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.     

Dismantling the Hyperconjugation of π-Conjugated Phosphorus Heterocycles

The development of π-extended phosphorus heterocycles has been rapidly increasing because of their unique optoelectronics properties, which are very often considered to be a consequence of special hyperconjugative interactions. However, the latter interactions have primarily been investigated within the five-membered species, phospholes, and they are often conceptually extrapolated to the rest of π-extended phosphorus heterocycles (including six-membered P-heterocycles) despite evident structural differences. Herein, we report, for the first time, a detailed investigation that sheds light on the hyperconjugative effects of a series of phosphorus heterocyclic systems by means of EDA and NBO calculations within a DFT framework. Our results lay the foundations for the future design of π-extended phosphorus heterocycles with improved optoelectronics properties.     

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   

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.     

Aromaticity in metallabenzenes

The electronic structure and bonding situation in 21 metallabenzenes (metal=Os, Ru, Ir, Rh, Pt, and Pd) were investigated at the DFT level (BP86/TZ2P) by using an energy decomposition analysis (EDA) of the interaction energy between various fragments. The aim of the work is to estimate the strength of the pi bonding and the aromatic character of the metallacyclic compounds. Analysis of the electronic structure shows that the metallacyclic moiety has five occupied pi orbitals, two with b1 symmetry and three with a2 symmetry, which describe the pi-bonding interactions. The metallabenzenes are thus 10 pi-electron systems. This holds for 16-electron and for 18-electron complexes. The pi bonding in the metallabenzenes results mainly from the b1 contribution, but the a2 contribution is not negligible. Comparison of the pi-bonding strength in the metallacyclic compounds with acylic reference molecules indicates that metallabenzenes should be considered as aromatic compounds whose extra stabilization due to aromatic conjugation is weaker than in benzene. The calculated aromatic stabilization energies (ASEs) are between 8.7 kcal mol(-1) for 13 and 37.6 kcal mol(-1) for 16 which is nearly as aromatic as benzene (ASE=42.5 kcal mol(-1)). The classical metallabenzene model compounds 1 and 4 exhibit intermediate aromaticity with ASE values of 33.4 and 17.6 kcal mol(-1). The greater stability of the 5d complexes compared with the 4d species appears not to be related to the strength of pi conjugation. From the data reported here there is no apparent trend or pattern which indicates a correlation between aromatic stabilization and particular ligands, metals, coordination numbers or charge. The lower metal-C5H5 binding energy of the 4d complexes correlates rather with weaker sigma-orbital interactions.     

Chemical Reactivity Controlled by Negative Hyperconjugation: A Theoretical Study

Negative hyperconjugation is a general phenomenon that can be observed in many areas of chemistry. The knowledge of its impact on structural parameters and conformational issues is well established, but little is known about its importance for chemical reactivity. Here we present a systematic study of different aspects of negative hyperconjugation on the reactivity of complex heterocyclic systems using density functional theory. Intermediates from the reaction of nitrogen‐based nucleophiles with bis(1,3,4‐thiadiazolo)‐1,3,5‐triazinium halides serve as benchmark systems to demonstrate the effects of negative hyperconjugation on bond lengths, on the relative stability of conformational isomers and transition structures and, most importantly, on the different reaction pathways of these species. The computational results provided here are in part supported by experiments reported elsewhere.     

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D₂Ch⋅⋅⋅A⁻ (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO−LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A⁻ to D₂Ch.     

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     

On the electronic structures of the 1,3-diboracyclobutane-1,3-diyls and their valence isomers with a B2E2 skeleton (E=N,P, As)

The concept of through-space versus through-bond interactions on the stabilization of biradical structures with a singlet or triplet ground state is evaluated for the 1,3-diboracyclobutane-1,3-diyls and related congeners. Singlet biradicals are favored when the intermediate units E feature singlet character (PH(2) (+), AsH(2) (+)), while E fragments with triplet character (NH(2) (+)) induce small energy separations between the lowest singlet and triplet states. These considerations are supported by quantum chemical calculations with energy optimization at 1) MCSCF level plus MR-MP2 correction, 2) MR-MP2 level, and 3) two different types of density functional levels for the planar (D(2h)) geometries. The singlet-triplet energy separations in the planar compounds increase with increasing singlet stability of the corresponding E fragments. In addition to this newly developed principal features for singlet stabilization, which primarily occurs in bonded structures with higher main-group elements, the corresponding valence isomers with bicyclobutane, cyclobutene and cis-butadiene structures are investigated.     

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.     

The Nature of Nonclassical Carbonyl Ligands Explained by Kohn–Sham Molecular Orbital Theory

When carbonyl ligands coordinate to transition metals, their bond distance either increases (classical) or decreases (nonclassical) with respect to the bond length in the isolated CO molecule. C−O expansion can easily be understood by π-back-donation, which results in a population of the CO's π*-antibonding orbital and hence a weakening of its bond. Nonclassical carbonyl ligands are less straightforward to explain, and their nature is still subject of an ongoing debate. In this work, we studied five isoelectronic octahedral complexes, namely Fe(CO)₆²⁺, Mn(CO)₆⁺, Cr(CO)₆, V(CO)₆⁻ and Ti(CO)₆²⁻, at the ZORA-BLYP/TZ2P level of theory to explain this nonclassical behavior in the framework of Kohn–Sham molecular orbital theory. We show that there are two competing forces that affect the C−O bond length, namely electrostatic interactions (favoring C−O contraction) and π-back-donation (favoring C−O expansion). It is a balance between those two terms that determines whether the carbonyl is classical or nonclassical. By further decomposing the electrostatic interaction ΔV_elstat into four fundamental terms, we are able to rationalize why ΔV_elstat gives rise to the nonclassical behavior, leading to new insights into the driving forces behind C−O contraction.     

Measurement and Applications of Long‐Range Heteronuclear Scalar Couplings: Recent Experimental and Theoretical Developments

The use of long‐range heteronuclear couplings, in association with ¹H–¹H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long‐range homo‐ and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J‐couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short‐ and long‐range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long‐range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium‐ to larger‐sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.     

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.     

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.     

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.     

Transition‐Metal Complexes of Tetrylones [(CO)5W‐E(PPh3)2] and Tetrylenes [(CO)5W‐NHE] (E=C–Pb): A Theoretical Study

Quantum chemical calculations at the BP86/TZVPP//BP86/SVP level are performed for the tetrylone complexes [W(CO)₅‐E(PPh₃)₂] ( W‐1 E ) and the tetrylene complexes [W(CO)₅‐NHE] ( W‐2 E ) with E=C–Pb. The bonding is analyzed using charge and energy decomposition methods. The carbone ligand C(PPh₃) is bonded head‐on to the metal in W‐1 C , but the tetrylone ligands E(PPh₃)₂ are bonded side‐on in the heavier homologues W‐1 Si to W‐1 Pb . The W? E bond dissociation energies (BDEs) increase from the lighter to the heavier homologues ( W‐1 C : D_e=25.1 kcal mol^?1; W‐1 Pb : D_e=44.6 kcal mol^?1). The W(CO)₅←C(PPh₃)₂ donation in W‐1 C comes from the σ lone‐pair orbital of C(PPh₃)₂, whereas the W(CO)₅←E(PPh₃)₂ donation in the side‐on bonded complexes with E=Si–Pb arises from the π lone‐pair orbital of E(PPh₃)₂ (the HOMO of the free ligand). The π‐HOMO energy level rises continuously for the heavier homologues, and the hybridization has greater p character, making the heavier tetrylones stronger donors than the lighter systems, because tetrylones have two lone‐pair orbitals available for donation. Energy decomposition analysis (EDA) in conjunction with natural orbital for chemical valence (NOCV) suggests that the W? E BDE trend in W‐1 E comes from the increase in W(CO)₅←E(PPh₃)₂ donation and from stronger electrostatic attraction, and that the E(PPh₃)₂ ligands are strong σ‐donors and weak π‐donors. The NHE ligands in the W‐2 E complexes are bonded end‐on for E=C, Si, and Ge, but side‐on for E=Sn and Pb. The W? E BDE trend is opposite to that of the W‐1 E complexes. The NHE ligands are strong σ‐donors and weak π‐acceptors. The observed trend arises because the hybridization of the donor orbital at atom E in W‐2 E has much greater s character than that in W‐1 E , and even increases for heavier atoms, because the tetrylenes have only one lone‐pair orbital available for donation. In addition, the W? E bonds of the heavier systems W‐2 E are strongly polarized toward atom E, so the electrostatic attraction with the tungsten atom is weak. The BDEs calculated for the W? E bonds in W‐1 E , W‐2 E and the less bulky tetrylone complexes [W(CO)₅‐E(PH₃)₂] ( W‐3 E ) show that the effect of bulky ligands may obscure the intrinsic W? E bond strength.     

Bonding in Endohedral Metallofullerenes as Studied by Quantum Theory of Atoms in Molecules

Metal–cage and intracluster bonding was studied in detail by quantum theory of atoms in molecules (QTAIM) for the four major classes of endohedral metallofullerenes (EMFs), including monometallofullerenes Ca@C₇₂, La@C₇₂, M@C₈₂ (M=Ca, Sc, Y, La), dimetallofullerenes Sc₂@C₇₆, Y₂@C₈₂, Y₂@C₇₉N, La₂@C₇₈, La₂@C₈₀, metal nitride clusterfullerenes Sc₃N@C_2n (2n=68, 70, 78, 80), Y₃N@C_2n (2n=78, 80, 82, 84, 86, 88), La₃N@C_2n (2n=88, 92, 96), metal carbide clusterfullerenes Sc₂C₂@C₆₈, Sc₂C₂@C₈₂, Sc₂C₂@C₈₄, Ti₂C₂@C₇₈, Y₂C₂@C₈₂, Sc₃C₂@C₈₀, as well as Sc₃CH@C₈₀ and Sc₄O_x@C₈₀ (x=2, 3), that is, 42 EMF molecules and ions in total. Analysis of the delocalization indices and bond critical point (BCP) indicators such as G_bcp/ρ_bcp, H_bcp/ρ_bcp, and |V_bcp|/G_bcp, revealed that all types of bonding in EMFs exhibit a high degree of covalency, and the ionic model is reasonable only for the Ca‐based EMFs. Metal–metal bonds with negative values of the electron‐density Laplacian were found in Y₂@C₈₂, Y₂@C₇₉N, Sc₄O₂@C₈₀, and anionic forms of La₂@C₈₀. A delocalized nature of the metal–cage bonding results in a topological instability of the electron density in EMFs with an unpredictable number of metal–cage bond paths and large elipticity values.