moderately high‐lying eigenvalues of the rotating shifted Tietz–Hua (RSTH) oscillator potential. The radial Schrödinger equation is solved efficiently by means of the diagonalization of the full Hamiltonian matrix, with the Laguerre or oscillator basis. Ro–vibrational bound state energies for 11 diatomic systems, namely , , , NO, CO, , , , , , and NO⁺, are calculated with high accuracy. Some of the energy states for molecules are reported here for the first time. The results of the last four molecules have been introduced for the first time using the oscillator basis. Higher accuracy is achieved by calculating the energy corresponding to the poles of the S‐matrix in the complex energy plane using the J‐matrix method. Furthermore, the bound states and the resonance energies for the newly proposed inverted Tietz–Hua IRSTH‐potential are calculated for the H₂‐molecule with scaled depth. A detailed analysis of variation of eigenvalues with n, quantum numbers is made. Results are compared with literature data, wherever possible. © 2015 Wiley Periodicals, Inc.     

Counter anion in Li+‐encapsulated C60 can further enhance the rate of Diels–Alder reaction: A DFT study

Density functional theory calculations were carried out to investigate the Diels–Alder cycloaddition between cyclopentadiene and C₆₀ after the encapsulation of Li⁺ ion with transition states identified and confirmed by intrinsic reaction coordinate calculations. Our results showed that the Li⁺‐encapsulation results in a lower energy barrier and the presence of counter anion can further reduce the energy barrier, making the trend in agreement with the experimental results. In addition, the influencing factors on the reactivity of Li⁺‐encapsulated fullerenes such as counter anion and the position of Li⁺ in C₆₀ were discussed. This study aims to provide a better understanding of Diels–Alder reaction with Endohedral Metallofullerenes to allow more efficient functionalization of fullerenes.     

The quantum dynamics of the reactions N+H2(HD,D2) and their vibrational excitation effect

The N(⁴S)+H₂ reaction and its isotopic variants have been investigated by means of time‐dependent quantum wave packet with split operator method on the ground state potential energy surface (Zhai and Han, J. Chem. Phys. 2011, 135, 104314). The reaction probabilities, integral cross sections, branching ratio of the integral cross sections, and effect of vibrational excitation of H₂, HD, and D₂ diatomic molecules are presented and discussed. The results reveal that the intramolecular isotopic effect is greater than the intermolecular one, and that the vibrational excitation of the diatomic molecules can promote the progress of this reaction. In addition, a limited number of rigorous Coriolis coupling calculations of the integral cross sections of the N(⁴S)+H₂ reaction have been carried out. Also shown is that since the Coriolis coupling plays a small part in this accurate quantum calculation, the cheaper centrifugal sudden calculations here reported are effective for this reactive system. © 2014 Wiley Periodicals, Inc.     

Prediction of the pH‐rate profile for dimethyl sulfide oxidation by hydrogen peroxide: The role of elusive H3O2+ Ion

Experimental kinetics of sulfide oxidation by hydrogen peroxide presents a pH‐dependent profile. In this article, it was carried out a detailed study of the mechanism and kinetics of dimethyl sulfide (DMS) oxidation by H₂O₂ in neutral, acid, and basic aqueous medium using ab initio calculations. The results point out that DMS oxidation in neutral aqueous medium occurs through its direct reaction with H₂O₂. In acid medium, cluster‐continuum model calculations shows that cluster is the best representation of the very reactive species. In basic medium, there is formation of the species. However, the pathway involving this species has high free energy barrier, making this pathway unfeasible. The theoretical pH‐rate profile is in good agreement with the experimental observations. © 2013 Wiley Periodicals, Inc.     

Pseudo Jahn–Teller origin tracking for symmetry breaking in halogenabenzene: How can a bird fly?

The cyclic iodabenzene molecule (CH)₅I was first introduced and characterized as planar configuration and zwitterionic valence structure by Glukhovtsev in 1991. Recently, it caused researchers' great interest due to the theoretical discovery of a stable bird‐like structure by Hoffmann et al. in 2017 which has similar electronic structure and charge distribution as well‐known Meisenheimer complex C₆H. Inspired by this, we continue to tell the halogenabenzene story by revealing the origin of the bird‐like structure and understanding how the electronic behavior affects the geometrical symmetry for a molecule. By combining the Pseudo Jahn–Teller effect (PJTE) theory with the ab initio calculations for halogenabenzenes (CH)₅X (X = F, Cl, Br, I) and C₆H, it is illustrated that the vibronic coupling of ¹A₁ ground state and ¹B₁ excited states with C_2v planar structure along the out‐of‐plane b₁ distortion triggers the symmetry breaking of planar configuration to form a preferred bird‐like structure. This interpretation can be also applied to explain their different stabilization energies by analyzing numerically the energy gaps of coupled electronic states and PJTE vibronic coupling parameters. Taking use of the PJTE formulation above, we also tracked the origin of restoring to be planar for (CH)₅X²⁺ cation, as well as their isoelectronic species (CH)₅O⁺ and (CH)₅N, and suggests an effective strategy to stabilize the planar configuration for halogenabenzenes.     

Four faces of the interaction between ions and aromatic rings

Non‐covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion–aromatic‐ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation–π (CP_⊥), co‐planar cation–π (CP_∥), perpendicular anion–π (AP_⊥), and co‐planar anion–π (AP_∥). To understand more than the basic features of these four interaction types, a systematic, high‐level quantum chemical study is performed, using the X^– + C₆H₆, M⁺ + C₆H₆, X^– + C₆F₆, and M⁺ + C₆F₆ model systems with X⁻ = H⁻, F⁻, Cl⁻, HCOO⁻, CH₃COO⁻ and M⁺ = H⁺, Li⁺, Na⁺, , CH₃ , whereby C₆H₆ and C₆F₆ represent an electron‐rich and an electron‐deficient π system, respectively. Benchmark‐quality interaction energies with small uncertainties, obtained via the so‐called focal‐point analysis (FPA) technique, are reported for the four interaction types. The computations reveal that the interactions lead to significant stabilization, and that the interaction energy order, given in kcal mol⁻¹ in parentheses, is CP_⊥ (23–37) > AP_⊥ (14–21) > CP_∥ (9–22) > AP_∥ (6–16). A natural bond orbital analysis performed leads to a deeper qualitative understanding of the four interaction types. To facilitate the future quantum chemical characterization of ion–aromatic‐ring interactions in large biomolecules, the performance of three density functional theory methods, B3LYP, BHandHLYP, and M06‐2X, is tested against the FPA benchmarks, with the result that the M06‐2X functional performs best. © 2017 Wiley Periodicals, Inc.     

The nature of the chemical bond in borazine (B3N3H6), boroxine (B3O3H3), carborazine (B2N2C2H6), and related species

The bonding problem in borazine (B₃N₃H₆), boroxine (B₃O₃H₃), and carborazine (B₂N₂C₂H₆) is successfully addressed through the consideration of the excited states of the constituent fragments, namely BH( ), NH( ), and CH( ). We propose the participation of resonant structures for all three species that help to explain the experimental findings. A discussion on the chemical pattern of the parental molecule benzene (C₆H₆) helps to make coherent the whole bonding analysis on the titled species.     

Comments on the carbon cluster C60 and on its complexes with alkaline elements

We have analyzed in the Hartree–Fock approximation the carbon cluster C₆₀ with a single-zeta [(9,5)/(2,1)] basis set and a double-zeta [(9,5)/(4,2)] basis set, the latter with and without 3d polarization functions. Estimates of the correlation energy correction were obained either using Becke's density functional theory or the Clementi–Chakravorty's electron–pair density approximation. The cluster's positive ion and singly and doubly charged negative ions have also been studied (doublets for C and C and singlet and triplet for C) and computed both with a doublezeta basis set and defferent geometries or a double-zeta plus polarization basis set. The geometries considered include the one obtained by quantum molecular dynamics using the Car–Parrinello approximation and two additional near this minimum. The computed ionization potential and electron affinity are in reasonable agreement with the experiments considering the basis sets adopted. A lithium, a sodium, or a potassium atom or the corresponding positive ions have been placed at the center of the cluster and have been shown to form stable complexes: C₆₀Li⁺, C₆₀Li, C₆₀Na⁺, C₆₀Na, C₆₀K⁺, and C₆₀K. In addition, preliminary data with a calcium atom are reported. Computations on model cluster C₅, C₆, and C₉ are also reported to show that one needs large basis sets, extended use of polarization functions, and correlation corrections for quantitative results, more accurate than ～5 kcal/mol per carbon atom, in the total energy, as in this work.     

How does the pH influences the Ru-NO coordination compounds?

The pH influence has important role in the bioavailability of coordination compounds. fac-[Ru(NO)Cl₂(κ³N⁴,N⁸,N¹¹[1-carboxypropyl]cyclam)]⁺, 1 , and the species found at different pHs, 2 - 4 , were investigated. One series of computational methodologies has been used to investigate these compounds. One special highlight is to interacting quantum atoms method, where the total interaction energy, , between two atoms has been used as base to estimate the chemical bonds strength. The deprotonation of -CO₂H, 1 ➔ 2 (pK_a = 3.3), creates a hydrogen bond in the complex 2 , N( 3 )-H⋯ ·OCO⁻, with a more favorable than the presents in 1 , N( 3 )-H⋯ ·OCOH. There are no changes in in Ru-NO bond. The second deprotonation occurs in the N(2) atom of the cyclam group, 2 ➔ 3 (pK_a = 8.0). It promotes an increase in the covalent character of Ru-N( 2 ). In contrast, there is no changes in Ru-N( 5 )O bond. For higher pHs, there is a 3 ➔ 4 equilibrium (pK_a = 11.5) and the conversion of Ru-N( 5 )O for Ru-N( 5 )O₂. The Ru-N( 5 ) of 4 shows a larger ionic character than 3 . Thus, Ru-NO in 1 - 4 has worthy stability about a large pH range, showing potential application as NO scavengers.     

Unexpected properties of non‐autoionizing doubly excited states of the H2 molecule

We present accurate calculations of the non‐autoionizing and doubly excited states of the H₂ molecule using full configuration interaction with Hartree–Fock molecular orbitals and Heitler–London atomic orbitals. We consider the united atom configurations from He(2p2p) up to He(2p8g) and dissociation products from H₂(2p + 2p) up to H₂(2p + 6?). Born–Oppenheimer calculations are carried out with extended and optimized Slater‐type orbitals for a total of 40 states, 10 for each symmetry, covering the internuclear distances from the united atom to dissociation, which, for some states, is reached beyond 100 a₀. Occurrences of repulsive states cleanly interlaced between bound states with many vibrational levels are reported. Some of the potential minima are deep enough to accommodate many vibrational levels (up to 50). Noteworthy large equilibrium minima, like R_eq = 46.0 a₀ in the state dissociating as (2p + 6h) and with 18 vibrational levels. The occurrence of vertical excitations from the singly excited manifolds is analyzed. Several states present double minima generated by avoided crossings, some with a strong ionic character. © 2016 Wiley Periodicals, Inc.     

Quantum control of electron‐proton symmetry breaking in dissociative ionization of H2 by intense laser pulses

Forward and backward electron/proton ionization/dissociation spectra from one‐dimensional non‐Born‐Oppenheimer H₂ molecule exposed to ultrashort intense laser pulses ( W/cm², λ = 800 nm) have been computed by numerically solving the time‐dependent Schrödinger equation. The resulting above‐threshold ionization and above‐threshold dissociation spectra exhibit the characteristic forward‐backward asymmetry and sensitivity to the carrier‐envelope phase (CEP), particularly for high energies. A general framework for understanding CEP effects in the asymmetry of dissociative ionization of H₂ has been established. It is found that the symmetry breaking of electron‐proton distribution with π periodic modulation occurs for all CEPs except for ( integer) and the largest asymmetry coming from the CEP of . At least one of the electron and proton distributions is asymmetric when measured simultaneously. Inspection of the nuclear and electron wave packet dynamics provides further information about the relative contribution of the gerade and ungerade states of to the dissociation channel and the time delay of electrons in asymmetric ionization. © 2014 Wiley Periodicals, Inc.     

Single‐ and double‐electron reductions of CO2 by using superalkalis: An ab initio study

CO₂, a major contributor to global warming, can be balanced by converting it into fuels. The reduction of CO₂ has been difficult due to its extremely high stability. Recently, single‐electron reduction of CO₂ by superalkalis has been proposed using quantum chemical methods. Herein, we report a systematic study on the single‐reduction of CO₂ by using typical superalkalis. Superalkalis are hypervalent species possessing lower ionization energies than alkali atoms. We have studied the interaction of CO₂ with FLi₂, OLi₃, and NLi₄ superalkalis using ab initio MP2 calculations. We notice that this interaction leads to stable superalkali‐CO₂ complexes in which the structure of CO₂ is bent due to electron transfer from superalkalis. This clearly reveals that the CO₂ can successfully be reduced to the anion. It has been also noticed that the size of superalkalis plays a crucial in the single‐electron reduction of CO₂. For instance, the binding energy of superalkali‐CO₂ complex and charge transfer to CO₂ decreases monotonically with the increase in the size of superalkali. We have also proposed that CO₂ can be further reduced to in case of the anionic complex such as (FLi₂ CO₂)‾. Thus, FLi₂ superalkali is also capable of double‐electron reduction of CO₂. These findings should provide new insights into CO₂‐activation as well as motivate further research in this direction.     

A theoretical study on cyclacenes: Analytical tight‐binding approach

We present a theoretical study of cyclacene molecules performed at tight‐binding level. The orbital energies and eigenvectors have been analytically computed, and exact expressions for the axial component of the total position spread and polarizability tensors have been obtained. In absence of dimerization, the system has a D_nh symmetry, where n is the number of hexagonal units. The energy bands present no gap at the Fermi level, and to this fact it corresponds a diverging (per‐electron) polarizability for in the direction of the system symmetry axis. The two (degenerate) components of the polarizability on the σ_h symmetry plane, conversely, remain finite for . The total position spread tensor presents a qualitatively different behavior, since all the three components of the position spread per electron remain finite for . The results are analyzed and discussed for both axial and planar components separately as these are affected differently with respect to the increasing system size. Both dipole polarizability and total position spread have been computed using an ab initio approach for the smallest systems, to compare the analytical tight‐binding expressions with a higher‐level theory.     

Electronic Structure of the Low-Lying States of the Triatomic MoS2 Molecule: The Building Block of 2D MoS2

Molybdenum disulfide (MoS₂) is the building component of 1D-monolayer, 2D-layered nanosheets and nanotubes having many applications in industry, and it is detected in various molecular systems observed in nature. Here, the electronic structure and the chemical bonding of sixteen low-lying states of the triatomic MoS₂ molecule are investigated, while the connection of the chemical bonding of the isolated MoS₂ molecule to the relevant 2D-MoS₂, is emphasized. The MoS₂ molecule is studied via DFT and multireference methodologies, i. e., MRCISD(+Q)/aug-cc-pVQZ(−PP)_Mo. The ground state, ³B₁, is bent (Mo−S=2.133 Å and ϕ(SMoS)=115.9°) with a dissociation energy to atomic products of 194.7 kcal/mol at MRCISD+Q. In the ground and in the first excited state a double bond is formed between Mo and each S atom, i. e., . These two states differ in which d electrons of Mo are unpaired. The Mo−S bond distances of the calculated states range from 2.108 to 2.505 Å, the SMoS angles range from 104.1 to 180.0°, and the Mo−S bonds are single or double. Potential energy curves and surfaces have been plotted for the ³B₁, ⁵A₁ and ⁵B₁ states. Finally, the low-lying septet states of the triatomic molecule are involved in the material as a building block, explaining the variety of its morphologies.     

Theoretical investigation of geometry and stability of small lithium‐iodide LinI (n = 2–6) clusters

We present theoretical investigation of the structural characteristics and stabilities of neutral and positively charged Li_nI (n = 2‐6) species. The structural isomers were found by using a randomized algorithm to search for minima structures, followed by B3LYP optimizations; the single‐point RCCSD(T)/cc‐pwCVTZ(‐PP) calculations were performed in order to compute relative energies, binding energies per atom, adiabatic and vertical ionization energies, and dissociation energies. Stability was compared to the pure lithium clusters; there is a typical odd‐even alternation; iodine doped clusters are more stable than pure lithium clusters. Lithium “cage” transfers its valence electron to the iodine atom to form neutral and cationic clusters. An electron departures the lithium cage upon ionization. An important reason for the larger stability of closed‐shell species is the existence of the HOMO 3c/2e natural bond orbitals. © 2013 Wiley Periodicals, Inc.