QM/MM simulation of liquid water with an adaptive quantum region.

The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.

Reactive Many-Body Expansion for a Protonated Water Cluster.

We generalize the standard many-body expansion technique that is used to approximate the total energy of a molecular system to enable the treatment of chemical reactions by quantum chemical techniques. By considering all possible assignments of atoms to monomer units of the many-body expansion and associating suitable weights with each, we construct a potential energy surface that is a smooth function of the nuclear positions. We derive expressions for this reactive many-body expansion energy and describe an algorithm for its evaluation, which scales polynomially with system size, and therefore will make the method feasible for future condensed phase simulations. We demonstrate the accuracy and smoothness of the resulting potential energy surface on a molecular dynamics trajectory of the protonated water hexamer, using the Hartree-Fock method for the many-body term and Møller-Plesset theory for the low order terms of the many-body expansion.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

Light absorption in silicon quantum dots embedded in silica

The photon absorption in Si quantum dots (QDs) embedded in SiO2 has been systematically investigated by varying several parameters of the QD synthesis. Plasma-enhanced chemical vapor deposition (PECVD) or magnetron cosputtering (MS) have been used to deposit, upon quartz substrates, single layer, or multilayer structures of Si-rich- SiO2 (SRO) with different Si content (43-46 at. %). SRO samples have been annealed for 1 h in the 450-1250 °C range and characterized by optical absorption measurements, photoluminescence analysis, Rutherford backscattering spectrometry and x-ray Photoelectron Spectroscopy. After annealing up to 900 °C SRO films grown by MS show a higher absorption coefficient and a lower optical bandgap (∼2.0 eV) in comparison with that of PECVD samples, due to the lower density of Si-Si bonds and to the presence of nitrogen in PECVD materials. By increasing the Si content a reduction in the optical bandgap has been recorded, pointing out the role of Si-Si bonds density in the absorption process in small amorphous Si QDs. Both the photon absorption probability and energy threshold in amorphous Si QDs are higher than in bulk amorphous Si, evidencing a quantum confinement effect. For temperatures higher than 900 °C both the materials show an increase in the optical bandgap due to the amorphous-crystalline transition of the Si QDs. Fixed the SRO stoichiometry, no difference in the optical bandgap trend of multilayer or single layer structures is evidenced. These data can be profitably used to better implement Si QDs for future PV technologies. © 2009 American Institute of Physics.

Coulomb effects in tunneling through a quantum dot stack

Tunneling through two vertically coupled quantum dots is studied by means of a Pauli master equation model. The observation of double peaks in the current-voltage characteristic in a recent experiment is analyzed in terms of the tunnel coupling between the quantum dots and the coupling to the contacts. Different regimes for the emitter chemical potential indicating different peak scenarios in the tunneling current are discussed in detail. We show by comparison with a density matrix approach that the interplay of coherent and incoherent effects in the stationary current can be fully described by this approach.

Communication: energy benchmarking with quantum Monte Carlo for water nano-droplets and bulk liquid water.

We show the feasibility of using quantum Monte Carlo (QMC) to compute benchmark energies for configuration samples of thermal-equilibrium water clusters and the bulk liquid containing up to 64 molecules. Evidence that the accuracy of these benchmarks approaches that of basis-set converged coupled-cluster calculations is noted. We illustrate the usefulness of the benchmarks by using them to analyze the errors of the popular BLYP approximation of density functional theory (DFT). The results indicate the possibility of using QMC as a routine tool for analyzing DFT errors for non-covalent bonding in many types of condensed-phase molecular system.

Growth, structural and optical properties of GaAs/AlGaAs Core/shell nanowires with and without quantum well shells

We have investigated the growth, structural properties and photoluminescence of novel GaAs/AlGaAs radial heterostructure nanowires, fabricated by metalorganic chemical vapour deposition. The effect of growth temperature on nanowire morphology is discussed. Strong photoluminescence is observed from GaAs nanowires with AlGaAs shells. Core/multishell nanowires, of GaAs cores clad in several alternating layers of thick AlGaAs barrier shells and thin GaAs quantum well shells, exhibit a blue-shifted photoluminescence peak believed to arise from quantum confinement effects. A novel two-temperature growth procedure for obtaining GaAs cores is introduced, and other nanowire heterostructures are addressed. © 2006 IEEE.

Quantum dots and nanowires for optoelectronic device applications

InGaAs quantum dots (QDs) and nanowires have been grown on GaAs by metal-organic chemical vapour deposition on GaAs (100) and (111)B substrates, respectively. InGaAs QD lasers were fabricated and characterised. Results show ground-state lasing at about 1150 nm in devices with lengths greater than 2.5 mm. We also observed a strong influence of nanowire density on nanowire height specific to nanowires with high indium composition. This dependency was attributed to the large difference of diffusion length on (111)B surfaces between In and Ga reaction species, with In being the more mobile species. Selective area epitaxy for applications in quantum-dot optoelectronic device integration is also discussed in this paper. ©2006 IEEE.

Structural and optical properties of axial and radial heterostructure III-V nanowires grown by metalorganic chemical vapour deposition

We have investigated the structural properties and photoluminescence of novel axial and radial heterostructure III-V nanowires, fabricated by metalorganic chemical vapour deposition. Segments of InGaAs have been incorporated within GaAs nanowires, to create axial heterostructure nanowires which exhibit strong photoluminescence. Photoluminescence is observed from radial heterostructure nanowires (core-shell nanowires), consisting of GaAs cores with AlGaAs shells. Core-multishell nanowires, of GaAs cores clad in several alternating layers of thick AlGaAs barrier shells and thin GaAs quantum well shells, exhibit a blue-shifted photoluminescence peak arising from quantum confinement effects. © 2006 Crown Copyright.

Quantum dots and nanowires for photonics applications

We review our results on integrated photonic devices fabricated using InGaAs quantum-dots. Selective-area metal organic chemical vapor deposition (MOCVD) is used to grow the active region with quantum dots emitting at different wavelengths for fabrication of the integrated devices. We will also review the structural and optical properties of III-V nanowires, and axial and radial nanowire heterostructures grown by MOCVD. In addition to binary nanowires, such as GaAs, InAs, and InP, we have demonstrated ternary InGaAs and AlGaAs nanowires. Core-shell nanowires consisting of GaAs cores with AlGaAs shells, and core-multishell nanowires with several alternating shells of AlGaAs and GaAs, exhibit strong photoluminescence. Axial segments of InGaAs have been incorporated within GaAs nanowires to form GaAs/InGaAs nanowire superlattices.