Multicentred QM/QM methods for overlapping model systems

An improved, more general method for performing multicentred integrated QM/QM calculations is presented. The new approach allows the multicentred approximation to be extended to overlapping model systems, removing a significant limitation of the original approach. The usefulness and numerical accuracy of the equations presented are confirmed via some applications to dipole–dipole, charge–dipole and charge–charge complexes. The method performs well for all of these complexes, which range from very weakly to very strongly bound and in which non-additivity effects on interaction energies range from 0.2 to 17kcalmol^?1.     

New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach

Molecular Diversity - SARS-CoV-2 Mpro, also known as the main protease or 3C-like protease, is a key enzyme involved in the replication process of the virus that is causing the COVID-19 pandemic....     

Hydrogen bonding in liquid water: An ab initio QM/MM MD simulation study

Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.     

Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase

Chorismate mutase provides an important test of theories of enzyme catalysis, and of modelling methods. The Claisen rearrangement of chorismate to prephenate in the enzyme has been modelled here by a combined quantum mechanics/molecular mechanics (QM/MM) method. Several pathways have been calculated. The sensitivity of the results to details of model preparation and pathway calculation is tested, and the results are compared in detail to previous similar studies and experiments. The potential energy barrier for the enzyme reaction is estimated at 24.5—31.6 kcal mol^?1 (AMl/CHARMM), and 2.7—11.9 kcal mol^?1 with corrections (e.g. B3LYP/6-31 + G(d)). In agreement with previous studies, the present analysis of the calculated paths provides unequivocal evidence of significant transition state stabilization by the enzyme, indicating that this is central to catalysis by the enzyme. The active site is exquisitely complementary to the transition state, stabilizing it more than the substrate, so reducing the barrier to reaction. A number of similar pathways for reaction exist in the protein, as expected. Small structural differences give rise to differences in energetic contributions. Major electrostatic contributions to transition state stabilization come in all cases from Arg90, Arg7, one or two water molecules, and Glu78 (Glu78 destabilizes the transition state less than the substrate), while Arg63 contributes significantly in one model.     

Quantum nonintegrability and the classical limit for usp(4) systems

We investigate the transition from integrability to chaos in a system built of usp(4) elements, both in the quantum case and in its classical limit, obtained using coherent states. This algebraic Hamiltonian consists in an integrable term plus a nonlinear perturbation, and we see that the level spacing distribution for the quantum system is well approximated by the Berry-Robnik-Brody distribution, and accordingly the classical limit displays mixed dynamics.     

Theoretical study of keto–enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method)

In this study, the tautomeric equilibrium between the keto and enol forms has been studied for five typical ketones and aldehydes: i‐butanal, acetaldehyde, acetone, acetylacetone, and dimedone. The level of theory used in the gas‐phase calculation was Becke, three‐parameter, Lee–Yang–Parr/6‐311G(d,p)//Becke, three‐parameter, Lee–Yang–Parr/6‐31G(d). The free energies of solvation were included in the calculation by using the free‐energy perturbation method based on Monte Carlo simulation, that is, the quantum mechanical/Monte Carlo/free‐energy perturbation method. Three different models, incorporating no‐water, one‐water, and two‐waters, were adopted. The results showed that in the gas phase the addition of water molecules to the reaction mechanism caused the activation barriers (ΔG^?_gas) to decrease by half relative to the water‐free mechanism, but there was no effect on the relative difference in free energy, ΔG_gas. The solvation effects (ΔG_sol), based on quantum mechanical/Monte Carlo/free‐energy perturbation calculations, were added to those of the gas‐phase results of the one‐water and two‐waters models. The two‐waters model produced values that were very consistent with the experimental data for all of the tautomers. The differences in the relative Gibbs free energy (ΔG_rxn) were less than 1.0 kcal mol^–1. In summary, the inclusion of solvent molecules in gas‐phase calculations plays a very important role in producing results consistent with experimental data. Copyright © 2012 John Wiley & Sons, Ltd.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

Quantum meaning of classical (field) theory for fermi systems

We investigate the cosmological consequences of a phase transition which is driven primarily by slow nucleation of bubbles of the new phase via the effectively zero temperature quantum tunneling process of Coleman and Callan. These bubbles will asymptotically fill an arbitrarily large fraction of the space, yet they never percolate. Instead they form finite clusters, with each cluster dominated by a single largest bubble. The large scale thermalization required by the original “inflationary universe” scenario does not take place. The Coleman-De Luccia formalism for bubble formation in curved space is reviewed, with minor extensions. We argue that a single uncollided bubble would contain much less total entropy than the observed universe, unless the Higgs field potential involves widely disparate mass scales, as in the new inflationary universe scenario. We also argue that finite clusters are unlikely to yield a homogeneous and isotropic region containing sufficient entropy. Thus, unless the Higgs potential has the special form required by the new inflationary scenario, it appears quite implausible that there was such a phase transition in our past.     

The QM/MM approach for wavefunctions,energies and response functions within self-consistent field and coupled cluster theories

This paper presents the coupled cluster/molecular mechanics (CC/MM) and self-consistent field/molecular mechanics (SCF/MM) approaches for wavefunctions, energies and response properties. Two physically different theories are derived, the mean-field and the direct-field interaction approaches, together with expressions for the optimization condition of both variational and non-variational wavefunctions and energies. Also derived are the linear response functions at the CC/MM and SCF/MM levels of theory, and the expressions are compared with the vacuum response functions.     

Quantum loop current in a C(60) molecular bridge

The existence of a quantum loop current in a C(60) molecular bridge is predicted using the Green's function method. The model for the molecular bridge consists of a C(60) molecule attached to one-dimensional conductive electrodes. It is shown that the loop current is related to the degeneracy of the energy levels of the C(60) molecule. Specific to this loop current is its magnitude which is much larger than that of the source-drain current. The associated magnetic moment also shows certain remarkable features such as its inversion with the energy across the molecular levels and the restriction of its direction onto a single plane.     

Low-dimensional systems: Quantum size effects and electronic properties of semiconductor microcrystallites (zero-dimensional systems) and some quasi-two-dimensional systems

This review is concerned with quantum confinement effects in low-dimensional semiconductor systems. The emphasis is on the optical properties, including luminescence, of nanometre-sized microcrystallites, also referred to as zerodimensional systems. There is some discussion on certain of the two-dimensional systems, such as thin films and layer structures. The increase in energy of excitation peaks (blue shift) as the radius R of a microcrystallite is reduced is treated theoretically, and experimental data when they are available are used to assess the reliability of the different models that have been used. These experiments normally make use of microcrystallites dispersed in a large-bandgap matrix such as glass, rocksalt, polymers, zeolites or liquids. Exciton binding energies E b are larger than for bulk semiconductors, and oscillator strengths are higher for the microcrystallites. The regimes of direct interest are as follows. Firstly there is the so-called weak-confinement regime where R is greater than the bulk exciton Bohr radius a B . Experimentally, semiconductors such as CuCl with a B , 7 Å, are suitable for study in this case. Secondly there is the moderate-confinement regime, where R , a B , and a h < R < a e , a h and a e being the hole and electron Bohr radii, respectively. Finally there is the strong-confinement regime, with R < a B , and R < a h , a e . For this case we are concerned with a ladder of discrete energy levels, as in molecular systems, rather than energy bands. The electrons and holes are treated as independent particles, and for excited states we refer to electron-hole pairs rather than excitons. Suitable materials for investigation in this regime are the II-VI semiconductors, and also GaAs and Ge, for which a B is relatively large. Although a number of different theoretical models have been used, none can be described as completely first-principles calculations, and there is room for improvement on this aspect. However, useful expressions have been developed by Brus and by Lippens and Lannoo, giving the energy of excited states as a function of R , in terms of the bulk energy gap, kinetic energy, Coulomb energy and correlation energy. Other phenomena discussed are firstly biexciton formation by the use of high intensity laser beams and secondly nonlinear optical effects. Strong nonlinearities and short decay times for excited states have been predicted, and the models developed cover both the resonant and the non-resonant cases. The possibility of using microcrystallites embedded at reasonable concentrations in a glass matrix in the field of optical communications and optical switching is also considered.     

Quantum tunneling through aromatic molecular junctions for molecular devices: A review

In this review article, we have outlined major factors which decide the electron transport properties through two probe aromatic molecular junctions using DFT + NEGF framework. We have discussed the nature of central molecule, doping of molecule, geometry of metal-molecule-metal junction, nature of electrode material and electrode orientations that can fluctuate the electrical conductance of aromatic molecular junctions. We investigate our study by considering various aromatic molecules from benzene, naphthalene, anthracene to fullerene and conclude our findings in this state of art review paper. All the concluded results are found to be closely analogous to previous findings.     

Quantum mechanical and molecular mechanical simulation approaches bridging length and time scales for simulation of interface reactions in realistic environments

Computer-assisted design of functional materials requires methods that are able to simultaneously describe these with the necessary accuracy at the relevant time and length scales. One such possibility is the combination of classical interatomic force fields with density-functional based tight-binding (DFTB), an efficient and accurate quantum method. We employ this combination to study porous silicon dioxide functionalized with imidazole, which is used as an additive to polymer electrolyte membranes (PEM) for fuel cells applications. We analyze the water density and the dynamics of the functional groups at different temperatures by molecular dynamics simulation, whereas we calculate DFTB free energy barriers for proton transport reactions within the functionalized surface at different water contents. Combining both results, a macroscopic picture of the proton diffusion is drawn. Furthermore, we simulate the adsorption reactions of different components of an epoxide adhesive system on gamma alumina, using a direct coupling of DFTB and classical modeling. This yields direct chemical insight, how water and excess protons at the interface weaken the adhesion between epoxy polymers and natively oxidized aluminium.     

Weak intermolecular interactions in an ionically bound molecular adsorbate: cyclopentadienyl/Cu(111)

The dissociative adsorption of cyclopentadiene (C(5)H(6)) on Cu(111) yields a cyclopentadienyl (Cp) species with strongly anionic characteristics. The Cp potential energy surface and frictional coupling to the substrate are determined from measurements of dynamics of the molecule together with density functional calculations. The molecule is shown to occupy degenerate threefold adsorption sites and molecular motion is characterized by a low diffusional energy barrier of 40±3 meV with strong frictional dissipation. Repulsive dipole-dipole interactions are not detected despite charge transfer from substrate to adsorbate.     

Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values

The rate-determining proton transfer step in the amine reduction reaction catalysed by the enzyme methylamine dehydrogenase has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. Variational transition state theory, combined with multidimensional tunnelling corrections, has been employed to calculate reaction rate constants, and hence deuterium kinetic isotope effects (KIE). To render these calculations computationally feasible, the electronic structure was described using a PM3 method with specific reaction parameters obtained by a fit to energetics obtained at a high level for a small model system. Compared to the use of standard parameters, these revised parameters result in a considerable improvement in the predicted KIE values and activation energy. For both methylamine and ethanolamine substrates, through-barrier, rather than over-barrier, motion is found to dominate with KIE values that are large and close to the experimental values. A major difference between the two substrates is that, for ethanolamine, different hydrogen bonding structures involving the substrate hydroxyl are possible, leading to very different potential energy surfaces with KIE values covering a considerable range. We speculate that this is the origin of the differing temperature behaviour observed for the KIEs of the two substrates.     

Synthesis,characterization, antibacterial evaluation, 2D-QSAR modeling and molecular docking studies for benzocaine derivatives

Molecular Diversity - Possible application of incorporating a well-known drug (benzocaine) with cyanoacetamide function to get a powerful synthon ethyl 4-cyanoacetamido benzoate. This synthetic...     

Photoinduced changes of mechanical stress in amorphous Ge-As-S(Se) film/Si substrate systems

Received: 16 April 1997/Accepted: 23 June 1997     

Quantum speed limit for qubit systems: Exact results

Given an initial state, a target state, and a driving Hamiltonian, how fast can the initial state evolve into the target state according to the Schröchinger dynamics? This problem arises in a variety of contexts such as quantum computation, quantum control, and in particular, the problem of maximum information processing rate of quantum systems, and has been studied extensively due to its fundamental importance. In this paper, we purse further the study in the qubit case in which the particular structure admits stronger results. We use the quantum fidelity as well as relative entropy as a figure of merit to characterize the closeness between a fixed initial qubit state and another one undergoing unitary evolution. We work out explicitly maximal and minimal fidelity and relative entropy by determining the closest and the farthest states to the target state and show that these results are unique for qubit systems. We also determine the minimal time for a state to evolve to the extremal states (that is, the farthest one evolved from the initial state in the sense of minimal fidelity or maximal relative entropy), which generalizes the celebrated Mandelstam–Tamm bound and the Margolus–Levitin bound for qubit systems. We further reveal an interesting fact that this minimal time is independent of the initial states.     

Investigation of photoprocesses in complex molecular systems (macroheterocycles)

Spectral properties and photophysical processes in two macroheterocycles consisting of two pairs of chemically bound fluorophors 1-(3,4-dicyanophenyl)-benzotriazole and 9,10-bis (4-aminophenyl)-anthracene (MI) and 1-(3,4- dicyanophenyl)-benzotriazole and rhodamine (MII) are examined by quantum-chemical and experimental methods. It is demonstrated that macroheterocycles are not bifluorophor molecules in classical understanding by virtue of their unique structure. All processes of electronic excitation energy deactivation in such systems proceed as in a single molecule, and electronic states in them are common with different relative contributions of molecular orbitals belonging to donor and acceptor fragments. The presence of identical fragments results in splitting of electronic states with the forbidden lower state from which the fluorescence is improbable.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 10, pp. 13–18, October, 2004.