Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra

The infrared (IR) and Raman spectra of eight substitutional carbon defects in silicon are computed at the quantum mechanical level by using a periodic supercell approach based on hybrid functionals, an all electron Gaussian type basis set and the CRYSTAL code. The single substitutional C _s case and its combination with a vacancy (C _sV and C _sSiV) are considered first. The progressive saturation of the four bonds of a Si atom with C is then examined. The last set of defects consists of a chain of adjacent carbon atoms C, with i = 1–3. The simple substitutional case, C _s, is the common first member of the three sets. All these defects show important, very characteristic features in their IR spectrum. One or two C related peaks dominate the spectra: at 596 cm⁻¹ for C _s (and C _sSiV, the second neighbor vacancy is not shifting the C _s peak), at 705 and 716 cm⁻¹ for C _sV, at 537 cm⁻¹ for C and C (with additional peaks at 522, 655 and 689 for the latter only), at 607 and 624 cm⁻¹, 601 and 643 cm⁻¹, and 629 cm⁻¹ for SiC, SiC, and SiC, respectively. Comparison with experiment allows to attribute many observed peaks to one of the C substitutional defects. Observed peaks above 720 cm⁻¹ must be attributed to interstitial C or more complicated defects.     

Aspartate: An interesting model for analyzing dipole-ion and ion pair interactions through its oppositely charged amine and acid groups

Anionic species of aspartic acid, Asp⁻, having a zwitterionic backbone and a deprotonated side chain, appears to be a good example for analyzing dipole-ion and ion pair interactions. Density functional theory calculations were herein performed to investigate the low energy conformers of Asp⁻ embedded in a dielectric continuum modeling an aqueous environment, through a scan of the potential energy as a function of the side chain (χ₁, χ₂) torsion angles. The most energetically favorable conformers having g⁺g⁻ and g⁻g⁺ side chain orientations are found to be stabilized by charge-enhanced intramolecular H-bonding involving the positively charged () and the two negatively charged (COO⁻) groups. These conformers were further used to analyze Asp⁻ + nW clusters (W: water, n = 1 or 3), and Asp⁻/Asp⁻ pair formation. COO⁻ groups were found to be the most attractive sites for hosting a water molecule (binding energy: −6.0 ± 1.5 kcal/mol), compared to groups (binding energy: −4.7 ± 1.1 kcal/mol). Energy separation between g⁺g⁻ and g⁻g⁺ conformers increases upon explicit hydration. Asp⁻/Asp⁻ ion pairs, stabilized by the interaction between the group of a partner and the COO⁻ group of the other, shows a quite constant binding energy (−8.1 ± 0.2 kcal/mol), whatever the pair type, and the relative orientation of the two interacting partners. This study suggests a first step to achieve a more realistic image of intermolecular interactions in aqueous environment, especially upon increasing concentration. It can also be considered as a preliminary attempt to assess the interactions of the Lys⁺…Asp⁻/Glu⁻ ion pairs stabilizing intra- and interchain interactions in proteins.     

Topological analysis of chemical bonding in the layered FePSe3 upon pressure-induced phase transitions

Two pressure-induced phase transitions have been theoretically studied in the layered iron phosphorus triselenide (FePSe₃ ). Topological analysis of chemical bonding in FePSe₃ has been performed based on the results of first-principles calculations within the periodic linear combination of atomic orbitals (LCAO) method with hybrid Hartree-Fock-DFT B3LYP functional. The first transition at about 6 GPa is accompanied by the symmetry change from to C2/m , whereas the semiconductor-to-metal transition (SMT) occurs at about 13 GPa leading to the symmetry change from C2/m to . We found that the collapse of the band gap at about 13 GPa occurs due to changes in the electronic structure of FePSe₃ induced by relative displacements of phosphorus or selenium atoms along the c-axis direction under pressure. The results of the topological analysis of the electron density and its Laplacian demonstrate that the pressure changes not only the interatomic distances but also the bond nature between the intralayer and interlayer phosphorus atoms. The interlayer P–P interactions are absent in two non-metallic FePSe₃ phases while after SMT the intralayer P–P interactions weaken and the interlayer P–P interactions appear.     

Mono-silicon isoelectronic replacement in CAl4: van't hoff/le bel carbon or not?

In cluster studies, the isoelectronic replacement strategy has been successfully used to introduce new elements into a known structure while maintaining the desired topology. The well-known penta-atomic 18 valence electron (ve) species and its Al⁻/Si or Al/Si⁺ isoelectronically replaced clusters CAl₃Si⁻, CAl₂Si₂, , and , all possess the same anti-van't Hoff/Le Bel skeletons, that is, nontraditional planar tetracoordinate carbon (ptC) structure. In this article, however, we found that such isoelectronic replacement between Si and Al does not work for the 16ve-CAl₄ with the traditional van't Hoff/Le Bel tetrahedral carbon (thC) and its isoelectronic derivatives CAl₃X (X = Ga/In/Tl). At the level of CCSD(T)/def2-QZVP//B3LYP/def2-QZVP, none of the global minima of the 16ve mono-Si-containing clusters CAl₂SiX⁺ (X = Al/Ga/In/Tl) maintains thC as the parent CAl₄ does. Instead, X = Al/Ga globally favors an unusual ptC structure that has one long C─X distance yet with significant bond index value, and X = In/Tl prefers the planar tricoordinate carbon. The frustrated formation of thC in these clusters is ascribed to the CSi bonding that prefers a planar fashion. Inclusion of chloride ion would further stabilize the ptC of CAl₂SiAl⁺ and CAl₂SiGa⁺. The unexpectedly disclosed CAl₂SiAl⁺ and CAl₂SiGa⁺ represent the first type of 16ve-cationic ptCs with multiple bonds. © 2019 Wiley Periodicals, Inc.     

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.     

Fluxional bonds in quasi-planar and half-sandwich (M = K,Rb, and Cs)

Detailed molecular orbital and bonding analyses reveal the existence of both fluxional σ- and π-bonds in the global minima C_s ( 1 ) and C_s MB₁₈ ( 3 ) and transition states C_s ( 2 ) and C_s ( 4 ) of dianion and monoanions (M = K, Rb, and Cs). It is the fluxional bonds that facilitate the fluxional behaviors of the quasi-planar and half-sandwich which possess energy barriers smaller than the difference of the corresponding zero-point corrections. © 2019 Wiley Periodicals, Inc.     

A Density Functional Theory Study on Nonlinear Optical Properties of Double Cage Excess Electron Compounds: Theoretically Design M[Cu(Ag)@(NH3)n](M = Be,Mg and Ca; n = 1–3)

In this work, we investigated the nonlinear optical (NLO) properties of excess electron electride molecules of M[Cu(Ag)@(NH₃)_n](M = Be, Mg and Ca; n = 1–3) using density functional theory (DFT). This electride molecules consist of an alkaline-earth (Be, Mg and Ca) together with transition metal (Cu and Ag) doped in NH₃ cluster. The natural population analysis of charge and their highest occupied molecular orbital suggests that the M[Cu(Ag)@(NH₃)_n] compound has excess electron like alkaline-earth metal form double cage electrides molecules, which exhibit a large static first hyperpolarizability () (electron contribution part) and one of which owns a peak value of 216,938 (a.u.) for Be[Ag@(NH₃)₂] and vibrational harmonic first hyperpolarizability () (nuclear contribution part) values and the ratio of /, namely, η values from 0.02 for Be[Ag@(NH₃)] to 0.757 for Mg[Ag@(NH₃)₃]. The electron density contribution in different regions on values mainly come from alkaline-earth and transition metal atoms by first hyperpolarizability density analysis, and also explains the reason why values are positive and negative. Moreover, the frequency-dependent values β(−2ω,ω,ω) are also estimated to make a comparison with experimental measures. © 2018 Wiley Periodicals, Inc.     

Mechanism of the O2(1Δg) generation from the Cl2/H2O2 basic aqueous solution explored by the combined ab initio calculation and nonadiabatic dynamics simulation

In the present work, mechanism of the O₂(¹Δ_g) generation from the reaction of the dissolved Cl₂ with H₂O₂ in basic aqueous solution has been explored by the combined ab initio calculation and nonadiabatic dynamics simulation, together with different solvent models. Three possible pathways have been determined for the O₂(¹Δ_g) generation, but two of them are sequentially downhill processes until formation of the OOCl⁻ complex with water, which are of high exothermic character. Once the complex is formed, singlet molecular oxygen is easily generated by its decomposition along the singlet-state pathway. However, triplet molecular oxygen of O₂() can be produced with considerable probability through nonadiabatic intersystem crossing in the ¹Δ_g/ intersection region. It has been found that the coupled solvent, heavy-atom, and nonadiabatic effects have an important influence on the quantum yield of the O₂(¹Δ_g) generation. © 2018 Wiley Periodicals, Inc.     

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN2 Reaction of and CH3Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N2) reactions of M_nNH₂⁽ⁿ⁻¹⁾ + CH₃Cl (M⁺ = Li⁺, Na⁺, K⁺, and MgCl⁺; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M⁺ and of solvation on the reaction profile and the stereochemical preference, that is, backside (S_N2-b) versus frontside attack (S_N2-f). The results were compared to the corresponding ion-pair S_N2 reactions involving F⁻ and OH⁻ nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N2 reactivity along the nucleophiles F⁻, OH⁻, and , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.     

Ab initio structure and vibration-rotation dynamics of germylene,GeH2

Accurate structure and potential energy surface of germylene, GeH₂, in its ground electronic state ¹A₁ were determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to sextuple-zeta quality. The Born-Oppenheimer equilibrium structural parameters for the ¹A₁ state are estimated to be r_e(GeH) = 1.5793 Å and ∠_e(HGeH) = 91.19^∘. The term value T_e for the lowest excited electronic state ã³B₁ of GeH₂ is predicted to be 9140 cm^–1. The vibration-rotation energy levels for the ¹A₁ state of the ⁷⁴GeH₂, ⁷⁴GeD₂, ⁷²GeH₂, and ⁷⁰GeH₂ isotopologues were determined using a variational approach and compared with the experimental data. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, spin-orbit, and adiabatic effects for prediction of the structure and vibration-rotation dynamics of the GeH₂ molecule is discussed. © 2019 Wiley Periodicals, Inc.     

A Computational Analysis of the Intrinsic Plasticity of Five-Coordinate Cu(II) Complexes and the Factors Leading to the Breakdown of the Orbital Directing Effect in Paddlewheel Secondary Building Units

Quantum chemical calculations on model copper paddlewheel (CPW) complexes of general formula [Cu₂(μ₂-O₂CR)₄L₂] establish two local coordination geometries at the metal centers depending on the balance between equatorial and axial ligand fields. When the equatorial field is stronger than the axial field (large ligand field asymmetry), dominates the stereochemical activity of the d⁹ shell resulting in a relatively rigid, “orbitally directed” planar or square pyramidal structure. However, if the axial field is significantly increased, or the equatorial field moderately weakened, a small ligand field asymmetry results and both and are involved in the stereochemical activity. This results in a “plastic,” distorted trigonal bipyramidal geometry where the former axial ligand moves into one of the original four equatorial positions. Linkers already used to synthesize zinc-dabco MOFs (dabco = 1,4-diazabicyclo[2.2.2]octane) are shown to generate plastic CPW secondary building unit analogs with potential implications for conferring breathing behavior for MOFs which would currently be assumed to be rigid. © 2019 Wiley Periodicals, Inc.     

Ab initio potential energy surface and vibration–rotation energy levels of germanium dicarbide,GeC2

The accurate ground‐state potential energy surface of germanium dicarbide, GeC₂, has been determined from ab initio calculations using the coupled‐cluster approach. The core–electron correlation, higher‐order valence‐electron correlation, and scalar relativistic effects were taken into account. The potential energy surface of GeC₂ was shown to be extraordinarily flat near the T‐shaped equilibrium configuration. The potential energy barrier to the linear CCGe configuration was predicted to be 1218 cm⁻¹. The vibration–rotation energy levels of some GeC₂ isotopologues were calculated using a variational method. The vibrational bending mode ν₃ was found to be highly anharmonic, with the fundamental wavenumber being only 58 cm⁻¹. Vibrational progressions due to this mode were predicted for the , , and states of GeC₂. © 2018 Wiley Periodicals, Inc.     

The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3‐iodanes): Facing the limit of the stationary quantum chemical approach

Trifluoromethylation of acetonitrile with 3,3‐dimethyl‐1‐(trifluoromethyl)?1λ³,2‐ benziodoxol is assumed to occur via reductive elimination (RE) of the electrophilic CF₃‐ligand and MeCN bound to the hypervalent iodine. Computations in gas phase showed that the reaction might also occur via an S_N2 mechanism. There is a substantial solvent effect present for both reaction mechanisms, and their energies of activation are very sensitive toward the solvent model used (implicit, microsolvation, and cluster‐continuum). With polarizable continuum model‐based methods, the S_N2 mechanism becomes less favorable. Applying the cluster‐continuum model, using a shell of solvent molecules derived from ab initio molecular dynamics (AIMD) simulations, the gap between the two activation barriers ( ) is lowered to a few kcal mol^?1 and also shows that the activation entropies ( ) and volumes ( ) for the two mechanisms differ substantially. A quantitative assessment of will therefore only be possible using AIMD. A natural bond orbital‐analysis gives further insight into the activation of the CF₃‐reagent by protonation. © 2014 Wiley Periodicals, Inc.     

Structure and electrochemical properties for complexes of nitrocompounds with inorganic ions: A theoretical approach

Reduction and oxidation (redox) reactions are widely used for removal of nitrocompounds from contaminated soil and water. Structures and redox properties for complexes of nitrocompounds, such as 2,4,6‐trinitrotoluene (TNT), 2,4‐dinitrotoluene (DNT), 2,4‐dinitroanisole (DNAN), and 5‐nitro‐2,4‐dihydro‐3H?1,2,4‐triazol‐3‐one (NTO), with common inorganic ions (Na⁺, Cl^?, ) were investigated at the SMD(Pauling)/PCM(Pauling)/MPWB1K/TZVP level of theory. Atoms in molecules (AIM) theory was applied to analyze the topological properties of the bond critical points involved in the interactions between the nitrocompounds and the ions. Topological analyses show that intermolecular interactions of the types O(N)…Na⁺, C‐H…Cl^?( ), and C…Cl^?( ) may be discussed as noncovalent closed‐shell interactions, while N‐H···Cl^?( ) hydrogen bonds are partially covalent in nature. Complexation causes significant decrease of redox activity of the nitrocompounds. Analysis of the reduction potentials of the complexes obtained through application of the Pourbaix diagram of an iron/water system revealed that sodium complexes of NTO might be reduced by metallic iron. © 2016 Wiley Periodicals, Inc.     

Vibrationally Resolved Inner-Shell Photoexcitation of the Molecular Anion C2−

Carbon 1s core-hole excitation of the molecular anion C₂⁻ has been experimentally studied at high resolution by employing the photon-ion merged-beams technique at a synchrotron light source. The experimental cross section for photo–double-detachment shows a pronounced vibrational structure associated with and core excitations of the C₂⁻ ground level and first excited level, respectively. A detailed Franck-Condon analysis reveals a strong contraction of the C₂⁻ molecular anion by 0.2 Å upon this core photoexcitation. The associated change of the molecule's moment of inertia leads to a noticeable rotational broadening of the observed vibrational spectral features. This broadening is accounted for in the present analysis which provides the spectroscopic parameters of the C₂⁻ and core-excited levels.     

Lithium–Lanthanide Bimetallic Metal–Organic Frameworks towards Negative Electrode Materials for Lithium-Ion Batteries

Novel lithium–lanthanide (Ln: cerium and praseodymium) bimetallic coordination polymers with formulas C₁₀H₂LnLiO₈ (Ln: Ce (CeLipma) and Pr (PrLipma)) and C₁₀H₃CeO₈ (Cepma) were prepared through a simple hydrothermal method. The three compounds were characterized by means of FTIR spectroscopy, X-ray diffraction, single-crystal X-ray diffraction, SEM, TEM, and X-ray photoelectron spectroscopy. The results of structural refinement show that they belong to triclinic symmetry and P space group with cerium (or praseodymium) and lithium cations, forming coordination bonds to oxygen atoms from different pyromellitic acid molecules, and leading to the construction of 3D structures. It is interesting to note that the frameworks exclude any coordination water and lattice water. As an electrode material for lithium-ion batteries, CeLipma exhibits a maximum capacity of 800.5 mAh g⁻¹ and a retention of 91.4 % after 50 cycles at a current density of 100 mA g⁻¹. The favorable electrochemical properties of the lanthanide coordination polymers show potential application prospects in the field of electrode materials.     

Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability

Pairwise-based methods such as the free energy perturbation (FEP) method have been widely deployed to compute the binding free energy differences between two similar host–guest complexes. The calculated pairwise free energy difference is either directly adopted or transformed to absolute binding free energy for molecule rank ordering. We investigated, through both analytic derivations and simulations, how the selection of pairs in the experiment could impact the overall prediction precision. Our studies showed that (1) the estimated absolute binding free energy () derived from calculated pairwise differences (ΔΔG) through weighted least squares fitting is more precise in prediction than the pairwise difference values when the number of pairs is more than the number of ligands and (2) prediction precision is influenced by both the total number of pairs and the specifically selected pairs, the latter being critically important when the number of calculated pairs is limited. Furthermore, we applied optimal experimental design in pair selection and found that the optimally selected pairs can outperform randomly selected pairs in prediction precision. In an illustrative example, we showed that, upon weighing ligand structure similarity into design optimization, the weighted optimal designs are more efficient than the literature reported designs. This work provides a new approach to assess retrospective pairwise-based prediction results, and a method to design new prospective pairwise-based experiments for molecular lead optimization. © 2019 Wiley Periodicals, Inc.