Assessment of the potential energy hypersurfaces in thymine within multiconfigurational theory: CASSCF vs. CASPT2

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected

Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra

Accurate ab initio modeling of spectroscopic signals in nonlinear electronic spectra, such as bidimensional (2D) spectra, requires the computation of the electronic transitions induced by the incoming pump/probe pulses, resulting in a challenging calculation of many electronic excited states. A protocol is thus required to evaluate the variations of spectral properties, like transition energies and dipole moments, with the computational level, and to estimate the sensitivity of the spectra to these variations. Such a protocol is presented here within the framework of complete and restricted active space self-consistent field (CASSCF/RASSCF) theory and its second-order perturbation theory extensions (CASPT2/RASPT2). The electronic excited-state manifolds of pyrimidine nucleobases (thymine, uracil, and cytosine) are carefully characterized in vacuo employing high-level RAS(0,0|10,8|2,12)//SS-RASPT2 calculations. The results provide a reference data set that can be used for optimizing computational efforts and costs, as required for studying computationally more demanding multichromophoric systems (e.g., di- and oligonucleotides). The spectroscopic signatures of the 2D electronic spectrum of a perfectly stacked uracil–cytosine dimer model are characterized, and experimental setups are proposed that can resolve non-covalent interchromophoric interactions in canonical pyrimidine nucleobase-stacked dimers

Quantum chemistry of the excited state: recent trends in methods developments and applications

Advances (2016–2017) in Quantum Chemistry of the Excited State (QCEX) are presented in this book chapter focusing firstly on developments of methodology and excited-state reaction-path computational strategies and secondly on the applications of QCEX to study light–matter interaction in distinct fields of biology, (nano)-technology, medicine and the environment. We highlight in this contribution developments of static and dynamic electron-correlation methods and methodological approaches to determine dynamical properties, recent examples of the roles of conical intersections, novel DNA spectroscopy and photochemistry findings, photo-sensitisation mechanisms in biological structures and the current knowledge on chemi-excitation mechanisms that give rise to light emission (in the chemiluminescence and bioluminescence phenomena)

Dissemination of Strongyloides stercoralis in a patient with systemic lupus erythematosus after initiation of albendazole: a case report

<p>Abstract</p> <p>Introduction</p> <p><it>Strongyloides stercoralis </it>infection affects hundreds of millions of people worldwide. As immigration rates and international travel increase, so does the number of cases of strongyloidiasis in the United States. Although described both in immigrant and in immunosuppressed populations, hyperinfection and dissemination of <it>S. stercoralis </it>following the initiation of antiparasitic medication is a previously unreported phenomenon.</p> <p>Case presentation</p> <p>Here we describe the case of a 38-year-old immunocompromised woman with systemic lupus erythematosus, who developed disseminated disease following treatment with albendazole (400 mg every 12 hours). Notably the patient was receiving oral prednisone (10 mg once daily), azathioprine (50 mg twice daily), and hydroxychloroquine (400 mg daily) at the time of hospitalization. The patient was subsequently treated successfully with ivermectin (200 mcg/kg daily).</p> <p>Conclusion</p> <p>The reader should be aware that dissemination of <it>S. stercoralis </it>can occur even after the initiation of antiparasitic medication.</p

Randomized Clinical Trial on Ivermectin versus Thiabendazole for the Treatment of Strongyloidiasis

Strongyloidiasis is the infection caused by the worm Strongyloides stercoralis. Due to its peculiar life cycle Strongyloides may remain indefinitely in the host, if not effectively cured. Although the disease is usually mild, in case of weakening of the host's immune defenses the worm may invade virtually all organs and tissues (disseminated strongyloidiasis, almost invariably fatal). The treatment must then reach the goal of the complete elimination of the parasite. Small size clinical trials showed similar, high efficacy of the two drugs ivermectin (used as a single dose) and thiabendazole (used twice daily for two consecutive days). All trials used as the criterion for cure the absence of larvae in stool exams. The latter however may easily miss the infection, falsely suggesting that the infection has been cured. This trial, using a test detecting specific Strongyloides antibodies as an additional and more sensitive diagnostic tool, confirms previous reports: the two drugs have similar efficacy but ivermectin is better tolerated and is therefore the first choice. However the cure rate was lower than 70% for the standard, single dose. The authors then conclude that a larger, multi center trial is needed to find the optimal dose schedule of ivermectin

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations

Improving the configuration of the predictable ACDC data cache for real-time systems

In real-time systems, analyzing the worst-case execution time (WCET) of a task in the presence of data caches is hard. The ACDC is a data cache that provides predictability, facilitating WCET analysis. It works by granting data cache replacement permission to specific load/store instructions. Nonetheless, knowing how to select these instructions to minimize the WCET, i.e., configuring the ACDC, is not trivial. In this paper, we propose four new methods to configure the ACDC, and compare them with existing methods. Unlike those in previous studies, our proposed methods provide specific ACDC configurations for the different phases of a given task, instead of a single ACDC configuration per task. We evaluate the WCET bounds obtained when using different ACDC configuration methods on the TACLeBench benchmark suite. Our results show that the most complex benchmarks work better with multiple-content configurations, which indicates that realistic tasks may also benefit from this kind of configuration. The methods proposed in this study improve the WCET in more than 60% of cases, with an average WCET improvement of nearly 5% and up to 50% in some cases

Computing the ultrafast and radiationless electronic excited state decay of cytosine and 5‐methyl‐cytosine cations: uncovering the role of dynamic electron correlation

Photoionisation in DNA, i.e. the process of photoinduced electron removal from the chromophoric species − the nucleobases − leading to their cationic form, has been scarcely studied despite being considered to be responsible for significant damaging instances in our genetic material. In this contribution we theoretically characterise the electronic ground and excited state decay pathways of cationic DNA nucleobase cytosine+ and its epigenetic derivative 5‐methyl‐cytosine+, including the effects of dynamic electron correlation on energies and geometries of minima and conical intersections. We do this by comparing the results of XMS‐CASPT2 calculations with CASSCF estimates and we find some significant differences between the results of these two methods. In particular, including dynamic electron correlation is found to significantly reduce the barrier to access the (D1/D0) conical intersection. We find notable similarities in both cytosine and 5‐methyl‐cytosine cations, accessible conical intersections in the vicinity of the Franck‐Condon region are found. This points towards an ultrafast depopulation of their electronic excited states. Moreover, the shape of the ground state potential energy surface strongly directs the decaying excited state population towards the cationic ground state minimum on ultrafast timescales, preventing photofragmentation and thus explaining their photostability

Molecular excited state calculations with adaptive wavefunctions on a quantum eigensolver emulation: reducing circuit depth and separating spin states

Ab initio electronic excited state calculations are necessary for the quantitative study of photochemical reactions, but their accurate computation on classical computers is plagued by prohibitive resource scaling. The Variational Quantum Deflation (VQD) is an extension of the quantum-classical Variational Quantum Eigensolver (VQE) algorithm for calculating electronic excited state energies, and has the potential to address some of these scaling challenges using quantum computers. However, quantum computers available in the near term can only support a limited number of quantum circuit operations, so reducing the quantum computational cost in VQD methods is critical to their realisation. In this work, we investigate the use of adaptive quantum circuit growth (ADAPT-VQE) in excited state VQD calculations, a strategy that has been successful previously in reducing the resources required for ground state energy VQE calculations. We also invoke spin restrictions to separate the recovery of eigenstates with different spin symmetry to reduce the number of calculations and accumulation of errors in computing excited states. We created a quantum eigensolver emulation package - Quantum Eigensolver Building on Achievements of Both quantum computing and quantum chemistry (QEBAB) – for testing the proposed adaptive procedure against two existing VQD methods that use fixed-length quantum circuits: UCCGSD-VQD and k-UpCCGSD-VQD. For a lithium hydride test case we found that the spin-restricted adaptive growth variant of VQD uses the most compact circuits out of the tested methods by far, consistently recovers adequate electron correlation energy for different nuclear geometries and eigenstates while isolating the singlet and triplet manifold. This work is a further step towards developing techniques which improve the efficiency of hybrid quantum algorithms for excited state quantum chemistry, opening up the possibility of exploiting real quantum computers for electronic excited state calculations sooner than previously anticipated

COBRAMM 2.0 A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results