Efficient Spin-Adapted Implementation of Multireference Algebraic Diagrammatic Construction Theory. I. Core-Ionized States and X-ray Photoelectron Spectra.

We present an efficient implementation of multireference algebraic diagrammatic construction theory (MR-ADC) for simulating core-ionized states and X-ray photoelectron spectra (XPS). Taking advantage of spin adaptation, automatic code generation, and density fitting, our implementation can perform calculations for molecules with more than 1500 molecular orbitals, incorporating static and dynamic correlation in the ground and excited electronic states. We demonstrate the capabilities of MR-ADC methods by simulating the XPS spectra of substituted ferrocene complexes and azobenzene isomers. For the ground electronic states of these molecules, the XPS spectra computed using the extended second-order MR-ADC method (MR-ADC(2)-X) are in a very good agreement with available experimental results. We further show that MR-ADC can be used as a tool for interpreting or predicting the results of time-resolved XPS measurements by simulating the core ionization spectra of azobenzene along its photoisomerization, including the XPS signatures of excited states and the minimum energy conical intersection. This work is the first in a series of publications reporting the efficient implementations of MR-ADC methods.

The Antiaromatic Nucleophilic Substitution Reaction (SNAAr) in Cycloheptatrienyl-Anion Containing Zwitterions with a Möbius-Aromatic Intermediate.

Antiaromatic nucleophilic substitution reactions in cycloheptatrienide pyridinium and phosphonium zwitterions with initial formation of a cycloheptatetraene intermediate are explored. The mechanism was supported by quantum chemical calculations, first-order reaction kinetics, and high-resolution mass spectrometry. The pyridinium zwitterion exhibited weak antiaromaticity, whereas the intermediate displayed Möbius aromaticity, as evidenced by nuclear independent chemical shift values and the shape of its HOMO. This study represents the eighth confirmed instance of a Möbius-aromatic organic species in its ground state.

Key role of cycloalkyne nature in alkyne-dye reagents for enhanced specificity of intracellular imaging by bioorthogonal bioconjugation.

Conjugates of benzothiophene-fused azacyclononyne BT9N-NH2 with fluorescent dyes were developed to visualise azidoglycans intracellularly. The significance of the cycloalkyne core was demonstrated by comparing new reagents with DBCO- and BCN-dye conjugates. To reduce non-specificity during intracellular bioconjugation using SPAAC, less reactive BT9N-dye reagents are preferred over highly reactive DBCO- and BCN-dye conjugates.

Synthesis and Biological Evaluation of a Series of New Hybrid Amide Derivatives of Triazole and Thiazolidine-2,4-dione.

A series of hybrid compounds with triazole and thiazolidine nuclei connected by a linker has been synthesized and extensively studied. Various synthetic methods for the target compounds have been tested. A microbiological assessment of the obtained compounds was carried out on strains of pathogenic fungi C. albicans, C. non-albicans, multidrug-resistant C. auris, Rhizopus arrhizus, Aspergillus spp. and some dermatophytes and other yeasts. The lowest obtained MIC values for target compounds lie between 0.003 µg/mL and 0.5 µg/mL and therefore the compounds are not inferior or several times better than commercial azole drugs. The length of the acylpiperazine linker has a limited effect on antifungal activity. Some bioisosteric analogues were tested in microbiological analysis, but turned out to be weaker than the leader in activity. The highest activity was demonstrated by a compound with para-chlorobenzylidene substituent in the thiazolidine fragment. Molecular modelling was used to predict binding modes of synthesized molecules and rationalize experimentally observed SAR. The leader compound is twice more effective in inhibiting the formation of germ tubes by Candida albicans yeast cells compared to voriconazole. An increased level of Pdr5, an azoles drug efflux pump was observed, but the increase is lower than that caused by azoles. The results can be useful for further development of more powerful and safe antifungal agents.

Quantifying spin contamination in algebraic diagrammatic construction theory of electronic excitations.

Algebraic diagrammatic construction (ADC) is a computationally efficient approach for simulating excited electronic states, absorption spectra, and electron correlation. Due to their origin in perturbation theory, the single-reference ADC methods may be susceptible to spin contamination when applied to molecules with unpaired electrons. In this work, we develop an approach to quantify spin contamination in the ADC calculations of electronic excitations and apply it to a variety of open-shell molecules starting with either the unrestricted (UHF) or restricted open-shell (ROHF) Hartree-Fock reference wavefunctions. Our results show that the accuracy of low-order ADC approximations [ADC(2) and ADC(3)] significantly decreases when the UHF reference spin contamination exceeds 0.05 a.u. Such strongly spin-contaminated molecules exhibit severe excited-state spin symmetry breaking that contributes to decreasing the quality of computed excitation energies and oscillator strengths. In a case study of phenyl radical, we demonstrate that spin contamination can significantly affect the simulated UV/Vis spectra, altering the relative energies, intensities, and order of electronic transitions. The results presented here motivate the development of spin-adapted ADC methods for open-shell molecules.

Consistent Second-Order Treatment of Spin-Orbit Coupling and Dynamic Correlation in Quasidegenerate N-Electron Valence Perturbation Theory.

We present a formulation and implementation of second-order quasidegenerate N-electron valence perturbation theory (QDNEVPT2) that provides a balanced and accurate description of spin-orbit coupling and dynamic correlation effects in multiconfigurational electronic states. In our approach, the energies and wave functions of electronic states are computed by treating electron repulsion and spin-orbit coupling operators as equal perturbations to the nonrelativistic complete active-space wave functions, and their contributions are incorporated fully up to the second order. The spin-orbit effects are described using the Breit-Pauli (BP) or exact two-component Douglas-Kroll-Hess (DKH) Hamiltonians within spin-orbit mean-field approximation. The resulting second-order methods (BP2- and DKH2-QDNEVPT2) are capable of treating spin-orbit coupling effects in nearly degenerate electronic states by diagonalizing an effective Hamiltonian expanded in a compact non-relativistic basis. For a variety of atoms and small molecules across the entire periodic table, we demonstrate that DKH2-QDNEVPT2 is competitive in accuracy with variational two-component relativistic theories. BP2-QDNEVPT2 shows high accuracy for the second- and third-period elements, but its performance deteriorates for heavier atoms and molecules. We also consider the first-order spin-orbit QDNEVPT2 approximations (BP1- and DKH1-QDNEVPT2), among which DKH1-QDNEVPT2 is reliable but less accurate than DKH2-QDNEVPT2. Both DKH1- and DKH2-QDNEVPT2 hold promise as efficient and accurate electronic structure methods for treating electron correlation and spin-orbit coupling in a variety of applications.

Simulating transient X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products with multireference algebraic diagrammatic construction theory.

Accurate simulations of transient X-ray photoelectron spectra (XPS) provide unique opportunities to bridge the gap between theory and experiment in understanding the photoactivated dynamics in molecules and materials. However, simulating X-ray photoelectron spectra along a photochemical reaction pathway is challenging as it requires accurate description of electronic structure incorporating core-hole screening, orbital relaxation, electron correlation, and spin-orbit coupling in excited states or at nonequilibrium ground-state geometries. In this work, we employ the recently developed multireference algebraic diagrammatic construction theory (MR-ADC) to investigate the core-ionized states and X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products (Fe(CO)4, Fe(CO)3) following excitation with 266 nm light. The simulated transient Fe 3p and CO 3σ XPS spectra incorporating spin-orbit coupling and high-order electron correlation effects are shown to be in a good agreement with the experimental measurements by Leitner et al. [J. Chem. Phys., 2018, 149, 044307]. Our calculations suggest that core-hole screening, spin-orbit coupling, and ligand-field splitting effects are similarly important in reproducing the experimentally observed chemical shifts in transient Fe 3p XPS spectra of iron carbonyl complexes. Our results also demonstrate that the MR-ADC methods can be very useful in interpreting the transient XPS spectra of transition metal compounds.

Structure and Dynamic Rearrangements of the Pt2dba3 and Pd2dba3 Complexes in Solution.

Although the tris(dibenzylideneacetone)diplatinum complex (Pt2dba3) is an important source of Pt(0) used in catalysis and materials science, its structure has not yet been fully elucidated. A thorough study of the three-dimensional structure of Pt2dba3 and its dynamic behavior in solution was carried out using NMR spectroscopy methods at a high field (600 MHz) and molecular modeling. The complex was shown to contain three dba ligands in the s-cis,s-trans, s-trans,s-cis, and s-trans,s-trans conformations, which are uniformly oriented around the Pt2 backbone. In solution, the Pt2dba3 and Pd2dba3 complexes undergo rapid dynamic rearrangements, as evidenced by the exchange between the signals of the olefin protons of various dba ligands in the EXSY NMR spectra. According to the experimental measurements, the activation energies of the rearrangements were estimated to be 19.9 ± 0.2 and 17.9 ± 0.2 kcal/mol for the platinum and palladium complexes, respectively. Three possible mechanisms for this chemical exchange process were considered within the framework of DFT calculations. According to the calculated data, M2dba3 complexes undergo fluxional isomerization involving successive rotations of the dihedral angles formed by the carbonyl group and the C═C bond. Dissociation of dba ligands does not occur within these processes.

Revealing the Mechanism of Combining Best Properties of Homogeneous and Heterogeneous Catalysis in Hybrid Pd/NHC Systems.

The formation of transient hybrid nanoscale metal species from homogeneous molecular precatalysts has been demonstrated by in situ NMR studies of catalytic reactions involving transition metals with N-heterocyclic carbene ligands (M/NHC). These hybrid structures provide benefits of both molecular complexes and nanoparticles, enhancing the activity, selectivity, flexibility, and regulation of active species. However, they are challenging to identify experimentally due to the unsuitability of standard methods used for homogeneous or heterogeneous catalysis. Utilizing a sophisticated solid-state NMR technique, we provide evidence for the formation of NHC-ligated catalytically active Pd nanoparticles (PdNPs) from Pd/NHC complexes during catalysis. The coordination of NHCs via C(NHC)-Pd bonding to the metal surface was first confirmed by observing the Knight shift in the 13C NMR spectrum of the frozen reaction mixture. Computational modeling revealed that as little as few NHC ligands are sufficient for complete ligation of the surface of the formed PdNPs. Catalytic experiments combined with in situ NMR studies confirmed the significant effect of surface covalently bound NHC ligands on the catalytic properties of the PdNPs formed by decomposition of the Pd/NHC complexes. This observation shows the crucial influence of NHC ligands on the activity and stability of nanoparticulate catalytic systems.

Dysregulation of cell state dynamics during early stages of serous endometrial carcinogenesis.

Serous endometrial carcinoma (SEC) constitutes about 10% of endometrial carcinomas and is one of the most aggressive and lethal types of uterine cancer. Due to the rapid progression of SEC, early detection of this disease is of utmost importance. However, molecular and cellular dynamics during the pre-dysplastic stage of this disease remain largely unknown. Here, we provide a comprehensive census of cell types and their states for normal, pre-dysplastic, and dysplastic endometrium in a mouse model of SEC. This model is associated with inactivation of tumor suppressor genes Trp53 and Rb1 , whose pathways are altered frequently in SEC. We report that pre-dysplastic changes are characterized by an expanded and increasingly diverse immature luminal epithelial cell populations. Consistent with transcriptome changes, cells expressing the luminal epithelial marker TROP2 begin to substitute FOXA2+ cells in the glandular epithelium. These changes are associated with a reduction in number and strength of predicted interactions between epithelial and stromal endometrial cells. By using a multi-level approach combining single-cell and spatial transcriptomics paired with screening for clinically relevant genes in human endometrial carcinoma, we identified a panel of 44 genes suitable for further testing of their validity as early diagnostic and prognostic markers. Among these genes are known markers of human SEC, such as C DKN2A, and novel markers, such as OAS2 and OASL, members of 2-5A synthetase family that is essential for the innate immune response. In summary, our results suggest an important role of the luminal epithelium in SEC pathogenesis, highlight aberrant cell-cell interactions in pre-dysplastic stages, and provide a new platform for comparative identification and characterization of novel, clinically relevant prognostic and diagnostic markers and potential therapeutic modalities.

Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli.

CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.

Quantum trapping and rotational self-alignment in triangular Casimir microcavities.

Casimir torque, a rotational motion driven by zero-point energy minimization, is a problem that attracts notable research interest. Recently, it has been realized using liquid crystal phases and natural anisotropic substrates. However, for natural materials, substantial torque occurs only at van der Waals distances of ~10 nm. Here, we use Casimir self-assembly with triangular gold nanostructures for rotational self-alignment at truly Casimir distances (100 to 200 nm separation). The interplay of repulsive electrostatic and attractive Casimir potentials forms a stable quantum trap, giving rise to a tunable Fabry-Pérot microcavity. This cavity self-aligns both laterally and rotationally to maximize area overlap between templated and floating flakes. The rotational self-alignment is sensitive to the equilibrium distance between the two triangles and their area, offering possibilities for active control via electrostatic screening manipulation. Our self-assembled Casimir microcavities present a versatile and tunable platform for nanophotonic, polaritonic, and optomechanical applications.

Color-tunable luminescence and temperature sensing properties of Bi3+/Sm3+ or Bi3+/Eu3+ codoped Ba2Gd2Ge4O13 phosphors.

Novel temperature-sensitive luminescent materials, Ba2Gd2Ge4O13 doped with Bi3+, Bi3+/Sm3+ or Bi3+/Eu3+ ions, have been prepared using a conventional solid-state reaction technique. The XRPD study has verified that all the synthesized germanates crystallize in the monoclinic system (space group C2/c, Z = 4). The crystal lattice of the compounds consists of zigzag chains of edge-sharing Me2O7 (Me = Bi3+, Eu3+ or Sm3+) dimers, [Ge4O13] units, and ten-coordinated Ba atoms. Under UV excitation the powders exhibit the luminescence corresponding to the 3P1 → 1S0 (310-550 nm) transition in Bi3+ and 4G5/2 → 6HJ (550-730 nm) in Sm3+ or 5D0 → 7FJ (570-720 nm) transitions in Eu3+ ions. Heating of Ba2Gd1.94Bi0.01Sm0.05Ge4O13 and Ba2Gd1.89Bi0.01Eu0.1Ge4O13 phosphors leads to an irregular decrease in the intensity of the main emission lines. It has been found that the fluorescence intensity ratio between a wide band in the 310-530 nm region and peaks at longer wavelengths may be successfully used as a temperature-dependent characteristic. Absolute/relative sensitivity values for Ba2Gd1.94Bi0.01Sm0.05Ge4O13 and Ba2Gd1.89Bi0.01Eu0.1Ge4O13 germanates reach 0.19% K-1/0.80% K-1 and 2.21% K-1/0.58% K-1, respectively. The above parameters indicate that Ba2Gd2Ge4O13:Bi3+/Sm3+ or Bi3+/Eu3+ samples can be used as potential luminescent materials for non-contact temperature measurement.

A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST.

NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.

Retroperitoneal Liposarcoma: Rational Extent of Surgery Tailored to Grade of Malignancy.

This study was aimed at determining the indications for combined and organ-preserving operations. The study included 190 patients with retroperitoneal liposarcoma (RLPS). The influence of the following factors on the overall survival (OS) and recurrence-free survival (RFS) were studied: involvement of adjacent organs in the tumor, volume of surgical intervention. OS and RFS were worse in pathologically confirmed visceral invasion in the both RLPS low grade and high grade (p = 0.000). In RLPS low grade, there was no significant difference in OS and RFS between the group of patients who underwent combined surgery without confirmed visceral invasion and the group of patients who underwent organ-preserving surgery (p > 0.080). In RLPS high grade, OS and RFS were higher in the group of patients who underwent combined surgery without confirmed visceral invasion than in the group of patients who underwent organ-preserving surgery (p < 0.050). In RLPS low grade, it is advisable to perform organ-preserving operations, including nephrosaving operations. In RLPS high grade, the organ-preserving operations worsen long-term results and prognosis. Combined operations including nephrectomy are justified in RLPS high grade.

Prediction of Recurrence-Free and Overall Survival in Retroperitoneal Well-Differentiated and Dedifferentiated Liposarcoma After Surgery.

This study was aimed at creating an effective model for predicting the course of the disease in retroperitoneal well-differentiated (WDLPS) and dedifferentiated (DDLPS) liposarcomas after surgery. The study included 111 patients with WDLPS and 74 patients with DDLPS. We developed a methodology for stratification of patients into prognostic groups. Overall survival (OS) and recurrence-free survival (RFS) were analyzed in accordance with it. The highest OS was achieved in the group "favorable prognosis," while the shortest OS was in the group "extremely poor prognosis" (p < 0.001). The median OS in the "favorable prognosis" group was 225 (95% CI, 174, 276) months; "intermediate prognosis" - 130 (95% CI, 115, 145) months; "poor prognosis" - 90 (95% CI, 79, 101) months; and "extremely poor prognosis" - 22 (95% CI, 15, 29) months. The highest RFS was achieved in the group "favorable prognosis," while the shortest RFS was achieved in the group "extremely poor prognosis" (p < 0.001). The median RFS in the "favorable prognosis" group was 80 (95% CI, 65, 95) months; "intermediate prognosis" - 47 (95% CI, 33, 61) months; "poor prognosis" - 26 (95% CI, 24, 28) months; "extremely poor prognosis" - 10 (95% CI, 6, 14) months. The method of predicting recurrence-free and overall survival demonstrates an adequate distribution of patients and the reliability of intergroup differences in the survival rate.

Chemical composition of the White Sea sponge Halichondriа panicea.

The extract of the White Sea sponge Halichondria panicea (Pallas, 1766) exhibits cytotoxic and cytostatic effects. The main part of the extract consists of hydrophilic low molecular weight compounds: free amino acids (13.9%), glucose (19.9%), polyatomic alcohols (glycerin and others) (6.1%), carboxylic acids (0.7%) and nitrogenous heterocycles (1.2%). Of the substances specific to the metabolome, bicyclic diketopiperazines (four derivatives), pyroglutamic acid, phenylacetic acid, and two steroids (3ß,5α)cholest-7-en-3-ol and dihydrocholesterol were identified. Toxicants characteristic of the genus Halichondria were not found in the White Sea sponge.

Conditions for the efficiency of optical limiting based on experiment and quantum chemical calculations.

The development of suitable protection against laser radiation has proven challenging due to the lack of predictive models. The purpose of this article is to exclude the existing drawback by creating a universal strategy based on correlations between experimental and theoretical data characterizing the nonlinear optical properties of absorbers, for which a series of low-symmetry penta(chloro)cyclotriphosphazene-substituted monophthalocyanines was chosen. To search for correlations on a small series of dyes, we used the advanced algorithm CORRELATO, which has been proven to construct even the most unusual relationships demonstrated in our previous works. Due to the reducing symmetry of molecules, large values of the nonlinear absorption coefficient (more than 3000 cm GW-1) and, as a result, wide dynamic ranges (up to 630) with a high degree of attenuation of nanosecond laser radiation (10-20 times) were achieved. The use of the finite-field DFT method has allowed the calculation of dipole moments, polarizabilities and hyperpolarizabilities. The numerical data obtained during the calculations were used in correlations of theory vs. experiment to derive mathematical expressions (inequalities) to assess the effectiveness of absorbers in limiting the power of laser radiation.

Manipulating stereoselectivity of parahydrogen addition to acetylene to unravel interconversion of ethylene nuclear spin isomers.

Symmetric molecules exist as distinct nuclear spin isomers (NSIMs). A deeper understanding of their properties, including interconversion of different NSIMs, requires efficient techniques for NSIM enrichment. In this work, selective hydrogenation of acetylene with parahydrogen (p-H2) was used to achieve the enrichment of ethylene NSIMs and to study their equilibration processes. The effect of the stereoselectivity of H2 addition to acetylene on the imbalance of ethylene NSIMs was experimentally demonstrated by using three different heterogeneous catalysts (an immobilized Ir complex and two supported Pd catalysts). The interconversion of NSIMs with time during ethylene storage was studied using NMR spectroscopy by reacting ethylene with bromine water, which rendered the p-H2-derived protons in the produced 2-bromoethan(2H)ol (BrEtOD) magnetically inequivalent, thereby revealing the non-equilibrium nuclear spin order of ethylene. A thorough analysis of the shape and transformation of the 1H NMR spectra of hyperpolarized BrEtOD allowed us to reveal the initial distribution of produced ethylene NSIMs and their equilibration processes. Comparison of the results obtained with three different catalysts was key to properly attributing the derived characteristic time constants to different ethylene NSIM interconversion processes: ∼3-6 s for interconversion between NSIMs with the same inversion symmetry (i.e., within g or u manifolds) and ∼1700-2200 s between NSIMs with different inversion symmetries (i.e., between g and u manifolds).

Fibroblasts and polymer composition are essential for bioengineering of airway epithelium on nonwoven scaffolds.

To make tissue engineering a truly effective tool, it is necessary to understand how the patterns of specific tissue development are modulated by and depend on the artificial environment. Even the most advanced approaches still do not fully meet the requirements of practical engineering of tracheobronchial epithelium. This study aimed to test the ability of the synthetic and natural nonwoven scaffolds to support the formation of morphological sound airway epithelium including the basement membrane (BM). We also sought to identify the potential role of fibroblasts in this process. Our results showed that nonwoven scaffolds are generally suitable for producing well-differentiated tracheobronchial epithelium (with cilia and goblet cells), while the structure and functionality of the equivalents appeared to be highly dependent on the composition of the scaffolds. Unlike natural scaffolds, synthetic ones supported the formation of the epithelium only when epithelial cells were cocultured with fibroblasts. Fibroblasts also appeared to be obligatory for basal lamina formation, regardless of the type of the nonwoven material used. However, even in the presence of fibroblasts, the synthetic scaffolds were unable to support the formation of the epithelium and of the BM (in particular, basal lamina) as effectively as the natural scaffolds did.