Search

Extracts of Eremophila phyllopoda subsp. phyllopoda showed alpha-glucosidase and PTP1B inhibitory activity with IC50 values of 19.6 and 13.6 mu g/mL, respectively. High-resolution alpha-glucosidase/PTP1B/radical scavenging profiling was performed to establish a triple high-resolution inhibition profile that allowed direct pinpointing of the constituents responsible for one or more of the observed bioactivities. Subsequent targeted isolation and purification by analytical-scale HPLC led to the identification of 21 previously undescribed serrulatane diterpenoids, eremophyllanes A-U, as well as two known serrulatane diterpenoids, 1 beta- trihydroxyserrulatane (8) and 1 alpha-trihydroxyserrulatane (10d), and five known furofuran lignans, (+)-piperitol (6), horsfieldin (7e), (-)-sesamin (9), (+)-sesamin (10h), and asarinin (10i). Their structures were elucidated by extensive analysis of HRMS and 1D and 2D NMR spectroscopic data. The relative configurations of the previously undescribed compounds were established by analysis of ROESY spectra as well as by DFT-GIAO NMR calculations followed by DP4+ probability analysis. The absolute configurations were determined by comparison of experimental and calculated ECD spectra. Serrulatane diterpenoids 7b and 14 exhibited alpha- glucosidase inhibitory activity with IC50 values of 28.4 and 64.2 mu M, respectively, while 11, 12, 14, and 15 exhibited PTP1B inhibitory activity with IC50 values ranging from 16.6 to 104.6 mu M. Hypothetical routes for formation of all identified serrulatane diterpenoids are proposed. Refereed/Peer-reviewed

We present an implementation of a damped response framework for calculating resonant inelastic X-ray scattering (RIXS) at the equation-of-motion coupled cluster singles and doubles (CCSD) and second-order approximate coupled cluster singles and doubles (CC2) levels of theory in the open-source program $e^T$. This framework lays the foundation for future extension to higher excitation methods (notably, the coupled cluster singles and doubles with perturbative triples, CC3) and to multilevel approaches. Our implementation adopts a fully relaxed ground state, and different variants of the core-valence separation projection technique to address convergence issues. Illustrative results are compared with those obtained within the frozen-core core-valence separated approach, available in Q-Chem, as well as with experiment. The performance of the CC2 method is evaluated in comparison with that of CCSD. It is found that, while the CC2 method is noticeably inferior to CCSD for X-ray absorption spectra, the quality of the CC2 RIXS spectra is often comparable to that of the CCSD level of theory, when the same valence excited states are probed. Finally, we present preliminary RIXS results for a solvated molecule in aqueous solution.

Calculations of first-order response wave functions in the X-ray regime often diverge within correlated frameworks such as equation-of-motion coupled-cluster singles and doubles (EOM-CCSD), a consequence of the coupling with the valence ionization continuum. Here, we extend our strategy of introducing a hierarchy of approximations to the EOM-EE-CCSD resolvent (or, inversely, the model Hamiltonian) involved in the response equations for the calculation of X-ray two-photon absorption (X2PA) cross sections. We exploit the frozen--core core--valence--separation (fc-CVS) scheme to first decouple the core and valence Fock spaces, followed by a separate approximate treatment of the valence resolvent. We demonstrate the robust convergence of X-ray response calculations within this framework and compare X2PA spectra of small benchmark molecules with the previously reported density functional theory results.

Nuclear spin-induced circular dichroism (NSCD) is a molecular effect of differential absorption of left- and right-circularly polarized light due to nuclear spins in the molecule. In this work, new tools for its calculation are presented. Analytic expressions for the computation of the B_K term of NSCD have been derived and implemented for the second-order coupled cluster singles and doubles (CC2) model. NSCD results obtained thereby for three derivatives of azobenzenes have been compared with results from time-dependent density functional theory (TD-DFT). The complementary information that could be obtained from NSCD measurements compared to NMR for these three species is discussed.

Coupled-cluster response theory offers a path to high-accuracy calculations of spectroscopic properties, such as magnetic circular dichroism (MCD). However, divergence or slow convergence issues or are often encountered for electronic transitions in high-energy regions with a high density of states. This is here addressed for MCD by an implementation of damped quadratic response theory for resolution-of-identity coupled cluster singles-and-approximate-doubles (RI-CC2), along with an implementation of the MCD A term from resonant response theory. Combined, damped and resonant response theory provide an efficient strategy to calculate MCD spectra over a broad frequency range and for systems that include highly symmetric molecules with degenerate excited states. The protocol is illustrated by application to Zink Tetrabenzoporphyrin in the energy region 2–8 eV and comparison to experimental data. Timings are reported for the resonant and damped approaches, showing that the greater part of the calculation time is consumed by the construction of the building 1blocks for the final MCD ellipticity. A recommendation on how to utilize the procedure is outlined.

The time-resolved x-ray absorption spectrum of the BT-1T cation (BT-1T+) is theoretically simulated in order to investigate the charge transfer reaction of the system. We employ both trajectory surface hopping and quantum dynamics to simulate the structural evolution over time and the changes in the state populations. To compute the static x-ray absorption spectra (XAS) of the ground and excited states, we apply both the time-dependent density functional theory and the coupled cluster singles and doubles method. The results obtained are in good agreement between the methods. It is, furthermore, found that the small structural changes that occur during the reaction have little effect on the static XAS. Hence, the tr-XAS can be computed based on the state populations determined from a nuclear dynamics simulation and one set of static XAS calculations, utilizing the ground state optimized geometry. This approach can save considerable computational resources, as the static spectra need not to be calculated for all geometries. As BT-1T is a relatively rigid molecule, the outlined approach should only be considered when investigating non-radiative decay processes in the vicinity of the Franck-Condon point.

Refereed/Peer-reviewed Discovery of sustainable and benign-by-design drugs to combat emerging health pandemics calls for new analytical technologies to explore the chemical and pharmacological properties of Nature’s unique chemical space. Here, we present a new analytical technology workflow, polypharmacology-labeled molecular networking (PLMN), where merged positive and negative ionization tandem mass spectrometry-based molecular networking is linked with data from polypharmacological high-resolution inhibition profiling for easy and fast identification of individual bioactive constituents in complex extracts. The crude extract of Eremophila rugosa was subjected to PLMN analysis for the identification of antihyperglycemic and antibacterial constituents. Visually easy-interpretable polypharmacology scores and polypharmacology pie charts as well as microfractionation variation scores of each node in the molecular network provided direct information about each constituent’s activity in the seven assays included in this proof-of-concept study. A total of 27 new noncanonical nerylneryl diphosphate-derived diterpenoids were identified. Serrulatane ferulate esters were shown to be associated with antihyperglycemic and antibacterial activities, including some showing synergistic activity with oxacillin in clinically relevant(epidemic) methicillin-resistant Staphylococcus aureus strains and some showing saddle-shaped binding to the active site of proteintyrosine phosphatase 1B. PLMN is scalable in the number and types of assays included and thus holds potential for a paradigm shift toward polypharmacological natural-products-based drug discovery.

Table-top x-ray spectroscopy measurements at the carbon K-edge complemented by ab initio calculations are used to investigate the influence of the bromine atom on the carbon core-valence transitions in bromobenzene cation (BrBz+). The electronic ground state of the cation is prepared by resonance-enhanced two-photon ionization of neutral bromobenzene (BrBz) and probed by x-rays produced by high-harmonic generation (HHG). Replacing one of the hydrogen atoms in benzene with a bromine atom shifts the transition from the 1sC* orbital of the carbon atom (C*) bonded to bromine by ~1 eV to higher energy in the x-ray spectrum compared to the other carbon atoms (C). The x-ray absorption spectra of neutral BrBz reveals the influence of the bromine atom on the x-ray absorption spectrum due to the 1sC* orbital, while the influence of the bromine atom on the cation spectrum is even more prominent. The x-ray spectrum of the cation is dominated by two relatively intense transitions, the 1sC→ π* and the 1sC*→ σ*(C*-Br), where the second transition is enhanced relative to the neutral BrBz. In addition, a doublet peak shape for these two transitions is observed in the experiment. The 1sC→ π* doublet peak shape arises due to the spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the two other unpaired electrons resulting from the transition from the 1sC core orbital to the fully vacant π* orbitals. The 1sC*→ σ* doublet peak shape results from several transitions involving σ* and vibrational C*-Br mode activation following the UV ionization, which demonstrates the impact of the C*-Br bond length on the core-valence transition as well as the relaxation geometry of BrBz+.

We investigate the resonant and non-resonant Auger spectra of ozone with a newly implemented multi-reference protocol based on the one-center approximation [Tenorio et al., J. Chem. Theory Comput. 2022, 18, 4387-4407]. The results of our calculations are compared to existing experimental data, where we elucidate the resonant Auger spectrum measured at 530.8 and 536.7 eV, that correspond to the 1sOT → π*(2b1) and 1sOT → σ*(7a1) resonances, and at 542.3 eV, which lies near the 1sOC → σ*(7a1) excited state and above the 1sOT−1 ionization threshold. Using molecular dynamics simulations, we demonstrate the relevance of few-femtoseconds nuclear dynamics in the resonant Auger spectrum of ozone following the 1sOT → π*(2b1) core-excitation.

We present an implementation of the [Formula: see text] term of Magnetic Circular Dichroism (MCD) within the Algebraic Diagrammatic Construction (ADC) scheme of the polarization propagator and its Intermediate State Representation. As illustrative results, the MCD spectra of the ADC variants ADC(2), ADC(2)-x, and ADC(3) of the molecular systems uracil, 2-thiouracil, 4-thiouracil, purine, hypoxanthine 1,4-naphthoquinone, 9,10-anthraquinone, and 1-naphthylamine are computed and compared with results obtained by using the Resolution-of-Identity Coupled-Cluster Singles and Approximate Doubles method, with literature Time-Dependent Density Functional Theory results, and with available experimental data.

Five new polyketides were isolated from the rare filamentous fungus Aspergillus californicus IBT 16748 including calidiol A (1); three phthalide derivatives califuranones A1, A2, and B (2-4); and a pair of enantiomers (-)-calitetralintriol A (-5) and (+)-calitetralintriol A (+5) together with four known metabolites (6-9). The structures of the new products were established by extensive spectroscopic analyses including HRMS and 1D and 2D NMR. The absolute configurations of two diastereomers 2 and 3 and the enantiomers (-5) and (+5) were assigned by comparing their experimental and calculated ECD data, whereas the absolute configuration of 4 was proposed by analogy. Compound 1 showed moderate activity against methicillin-resistant Staphylococcus aureus.

We report on single- and double-charge photofragment formation by synchrotron radiation, following C 1s core excitation and ionization and Cl 2p inner excitation and ionization of chlorobenzene, C6H5Cl. From a comparison of experimental near-edge X-ray absorption fine structure spectra and theoretical ab initio calculations, the nature of various core and inner shell transitions of the molecule and pure atomic features were identified. To shed light on the normal Auger processes following excitation or ionization of the molecule at the Cl 2p or C 1s sites, we addressed the induced ionic species formation. With energy resolved electron spectra and ion time-of-flight spectra coincidence measurements, the ionic species were correlated with binding energy regions and initial states of vacancies. We explored the formation of the molecular dication C6H5Cl2+, the analogue benzene dication C6H42+, and the singly charged species produced by single loss of a carbon atom, C5HnCl+. The appearance and intensities of the spectral features associated with these ionic species are shown to be strongly site selective and dependent on the energy ranges of the Auger electron emission. Unexpected intensities for the analogue double charged benzene C6H42+ ion were observed with fast Auger electrons. The transitions leading to C6H5Cl2+ were identified from the binding energy representation of high resolution electron energy spectra. Most C6H5Cl2+ ions decay into two singly charged moieties, but intermediate channels are opened leading to other heavy dicationic species, C6H42+ and C6H4Cl2+, the channel leading to the first of these being much more favored than the other.

A methodology to calculate the decay rates of normal and resonant Auger processes in atoms and molecules based on the One-Center Approximation (OCA) using atomic radial Auger integrals is implemented within the restricted-active-space self-consistent-field (RASSCF) and multi-state restricted-active-space perturbation theory of second order (MS-RASPT2) frameworks as part of the OpenMolcas project. To ensure an unbiased description of the correlation and relaxation effects on the initial core excited/ ionized states and the final cationic states, their wave functions are optimized independently, whereas the Auger matrix elements are computed with a biorthonormalized set of molecular orbitals within the state-interaction (SI) approach. As a decay of an isolated resonance, the computation of Auger intensities involves matrix elements with one electron in the continuum. However, treating ionization and autoionization problems can be overwhelmingly complicated for non-experts because of many peculiarities in comparison to bound-state electronic structure theory. One of the advantages of our approach is that, by projecting the intensities on the atomic center bearing the core hole and using precalculated atomic radial two-electron integrals, the Auger decay rates can be easily obtained directly with OpenMolcas, avoiding the need to interface it with external programs to compute matrix elements with the photoelectron wave function. The implementation is tested on the Ne atom, for which numerous theoretical and experimental data are available for comparison, as well as on a set of prototype closed- and open-shell molecules, namely, CO, N2, HNCO, H2O, NO2, and C4N2H4 (pyrimidine).

The iterative subspace algorithm to solve the complex linear response equation of damped coupled cluster response theory presented, up to CCSD level, by Kauczor et al., J. Chem. Phys., 2013, 139, 211102, and recently extended to the solution of the complex left response multipliers by Faber and Coriani, J. Chem. Theory Comput., 2019, 15, 520, has been modified to include a core-valence separation projection step in the iterative procedure. This allows one to overcome serious convergence issues that specifically manifest themselves at the CCSD level when addressing core-related spectroscopic effects using large basis sets. The spectra, obtained adopting the new scheme for X-ray absorption and circular dichroism, as well as resonant inelastic-X-ray scattering, are presented and discussed. Core-valence separated results for non-resonant X-ray emission are also reported.

We present several strategies for computing electronic circular dichroism (CD) spectra across different frequency ranges at the equation-of-motion coupled-cluster singles and doubles level of theory. CD spectra of both ground and electronically excited states are discussed. For selected cases, the approach is compared with coupled-cluster linear response results as well as time-dependent density functional theory. The extension of the theory to include the effect of spin-orbit coupling is presented and illustrated by calculations of X-ray CD spectra at the

We present a theoretical model to compute the accurate photoionization dynamical parameters (cross-sections, asymmetry parameters and orbital, or cross-section, ratios) from Dyson orbitals obtained with the multi-state complete active space perturbation theory to the second order (MS-CASPT2) method. Our new implementation of Dyson orbitals in OpenMolcas takes advantage of the full Abelian symmetry point group and has the corrected normalization. The Dyson orbitals are coupled to an accurate description of the electronic continuum obtained with a multicentric B-spline basis at the DFT and TD-DFT levels. Two prototype diatomic molecules, i.e., CS and SiS, have been chosen due to their smallness, which hides important correlation effects. These effects manifest themselves in the appearance of well-characterized isolated satellite bands in the middle of the valence region. The rich satellite structures make CS and SiS the perfect candidates for a computational study based on our highly accurate MS-CASPT2/B-spline TD-DFT protocol.

The experimental and theoretical determination of the mean excitation energy,I(0), and the stopping power, S(v), of a material is of great interest in particle andmaterial physics, as well as radiation therapy. For calculations of I(0), the complete set of electronic transitions in a given basis set is required, effectively limiting such calculations to systems with a small number of electrons, even at the random-phase approximation (RPA)/time-dependent Hartree-Fock (TDHF) or time-dependent density functional theory (TDDFT) level. To overcome such limitations, we present here the implementation of a Lanczos algorithm adapted for the paired RPA/TDHF eigenvalue problem in the Dalton program and show that it provides good approximations of the entire RPA eigenspectra in a reduced space. We observe rapid convergence of I(0) with the number of Lanczos vectors as the algorithm favors the transitions with large contributions. In most cases, the algorithm recovers RPA I(0) values of up to 0.5 % accuracy at less than a quarter of the full space size. The algorithm not only exploits the RPA paired structure to save computational resources, but it is also preserves certain sum-over-states properties, as first demonstrated by Johnson et al. [Comput. Phys. Commun. 1999, 120, 155]. The block Lanczos RPA solver, as presented here, thus shows promise for computing mean excitation energies for systems larger than what was computationally feasible before.

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the pi pi* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying n pi* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the n pi* state. Finally, ESA spectra have been computed from the minima of the lowest energy pi pi* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.

We present an efficient implementation of ground and excited state CCSD gradients based on Cholesky-decomposed electron repulsion integrals. Cholesky decomposition, like density-fitting, is an inner projection method, and thus similar implementation schemes can be applied for both methods. One well-known advantage of inner projection methods, which we exploit in our implementation, is that one can avoid storing large V3O and V4 arrays by instead considering three-index intermediates. Furthermore, our implementation does not require the formation and storage of Cholesky vector derivatives. The new implementation is shown to perform well, with less than 10% of the time spent calculating the gradients in geometry optimizations. The computational time spent per optimization cycle are furthermore found to be significantly lower compared to other implementations based on an inner projection method. We illustrate the capabilities of the implementation by optimizing the geometry of the retinal molecule (C20H28O) at the CCSD/aug-cc-pVDZ level of theory., Comment: 12 pages, 1 figure

The computation of Dyson orbitals and corresponding ionization energies has been implemented within the equation of motion coupled cluster singles, doubles and perturbative triples (EOM-CC3) method. Coupled to an accurate description of the electronic continuum via a time-dependent density functional approach using a multicentric B-spline basis, this yields highly accurate photoionization dynamical parameters (cross-sections, branching ratios, asymmetry parameters and dichroic coefficients) for primary (1h) states as well as satellite states of (2h1p) character. Illustrative results are presented for the molecular systems H2O, H2S, CS, CS2 and (S)-propylene oxide (a.k.a. methyloxirane).

We have measured, analyzed, and simulated the ground state valence photoelectron spectrum, x-ray absorption (XA) spectrum, x-ray photoelectron (XP) spectrum as well as normal and resonant Auger–Meitner electron (AE) spectrum of oxazole at the carbon, oxygen, and nitrogen K-edge in order to understand its electronic structure. Experimental data are compared to theoretical calculations performed at the coupled cluster, restricted active space perturbation theory to second-order and time-dependent density functional levels of theory. We demonstrate (1) that both N and O K-edge XA spectra are sensitive to the amount of dynamical electron correlation included in the theoretical description and (2) that for a complete description of XP spectra, additional orbital correlation and orbital relaxation effects need to be considered. The normal AE spectra are dominated by a singlet excitation channel and well described by theory. The resonant AE spectra, however, are more complicated. While the participator decay channels, dominating at higher kinetic energies, are well described by coupled cluster theory, spectator channels can only be described satisfactorily using a method that combines restricted active space perturbation theory to second order for the bound part and a one-center approximation for the continuum.

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, i.e. equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for Thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are also consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the pp states (one for pyrimidine, two for purines) associated with the lowest energy absorption band, and for the close-lying np state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effect by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the np state. Finally, ESA spectra have been computed from the minima of the lowest energy pp state, and are consistent with the available experimental transient absorption spectra of the nucleosides in solution, providing a final validation of our computational approach.

We present several strategies for computing electronic circular dichroism (CD) spectra across different frequency ranges at the equation-of-motion coupled-cluster singles and doubles level of theory. CD spectra of both ground and electronically excited states are discussed. For selected cases, the approach is compared with coupled-cluster linear response results as well as time-dependent density functional theory. The extension of the theory to include the effect of spin-orbit coupling is presented and illustrated by calculations of X-ray CD spectra at the L edge.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design. This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

A highly correlated combination of the equation-of-motion coupled cluster (EOM-CC) Dyson orbital and the multicentric B-spline time-dependent density functional theory (TDDFT)-based approach is proposed and implemented within the single-channel approximation to describe molecular photoionization processes. The twofold objective of the approach is to capture interchannel coupling effects, missing in the B-spline DFT treatment, and to explore the response of Dyson orbitals to strong correlation effects and its influence on the photoionization observables. We validate our scheme by computing partial cross sections, branching ratios, asymmetry parameters, and molecular frame photoelectron angular distributions of simple molecules. Finally, the method has been applied to the study of photoelectron spectra of the Ni(C3H5)2 molecule, where giant correlation effects completely destroy the Koopmans picture.

Double-Core Hole (DCH) states of small molecules are assessed with the restrictedactive space self-consistent field (RASSCF) and multi-state restricted active space perturbationtheory of second order (MS-RASPT2) approximations. To ensure an unbiaseddescription of the relaxation and correlation effects on the DCH states, the neutralground state and DCH wave functions are optimized separately, whereas the spectralintensities are computed with a biorthonormalized set of molecular orbitals within thestate-interaction (SI) approximation. Accurate shake-up satellites binding energies andintensities of double-core-ionized states (K-2) are obtained for H2O, N2, CO and C2H2n(n=1–3). The results are analyzed in detail and show excellent agreement with recent theoretical and experimental data. The K^{-2} shake-up spectra of H2O and the C2H2n molecules are here completely characterized for the first time.

The excited states of the three radical derivatives of guanine, i.e. guanine cation (G+) and its two main deprotonated derivatives (G-H1 and G-H2) have been characterized in the Franck-Condon region by TD-DFT, using different functionals, CASPT2, and EOM-EE-CCSD calculations. In the gas phase, all the methods provide a similar description of the main spectral features, the pictures provided by TD-DFT, with long range corrected functionals, and EOM-EE-CCSD being very close. Solvent effects are then taken into account by a mixed discrete-continuum approach, including five water molecules of the first solvation shell and the Polarizable Continuum Model (PCM). The vibronic absorption line-width has finally been simulated at the TD-M052X level by a time dependent method within the harmonic approximation. The resulting absorption spectra are in good agreement with their experimental counterparts, providing useful indications on the use of PCM/TD-DFT based approaches to interpret the spectra of guanine based radicals within DNA.

Double-Core Hole (DCH) states of small molecules are assessed with the restrictedactive space self-consistent field (RASSCF) and multi-state restricted active space perturbationtheory of second order (MS-RASPT2) approximations. To ensure an unbiaseddescription of the relaxation and correlation effects on the DCH states, the neutralground state and DCH wave functions are optimized separately, whereas the spectralintensities are computed with a biorthonormalized set of molecular orbitals within thestate-interaction (SI) approximation. Accurate shake-up satellites binding energies andintensities of double-core-ionized states (K-2) are obtained for H2O, N2, CO and C2H2n(n=1–3). The results are analyzed in details and show excellent agreement with recentexperimental data.

We report an implementation of the core-valence separation approach to the four-component relativistic Hamiltonian-based equation-of-motion coupled-cluster with singles and doubles theory (CVS-EOM-CCSD) for the calculation of relativistic core-ionization potentials and core-excitation energies. With this implementation, which is capable of exploiting double group symmetry, we investigate the effects of the different CVS-EOM-CCSD variants and the use of different Hamiltonians based on the exact two-component (X2C) framework on the energies of different core-ionized and -excited states in halogen- (CH3I, HX, and X-, X = Cl-At) and xenon-containing (Xe, XeF2) species. Our results show that the X2C molecular mean-field approach [Sikkema, J.; J. Chem. Phys. 2009, 131, 124116], based on four-component Dirac-Coulomb mean-field calculations (2DCM), is capable of providing core excitations and ionization energies that are nearly indistinguishable from the reference four-component energies for up to and including fifth-row elements. We observe that two-electron integrals over the small-component basis sets lead to non-negligible contributions to core binding energies for the K and L edges for atoms such as iodine or astatine and that the approach based on Dirac-Coulomb-Gaunt mean-field calculations (2DCGM) are significantly more accurate than X2C calculations for which screened two-electron spin-orbit interactions are included via atomic mean-field integrals.

Expressions for the calculation of rotatory strengths using the algebraic diagrammatic construction (ADC) scheme of the polarization propagator in both length and velocity gauges have been implemented. This enables the simulation of electronic circular dichroism (ECD) spectra at the ADC level up to third order of perturbation theory. The ADC(n) methods produce rotatory strengths of comparable accuracy to those obtained with coupled cluster methods of corresponding approximation levels, as evaluated for methyloxirane, methylthiirane, dimethyloxirane, dimethylthiirane, hydrogen peroxide, and dihydrogen disulfide. ECD spectra of (1R)-camphor, (1R)-norcamphor, and (1R)-fenchone computed at the third order ADC(3) level of theory are shown to agree very favorably with experimental gas phase spectra, demonstrating the usefulness of ADC for the calculation of chiro-optical properties of organic molecules. ADC(2) in combination with the polarizable continuum model is shown to successfully reproduce the ECD spectrum of the L-epinephrine enantiomer in water, further demonstrating the applicability of this approach.

We present the first investigation of excited state dynamics by resonant Auger-Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a {\pi}{\pi}* excited state, thymine is known to undergo internal conversion to an n{\pi}* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state {\pi}* resonances of thymine (see our previous study Wolf et al., Nat. Commun., 2017, 8, 29). We resolve and compare the Auger-Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the n{\pi}* state signatures the appearance of additional resonant Auger-Meitner contributions at photon energies between the n{\pi}* state and the ground state resonances. We assign these contributions to population transfer from the n{\pi}* state to a {\pi}{\pi}* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited {\pi}{\pi}* singlet state which we have not observed in our previous study.

The recent development of liquid jet and liquid leaf sample delivery systems allows for accurate measurements of soft X-ray absorption spectra in transmission mode of solutes in a liquid environment. As this type of measurement becomes increasingly accessible, there is a strong need for reliable theoretical methods for assisting in the interpretation of the experimental data. Coupled cluster methods have been extensively developed over the past decade to simulate X-ray absorption in the gas phase. Their performance for solvated species, on the contrary, remains largely unexplored. Here, we investigate the current state of the art of coupled cluster modeling of nitrogen K-edge X-ray absorption of aqueous ammonia and ammonium based on quantum mechanics/molecular mechanics, where both the level of coupled cluster calculations and polarizable embedding are scrutinized. The results are compared to existing experimental data as well as simulations based on transition potential density functional theory.

A time-dependent equation of motion coupled cluster singles and doubles (TD-EOM-CCSD) method is implemented, which uses a reduced basis calculated with the asymmetric band Lanczos algorithm. The approach is used to study weak-field processes in small molecules induced by ultrashort valence pump and core probe pulses. We assess the reliability of the procedure by comparing TD-EOM-CCSD absorption spectra to spectra obtained from the time-dependent coupled-cluster singles and doubles (TDCCSD) method and observe that spectral features can be reproduced for several molecules, at much lower computational times. We discuss how multiphoton absorption and symmetry can be handled in the method and general features of the core-valence separation (CVS) projection technique. We also model the transient absorption of an attosecond X-ray probe pulse by the glycine molecule., Comment: 15 pages and 5 figures

A detailed description of a method proposed to compute total photoionization and photodetachment cross sections of atoms and molecules relying just on L\(^2\) basis sets is presented. The method consists of an analytical continuation procedure based on Pade approximants. It has the advantage of treating the discrete and continuum part of the spectra at the same level with a flexible choice of the correlated electronic structure approximations. Herein, we present results obtained at the coupled cluster singles and doubles (CCSD) and time-dependent density functional theory (TDDFT) level. Examples of L\(^2\) basis sets adequate and inadequate to reproduce the continuum region of the spectrum are given for the CCSD photoionization cross section of He. Also, a brief review of recent applications of the method is presented, together with original TDDFT results for the total photoionization cross section of formic acid, HCOOH, and the photodetachment cross section of the formate anion, HCOO\(^-\).

An implementation of a complex solver for the solution of the response equations required to compute the complex response functions of damped response theory is presented for the resolution-of-identity (RI) coupled-cluster singles and approximate doubles CC2 method. The implementation uses a partitioned formulation that avoids the storage of double excitation amplitudes to make it applicable to large molecules. The solver is the keystone element for the development of the damped coupled-cluster response formalism for linear and nonlinear effects in resonant frequency regions at the RI-CC2 level of theory. Illustrative results are reported for the one-photon absorption cross section of C60, the electronic circular dichroism of $n$-helicenes ($n$ = 5, 6, 7), and the $C_6$ dispersion coefficients of a set of selected organic molecules and fullerenes., Comment: Submitted to J. Chem. Phys., Dec. 2020

The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s → π* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities—in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange–correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2–0.3 eV and ∼10%, respectively, as compared to 0.3–0.6 eV and ∼20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.

A theoretical study of CF2Cl2 and CH2Cl2 photoabsorption spectra and photofragmentation profiles at the chlorine K-edge is presented. We simulated the NEXAFS spectra at the Core-Valence Separated Coupled Cluster Singles and Doubles (CVS-CCSD) level and interpreted the photofragmentation profile in terms of the potential energy surfaces (PES) computed at the complete active space self-consistent field (CASSCF) level along the C–Cl bond cleavage for the 1sCl → σ*C-Cl' 1sCl → 7b2, and 1sCl → ∞ states. the PES of CF2Cl2 shows that the chlorine's 1s → σ* transition tends to fragment into the CF2Cl* radical and the Cl (1s12s22p63s23p6) excited atom, whereas the 1sCl → 7b2, and 1sCl → ∞ states are less prone to undergo this fragmentation channel. The same tendency was observed for the CH2Cl2 molecule, suggesting that the F atom has little influence on the PES

Eremophila (Scrophulariaceae) is a genus of Australian desert plants, which have been used by Australian Aboriginal people for various medicinal purposes. Crude extracts of the leaf resin of Eremophila glabra (R.Br.) Ostenf. showed α-glucosidase and protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with IC50 values of 19.3 ± 1.2 μg/mL and 11.8 ± 2.1 μg/mL, respectively. Dual α-glucosidase/PTP1B high-resolution inhibition profiling combined with HPLC-PDA-HRMS and NMR were used to isolate and identify the compounds providing these activities. This resulted in isolation of seven undescribed serrulatane diterpenoids, eremoglabrane A-G, together with nine previously identified serrulatane diterpenoids and flavonoids. Three of the serrulatane diterpenoids showed PTP1B inhibitory activities with IC50 values from 63.8 ± 5.8 μM to 104.5 ± 25.9 μM.

We present a computational study of the one-photon and excited-state absorption from the two lowest-energy excited states of uracil in the gas phase: an n?pi* dark state(1n) and the lowest-energy bright ??? pi-pi* state (1?pi). The predictions of six di?fferent linear response electronic structure methods, namely TD-CAM-B3LYP, EOM-CCSD,EOM-CC3, ADC(2), ADC(2)-x and ADC(3) are critically compared. In general, the spectral shapes predicted by TD-CAM-B3LYP, EOM-CCSD, EOM-CC3 and ADC(3) are fairly similar, though the quality of TD-CAM-B3LYP slightly deteriorates in the high energy region. Computing the spectra at some key structures on the di?fferent potential energy surfaces (PES), i.e. the Franck-Condon point, the 1n minimum,and structures representative of di?fferent regions of the 1? PES, we obtain important insights into the shift of the excited-state absorption spectra, following the motion of thewavepacket on the excited state PES. Though 1pi ? has larger excited-state absorption than 1n, some spectral regions are dominated by these latter signals. Aside from itsmethodological interest, we thus obtain interesting indications to interpret transient absorption spectra to disentangle the photoactivated dynamics of nucleobases.

The UV-Vis absorption and Magnetic Circular Dichroism spectra of naphthalene and some of its derivatives have been simulated at the Coupled Cluster Singles andApproximate Doubles (CC2) level of theory, and at the Time-Dependent Density Functional Theory level (TD-DFT) using the B3LYP and CAM-B3LYP functionals. DFT and CC2 predict in general opposite energetic ordering of the Lb and La transitions (in gas phase), as previously observed in adenine. The CC2 simulations of UV and MCD spectra show the best agreement with the experimental data. Analysis of the Cartesiancomponents of the electric dipole transition strengths and the magnetic dipole transition moment between the excited states have been considered in the interpretationof the electronic transitions and the Faraday B term inversion among the naphthalenederivatives.

We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. Ahttp://dx.doi.org/10.1021/acs.jpca.0c08736]. We show that the 1sC → π transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the π-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC → π* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the 1sC → π* band of the cation is attributed to the interplay between the coupling of the core → π* excitation with the unpaired electron in the π-subshell and the Jahn–Teller distortion. The calculations attribute most of the splitting (∼1–1.2 eV) to the spin coupling, which is visible already at the Franck–Condon structure, and we estimate the additional splitting due to structural relaxation to be around ∼0.1–0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn–Teller effect in the benzene cation.

We report a theoretical investigation and elucidation of the x-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization as well as the experimental measurement ofthe carbon K-edge spectra of both species using a table-top high-harmonic generation (HHG) source have been described in a companion paper [M. Epshtein et al., J. Am.Chem. Soc., submitted. Available on ChemRxiv]. We show that the 1sC -> pi transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presenceof the unpaired (spectator) electron in the pi-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC ->pi* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation.The prominent split structure of the 1sC -> pi* band of the cation is attributed to the interplay between the coupling of the core -> pi* excitation with the unpaired electronin the pi-subshell and the Jahn-Teller distortion. The calculations attribute most ofthe splitting (~1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and estimate the additional splitting due to structural relaxation tobe around ~0.1-0.2 eV. These results suggest that x-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Tellereffect in benzene cation.