Molecular second-quantized Hamiltonian:Electron correlation and non-adiabatic coupling treated on an equal footing

We introduce a new theoretical and computational framework for treating molecular quantum mechanics without the Born–Oppenheimer approximation. The molecular wavefunction is represented in a tensor-product space of electronic and vibrational basis functions, with electronic basis chosen to reproduce the mean-field electronic structure at all geometries. We show how to transform the Hamiltonian to a fully second-quantized form with creation/annihilation operators for electronic and vibrational quantum particles, paving the way for polynomial-scaling approximations to the tensor-product space formalism. In addition, we make a proof-of-principle application of the new Ansatz to the vibronic spectrum of C2

Direct quantum dynamics using variational Gaussian wavepackets and Gaussian process regression

The method of direct variational quantum nuclear dynamics in a basis of Gaussian wavepackets, combined with the potential energy surfaces fitted on-the-fly using Gaussian process regression, is described together with its implementation. Enabling exact and efficient analytic evaluation of Hamiltonian matrix elements, this approach allows for black-box quantum dynamics of multidimensional anharmonic molecular systems. Example calculations of intra-molecular proton transfer on the electronic ground state of salicylaldimine are provided, and future algorithmic improvements as well as the potential for multiple-state non-adiabatic dynamics are discussed

Toward accurate QM/MM reaction barriers with large QM regions using domain based pair natural orbital coupled cluster theory

The hydroxylation reaction catalyzed by p-hydroxybenzoate hydroxylase and the Baeyer–Villiger reaction catalyzed by cyclohexanone monooxygenase are investigated by means of quantum mechanical/molecular mechanical (QM/MM) calculations at different levels of QM theory. The geometries of the stationary points along the reaction profile are obtained from QM/MM geometry optimizations, in which the QM region is treated by density functional theory (DFT). Relative energies are determined from single-point QM/MM calculations using the domain-based local pair natural orbital coupled cluster DLPNO-CCSD(T) method as QM component. The results are compared with single-point DFT/MM energies obtained using popular density functionals and with available experimental and computational data. It is found that the choice of the QM method strongly affects the computed energy profiles for these reactions. Different density functionals provide qualitatively different energy barriers (variations of the order of 10 kcal/mol in both reactions), thus limiting the confidence in DFT/MM computational predictions of energy profiles. On the other hand, the use of the DLPNO-CCSD(T) method in conjunction with large QM regions and basis sets makes it possible to achieve high accuracy. A critical discussion of all the technical aspects of the calculations is given with the aim of aiding computational chemists in the application of the DLPNO-CCSD(T) methodology in QM/MM calculations

Electron and nuclear dynamics following ionisation of modified bismethylene-adamantane

We have simulated the coupled electron and nuclear dynamics using the Ehrenfest method upon valence ionisation of modified bismethylene-adamantane (BMA) molecules where there is an electron transfer between the two π bonds. We have shown that the nuclear motion significantly affects the electron dynamics after a few fs when the electronic states involved are close in energy. We have also demonstrated how the non-stationary electronic wave packet determines the nuclear motion, more precisely the asymmetric stretching of the two π bonds, illustrating “charge-directed reactivity”. Taking into account the nuclear wave packet width results in the dephasing of electron dynamics with a half-life of 8 fs; this eventually leads to the equal delocalisation of the hole density over the two methylene groups and thus symmetric bond lengths

Novel long-chain neurotoxins from Bungarus candidus distinguish the two binding sites in muscle-type nicotinic acetylcholine receptors

αδ-Bungarotoxins, a novel group of long-chain α-neurotoxins, manifest different affinity to two agonist/competitive antagonist binding sites of muscle-type nicotinic acetylcholine receptors (nAChRs), being more active at the interface of α–δ subunits. Three isoforms (αδ-BgTx-1–3) were identified in Malayan Krait (Bungarus candidus) from Thailand by genomic DNA analysis; two of them (αδ-BgTx-1 and 2) were isolated from its venom. The toxins comprise 73 amino acid residues and 5 disulfide bridges, being homologous to α-bungarotoxin (α-BgTx), a classical blocker of muscle-type and neuronal α7, α8, and α9α10 nAChRs. The toxicity of αδ-BgTx-1 (LD50 = 0.17–0.28 µg/g mouse, i.p. injection) is essentially as high as that of α-BgTx. In the chick biventer cervicis nerve–muscle preparation, αδ-BgTx-1 completely abolished acetylcholine response, but in contrast with the block by α-BgTx, acetylcholine response was fully reversible by washing. αδ-BgTxs, similar to α-BgTx, bind with high affinity to α7 and muscle-type nAChRs. However, the major difference of αδ-BgTxs from α-BgTx and other naturally occurring α-neurotoxins is that αδ-BgTxs discriminate the two binding sites in the Torpedo californica and mouse muscle nAChRs showing up to two orders of magnitude higher affinity for the α–δ site as compared with α–ε or α–γ binding site interfaces. Molecular modeling and analysis of the literature provided possible explanations for these differences in binding mode; one of the probable reasons being the lower content of positively charged residues in αδ-BgTxs. Thus, αδ-BgTxs are new tools for studies on nAChRs

The Molpro quantum chemistry package

Molpro is a general purpose quantum chemistry software package with a long development history. It was originally focused on accurate wavefunction calculations for small molecules but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding, and anharmonic vibrational spectra. In addition to conventional input-file specification of calculations, Molpro calculations can now be specified and analyzed via a new graphical user interface and through a Python framework

A complete description of tunnelling using direct quantum dynamics simulation: Salicylaldimine proton transfer

We demonstrate here conclusively that the variational multiconfiguration Gaussian (vMCG) method converges to the grid based full quantum dynamics multiconfiguration time-dependent Hartree result for a tunnelling problem in many dimensions, using the intramolecular proton transfer in salicylaldimine as a model system. The 13-dimensional model potential energy surface was obtained from Hartree Fock energies with the 6-31G* basis set and the expectation value of the flux operator along the transition mode was used as a benchmark characteristic. As well as showing excellent convergence of the vMCG method on the model surface using a local harmonic approximation and a moderate number of basis functions, we show that the direct dynamics version of the vMCG also performs very well, usually needs the same number of Gaussians to converge, and converges to exact results if those are obtained on an accurately fitted surface. Finally, we make an important observation that the width of the Gaussian basis functions must be chosen very carefully to obtain accurate results with the use of the frozen-width approximation

Quantum Mechanical/Molecular Mechanical Study on the Enantioselectivity of the Enzymatic Baeyer–Villiger Reaction of 4‑Hydroxycyclohexanone

We report a combined quantum mechanical/molecular mechanical (QM/MM) study of the effect of mutations of the Phe434 residue in the active site of cyclohexanone monooxygenase (CHMO) on its enantioselectivity toward 4-hydroxycyclohexanone. In terms of our previously established model of the enzymatic Baeyer–Villiger reaction, enantioselectivity is governed by the preference toward the equatorial ((<i>S</i>)-selectivity) or axial ((<i>R</i>)-selectivity) conformation of the substituent at the C4 carbon atom of the cyclohexanone ring in the Criegee intermediate and the subsequent rate-limiting transition state for migration (TS2). We assess the enantiopreference by locating all relevant TS2 structures at the QM/MM level. In the wild-type enzyme we find that the axial conformation is energetically slightly more stable, thus leading to a small excess of (<i>R</i>)-product. In the Phe434Ser mutant, there is a hydrogen bond between the serine side chain and the equatorial substrate hydroxyl group that is retained during the whole reaction, and hence there is pronounced reverse (<i>S</i>)-enantioselectivity. Another mutant, Phe434Ile, is shown to preserve and enhance the (<i>R</i>)-selectivity. All these findings are in accordance with experiment. The QM/MM calculations allow us to explain the effect of point mutations on CHMO enantioselectivity for the first time at the molecular level by an analysis of the specific interactions between substrate and active-site environment in the TS2 structures that satisfy the basic stereoelectronic requirement of anti-periplanarity for the migrating σ-bond