Bonding character of intermediates in on-surface Ullmann reactions revealed with energy decomposition analysis

On-surface synthesis has become a thriving topic in surface science. The Ullmann coupling reaction is the most applied synthetic route today, but the nature of the organometallic intermediate is still under discussion. We investigate the bonding nature of prototypical intermediate species (phenyl, naphthyl, anthracenyl, phenanthryl, and triphenylenyl) on the Cu(111) surface with a combination of plane wave and atomic orbital basis set methods using density functional theory calculations with periodic boundary conditions. The surface bonding is shown to be of covalent nature with a polarized shared-electron bond supported by π-back donation effects using energy decomposition analysis for extended systems (pEDA). The bond angle of the intermediates is determined by balancing dispersion attraction and Pauli repulsion between adsorbate and surface. The latter can be significantly reduced by adatoms on the surface. We furthermore investigate how to choose computational parameters for pEDA of organic adsorbates on metal surfaces efficiently and show that bonding interpretation requires consistent choice of the density functional.     

Atomic decomposition of identity: General formalism for population analysis and energy decomposition

The concept of “atomic resolution of identity” has been introduced, leading to a very simple general formalism for generating different decomposition schemes of molecular quantities. Thus, different population analysis and energy partitioning schemes can be treated as special cases of a common framework. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Direct estimate of the strength of conjugation and hyperconjugation by the energy decomposition analysis method

The intrinsic strength of pi interactions in conjugated and hyperconjugated molecules has been calculated using density functional theory by energy decomposition analysis (EDA) of the interaction energy between the conjugating fragments. The results of the EDA of the trans-polyenes H2C=CH-(HC=CH)n-CH=CH2 (n = 1-3) show that the strength of pi conjugation for each C=C moiety is higher than in trans-1,3-butadiene. The absolute values for the conjugation between Si=Si pi bonds are around two-thirds of the conjugation between C=C bonds but the relative contributions of DeltaE pi to DeltaE orb in the all-silicon systems are higher than in the carbon compounds. The pi conjugation between C=C and C=O or C=NH bonds in H2C=CH--C(H)=O and H2C=CH-C(H)=NH is comparable to the strength of the conjugation between C=C bonds. The pi conjugation in H2C=CH-C(R)=O decreases when R = Me, OH, and NH2 while it increases when R = halogen. The hyperconjugation in ethane is around a quarter as strong as the pi conjugation in ethyne. Very strong hyperconjugation is found in the central C-C bonds in cubylcubane and tetrahedranyltetrahedrane. The hyperconjugation in substituted ethanes X3C-CY3 (X,Y = Me, SiH3, F, Cl) is stronger than in the parent compound particularly when X,Y = SiH3 and Cl. The hyperconjugation in donor-acceptor-substituted ethanes may be very strong; the largest DeltaE pi value was calculated for (SiH3)3C-CCl3 in which the hyperconjugation is stronger than the conjugation in ethene. The breakdown of the hyperconjugation in X3C-CY3 shows that donation of the donor-substituted moiety to the acceptor group is as expected the most important contribution but the reverse interaction is not negligible. The relative strengths of the pi interactions between two C=C double bonds, one C=C double bond and CH3 or CMe3 substituents, and between two CH3 or CMe3 groups, which are separated by one C-C single bond, are in a ratio of 4:2:1. Very strong hyperconjugation is found in HC[triple bond]C-C(SiH3)3 and HC[triple bond]C-CCl3. The extra stabilization of alkenes and alkynes with central multiple bonds over their terminal isomers coming from hyperconjugation is bigger than the total energy difference between the isomeric species. The hyperconjugation in Me-C(R)=O is half as strong as the conjugation in H2C=CH-C(R)=O and shows the same trend for different substituents R. Bond energies and lengths should not be used as indicators of the strength of hyperconjugation because the effect of sigma interactions and electrostatic forces may compensate for the hyperconjugative effect.     

SurfinPES: Performing automated analysis of activation strain,energy decomposition,and reaction force

Analyzing activation strain, energy decomposition, and reaction force models is crucial for studying chemical reactivity and gaining quantitative insights into the factors that control energy barriers. However, manually preparing and processing the necessary data can be challenging and prone to errors. To address this issue, we introduce SurfinPES, a Python-based module in Eyringpy that automates data extraction and processing for these analyses. SurfinPES also allows monitoring of the evolution of primitive properties (geometrical and electronic) along the reaction coordinate. The module is user-friendly with a simple input format, making it accessible to any user in the field of computational chemistry.     

The nature of the chemical bond revisited: an energy-partitioning analysis of nonpolar bonds

The nature of the chemical bond in nonpolar molecules has been investigated by energy-partitioning analysis (EPA) of the ADF program using DFT calculations. The EPA divides the bonding interactions into three major components, that is, the repulsive Pauli term, quasiclassical electrostatic interactions, and orbital interactions. The electrostatic and orbital terms are used to define the nature of the chemical bond. It is shown that nonpolar bonds between main-group elements of the first and higher octal rows of the periodic system, which are prototypical covalent bonds, have large attractive contributions from classical electrostatic interactions, which may even be stronger than the attractive orbital interactions. Fragments of molecules with totally symmetrical electron-density distributions, like the nitrogen atoms in N(2), may strongly attract each other through classical electrostatic forces, which constitute 30.0 % of the total attractive interactions. The electrostatic attraction can be enhanced by anisotropic charge distribution of the valence electrons of the atoms that have local areas of (negative) charge concentration. It is shown that the use of atomic partial charges in the analysis of the nature of the interatomic interactions may be misleading because they do not reveal the topography of the electronic charge distribution. Besides dinitrogen, four groups of molecules have been studied. The attractive binding interactions in H(n)E-EH(n) (E=Li to F; n=0-3) have between 20.7 (E=F) and 58.4 % (E=Be) electrostatic character. The substitution of hydrogen by fluorine does not lead to significant changes in the nature of the binding interactions in F(n)E-EF(n) (E=Be to O). The electrostatic contributions to the attractive interactions in F(n)E-EF(n) are between 29.8 (E=O) and 55.3 % (E=Be). The fluorine substituents have a significant effect on the Pauli repulsion in the nitrogen and oxygen compounds. This explains why F(2)N-NF(2) has a much weaker bond than H(2)N-NH(2), whereas the interaction energy in FO-OF is much stronger than in HO-OH. The orbital interactions make larger contributions to the double bonds in HB=BH, H(2)C=CH(2), and HN=NH (between 59.9 % in B(2)H(2) and 65.4 % in N(2)H(2)) than to the corresponding single bonds in H(n)E-EH(n). The orbital term Delta E(orb) (72.4 %) makes an even greater contribution to the HC triple bond CH triple bond. The contribution of Delta E(orb) to the H(n)E=EH(n) bond increases and the relative contribution of the pi bonding decreases as E becomes more electronegative. The pi-bonding interactions in HC triple bond CH amount to 44.4 % of the total orbital interactions. The interaction energy in H(3)E-EH(3) (E=C to Pb) decreases monotonically as the element E becomes heavier. The electrostatic contributions to the E-E bond increases from E=C (41.4 %) to E=Sn (55.1 %) but then decreases when E=Pb (51.7 %). A true understanding of the strength and trends of the chemical bonds can only be achieved when the Pauli repulsion is considered. In an absolute sense the repulsive Delta E(Pauli) term is in most cases the largest term in the EPA.     

A hybrid approach combining energy density analysis with the interaction energy decomposition method

We propose a new analysis technique for characterizing molecular interactions that combines an energy decomposition scheme, such as the Kitaura-Morokuma decomposition method, with energy density analysis, which partitions the total energy of the system into atomic contributions. The combined scheme, termed Interaction-EDA, enables us to estimate the local contribution of interaction energy components, such as electrostatic, exchange, polarization, and charge transfer. The evaluation of the local interaction energy is rather important in large systems. For a numerical assessment, the Interaction-EDA method is applied to the process of CO adsorption on Si(100) - (2 x 1) surface.     

A multipolar approach to the interatomic covalent interaction energy

Interatomic exchange‐correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp ) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities and , we examine in this work the mp approach to approximate the interatomic exchange‐correlation (xc) energies of the Interacting Quantum Atoms method. We show that the full xc mp series is quickly divergent for directly bonded atoms (1–2 pairs) albeit it works reasonably well most times for 1– n (n > 2) interactions. As with conventional perturbation theory, we show numerically that the xc series is asymptotically convergent and that, a truncated xc mp approximation retaining terms up to usually gives relatively accurate results, sometimes even for directly bonded atoms. Our findings are supported by extensive numerical analyses on a variety of systems that range from several standard hydrogen bonded dimers to typically covalent or aromatic molecules. The exact algebraic relationship between the monopole‐monopole xc mp term and the inter‐atomic bond order, as measured by the delocalization index of the quantum theory of atoms in molecules, is also established. © 2017 Wiley Periodicals, Inc.     

Kinetic energy decomposition scheme based on information theory

We proposed a novel kinetic energy decomposition analysis based on information theory. Since the Hirshfeld partitioning for electron densities can be formulated in terms of Kullback–Leibler information deficiency in information theory, a similar partitioning for kinetic energy densities was newly proposed. The numerical assessments confirm that the current kinetic energy decomposition scheme provides reasonable chemical pictures for ionic and covalent molecules, and can also estimate atomic energies using a correction with viral ratios.     

Partitioning of atomization energy

The present work provides a technique for partitioning the atomization energy of a molecule into diatomic contributions. The method is largely based on the redistribution of the kinetic energy term in Mayer's energy partitioning and uses free‐atom energies as a reference. The comparison of Mayer's original method, the alternative Ichikawa–Yoshida approach, and the new atomization energy partitioning (AEP) shows that the new approach has advantages in describing trends in diatomic energies in molecules with triple bonds, as well as for hydrogen bonds. The proposed AEP is a viable alternative to Mayer's energy partitioning method. © 2007 Wiley Periodicals, Inc. Int. J. Quantum Chem, 2008     

Comment on “Realization of Lewis Basic Sodium Anion in the NaBH3− Cluster”

We challenge the interpretation of the chemical bond in NaBH₃^? proposed by Liu et al. We argue that NaBH₃^? has an electron‐sharing Na?BH₃^? covalent bond rather than a dative bond Na^?→BH₃.     

An energy decomposition scheme applicable to strongly interacting systems

An energy decomposition scheme useful for the analysis of the coupled types of interactions in strongly interacting systems is developed within the Hartree-Fock approximation. A dominant characteristic of the scheme is that it involves the interactions between vacant orbitals of component molecules, as can be justified from the third-order perturbation theory. On the basis ofab initio molecular orbital calculations, the utility of the scheme is illustrated for the BH₃-NH₃ complexation and the S_N2 reaction of CH₄ with H^–. It is found that the charge transfer from electron donor (i.e. NH₃ or H^–) to acceptor (i.e. BH₃ or CH₄) is strongly coupled with the polarization of the acceptor, to contribute appreciably to the stabilization of the entire system. A specific role of this coupling mode in the progress of reactions is discussed.     

Comment on “Realization of Lewis Basic Sodium Anion in the NaBH3− Cluster”

We challenge the interpretation of the chemical bond in NaBH₃⁻ proposed by Liu et al. We argue that NaBH₃⁻ has an electron-sharing Na−BH₃⁻ covalent bond rather than a dative bond Na⁻→BH₃.     

Thermal decomposition kinetics of natural fibers: Activation energy with dynamic thermogravimetric analysis

Dynamic TG analysis under nitrogen was used to investigate the thermal decomposition processes of 10 types of natural fibers commonly used in the polymer composite industry. These fibers included wood, bamboo, agricultural residue, and bast fibers. Various degradation models including the Kissinger, Friedman, Flynn-Wall-Ozawa, and modified Coats-Redfern methods were used to determine the apparent activation energy of these fibers. For most natural fibers approximately 60% of the thermal decomposition occurred within a temperature range between 215 and 310 °C. The result also showed that an apparent activation energy of 160-170 kJ/mol was obtained for most of the selected fibers throughout the polymer processing temperature range. These activation energy values allow developing a simplified approach to understand the thermal decomposition behavior of natural fibers as a function of polymer composite processing.     

Is This a Chemical Bond? A Theoretical Study of Ng2@C60 (Ng=He,Ne, Ar,Kr, Xe)

Quantum-chemical calculations using DFT (BP86) and ab initio methods (MP2, SCS-MP2) have been carried out for the endohedral fullerenes Ng2@C60 (Ng=He-Xe). The nature of the interactions has been analyzed with charge- and energy-partitioning methods and with the topological analysis of the electron density (Atoms-in-Molecules (AIM)). The calculations predict that the equilibrium geometries of Ng2@C60 have D3d symmetry when Ng=Ne, Ar, Kr, while the energy-minimum structure of Xe2@C60 has D5d symmetry. The precession movement of He2 in He2@C60 has practically no barrier. The Ng--Ng distances in Ng2@C60 are much shorter than in free Ng2. All compounds Ng2@C60 are thermodynamically unstable towards loss of the noble gas atoms. The heavier species Ar2@C60, Kr2@C60, and Xe2@C60 are high energy compounds which are at the BSSE corrected SCS-MP2/TZVPP level in the range 96.7-305.5 kcal mol(-1) less stable than free C60+2 Ng. The AIM method reveals that there is always an Ng--Ng bond path in Ng2@C60. There are six Ng--C bond paths in (D3d) Ar2@C60, Kr2@C60, and Xe2@C60, whereas the lighter D3d homologues He2@C60 and Ne2@C60 have only three Ng--C2 paths. The calculated charge distribution and the orbital analysis clearly show that the bonding situation in Xe2@C60 significantly differs from those of the lighter homologues. The atomic partial charge of the [Xe2] moiety is +1.06, whereas the charges of the lighter dimers [Ng2] are close to zero. The a2u HOMO of (D3d) Xe2@C60 in the 1A1g state shows a large mixing of the highest lying occupied sigma* orbital of [Xe2] and the orbitals of the C60 cage. There is only a small gap between the a2u HOMO of Xe2@C60 and the eu LUMO and the a2u LUMO+1. The calculations show that there are several triplet states which are close in energy to each other and to the 1A1g state. The bonding analysis suggests that the interacting species in Xe2@C60 are the charged species Xe2q+ and C60q-, where 1相似文献   

Chemical Bonding in Silicon Carbonyl Complexes

Although silylene-carbonyl complexes are known for decades, only recently isolable examples have been accomplished. In this work, the bonding situation is re-evaluated to explain the origins of their remarkable stability within the Kohn-Sham molecular orbital theory framework. It is shown that the chemical bond can be understood as CO interaction with the silylene via a donor-acceptor interaction: a σ-donation from the σ_CO into the empty p-orbital of silicon, and a π-back donation from the sp² lone pair of silicon into the π*_CO antibonding orbitals. Notably, it was established that the driving force behind the surprisingly stable Si−CO compounds, however, is another π-back donation from a perpendicular bonding R−Si σ-orbital into the π*_CO antibonding orbitals. Consequently, the pyramidalization of the central silicon atom cannot be associated with the strength of the π-back donation, in sharp contrast to the established chemical bonding model. Considering this additional bonding interaction not only shed light on the bonding situation, but is also an indispensable key for broadening the scope of silylene-carbonyl chemistry.     

HCCO自由基与水分子氢键复合物的从头算研究

在MP2/aug-cc-pvdz水平下,对二体氢键复合物H2O…HCCO(Ⅰ)和HCCO…H2O(Ⅱ)以及三体氢键复合物(H2O)2…HCCO(Ⅲ),H2O…H2O…HCCO(Ⅳ)和H2O…HCCO…H2O(Ⅴ)的几何和相互作用能进行了计算.轨道分析表明Ⅲ中HCCO中的H(1),C(2)通过2个氢键与2个水分子形成了环...     

Model-free kinetics analysis of decomposition of polypropylene over Al-MCM-41

Both thermal and catalytic decomposition of PP sample is studied to understand the effect of catalyst (Al-MCM-41) on the decomposition behaviour. Mesoporous catalyst (Al-MCM-41) is synthesized by sol–gel methods and characterized by X-ray diffraction (XRD) analysis and nitrogen adsorption study. The optimum catalyst composition is found to be around 18.5 wt%, where the reduction in maximum decomposition temperature is around 103 °C. The nonlinear Vyazovkin model-free technique is applied to evaluate the quantitative information on variation of E with for PP sample under both catalytic and noncatalytic nonisothermal conditions.

The constant pattern behaviour of the TG curves and the similar trend on variation of E with for both catalytic and noncatalytic decomposition of PP indicates similar mechanism involved during decomposition. The only effect of catalyst is observed in the form of reduction of the temperature and the activation energy. The literature reported data on such variation are compared with the results of the present study. Results show that Al-MCM-41 is superior to the ZSM-5 catalyst in terms of catalyst loading due to the existence of larger external macropore and mesopore surface in it.     

In-Situ Electronegativity and the Bridging of Chemical Bonding Concepts

One challenge in chemistry is the plethora of often disparate models for rationalizing the electronic structure of molecules. Chemical concepts abound, but their connections are often frail. This work describes a quantum-mechanical framework that enables a combination of ideas from three approaches common for the analysis of chemical bonds: energy decomposition analysis (EDA), quantum chemical topology, and molecular orbital (MO) theory. The glue to our theory is the electron energy density, interpretable as one part electrons and one part electronegativity. We present a three-dimensional analysis of the electron energy density and use it to redefine what constitutes an atom in a molecule. Definitions of atomic partial charge and electronegativity follow in a way that connects these concepts to the total energy of a molecule. The formation of polar bonds is predicted to cause inversion of electronegativity, and a new perspective of bonding in diborane and guanine−cytosine base-pairing is presented. The electronegativity of atoms inside molecules is shown to be predictive of pK_a.