Insights into localization, energy ordering, and substituent effect in excited states of azobenzenes from coupled cluster calculations of nuclear spin-induced circular dichroism.

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. Specifically, analytic expressions for the computation of the 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.

Auger-Meitner and X-ray Absorption Spectra of Ethylene Cation: Insight into Conical Intersection Dynamics.

We present a theoretical investigation of the near-edge X-ray absorption fine structure and the Auger-Meitner decay spectra of ethylene and its cation. Herein, we demonstrate that our method, coupled with the nuclear ensemble approach, successfully reproduces the natural bandwidth structure of the experimental resonant Auger-Meitner decay spectra of ethylene, which is not very well reproduced within the Franck-Condon approximation. Furthermore, we analyze the Auger-Meitner decay spectra of the ethylene cation in light of minimum energy conical intersection structures involving the two lowest cationic states (D1 and D0), providing valuable insights into the ultrafast D1/D0 relaxation dynamics. Our results suggest that Auger-Meitner electron spectroscopy can help elucidate the mechanism behind the initial 20 fs of the relaxation dynamics.

Electric Field Gradient Calculations for Ice VIII and IX Using Polarizable Embedding: A Comparative Study on Classical Computers and Quantum Simulators.

We test the performance of the polarizable embedding variational quantum eigensolver self-consistent field (PE-VQE-SCF) model for computing electric field gradients with comparisons to conventional complete active space self-consistent-field (CASSCF) calculations and experimental results. We compute quadrupole coupling constants for ice VIII and ice IX. We find close agreement of the quantum-computing PE-VQE-SCF results with the results from the classical PE-CASSCF calculations and with experiment. Furthermore, we observe that the inclusion of the environment is crucial for obtaining results that match the experimental data. The calculations for ice VIII are within the experimental uncertainty for both CASSCF and VQE-SCF for oxygen and lie close to the experimental value for ice IX as well. With the VQE-SCF, which is based on an adaptive derivative-assembled problem-tailored (ADAPT) ansatz, we find that the inclusion of the environment and the size of the different basis sets do not directly affect the gate counts. However, by including an explicit environment, the wavefunction and therefore the optimization problem become more complicated, which usually results in the need to include more operators from the operator pool, thereby increasing the depth of the circuit.

Genome-Driven Discovery of Hygrocins in Streptomyces rapamycinicus.

Ansamycins, represented by the antituberculosis drug rifamycin, are an important family of natural products. To obtain new ansamycins, Streptomyces rapamycinicus IMET 43975 harboring an ansamycin biosynthetic gene cluster was fermented in a 50 L scale, and subsequent purification work led to the isolation of five known and four new analogues, where hygrocin W (2) belongs to benzoquinonoid ansamycins, and the other three hygrocins, hygrocins X-Z (6-8), are new seco-hygrocins. The structures of ansamycins (1-8) were determined by the analysis of spectroscopic (1D/2D NMR and ECD) and MS spectrometric data. The Baeyer-Villiger enzyme which catalyzed the ester formation in the ansa-ring was confirmed through in vivo CRISPR base editing. The discovery of these compounds further enriches the structural diversity of ansamycins.

Divergences in classical and quantum linear response and equation of motion formulations.

Calculating molecular properties using quantum devices can be performed through the quantum linear response (qLR) or, equivalently, the quantum equation of motion (qEOM) formulations. Different parameterizations of qLR and qEOM are available, namely naïve, projected, self-consistent, and state-transfer. In the naïve and projected parameterizations, the metric is not the identity, and we show that it depends on redundant orbital rotations. This dependency may lead to divergences in the excitation energies for certain choices of the redundant orbital rotation parameters in an idealized noiseless setting. Furthermore, this leads to a significant variance when calculations include statistical noise from finite quantum sampling.

The x-ray absorption spectrum of the tert-butyl radical: An experimental and computational investigation.

We report the x-ray absorption spectrum (XAS) of the tert-butyl radical, C4H9. The radical was generated pyrolytically from azo-tert-butane, and the XAS of the pure radical was obtained by subtraction of spectra recorded at different temperatures. The bands in the XAS were assigned by ab initio calculations that are in very good agreement with the experimental data. The lowest energy signal in the XAS is assigned to the C1s electron transition from the central carbon atom to the singly occupied molecular orbital (SOMO), while higher transitions correspond to C1s excitations from terminal carbon atoms. Furthermore, we investigated the fragmentation of the radical following resonant C1s excitation by electron-ion-coincidence spectroscopy. Several fragmentation channels were identified. The C1s excitation of the terminal carbons is associated with a stronger fragmentation tendency compared to the lowest C1s excitation of the central carbon into the SOMO. For this core excited state, we still observe an intact parent ion, C4H9+, and a comparatively higher tendency to dissociate into CH3+ + C3H6+.

The variational quantum eigensolver self-consistent field method within a polarizable embedded framework.

We formulate and implement the Variational Quantum Eigensolver Self Consistent Field (VQE-SCF) algorithm in combination with polarizable embedding (PE), thereby extending PE to the regime of quantum computing. We test the resulting algorithm, PE-VQE-SCF, on quantum simulators and demonstrate that the computational stress on the quantum device is only slightly increased in terms of gate counts compared to regular VQE-SCF. On the other hand, no increase in shot noise was observed. We illustrate how PE-VQE-SCF may lead to the modeling of real chemical systems using a simulation of the reaction barrier of the Diels-Alder reaction between furan and ethene as an example.

Signatures of the Bromine Atom and Open-Shell Spin Coupling in the X-ray Spectrum of the Bromobenzene Cation.

Tabletop 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 the 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). Moreover, in BrBz+, the X-ray spectrum is dominated by two relatively intense transitions, 1sC→π* and 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 activations following the UV ionization, which demonstrates the impact of the C*-Br bond length on the core-valence transition as well as on the relaxation geometry of BrBz+.

Polypharmacology-Labeled Molecular Networking: An Analytical Technology Workflow for Accelerated Identification of Multiple Bioactive Constituents in Complex Extracts.

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 non-canonical 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 protein-tyrosine 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.

New Implementation of an Equation-of-Motion Coupled-Cluster Damped-Response Framework with Illustrative Applications to Resonant Inelastic X-ray Scattering.

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 eT. 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.

Electronic Characterization of Glycolaldehyde: Experimental and Theoretical Insights from the Core- and Valence-Level Spectroscopy.

The core-level electron excitation and ionization spectra of glycolaldehyde have been investigated by photoabsorption and photoemission spectroscopy at both carbon and oxygen K-edges; the valence ionization spectra were also recorded by photoelectron spectroscopy in the UV-vis region. The spectra are interpreted by means of ab initio calculations based on the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) and coupled cluster singles, doubles, and perturbative are in good agreement with the experimental results, and many of the observed features are assigned. The photoabsorption spectra are not only dominated by transitions from core-level orbitals to unoccupied π and σ orbitals but also show structures due to Rydberg transitions.

Characterization of Serrulatane Diterpenoids in Eremophila phyllopoda subsp. phyllopoda by Triple High-Resolution α-Glucosidase/PTP1B/Radical Scavenging Profiling, NMR Spectroscopy, DFT-GIAO NMR, and Electronic Circular Dichroism Calculations.

Extracts of Eremophila phyllopoda subsp. phyllopoda showed α-glucosidase and PTP1B inhibitory activity with IC50 values of 19.6 and 13.6 µg/mL, respectively. High-resolution α-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, 1ß-trihydroxyserrulatane (8) and 1α-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 α-glucosidase inhibitory activity with IC50 values of 28.4 and 64.2 µM, respectively, while 11, 12, 14, and 15 exhibited PTP1B inhibitory activity with IC50 values ranging from 16.6 to 104.6 µM. Hypothetical routes for formation of all identified serrulatane diterpenoids are proposed.

Orthogonal Reversed-Phase C18 and Pentafluorophenyl HPLC Separation for Phytochemical Profiling of Serrulatanes in Eremophila denticulata.

Serrulatanes constitute a class of unique diterpenoids derived from all-Z nerylneryl diphosphate rather than the conventional all-E diterpenoid precursor geranylgeranyl diphosphate and thus provide an intriguing expansion of the chemical space of plant specialized metabolites. Plants of the Australian Eremophila genus are rich sources of structurally diverse serrulatanes. Here, we report the identification of 15 hitherto undescribed serrulatanes (eremoculatanes A-N), together with 16 previously reported compounds, from the EtOAc extract of Eremophila denticulata leaves. Isolation was performed by a combined use of systematic HPLC-PDA-HRMS-based phytochemical profiling and orthogonal reversed-phase C18 and pentafluorophenyl separations. Among the new compounds isolated, eremoculatane A contains a C12 backbone, for which the configuration was established by comparison of experimentally measured and theoretically calculated ECD spectra. The antihyperglycemic and antibacterial activities of the E. denticulata extract were investigated by high-resolution inhibition profiling, and they indicated that major constituents, mainly serrulatanes and flavonoids, contributed to the observed activity of the extract. One flavonoid, eupafolin (4), displayed moderate α-glucosidase inhibitory activity with an IC50 value of 41.3 µM, and four serrulatanes (8, 9, 19g, and 19j) showed more than 50% PTP1B inhibition at 200 µM.

Identification of new PTP1B-inhibiting decipiene diterpenoid esters from Eremophila clarkei by high-resolution PTP1B inhibition profiling, enzyme kinetics analysis, and molecular docking.

In this study, an extract of the leaves of Eremophila clarkei Oldfield & F.Muell. showed protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with an IC50 value of 33.0 µg/mL. The extract was therefore investigated by high-resolution PTP1B inhibition profiling to pinpoint the constituents responsible for the activity. Subsequent isolation and purification using analytical-scale HPLC led to identification of eight previously undescribed decipiene diterpenoids, eremoclarkanes A-H, as well as eremoclarkic acid, a biogenetically related new phenolic acid. In addition, one known decipiene diterpenoid and ten known O-methylated flavonoids were isolated. The structures of the isolated compounds were elucidated by extensive analysis of their HRMS and 1D and 2D NMR spectra. The absolute configuration of decipiene diterpenoids was determined by comparison of experimental and calculated ECD spectra. The flavonoid hispidulin (2b) and the four decipiene diterpenoids 13a, 13b, 13f, and 14b exhibited PTP1B inhibitory activity with IC50 values ranging from 22.8 to 33.6 µM. This is the first report of PTP1B inhibitory activity of decipienes, and enzyme kinetics revealed that 13a and 13b are competitive inhibitors of PTP1B, whereas 13f and 14b displayed mixed-type-mode inhibition of PTP1B. Finally, molecular docking indicated that 13a, 13b, 13f, and 14b showed comparable binding affinity towards the active and/or allosteric site of PTP1B enzyme. Structure-activity relationship (SAR) of the identified O-methylated flavonoids and decipiene diterpenoids towards PTP1B is discussed. Plausible enzymatic and photochemically driven routes for the formation of the decipienes and conversion products thereof are presented and discussed.

Description of the KLL Auger-Meitner decay spectra of argon following primary and satellite core-ionized states.

The K-edge photoelectron and KLL Auger-Meitner decay spectra of Argon have been investigated computationally at the restricted active space perturbation theory to the second order level using biorthonormally transformed orbital sets. Binding energies were computed for the Ar 1s primary ionization, as well as for satellite states originated from shake-up and shake-off processes. Based on our calculations, the contributions of shake-up and shake-off states to the KLL Auger-Meitner spectra of Argon have been completely elucidated. Our results are compared with recent state-of-the-art experimental measurements on Argon.

Disentangling the resonant Auger spectra of ozone: overlapping core-hole states and core-excited state dynamics.

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.

Multi-electron excitation contributions towards primary and satellite states in the photoelectron spectrum.

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).

Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study.

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 ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* 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 nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.

A tale of two vectors: A Lanczos algorithm for calculating RPA mean excitation energies.

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 and material physics and 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 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 approximation 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 also preserves certain sum-over-states properties, as first demonstrated by Johnson et al. [Comput. Phys. Commun. 120, 155 (1999)]. 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.

Efficient implementation of molecular CCSD gradients with Cholesky-decomposed electron repulsion integrals.

We present an efficient implementation of ground and excited state coupled cluster singles and doubles (CCSD) gradients based on Cholesky-decomposed electron repulsion integrals. Cholesky decomposition and density fitting are both inner projection methods, 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. Furthermore, the computational time per optimization cycle is significantly lower compared to other implementations based on an inner projection method. We showcase the capabilities of the implementation by optimizing the geometry of the retinal molecule (C20H28O) at the CCSD/aug-cc-pVDZ level of theory.