Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles

The ground state intermolecular potential of bimolecular complexes of N-heterocycles is analysed for the impact of different terms of the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, dispersion and other contributions are tested for a good performance at both short- and long-distance sides of the potential energy surface for various alignments of the pyrrole dimer as well as the cytosine-uracil complex. The integration of a DFT/CC density embedding scheme and dispersion terms from the effective fragment potential (EFP) method is found to provide very good agreement with the reference CCSD(T) potential overall, but a QM/MM approach using CHELPG atomic point charges for the electrostatic interaction augmented by EFP dispersion and Pauli repulsion contributions comes also close. Both of these schemes has the advantage of not relying on predefined force fields, rather the interaction parameters can be obtained for the system under study, therefore excellent candidates for ab initio modeling.

Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles

The ground state intermolecular potential of bimolecular complexes of N-heterocycles is analysed for the impact of different terms of the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, dispersion and other contributions are tested for a good performance at both short- and long-distance sides of the potential energy surface for various alignments of the pyrrole dimer as well as the cytosine-uracil complex. The integration of a DFT/CC density embedding scheme and dispersion terms from the effective fragment potential (EFP) method is found to provide very good agreement with the reference CCSD(T) potential overall, but a QM/MM approach using CHELPG atomic point charges for the electrostatic interaction augmented by EFP dispersion and Pauli repulsion contributions comes also close. Both of these schemes has the advantage of not relying on predefined force fields, rather the interaction parameters can be obtained for the system under study, therefore excellent candidates for ab initio modeling.

Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding

The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin–orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C–At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.

Very weak bonds to artificial atoms formed by quantum corrals

We explored the bonding properties of the quantum corral (a circle of 48 iron atoms placed on a copper surface) reported by Crommie, Lutz and Eigler in 1993, along with variants, as an artificial atom using an atomic force microscope (AFM). The original corral geometry confines 102 electrons to 28 discrete energy states, and we find that these states can form a bond to the front atom of the AFM with an energy of about 5 millielectron volts. The measured forces are about 1/1000 of typical forces in atomically resolved AFM. The confined electrons showed covalent attraction to metal tips and Pauli repulsion to CO-terminated tips. The repulsion at close distance was evident from the response of corral states created by deliberately placing single iron atoms inside the corral. The forces scaled appropriately with a 24-atom corral.

From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.

An Isolable Mononuclear Palladium(I) Amido Complex

Mononuclear Pd(I) species are putative intermediates in Pd-catalyzed reactions, but our knowledge about them is limited due to difficulties in accessing them. Herein, we report the isolation of a Pd(I) amido complex, [(BINAP)Pd(NHArTrip )] (BINAP = 2,2′- bis(diphenylphosphino)-1,1′-binaphthalene, ArTrip = 2,6-bis(2’,4’,6’-triisopropylphenyl)phenyl), from the reaction of (BINAP)PdCl2 with LiNHArTrip. This Pd(I) amido species has been characterized by X-ray crystallography, electron paramagnetic resonance, and multi-edge Pd Xray absorption spectroscopy. Theoretical study revealed that, while the 3-electron-2-center π interaction between Pd and N in the Pd(I) complex imposes severe Pauli repulsion in its Pd–N bond, pronounced attractive inter-ligand dispersion force aids its stabilization. In accord with its electronic features, reactions of homolytic Pd–N bond cleavage and deprotonation of primary amines are observed on the Pd(I) amido complex.

An Isolable Mononuclear Palladium(I) Amido Complex

Mononuclear Pd(I) species are putative intermediates in Pd-catalyzed reactions, but our knowledge about them is limited due to difficulties in accessing them. Herein, we report the isolation of a Pd(I) amido complex, [(BINAP)Pd(NHArTrip )] (BINAP = 2,2′- bis(diphenylphosphino)-1,1′-binaphthalene, ArTrip = 2,6-bis(2’,4’,6’-triisopropylphenyl)phenyl), from the reaction of (BINAP)PdCl2 with LiNHArTrip. This Pd(I) amido species has been characterized by X-ray crystallography, electron paramagnetic resonance, and multi-edge Pd Xray absorption spectroscopy. Theoretical study revealed that, while the 3-electron-2-center π interaction between Pd and N in the Pd(I) complex imposes severe Pauli repulsion in its Pd–N bond, pronounced attractive inter-ligand dispersion force aids its stabilization. In accord with its electronic features, reactions of homolytic Pd–N bond cleavage and deprotonation of primary amines are observed on the Pd(I) amido complex.

Guanidine–Amide-Catalyzed Aza-Henry Reaction of Isatin-Derived Ketimines: Origin of Selectivity and New Catalyst Design

Density functional theory (DFT) calculations were performed to investigate the mechanism and the enantioselectivity of the aza-Henry reaction of isatin-derived ketimine catalyzed by chiral guanidine–amide catalysts at the M06-2X-D3/6-311+G(d,p)//M06-2X-D3/6-31G(d,p) (toluene, SMD) theoretical level. The catalytic reaction occurred via a three-step mechanism: (i) the deprotonation of nitromethane by a chiral guanidine–amide catalyst; (ii) formation of C–C bonds; (iii) H-transfer from guanidine to ketimine, accompanied with the regeneration of the catalyst. A dual activation model was proposed, in which the protonated guanidine activated the nitronate, and the amide moiety simultaneously interacted with the ketimine substrate by intermolecular hydrogen bonding. The repulsion of CPh3 group in guanidine as well as N-Boc group in ketimine raised the Pauli repulsion energy (∆EPauli) and the strain energy (∆Estrain) of reacting species in the unfavorable si-face pathway, contributing to a high level of stereoselectivity. A new catalyst with cyclopropenimine and 1,2-diphenylethylcarbamoyl as well as sulfonamide substituent was designed. The strong basicity of cyclopropenimine moiety accelerated the activation of CH3NO2 by decreasing the energy barrier in the deprotonation step. The repulsion between the N-Boc group in ketimine and cyclohexyl group as well as chiral backbone in the new catalyst raised the energy barrier in C–C bond formation along the si-face attack pathway, leading to the formation of R-configuration product. A possible synthetic route for the new catalyst is also suggested.