Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients.

Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated.

Quasi-atomic orbital analysis of halogen bonding interactions.

A quasi-atomic orbital analysis of the halogen bonded NH3⋯XF complexes (X = F, Cl, Br, and I) is performed to gain insight into the electronic properties associated with these σ-hole interactions. It is shown that significant sharing of electrons between the nitrogen lone pair of the ammonia molecule and the XF molecule occurs, resulting in a weakening of the X-F bond. In addition, the N-X bond shows increasing covalent character as the size of the halogen atom X increases.

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures.

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g.

Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory.

We propose to generalize the previously developed two-layer permuted adaptive-partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms as QM or MM on-the-fly in dynamics simulations, to multilayer adaptive-partitioning algorithms that enable multiple levels of theory. In this work, we formulate two new algorithms that smoothly interpolate the energy between two QM (Q1 and Q2) levels of theory. The first "permuted adaptive-partitioning" scheme is based on the weighted many-body expansion of the potential, as in the adaptive-partitioning QM/MM.

Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.

A new method called QM-VM2 is presented that efficiently combines statistical mechanics with quantum mechanical (QM) energy potentials in order to calculate noncovalent binding free energies of host-guest systems. QM-VM2 efficiently couples the use of semi-empirical QM (SEQM) energies and geometry optimizations with an underlying molecular mechanics (MM) based conformational search, to find low SEQM energy minima, and allows for processing of these minima at higher levels of ab initio QM theory. A progressive geometry optimization scheme is introduced as a means to increase conformational sampling efficiency.

Why is SiH Not Linear? An Intrinsic Quasi-Atomic Bonding Analysis.

The molecular energy of SiH geometric structures increases in the order dibridged < -bent < linear, in contrast to acetylene, CH, for which the linear structure is the global minimum. In this study, the intra-atomic (antibonding) and bonding contributions to the total molecular energy of these valence isoelectronic molecules are computed by expressing the density matrices of the full valence space multiconfiguration self-consistent field wave function in terms of quasi-atomic orbitals. The analysis shows that the -atomic contributions to the molecular energy become favorable in the order dibridged → -bent → linear for both CH and SiH.

Recent developments in the general atomic and molecular electronic structure system.

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory.

Quantum Mechanical Modeling of the Interactions between Noble Metal (Ag and Au) Nanoclusters and Water with the Effective Fragment Potential Method.

Explicit solvent interactions can significantly alter the physical and chemical properties of noble metal (., gold and silver) nanoclusters. In order to compute these solvent interactions at a reasonable computational cost, a quantum mechanical (QM)/molecular mechanics (MM) approach, where the metal nanocluster is treated with full QM and the water molecules are treated with a MM force field, can be used.

Accuracy of the PM6 and PM7 Methods on Bare and Thiolate-Protected Gold Nanoclusters.

Semiempirical quantum mechanical (SEQM) methods offer an attractive middle ground between fully ab initio quantum chemistry and force-field simulations, allowing for a quantum mechanical treatment of the system at a relatively low computational cost. However, SEQM methods have not been frequently utilized in the study of transition metal systems, mostly due to the difficulty in obtaining reliable parameters. This paper examines the accuracy of the PM6 and PM7 semiempirical methods to predict geometries, ionization potentials, and HOMO-LUMO energy gaps of several bare gold clusters (Au) and thiolate-protected gold nanoclusters (AuSNCs).

Benchmarking of the R Anisotropic Dispersion Energy Term on the S22 Dimer Test Set.

The effects of including the anisotropic E term to the dispersion energy in addition to the leading E term are examined by using the effective fragment potential (EFP) method on the S22 test set. In this study, the full anisotropic E term is computed whereas the isotropic and spherical approximations are used for the E term. It is found that the E term is positive for hydrogen-bonded complexes and has a magnitude that can be as large as 50% of E, giving rise to larger intermolecular distances than those obtained with E alone.

Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 Test Set.

The usual modeling of dispersion interactions in density functional theory (DFT) is often limited by the use of empirically fitted parameters. In this study, the accuracies of the popular empirical dispersion corrections and the first-principles derived effective fragment potential (EFP) dispersion correction are compared by computing the DFT-D and HF-D equilibria interaction energies and intermolecular distances of the S22 test set dimers. Functionals based on the local density approximation (LDA) and generalized gradient approximation (GGA), as well as hybrid functionals, are compared for the DFT-D calculations using coupled cluster CCSD(T) at the complete basis set (CBS) limit as the reference method.

Dispersion Interactions in Water Clusters.

The importance of dispersion forces in water clusters is examined using the effective fragment potential (EFP) method. Since the original EFP1 water potential does not include dispersion, a dispersion correction to the EFP1 potential (EFP1-D) was derived and implemented. The addition of dispersion to the EFP1 potential yields improved geometries for water clusters that contain 2-6 molecules.

Derivation and Implementation of the Gradient of the R(-7) Dispersion Interaction in the Effective Fragment Potential Method.

The dispersion interaction energy may be expressed as a sum over R(-n) terms, with n ≥ 6. Most implementations of the dispersion interaction in model potentials are terminated at n = 6. Those implementations that do include higher order contributions commonly only include even power terms, despite the fact that odd power terms can be important.

Time-dependent density functional theory study of the luminescence properties of gold phosphine thiolate complexes.

The origin of the emission of the gold phosphine thiolate complex (TPA)AuSCH(CH3)2 (TPA = 1,3,5-triaza-7-phosphaadamantanetriylphosphine) is investigated using time-dependent density functional theory (TDDFT). This system absorbs light at 3.6 eV, which corresponds mostly to a ligand-to-metal transition with some interligand character.

Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work.

Quantum mechanical origin of the plasmon: from molecular systems to nanoparticles.

The surface plasmon resonance (SPR) of noble metal nanoparticles is reviewed in terms of both classical and quantum mechanical approaches. The collective oscillation of the free electrons responsible for the plasmon is well described using classical electromagnetic theory for large systems (from about 10 to 100 nm). In cases where quantum effects are important, this theory fails and first principle approaches like time-dependent density functional theory (TDDFT) must be used.

Quantum coherent plasmon in silver nanowires: a real-time TDDFT study.

A plasmon-like phenomenon, arising from coinciding resonant excitations of different electronic characteristics in 1D silver nanowires, has been proposed based on theoretical linear absorption spectra. Such a molecular plasmon holds the potential for anisotropic nanoplasmonic applications. However, its dynamical nature remains unexplored.

Plasmon resonance analysis with configuration interaction.

Dipole plasmon resonances are described quantum mechanically using configuration interaction (CI). A fictitious system of three interacting configurations is considered, which yields three excited states. Excited states energies and oscillator strengths are derived from the eigenvalues and eigenvectors of the CI matrix, where the diagonal elements α(i) (i = 1, 2, 3) correspond to the interacting one-electron transition energies and the off-diagonal elements β(ij) correspond to the coupling between these configurations.

Theoretical analysis of the optical excitation spectra of silver and gold nanowires.

The excitation spectra of linear atomic chains of silver and gold with various sizes have been calculated using time-dependent density functional theory. Silver chains show longitudinal and transverse peaks as well as a low-intensity d-band. The longitudinal peak, corresponding to the HOMO-LUMO transition (along the main axis of the chain), shifts linearly to the red as the length of the system increases, consistent with the particle-in-a-box model.

Development of a charge-perturbed particle-in-a-sphere model for nanoparticle electronic structure.

The complex surface structure of gold-thiolate nanoparticles is known to affect the calculated density functional theory (DFT) excitation spectra. However, as the nanoparticle size increases, it becomes impractical to calculate the excitation spectrum using DFT. In this study, a new method is developed to determine the energy levels of the thiolate-protected gold nanoparticles [Au(25)(SR)(18)](-), Au(102)(SR)(44) and Au(144)(SR)(60).