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.     

On the accurate estimation of free energies using the jarzynski equality

The Jarzynski equality is one of the most widely celebrated and scrutinized nonequilibrium work theorems, relating free energy to the external work performed in nonequilibrium transitions. In practice, the required ensemble average of the Boltzmann weights of infinite nonequilibrium transitions is estimated as a finite sample average, resulting in the so-called Jarzynski estimator, . Alternatively, the second-order approximation of the Jarzynski equality, though seldom invoked, is exact for Gaussian distributions and gives rise to the Fluctuation-Dissipation estimator . Here we derive the parametric maximum-likelihood estimator (MLE) of the free energy considering unidirectional work distributions belonging to Gaussian or Gamma families, and compare this estimator to . We further consider bidirectional work distributions belonging to the same families, and compare the corresponding bidirectional to the Bennett acceptance ratio () estimator. We show that, for Gaussian unidirectional work distributions, is in fact the parametric MLE of the free energy, and as such, the most efficient estimator for this statistical family. We observe that and perform better than and , for unidirectional and bidirectional distributions, respectively. These results illustrate that the characterization of the underlying work distribution permits an optimal use of the Jarzynski equality. © 2018 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.     

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.     

Efficient singular-value decomposition of the coupled-cluster triple excitation amplitudes

We demonstrate a novel technique to obtain singular-value decomposition (SVD) of the coupled-cluster triple excitations amplitudes, . The presented method is based on the Golub-Kahan bidiagonalization strategy and does not require to be stored. The computational cost of the method is comparable to several coupled cluster singles and doubles (CCSD) iterations. Moreover, the number of singular vectors to be found can be predetermined by the user and only those singular vectors which correspond to the largest singular values are obtained at convergence. We show how the subspace of the most important singular vectors obtained from an approximate triple amplitudes tensor can be used to solve equations of the CC3 method. The new method is tested for a set of small and medium-sized molecular systems in basis sets ranging in quality from double- to quintuple-zeta. It is found that to reach the chemical accuracy (≈1 kJ/mol) in the total CC3 energies as little as 5 − 15% of SVD vectors are required. This corresponds to the compression of the amplitudes by a factor of about 0.0001 − 0.005 . Significant savings are obtained also in calculation of interaction energies or rotational barriers, as well as in bond-breaking processes. © 2019 Wiley Periodicals, Inc.     

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.     

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.     

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.     

Fluorine Substitution of TCNQ Alters the Redox-Driven Catalytic Pathway for the Ferricyanide-Thiosulfate Reaction

Mechanistic variation in catalysis through substituent-based redox tuning is well established. Fluorination of TCNQ (TCNQ=tetracyanoquinodimethane) provides ~850 mV variation in the redox potentials of the and (n=0, 2, 4) processes. With , catalysis of the kinetically very slow ferrocyanide-thiosulfate redox reaction in aqueous solution occurs via a mechanism in which the catalyst is reduced to when reacting with which is oxidised to . Subsequently, reacts with to form and reform the catalyst, in another thermodynamically favoured process. An analogous mechanism applies with as a catalyst. In contrast, since the reaction of with is thermodynamically unfavourable, an alternative mechanism is required to explain the catalytic activity observed in this non-fluorinated system. Here, upon addition of , reduction of to occurs with concomitant oxidation of to , which then acts as the catalyst for oxidation. Thermodynamic data explain the observed differences in the catalytic mechanisms. (n=0, 4) also act as catalysts for the ferricyanide-thiosulfate reaction in aqueous solution. The present study shows that homogeneous pathways are available following addition of these dissolved materials. Previously, these (n=0, 4) coordination polymers have been regarded as insoluble in water and proposed as heterogeneous catalysts for the ferricyanide-thiosulfate reaction. Details and mechanistic differences were established using UV-visible spectrophotometry and cyclic voltammetry.     

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.     

Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields**

Intricate behaviour of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic and kinetic potentials and electron density allowed partitioning any molecules and crystals into atomic - and potential-based -basins; -basins explicitly account for the electron exchange effect, which is missed for -ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero-flux surfaces of - and -basins. The gap between - and -basins represents the charge transfer, while the gap between - and -basins is a real-space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of -, -, and - basin boundaries between interacting atoms was proposed. The position of -boundary between - and -ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an H⋅⋅⋅O hydrogen bond is, the deeper hydrogen atom's -basin penetrates oxygen atom's -basin, while for covalent bonds a -boundary closely approaches a -one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the -basin of an electron occupier atom.     

Oxidation of methylamine

A detailed chemical kinetic model for oxidation of methylamine has been developed, based on theoretical work and a critical evaluation of data from the literature. The rate coefficients for the reactions of CHNH + O CHNH / CHNH + HO, CHNH + H CH + NH, CHNH CHNH, and CHNH + O CHNH + HO were calculated from ab initio theory. The mechanism was validated against experimental results from batch reactors, flow reactors, shock tubes, and premixed flames. The model predicts satisfactorily explosion limits for CHNH and its oxidation in a flow reactor. However, oxidation in the presence of nitric oxide, which strongly promotes reaction at lower temperatures, is only described qualitatively. Furthermore, calculated flame speeds are higher than reported experimental values; the model does not capture the inhibiting effect of the NH group in CHNH compared to CH. More work is desirable to confirm the products of the CHNH + NO reaction and to look into possible pathways to NH in methylamine oxidation.     

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.     

Cover Feature: How Different are the Diamagnetic and Paramagnetic Contributions to Off-Nucleus Shielding in Aromatic and Antiaromatic Rings? (ChemPhysChem 9/2023)

The spatial variations in the diamagnetic and paramagnetic contributions to the off-nucleus isotropic shielding, , and to the zz component of the off-nucleus shielding tensor, , around benzene (C₆H₆) and cyclobutadiene (C₄H₄) are investigated using complete-active-space self-consistent field wavefunctions. Despite the substantial differences between and around the aromatic C₆H₆ and the antiaromatic C₄H₄, the diamagnetic and paramagnetic contributions to these quantities, and , and and , are found to behave similarly in the two molecules, shielding and deshielding, respectively, each ring and its surroundings. The different signs of the most popular aromaticity criterion, the nucleus-independent chemical shift (NICS), in C₆H₆ and C₄H₄ are shown to follow from a change in the balance between the respective diamagnetic and paramagnetic contributions. Thus, the different NICS values for antiaromatic and antiaromatic molecules cannot be attributed to differences in the ease of access to excited states only; differences in the electron density, which determines the overall bonding picture, also play an important role.     

Simulations of a weakly conducting droplet under the influence of an alternating electric field

We investigate the electrohydrodynamics of an initially spherical droplet under the influence of an external alternating electric field by conducting axisymmetric numerical simulations using a charge-conservative volume-of-fluid based finite volume flow solver. The mean amplitude of shape oscillations of a droplet subjected to an alternating electric field for leaky dielectric fluids is similar to the steady-state deformation under an equivalent root mean squared direct electric field for all possible electrical conductivity ratio and permittivity ratio of the droplet to the surrounding fluid. In contrast, our simulations for weakly conducting media show that this equivalence between alternating and direct electric fields does not hold for . Moreover, for a range of parameters, the deformation obtained using the alternating and direct electric fields is qualitatively different, that is, for low and high , the droplet becomes prolate under alternating electric field but deforms to an oblate shape in the case of the equivalent direct electric field. A parametric study is conducted by varying the time period of the applied alternating electric field, the permittivity and the electrical conductivity ratios. It is observed that while increasing has a negligible effect on the deformation dynamics of the droplet for , it enhances the deformation of the droplet when for both alternating and direct electric fields. We believe that our results may be of immense consequence in explaining the morphological evolution of droplets in a plethora of scenarios ranging from nature to biology.     

Transport of hydrated nitrate and nitrite ions through graphene nanopores in aqueous medium

Nitrate () and nitrite () ions are naturally occurring inorganic ions that are part of the nitrogen cycle. High doses of these ions in drinking water impose a potential risk to public health. In this work, molecular dynamics simulations are carried out to study the passage of nitrate and nitrite ions from water through graphene nanosheets (GNS) with hydrogen-functionalized narrow pores in presence of an external electric field. The passage of ions through the pores is investigated through calculations of ion flux, and the results are analyzed through calculations of various structural and thermodynamic properties such as the density of ions and water, ion–water radial distribution functions, two-dimensional density distribution functions, and the potentials of mean force of the ions. Current simulations show that the nitrite ions can pass more in numbers than the nitrate ions in a given time through GNS hydrogen-functionalized pore of different geometry. It is found that the nitrite ions can permeate faster than the nitrate ions despite the former having higher hydration energy in the bulk. This can be explained in terms of the competition between the number density of the ions along the pore axis and the free energy barrier calculated from the potential of mean force. Also, an externally applied electric field is found to be important for faster permeation of the nitrite over the nitrate ions. The current study suggests that graphene nanosheets with carefully created pores can be effective in achieving selective passage of ions from aqueous solutions.     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .