Shape resonance induced electron attachment to cytosine: The effect of aqueous media

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.

State-specific frozen natural orbital for reduced-cost algebraic diagrammatic construction calculations: The application to ionization problem

We have developed a reduced-cost algebraic diagrammatic construction (ADC) method based on state-specific frozen natural orbital and natural auxiliary functions. The newly developed method has been benchmarked on the GW100 test set for the ionization problem. The use of state-specific natural orbitals drastically reduces the size of the virtual space with a systematically controllable accuracy and offers a significant speedup over the standard ionization potential (IP)-ADC(3) method. The accuracy of the method can be controlled by two thresholds and nearly a black box to use. The inclusion of the perturbative correction significantly improves the accuracy of the calculated IP values, and the efficiency of the method has been demonstrated by calculating the IP of a molecule with 60 atoms and more than 2216 basis functions.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

Electron Attachment to DNA: The Protective Role of Amino Acids

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Electron Attachment to Wobble Base Pairs

We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.

A low-cost four-component relativistic equation of motion coupled cluster method based on frozen natural spinors: Theory, Implementation and Benchmark

<p>We present the theory and the implementation of a low-cost four-component relativistic equation of motion coupled cluster method for ionized states based on frozen natural spinors. A single threshold (natural spinor occupancy) can control the accuracy of the calculated ionization potential values. Frozen natural spinors can significantly reduce the computational cost for valence and core-ionization energies with systematically controllable accuracy. The convergence of the ionization potential values with respect to the natural spinor occupancy threshold becomes slower with the increase in basis set dimension. However, the use of a natural spinor threshold of 10-5 and 10-6 gives excellent agreement with experimental results for valence and core ionization energies, respectively.</p>

Observation of Myocardial Involvement in Patients Recovered From COVID-19 by Using Cardiac Magnetic Resonance Imaging, In a Tertiary Care Hospital, Bangladesh

It was previously reported that coronavirus caused myocardial injury in hospitalized patients. However, delayed cardiac involvement in symptomatic patient recovery from COVID-19 is not yet well known. The objective of this study was to evaluate cardiac involvement by using cardiac magnetic resonance (CMR) in symptomatic post-COVID-19 recovered patients. Thirty (30) patients who recovered from COVID-19 and had recently reported cardiac symptoms were studied in a prospective observational study performed at Popular Medical College Hospital, Dhaka, Bangladesh from March 2021 to September 2021. They underwent CMR examinations. CMR scanning protocol included the following: black blood, cine sequence, both short-axis and long-axis, T2-weight short tau inversion recovery (STIR) sequence, T2- weighted imaging (T2WI) and late gadolinium enhancement (LGE) and quantitative mapping sequences-native T1/T2 mapping and post-contrast T1 mapping. Myocardial edema and late gadolinium enhancement were assessed in all patients. Quantitative evaluation of native T1/T2 and ECV value and cardiac function were evaluated. There were 30 people in all in this study. The average age of the participants in the study was 36.6 years. Fourteen (46.6%) of the patients had abnormal cardiac MRI results, while the remaining 15(53.3%) had negative CMR findings. Among positive findings patients, 8(57.1%) of 14 had increased T2 signal. Increased myocardial edema was found in the same no of patients, involving 53.2% (128 of 224) of LV segments. Only 2 cases (2 of 14) showed mid myocardial and subepicardial LGE, involving 18 of 224, 8.03% of myocardial segments. Global native T1, T2 and ECV values are significantly elevated in all CMR positive findings patients. Native T1 1231ms (IQR: 1281.25-1257.5 versus 1155.5 (IQR: 1137.25-1172.75), T2 40 (IQR: 34.5-43.25) versus 35.5 (IQR: 34-37), ECV 31 (29.75-33.25) versus 23.5 (21.25-24.0), p<0.001; p<0.011 and p<0.001 respectively. Reduced RV functional were found in positive as compared with negative CMR findings patients, EF, 32.05 (IQR: 25.25-39.0) versus 54.5 (IQR: 52.0-57.75) and EDV, 117.5 (IQR: 102.0-134.25) versus 95.0 (IQR: 71.75-99.75), p<0.001 and p<0.001 respectively. In this study cardiac involvement was found in the post-COVID-19 recovered patient with cardiac symptoms. Cardiac MRI findings included myocardial edema, fibrosis and reduced right ventricular function. So attention should be paid to symptomatic post-COVID-19 recovered patients.

Pair Natural Orbital Equation-of-Motion Coupled-Cluster Method for Core Binding Energies: Theory, Implementation, and Benchmark

We present the theory and implementation of a lower scaling core-valence separated equation-of-motion coupled-cluster approach based on domain-based local pair natural orbitals for core binding energies. The accuracy of the new method has been compared with that of the standard equation-of-motion coupled-cluster method and experimentally measured results. The use of pair natural orbitals significantly reduces the computation cost and can be applied to large molecules.

A reduced cost four-component relativistic coupled cluster method based on natural spinors

We present the theory, implementation, and benchmark results for a frozen natural spinors based reduced cost four-component relativistic coupled cluster method. The natural spinors are obtained by diagonalizing the one-body reduced density matrix from a relativistic second-order Møller-Plesset calculation based on a four-component Dirac-Coulomb Hamiltonian. The correlation energy in the coupled cluster method converges more rapidly with respect to the size of the virtual space in the frozen natural spinor basis than that observed in the standard canonical spinors obtained from the Dirac-Hartree-Fock calculation. The convergence of properties is not smooth in the frozen natural spinor basis. However, the inclusion of the perturbative correction smoothens the convergence of the properties with respect to the size of the virtual space in the frozen natural spinor basis and greatly reduces the truncation errors in both energy and property calculations. The accuracy of the frozen natural spinor based coupled cluster methods can be controlled by a single threshold and is a black box to use.

A similarity transformed second-order approximate coupled cluster method for the excited states: Theory, implementation, and benchmark

We present a novel and cost-effective approach of using a second similarity transformation of the Hamiltonian to include the missing higher-order terms in the second-order approximate coupled cluster singles and doubles (CC2) model. The performance of the newly developed ST-EOM-CC2 model has been investigated for the calculation of excitation energies of valence, Rydberg, and charge-transfer excited states. The method shows significant improvement in the excitation energies of Rydberg and charge-transfer excited states as compared to the conventional CC2 method while retaining the good performance of the latter for the valence excited state. This method retains the charge-transfer separability of the charge-transfer excited states, which is a significant advantage over the traditional CC2 method. A second order many-body perturbation theory variant of the new method is also proposed.

A Core-Valence Separated Similarity Transformed EOM-CCSD Method for Core-Excitation Spectra

We present the theory and implementation of a core-valence separated similarity transformed EOM-CCSD (STEOM-CCSD) method for K-edge core excitation spectra. The method can select an appropriate active space using CIS natural orbitals and near "black box" to use. The second similarity transformed Hamiltonian is diagonalized in the space of single excitation. Therefore, the final diagonalization step is free from the convergence problem arising due to the coupling of the core-excited states with the continuum of doubly excited states. Convergence trouble can appear for the preceding core-ionized state calculation in STEOM-CCSD. A core-valence separation (CVS) scheme compatible with the natural orbital based active space selection (CVS-STEOM-CCSD-NO) is implemented to overcome the problem. The CVS-STEOM-CCSD-NO has a similar accuracy to that of the standard CVS-EOM-CCSD method but comes with a lower computational cost. The modification required in the CVS scheme to make use of the CIS natural orbital is highlighted. The suitability of the CVS-STEOM-CCSD-NO method for chemical application is demonstrated by simulating the K-edge spectra of glycine and thymine.

Doorway Mechanism for Electron Attachment Induced DNA Strand Breaks

We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ*-type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism can explain the relative rates of electron attachment induced bond cleavages in genetic materials.

An efficient Fock space multi-reference coupled cluster method based on natural orbitals: Theory, implementation, and benchmark

We present a natural orbital-based implementation of the intermediate Hamiltonian Fock space coupled-cluster method for the (1, 1) sector of Fock space. The use of natural orbitals significantly reduces the computational cost and can automatically choose an appropriate set of active orbitals. The new method retains the charge transfer separability of the original intermediate Hamiltonian Fock space coupled-cluster method and gives excellent performance for valence, Rydberg, and charge-transfer excited states. It offers significant computational advantages over the popular equation of motion coupled cluster method for excited states dominated by single excitations.

Electron Attachment to Cytosine: The Role of Water

We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.

Retraction: A highly concise and practical route to clavaminols, sphinganine and (+)-spisulosine via indium mediated allylation of α-hydrazino aldehyde and a theoretical insight into the stereochemical aspects of the reaction

[This retracts the article DOI: 10.1039/C3RA43048K.].

Photolysis of cell-permeant caged inositol pyrophosphates controls oscillations of cytosolic calcium in a β-cell line

β-Cells respond directly to the intracellular photochemical release of caged inositol pyrophosphate isomers with modulations of oscillations in cytosolic Ca²⁺.

Among many cellular functions, inositol pyrophosphates (PP-InsPs) are metabolic messengers involved in the regulation of glucose uptake, insulin sensitivity, and weight gain. However, their mechanisms of action are still poorly understood. So far, the influence of PP-InsPs on cellular metabolism has been studied by overexpression or knockout/inhibition of relevant metabolizing kinases (IP6Ks, PPIP5Ks). These approaches are, inter alia, limited by time-resolution and potential compensation mechanisms. Here, we describe the synthesis of cell-permeant caged PP-InsPs as tools to rapidly modulate intracellular levels of defined isomers of PP-InsPs in a genetically non-perturbed cellular environment. We show that caged prometabolites readily enter live cells where they are enzymatically converted into still inactive, metabolically stable, photocaged PP-InsPs. Upon light-triggered release of 5-PP-InsP₅, the major cellular inositol pyrophosphate, oscillations of intracellular Ca²⁺ levels in MIN6 cells were transiently reduced to spontaneously recover again. In contrast, uncaging of 1-PP-InsP₅, a minor cellular isomer, was without effect. These results provide evidence that PP-InsPs play an active role in regulating [Ca²⁺]_i oscillations, a key element in triggering exocytosis and secretion in β-cells.

Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones

Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T₀ ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.

A simple scheme for calculating approximate transition moments within the equation of motion expectation value formalism

A simple scheme for calculating approximate transition moments within the framework of the equation of motion coupled cluster method is proposed. It relies on a matrix inversion technique to calculate the excited state left eigenvectors and requires no additional cost over that of the excitation energy calculation. The new approximation gives almost identical UV-Vis spectra to that obtained using the standard equation of motion coupled cluster method with single and double excitations for molecules in a standard test set.

Electron Detachment and Subsequent Structural Changes of Water Clusters

A cost-effective equation of motion coupled cluster method, EOMIP-CCSD(2), is used to investigate vertical and adiabatic ionization potential as well as ionization-induced structural changes of water clusters and compared with CCSD(T), CASPT2, and MP2 methods. The moderate N(5) scaling and low storage requirement yields EOMIP-CCSD(2) calculation feasible even for reasonably large molecules and clusters with accuracy comparable to CCSD(T) method at much cheaper computational cost. Our calculations shed light on the authenticity of EOMIP-CCSD(2) results and establish a reliable method to study of ionization energy of molecular clusters. We have further investigated the performance of several classes of DFT functionals for ionization energies of water clusters to benchmark the results and to get a reliable functionals for the same.

Ground state of naphthyl cation: singlet or triplet?

We present a benchmark theoretical investigation on the electronic structure and singlet-triplet(S-T) gap of 1- and 2-naphthyl cations using the CCSD(T) method. Our calculations reveal that the ground states of both the naphthyl cations are singlet, contrary to the results obtained by DFT/B3LYP calculations reported in previous theoretical studies. However, the triplet states obtained in the two structural isomers of naphthyl cation are completely different. The triplet state in 1-naphthyl cation is (π,σ) type, whereas in 2-naphthyl cation it is (σ,σ') type. The S-T gaps in naphthyl cations and the relative stability ordering of the singlet and the triplet states are highly sensitive to the basis-set quality as well as level of correlation, and demand for inclusion of perturbative triples in the coupled-cluster ansatz.

Structure, stability, and properties of the trans peroxo nitrate radical: the importance of nondynamic correlation

We report a comparative single-reference and multireference coupled-cluster investigation on the structure, potential energy surface, and IR spectroscopic properties of the trans peroxo nitrate radical, one of the key intermediates in stratospheric NOX chemistry. The previous single-reference ab initio studies predicted an unbound structure for the trans peroxo nitrate radical. However, our Fock space multireference coupled-cluster calculation confirms a bound structure for the trans peroxo nitrate radical, in accordance with the experimental results reported earlier. Further, the analysis of the potential energy surface in FSMRCC method indicates a well-behaved minima, contrary to the shallow minima predicted by the single-reference coupled-cluster method. The harmonic force field analysis, of various possible isomers of peroxo nitrate also reveals that only the trans structure leads to the experimentally observed IR peak at 1840 cm(-1). The present study highlights the critical importance of nondynamic correlation in predicting the structure and properties of high-energy stratospheric NOx radicals.

Hepatitis B vaccination with or without hepatitis B immunoglobulin at birth to babies born of HBsAg-positive mothers prevents overt HBV transmission but may not prevent occult HBV infection in babies: a randomized controlled trial

Vertical transmission of Hepatitis B virus HBV can result in a state of chronic HBV infection and its complications. HBV vaccination with or without hepatitis B immunoglobulin (HBIG) prevents transmission of overt infection to the babies. However, whether it also prevents occult HBV infection in babies is not known. Consecutive pregnant women of any gestation found to be HBsAg positive were followed till delivery, and their babies were included in the study. Immediately after delivery, babies were randomized to receive either HBIG or placebo in addition to recombinant HBV vaccine (at 0, 6, 10 and 14 weeks). The primary end-point of the study, assessed at 18 weeks of age, was remaining free of any HBV infection (either overt or occult) plus the development of adequate immune response to vaccine. The babies were further followed up for a median of 2 years of age to determine their eventual outcome. Risk factors for HBV transmission and for poor immune response in babies were studied. Of the 283 eligible babies, 259 were included in the trial and randomized to receive either HBIG (n=128) or placebo (n=131) in addition to recombinant HBV vaccine. Of the 222 of 259 (86%) babies who completed 18 weeks of follow-up, only 62/222 (28%) reached primary end-point. Of the remaining, 6/222 (3%) developed overt HBV infection, 142/222 (64%) developed occult HBV infection, and 12/222 (5%) had no HBV infection but had poor immune response. All 6 overt infections occurred in the placebo group (P=0.030), while occult HBV infections were more common in the HBIG group (76/106 [72%] vs. 66/116 [57%]; P=0.025). This may be due to the immune pressure of HBIG. There was no significant difference between the two groups in frequency of babies developing poor immune response or those achieving primary end-point. The final outcome of these babies at 24 months of age was as follows: overt HBV infection 4%, occult HBV infection 42%, no HBV infection but poor immune response 8% and no HBV infection with good immune response 28%. Women who were anti-HBe positive were a low-risk group, and their babies were most likely to remain free of HBV infection (occult or overt) and had good immune response to the vaccine. Maternal HBeAg-positive status and negativity for anti-HBe predicted not only overt but also any infection (both overt and occult) in babies. In addition, high maternal HBV DNA and treatment with vaccine alone were significant factors for overt HBV infection in babies. The current practice of administration of vaccine with HBIG at birth to babies born of HBsAg-positive mothers is not effective in preventing occult HBV infection in babies, which may be up to 40%. Because the most important risk factors for mother-to-baby transmission of HBV infection are the replicative status and high HBV DNA level in mothers; it will be worthwhile investigating the role of antivirals and HBIG administration during pregnancy to prevent mother-to-child transmission of HBV infection.