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.

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.

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.

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.

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.

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.

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.

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.

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.

Ligand effects in the formation of tertiary carbanions from substituted tertiary aromatic amides.

Reaction of 2-isopropyl-(N,N-diisopropyl)-benzamide 5 with tBuLi in ether results in ortho deprotonation and the formation of a hemisolvate based on a tetranuclear dimer of (5-Li(o))(2)⋅Et(2)O. The solid-state structure exhibits a dimer core in which the amide oxygen atoms fail to stabilize the metal ions but are instead available for interaction with two metalated monomers that reside peripheral to the core. Reaction of 5 with tBuLi in the presence of the tridentate Lewis base PMDTA (N,N,N',N'',N''-pentamethyldiethylenetriamine) takes a different course. In spite of the tertiary aliphatic group at the 2-position in 5, X-ray crystallography revealed that a remarkable benzylic (lateral) deprotonation had occurred, giving the tertiary benzyllithium 5-Li(l)⋅PMDTA. The solid-state structure reveals that amide coordination and solvation by PMDTA combine to distance the Li(+) ion from the deprotonated α-C of the 2-iPr group (3.859(4) Å), thus giving an essentially flat tertiary carbanion and a highly distorted aromatic system. DFT analysis suggests that the metal ion resides closer to the carbanion center in solution. In line with this, the same (benzylic) deprotonation is noted if the reaction is attempted in the presence of tridentate diglyme, with X-ray crystallography revealing that the metal is now closer to the tertiary carbanion (2.497(4) Å). Electrophilic quenches of lithiated 5 have allowed, for the first time, the formation of quaternary benzylic substituents by lateral lithiation.

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.

Cadmium sulfide and cadmium phosphide thin films from a single cadmium compound.

Aerosol-assisted chemical vapor deposition of Cd[(SP(i)Pr(2))(2)N](2) leads to the growth of cadmium sulfide and/or phosphide thin films on glass. Decomposition of the precursor has been studied by pyrolysis-gas chromatography/mass spectrometry and modeled by density functional theory.

The structure and interaction energies of the weak complexes of CHClF2 and CHF3 with HCCH: a test of density functional theory methods.

The structure and interaction energies of the weak non-covalent complexes of CHClF(2) and CHF(3) with HCCH have been predicted using a number of density functional based approaches, and compared with both high resolution spectroscopic data recently reported by Sexton et al. [Phys. Chem. Chem. Phys., 2010, 12, 14263-14270], and with high level benchmark calculations reported herein. We find that this is another case where the M05 and M06 families of functionals, as well as the DFT-D approach, are competitive with the more costly wavefunction based methods. We highlight the problem of deriving unique intermolecular structural parameters from the experimental microwave data.

The origin of the conformational preference of N,N'-diaryl-N,N'-dimethyl ureas.

Poly aromatic ureas and poly aromatic amides are important classes of foldamers-oligomers with well defined conformations. We have explored the origins of the conformational preference of some N,N'-diaryl-N,N'-dimethyl ureas by a combination of NMR spectroscopy and electronic structure calculations using both a recently developed density functional (M06-2X) and a DFT approach (DFT-D) having empirical corrections for dispersive interactions. We have validated the DFT-D approach for structures of this type using high level wavefunction calculations, (CCSD(T)), of the unsubstituted N,N'-diphenyl-N,N'-dimethyl urea. For the N,N'-diaryl-N,N'-dimethyl ureas we have identified a number of 'endo' conformers (i.e. having an E,E geometrical conformation about the two urea C-N bonds), both π- and tert-butyl-stacked, as well as 'exo' structures (having a Z geometrical conformation about at least one of the C-N bonds), and have computed the relative energies of these conformers as well as the barriers for their interconversion. We find that the relative energies of the 'endo' structures closely follow the relative values of the dispersive interactions. The calculations have allowed us to associate different conformers with the various peaks in the NMR spectra, which point to relatively small differences in energy between the conformers. Somewhat larger energy differences are predicted by the two computational approaches, with the M06-2X functional performing the better of the two. It is suggested that the continuum model employed may not be sufficiently accurate to reflect the solvation of the various conformers.

The effects of perfluorination on carbohydrate-pi interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin.

The effect of benzene fluorination on C-H...pi interactions is studied using a number of computational methods applied to a range of intermolecular complexes. High level wavefunction methods (CCSD(T)) predict a slightly greater interaction energy for complexes of benzene with methane or fucose, compared to corresponding complexes involving hexafluorobenzene. A number of more approximate treatments, DFT with the M06-2X functional, PM3-D* and MM methods, give interaction energies within 1 kcal mol(-1) of the high level values, and also correctly predict that the interaction energy is slightly greater for benzene compared to hexafluorobenzene. However, the DFT-D model used here predicts that the interaction energy is slightly greater for hexafluorobenzene. Molecular dynamics simulations, employing the GLYCAM-06 force field, validated here, are used to model the complexes of benzene and hexafluorobenzene with beta-cyclodextrin in aqueous solution. We predict the binding free energies of the complexes to be within 0.5 kcal mol(-1), and suggest that the different chemical shifts of the H5 protons observed in the two complexes arise from their slightly different structures, rather than from different binding energies.

N to C aryl migration in lithiated carbamates: alpha-arylation of benzylic alcohols.

We report a new mode of reactivity displayed by lithiated O-benzyl carbamates carrying an N-aryl substituent: upon lithiation, the N-aryl group is transferred cleanly from N to C. An arylation of the carbamate results, providing a route to alpha,alpha-arylated secondary or tertiary alcohols. We also report density functional theory calculations supporting the proposal that arylation proceeds through a dearomatizing attack on the aromatic ring, a significantly lower energy pathway than the 1,2-acyl transfer observed with related N-alkyl carbamates.

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.

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.

Claisen rearrangement of aliphatic allyl vinyl ethers in the presence of copper(II) bisoxazoline.

The Claisen rearrangement of 1-methyl-2-isopropyoxycarbonyl-6-propyl allyl vinyl ether catalyzed by copper(II) bisoxazoline (Cu-box) has been investigated using density functional theory. Both the phenyl- and tert-butyl-substituted Cu-box systems have been studied. Three different reaction media (vacuum, CH2Cl2, CH3CN) have been considered. In vacuum, the phenyl Cu-box catalyzed reaction yields a (1R,6R) configured major product with a low selectivity. The solvent induces a higher selectivity and a reversal of the absolute configuration (1S,6S). However, the tert-butyl Cu-box catalyzed reaction yields (1R,6R) as the major product both in the gas phase and in the solvent with a good selectivity. Although chair-like TSs are lower in energy than boat-like TSs, the energy difference is small. This is because in the presence of the catalyst the distance between the allyl and vinyl parts of the substrate is relatively large, and thus the steric repulsion between them is smaller than would normally be expected for boat-like structures. The enantioselectivity of tert-butyl Cu-box originates from the steric interactions between the substrate and the catalyst, which are less important for the phenyl Cu-box where the enantioselectivity is determined by the solvent effects.