Extending Hirshfeld‐I to bulk and periodic materials

In this work, a method is described to extend the iterative Hirshfeld‐I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudopotential‐based electron density distributions, and it is shown that high‐quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of grids containing (precalculated) electron densities makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems. The conceptual issue of obtaining reference densities for anions is discussed, and the delocalization problem for anionic reference densities originating from the use of a plane wave basis set is identified and handled. © 2012 Wiley Periodicals, Inc.     

Atomic charges,dipole moments,and Fukui functions using the Hirshfeld partitioning of the electron density

In the Hirshfeld partitioning of the electron density, the molecular electron density is decomposed in atomic contributions, proportional to the weight of the isolated atom density in the promolecule density, constructed by superimposing the isolated atom electron densities placed on the positions the atoms have in the molecule. A maximal conservation of the information of the isolated atoms in the atoms-in-molecules is thereby secured. Atomic charges, atomic dipole moments, and Fukui functions resulting from the Hirshfeld partitioning of the electron density are computed for a large series of molecules. In a representative set of organic and hypervalent molecules, they are compared with other commonly used population analysis methods. The expected bond polarities are recovered, but the charges are much smaller compared to other methods. Condensed Fukui functions for a large number of molecules, undergoing an electrophilic or a nucleophilic attack, are computed and compared with the HOMO and LUMO densities, integrated over the Hirshfeld atoms in molecules.     

Probing Rapidly‐Ionizing Super‐Atom Molecular Orbitals in C60: A Computational and Femtosecond Photoelectron Spectroscopy Study

Super‐atom molecular orbitals (SAMOs) are diffuse hydrogen‐like orbitals defined by the shallow potential at the centre of hollow molecules such as fullerenes. The SAMO excited states differ from the Rydberg states by the significant electronic density present inside the carbon cage. We provide a detailed computational study of SAMO and Rydberg states and an experimental characterization of SAMO excited electronic states for gas‐phase C₆₀ molecules by photoelectron spectroscopy. A large band of 500 excited states was computed using time‐dependent density functional theory. We show that due to their diffuse character, the photoionization widths of the SAMO and Rydberg states are orders of magnitude larger than those of the isoenergetic non‐SAMO excited states. Moreover, in the range of kinetic energies experimentally measured, only the SAMO states photoionize significantly on the timescale of the femtosecond laser experiments. Single photon ionization of the SAMO states dominates the photoelectron spectrum for relatively low laser intensities. The computed photoelectron spectra and photoelectron angular distributions are in good agreement with the experimental results.     

Reply to ‘comment on “extending Hirshfeld‐I to bulk and periodic materials”’

The issues raised in the comment by Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO $$_3$$ , and La $$_2$$ Ce $$_2$$ O $$_7$$ , using our previously presented method for calculating Hirshfeld‐I charges in solids (Vanpoucke et al., J. Comput. Chem. doi: 10.1002/jcc.23088). It is shown that the use of pseudovalence charges is sufficient to retrieve the full all‐electron Hirshfeld‐I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over 200 atoms, underlining the relatively low cost for large systems. A number of theoretical issues are formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on “expectations” for atomic charges. © 2012 Wiley Periodicals, Inc.     

TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems

We introduce Topo MS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared‐memory parallel approach, Topo MS provides scalable, numerically robust, and topologically consistent analysis. Topo MS can be used as a command‐line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of Topo MS and compares it with state‐of‐the‐art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero‐de‐la‐Roza et al., Comput. Phys. Commun. 2014, 185, 1007). Topo MS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine‐grid solution, robustness against lattice bias, and topological consistency. Topo MS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc.     

Performance of 3D‐space‐based atoms‐in‐molecules methods for electronic delocalization aromaticity indices

Several definitions of an atom in a molecule (AIM) in three‐dimensional (3D) space, including both fuzzy and disjoint domains, are used to calculate electron sharing indices (ESI) and related electronic aromaticity measures, namely, I_ring and multicenter indices (MCI), for a wide set of cyclic planar aromatic and nonaromatic molecules of different ring size. The results obtained using the recent iterative Hirshfeld scheme are compared with those derived from the classical Hirshfeld method and from Bader's quantum theory of atoms in molecules. For bonded atoms, all methods yield ESI values in very good agreement, especially for C–C interactions. In the case of nonbonded interactions, there are relevant deviations, particularly between fuzzy and QTAIM schemes. These discrepancies directly translate into significant differences in the values and the trends of the aromaticity indices. In particular, the chemically expected trends are more consistently found when using disjoint domains. Careful examination of the underlying effects reveals the different reasons why the aromaticity indices investigated give the expected results for binary divisions of 3D space. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Four‐center integrals for Gaussian and exponential functions

The shift operator technique is used for deriving, in a unified manner, the master formulas for the four‐center repulsion integrals involving Gaussian (GTO), Slater (STO), and Bessel (BTO) basis functions. Moreover, for the two classes of exponential‐type functions (ETO), i.e., STO and BTO, we give the expressions corresponding to both the Gauss and Fourier transforms. From the comparison of the master formulas of GTO and ETO, we conclude that ETO can perform more efficiently than GTO, and we remark the points where the effort must be focused to carry out this possibility. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 16–28, 2001     

复合物HNO···H2O2内N-H···O蓝移氢键的理论研究

A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complexHNO…H_2O_2 was conducted by employment of both standard and counterpoise-corrected methods to calculate thegeometric structures and vibrational frequencies at the MP2/6-31G(d),MP2/6-31 G(d,p),MP2/6-311 q G(d,p),B3LYP/6-31G(d),B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels.In the H-bond N-H…O,the calcu-lated blue shift of N-H stretching frequency is in the vicinity of 120 cm~(-1) and this is indeed the largest theoreticalestimate of a blue shift in the X-H…Y H-bond ever reported in the literature.From the natural bond orbital analy-sis,the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O,the hyperconjugation was inhibited due to the existence of significant elec-tron density redistribution effect,and the large blue shift of the N-H stretching frequency was prominently due tothe rehybridization of sp~n N-H hybrid orbital.     

Analysis of the Electronic Structure of Aqueous Urea and Its Derivatives: A Systematic Soft X‐Ray–TD‐DFT Approach

Soft X‐ray emission (XE), absorption (XA), and resonant inelastic scattering (RIXS) experiments have been conducted at the nitrogen K‐edge of urea and its derivatives in aqueous solution and were compared with density functional theory and time‐dependent density functional theory calculations. This comprehensive study provides detailed information on the occupied and unoccupied molecular orbitals of urea, thiourea, acetamide, dimethylurea, and biuret at valence levels. By identifying the electronic transitions that contribute to the experimental spectral features, the energy gap between the highest occupied and the lowest unoccupied molecular orbital of each molecule is determined. Moreover, a theoretical approach is introduced to simulate resonant inelastic X‐ray scattering spectra by adding an extra electron to the lowest unoccupied molecular orbital, thereby mimicking the real initial state of the core‐electron absorption before the subsequent relaxation process.     

Comment on “Extending Hirshfeld‐I to bulk and periodic materials”

In recent years, several methods have been developed that partition the electron density among atoms using spherically symmetric atomic weights. D. E. P. Vanpoucke, P. Bultinck, and I. Van Driessche (J. Comput. Chem. 2012, doi: 10.1002/jcc.23088) recently reported a periodic implementation of the Hirshfeld‐I method that uses a combination of Becke‐style and uniform integration grids and modified atomic reference densities to compute net atomic charges in periodic materials. Herein, this method is discussed in the context of earlier periodic implementations of the Hirshfeld‐I method, the Iterated Stockholder Atoms method, and the density derived electrostatic and chemical method.     

Trap mechanism based on frontier molecular orbitals of additives in polyethylene insulators: A theoretical study and molecular design strategy

In this work, the energy gaps (E_g) of highest occupied orbitals and lowest unoccupied orbitals, trap energies (E_t(e) and E_t(h)) and excited energies of polyethylene model compound, typical defect compound, acetophonene, and 33 designed additives are obtained using density functional method at B3LYP/6–311+G(d, p) level. The correlation between trapping‐electrons (holes) abilities of additives and molecular frontier orbitals is established, and a new understanding for trap mechanism based on chemical molecular orbital levels is given for the first time which could be used to filter qualitative additives as voltage stabilizers of polyethylene. The role of trap energies and the energy gaps on discussing space charge accumulation and electric breakdown is analyzed in detail. A molecular design strategy for potential additives of cross‐linked polyethylene insulated high‐voltage cable is shown based on conjugation effect, substituents character, and polycyclic aromatic compounds. © 2015 Wiley Periodicals, Inc.     

Metal Olefin Complexes: Revisiting the Dewar−Chatt−Duncanson Model and Deriving Reactivity Patterns from Carbon‐13 NMR Chemical Shift

Metal olefin complexes that are ubiquitous intermediates in catalysis are investigated by a detailed analysis of their ¹³C‐NMR chemical shift tensors. This analysis allows evidencing specific electronic features, namely the olefin‐to‐metal σ‐donation and the metal‐to‐olefin π‐backdonation as proposed in the Dewar?Chatt?Duncanson model. Apart from these interactions, the chemical shift tensor analysis reveals an additional ligand‐to‐metal π‐donation of the olefin σ(C=C) orbital in systems with suitably oriented vacant d‐orbitals. This interaction which is not accounted for in the Dewar?Chatt?Duncanson model explains the reactivity of this type of metal olefin complexes towards oxidative cyclization (olefin insertion) and protonolysis.     

Structural properties and the effect of 2,6‐diaminoanthraquinone on G‐tetrad,non‐G‐tetrads,and mixed tetrads—A density functional theory study

Telomerase inhibitor causes the attrition of telomere length and consequently leading to senescence which require a lag period for cancer cells to stop proliferating. Telomeric sequences form quadruplex structures stabilized by tetrads. The structural and electronic properties related with interaction of 2,6‐diaminoanthraquinone and tetrads are the key step to elucidate the anticancer activity. The present study has been focused on the stability of the isolated tetrads and the effect of interaction of 2,6‐diaminoanthraquinone with G‐tetrad, non‐G‐tetrads, and mixed tetrads using density functional theory method in both gas and aqueous phases. The solvent interaction with the molecular systems has increased the stability of the isolated tetrads and complexes. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The atoms in molecules theory and natural bond orbital analysis have been performed to study the nature of hydrogen bonds in the inhibitor interacting complexes. The linear correlation is shown between electron density [ρ(r)], and its Laplacian [(²ρ(r)] at the bond critical points. The strong binding nature of 2,6‐diaminoanthraquinone with studied tetrads reveals that this inhibitor is suitable to stabilize the above tetrads and inhibit the telomerase activity. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A Full Topological Analysis of Unstable and Metastable Bond Critical Points

Researchers are developing conceptually based models linking the structure and dynamics of molecular charge density to certain properties. Here we report on our efforts to identify features within the charge density that are indicative of instability and metastability. Towards this, we use our extensions to the quantum theory of atoms in molecules that capitalize on a molecule’s ridges to define a natural simplex over the charge density. The resulting simplicial complex can be represented at various levels by its 0‐, 1‐, and 2‐skeleton (dependent sets of points, lines, and surfaces). We show that the geometry of these n‐skeletons retains critical information regarding the structure and stability of molecular systems while greatly simplifying charge density analysis. As an example, we use our methods to uncover the fingerprints of instability and metastability in two much‐discussed systems, that is, the di‐benzene complex and the He and adamantane inclusion complex.