The accuracies of effective interactions in downfolding coupled-cluster approaches for small-dimensionality active spaces.

This paper evaluates the accuracy of the Hermitian form of the downfolding procedure using the double unitary coupled cluster (DUCC) ansatz on the benchmark systems of linear chains of hydrogen atoms, H6 and H8. The computational infrastructure employs the occupation-number-representation codes to construct the matrix representation of arbitrary second-quantized operators, allowing for the exact representation of exponentials of various operators. The tests demonstrate that external amplitudes from standard single-reference coupled cluster methods that sufficiently describe external (out-of-active-space) correlations reliably parameterize the Hermitian downfolded effective Hamiltonians in the DUCC formalism. The results show that this approach can overcome the problems associated with losing the variational character of corresponding energies in the corresponding SR-CC theories.

Quantum Flow Algorithms for Simulating Many-Body Systems on Quantum Computers.

We conducted quantum simulations of strongly correlated systems using the quantum flow (QFlow) approach, which enables sampling large subspaces of the Hilbert space through coupled variational problems in reduced dimensionality active spaces. Our QFlow algorithms significantly reduce circuit complexity and pave the way for scalable and constant-circuit-depth quantum computing. Our simulations show that QFlow can optimize the collective number of wave function parameters without increasing the required qubits using active spaces having an order of magnitude fewer number of parameters.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape.

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

Sub-system self-consistency in coupled cluster theory.

In this article, we provide numerical evidence indicating that the single-reference coupled-cluster (CC) energies can be calculated alternatively to their copybook definition. We demonstrate that the CC energy can be reconstructed by diagonalizing the effective Hamiltonians describing correlated sub-systems of the many-body system. In the extreme case, we provide numerical evidence that the CC energy can be reproduced through the diagonalization of the effective Hamiltonian describing sub-system composed of a single electron. These properties of the CC formalism can be exploited to design protocols to define effective interactions in sub-systems used as probes to calculate the energy of the entire system and introduce a new type of self-consistency for approximate CC approaches.

High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference validation.

Quantum chemical calculations on atomistic systems have evolved into a standard approach to studying molecular matter. These calculations often involve a significant amount of manual input and expertise, although most of this effort could be automated, which would alleviate the need for expertise in software and hardware accessibility. Here, we present the AutoRXN workflow, an automated workflow for exploratory high-throughput electronic structure calculations of molecular systems, in which (i) density functional theory methods are exploited to deliver minimum and transition-state structures and corresponding energies and properties, (ii) coupled cluster calculations are then launched for optimized structures to provide more accurate energy and property estimates, and (iii) multi-reference diagnostics are evaluated to back check the coupled cluster results and subject them to automated multi-configurational calculations for potential multi-configurational cases. All calculations are carried out in a cloud environment and support massive computational campaigns. Key features of all components of the AutoRXN workflow are autonomy, stability, and minimum operator interference. We highlight the AutoRXN workflow with the example of an autonomous reaction mechanism exploration of the mode of action of a homogeneous catalyst for the asymmetric reduction of ketones.

TAMM: Tensor algebra for many-body methods.

Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks.

Small intestinal bacterial overgrowth in Alzheimer's disease.

The results of animal studies and clinical data support the gut microbiota contribution to the pathogenesis of Alzheimer's disease (AD). The aim of this pilot study was to evaluate the prevalence of small intestinal bacterial overgrowth (SIBO) and fecal markers of intestinal inflammation and permeability in AD patients. The study was conducted in 45 AD patients and 27 controls. Data on comorbidities, pharmacotherapy, and gastrointestinal symptoms were acquired from medical records and a questionnaire. SIBO was evaluated using lactulose hydrogen breath test. Fecal calprotectin and zonulin levels were assessed by ELISA assays. The positive result of SIBO breath test was found in 49% of the AD patients and 22% of the controls (p = 0.025). The comparative analysis between SIBO-positive and SIBO-negative AD patients with respect to the degree of cognitive impairment, comorbidities and used medications did not reveal any statistically significant difference, except for less common heartburn in SIBO-positive AD patients than in SIBO-negative ones (9 vs 35%, p = 0.038). The median fecal calprotectin and zonulin levels in the AD group compared to the control group amounted to 43.1 vs 64.2 µg/g (p = 0.846) and 73.5 vs 49.0 ng/ml (p = 0.177), respectively. In the AD patients there was no association between the presence of SIBO and fecal calprotectin level. Patients with AD are characterized by higher prevalence of SIBO not associated with increased fecal calprotectin level that may be related to anti-inflammatory effect of cholinergic drugs used in the treatment of AD.

Coupled cluster downfolding methods: The effect of double commutator terms on the accuracy of ground-state energies.

Downfolding coupled cluster techniques have recently been introduced into quantum chemistry as a tool for the dimensionality reduction of the many-body quantum problem. As opposed to earlier formulations in physics and chemistry based on the concept of effective Hamiltonians, the appearance of the downfolded Hamiltonians is a natural consequence of the single-reference exponential parameterization of the wave function. In this paper, we discuss the impact of higher-order terms originating in double commutators. In analogy to previous studies, we consider the case when only one- and two-body interactions are included in the downfolded Hamiltonians. We demonstrate the efficiency of the many-body expansions involving single and double commutators for the unitary extension of the downfolded Hamiltonians on the example of the beryllium atom, and bond-breaking processes in the Li2 and H2O molecules. For the H2O system, we also analyze energies obtained with downfolding procedures as functions of the active space size.

Real-time equation-of-motion CC cumulant and CC Green's function simulations of photoemission spectra of water and water dimer.

Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses the results obtained with the real-time equation-of-motion CC cumulant (RT-EOM-CC) approach and CC Green's function (CCGF) approaches in applications to the water and water dimer molecules. We compare the ionization potentials obtained with these methods for the valence region with the results obtained with the coupled-cluster with singles, doubles, and perturbative triples formulation as a difference of energies for N and N - 1 electron systems. All methods show good agreement with each other. They also agree well with the experiment with errors usually below 0.1 eV for the ionization potentials. We also analyze unique features of the spectral functions, associated with the position of satellite peaks, obtained with the RT-EOM-CC and CCGF methods employing single and double excitations, as a function of the monomer OH bond length and the proton transfer coordinate in the dimer. Finally, we analyze the impact of the basis set effects on the quality of calculated ionization potentials and find that the basis set effects are less pronounced for the augmented-type sets.

Massively parallel quantum chemical density matrix renormalization group method.

We present, to the best of our knowledge, the first attempt to exploit the super-computer platform for quantum chemical density matrix renormalization group (QC-DMRG) calculations. We have developed the parallel scheme based on the in-house MPI global memory library, which combines operator and symmetry sector parallelisms, and tested its performance on three different molecules, all typical candidates for QC-DMRG calculations. In case of the largest calculation, which is the nitrogenase FeMo cofactor cluster with the active space comprising 113 electrons in 76 orbitals and bond dimension equal to 6000, our parallel approach scales up to approximately 2000 CPU cores.

Quantum simulations employing connected moments expansions.

Further advancement of quantum computing (QC) is contingent on enabling many-body models that avoid deep circuits and excessive use of CNOT gates. To this end, we develop a QC approach employing finite-order connected moment expansions (CMX) and affordable procedures for initial state preparation. We demonstrate the performance of our approach employing several quantum variants of CMX through the classical emulations on the H2 molecule potential energy surface and the Anderson model with a broad range of correlation strength. The results show that our approach is robust and flexible. Good agreement with exact solutions can be maintained even at the dissociation and strong correlation limits.

Sub-system quantum dynamics using coupled cluster downfolding techniques.

In this paper, we discuss extending the sub-system embedding sub-algebra coupled cluster formalism and the double unitary coupled cluster (DUCC) ansatz to the time domain. An important part of the analysis is associated with proving the exactness of the DUCC ansatz based on the general many-body form of anti-Hermitian cluster operators defining external and internal excitations. Using these formalisms, it is possible to calculate the energy of the entire system as an eigenvalue of downfolded/effective Hamiltonian in the active space, which is identifiable with the sub-system of the composite system. It can also be shown that downfolded Hamiltonians integrate out Fermionic degrees of freedom that do not correspond to the physics encapsulated by the active space. In this paper, we extend these results to the time-dependent Schrödinger equation, showing that a similar construct is possible to partition a system into a sub-system that varies slowly in time and a remaining sub-system that corresponds to fast oscillations. This time-dependent formalism allows coupled cluster quantum dynamics to be extended to larger systems and for the formulation of novel quantum algorithms based on the quantum Lanczos approach, which has recently been considered in the literature.

Green's function coupled cluster simulation of the near-valence ionizations of DNA-fragments.

Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation and the exploration of the potential application of DNA strands in nanoelectronics. In this work, by employing our recently developed Green's function coupled-cluster library on supercomputing facilities, we have studied the spectral functions of several guanine-cytosine (G-C) base pair structures ([G-C]n, n = 1-3) for the first time in a relatively broad near-valence regime ([-25.0, -5.0] eV) in the coupled-cluster with singles and doubles level. Our focus is to give a preliminary many-body coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p⟩'s in the ionized wave functions of the considered G-C base pair systems. The leading |2h, 1p⟩'s associated with the main ionizations from the cytosine part of the G-C base pairs feature a transition from the intra-base-pair cytosine π → π* excitation to the inter-base-pair electron excitation as the size of G-C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.

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.

Quantum simulations of excited states with active-space downfolded Hamiltonians.

Many-body techniques based on the double unitary coupled cluster (DUCC) ansatz can be used to downfold electronic Hamiltonians into low-dimensional active spaces. It can be shown that the resulting dimensionality reduced Hamiltonians are amenable for quantum computing. Recent studies performed for several benchmark systems using phase estimation (PE) algorithms for quantum computers demonstrated that these formulations can recover a significant portion of ground-state dynamical correlation effects that stem from the electron excitations outside of the active space. These results have also been confirmed in studies of ground-state potential energy surfaces using quantum simulators. In this letter, we study the effectiveness of the DUCC formalism in describing excited states. We also emphasize the role of the PE formalism and its stochastic nature in discovering/identifying excited states or excited-state processes in situations when the knowledge about the true configurational structure of a sought after excited state is limited or postulated (due to the specific physics driving excited-state processes of interest). In this context, we can view PE algorithms as an engine for verifying various hypotheses for excited-state processes and providing statistically meaningful results that correspond to the electronic state(s) with the largest overlap with a postulated configurational structure. We illustrate these ideas on examples of strongly correlated molecular systems, characterized by small energy gaps and high density of quasidegenerate states around the Fermi level.

Downfolding of many-body Hamiltonians using active-space models: Extension of the sub-system embedding sub-algebras approach to unitary coupled cluster formalisms.

In this paper, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced complete active space (CAS) effective Hamiltonian. In contrast to the standard single-reference SES-CC theory, the unitary CC approach results in a Hermitian form of the effective Hamiltonian. Additionally, for the double unitary CC (DUCC) formalism, the corresponding CAS eigenvalue problem provides a rigorous separation of external cluster amplitudes that describe dynamical correlation effects-used to define the effective Hamiltonian-from those corresponding to the internal (inside the active space) excitations that define the components of eigenvectors associated with the energy of the entire system. The proposed formalism can be viewed as an efficient way of downfolding many-electron Hamiltonian to the low-energy model represented by a particular choice of CAS. In principle, this technique can be extended to any type of CAS representing an arbitrary energy window of a quantum system. The Hermitian character of low-dimensional effective Hamiltonians makes them an ideal target for several types of full configuration interaction type eigensolvers. As an example, we also discuss the algebraic form of the perturbative expansions of the effective DUCC Hamiltonians corresponding to composite unitary CC theories and discuss possible algorithms for hybrid classical and quantum computing. Given growing interest in quantum computing, we provide energies for H2 and Be systems obtained with the quantum phase estimator algorithm available in the Quantum Development Kit for the approximate DUCC Hamiltonians.

Green's function coupled cluster formulations utilizing extended inner excitations.

In this paper, we analyze new approximations of the Green's function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i(n, m) method, where the excitation level of the inner auxiliary operators (m) used to describe the ionization potential and electron affinity effects in the N - 1 and N + 1 particle spaces is higher than the excitation level (n) used to correlate the ground-state coupled cluster wave function for the N-electron system. Furthermore, we reveal the so-called "n + 1" rule in this category [or the GFCC-i(n, n + 1) method], which states that in order to maintain size-extensivity of the Green's function matrix elements, the excitation level of inner auxiliary operators X p (ω) and Y q (ω) cannot exceed n + 1. We also discuss the role of the moments of coupled cluster equations that in a natural way assures these properties. Our implementation in the present study is focused on the first approximation in this GFCC category, i.e., the GFCC-i(2,3) method. As our first practice, we use the GFCC-i(2,3) method to compute the spectral functions for the N2 and CO molecules in the inner and outer valence regimes. In comparison with the Green's function coupled cluster singles, doubles results, the computed spectral functions from the GFCC-i(2,3) method exhibit better agreement with the experimental results and other theoretical results, particularly in terms of providing higher resolution of satellite peaks and more accurate relative positions of these satellite peaks with respect to the main peak positions.

Electronic Structure and Stability of [B12X12]2- (X = F-At): A Combined Photoelectron Spectroscopic and Theoretical Study.

The stability and electron loss process of numerous multiply charged anions (MCAs) have been traditionally explained in terms of the classical Coulomb interaction between spatially separated charged groups. An understanding of these processes in MCAs with not well-separated excess charges is still lacking. We report the surprising properties and physical behavior of [B12X12]2-, X = F, Cl, Br, I, At, which are MCAs with not well-separated excess charges and cannot be described by the prevailing classical picture. In this series of MCAs, comprising a "boron core" surrounded by a "halogen shell", the sign of the total charge in these two regions changes along the halogen series from X = F-At. With the aid of experimental photoelectron spectroscopy and highly correlated ab initio electronic structure calculations, we demonstrate that the trend in the electronic stability of these MCAs is determined by the interplay between the Coulomb (de)stabilization originating from the "boron core" and "halogen shell" and the extension of the overlap between the orbitals from both regions. The second excess electron is always taken from the most positively charged region, viz., the "boron core" for X = F, Cl, and the surrounding "halogen shell" for X = I, At. This change in the physical behavior is attributed to the position of the highest occupied molecular orbital, which dwells in a region that is spatially separated from the one containing the excess negative charge. The unusual intrinsic electronic structure of the [B12X12]2- MCAs provides the basis for a molecular level understanding of their observed unique physical and chemical properties and a new paradigm for understanding the properties of these MCAs with not well-separated charges that departs from the prevailing model used for spatially separated charges that is based on their classical Coulomb interaction.

Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution.

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.

Coupled Cluster Studies of Ionization Potentials and Electron Affinities of Single-Walled Carbon Nanotubes.

In this paper, we apply equation-of-motion coupled cluster (EOM-CC) methods in the studies of the vertical ionization potentials (IPs) and electron affinities (EAs) for a series of single-walled carbon nanotubes (SWCNT). The EOM-CC formulations for IPs and EAs employing excitation manifolds spanned by single and double excitations (IP/EA-EOM-CCSD) are used to study the IPs and EAs of the SWCNTs as a function of the nanotube length. Several armchair nanotubes corresponding to C20nH20 models with n = 2-6 have been used in benchmark calculations. In agreement with previous studies, we demonstrate that the electronegativity of C20nH20 systems remains, to a large extent, independent of the nanotube length. We also compare IP/EA-EOM-CCSD results with those obtained with coupled cluster models with single and double excitations corrected by perturbative triples, CCSD(T), and density functional theory (DFT) using global and range-separated hybrid exchange-correlation functionals.