A CC2 dielectric continuum model and a CC2 molecular mechanics model

In this paper we present theory and applications for the second-order approximate singles and doubles coupled cluster (CC2) electronic structure method coupled to either a dielectric continuum (the CC2/DC model) or a molecular mechanical intermolecular force field (the CC2/MM model). Calculations of the interaction energy, solvation energy, electric dipole moment and electric quadrupole moment of liquid water are presented using the correlated CC2 approach. The results are compared to the corresponding results using the uncorrelated Hartree-Fock (HF) and the correlated coupled cluster singles and doubles (CCSD) methods. Also, a hierarchy in the coupling between the quantum mechanical (QM) and the molecular mechanical (MM) part of the system is investigated in the QM/MM model for the three different electronic structure methods.     

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.     

The UV-vis absorption spectrum of the flavonol quercetin in methanolic solution: A theoretical investigation

The UV-vis absorption spectrum of the solvated quercetin molecule in methanol was investigated theoretically by means of an elegant type of QM/MM scheme better known as sequential Monte Carlo/quantum mechanics (S-MC/QM) methodology. A set of 125 uncorrelated Monte Carlo molecular liquid structures were properly selected through the autocorrelation function of the energy in order to be used in the quantum mechanical calculations. These molecular liquid structures were obtained by means of the radial and minimum distance distribution functions. A detailed account of the pattern of hydrogen bond structures obtained in this study is also available. The computed results obtained here were directly compared with the available experimental data in order to validate our theoretical model and through this comparison a very good conformity between theoretical and available experimental results was found.     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACT

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.     

Docking accuracy enhanced by QM-derived protein charges

Effects of protein polari sation on docking accuracy were investigated using molecular docking programme AutoDock 4 in which topology-specific empirical Gasteiger charges were replaced with Polarised protein-specific charges (PPC) to represent quantum mechanics- polarised protein. Docking was successfully conducted for 50 diverse protein–ligand complexes. The docking with PPC charges shows a decrease in the root-mean-square deviation (RMSD) values of ligands compared to those from the docking with Gasteiger charges. Ligand binding orientations and their key interactions such as hydrogen bonding interactions in X-ray structures were substantially reproduced in complexes docked using PPC scheme with 98% of the RMSDs of the best docking poses less than 2 Å compared to 74% in the docking with Gasteiger charges. Considerable improvements in docking accuracy were observed by simply altering the atomic partial charges in the scoring function, which reflects the importance of protein polarisation in molecular docking. Further research can be carried out to (1) include polarisation of both ligands and proteins to account for polarisation effects within protein and between protein and ligand, and (2) develop a PPC-based scoring function to increase the docking accuracies for protein–ligand complexes from a larger variety of protein families.     

Investigation of dodecylammonium adsorption on mica,albite and quartz surfaces by QM/MM simulation

The absorption mechanisms of collector and mineral surface structures play important roles in studies of lepidolite flotation. In this work, quantum mechanics (QM) and hybrid quantum mechanics/molecular mechanics (MM) methods were implemented to investigate the flotation mechanisms of lepidolite from muscovite, quartz and albite. The crystal structures, electron density distributions, bonds and the densities of states of lepidolite were calculated and compared with those of muscovite. The adsorption structures and energies of monomer dodecylammonium (DDA) on the three different minerals were also calculated. The headgroup of the DDA cation was found to adsorb on the surface of minerals, with its hydrophobic tail stretching into the vacuum slab, approximately perpendicular to the surface. Simulation results indicate that the purity of fine lepidolite is limited by the existence of muscovite, due to their similarities in surficial structure and properties. Other gangues were found to be removed efficiently with the use of acidic conditions. The results are in good agreement with other experiments. Compared with simple MM simulations, the use of the QM/MM methods to investigate the adsorption on minerals without specific forcefield parameters was concluded to be a more accurate method to attain monomer surfactant–mineral adsorption energies.     

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.     

Solvent effects on optical excitations of poly <Emphasis Type="Italic">para</Emphasis> phenylene ethynylene studied by QM/MM simulations based on many-body Green's functions theory

Electronic excitations in dilute solutions of poly para phenylene ethynylene (poly-PPE) are studied using a QM/MM approach combining many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation with polarizable force field models. Oligomers up to a length of 7.5?nm (10 repeat units) functionalized with nonyl side chains are solvated in toluene and water, respectively. After equilibration using atomistic molecular dynamics (MD), the system is partitioned into a quantum region (backbone) embedded into a classical (side chains and solvent) environment. Optical absorption properties are calculated solving the coupled QM/MM system self-consistently and special attention is paid to the effects of solvents. The model allows to differentiate the influence of oligomer conformation induced by the solvation from electronic effects related to local electric fields and polarization. It is found that the electronic environment contributions are negligible compared to the conformational dynamics of the conjugated PPE. An analysis of the electron-hole wave function reveals a sensitivity of energy and localization characteristics of the excited states to bends in the global conformation of the oligomer rather than to the relative of phenyl rings along the backbone.     

Small silver clusters at paramagnetic defects of silica surfaces: A density functional embedded-cluster study

We studied the interaction of small Ag_n clusters (n = 1–4) with paramagnetic defect centers of a dehydroxylated silica surface using an all-electron scalar relativistic density functional method. The surface and adsorption complexes on it were modeled with an accurate quantum mechanics/molecular mechanics (QM/MM) scheme of embedding QM clusters in an elastic polarizable environment, described at the molecular mechanics level (MM). We analyzed two types of frequent point defects as sites for trapping and growing of Ag clusters: a silicon atom with a dangling bond (E′ center), ≡ Si?, and a non-bridging oxygen center (NBO), ≡ Si–O?. The Ag clusters interact with these paramagnetic centers forming strong covalent metal-defect bonds. The high adsorption energy allows one to consider the NBO and E′ sites as traps of single Ag atoms and as centers of cluster growth. We also explored the effect of adsorption on observable electronic properties of the silver clusters and of the defects of the silica surface.     

CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities

We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR intensity data on reversibly forming weak complexes. In this approach, the global minimum for the bound-ligand conformation is obtained by a hybrid structure refinement method involving CORCEMA calculation of intensities and simulated annealing optimization of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints and the NOE R-factor as the pseudo-energy function to be minimized. This method is illustrated using simulated STD data sets for typical carbohydrate and peptide ligands. Our procedure also allows for the optimization of side chain torsion angles of protein residues within the binding pocket. This procedure is useful in refining and improving initial models based on crystallography or computer docking or other algorithms to generate models for the bound ligand (e.g., a lead compound) within the protein binding pocket compatible with solution STD-NMR data. This method may facilitate structure-based drug design efforts.     

Optimization of semiconductor quantum devices by evolutionary search

A novel simulation strategy is proposed for searching for semiconductor quantum devices that are optimized with respect to required performances. Based on evolutionary programming, a technique that implements the paradigm of genetic algorithms in more-complex data structures than strings of bits, the proposed algorithm is able to deal with quantum devices with preset nontrivial constraints (e.g., transition energies, geometric requirements). Therefore our approach allows for automatic design, thus avoiding costly by-hand optimizations. We demonstrate the advantages of the proposed algorithm through a relevant and nontrivial application, the optimization of a second-harmonic-generation device working in resonance conditions.     

Quantum Boltzmann equation solved by Monte Carlo method for nano-scale semiconductor devices simulation

A two-dimensional (2D) full band self-consistent ensemble Monte Carlo (MC) method for solving the quantum Boltzmann equation, including collision broadening and quantum potential corrections, is developed to extend the MC method to the study of nano-scale semiconductor devices with obvious quantum mechanical (QM) effects. The quantum effects both in real space and momentum space in nano-scale semiconductor devices can be simulated. The effective mobility in the inversion layer of n and p channel MOSFET is simulated and compared with experimental data to verify this method. With this method 50nm ultra thin body silicon on insulator MOSFET are simulated. Results indicate that this method can be used to simulate the 2D QM effects in semiconductor devices including tunnelling effect.     

Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用

对人类免疫缺陷病毒（HIV-1）蛋白酶-抑制剂复合物分别在AMBER力场及极化专一性蛋白电荷（PPC）下进行10 ns的分子动力学模拟（MD）,并用MM/PBSA方法计算结合自由能.PPC是基于线性标度的量子力学计算的静电势拟合的蛋白质电荷,能够更准确地描述蛋白质所处的静电环境.结果表明：PPC电荷计算的结合自由能比AMBER力场计算的结合自由能更接近实验值.     

Spectrum of electron-hole states of the Si/Ge structure with Ge quantum dots

The lateral photoconductivity spectra of Si/Ge multilayer structures with Ge quantum dots of various sizes are investigated. We observed optical transition lines between the hole levels of quantum dots and electronic states of Si. This enabled us to construct a detailed energy level diagram of the electron-hole spectrum of the Si/Ge structures. It is shown that the hole levels of Ge quantum dots are successfully described by the “quantum box” model using the actual sizes of Ge islands. It I found that the position of the longwavelength photosensitivity boundary of Si/Ge structures with Ge quantum dots can be controlled by changing the growth parameters.     

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.     

Relaxation of mechanical stresses in an array of Ge quantum dots obtained in Si

Raman scattering on optical phonons in Si/Ge/Si structures with Ge quantum dots grown by molecular beam epitaxy at low temperatures 200–300°C has been investigated. A pseudomorphic state of an array of Ge quantum dots to a Si matrix with an ideally sharp interface has been obtained. Features associated with the inelastic relaxation of mechanical stresses have been revealed in the Raman spectrum. Two mechanisms of stress relaxation are separated. It has been shown that the spectrum of the electronic states of the array differs significantly from the set of the discrete levels of a single quantum dot, because the relaxation is inhomogeneous.