Topological Analysis Of Electron Density Research Articles

Anti-Symmetric Electromagnetic Interactions' Response in Electron Circular Dichroism and Chiral Origin of Periodic, Complementary Twisted Angle in Twisted Bilayer Graphene.

Many novel physical properties of twisted bilayer graphene have been discovered and studied successively, but the physical mechanism of the chiral modulation of BLG by a twisted angle lacks theoretical research. In this work, the density functional theory, the wavefunction analysis of the excited state, and the quantum theory of atoms in molecules are used to calculate and analyze the anti-symmetric chiral characteristics of zigzag-edge twisted bilayer graphene quantum dots based on periodic complementary twisted angles. The analysis of the partial density of states shows that Moiré superlattices can effectively adjust the contribution of the atomic basis function of the fragment to the transition dipole moment. The topological analysis of electron density indicates that the Moiré superlattices structure can enhance the localization of the system, increasing the electron density of the Moiré central ring, reducing the electron surge capacity in general and inducing the reversed helical properties of the top and underlying graphene, which can be used as the origin of the chiral discrimination; it also reveals the mole in the superlattice chiral physical mechanism. On this basis, we will also study the nonlinear optical properties of twisted bilayer graphene based on a twisted angle.

On the influence of pnictogen bonding on acidity

The pnictogen-bonded systems with general formula – HA/PnX3 (where HA = HBr, HCl, H2O, NH3, CH3NH2, (CH3)2NH, Pn = P, As, Sb, Bi, X = H, F) were investigated with the aim of assessing the influence of the electron density flow upon the pnictogen bond formation on the acidity of resulting system. The results of calculations indicate that said influence is significant in most cases. The formation of HA/PnX3 pnictogen bonded acid may be assisted by creation of hydrogen bonds leading to a further increase in acidity. As measured by the bond degree parameter, pnictogen bonds formed by the studied systems were found to exhibit a covalence degree higher than that of hydrogen bonds. The relationship between the structure and acidity was elucidated with the use of the electron density topology analysis.

Enhancing first-principles simulations of complex solid-state ion conductors using topological analysis of procrystal electron density

Atomistic-level understanding of ion migration mechanisms holds the key to design high-performance solid-state ion conductors for a breadth of electrochemical devices. First-principles simulations play an important role in this quest. Yet, these methods are generally computationally-intensive, with limited access to complex, low-symmetry structures, such as interfaces. Here we show how topological analysis of the procrystal electron density can be applied to efficiently mitigate this issue. We discuss how this methodology goes beyond current state of the art capabilities and demonstrate this with two examples. In the first, we examine Li-ion transport across grain boundaries in Li3ClO electrolyte. Then, we compute diffusion coefficients as a function of charge carrier concentration in spinel LiTiS2 electrode material. These two case studies do not exhaust the opportunities and might constitute motivations for still more complex applied materials.

The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength.

In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me3PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.

The Complexation between Siloxane Species and Methylsiloxane: Electronic Structure, Thermodynamic, and Interaction Characteristics

AbstractThe interaction between organosiloxane materials and siloxane species has attracted extensive attention in the protection of cultural relics due to their bonding characteristics. In this context, detailed studies of the complexation between siloxane species and methylsiloxane were explored using various computational methods. The complex molecular structures and their electronic excitation characteristics were predicted. The strong covalent interactions of Si−O bond between siloxane and methylsiloxane are checked by topological analysis of electron density and obvious charge transfer. Thermodynamic results show that these types of complexes are considerable stability. The energy barrier of oxygen molecules to pass through the pores between methylsiloxane and silica close to 19 eV, indicating that this type of coating does not peel off easily. Moreover, IR and UV‐vis spectrum were predicted. The microscopic mechanism will give theoretical direction for theoretical guidance for practical applications of the coating in the protection of stone artifacts.

Missing Recipe in the Na‐B Bond in NaBH3–Cluster

AbstractThe multifaceted little Na−B bond in NaBH3‐cluster has been the subject of many recent studies. Many proposals have been put forward for the complete understanding of the chemical bonding in NaBH3‐cluster. However, none of the studies provided a complete picture. Herein, the missing recipe of the chemical bonding in NaBH3‐cluster has been identified which completes the description. Our calculations reveal that the chemical bonding in NaBH3‐cluster is more multifaceted than ever thought. Our finding suggests that the NaBH3‐cluster features a Na−B one electron bond which is assisted by three 3‐centre‐2‐electron Na‐B−H bond. Detailed topological analyses of electron density and electron localization function at the correlated level reveal such a bonding situation. This missing 3‐centre‐2‐electron Na‐B−H bond completes the description of chemical bonding in NaBH3‐cluster which is at‐per with the well established bonding scenario for electron deficient compounds. Similar bonding scenario is observed in KBH3−, CuBH3‐and AuBH3−clusters, further lending support to the complete picture of bonding.

Origin of the low formation energy of oxygen vacancies in CeO2

Oxygen vacancies play a crucial role in determining the catalytic properties of Ce-based catalysts, especially in oxidation reactions. The design of catalytic activity requires keen insight into oxygen vacancy formation mechanisms. In this work, we investigate the origin of oxygen vacancies in CeO2 from the perspective of electron density via high-energy synchrotron powder x-ray diffraction. Multipole refinement results indicate that there is no obvious hybridization between bonded Ce and O atoms in CeO2. Subsequent quantitative topological analysis of the experimental total electron density reveals the closed-shell interaction behavior of the Ce–O bond. The results of first-principles calculation indicate that the oxygen vacancy formation energy of CeO2 is the lowest among three commonly used redox catalysts. These findings indicate the relatively weak bond strength of the Ce–O bond, which induces a low oxygen vacancy formation energy for CeO2 and thus promotes CeO2 as a superior catalyst for oxidation reactions. This work provides a new direction for design of functional metal oxides with high oxygen vacancy concentrations.

Ab initio study of CsBiO[formula omitted] oxide-perovskite, dynamical stability and bonding analysis

The quest for a new stable oxide perovskite is a crucial challenge for use in many fields of applications. However, the Jahn-Teller effect in conjunction with symmetry-breaking distortion in some compounds acts as a key ingredient for several intriguing quantum phenomena causing instability in the ideal cubic structure. Using density functional theory (DFT) calculations, we find that the CsBiO3 compound is rather stable in a distorted tetragonal structure than in an ideal cubic one. To analyze this stability, we investigated deeply the thermodynamic and dynamical properties of the title compound. The results suggest that the octahedral distortion is due to the anti-symmetric breathing modes moving the BiO6 octahedra. Both electronic and topological analyses of electron density showed that these distortions found their origin in the sp lone pair bonds in the Bi units.

Rietveld Refinement and X-ray Absorption Study on the Bonding States of Lanthanum-Based Perovskite-Type Oxides La1−xCexCoO3

Metal-oxygen bonding of the Ce-doped LaCoO3 system remains largely unexplored despite extensive studies on its magnetic properties. Here, we investigate the structure and local structure of nanoscale La1−xCexCoO3, with x = 0, 0.2, and 0.4, using the Rietveld refinement and synchrotron X-ray absorption techniques, complemented by topological analysis of experimental electron density and electron energy distribution. The Rietveld refinement results show that LaCoO3 subject to Ce addition is best interpretable by a model of cubic symmetry in contrast to the pristine LaCoO3, conventionally described by either a monoclinic model or a rhombohedral model. Ce4+/Co2+ are more evidently compatible dopants than Ce3+ for insertion into the main lattice. X-ray absorption data evidence the partially filled La 5d-band of the pristine LaCoO3 in accordance with the presence of La–O bonds with the shared-type atomic interaction. With increasing x, the increased Ce spectroscopic valence and enhanced La–O ionic bonding are noticeable. Characterization of the local structures around Co species also provides evidence to support the findings of the Rietveld refinement analysis.

Influence of pseudo-polymorphism on the structure and thermal behavior of the new barium β-diketonate complexes [Ba(adtfa)2(18-crown-6)] and [Ba(adtfa)2(18-crown-6)](CDCl3)2

The new barium β-diketonate complexes with 18-crown-6 [Ba(adtfa)2(18-crown-6)] (1) and [Ba(adtfa)2(18-crown-6)](CDCl3)2 (2) (adtfa = 1,1,1-trifluoro-4-(1-adamantyl)-2,4-butanedionato, 18-crown-6 = 1,4,7,10,13,16-hexaoxacycloocta-decane) were synthesized and characterized by elemental analysis, IR-, 1H NMR-spectroscopy and X-ray diffraction analysis. The mutual arrangement of the β-diketonate ligands relative to the barium atoms in 1 and 2 was found to be different. The nature of chemical interactions and charges distribution in 1 and 2 was investigated using an experimental-theoretical approach based on crystal (asymmetric unit–cell aspherical scattering factor) and molecular (whole–molecule aspherical scattering factor) invarioms within the framework of Bader theory. It was shown that the less favorable conformation of complex 2 is stabilized in the crystal by the higher energy of intermolecular interactions as compared to 1. The energy of intermolecular interactions (94.3 kJ/mol) in 1 was estimated by electron density topological analysis and agrees well with the experimentally obtained sublimation enthalpy (83.2 ± 1.1 kJ/mol).

Investigation of polar crystalline materials containing hydrochlorothiazide: electron density distribution and optical properties

The polar hydrochlorothiazide polymorph (I) (systematic name: 6-chloro-1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide, C7H8ClN3O4S2) and, recently designed by us, the polar 2-aminopyridine hydrochlorothiazide water <1/1/1> (C7H8ClN3O4S2·C5H6N2·H2O), (II), have been investigated. The crystal structures of both materials were determined using the single-crystal X-ray diffraction technique. The intermolecular interactions in (I) and (II) were studied in detail via topological electron-density analysis. The obtained results showed hydrogen bonds with a character intermediate between closed-shell and shared-shell in both crystal structures. The most important hydrogen bonds in (I) are formed between sulfonamide groups, whereas in (II), water molecules play a crucial role as they interconnect 2-aminopyridine and hydrochlorothiazide molecules. Calculations of the optical properties revealed that both materials exhibit large linear birefringence, twice that of calcite. The theoretically predicted second harmonic generation efficiency is four times and five times larger than that of KH2PO4 for (I) and (II), respectively. The information gathered on intermolecular interactions and structure–property correlations was used to identify the best strategies for the future design of new functional materials of this kind.

Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion.

An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc+/2+–water bond as a noncovalent bond while Sc3+–OH2, Sc2+–OH, and Sc+–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.

Aqueous solvation study of melatonin using ab initio molecular dynamics

Melatonin is an essential human hormone produced mainly by the pineal gland from the amino acid tryptophan; it has several types of bioactivity, such as regulation of circadian rhythm, antioxidant, and DNA protection. Despite the importance of melatonin in the human body, studies on the interaction of melatonin with water molecules, considered explicitly, are quite limited in the literature. Thus, the present work reports a study on the effects of aqueous solvation on the geometric and electronic parameters of melatonin using Car-Parrinello Molecular Dynamics (CPMD). The CPMD results show that the aqueous solvation of melatonin affects mainly C14-O2 (2.176%), N17-C14 (2.169%), and N16-H21 (1.079%) bond lengths as well as O1-C3-C4 (4.37%) and O1-C3-C8 (4.241%) bond angles. These effects are attributed mainly to the H-bond formation between O1, O2, H21, and H30 melatonin sites and water molecules. The topological analysis of the H-bond electron density shows that the H-bond strength varies from weak to intermediate intensities, except for the O2 site – where it varies from weak to strong. The energetic aspect of the H-bonds was investigated using Helmholtz free energy, and the radial distribution function was employed to assess the mean residence time of the water atoms inside the first shell. The supramolecular arrangement of melatonin in the solid-state was investigated using the Hirshfeld surface technique. These findings deepen the knowledge of melatonin chemistry in the human body and help develop explanations for its biological activities.

Examining a Transition from Supramolecular Halogen Bonding to Covalent Bonds: Topological Analysis of Electron Densities and Energies in the Complexes of Bromosubstituted Electrophiles.

The transition from weak (noncovalent) interactions to fully developed covalent bonds is examined using the quantum theory of atoms in molecules in a series of halogen-bonded (XB) complexes of bromosubstituted electrophiles, RBr, with 1,4-diazabicyclo[2.2.2]octane (DABCO) and Cl– and Br– anions. The gradual decrease in the XB lengths in these associations, dBr···Y (where Y = Cl–, Br–, or N), was accompanied by the exponential increase in the binding energies and charge transfer, as well as electron densities and magnitudes of the kinetic and potential energy densities at the bond critical points (BCPs) on the Br···Y bond path. These indices, as well as characteristics of the adjacent bonds in the XB donor, followed remarkably close trend lines when plotted against the normalized XB length RBrY = dBr···Y/(rBr + rY) (where rBr and rY are the van der Waals radii) regardless of the methods [MP2/6-311+G(d,p) or M062X/6-311+G(d,p)], media (gas phase or dichloromethane), and nucleophiles (Cl–, Br–, or DABCO). In the systems with an RBrY higher than about 0.78, the energy densities H(r) at BCPs at the Br···Y bond path were small and positive, and XBs did not substantially affect the characteristics of the adjacent R–Br covalent bond in the XB donor. Accordingly, the XB can be identified as noncovalent in this range. In the complexes with RBrY values between about 0.67 and 0.78, energy densities H(r) at Br···Y BCPs were negative, and their magnitudes increased with the decrease in the Br···Y separation. In this range, formation of XBs was accompanied by the increase in the R–Br bond length in the XB donor and the decrease in the magnitude of the (negative) H(r) values at the BCPs of the R–Br bonds. XBs can be classified as partially covalent in this RBrY range. At an RBrY less than about 0.67, electron densities were larger, and energy densities were more negative at BCPs of the Br···Y bond than those at BCPs of the R–Br bond in the XB donor. This indicates that Br···Y bonds were stronger than R–Br bonds, and these (Br···Y) XBs can be regarded as essentially covalent. The synchronous change of a variety of (R–Br and Br···Y) bonding characteristics with RBrY suggests that the normalized XB bond length can be used as a basic parameter in the identification of the type of intermolecular interaction. A continuity of these characteristics suggests an inherent relationship between limiting (covalent and noncovalent) types of XBs and thus an onset of molecular–orbital interactions in the weaker bonds.

Influence of multiple and cooperative hydrogen bonding on the acidity of polyhydroxylated piperidines: electron density topological analysis

Hydrogen bonds are the presiding concepts for arranging the three-dimensional forms of biological molecules like proteins, carbohydrates, and nucleic acids, and act as guides for proton transfer reactions. Gas-phase acidity and pKa calculations in dimethyl sulfoxide on a line of polyhydroxylated piperidines specify that multiple hydrogen bonds lead to enhance acidities. The gas-phase acidity (GPA) of polyhydroxylated piperidines was investigated by MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. For each structure, varied primary and secondary hydroxyl groups were deprotonated. The natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have also been used to realize the character of the hydrogen bonding interactions in these compounds. The results show by adding each hydroxyl group, ΔHacid in the gas phase becomes less endothermic and pKa value in the solution phase will decrease. Therefore, intramolecular hydrogen bonds lead to enhance the acid strength. In both the gas and solution phases, the β-nojirimycin-OH2 (β-1-OH2) was found to be the most acidic compound with calculated GPA of 349.4 kcal·mol-1 and the pKa value of 22.0 (8.0 pKa units more acidic than 1-propanol). It was also shown, by applying the polarized continuum model (PCM), there is a superior linear correlation with the GPAs of polyhydroxylated piperidines and their calculated pKa (DMSO) values.

Substituted hydrocarbon: a CCSD(T) and local vibrational mode investigation

Substituent effects on the carbon–carbon bonds of hydrocarbons have been a topic of interest within the past seven decades as resultant information would enable one to tune the activity of CC bonds. However, current assessments of the C≡C, C=C, and C−C bond strength of acetylene, ethylene, and ethane as well as their derivatives rely on indirect measures such as bond length and bond dissociation enthalpy. In this work, we introduce a quantitative measure of the intrinsic strength of C≡C, C=C, and C−C bonds for a set of 40 hydrocarbon systems consisting of 3 parent structures, 36 hydrocarbon derivatives involving CF3, CH3, CHO, F, NH2, or OH groups, and a conjugated system, based on vibrational spectroscopy. Local mode force constants (CC) were computed at the CCSD(T)/cc-pVTZ level of theory for systems 1–32 and 34–40 and CCSD(T)/cc-pVDZ for 33. From (CC), we derived related bond strength orders BSO n(CC) in order to provide quantitative measures of intrinsic bond strength. Topological electron density and natural population analyses were carried out as to analyze the nature of these bonds and complement bond strength measures. For substituted hydrocarbon systems, we found the strengthening/weakening of the CC bonds occurs as the covalent nature of the bond increases/decreases by means of varying charge delocalizations. Our findings provide new guidelines for desirably modulating C≡C, C=C, and C−C bond strength and for the design of prospective pathways for bond cleavage reactions.

Tautomeric equilibrium, proton affinity and mass spectrometry fragmentation of flexible hydrogen-bonded precursors and rigid hbox {N}longrightarrow hbox {BF}_2 fluorescent dyes

The stability of two groups of conformationally locked molecules, similar in topology, but differing only by the type of the bridge rigidifying their structure, is studied. The series of the less-rigid 2-phenacylheterocyclic compounds and their stiff difluoroboranyl derivatives are investigated for the determination of the effect of hbox {NCH}_3/S/O replacement in a five-membered heterocyclic ring and the presence of a strong electron-donating group on the tautomeric equilibrium, protonation affinity, and fragmentation pattern observed in the structural elucidation by means of mass spectrometry technique. The results of the omega B97X-D/6-311++G(d,p) calculations, the topological analysis of electron density as well as the experimental MS measurements show the importance of the number of heteroatoms, their properties, and location in the molecule for the rational design of the systems of desired stable tautomers or the favorable protonation sites. The obtained data allow for the understanding of the fundamentals of the novel highly fluorescent difluoroborates fragmentation behavior, vital for their structural elucidation with the application of high-resolution tandem mass spectrometry methods.

Prediction of a stable helium-hydrogen compound: First-principles simulations

Despite extensive experimental and theoretical work, consensus on the crystal structure and stability of the helium-hydrogen system is lacking. In this study, we investigate the possibility of helium forming a stable compound with hydrogen by using a first-principles structure search method. As a result of first-principles simulations, we predict a helium-hydrogen compound that is mechanically stable below 8 GPa with a $\mathrm{He}{({\mathrm{H}}_{2})}_{3}$ stoichiometry. Topological analysis of electron density at the bond critical points shows that there exists a quantifiable level of van der Waals interaction between helium and hydrogen in this $\mathrm{He}{({\mathrm{H}}_{2})}_{3}$ crystal. Our current results provide a case of weak interaction in a mixed hydrogen-helium system, offering insights for the evolution of interiors of giant planets such as Jupiter and Saturn.

Assessing the Intrinsic Strengths of Ion–Solvent and Solvent–Solvent Interactions for Hydrated Mg2+ Clusters

Information resulting from a comprehensive investigation into the intrinsic strengths of hydrated divalent magnesium clusters is useful for elucidating the role of aqueous solvents on the Mg2+ ion, which can be related to those in bulk aqueous solution. However, the intrinsic Mg–O and intermolecular hydrogen bond interactions of hydrated magnesium ion clusters have yet to be quantitatively measured. In this work, we investigated a set of 17 hydrated divalent magnesium clusters by means of local vibrational mode force constants calculated at the ωB97X-D/6-311++G(d,p) level of theory, where the nature of the ion–solvent and solvent–solvent interactions were interpreted from topological electron density analysis and natural population analysis. We found the intrinsic strength of inner shell Mg–O interactions for [Mg(H2O)n]2+ (n = 1–6) clusters to relate to the electron density at the bond critical point in Mg–O bonds. From the application of a secondary hydration shell to [Mg(H2O)n]2+ (n = 5–6) clusters, stronger Mg–O interactions were observed to correspond to larger instances of charge transfer between the lp(O) orbitals of the inner hydration shell and the unfilled valence shell of Mg. As the charge transfer between water molecules of the first and second solvent shell increased, so did the strength of their intermolecular hydrogen bonds (HBs). Cumulative local vibrational mode force constants of explicitly solvated Mg2+, having an outer hydration shell, reveal a CN of 5, rather than a CN of 6, to yield slightly more stable configurations in some instances. However, the cumulative local mode stretching force constants of implicitly solvated Mg2+ show the six-coordinated cluster to be the most stable. These results show that such intrinsic bond strength measures for Mg–O and HBs offer an effective way for determining the coordination number of hydrated magnesium ion clusters.

Stabilization of group 14 elements E = C, Si, Ge by hetero-bileptic ligands cAAC, MCOn with push-pull mechanism.

The stability and bonding of a series of hetero-diatomic molecules with general formula (cAAC)EM(CO)n , where cAAC = cyclic alkyl(amino) carbene; E = group 14 elements (C, Si, and Ge); M = transition metal (Ni, Fe, and Cr) have been studied by quantum chemical calculations using density functional theory (DFT) and energy decomposition analysis-natural orbital chemical valence (EDA-NOCV). The equilibrium geometries were calculated at the BP86/def2-TZVPP level of theory. The tri-coordinated group 14 complex (1a, 4a, and 7a) in which one of the CO groups is migrated to the central group 14 element from adjacent metal is theoretically found to be more stable when the central atom (E) is carbon. On the other hand, the two-coordinate group 14 element containing metal-complexes (2, 5, 8, 3, 6, and 9) are found to be more stable with their corresponding heavier analogues. The electronic structures of all the molecules have been analyzed by molecular orbital, topological analysis of electron density and natural bond orbital (NBO) analysis at the M06/def2-TZVPP//BP86/def2-TZVPP level of theory. The nature of the cAACE and EM bonds has been studied by EDA-NOCV calculations at BP86-D3(BJ)/TZ2P level of theory. The EDA analysis suggests that the bonding of cAACC(CO) can be best represented by electron sharing σ and π interactions, whereas, C(CO)M(CO)n-1 by dative σ and π interactions. On the other hand, EDA-NOCV calculations suggests both dative σ and π interactions for cAACE and EM(CO)n bonds of the corresponding Si and Ge analogues having stronger σ- and relatively weaker π-bonds. The topological analysis of electron density supports the closed-shell interaction for the Si and Ge complexes and open-shell interaction for the carbon complexes. The calculated proton affinity and hydride affinity values corroborated well with the present bonding description. This class of complexes might act as efficient future catalysts for different organic transformations due to the presence of electron rich group 14 element and metal carbonyl.