Topological Analysis Of Electron Density Research Articles

Local vibrational mode analysis of ion-solvent and solvent-solvent interactions for hydrated Ca2+ clusters.

Hydrated calcium ion clusters have received considerable attention due to their essential role in biological processes such as bone development, hormone regulation, blood coagulation, and neuronal signaling. To better understand the biological role of the cation, the interactions between the Ca2+ ions and water molecules have been frequently investigated. However, a quantitative measure for the intrinsic Ca-O (ion-solvent) and intermolecular hydrogen bond (solvent-solvent) interactions has been missing so far. Here, we report a topological electron density analysis and a natural population analysis to analyze the nature of these interactions for a set of 14 hydrated calcium clusters via local mode stretching force constants obtained at the ωB97X-D/6-311++G(d,p) level of theory. The results revealed that the strength of inner Ca-O interactions for Ca(H2O)n 2+ (n = 1-8) clusters correlates with the electron density. The application of a second hydration shell to Ca(H2O)n 2+ (n = 6-8) clusters resulted in stronger Ca-O interactions where a larger electron charge transfer between lp(O) of the first hydration shell and the lower valence of Ca prevailed. The strength of the intermolecular hydrogen bonds, formed between the first and second hydration shells, became stronger when the charge transfers between hydrogen bond (HB) donors and HB acceptors were enhanced. From the local mode stretching force constants of implicitly and explicitly solvated Ca2+, we found the six-coordinated cluster to possess the strongest stabilizations, and these results prove that the intrinsic bond strength measures for Ca-O and hydrogen bond interactions form new effective tools to predict the coordination number for the hydrated calcium ion clusters.

Argentophillic interactions in argentum chalcogenides: First principles calculations and topological analysis of electron density.

The plasticity of Ag2 S and Ag2 Se crystals important for applications is associated mainly with AgAg metallophilic bonds, which are related to van der Waals interactions and therefore are not directed. This is demonstrated by the first principles DFT M06 LCAO calculations of Ag2 X (X = S, Se) crystals (periodic model) and hypothetical molecules Xn Ag2n (X = S, Se; n = 1, 2, 4) in gas phase (molecular model). A topological analysis of the calculated electron density, was performed both for periodic and molecular models of Ag2 X (X = S, Se). It was found that Ag-Ag interatomic distances are close in periodic and molecular models. The numerical values of electron density, its Laplacian, kinetic, and potential energy densities are also close in both models and confirm the existence of AgAg metallophilic bonds.

Metal–Metal and Metal–Ligand Bonding in Trinuclear Vinylidene Rhenium-Iron-Platinum Complex Studied by Topological Analysis of Electron Density

Metal–metal and metal–ligand bonding in vinylidene ReFePt complex was studied by density functional method and topological analysis of electron density. Topological analysis did not found direct bonding between the metal atoms pointing to indirect metal–metal interaction mediated via the bridging vinylidene ligand. At the same time, the delocalization index δ(Fe,Pt) reveals the strong Fe–Pt interaction that allows for supposing a chemical bonding between these atoms

Hirshfeld surface, charge density and site selectivity studies of 1-(2-Methyl-5-nitro-1H-imidazol-1-yl)-acetone

Extensive quantum chemical calculations were carried out for the molecule with B3LYP/6311G++(d,p) level of theory. The molecular packing of the crystal is stabilized by CH…N and CH…O interactions and those interactions were investigated through Hirshfeld surface analysis. Aspherical distribution of charges was estimated using Hansen-Coppens multipole formalism and the effect of temperature on charge density was analyzed. Bader’s AIM theory was used to perform the topological analysis of electron density which disclose the strength and nature of atom-atom interaction. Stability of the molecule arising from hyper conjugative interactions and charge delocalization was examined using Natural Bond Orbital analysis and it also confirms the existence of CH…N and CH…O hydrogen bonds. Frontier Molecular Orbital analysis was carried out and the molecule is found to be a good electrophile with the electrophilicity index of 9.7349 eV. Molecular Electrostatic Potential was used to identify the possible reactive locations of the molecule.

Mechanistic insights into the reaction Cp2Nb(CO)H (Cp = η5-C5H5) with acetylenedicarboxylic acid (ADCA): DFT studies

The insertions of unsaturated molecules into metal-hydride bonds are very common steps in industrial catalytic reactions such as olefinic isomerization, hydrogenation and hydroformylation. In this paper, the reaction mechanism of Cp2Nb(CO)H (Cp = η5-C5H5) with acetylenedicarboxylic (ADCA) has been investigated based on density functional theory calculations. Kinetic calculation and topological analyses of electron density have been conducted. The calculated results show that the reaction can proceed easily even at very low temperature. (Z)-pro Cp2Nb(CO)(η1-(Z)–HOOCC = CHCOOH) and the isomer (E)-pro can be got via two parallel steps. The yield rate of (E)-pro is larger than that of (Z)-pro because of its lower energy barrier. In addition, the carboxylato-containing niobocene compound Cp2Nb(CO)(k1-OOCC(H)= CHCOOH) can also be got as the most stable product through a proton transfer process. Along the reaction pathway, there is a η2-(C, C)-Nb agostic structure. The results provide useful informations and theoretical predictions on much more insertion reactions.

Synthesis, crystal structure and electron density analysis of a sulfanyl 2-pyridone analogue: Tautomeric preference and conformation locking by S···O chalcogen bonding

The effect of intra-molecular chalcogen bonding involving S(sp3)···O(sp2) interaction in locking the molecular conformation has been investigated in 2-hydroxy-5-(4-methoxybenzoyl)-6-(methylsulfanyl)nicotinonitrile. The compound has been synthesized in a one-pot synthetic method and structurally characterized by NMR, FT-IR spectroscopic techniques and single crystal X-ray diffraction. The strength and n→σ∗ nature of the S···O interaction have been revealed by electron density topological analysis and second order perturbation energy estimation of orbital interaction. Among the two possible tautomers, the molecule prefers the relatively less stable one in the solid-state. A rare but robust hydroxyl-nitrile supramolecular synthon identified in the structure helps to understand this tautomeric preference.

The nature of multiple boron-nitrogen bonds studied using electron localization function (ELF), electron density (AIM), and natural bond orbital (NBO) methods

Local nature of the boron-nitrogen (BN) bonding with different formal multiplicities (B≡N, B=N, B-N) have been investigated for 25 experimentally established organoboron molecules in both real and the Hilbert space, using topological analysis of electron localization function (ELF), electron density (AIM), and natural bond orbital (NBO) method. Each BN bond has been represented (ELF) by the bonding disynaptic attractor V(B,N), with the basin electron population between 5.72e and 1.83e, confirming possible existence of all the three bond types. A covalent character of bonding can be associated with the dative mechanism due to the V(B,N) bonding basin formed mainly (91–96%) by the N electron density. Similarly, the NBO method shows 2-center natural orbitals, consisting largely of the hybrids from the N atom. The AIM analysis yields the features typical for shared (H(3,−1)(r) < 0) and closed-shell (∇2ρ(3,−1)(r) > 0) interactions. The delocalization indices, describing electron exchanges between B and N quantum atoms, are smaller than 1.5, even for formally very short triple B≡N bonds.Graphical abstract.

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.

New insight into the structure-property relationships from chemical bonding analysis: Application to thermoelectric materials

Structure-property relationships are indisputably important to deeply understand the nature of materials. The main direction pursued to investigate these relations is based on the chemical bonding concept. The integral and local properties of chemical bonding determined from the topological analysis of electron density by combining the quantum theory of atoms in molecules (AIM) and DFT calculations can aid to build a bridge between the atomic structure and the intrinsic properties of materials. In this paper, the electronic and thermal transport properties of thermoelectric materials in the Cu–Sb–Se system have been analysed by coupling energy densities relationships and corresponding electron density Laplacian distribution for specific interactions. The asset of this method is to directly highlight the influence of lone pair electrons and atomic fluctuations on interatomic interactions as well as the coupling effect of weak bonds, which offers a new approach to design and search for materials with low thermal conductivity at low calculation cost.

Theoretical study on the intermolecular interactions between energetic oxidizer and pyrazine - 1, 4 - dioxide

Based on density functional theory (DFT), the intermolecular interaction between two kinds of energetic oxidizer (ammonium perchlorate (AP) and ammonium dinitramide (ADN)) and pyrazine - 1, 4 - dioxide (PDO) was studied. Under the calculation level of B3LYP // 6-311++G**, three AP-PDO complexes and six ADN-PDO complexes were optimized to obtain their stable structures. Electron density topological analysis and reduced density gradient analysis were used to analyze the types of intermolecular interaction. The change of electrostatic potential (ESP) before and after the formation of the composite was compared, and the oxygen balance of the composite was analyzed at different molar ratios. The results show that both AP-PDO and ADN-PDO have hydrogen bonds and van der Waals interactions between the two compounds, and there was hope for the synthesis of cocrystallization. After the formation of the complex, the Vs, max of electrostatic potential was decreased compared with the simple substance. According to the oxygen balance performance, the optimal molar ratios of AP-PDO and ADN-PDO for cocrystal formation were 3:2 and 2:1, and the oxygen balance were −1.4 % and 0, respectively. The results are helpful for the application of cocrystallization technique in the field of ionic salt containing energy.

Topological analysis of electron density in half-Heusler ZrXBi (X = Co, Rh) compounds: A density functional theory study accompanied by Bader’s quantum theory of atoms in molecules

Here, we study the electron charge densities (ECDs) of two half-Heusler compounds, i.e. ZrCoBi and ZrRhBi, from topological point of view using the combination of DFT and quantum theory of atoms in molecules (DFT + QTAIM). We also investigate the structural properties and electronic structures of these compounds including DOSs, band structures and electron charge densities (ECDs) as well as the thermoelectric parameters including Seebeck coefficient and electrical conductivity. Furthermore, the effects of pressure on the properties of these compounds are investigated. The DFT + QTAIM calculations show that the compounds under study have similar numbers and types of critical points, but different bonds properties. The bonds of the Rh-case are more stable than those of the Co-case. Moreover, the ECD values at bonds of Rh-case are more than the Co-case. Imposing pressure affects some properties of the bonds in both cases, but does not change the numbers and types of their critical points. Based on our electronic structure calculations, Co-case has sharper valence DOSs near the Fermi level and larger band gap compared to the Rh-case. We have also observed flatter bands in the Co-case near the Fermi level compared to the Rh-case. In the anticipation of further study, the presented results may provide fundamental information which can pave the way for the study on the thermoelectric efficiencies of these interesting thermoelectric materials. In agreement with the electronic structure, our thermoelectric calculations show higher Seebeck coefficient and lower electrical conductivity for ZrCoBi than ZrRhBi.

The performance of the single-walled carbon nanotube covalently modified with polyethylene glycol to delivery of Gemcitabine anticancer drug in the aqueous environment

A computational investigation of Gemcitabine drug adsorption on the single-walled carbon nanotube covalently modified with polyethylene glycol in a series of the configurations is studied using density functional theory calculations. It is observed that O…H hydrogen bonds are the dominating intermolecular interactions during the complex formation between anti-cancer drug and the nanotube. The studied hydrogen-bonded complexes are treated theoretically to elucidate the nature of the intermolecular hydrogen bonds, geometrical structures, the binding energy and electron density topological analysis. The existence of the bond critical points between hydrogen and the electronegative atoms and their concomitant bond paths which connect the bond critical points to the two interacting atoms confirm by Quantum Theory of Atoms in Molecules method. In addition, considering the charge transfer for all of the adsorbed configurations reveals the capability of the drug molecule to accept precisely the electron from the functionalized carbon nanotube during the drug adsorption on external surface of the carbon nanotube. Also, the effect of weight percent of polyethylene glycol on the drug adsorption strength is investigated by molecular dynamics simulations. Communicated by Ramaswamy H. Sarma

Characterizing local metallic bonding variation induced by external perturbation.

The subtle variation of metallic bonding, induced by external influence, plays an essential role in determining physical, mechanical, and chemical properties of metals. However, it is extremely difficult to describe this variation because of the delocalization nature of metallic bonding. Here, we utilize the reduced density gradient and topological analysis of electron density to capture the local metallic bonding variations (LMBV) caused by lattice distortion and carrier injection in many face-centered cubic (fcc) metals. We find that the LMBV determines the traits of fcc metals such as strength, malleability, and ductility. Moreover, the fcc metals can become more flexible/stronger with the electron/hole injection, providing an important guidance to tune metals for desired mechanical properties.

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

Topological Analysis of Electron Density in Large Biomolecular Systems.

A great step toward describing the structure of the molecular electron was made in the era of quantum chemical methods. Methods play a very important role in the prediction of molecular properties and in the description of the reactivity of compounds, which cannot be overestimated. There are many works, books, and articles on quantum methods, their applications, and comparisons. At the same time, quantum methods of a high level of theory, which give the most accurate results, are time-consuming, which makes them almost impossible to describe large complex molecular systems, such as macromolecules, enzymes, supramolecular compounds, crystal fragments, and so on. To propose an approach that allows real-time estimation of electron density in large systems, such as macromolecules, nanosystems, proteins. AlteQ approach was applied to the tolopogical analysis of electron density for "substrate - cytochrome" complexes. The approach is based on the use of Slater's type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of "CYP3A4 - substrate" complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular "CYP3A4 - substrate" space was performed. Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. Relationship of pKM (KM is Michaelis constant) with the maximal value of the second Laplacian eigen value of electron density at the critical points and energy of complex formation computed using MM3 force field was determined. It was shown that significant number of (3,-1) bond critical points are located in the intermolecular space between the enzyme site and groups of substrate atoms eliminating during metabolism processes.

CarNit4 – A new polymeric energetic material based on poly(1,5-tetrazolediyl)

In this paper, a theoretical design and characterization of a novel nitrogen-rich polymeric material (CarNit4) based on 1,5-tetrazolediyl unit was performed using density functional theory. The theoretical analysis includes crystal structure prediction, estimation of dynamical and mechanical stability of the monoclinic (space group P21) crystal, topological analysis of electron density, band structure and spectral (IR, Raman, UV, NMR) characterization as well as detonation and propulsive properties calculation. The modeling of both the crystalline and amorphous phases reveals high enthalpies of formation and densities. Detonation and propulsive properties of CarNit4 as a single explosive are close to that of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). However, mixing of CarNit4 with oxidants (gaseous O2) improves sharply the propulsive properties which become much higher than that of RDX. The same effect on detonation velocity and pressure is expected for formulations of CarNit4 with various positive oxygen balance explosives. Decomposition of CarNit4 in the presence of O2 demonstrates the highest propulsive parameters under oxidation to carbon monoxide rather than carbon dioxide.

Comparative Analysis of Hydrogen, van der Waals, and Halogen Bonds in Ammonia Complexes with HCl and ClF Molecules

Quantum chemical calculations of molecular complexes formed by ammonia and methanide (electron pair donor) with HCl and ClF molecules (acceptor) at different mutual orientations are performed by the MP2 method of second-order Moller–Plesset perturbation theory using Dunning’s correlation-consistent aug-cc-pVTZ basis set, augmented by diffuse functions. An elongation in the covalent bond of the acceptor and a red shift in the corresponding IR band are observed for all complexes. NBO analysis and topological analysis of electron density are performed and maps of electron density shift upon complexation are plotted. The structure of the transition state for interconversion of NH3···HCl and NH3···ClH complexes corresponding to minima on the potential energy surface is calculated. The transition between configurations is accompanied by evolution of the intermolecular bond path with the N···H contact critical point being replaced by the critical point for the N···Cl contact. Calculated data supplemented by a comparative analysis of potential interaction curves indicate a similar nature of intermolecular binding in the H3N and HCl complexes with different orientations of monomers.

Charge densities in actinide compounds: strategies for data reduction and model building.

The data quality requirements for charge density studies on actinide compounds are extreme. Important steps in data collection and reduction required to obtain such data are summarized and evaluated. The steps involved in building an augmented Hansen-Coppens multipole model for an actinide pseudo-atom are provided. The number and choice of radial functions, in particular the definition of the core, valence and pseudo-valence terms are discussed. The conclusions in this paper are based on a re-examination and improvement of a previously reported study on [PPh4][UF6]. Topological analysis of the total electron density shows remarkable agreement between experiment and theory; however, there are significant differences in the Laplacian distribution close to the uranium atoms which may be due to the effective core potential employed for the theoretical calculations.

Organometallic complexes of carbon nanotori.

New organometallic complexes of carbon nanotori were designed and theoretically described by means of density functional theory. After a systematic structural search, it was found that energetically favorable complexes were formed by the metal atoms Cr and Ni, both located at the center of a nanotorus with diameter around 5Å and 120 carbon atoms. The nature of the metal-nanotorus interaction shows a partial polar-covalent character, different from those found in other well-known organometallic compounds. Interactions were studied through molecular orbitals and thermodynamic stability. Ten bonds are set up between the metal atom and nanotorus, confirmed by electron density topology analysis, showing ten bond critical points among the metal atoms and the surrounding carbon atoms. The response of the induced electron current caused by a magnetic field perpendicular to the nanotorus was analyzed to explain the electron delocalization and aromaticity of the complexes. Only in the case of the chromium complex, the electron density is fully delocalized on the whole complex. According to a geometry-based index of aromaticity, interaction with the metal atom only changes the aromatic character of the carbon rings slightly. Also, induced currents were used to elucidate the presence of a ferrotoroidal behavior. The isolated nanotorus and its compound with a single Ni atom have well-defined ferrotoroidal behavior because they present broken symmetries and could help to design a topological insulator. Meanwhile, the nanotorus with a Cr atom at the center lacks ferrotoroidal behavior as a consequence of the absence of magnetic vortices. Graphical abstract Organometallic complex of carbon nanotoruswith chromium and induced currents on it by applying an external magnetic field.

Probing the structures, electronic and bonding properties of multidecker lanthanides: Neutral and anionic Lnn(COT)m (Ln = Ce, Nd, Eu, Ho and Yb; n, m = 1, 2) complexes

The ground state structures of neutral and anionic Lnn(COT)m (Ln = Ce, Nd, Eu, Ho and Yb; n, m = 1, 2) complexes have been identified by density functional theory. Ln(COT)1,20/- and Ln2(COT)20/- complexes are found to possess sandwich ground state structures in which Ln atoms and COT molecules are alternately stacked except for Nd2COT20/-. Our calculated AEA and VDE values show good agreement with the available experimental values, which validates that our obtained ground state structures are credible. Based on the frontier molecular orbitals, we find that the bond formation between the 4f electrons of Ln atoms and the π clouds of COT molecules is weak. Then, the bond strength within these complexes is further analyzed based on the topological analysis of electron density at bond critical point. By analyzing Hirshfeld charge, we find Lnn(COT)m0/- are charge-transfer complexes with weak bonding feature.