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.

Proton Transfer in 1,2,4-Triazolium Dinitramide: Effect of Aqueous Microsolvation.

The gas phase proton transfer process in 1,2,4-triazolium dinitramide (TD) was studied using second-order perturbation theory to determine how the presence of one and two water molecules modifies the potential energy surface that connects the ion pair to the neutral pair. The presence of one water molecule can introduce small proton transfer energy barriers that separate the ion pair from the lower-energy neutral pair. These energy barriers are easily surmounted.

Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method.

The Claisen rearrangement of chorismate to prephenate is mapped across the entire reaction pathway using the fragment molecular orbital (FMO) method. Three basis sets (6-31G(d), cc-pVDZ, and pcseg-1) are studied to provide guidance toward obtaining high accuracy with the FMO method on such systems. Using a fragmentation scheme of one residue per fragment, the FMO method using the 6-31G(d) basis set and second-order Møller-Plesset perturbation theory (MP2) with the hybrid orbital projection fragmentation scheme provides the most reliable results across the entire reaction pathway.

Ab Initio Multiple Spawning Method for Intersystem Crossing Dynamics: Spin-Forbidden Transitions between (3)B1 and (1)A1 States of GeH2.

Dynamics at intersystem crossings are fundamental to many processes in chemistry, physics, and biology. The ab initio multiple spawning (AIMS) method was originally developed to describe internal conversion dynamics at conical intersections where derivative coupling is responsible for nonadiabatic transitions between electronic states with the same spin multiplicity. Here, the applicability of the AIMS method is extended to intersystem crossing dynamics in which transitions between electronic states with different spin multiplicities are mediated by relativistic spin-orbit coupling.

Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster.

Ab initio investigation of the aqueous solvation of the nitrate ion.

The surface affinity of the nitrate ion in aqueous clusters is investigated with a variety of theoretical methods. A sampling of structures in which the nitrate ion is solvated by 32 water molecules is optimized using second order Møller-Plesset perturbation theory (MP2). Four of these MP2 optimized structures are used as starting points for fully ab initio molecular dynamics simulations at the dispersion corrected restricted Hartree-Fock (RHF-D) level of theory.

Surface affinity of the hydronium ion: the effective fragment potential and umbrella sampling.

The surface affinity of the hydronium ion in water is investigated with umbrella sampling and classical molecular dynamics simulations, in which the system is described with the effective fragment potential (EFP). The solvated hydronium ion is also explored using second order perturbation theory for the hydronium ion and the empirical TIP5P potential for the waters. Umbrella sampling is used to analyze the surface affinity of the hydronium ion, varying the number of solvent water molecules from 32 to 256.

Efficient and accurate fragmentation methods.

Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems.

Fully Integrated Effective Fragment Molecular Orbital Method.

In this work, the effective fragment potential (EFP) method is fully integrated (FI) into the fragment molecular orbital (FMO) method to produce an effective fragment molecular orbital (EFMO) method that is able to account for all of the fundamental types of both bonded and intermolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the method is tested and compared to both the standard FMO method as well as to fully ab initio methods. It is shown that the FIEFMO method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%.

Geometry optimizations of open-shell systems with the fragment molecular orbital method.

The ability to perform geometry optimizations on large molecular systems is desirable for both closed- and open-shell species. In this work, the restricted open-shell Hartree-Fock (ROHF) gradients for the fragment molecular orbital (FMO) method are presented. The accuracy of the gradients is tested, and the ability of the method to reproduce adiabatic excitation energies is also investigated.

The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters.

Two electronic structure methods, the fragment molecular orbital (FMO) and systematic molecular fragmentation (SMF) methods, that are based on fragmenting a large molecular system into smaller, more computationally tractable components (fragments), are presented and compared with fully ab initio results for the predicted binding energies of water clusters. It is demonstrated that, even when explicit three-body effects are included (especially necessary for water clusters due to their complex hydrogen-bonded networks) both methods present viable, computationally efficient alternatives to fully ab initio quantum chemistry.

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method.

Benchmark timings are presented for the fragment molecular orbital method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 basis functions, using second order perturbation theory and an augmented and polarized double-ζ basis set, takes ∼7 min on 131 072 cores.

Open-Shell Formulation of the Fragment Molecular Orbital Method.

Performing accurate calculations on large molecular systems is desirable for closed- and open-shell systems. In this work, the fragment molecular orbital method is extended to open-shell systems and implemented in the GAMESS (General Atomic and Molecular Electronic Structure System) program package. The accuracy of the method is tested, and the ability to reproduce reaction enthalpies is demonstrated.

Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies.

The systematic fragmentation method fragments a large molecular system into smaller pieces, in such a way as to greatly reduce the computational cost while retaining nearly the accuracy of the parent ab initio electronic structure method. In order to attain the desired (sub-kcal/mol) accuracy, one must properly account for the nonbonded interactions between the separated fragments. Since, for a large molecular species, there can be a great many fragments and therefore a great many nonbonded interactions, computations of the nonbonded interactions can be very time-consuming.

Accurate methods for large molecular systems.

Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g.