RT-EOM-CCSD Calculations of Inner and Outer Valence Ionization Energies and Spectral Functions

Photoelectron spectroscopy (PES) is a standard experimental method for material characterization, but its interpretation can be hampered by its reliance on standard materials. To facilitate the study of unknown systems, theoretical methods are desirable. Here, we present a real-time equation-of-motion coupled cluster (RT-EOM-CC) approach for valence PES, extending our core-level development. We demonstrate that RT-EOM-CC yields ionization energies and spectral functions in good agreement with experimental and CI-based results, even for some more correlated cases.

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.

NWChem: Recent and Ongoing Developments

This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0). Specifically, we focus on functionality, along with input blocks, that is accessible in the current stable release (NWChem 7.2.0) and in the "master" development branch, interfaces to quantum computing simulators, interfaces to external libraries, the NWChem github repository, and containerization of NWChem executable images. Some ongoing developments that will be available in the near future are also discussed.

A Perspective on Sustainable Computational Chemistry Software Development and Integration

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

Avelumab or talazoparib in combination with binimetinib in metastatic pancreatic ductal adenocarcinoma: dose-finding results from phase Ib of the JAVELIN PARP MEKi trial

BACKGROUND

Combinations of avelumab [anti-programmed death-ligand 1 (anti-PD-L1)] or talazoparib [poly(adenosine diphosphate ribose) polymerase (PARP) inhibitor] with binimetinib (MEK inhibitor) were expected to result in additive or synergistic antitumor activity relative to each drug administered alone. Here, we report phase Ib results from JAVELIN PARP MEKi, which investigated avelumab or talazoparib combined with binimetinib in metastatic pancreatic ductal adenocarcinoma (mPDAC).

PATIENTS AND METHODS

Patients with mPDAC that had progressed with prior treatment received avelumab 800 mg every 2 weeks plus binimetinib 45 mg or 30 mg two times daily (continuous), or talazoparib 0.75 mg daily plus binimetinib 45 mg or 30 mg two times daily (7 days on/7 days off). The primary endpoint was dose-limiting toxicity (DLT).

RESULTS

A total of 22 patients received avelumab plus binimetinib 45 mg (n = 12) or 30 mg (n = 10). Among DLT-evaluable patients, DLT occurred in five of 11 patients (45.5%) at the 45-mg dose, necessitating de-escalation to 30 mg; DLT occurred in three of 10 patients (30.0%) at the 30-mg dose. Among patients treated at the 45-mg dose, one (8.3%) had a best overall response of partial response. Thirteen patients received talazoparib plus binimetinib 45 mg (n = 6) or 30 mg (n = 7). Among DLT-evaluable patients, DLT occurred in two of five patients (40.0%) at the 45-mg dose, necessitating de-escalation to 30 mg; DLT occurred in two of six patients (33.3%) at the 30-mg dose. No objective responses were observed.

CONCLUSIONS

Combinations of avelumab or talazoparib plus binimetinib resulted in higher-than-expected DLT rates. However, most DLTs were single occurrences, and the overall safety profiles were generally consistent with those reported for the single agents.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.govNCT03637491; https://clinicaltrials.gov/ct2/show/NCT03637491.

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.

Modeling Singlet Fission on a Quantum Computer

We demonstrate a practical application of quantum computing by using it to investigate the linear H₄ molecule as a simple model for singlet fission. We use the Peeters-Devreese-Soldatov energy functional to calculate the necessary energetics based on the moments of the Hamiltonian estimated on the quantum computer. To reduce the number of required measurements, we use several independent strategies: 1) reduction of the size of the relevant Hilbert space by tapering off qubits; 2) measurement optimization via rotations to eigenbases shared by groups of qubit-wise commuting Pauli strings; and 3) parallel execution of multiple state preparation and measurement operations using all 20 qubits available on the Quantinuum H1-1 quantum hardware. Our results meet the energetic requirements for singlet fission, are in excellent agreement with exact transition energies (for the chosen one-particle basis), and outperform classical methods considered computationally feasible for singlet fission candidates.

Real-Time Equation-of-Motion Coupled-Cluster Cumulant Green's Function Method: Heterogeneous Parallel Implementation Based on the Tensor Algebra for Many-Body Methods Infrastructure

We report the implementation of the real-time equation-of-motion coupled-cluster (RT-EOM-CC) cumulant Green's function method [ J. Chem. Phys. 2020, 152, 174113] within the Tensor Algebra for Many-body Methods (TAMM) infrastructure. TAMM is a massively parallel heterogeneous tensor library designed for utilizing forthcoming exascale computing resources. The two-body electron repulsion matrix elements are Cholesky-decomposed, and we imposed spin-explicit forms of the various operators when evaluating the tensor contractions. Unlike our previous real algebra Tensor Contraction Engine (TCE) implementation, the TAMM implementation supports fully complex algebra. The RT-EOM-CC singles (S) and doubles (D) time-dependent amplitudes are propagated using a first-order Adams-Moulton method. This new implementation shows excellent scalability tested up to 500 GPUs using the Zn-porphyrin molecule with 655 basis functions, with parallel efficiencies above 90% up to 400 GPUs. The TAMM RT-EOM-CCSD was used to study core photoemission spectra in the formaldehyde and ethyl trifluoroacetate (ESCA) molecules. Simulations of the latter involve as many as 71 occupied and 649 virtual orbitals. The relative quasiparticle ionization energies and overall spectral functions agree well with available experimental results.

Triple Excitations in Green's Function Coupled Cluster Solver for Studies of Strongly Correlated Systems in the Framework of Self-Energy Embedding Theory

Embedding theories became important approaches used for accurate calculations of both molecules and solids. In these theories, a small chosen subset of orbitals is treated with an accurate method, called an impurity solver, capable of describing higher correlation effects. Ideally, such a chosen fragment should contain multiple orbitals responsible for the chemical and physical behavior of the compound. Handling a large number of chosen orbitals presents a very significant challenge for the current generation of solvers used in the physics and chemistry community. Here, we develop a Green's function coupled cluster singles doubles and triples (GFCCSDT) solver that can be used for a quantitative description in both molecules and solids. This solver allows us to treat orbital spaces that are inaccessible to other accurate solvers. At the same time, GFCCSDT maintains high accuracy of the resulting self-energy. Moreover, in conjunction with the GFCCSD solver, it allows us to test the systematic convergence of computational studies. Developing the CC family of solvers paves the road to fully systematic Green's function embedding calculations in solids. In this paper, we focus on the investigation of GFCCSDT self-energies for a strongly correlated problem of SrMnO₃ solid. Subsequently, we apply this solver to solid MnO showing that an approximate variant of GFCCSDT is capable of yielding a high accuracy orbital resolved spectral function.

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.

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.

Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase

Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis. Theoretical methods can provide such quantification but are often hindered by the innate complexity of electron correlation and dynamic relaxation of solvent environments. We present and validate a protocol for calculating the redox potentials of the ferrocene/ferrocenium redox pair in acetonitrile. Equation-of-motion and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in the ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrates the ability of modern computational methods to predict absolute redox potentials quantitatively and to quantify the correlation of dynamic effects, which underlie their origin.

Optimized Quantum Phase Estimation for Simulating Electronic States in Various Energy Regimes

While quantum algorithms for simulations exhibit better asymptotic scaling than their classical counterparts, they currently cannot be accurately implemented on real-world devices. Instead, chemists and computer scientists rely on costly classical simulations of these quantum algorithms. In particular, the quantum phase estimation (QPE) algorithm is among several approaches that has attracted much attention in recent years due to its genuine quantum character. However, it is memory-intensive to simulate and intractable for moderate system sizes. This paper discusses the performance and applicability of QPESIM, a new simulation of the QPE algorithm designed to take advantage of modest computational resources. In particular, we demonstrate the versatility of QPESIM in simulating various electronic states by examining the ground and core-level states of H₂O. For these states, we also discuss the effect of the active-space size on the quality of the calculated energies. For the high-energy core-level states, we demonstrate that new QPE simulations for active spaces defined by 15 active orbitals significantly reduce the errors in core-level excitation energies compared to earlier QPE simulations using smaller active spaces.

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 results obtained with the real-time equation-of-motion CC cumulant approach (RT-EOM-CC), 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 CCSD(T) 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 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.

Real-Time Equation-of-Motion CCSD Cumulant Green's Function

Many-body excitations in X-ray photoemission spectra have been difficult to simulate from first principles. We have recently developed a cumulant-based one-electron Green's function method using the real-time coupled-cluster-singles equation-of-motion approach (RT-EOM-CCS) that provides a general framework for treating these problems. Here we extend this approach to include double excitations in the ground-state energy and in the coupled cluster amplitudes, which have been implemented using subroutines generated by the Tensor Contraction Engine (TCE). As in the case of the singles approximation, RT-EOM-CCSD yields a nonperturbative cumulant form of the Green's function in terms of the time-dependent cluster amplitudes, adding nonlinear corrections to the traditional cumulant forms. The extended approach is applied to the core-hole spectral function for small molecular systems. We find that, when core-optimized basis sets are used, the doubles contributions reduce the mean absolute errors in the core binding energies of the 10e systems from 0.8 to 0.3 eV. They also significantly improve the quasiparticle-satellite gap by reducing its overestimation from about 3-5 to about 0-1 eV in CH₄, NH₃, and H₂O, and also improving the overall shape of the satellite features. Finally, we demonstrate the application of the new implementation to the larger, classical XPS ESCA series of molecules and show that the singles approximation can be paired with a modest basis set to study carbon speciation.

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.

Equation-of-Motion Coupled-Cluster Cumulant Green's Function for Excited States and X-Ray Spectra

Green’s function methods provide a robust, general framework within many-body theory for treating electron correlation in both excited states and x-ray spectra. Conventional methods using the Dyson equation or the cumulant expansion are typically based on the GW self-energy approximation. In order to extend this approximation in molecular systems, a non-perturbative real-time coupled-cluster cumulant Green’s function approach has been introduced, where the cumulant is obtained as the solution to a system of coupled first order, non-linear differential equations. This approach naturally includes non-linear corrections to conventional cumulant Green’s function techniques where the cumulant is linear in the GW self-energy. The method yields the spectral function for the core Green’s function, which is directly related to the x-ray photoemission spectra (XPS) of molecular systems. The approach also yields very good results for binding energies and satellite excitations. The x-ray absorption spectrum (XAS) is then calculated using a convolution of the core spectral function and an effective, one-body XAS. Here this approach is extended to include the full coupled-cluster-singles (CCS) core Green’s function by including the complete form of the non-linear contributions to the cumulant as well as all single, double, and triple cluster excitations in the CC amplitude equations. This approach naturally builds in orthogonality and shake-up effects analogous to those in the Mahan-Noizeres-de Dominicis edge singularity corrections that enhance the XAS near the edge. The method is illustrated for the XPS and XAS of NH₃.

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.

Quantum Solvers for Plane-Wave Hamiltonians: Abridging Virtual Spaces Through the Optimization of Pairwise Correlations

For many-body methods such as MCSCF and CASSCF, in which the number of one-electron orbitals is optimized and independent of the basis set used, there are no problems with using plane-wave basis sets. However, for methods currently used in quantum computing such as select configuration interaction (CI) and coupled cluster (CC) methods, it is necessary to have a virtual space that is able to capture a significant amount of electron-electron correlation in the system. The virtual orbitals in a pseudopotential plane-wave Hartree-Fock calculation, because of Coulomb repulsion, are often scattering states that interact very weakly with the filled orbitals. As a result, very little correlation energy is captured from them. The use of virtual spaces derived from the one-electron operators has also been tried, and while some correlations are captured, the amount is quite low. To overcome these limitations, we have been developing new classes of algorithms to define virtual spaces by optimizing orbitals from small pairwise CI Hamiltonians, which we term as correlation optimized virtual orbitals with the abbreviation COVOs. With these procedures, we have been able to derive virtual spaces, containing only a few orbitals, which are able to capture a significant amount of correlation. The focus in this manuscript is on using these derived basis sets to target full CI (FCI) quality results for H2 on near-term quantum computers. However, the initial results for this approach were promising. We were able to obtain good agreement with FCI/cc-pVTZ results for this system with just 4 virtual orbitals, using both FCI and quantum simulations. The quality of the results using COVOs suggests that it may be possible to use them in other many-body approaches, including coupled cluster and Møller-Plesset perturbation theories, and open up the door to many-body calculations for pseudopotential plane-wave basis set methods.

Toward Quantum Computing for High-Energy Excited States in Molecular Systems: Quantum Phase Estimations of Core-Level States

This paper explores the utility of the quantum phase estimation (QPE) algorithm in calculating high-energy excited states characterized by the promotion of electrons occupying core-level shells. These states have been intensively studied over the last few decades, especially in supporting the experimental effort at light sources. Results obtained with QPE are compared with various high-accuracy many-body techniques developed to describe core-level states. The feasibility of the quantum phase estimator in identifying classes of challenging shake-up states characterized by the presence of higher-order excitation effects is discussed. We also demonstrate the utility of the QPE algorithm in targeting excitations from specific centers in a molecule. Lastly, we discuss how the lowest-order Trotter formula can be applied to reducing the complexity of the ansatz without affecting the error.

Solving Coupled Cluster Equations by the Newton Krylov Method

We describe using the Newton Krylov method to solve the coupled cluster equation. The method uses a Krylov iterative method to compute the Newton correction to the approximate coupled cluster amplitude. The multiplication of the Jacobian with a vector, which is required in each step of a Krylov iterative method such as the Generalized Minimum Residual (GMRES) method, is carried out through a finite difference approximation, and requires an additional residual evaluation. The overall cost of the method is determined by the sum of the inner Krylov and outer Newton iterations. We discuss the termination criterion used for the inner iteration and show how to apply pre-conditioners to accelerate convergence. We will also examine the use of regularization technique to improve the stability of convergence and compare the method with the widely used direct inversion of iterative subspace (DIIS) methods through numerical examples.

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.

Real-Time Coupled-Cluster Approach for the Cumulant Green's Function

Green's function methods within many-body perturbation theory provide a general framework for treating electronic correlations in excited states and spectra. Here, we develop the cumulant form of the one-electron Green's function using a real-time coupled-cluster equation-of-motion approach, in an extension of our previous study (Rehr J.; et al. J. Chem. Phys. 2020, 152, 174113). The approach yields a nonperturbative expression for the cumulant in terms of the solution to a set of coupled first-order, nonlinear differential equations. The method thereby adds nonlinear corrections to traditional cumulant methods, which are linear in the self-energy. The approach is applied to the core-hole Green's function and is illustrated for a number of small molecular systems. For these systems, we find that the nonlinear contributions yield significant improvements, both for quasiparticle properties such as core-level binding energies and for inelastic losses that correspond to satellites observed in photoemission spectra.

Resource-Efficient Chemistry on Quantum Computers with the Variational Quantum Eigensolver and the Double Unitary Coupled-Cluster Approach

Applications of quantum simulation algorithms to obtain electronic energies of molecules on noisy intermediate-scale quantum (NISQ) devices require careful consideration of resources describing the complex electron correlation effects. In modeling second-quantized problems, the biggest challenge confronted is that the number of qubits scales linearly with the size of the molecular basis. This poses a significant limitation on the size of the basis sets and the number of correlated electrons included in quantum simulations of chemical processes. To address this issue and enable more realistic simulations on NISQ computers, we employ the double unitary coupled-cluster (DUCC) method to effectively downfold correlation effects into the reduced-size orbital space, commonly referred to as the active space. Using downfolding techniques, we demonstrate that properly constructed effective Hamiltonians can capture the effect of the whole orbital space in small-size active spaces. Combining the downfolding preprocessing technique with the variational quantum eigensolver, we solve for the ground-state energy of H₂, Li₂, and BeH₂ in the cc-pVTZ basis using the DUCC-reduced active spaces. We compare these results to full configuration-interaction and high-level coupled-cluster reference calculations.

Exploiting chemistry and molecular systems for quantum information science

The power of chemistry to prepare new molecules and materials has driven the quest for new approaches to solve problems having global societal impact, such as in renewable energy, healthcare and information science. In the latter case, the intrinsic quantum nature of the electronic, nuclear and spin degrees of freedom in molecules offers intriguing new possibilities to advance the emerging field of quantum information science. In this Perspective, which resulted from discussions by the co-authors at a US Department of Energy workshop held in November 2018, we discuss how chemical systems and reactions can impact quantum computing, communication and sensing. Hierarchical molecular design and synthesis, from small molecules to supramolecular assemblies, combined with new spectroscopic probes of quantum coherence and theoretical modelling of complex systems, offer a broad range of possibilities to realize practical quantum information science applications.

Improved sample preparation method for fast LC-MS/MS analysis of vitamin D metabolites in serum

Despite the fact that more than 90% of vitamin D analysis are performed using immuno-enzymatic techniques, it is liquid chromatography coupled with tandem mass spectrometry that is currently the reference method. It allows for specific and selective analysis of all relevant vitamin D metabolites from a variety of biological materials, including serum or a dried blood spot. This paper presents development of a fast, cheap and high-throughput method of serum sample preparation using protein precipitation. For this purpose, organic solvent is used. Several substances were tested, including acetonitrile, methanol and their mixtures with zinc sulfate. However, the highest recovery values for the vitamin D metabolites were obtained for acetonitrile, with an organic solvent to serum ratio of 8:1. The preparation of a sample is carried out in 96-well plates and takes an hour and a half, together with a derivatization reaction using Cookson-type reagent 4-(4'-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione. Due to the fact that vitamin D metabolites are bound to proteins, the relationship between the content of organic solvent in the sample preparation process and their release from the protein complex was examined. The results indicate that the organic solvent content should be 30-70% in order to completely release the tested compounds from the proteins. In addition, the developed chromatographic method has eliminated false positive signals for the 24,25(OH)₂D₃ metabolite. Total analysis time is 5.5 min., while maintaining resolution necessary to separate the analyzed compounds.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Equation of motion coupled-cluster cumulant approach for intrinsic losses in x-ray spectra

We present a combined equation of motion coupled-cluster cumulant Green's function approach for calculating and understanding intrinsic inelastic losses in core level x-ray absorption spectra (XAS) and x-ray photoemission spectra. The method is based on a factorization of the transition amplitude in the time domain, which leads to a convolution of an effective one-body absorption spectrum and the core-hole spectral function. The spectral function characterizes intrinsic losses in terms of shake-up excitations and satellites using a cumulant representation of the core-hole Green's function that simplifies the interpretation. The one-body spectrum also includes orthogonality corrections that enhance the XAS at the edge.

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.

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.

Approximate Green's Function Coupled Cluster Method Employing Effective Dimension Reduction

The Green's function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structure of molecular and periodic systems, especially when electrons of the system are strongly correlated. However, in order for the GFCC to become a method that may be routinely used in the electronic structure calculations, robust numerical techniques and approximations must be employed to reduce its extremely high computational overhead. In our recent studies, it has been demonstrated that the GFCC equations can be solved directly in the frequency domain using iterative linear solvers, which can be easily distributed in a massively parallel environment. In the present work, we demonstrate a successful application of model-order-reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires high-resolution descriptions of spectral function, instead of solving the GFCC linear equation of full dimension for every single frequency point of interest, an efficiently solvable linear system model of a reduced dimension may be built upon projecting the original GFCC linear system onto a subspace. From this reduced order model is obtained a reasonable approximation to the full dimensional GFCC linear equations in both interpolative and extrapolative spectral regions. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some selected frequencies within the spectral region of interest. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The method is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems such as carbon monoxide, 1,3-butadiene, benzene, and adenine. To reach the same level of accuracy as that of the original GFCC method, the application of MOR in the GFCC method is able to significantly lower the original computational cost for the aforementioned molecules in designated frequency regimes. As a byproduct, the reduced order model obtained by this method is found to provide a high-quality initial guess, which improves the convergence rate for the existing iterative linear solver.

Brain-Gut-Microbiota Axis in Alzheimer's Disease

Disturbances along the brain-gut-microbiota axis may significantly contribute to the pathogenesis of neurodegenerative disorders. Alzheimer's disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid beta (Aβ) plaques and neurofibrillary tangles. Alterations in the gut microbiota composition induce increased permeability of the gut barrier and immune activation leading to systemic inflammation, which in turn may impair the blood-brain barrier and promote neuroinflammation, neural injury, and ultimately neurodegeneration. Recently, Aβ has also been recognized as an antimicrobial peptide participating in the innate immune response. However, in the dysregulated state, Aβ may reveal harmful properties. Importantly, bacterial amyloids through molecular mimicry may elicit cross-seeding of misfolding and induce microglial priming. The Aβ seeding and propagation may occur at different levels of the brain-gut-microbiota axis. The potential mechanisms of amyloid spreading include neuron-to-neuron or distal neuron spreading, direct blood-brain barrier crossing or via other cells as astrocytes, fibroblasts, microglia, and immune system cells. A growing body of experimental and clinical data confirms a key role of gut dysbiosis and gut microbiota-host interactions in neurodegeneration. The convergence of gut-derived inflammatory response together with aging and poor diet in the elderly contribute to the pathogenesis of AD. Modification of the gut microbiota composition by food-based therapy or by probiotic supplementation may create new preventive and therapeutic options in AD.

Development of a method for multiple vitamin D metabolite measurements by liquid chromatography coupled with tandem mass spectrometry in dried blood spots

There are two forms of vitamin D which are essential to the human body, i.e. vitamin D2 (ergocalciferol) and vitamin D3 (cholecalciferol). The inactive metabolites of vitamin D are commonly used for quantitative analysis because of their longer half-life, stability, and relatively high blood concentrations. This paper presents the development of a high-throughput and sensitive method for determining four vitamin D metabolites in dried blood spots using liquid chromatography coupled with tandem mass spectrometry. This method allows for the determination of 25(OH)D2 and 25(OH)D3 concentrations, as well as the epimeric form 3-epi-25(OH)D3 and 24,25(OH)2D3. The analyzed material is capillary blood taken from the fingertip, deposited on filter paper. Four different chromatographic columns were tested to separate all compounds, in particular, the epimeric form. The column of choice was F5 (Phenomenex, Torrance, CA, USA). In order to prove the consistency between the results for DBS, used as an alternative biological matrix, and serum, comparative studies of these two materials were carried out in nearly 100 individuals. The results indicated their positive correlation. The evaluation of short-term stability of metabolites in DBS within the month showed no change in metabolite concentration. During the validation, the impact of the matrix on the ionization of the tested compounds was evaluated. Capillary blood and venous blood collected for different anticoagulants were also compared. The smallest differences in the results were obtained for citrate. In order to achieve a limit of quantitation of 0.2 ng ml-1, sample preparation involved derivatization using a Cookson-type reagent, 4-(4'-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD).

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.

Green's Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems

In this paper, we present an efficient implementation for the analytical energy-dependent Green's function coupled-cluster with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of realistic molecular systems. Because of its algebraic structure, the presented method is highly scalable and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where a many-body effect becomes significant and the single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing the computed spectral functions by our GFCCSD method with experimental photoelectron spectra as well as the theoretical ionization potentials obtained from other methods. It turns out the GFCCSD method is able to provide a qualitative or semiquantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main ionic states, a larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher-order many-body terms to be included in the GFCC implementation.

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.

Diagnostic challenges in celiac disease

Diagnosis of celiac disease in adults is currently based on serologic tests in combination with histopathological assessment of small intestinal biopsy specimens. High titers of celiac-specific antibodies in immunocompetent patients with villous atrophy in a good quality biopsy sample allow us to state a confident diagnosis. The relief of symptoms and histological improvement after embarking on a gluten free diet further support the initial diagnosis. However, in some cases, these conditions are not fulfilled, which requires a critical evaluation of laboratory and histopathology results and a consideration of other potential causes for the observed pathologies. To avoid diagnostic uncertainty, both biopsy and laboratory testing should be performed on a diet containing gluten. Immune deficiency, cross reaction of antibodies and possibilities of seronegative or latent celiac disease should be considered while evaluating serology results. Uneven distribution and variable intensity of histopathological changes in the small intestine along with multiple disorders presenting a similar specimen image may lead to invalid biopsy results. Additional laboratory testing and careful examination of a patient's history may deliver important data for a differential diagnosis and a more specific biopsy evaluation. Persistence or recurrence of symptoms, despite the ongoing treatment, requires a revision of the initial diagnosis, an evaluation of the gluten free diet and a search for concurrent disorders or complications.

Electronic π-to-π* Excitations of Rhodamine Dyes Exhibit a Time-Dependent Kohn-Sham Theory "Cyanine Problem"

The longest-wavelength π-to-π* electronic excitations of rhodamine-like dyes (RDs) with different group 16 heteroatoms (O, S, Se, Te) have been investigated. Time-dependent Kohn-Sham theory (TDKST) calculations were compared with coupled-cluster (CC) and equations-of-motion (EOM) CC results for π-to-π* singlet and triplet excitations. The RDs exhibit characteristics in the TDKST calculations that are very similar to previously investigated cyanine dyes, in the sense that the singlet energies obtained with nonhybrid functionals are too high compared with the CC results at the SD(T) level. The errors became increasingly larger for functionals with increasing amounts of exact exchange. TDKST with all tested functionals led to severe underestimations of the corresponding triplet excitations and overestimations of the singlet-triplet gaps. Long-range-corrected range-separated exchange and "optimal tuning" of the range separation parameter did not significantly improve the TDKST results. A detailed analysis suggests that the problem is differential electron correlation between the ground and excited states, which is not treated sufficiently by the relatively small integrals over the exchange-correlation response kernel that enter the excitation energy expression. Numerical criteria are suggested that may help identify "cyanine-like" problems in TDKST calculations of excitation spectra.