Quantum Chemical Topology Analysis Research Articles

Atomistically informed hierarchical modeling for revisiting the constituent structures from heredity and nano-micro mechanics of sheath-core carbon fiber.

To better understand the heterogeneous anisotropic nanocomposite features and provide reliable underlying constitutive parameters of carbon fiber for continuum-level simulations, hierarchical modeling approaches combining quantum chemistry, molecular dynamics, numerical and analytical micromechanics are employed for studying the structure-performance relationships of the precursor-inherited sheath-core carbon fiber layers. A robust debonding force field is derived from energy matching protocols, including bond dissociation enthalpy calculations and rigid-constraint potential energy surface scan. Logistic long range bond stretching curves with exponential parameters and shifted force vdW curves are designed to diminish energy perturbations. The pseudo-crystalline microstructure is proposed and validated using virtual wide angle X-ray diffraction patterns and bond-orientational order parameters. The distribution or alignment features of the nanocomposite microstructures are collected from quantum chemical topology analysis and normal vector extractions. Non-equilibrium tensile loading simulation predicts the decomposed strain energy contributions, principal-axis modulus, strength limit, localized stress, and fracture morphologies of the model. Finally, an atomistically-informed stiffness prediction model combining numerical homogenization and analytical self-consistent Eshelby-Mori-Tanaka-type effective mean field micromechanics theory is proposed, giving a successful estimation of the overall stiffness matrix of the sheath-core carbon fiber system. The hierarchical models in combination with the carbonization reaction template will help in providing efficient and feasible schemes for the synergistic process-performance control of distinct types of carbon fiber.

Interaction between organic molecules and a gold nanoparticle: a quantum chemical topological analysis

The ligands at the surface of a gold nanoparticle (GNP) have a significant influence on the optical and physical properties, that may render different functionalities to the GNP. Therefore, there is a need in understanding the nature of the interaction at atomic resolution in order to allow rational design of GNPs with desired physico-chemical properties. The interaction between Au $$_{79}$$ and a series of small organic molecules has been systematically studied at the quantum mechanical level : methane, methanol, formic acid, hydrogen sulfide, benzene, and ammonia. The reactivity of Au $$_{79}$$ has been first analyzed by performing the condensed Fukui analysis to emphasize that the surface of Au $$_{79}$$ is dominated by electrophilic sites, with higher reactivity at the corner and edge atoms. The net charge transfer flowing from the organic molecules toward Au $$_{79}$$ comes from the electrophilic behavior of the GNP. Furthermore, the shape of the frontier molecular orbitals of Au $$_{79}$$ and of the incoming organic molecules has been found to dictate the preferred orientation of the adsorption. Several quantum chemical topological analyses of the electron density have been performed to further classify the interactions to weak dispersive or van der Waals interactions in methane and stronger non-covalent interactions in ammonia, benzene, hydrogen sulfide, methanol, and formic acid. The analysis of the electron localization function (ELF), on the other hand, provides more insight about the charge transfer, as the population of the basins of the organic molecules has decreased after interacting with Au $$_{79}$$ .

Structure and Characterization of an Americium Bis(O,O'-diethyl)dithiophosphate Complex.

A facile synthesis of an americium complex with a sulfur-donor ligand has been developed, allowing characterization of americium bonding from multiple perspectives via several techniques. Reaction of 243Am with S2P(OEt)2- yields the tetrakis complex [Am(S2P(OEt)2)4]- that can be crystallized as the tetraphenylarsonium salt. Structures obtained from single crystal X-ray diffraction show bond length discrepancies from the neodymium analogue consistent with the soft-donor bond enhancement common to actinides. Solid state optical spectroscopy confirms interaction of the ligand with 5f orbitals. 31P nuclear magnetic reflects the minor paramagnetism of Am(III). Computational investigations through CASSCF calculations, ligand-field density functional theory, and quantum chemical topological analysis allow a quantification of covalency or orbital interaction effects via total energy density and nephelauxetic parameters, both of which indicate greater covalency in the americium species than in the neodymium analogue or the americium aquo complex.

Partitioning a Molecule into the Atomic Basins and the Resultant Atomic Charges from Quantum Chemical Topology Analysis of the Kohn-Sham Potential.

Quantum chemical topology (QCT) solidifies the chemical basic concepts demonstrating how a molecular system is intrinsically partitioned into its components and what the interaction lines between them are. Here, QCT analysis using a Kohn-Sham one-electron potential (KSpot) in KS equation as a scalar function is initiated and explored, showing KSpot and its resultant electron force lines have novel spatial features which reveal that an atom in a molecule is a spatial basin governed by its nucleus as a 3D-attractor that terminates all the electron force lines defined by the negative gradient of KSpot and that a chemical bond line is just a minimum path of KSpot for the electron motion. Particularly, the atomic charges from this KSpot QCT analysis are moderate and good, having much lower dependence on basis sets chosen for computation. This may provide a platform for the study of molecular structures and properties, intra- and intermolecular electrostatic interaction, energy decomposition, and construction of force field.

QCT analysis of molecules containing the first and second period elements based on the PAEM

Quantum chemical topology (QCT) is a branch of theoretical chemistry. We use QCT based on the potential acting on one electron in a molecule (PAEM) to systematically investigate polyatomic molecules containing the first and second period elements. The results and analyses for five series of molecules containing the first and second period elements are presented. The calculated topological characteristics of these molecules, namely, the partitions into atoms, the atomic charges and the absolute value of the PAEM at the bond critical point called Dpb, are compared with those obtained from the quantum theory of atoms in molecules (QTAIM). The values of the PAEMQCT atomic charge are moderate; they are smaller than those obtained from the QTAIM and larger than those obtained from the Hirshfeld method. In PAEMQCT, the Dpb can be utilized to measure the strength of the chemical bond, while in QTAIM method, the electron density at the bcp is related to the bond strength. There is a good linear correlation between the Dpb at the bcp in PAEMQCT and the electron density at the bcp in QTAIM, and their correlation coefficient R is 0.9165.

Li-decorated Pmmn8 phase of borophene for hydrogen storage. A van der Waals corrected density-functional theory study

We performed standard and van der Waals-corrected density functional theory calculations to investigate the hydrogen storage capacity of a phase of borophene with Pmmn symmetry and nonzero thickness. This borophene sheet (Pmmn8) has 8 atoms in its unit cell and is more stable than the planar α sheet and that the corrugated Pmmn2 sheet (2 atoms in the unit cell). Our results show that, in pristine form, the Pmmn8 sheet is not suited for hydrogen storage applications. However, decoration with Li atoms and strain increase the hydrogen storage ability of the sheet. We performed also a detailed quantum chemical topological analysis that shows that the BLi interaction in the hydrogenated Li-decorated Pmmn8 sheet is ionic. Our results for the adsorption of H2 on the Li-decorated Pmmn8 sheet are compared with those obtained for the adsorption of H2 on Ti-decorated zigzag graphene nanoribbons.

Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis.

In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.

From micro-to macroscopic: Understanding optical properties in zinc-blend-derived materials Cu2ZnYX4(X = S, Se, Te, Y = Si, Ge, Sn) by means of the quantum chemical topology analysis

Intensive calculations in the framework of the density functional theory (DFT) scheme have been carried out in order to predict accurately the dynamical stability and electronic properties of the zinc-blend-derived Cu2ZnYX4(X = S, Se, Te, Y = Si, Ge, Sn) compounds. Emphasis is also placed on the optical properties of the defect chalcopyrite compounds. Advantages of the analysis of the topology of the electron localization function (ELF) to provide microscopic point of view of the chemical bonding in solids are illustrated. A relationship between polarization of bonds and origin-independent atomic contributions to electric dipoles in the Cu2ZnYX4(X = S, Se, Te, Y = Si, Ge, Sn) defect chalcopyrite compounds is highlighted. In fact, what makes these compounds most interesting is a rich collection of S–Y long-distance bond paths. The ELF attractors do not systematically localize on the bond midpoint and their localization depends on electronegativity differences between the atoms forming the X–Y bond and on the nature of the chemical environment. Particularly, we show that the charge transfer remains generally the main contribution to the local bond dipole contribution. The compound which exhibits perturbed S lone pair is the more promising for nonlinear optical properties.

Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis

This study aims to identify the origin of the extra stability of alloxan, a biologically active pyrimidine. To achieve this goal, detailed DFT computations and quantum dynamics simulations have been performed to establish the most stable conformation and the global minimum structure on the alloxan potential energy surface. The effects of the solvent, basis set, and DFT method have been examined to validate the theoretical model adopted throughout the work. Two non-covalent intermolecular dimers of alloxan, the H-bonded and dipolar dimers, have been investigated at the ωB97X-D and M06-2X levels of theory using the triple zeta 6-311++G** to establish their relative stability. Quantum chemical topology features and natural bond orbital analysis (NBO) have been performed to identify and characterize the forces that govern the structures and underlie the extra stability of alloxan.

Chemical structure and reactivity by means of quantum chemical topology analysis

Chemical structure and bonding are key features and concepts in chemical systems which are used in deriving structure–property relationships, and hence in predicting physical and chemical properties of compounds. Even though the contemporary high standards in determination, using both theoretical methods and experimental techniques, questions of chemical bonds as well as their evolution along a reaction pathway are still highly controversial. This paper presents a working methodology to determine the structure and chemical reactivity based on the quantum chemical topology analysis. QTAIM and ELF frameworks, based on the topological analysis of the electron density and the electron localization function, respectively, have been used. We have selected two examples studied by the present approach, to show its potential: (i) QTAIM study on the α-Ag2WO4, for the simulation of Ag nucleation and formation on α-Ag2WO4 provoked in this crystal by the electron-beam irradiation. (ii) An ELF and Thom’s catastrophe theory study for the reaction pathway associated with the decomposition of stable planar hypercoordinate carbon species, CN3Mg3+.

Unraveling reaction mechanisms by means of Quantum Chemical Topology Analysis

A chemical reaction can be understood in terms of geometrical changes of the molecular structures and reordering of the electronic densities involved in the process; therefore, identifying structural and electronic density changes taking place along the reaction coordinate renders valuable information on reaction mechanism. Understanding the atomic rearrangements that occur during chemical reactions is of great importance, and this perspective aims to highlight the major developments in quantum chemical topology analysis, based on the combination of electron localization function and catastrophe theory as useful tools in elucidating the bonding and reactivity patterns of molecules. It reveals all the expected, but still ambiguous, elements of electronic structure extensively used by chemists. The chemical bonds determine chemical reactivity, and this technique offers the possibility of their visualization, allowing chemists to understand how atoms bond, how and where bonds are broken/formed along a given reaction pathway at a most fundamental level, and so, better following and understanding the changes in the bond pattern. Their results clearly herald a new era, in which the atomic imaging of chemical bonds will constitute a new method for examining chemical structures and reaction mechanisms. The important feature of this procedure is that in practice the scope of its values is system‐independent. In addition, from a practical point of view, it is cheap to calculate and implement because wave functions are the required input, which are easily available from standard calculations. To capture these results two reaction mechanisms: isomerization of C(BH)2carbene and the thermal cycloheptatriene‐norcaradiene isomerizations have been selected, indicating both the generality and utility of this type of analysis. © 2014 Wiley Periodicals, Inc.

A quantum chemical topological analysis of the C-C bond formation in organic reactions involving cationic species.

ELF topological analysis of the ionic Diels-Alder (I-DA) reaction between the N,N-dimethyliminium cation and cyclopentadiene (Cp) has been performed in order to characterise the C-C single bond formation. The C-C bond formation begins in the short range of 2.00-1.96 Åvia a C-to-C pseudoradical coupling between the most electrophilic center of the iminium cation and one of the two most nucleophilic centers of Cp. The electron density of the pseudoradical center generated at the most electrophilic carbon of the iminium cation comes mainly from the global charge transfer which takes place along the reaction. Analysis of the global reactivity indices indicates that the very high electrophilic character of the iminium cation is responsible for the negative activation energy found in the gas phase. On the other hand, the analysis of the radical P(k)(o) Parr functions of the iminium cation, and the nucleophilic P(k)(-) Parr functions of Cp makes the characterisation of the most favourable two-center interaction along the formation of the C-C single bond possible.

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron-oxo porphyrin π-cation radical complex Por(·+) Fe(IV)=O (S-H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon-carbon bonds in porphyrin moiety. The double C=C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V(i=1,2)(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)(i=1-20) after complexation with the Fe cation. The iron-nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)(i=1-4), where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron-oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe(δ+)···O(δ-), as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge-shift bond. The Fe-S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (-0.43e to 0.50e) and S-H bond (-0.55e to 0.52e).

How a Quantum Chemical Topology Analysis Enables Prediction of Electron Density Transfers in Chemical Reactions. The Degenerated Cope Rearrangement of Semibullvalene.

Recent works on the reaction mechanism for the degenerated Cope rearrangement (DCR) of semibullvalene (SBV) in the ground state prompted us to investigate this complex rearrangement in order to assign experimentally observed contrast features in the simulated electron distribution. We present a joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) as a powerful tool to analyze the electron density transfers along the DCR. The progress of the reaction is monitored by the structural stability domains of the topology of ELF, while the change between them is controlled by turning points derived from CT. The ELF topological analysis shows that the DCR of SBV corresponds to asynchronous electron density rearrangement taking place in three consecutive stages. We show how the pictures anticipated by drawing Lewis structures of the rearrangement correlate with the experimental data and time-dependent quantum description of the process.

The Asymptotic Behavior of the Dipole and Quadrupole Moment of a Single Water Molecule from Gas Phase to Large Clusters: A QCT Analysis

Water undergoes important electrostatic changes within clusters and the liquid phase, in particular the enhancement of the dipole moment of a central water molecule. We systematically investigate the effect that increasing cluster size (up to 21‐mer) has on the dipole and quadrupole moments of a water molecule located at the centre of a cluster. Using hundreds of clusters, sampled from a Molecular Dynamics simulation, molecular multipole moments are reconstructed from the atomic multipole moments. These atomic multipole moments are obtained by Quantum Chemical Topology (QCT) from the ab initio electron densities of water clusters, calculated at three levels of theory, viz. B3LYP/6‐311+G(2d,p), B3LYP/aug‐cc‐pVTZ and MP2/6‐311+G(2d,p). There is a substantial increase in the average dipole moment with increasing cluster size, with asymptotic behavior emerging.

Comparative Static and Dynamic Study of a Prototype SN2 Reaction.

Ab initio molecular-dynamic simulations, using density functional theory (DFT) and the recent atom-centered density-matrix propagation method (ADMP), were used to study the bond formation process in a prototypical SN2 reaction, namely the Walden inversion. Using the real space partition schemes of both electronic density and electron localization function gradient fields, we analyzed different quantum chemical topology (QCT) properties along the ADMP trajectory. In particular, atomic charges derived from the Bader's atoms-in-molecules (AIM) theory were used to analyze intra- and intermolecular charge transfers between atoms, while the electronic population of the forming bonding basin obtained from the electron localization function (ELF) gradient field was employed to describe the bond formation process. These results were compared to the corresponding QCT properties issuing from a static approach based on the intrinsic reaction path (IRP). Although similar features are found for both static and dynamic approaches, the dynamic QCT analysis provides some explanation of the differences observed during the formation of the ion-molecule complex. In particular, it suggests a stronger electron exchange leading to an effective maximization of both covalent and noncovalent interactions.

High-rank quantum topological electrostatic potential: Molecular dynamics simulation of liquid hydrogen fluoride

Five bulk properties of liquid hydrogen fluoride were obtained by a molecular dynamics simulation at five temperatures between 203 and 273 K. The rigid-body interaction potential was designed with emphasis on the electrostatic contribution. The potential was expanded in spherical tensor multipole moments, and its corresponding Ewald summations, containing all possible interaction up to L=5 (i.e., monopole–hexadecapole, dipole–octopole, quadrupole–quadrupole). The moments were generated by a quantum chemical topological analysis of the electron density of the geometry-optimized monomer at the MP2/aug-cc-pVTZ level. Only two parameters in the Lennard-Jones part of the potential were adjusted to the experimental density and radial distribution functions. Agreement with experiment is excellent for the total energy and the density, and reasonable (with even overall performance) for the diffusion coefficient, the isobaric heat capacity and the thermal expansion coefficient. Chains of hydrogen-bonded HF monomers up to 10 molecules are quite common in the liquid and they more or less retain the relative orientation of the HF monomers in the gas-phase dimer.