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. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

We report on the findings of a blind challenge devoted to determining the frozencore, full configuration interaction (FCI) ground state energy of the benzene molecule in a standard correlation-consistent basis set of double-ζ quality. As a broad international endeavour, our suite of wave function-based correlation methods collectively represents a diverse view of the high-accuracy repertoire offered by modern electronic structure theory. In our assessment, the evaluated high-level methods are all found to qualitatively agree on a final correlation energy, with most methods yielding an estimate of the FCI value around −863 mE H. However, we find the root-mean-square deviation of the energies from the studied methods to be considerable (1.3 mE H), which in light of the acclaimed performance of each of the methods for smaller molecular systems clearly displays the challenges faced in extending reliable, near-exact correlation methods to larger systems. While the discrepancies exposed by our study thus emphasize the fact that the current state-of-the-art approaches leave room for improvement, we still expect the present assessment to provide a valuable community resource for benchmark and calibration purposes going forward.

We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.

SUMMARY Understanding the relative contributions of genetic and epigenetic abnormalities to acute myeloid leukemia (AML) should assist integrated design of targeted therapies. In this study, we generated induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements and found that they retained leukemic mutations but reset leukemic DNA methylation/gene expression patterns. AML-iPSCs lacked leukemic potential, but when differentiated into hematopoietic cells, they reacquired the ability to give rise to leukemia in vivo and reestablished leukemic DNA methylation/gene expression patterns, including an aberrant MLL signature. Epigenetic reprogramming was therefore not sufficient to eliminate leukemic behavior. This approach also allowed us to study the properties of distinct AML subclones, including differential drug susceptibilities of KRAS mutant and wild-type cells, and predict relapse based on increased cytarabine resistance of a KRAS wild-type subclone. Overall, our findings illustrate the value of AML-iPSCs for investigating the mechanistic basis and clonal properties of human AML.

The full and active-space doubly electron-attached (DEA) and doubly ionized (DIP) equation-of-motion coupled-cluster (EOMCC) methods with up to 4-particle-2-hole (4p-2h) and 4-hole-2-particle (4h-2p) excitations are developed. By examining bond breaking in F2 and low-lying singlet and triplet states in the methylene, (HFH)(-), and trimethylenemethane biradicals, we demonstrate that the DEA- and DIP-EOMCC methods with an active-space treatment of 4p-2h and 4h-2p excitations reproduce the results of the analogous full calculations at the small fraction of the computer effort, while improving the DEA/DIP-EOMCC theories truncated at 3p-1h/3h-1p excitations.

We propose a new approach to the determination of accurate electronic energies that are equivalent to the results of high-level coupled-cluster (CC) calculations. The approach is based on merging the CC(P;Q) formalism, which corrects energies obtained with an arbitrary truncation in the cluster operator, with the stochastic configuration interaction and CC ideas. The advantages of the proposed methodology are illustrated by molecular examples, where the goal is to recover the energetics obtained in the CC calculations with a full treatment of singly, doubly, and triply excited clusters.

Extensive photochemical and spectroscopic properties of the V − B defect in hexagonal boron nitride are calculated, concluding that the observed photoemission associated with recently observed optically detected magnetic resonance is most likely of (1) 3 E → (1) 3 A 2 origin. Rapid intersystem crossing from the defect's triplet to singlet manifolds explains the observed short excited-state lifetime and very low quantum yield. New experimental results reveal smaller intrinsic spectral bandwidths than previously recognized, interpreted in terms of spectral narrowing and zero-phonon-line shifting induced by the Jahn-Teller effect. Different types of computational methods are applied to map out the complex triplet and singlet defect manifolds, including the doubly ionized formulation of the equation-of-motion coupled-cluster theory that is designed to deal with the open-shell nature of defect states, and mixed quantum-mechanics/molecular-mechanics schemes enabling 5763-atom simulations. Two other energetically feasible spectral assignments from among the singlet and triplet manifolds are considered, but ruled out based on inappropriate photochemical properties.

We have recently developed a flexible form of the method of moments of coupled-cluster (CC) equations and the CC(P;Q) hierarchy, which enable one to correct the CC and equation-of-motion CC energies obtained with unconventional truncations in the cluster and excitation operators [Shen, J.; Piecuch, P. Chem. Phys.2012, 401, 180; J. Chem. Phys.2012, 136, 144104]. One of the CC(P;Q) methods is a novel hybrid scheme, abbreviated as CC(t;3), in which the results of CC calculations with singles, doubles, and active-space triples, termed CCSDt, are corrected for the triple excitations missing in CCSDt using the expressions that are reminiscent of the completely renormalized (CR) CC approach known as CR-CC(2,3). We demonstrate that the total electronic energies of the lowest singlet and triplet states, and the singlet-triplet gaps in biradical systems, including methylene, (HFH)(-), and trimethylenemethane, resulting from the CC(t;3) calculations agree with those obtained with the full CC approach with singles, doubles, and triples to within fractions of a millihartree, improving the results of the noniterative triples CCSD(T), CCSD(2)T, and CR-CC(2,3) and hybrid CCSD(T)-h calculations, and competing with the best multireference CC data.