Many-body expansion of the Fock matrix in the fragment molecular orbital method

Importance of Charge Balance for the Embedding of Zwitterionic Solutes in the Fragment Molecular Orbital Method

Three new schemes of induced solvent charges for the auxiliary polarization formulation of the fragment molecular orbital method are proposed and compared to the original approach. It is found that the charge balance of the solute and solvent embeddings is crucial for maintaining a proper gap between occupied and virtual orbitals of fragments for zwitterionic systems in solution. The original instability is eliminated with the new scheme of fragment-specific solvent charges. The developed stable embedding method is applied to perform MP2/aug-cc-pVTZ calculations of a protein-ligand complex containing 1102 amino acid residues.

Many-Body Expansion-Based Quantum Mechanical Force Field for Cyclotrimethylene Trinitramine under High Pressure

RDX undergoes pressures of approximately 30-50 GPa during detonation, leading to significant changes in intermolecular interactions. Accurately describing these interactions is crucial for understanding the energy transfer in the detonation process. To address this, this work introduces a many-body expansion-based quantum mechanical force field (MB-QMFF) to accurately describe RDX's intermolecular interactions under high pressures. Using MB-QMFF, we evaluated various density functionals and found that the M062X functional with GD3 dispersion correction provided the highest accuracy. Regarding intermolecular forces, two-body interactions were the most significant, with three-body interactions being negligible. Additionally, we investigated intermolecular energy variations at different densities (or pressures). The results clearly demonstrate an accurate description of intermolecular interactions by the MB-QMFF scheme. Therefore, we believe that the MB-QMFF scheme can serve as a foundation for the development of RDX-specific force fields and pave the way for future studies on the detonation process of RDX.

Development and testing of an algorithm for efficient MP2/CCSD(T) energy estimation of molecular clusters with the 2-body approach

This work reports the development and testing of an automated algorithm for estimating the energies of weakly bound molecular clusters employing correlated theory. Firstly, the monomers and dimers of (homo/hetero) clusters are identified, and the sum of one-body and two-body contributions to correlation energy is calculated. The addition of this contribution to the Hartree-Fock full calculation (FC) energies provides a good estimate of the total energies at Møller-Plesset second-order perturbation theory (MP2)/coupled-cluster method with singles and doubles (CCSD) (T)-level theory using augmented Dunning basis sets. The estimated energies for several test clusters show an excellent agreement with their FC counterparts, with a substantial wall-clock time saving employing off-the-shelf hardware. Furthermore, the complete basis set (CBS) limit for MP2 energy computed using the two-body approach also agrees with its CBS energy with its FC counterpart.

Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method

Fast parameterized methods such as density-functional tight-binding (DFTB) facilitate realistic calculations of large molecular systems, which can be accelerated by the fragment molecular orbital (FMO) method. Fragmentation facilitates interaction analyses between functional parts of molecular systems. In addition to DFTB, other parameterized methods combined with FMO are also described. Applications of FMO methods to biochemical and inorganic systems are reviewed.

Computational Methods for Biochemical Simulations Implemented in GAMESS

Computational methods for modeling biochemical processes implemented in GAMESS package are reviewed; in particular, quantum mechanics combined with molecular mechanics (QM/MM), semi-empirical, and fragmentation approaches. A detailed summary of capabilities is provided for the QM/MM implementation in QuanPol program and the fragment molecular orbital (FMO) method. Molecular modeling and visualization packages useful for biochemical simulations with GAMESS are described. GAMESS capabilities with corresponding references are tabulated for reader's convenience.

Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.

Revisiting the Charge-Transfer States at Pentacene/C60 Interfaces with the GW/Bethe-Salpeter Equation Approach

Molecular orientations and interfacial morphologies have critical effects on the electronic states of donor/acceptor interfaces and thus on the performance of organic photovoltaic devices. In this study, we explore the energy levels and charge-transfer states at the organic donor/acceptor interfaces on the basis of the fragment-based GW and Bethe-Salpeter equation approach. The face-on and edge-on orientations of pentacene/C60 bilayer heterojunctions have employed as model systems. GW+Bethe-Salpeter equation calculations were performed for the local interface structures in the face-on and edge-on bilayer heterojunctions, which contain approximately 2000 atoms. Calculated energy levels and charge-transfer state absorption spectra are in reasonable agreements with those obtained from experimental measurements. We found that the dependence of the energy levels on interfacial morphology is predominantly determined by the electrostatic contribution of polarization energy, while the effects of induction contribution in the edge-on interface are similar to those in the face-on. Moreover, the delocalized charge-transfer states contribute to the main absorption peak in the edge-on interface, while the face-on interface features relatively localized charge-transfer states in the main absorption peak. The impact of the interfacial morphologies on the polarization and charge delocalization effects is analyzed in detail.

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. 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.

Pseudo-fragment approach for extended systems derived from linear-scaling DFT

We present a computational approach which is tailored for reducing the complexity of the description of extended systems at the density functional theory level. We define a recipe for generating a set of localized basis functions which are optimized either for the accurate description of pristine, bulk-like Wannier functions, or for the in situ treatment of deformations induced by defective constituents such as boundaries or impurities. Our method enables one to identify the regions of an extended system which require dedicated optimization of the Kohn-Sham degrees of freedom, and provides the user with a reliable estimation of the errors-if any-induced by the locality of the approach. Such a method facilitates on the one hand an effective reduction of the computational degrees of freedom needed to simulate systems at the nanoscale, while in turn providing a description that can be straightforwardly put in relation to effective models, like tight binding Hamiltonians. We present our methodology with SiC nanotube-like cages as a test bed. Nonetheless, the wavelet-based method employed in this paper makes possible calculation of systems with different dimensionalities, including slabs and fully periodic systems.

Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited

The photoinduced electron transfer (ET) reaction of cyclobutane pyrimidine dimer (CPD) photolyase plays an essential role in its DNA repair reaction, and the molecular mechanism of the ET reaction has attracted a large number of experimental and theoretical studies. We investigated the quantum mechanical nature of their ET reactions, characterized by multiple ET pathways of the CPD photolyase derived from Anacystis nidulans. Using the generalized Mulliken-Hush (GMH) method and the bridge green function (GF) methods, we estimated the electronic coupling matrix element, T_DA, to be 36 ± 30 cm^-1 from the donor (FADH^-) to the acceptor (CPD). The estimated ET time was 386 ps, in good agreement with the experimental value (250 ps) in the literature. Furthermore, we performed the molecular dynamics (MD) simulations and ab initio molecular orbital (MO) calculations, and explored the electron tunneling pathway. We examined 20 different structures during the MD trajectory and quantitatively evaluated the electron tunneling currents for each of them. As a result, we demonstrated that the ET route via Asn349 was the dominant pathway among the five major routes via (Adenine/Asn349), (Adenine/Glu283), (Adenine/Glu283/Asn349/Met353), (Met353/Asn349), and (Asn349), indicating that Asn349 is an essential amino acid residue in the ET reaction.