我们先前介绍的QTPIE（电荷转移与极化电流平衡）模型（J.Chen和T. J. Martinez，Chem.Phys.Lett. 438，315（2007））是具有正确渐近行为的波动电荷模型。与大多数其他波动电荷模型不同，QTPIE是根据电荷转移变量和成对电负性而不是原子电荷变量和电负性来制定的。QTPIE中电负性的成对特征避免了键断裂时的假电荷转移。然而，增加的变量数量导致相当大的计算费用和秩亏的工作方程组，这是数值上的不便。在这里，我们表明，QTPIE可以完全重新制定的原子电荷变量，从而大大降低了计算复杂性。原子和键变量之间的转换通常适用于任意波动电荷模型，并揭示了一个潜在的拓扑框架，可用于理解波动电荷模型和经典电路理论之间的关系。
英文摘要：
Our previously introduced QTPIE (charge transfer with polarization current equilibration) model (J. Chen and T. J. Martinez, Chem. Phys. Lett. 438, 315 (2007)) is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE avoids spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models, and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits.
A bismuth bond, a type of pnictogen bonding interaction, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region of a covalently or coordinately bonded bismuth atom and the nucleophilic region in another, or the same, molecular entity. In this review, we report on the signatory details of bismuth bonding in several crystalline systems, along with other non-covalent interactions such as hydrogen and halogen bonds, which are important driving forces in the rational design of various types of materials. Illustrative crystal structures wer…
We present an intuitive and general analytical approximation estimating the energy of covalent single and double bonds between participating atoms in terms of their respective nuclear charges with just three parameters, $[{E_\text{AB} \approx a - b Z_\text{A} Z_\text{B} + c (Z_\text{A}^{7/3} + Z_\text{B}^{7/3})}]$. The functional form of our expression models an alchemical atomic energy decomposition between participating atoms A and B. After calibration, reasonably accurate bond energy estimates are obtained for hydrogen-saturated diatomics composed of $p$-block elements coming from the same …
Charge transfer among individual atoms in a molecule is the key concept in the modern electronic theory of chemical bonding. In this work, we defined an atomic region between two atoms by Slater orbital exponents of valence electrons and suggested a method for analytical calculation of charge penetration between all atoms in a molecule. Computation of charge penetration amount is self-consistently performed until each orbital exponent converges to its certain values respectively. Charge penetration matrix was calculated for ethylene and MgO, and bonding charge and its distribution were analyze…
Fluctuating-charge models are computationally efficient methods of treating polarization and charge-transfer phenomena in molecular mechanics and classical molecular dynamics simulations. They are also theoretically appealing as they are minimally parameterized, with parameters corresponding to the chemically important concepts of electronegativities and chemical hardness. However, they are known to overestimate charge transfer for widely separated atoms, leading to qualitative errors in the predicted charge distribution and exaggerated electrostatic properties. We present the charge transfer …
By leveraging the fundamental doctrine of The Quantum Theory of Atoms in Molecules---the partitioning of the electron charge density ($ρ$) into regions bounded by surfaces of zero flux---we map the gradient field of $ρ$ onto a 2D space called the gradient bundle condensed charge density ($\cal{P}$). The topology of $\cal{P}$ appears to correlate with regions of chemical significance in $ρ$. The bond wedge is defined as the image in $ρ$ of the basin of attraction in $\cal{P}$, analogous to the Bader atom, which is the basin of attraction in $ρ$. A bond bundle is defined as the union of bond wed…
In a recent paper [J. Organomet. Chem. (2013) doi: 10.1016 /j.jorganchem. 2013.03.047] analyzing the bonding mode of Trimethylenemethane (TMM) with some metal carbonyls, Mousavi and Frenking have declared the absence of bond paths, the so-called missed bond paths, between metal atoms and terminal carbon atoms in several complexes. In this communication, it is first demonstrated that the presupposition of the equivalence of a bond path and a chemical bond within the context of the quantum theory of atoms in molecules (QTAIM) is superficial and basically flawed which is not only against with the…
A vector-based representation of the chemical bond is introduced that we refer to as the bond-path frame-work set = $\mathbb{B} = \{p, q, r\}$, where $p$, $q$ and $r$ represent three paths with corresponding eigenvector-following path lengths $\mathbb{H}^{*},\mathbb{H}$ and the familiar quantum theory of atoms in molecules (QTAIM) bond-path length. The eigenvector-following path lengths $\mathbb{H}^{*}$ and $\mathbb{H}$ are constructed along the bond-path from the $\underline{\mathbf{\mathit{e}}}_{1}$ and $\underline{\mathbf{\mathit{e}}}_{2}$ Hessian eigenvectors respectively, which correspond…
A two-orbital two-electron diatomic model resembling LiH is used to investigate the differences between the exact Löwdin-Shull and approximate Hartree-Fock-Bogoliubov and Baerends-Buijse density matrix functionals in the medium- to long-distance dissociation region. In case of homolytic dissociation (one electron on each atom), the approximate functionals fail to generate the correct energy due to a compromise between the Hartree-Fock component (which favors partial charge transfer) and the strong correlation component (which hampers charge transfer). The exact functional is able to generate t…
APLIP is a method for using a STIRAP-like three-state configuration with two laser pulses for continuous extension of a molecular bond, introduced in 1998. It is based on time-dependent light-induced potential surfaces (LIP). In VibLIP one extends the idea into a method for tailoring the vibrational state while changing the electronic state, introduced in 2000. Here I discuss the extension of both methods to situations that involve more than three electronic states, and note the possibility of using the method on adiabatic transport of atoms between microtraps or equivalent structures.
Recently it has been proposed that the positron, the anti-particle analog of the electron, is capable of forming an anti-matter bond in a composite system of two hydride anions and a positron [Angew. Chem. Int. Ed. 57, 8859 (2018)]. In order to dig into the nature of this novel bond the newly developed multi-component quantum theory of atoms in molecules is applied to this positronic system. The topological analysis reveals that this species is composed of two atoms in molecules, each containing a proton and half of the electronic and the positronic populations. Further analysis elucidates tha…
Chemical bonding concepts emerge naturally from maximally entangled atomic orbitals
Ludwig-Maximilians-Universität München（慕尼黑大学）；Munich Center for Quantum Science and Technology (MCQST)（慕尼黑量子科学与技术中心）；Donostia International Physics Center (DIPC)（圣塞巴斯蒂安国际物理中心）
A double-index atomic partitioning of the molecular first-order density matrix is proposed. Contributions diagonal in the atomic indices correspond to atomic density matrices, whereas off-diagonal contributions carry information about the bonds. The resulting matrices have good localization properties, in contrast to single-index atomic partitioning schemes of the molecular density matrix. It is shown that the electron density assigned to individual atoms, when derived from the density matrix partitioning, can be made con- sistent with well-known partitions of the electron density over AIM bas…
The structure of Ge$_{20}$Sb$_{10}$S$_{70}$, Ge$_{23}$Sb$_{12}$S$_{65}$ and Ge$_{26}$Sb$_{13}$S$_{61}$ glasses was investigated by neutron diffraction (ND), X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS) measurements at the Ge and Sb K-edges as well as Raman scattering. For each composition, large scale structural models were obtained by fitting simultaneously diffraction and EXAFS data sets in the framework of the reverse Monte Carlo (RMC) simulation technique. Ge and S atoms have 4 and 2 nearest neighbors, respectively. The structure of these glasses can be describ…
Hydrogen bond is often assumed to be a purely electrostatic interaction between a electron-deficient hydrogen atom and a region of high electron density. Here, for the first time, we directly image hydrogen bond in real space by room-temperature scanning tunneling microscopy (STM) with the assistance of resonant tunneling effect in double barrier mode. STM observations demonstrate that the C=O:HO hydrogen bonds lifted several angstrom meters above metal surfaces appear shuttle-like features with a significant contrast along the direction connected the oxygen and hydrogen atoms of a single hydr…
This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect a part of materials' nature. First, a material is separated into local structures; and then represented as matrices, each of which is computed by using information about the corresponding chemical bond as well as orbital-field matrices of two related atoms. After that, all local structures of the material are utilized by using the statistics point of view. …
The geometric--arithmetic indices are widely considered in the chemical graph theory in the last decade. The reason of introducing new indices is to gain prediction of target properties of considered molecules that is better than the prediction obtained by already known indices. In the case of the fifth geometric--arithmetic index hitherto no ability of prediction of some molecule property has been considered. In this paper we investigate correlations between the fifth geometric--arithmetic index and some other degree--based topological indices on the family of octane isomers and polyaromatic …
First-principles calculations and analysis of the thermodynamic, structural, and electronic properties of liquid SiO$_2$ characterize the bonded-to-atomic transition at 0.1--1.6 TPa and 10$^4$--10$^5$ K (1--7 eV), the high-energy-density regime relevant to understanding planetary interiors. We find strong ionic bonds that become short-lived due to high kinetics during the transition, with sensitivity of the transition temperature to pressure, and our calculated Hugoniots agree with past experimental data. These results reconcile previous experimental and theoretical findings by clarifying the …
An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two diabatic states and has a simple chemically motivated form for its matrix elements. The model gives insight into the "H-bond puzzle", describes different classes of bonds, and empirical correlations between the donor-acceptor distance R and binding energies, bond lengths, and the softening of vibrational frequencies. A key prediction is the UV photo-dissociati…
