Atomic Partitioning of the MPn (n = 2, 3, 4) Dynamic Electron Correlation Energy by the Interacting Quantum Atoms Method: A Fast and Accurate Electrostatic Potential Integral Approach.

Recently, the quantum topological energy partitioning method called interacting quantum atoms (IQA) has been extended to MPn (n = 2, 3, 4) wave functions. This enables the extraction of chemical insight related to dynamic electron correlation. The large computational expense of the IQA-MPn approach is compensated by the advantages that IQA offers compared to older nontopological energy decomposition schemes. This expense is problematic in the construction of a machine learning training set to create kriging models for topological atoms. However, the algorithm presented here markedly accelerates the calculation of atomically partitioned electron correlation energies. Then again, the algorithm cannot calculate pairwise interatomic energies because it applies analytical integrals over whole space (rather than over atomic volumes). However, these pairwise energies are not needed in the quantum topological force field FFLUX, which only uses the energy of an atom interacting with all remaining atoms of the system that it is part of. Thus, it is now feasible to generate accurate and sizeable training sets at MPn level of theory. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Initial Studies Directed toward the Rational Design of Aqueous Graphene Dispersants.

This study presents preliminary experimental data suggesting that sodium 4-(pyrene-1-yl)butane-1-sulfonate (PBSA), 5, an analogue of sodium pyrene-1-sulfonate (PSA), 1, enhances the stability of aqueous reduced graphene oxide (RGO) graphene dispersions. We find that RGO and exfoliated graphene dispersions prepared in the presence of 5 are approximately double the concentration of those made with commercially available PSA, 1. Quantum mechanical and molecular dynamics simulations provide key insights into the behavior of these molecules on the graphene surface. The seemingly obvious introduction of a polar sulfonate head group linked via an appropriate alkyl spacer to the aromatic core results in both more efficient binding of 5 to the graphene surface and more efficient solvation of the polar head group by bulk solvent (water). Overall, this improves the stabilization of the graphene flakes by disfavoring dissociation of the stabilizer from the graphene surface and inhibiting reaggregation by electrostatic and steric repulsion. These insights are currently the subject of further investigations in an attempt to develop a rational approach to the design of more effective dispersing agents for rGO and graphene in aqueous solution.

The deposition of cadmium selenide and cadmium phosphide thin films from cadmium thioselenoimidodiphosphinate by AACVD and the formation of an aromatic species.

Aerosol-assisted chemical vapour deposition (AACVD) of Cd[(SPiPr2)(SePiPr2)N]2 yields hexagonal cadmium selenide and monoclinic cadmium phosphide films on glass substrates between 475 and 525 °C at different argon flow rates. The films were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), energy dispersive analysis of X-rays (EDAX) and X-ray photoelectron spectroscopy (XPS). All the results of XRD, EDAX and XPS are in agreement with our previous investigations on Cd[(SePiPr2)2N]2. A breakdown mechanism is proposed based on mass spectra and density functional theory calculations. A large peak at m/z 207 in the mass spectra, previously assigned by us as a new aromatic species, is also observed for this complex.

Decomposition of Møller-Plesset Energies within the Quantum Theory of Atoms-in-Molecules.

We discuss two main approaches to decompose the Møller-Plesset perturbation theory molecular energies into atomic contributions within the interacting quantum atoms (IQA) formalism, as implemented in the programs Morphy and AIMAll. For this purpose, the so-called intraatomic energies (also known as self-energies) of a representative set of 55 small molecules are compared with each other. The origin of the possible discrepancies between both approaches is analyzed, and linear models linking the two approaches are proposed for each atom type.

Revitalizing the concept of bond order through delocalization measures in real space.

Ab initio quantum chemistry is an independent source of information supplying an ever widening group of experimental chemists. However, bridging the gap between these ab initio data and chemical insight remains a challenge. In particular, there is a need for a bond order index that characterizes novel bonding patterns in a reliable manner, while recovering the familiar effects occurring in well-known bonds. In this article, through a large body of calculations, we show how the delocalization index derived from Quantum Chemical Topology (QCT) serves as such a bond order. This index is defined in a parameter-free, intuitive and consistent manner, and with little qualitative dependency on the level of theory used. The delocalization index is also able to detect the subtler bonding effects that underpin most practical organic and inorganic chemistry. We explore and connect the properties of this index and open the door for its extensive usage in the understanding and discovery of novel chemistry.

Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease.

The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor. Chem. Acc. 2017, 136, 86], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here, the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17 689 individual IQA terms to be calculated). When REG and IQA work together it is possible to determine a reaction mechanism at atomistic resolution from data directly derived from quantum calculations, without arbitrary parameters. Moreover, the mechanism determined by this novel method gives concrete insight into how the active site residues catalyse peptide hydrolysis.

Machine Learning of Dynamic Electron Correlation Energies from Topological Atoms.

We present an innovative method for predicting the dynamic electron correlation energy of an atom or a bond in a molecule utilizing topological atoms. Our approach uses the machine learning method Kriging (Gaussian Process Regression with a non-zero mean function) to predict these dynamic electron correlation energy contributions. The true energy values are calculated by partitioning the MP2 two-particle density-matrix via the Interacting Quantum Atoms (IQA) procedure. To our knowledge, this is the first time such energies have been predicted by a machine learning technique. We present here three important proof-of-concept cases: the water monomer, the water dimer, and the van der Waals complex H2···He. These cases represent the final step toward the design of a full IQA potential for molecular simulation. This final piece will enable us to consider situations in which dispersion is the dominant intermolecular interaction. The results from these examples suggest a new method by which dispersion potentials for molecular simulation can be generated.

The Transferability of Topologically Partitioned Electron Correlation Energies in Water Clusters.

The electronic effects that govern the cohesion of water clusters are complex, demanding the inclusion of N-body, Coulomb, exchange and correlation effects. Here we present a much needed quantitative study of the effect of correlation (and hence dispersion) energy on the stabilization of water clusters. For this purpose we used a topological energy partitioning method called Interacting Quantum Atoms (IQA) to partition water clusters into topological atoms, based on a MP2/6-31G(d,p) wave function, and modified versions of GAUSSIAN09 and the Quantum Chemical Topology (QCT) program MORFI. Most of the cohesion in the water clusters provided by electron correlation comes from intramolecular energy stabilization. Hydrogen bond-related interactions tend to largely cancel each other. Electron correlation energies are transferable in almost all instances within 1 kcal mol-1 . This observed transferability is very important to the further development of the QCT force field FFLUX, especially to the future modelling of liquid water.

Quantifying Electron Correlation of the Chemical Bond.

The Interacting Quantum Atoms (IQA) method is used to analyze the correlated part of the Møller-Plesset (MP) perturbation theory two-particle density matrix. Such an analysis determines the effects of electron correlation within atoms and between atoms, which covers both bonds and nonbonded through-space atom-atom interactions within a molecule or molecular complex. Electron correlation lowers the energy of the atoms at either end of a bond, but for the bond itself, it can be stabilizing or destabilizing. Bonds are described in a two-dimensional world of exchange and charge transfer, where covalency is not the opposite of ionicity.

Aerosol-assisted CVD of cadmium diselenoimidodiphosphinate and formation of a new iPr2N2P3+ ion supported by combined DFT and mass spectrometric studies.

Aerosol-assisted chemical vapour deposition (AACVD) of Cd[(SePiPr2)2N]2 is shown to deposit cadmium selenide and/or cadmium phosphide on glass substrates, depending upon the growth conditions. The phase, structure, morphology and composition of the films were characterised by X-ray powder diffraction (XRD), scanning electron microscopy, energy dispersive X-ray analysis and X-ray photoelectron spectroscopy. The XRD indicated a hexagonal phase for cadmium selenide, whilst cadmium phosphide was monoclinic. Pyrolysis gas chromatography-mass spectrometry and density functional theory were used to deduce a breakdown mechanism for the deposition that favoured the formation of a new aromatic iPr2N2P3+ ion.

Accurate prediction of adsorption energies on graphene, using a dispersion-corrected semiempirical method including solvation.

The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can predict the adsorption energies of unsaturated hydrocarbons and the effect of substitution on these values to an accuracy comparable to DFT values and in good agreement with the experiment. The adsorption energies of TCNE, TCNQ, and a number of sulfonated pyrenes are also predicted, along with the effect of hydration using the COSMO model.

Forming a ruthenium isomerisation catalyst from Grubbs II: a DFT study.

A DFT investigation into the mechanism for the decomposition of Grubbs 2nd generation pre-catalyst (2) in the presence of methanol, is presented. Gibbs free energy profiles for decomposition of the pre-catalyst (2) via two possible mechanisms were computed. We predict that decomposition following tricyclohexylphosphane dissociation is most favoured compared to direct decomposition of the pre-catalyst (2). However, depending on the reaction conditions, an on-pathway mechanism may be competitive with ruthenium hydride formation.

Reactions of Cp2M (M = Ni, V) with dilithium diamido-aryl reagents; retention and oxidation of the transition metal ions.

The reactions of dilithium 1,2-diamidobenzene, [1,2-(HN)2C6H4]Li2 (L(1)H2)Li2, and dilithium 1,8-diamidonaphthalene, [1,8-(NH)2C10H6]Li2 (L(2)H2)Li2, with Cp2Ni and Cp2V have been used to obtain the new complexes (L(2)H2)2Ni{Li(THF)2}2 (3), (L(2)H2)3V{Li(THF)2}3 (4) and (L(1)H2)6Ni6·{[(L(1)H2)3(L(1)H)3Ni6Li(THF)](2-)·2[Li(THF)4](+)} (5), in which retention or oxidation of the initial metal(ii) centre is observed. Whereas 3 and 4 contain one transition metal ion within ion-paired structures, 5 has a complicated co-crystalline composition which contains octahedral Ni6-cages constructed from six square-planar (16e) Ni(II) centres.

Insights into the activity and specificity of Trypanosoma cruzi trans-sialidase from molecular dynamics simulations.

Trypanosoma cruzitrans-sialidase (TcTS), which catalyzes the transfer or hydrolysis of terminal sialic acid residues, is crucial to the development and proliferation of the T. cruzi parasite and thus has emerged as a potential drug target for the treatment of Chagas disease. We here probe the origin of the observed preference for the transfer reaction over hydrolysis where the substrate for TcTS is the natural sialyl donor (represented in this work by sialyllactose). Thus, acceptor lactose preferentially attacks the sialyl-enyzme intermediate rather than water. We compare this with the weaker preference for such transfer shown by a synthetic donor substrate, 4-methylumbelliferyl α-d-acetylneuraminide. For this reason, we conducted molecular dynamics simulations of TcTS following its sialylation by the substrate to examine the behavior of the asialyl leaving group by the protein. These simulations indicate that, where lactose is released, this leaving group samples well-defined interactions in the acceptor site, some of which are mediated by localized water molecules; also, the extent of the opening of the acceptor site to solvent is reduced as compared with those of unliganded forms of TcTS. However, where there is release of 4-methylumbelliferone, this leaving group explores a range of transient poses; surrounding active site water is also more disordered. The acceptor site explores more open conformations, similar to the case in which the 4-methylumbelliferone is absent. Thus, the predicted solvent accessibility of sialylated TcTS is increased when 4-methylumbelliferyl α-d-acetylneuraminide is the substrate compared to sialyllactose; this in turn is likely to contribute to a greater propensity for hydrolysis of the covalent intermediate. These computational simulations, which suggest that protein flexibility has a role in the transferase/sialidase activity of TcTS, have the potential to aid in the design of anti-Chagas inhibitors effective against this neglected tropical disease.

Reversible aryl migrations in metallated ureas: controlled inversion of configuration at a quaternary carbon atom.

Deprotonation with strong bases of N-vinyl ureas carrying an N'-aryl substituent leads to migration of the N'-aryl group from N to C via an allyllithium; with weaker bases and electron-deficient aryl rings the direction of the migration reverses, and aryl substituents α to the urea N atom may migrate from C to N.

Lithium choreography: intramolecular arylations of carbamate-stabilised carbanions and their mechanisms probed by in situ IR spectroscopy and DFT calculations.

Deprotonation of O-allyl, O-propargyl or O-benzyl carbamates in the presence of a lithium counterion leads to carbamate-stabilised organolithium compounds that may be quenched with electrophiles. We now report that when the allylic, propargylic or benzylic carbamate bears an N-aryl substituent, an aryl migration takes place, leading to stereochemical inversion and C-arylation of the carbamate α to oxygen. The aryl migration is an intramolecular S(N) Ar reaction, despite the lack of anion-stabilising aryl substituents. Our in situ IR studies reveal a number of intermediates along the rearrangement pathway, including a "pre-lithiation complex," the deprotonated carbamate, the rearranged anion, and the final arylated carbamate. No evidence was obtained for a dearomatised intermediate during the aryl migration. DFT calculations predict that during the reaction the solvated Li cation moves from the carbanion centre, thus freeing its lone pair for nucleophilic attack on the remote phenyl ring. This charge separation leads to several alternative conformations. The one having Li(+) bound to the carbamate oxygen gives rise to the lowest-energy transition structure, and also leads to inversion of the configuration. In agreement with the IR studies, the DFT calculations fail to locate a dearomatised intermediate.

Lithiated tertiary carbanions display variable coordination modes: evidence from DFT and NMR studies.

Density functional calculations reveal that, whereas the reaction of 2-propyl-N,N-diisopropylbenzamide (6) with tBuLi in the presence of potentially tridentate donor ligands may result in lateral deprotonation of 6, the behavior of the Lewis base is non-trivial. The ability of N and O donor centers in the co-solvent to resist Li(+) coordination is found to be synonymous with interaction of lithium with the formally deprotonated carbanion center. Low-energy structures have been identified whose predicted (1)H and (13)C NMR spectroscopic shifts are in excellent agreement with experiment. Reaction of 2-isopropyl-N,N-diisopropylbenzamide (5) with tBuLi in the presence of bidentate Lewis base N,N,N',N'-tetramethylethylenediamine (TMEDA) yields material that is suggested by NMR spectroscopy to be laterally deprotonated and to have the formulation 5-Li(l)·TMEDA. In spite of the tertiary aliphatic group at the 2-position in 5, X-ray crystallography reveals that the crystalline material isolated from the treatment of 5/(-)-sparteine with tBuLi is a lateral lithiate in which amide coordination and solvation by bidentate Lewis base results in the Li(+) ion interacting with the deprotonated α-C of the 2-iPr group (2.483(8) Å). The tertiary carbanion center remains essentially flat and the adjacent aromatic system is highly distorted. The use of a chiral co-solvent results in two diastereomeric conformers, and their direct observation in solution suggests that interconversion is slow on the NMR timescale.

On the control of secondary carbanion structure utilising ligand effects during directed metallation.

N,N-Diisopropyl-2-propylbenzamide 6-H undergoes lateral deprotonation by t-BuLi in the presence of the Lewis base PMDTA (N,N,N',N″,N″-pentamethyldiethylenetriamine) to give a benzyllithium 6-Li(l)·PMDTA that incorporates a trigonal planar secondary carbanion. In the solid state, the amide directing group and the PMDTA additive work together to abstract the metal ion from the deprotonated α-C of the propyl group (4.107(4) Å). A short distance of 1.376(3) Å is observed between the deprotonated carbon centre and a planar aromatic system that shows a pattern of bond lengths which contrasts with that reported for related tertiary carbanion systems. Analogous benzylic deprotonation is seen if 6-H is treated with t-BuLi in the presence of diglyme to give 6-Li(l)·DGME. X-ray crystallography now shows that the metal ion more closely approaches the tertiary carbanion (2.418(6) Å) but that the planarity of the deprotonated carbon centre and the bonding pattern in the organic anion seen in the PMDTA complex are retained. DFT analysis corroborates both the short distance between aromatic ring and carbanion centre and the unperturbed nature of aromaticity in 6-Li(l)·L (L = Lewis base). The observation of two structure-types for the carbanion in solution is explained theoretically and by NMR spectroscopy in terms of cis and trans isomerism imparted by partial double bond character in the arene-(α-C) bond.

Is nevirapine atropisomeric? Experimental and computational evidence for rapid conformational inversion.

The non-nucleoside reverse transcriptase inhibitor nevirapine displays in its room temperature (1)H-NMR spectrum signals characteristic of a chiral compound. Following suggestions in the recent literature that nevirapine may display atropisomerism-and therefore be a chiral compound, due to slow interconversion between two enantiomeric conformers-we report the results of an NMR and computational study which reveal that while nevirapine does indeed possess two stable enantiomeric conformations, they interconvert with a barrier of about 76 kJ mol(-1) at room temperature. Nevirapine has a half life for enantiomerisation at room temperature of the order of seconds, is not atropisomeric, and cannot exist as separable enantiomers.

Why is RCM favoured over dimerisation? Predicting and estimating thermodynamic effective molarities by solution experiments and electronic structure calculations.

The thermodynamic effective molarities of a series of simple cycloalkenes, synthesised from α,ω-dienes by reaction with Grubbs' second generation precatalyst, have been evaluated. Effective molarities were measured from a series of small scale metathesis reactions and agreed well with empirical predictions derived from the number of rotors and the product ring strain. The use of electronic structure calculations (at the M06-L/6-311G** level of theory) was explored for predicting thermodynamic effective molarities in ring-closing metathesis. However, it was found that it was necessary to apply a correction to DFT-derived free energies to account for the entropic effects of solvation.