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A general formulation of the strong coupling between photons confined in a cavity and molecular electronic states is developed for the state-interaction state-average spin-restricted ensemble-referenced Kohn–Sham method. The light–matter interaction is included in the Jaynes–Cummings model, which requires the derivation and implementation of the analytical derivatives of the transition dipole moments between the molecular electronic states. The developed formalism is tested in the simulations of the nonadiabatic dynamics in the polaritonic states resulting from the strong coupling between the cavity photon mode and the ground and excited states of the penta-2,4-dieniminium cation, also known as PSB3. Comparison with the field-free simulations of the excited-state decay dynamics in PSB3 reveals that the light–matter coupling can considerably alter the decay dynamics by increasing the excited state lifetime and hindering photochemically induced torsion about the C=C double bonds of PSB3. The necessity of obtaining analytical transition dipole gradients for the accurate propagation of the dynamics is underlined. [ABSTRACT FROM AUTHOR]

The photophysical properties of a series of recently synthesized single benzene fluorophores were investigated using ensemble density functional theory calculations. The energetic stability of the ground and excited state species were counterposed against the aromaticity index derived from local vibrational modes. It was found that the large Stokes shift of the fluorophores (up to ca. 5800 cm −1) originates from the effect of electron donating and electron withdrawing substituents rather than π‐delocalization and related (anti‐)aromaticity. On the basis of nonadiabatic molecular dynamics simulations, the absence of fluorescence from one of the regioisomers was explained by the occurrence of easily accessible S 1/S 0 conical intersections below the vertical excitation energy level. It is demonstrated in the manuscript that the analysis of local mode force constants and the related aromaticity index represent a useful tool for the characterization of π‐delocalization effects in π‐conjugated compounds. [ABSTRACT FROM AUTHOR]

Conical intersections control excited state reactivity, and thus, elucidating and predicting their geometric and energetic characteristics are crucial for understanding photochemistry. Locating these intersections requires accurate and efficient electronic structure methods. Unfortunately, the most accurate methods (e.g., multireference perturbation theories such as XMS-CASPT2) are computationally challenging for large molecules. The state-interaction state-averaged restricted ensemble referenced Kohn–Sham (SI-SA-REKS) method is a computationally efficient alternative. The application of SI-SA-REKS to photochemistry was previously hampered by a lack of analytical nuclear gradients and nonadiabatic coupling matrix elements. We have recently derived analytical energy derivatives for the SI-SA-REKS method and implemented the method effectively on graphical processing units. We demonstrate that our implementation gives the correct conical intersection topography and energetics for several examples. Furthermore, our implementation of SI-SA-REKS is computationally efficient, with observed sub-quadratic scaling as a function of molecular size. This demonstrates the promise of SI-SA-REKS for excited state dynamics of large molecular systems. [ABSTRACT FROM AUTHOR]

The use of the mixed reference (MR) reduced density matrix, which combines reduced density matrices of the MS = +1 and -1 triplet-ground states, is proposed in the context of the collinear spin-fliptime-dependent density functional theory (SF-TDDFT) methodology. The time-dependent Kohn-Sham equation with the mixed state is solved by the use of spinor-like open-shell orbitals within the linear response formalism, which enables to generate additional configurations in the realm of TD-DFT. The resulting MR-SF-TDDFT computational scheme has several advantages before the conventional collinear SF-TDDFT. The spin-contamination of the response states of SF-TDDFT is nearly removed. This considerably simplifies the identification of the excited states, especially in the "black-box" type applications, such as the automatic geometry optimization, reaction path following, or molecular dynamics simulations. With the new methodology, the accuracy of the description of the excited states is improved as compared to the collinear SF-TDDFT. Several test examples, which include systems typified by strong non-dynamic correlation, orbital (near) degeneracy, and conical intersections, are given to illustrate the performance of the new method. [ABSTRACT FROM AUTHOR]

An extended variant of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, the REKS(4,4) method, designed to describe the ground electronic states of strongly multireference systems is modified to enable calculation of excited states within the time-independent variational formalism. The new method, the state-interaction state-averaged REKS(4,4), i.e., SI-SA-REKS(4,4), is capable of describing several excited states of a molecule involving double bond cleavage, polyradical character, or multiple chromophoric units. We demonstrate that the newmethod correctly describes the ground and the lowest singlet excited states of a molecule (ethylene) undergoing double bond cleavage. The applicability of the new method for excitonic states is illustrated with π stacked ethylene and tetracene dimers. We conclude that the new method can describe a wide range of multireference phenomena. [ABSTRACT FROM AUTHOR]

The state-averaged (SA) spin restricted ensemble referenced Kohn-Sham(REKS) method and its state interaction (SI) extension, SI-SA-REKS, enable one to describe correctly the shape of the ground and excited potential energy surfaces of molecules undergoing bond breaking/bond formation reactions including features such as conical intersections crucial for theoretical modeling of non-adiabatic reactions. Until recently, application of the SA-REKS and SI-SA-REKS methods to modeling the dynamics of such reactions was obstructed due to the lack of the analytical energy derivatives. In this work, the analytical derivatives of the individual SA-REKS and SI-SA-REKS energies are derived. The final analytic gradient expressions are formulated entirely in terms of traces of matrix products and are presented in the form convenient for implementation in the traditional quantum chemical codes employing basis set expansions of the molecular orbitals. The implementation and benchmarking of the derived formalism will be described in a subsequent article of this series. [ABSTRACT FROM AUTHOR]

The spin-restricted ensemble-referenced Kohn-Sham (REKS) method is based on an ensemble representation of the density and is capable of correctly describing the non-dynamic electron correlation stemming from (near-)degeneracy of several electronic configurations. The existing REKS methodology describes systems with two electrons in two fractionally occupied orbitals. In thiswork, the REKS methodology is extended to treat systems with four fractionally occupied orbitals accommodating four electrons and self-consistent implementation of the REKS(4,4) method with simultaneous optimization of the orbitals and their fractional occupation numbers is reported. The new method is applied to a number of molecular systems where simultaneous dissociation of several chemical bonds takes place, as well as to the singlet ground states of organic tetraradicals 2,4-didehydrometaxylylene and 1,4,6,9-spiro[4.4]nonatetrayl. [ABSTRACT FROM AUTHOR]

The analytical gradient for the two-component Normalized Elimination of the Small Component (2c-NESC) method is presented. The 2c-NESC is a Dirac-exact method that employs the exact two-component one-electron Hamiltonian and thus leads to exact Dirac spin-orbit (SO) splittings for one-electron atoms. For many-electron atoms and molecules, the effect of the two-electron SO interaction is modeled by a screened nucleus potential using effective nuclear charges as proposed by Boettger [Phys. Rev. B 62, 7809 (2000)]. The effect of spin-orbit coupling (SOC) on molecular geometries is analyzed utilizing the properties of the frontier orbitals and calculated SO couplings. It is shown that bond lengths can either be lengthened or shortened under the impact of SOC where in the first case the influence of low lying excited states with occupied antibonding orbitals plays a role and in the second case the j j-coupling between occupied antibonding and unoccupied bonding orbitals dominates. In general, the effect of SOC on bond lengths is relatively small (=5% of the scalar relativistic changes in the bond length). However, large effects are found for van der Waals complexes Hg2 and Cn2, which are due to the admixture of more bonding character to the highest occupied spinors. [ABSTRACT FROM AUTHOR]

State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor-acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene-perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods. [ABSTRACT FROM AUTHOR]

Electron transfer in the ground and excited states of a model donor-acceptor (D-A) system is investigated using the single-reference and multi-reference density functional theory (DFT) methods. To analyze the results of the calculations, a simple two-site multi-reference model was derived that predicts a stepwise electron transfer in the S0 state and a wave-like dependence of the S1 electron transfer on the external stimulus. The standard single-reference Kohn-Sham (KS) DFT approach and the time-dependent DFT (TDDFT) method failed to describe the correct dependence of the S0 and S1 electron transfer on the external electric field applied along the donor-acceptor system. The multi-reference DFT approach, the spin-restricted ensemble-referenced KS (REKS) method, was able to successfully reproduce the correct behavior of the S0 and S1 electron transfer on the applied field. The REKS method was benchmarked against experimentally measured gas phase charge transfer excitations in a series of organic donor-acceptor complexes and displayed its ability to describe this type of electronic transitions with a very high accuracy, mean absolute error of 0.05 eV with the use of the standard range separated density functionals. On the basis of the calculations undertaken in this work, it is suggested that the non-adiabatic coupling between the S0 and S1 states may interfere with the electron transfer in a weakly coupled donor-acceptor system. It is also suggested that the electronic excitation of a D+-A- system may play a dual role by assisting the further electron transfer at certain magnitudes of the applied electric field and causing the backward transfer at lower electric field strengths. [ABSTRACT FROM AUTHOR]

Computational investigation of the longest wavelength excitations in a series of cyanines and linear n-acenes is undertaken with the use of standard spin-conserving linear response time-dependent density functional theory (TD-DFT) as well as its spin-flip variant and a ΔSCF method based on the ensemble DFT. The spin-conserving linear response TD-DFT fails to accurately reproduce the lowest excitation energy in these π-conjugated systems by strongly overestimating the excitation energies of cyanines and underestimating the excitation energies of n-acenes. The spin-flip TD-DFT is capable of correcting the underestimation of excitation energies of n-acenes by bringing in the non-dynamic electron correlation into the ground state; however, it does not fully correct for the overestimation of the excitation energies of cyanines, for which the non-dynamic correlation does not seem to play a role. The ensemble DFT method employed in this work is capable of correcting for the effect of missing non-dynamic correlation in the ground state of n-acenes and for the deficient description of differential correlation effects between the ground and excited states of cyanines and yields the excitation energies of both types of extended π-conjugated systems with the accuracy matching high-level ab initio multireference calculations. [ABSTRACT FROM AUTHOR]

A new family of light driven molecular rotary motors, which can be synthesized from easily available precursor compounds and which are capable of completing a full 360° revolution by two photoisomerization steps only, is proposed. The non-adiabatic molecular dynamic simulations show that the photoisomerization steps of the motor's working cycle occur on an ultrafast time scale (ca. 200–300 fs), have a very high quantum yield of isomerization (0.91–0.97), and display high selectivity of torsion in the same direction. It is expected that the new motor should remain operational at lower temperatures than the currently existing motors. [ABSTRACT FROM AUTHOR]

Utilizing the analytic derivative formalism for the Mössbauer isomer shift in connection with the Dirac-exact two-component Normalized Elimination of the Small Component (2c-NESC) method a new approach to the analytic calculation of the contact densities at the nuclei has been developed and implemented in the general purpose NESC programme. The new approach is applied to the calculation of the contact densities as well as contact density differences in several iodine-, gold-, and mercury-containing molecules. Substantial differences between the contact densities obtained by the spin-free 1c-NESC method and the 2c-NESC method are found, which demonstrate the importance of spin-orbit coupling. However, the influence of spin-orbit coupling on the contact density differences between the sample and the reference nuclei is found to be modest. This result suggests that a low-cost determination of accurate contact densities at the nuclei can be achieved by combining the 1c-NESC densities obtained at the correlated wavefunction level of theory with the contact density differences obtained at the 2c-NESC/DFT level. [ABSTRACT FROM AUTHOR]

The dynamics of the ring opening in the state of cyclohexa-1,3-diene (CHD) is studied by a new direct mixed quantum-classical non-adiabatic dynamics approach which employs the decoherence-induced surface hopping based on the exact factorisation (DISH-XF) molecular dynamics method in connection with the state-interaction state-averaged spin-restricted ensemble-referenced Kohn–Sham (SI-SA-REKS, or SSR) electronic structure method. The critical species on the and PESs of CHD were studied using the SSR method and the minimum energy pathways (MEPs) were optimised. The obtained vertical excitation energies are in good agreement (within ca. 5–6 kcal/mol) with the experimental values. The optimised geometry of the / minimum energy conical intersection (MECI) agrees well with the previously obtained MSPT2 geometry. The DISH-XF/SSR non-adiabatic molecular dynamics (NAMD) simulations of ring opening in CHD predict the exponential decay constant fs in a reasonable agreement with an experimental estimate (230±30 fs). The calculated product branching ratio (CHD:HT = 64:36) is in agreement with the recent experimental measurement (70:30). The NAMD trajectories are analysed in terms of the vibrational normal modes and the obtained branching ratio is explained by persistent stretching of the fissile bond when the trajectories propagate on the PES. [ABSTRACT FROM AUTHOR]

It is estimated that 72% of the worldwide primary energy consumption is lost as waste heat. Thermoelectric Generators (TEGs) are a possible solution to convert a part of this energy into electricity and heat for space heating. However, for their deployment a proven long-term operation is required. Therefore, this research investigates the long-term stability of TEGs on system level in air and argon atmosphere under thermal cycling up to 543 K. The layout of the examined test objects resembles a TEG in stack design. The results show that the maximal output power of the test object in air reaches a plateau at 57% of the initial power after 50 cycles caused by an increased electrical resistance of the system. Whereas the test object in argon atmosphere shows no significant degradation of electrical power or resistance. The findings represent a step towards the understanding of the long-term stability of TEGs and can be used as a guideline for design decisions. [ABSTRACT FROM AUTHOR]

The normalized elimination of the small component method is a first principles two-component relativistic approach that leads to the Dirac-exact description of one-electron systems. Therefore, it is an ideal starting point for developing procedures, by which first- and second-order response properties can be routinely calculated. We present algorithms and methods for the calculation of molecular response properties such as geometries, dipole moments, hyperfine structure constants, vibrational frequencies and force constants, electric polarizabilities, infrared intensities and so forth. The described formalisms are applied to molecules containing mercury and other heavy elements, which require a relativistic treatment. Perspectives for the future development and application of Dirac-exact methods are outlined. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

[Display omitted] • Ehrenfest Force F (r) applied to the two C-O ring-opening photo-reactions of oxirane. • Ehrenfest Force trajectories and hybrid stress tensor trajectory calculated with the F (r) BCP s. • Torsion of the CH 2 group facilitated the photo-reaction pathway towards the CI. • Torsion of CH 2 group induced symmetry breaking evident from S 0 and S 1 F (r) trajectories. • Agreement found between the Ehrenfest Force and hybrid stress tensor trajectories. Ehrenfest Force F (r) trajectories were constructed for the C-O ring-opening photo-reactions of oxirane. The F (r) trajectories were constructed in an eigenvector-space corresponding to bond-flexing, bond-twist and bond-anharmonicity associated with the least and most preferred directions of charge density accumulation and bond critical point (BCP) sliding respectively. The presence of the torsion of a CH 2 group for one of the photo-reactions led to greater symmetry breaking and greater reaction pathway preference. Consistency was found from hybrid Ehrenfest Force F (r) trajectories that were constructed using the Ehrenfest Force F (r) BCP s and the stress tensor eigenvectors. [ABSTRACT FROM AUTHOR]

The non-adiabatic dynamics of furan excited in the ππ* state (S2 in the Franck–Condon geometry) was studied using non-adiabatic molecular dynamics simulations in connection with an ensemble density functional method. The time-resolved photoelectron spectra were theoretically simulated in a wide range of electron binding energies that covered the valence as well as the core electrons. The dynamics of the decay (rise) of the photoelectron signal were compared with the excited-state population dynamics. It was observed that the photoelectron signal decay parameters at certain electron binding energies displayed a good correlation with the events occurring during the excited-state dynamics. Thus, the time profile of the photoelectron intensity of the K-shell electrons of oxygen (decay constant of 34 ± 3 fs) showed a reasonable correlation with the time of passage through conical intersections with the ground state (47 ± 2 fs). The ground-state recovery constant of the photoelectron signal (121 ± 30 fs) was in good agreement with the theoretically obtained excited-state lifetime (93 ± 9 fs), as well as with the experimentally estimated recovery time constant (ca. 110 fs). Hence, it is proposed to complement the traditional TRPES observations with the trXPS (or trNEXAFS) measurements to obtain more reliable estimates of the most mechanistically important events during the excited-state dynamics. [ABSTRACT FROM AUTHOR]

Molecular emitters simultaneously generating light at different wavelengths have wide applications. With a small molecule, however, it is challenging to realize two independent radiative pathways. We invented the first examples of dual‐emissive single‐benzene fluorophores (SBFs). Two emissive tautomers are generated by synthetic modulation of the hydrogen bond acidity, which opens up pathways for excited‐state proton transfer. White light is produced by a delicate balance between the energy and intensity of the emission from each tautomer. We show that the excited‐state antiaromaticity of the benzene core itself dictates the proton movements driving the tautomer equilibrium. Using this simple benzene platform, a fluorinated SBF was synthesized with a record high solubility in perfluorocarbon solvents. White light‐emitting devices and multicolor imaging of perfluorocarbon nanodroplets in live cells demonstrate the practical utility of these molecules. [ABSTRACT FROM AUTHOR]

Molecular emitters simultaneously generating light at different wavelengths have wide applications. With a small molecule, however, it is challenging to realize two independent radiative pathways. We invented the first examples of dual‐emissive single‐benzene fluorophores (SBFs). Two emissive tautomers are generated by synthetic modulation of the hydrogen bond acidity, which opens up pathways for excited‐state proton transfer. White light is produced by a delicate balance between the energy and intensity of the emission from each tautomer. We show that the excited‐state antiaromaticity of the benzene core itself dictates the proton movements driving the tautomer equilibrium. Using this simple benzene platform, a fluorinated SBF was synthesized with a record high solubility in perfluorocarbon solvents. White light‐emitting devices and multicolor imaging of perfluorocarbon nanodroplets in live cells demonstrate the practical utility of these molecules. [ABSTRACT FROM AUTHOR]

Cosmic dust transports information about the composition and evolution of distant realms over space and time. Dust sources may be in our local neighbourhood, such as the surfaces of moons and small bodies, or further away, in the galactic environment. The interior of moons like Io or Enceladus are well known dust sources in our solar system. Dust grains are therefore like probes, giving us the opportunity to investigate these objects at a distance. Thus, a new field of activity has been born: Dust Astronomy. The ultimate tool for Dust Astronomy is a dust observatory which was never been flown so far. Until today, all our knowledge is based on smaller individual dust detectors flown on various interplanetary spacecraft. Recently, a new generation of dust telescopes, which can be combined to a full dust observatory, became available. The scientific goal of such an observatory is to characterise our micrometeoroid environment with high precision and sensitivity and to record an inventory of various dust populations from asteroidal, cometary and interstellar dust sources. Two competitive studies on a Dust Astronomy mission were performed as part of a master's course, including mission analysis and spacecraft design. The goal was to demonstrate the feasibility of an observatory reaching the main asteroid belt with a minimum spacecraft mass using electric propulsion. Additional secondary payloads supporting the primary objective were selected as well. The results prove that small probes with less than 700 kg mass are capable of placing an array of dust telescopes deep in the asteroid belt, leading to a huge leap in Dust Astronomy and our knowledge about the local dust environment. • First presentation of feasibility studies for a dust observatory between Earth and asteroid belt. • A dust observatory is a tool for dust astronomy and studies interplanetary and interstellar dust fluxes in our solar system. • The observatories reach the asteroid belt within 7 years using electric propulsion. • Two full mission studies were performed by a small satellite project. [ABSTRACT FROM AUTHOR]

The formulations and performances of spin‐restricted ensemble‐referenced KS and mixed‐reference spin‐flip time‐dependent density functional theory incorporating strong correlations into density functional theories are documented. As a result of balanced dynamic and nondynamic correlation, they are capable of describing strongly correlated challenging systems including diradicals, bond dissociation, conical intersections, doubly excited states, and so on, overcoming the limitations of current density functional theories. [ABSTRACT FROM AUTHOR]

Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 À or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems. [ABSTRACT FROM AUTHOR]

Graphical abstract Top (photoreaction pathway leading back to the ring-closed reactant): QTAIM bond-path framework sets for the S 0 state; B 0 = { p 0 , q 0 , r 0 } (left panel), the S 1 state; B 1 = { p 1 , q 1 , r 1 } (middle panel) corresponding a to nudged elastic band (NEB) path length = 13.18 Å. Variation of the local total energy density H (r b) for the S 0 and S 1 states with the NEB of the fissile bond (right panel). Bottom: The corresponding results for the photoreaction pathway leading forward to the ring-opened product. Highlights • QTAIM provided an explanation of the direction of the ring-opening photoreactions. • Bond-path framework sets B compared for MEPs of ring-opening photoreactions in DHCL. • Less efficient MEP explained by "sticky" ring-opening bond resisting ring-opening. • No oscillation in chemical character of ring-opening bond of MEP that led to reactant. • Stress tensor stiffness confirmed explanation of ring-opening pathways. Abstract The factors underlying two possible pathways for the Dihydrocostunolide (DHCL) photochemical ring-opening reaction were investigated; the first pathway returned to the ring-closed conformation of the reactant and the second pathway progressed to the ring-opened product. High-level multi-reference DFT methods were used to optimize the two pathways and the density was analyzed using QTAIM and the stress tensor. Oscillations in the chemical character of the fissile bond were found for the first pathway before and after the conical intersection that steered the reaction back to reactant. Conversely, this behavior was absent for the second pathway that led forward to the product. [ABSTRACT FROM AUTHOR]

Malignant transformation is associated with loss of cell differentiation, anaplasia. Transcription factors gli, required for embryonic development, may be involved in this process. We studied the activity of transcription factors gli in high-grade gliomas and their role in maintenance of stem cell state and glioma cell survival. 20 glioma cell lines and a sample of a normal adult brain tissue were used in the present study. We found the expression of gli target genes, including GLI1 and FOXM1, in all tested glioma cell lines, but not in the normal tissue. Interestingly, the expression of gli target genes in some glioma cell lines was observed together with a high level of their transcriptional repressor, Gli3R. Knockdown of GLI3 in one of these lines resulted in decrease of gli target gene expression. These data suggest that Gli3R does not prevent the gli target genes transcription, and gli3 acts in glioma cells more as an activator, than a repressor of transcription. We observed that gli regulated the expression of such genes, as SOX2 or OCT4 that maintain stem cell state, and TET1, involving in DNA demethylation. Treatment with GANT61 or siRNA against GLI1, GLI2, or GLI3 could result in complete glioma cell death, while cyclopamine had a weaker and line-specific effect on glioma cell survival. Thus, the gli transcription factors are abnormally active in high-grade gliomas, regulate expression of genes, maintaining the stem cell state, and contribute to glioma cell survival. [ABSTRACT FROM AUTHOR]

Graphical abstract Top: QTAIM bond-path frame-work set B corresponding to the C.I planar configuration, where the ( p 0 , q 0)-paths (left panel) for S 0 and ( p 1 , q 1)-paths (middle panel) for the S 1 states are presented with ( p 0 , p 1)-paths (pale-blue) and ( q 0 , q 1)-paths (magenta) with a magnification factor of ×5. Variations of the ellipticity ε profiles (right panel) for the S 0 and S 1 states along the bond-path ( r ) associated with the torsional C2-C6 BCP. Bottom: The corresponding stress tensor B σ are presented also with a magnification factor of ×5 and the variations of the stress tensor ellipticity ε σ profiles (right panel). Highlights • Present QTAIM and stress tensor 3-D bond-path framework sets B , B σ and B σH for fulvene. • Provide a 3-D bonding morphology of the ground S 0 and first S 1 excited states of fulvene. • Demonstrated variation of B , B σ and B σH with torsion and bond length alternation (BLA). • Compare two versions of the stress tensor B σ , B σH and find best approximation to QTAIM B. • Higher degree of asymmetry and lower ellipticity ε for the S 1 than S 0 electronic state. Abstract We present, for the ground and first excited states of fulvene, the complete 3-D bond-path framework set B = {(p 0 , p 1), (q 0 , q 1), (r 0 , r 1)} from the quantum theory of atoms in molecules (QTAIM) and B σH = {(p σH0 , p σH1), (q σH0 , q σH1), (r 0 , r 1)} and B σ = {(p σ0 , p σ1), (q σ0 , q σ1), (r 0 , r 1)} from the stress tensor within the QTAIM partitioning. We find that both the QTAIM bond-path framework sets B = {(p 0 , p 1), (q 0 , q 1), (r 0 , r 1)} and the stress tensor B σ = {(p σ0 , p σ1), (q σ0 , q σ1), (r 0 , r 1)} provide a quantitative 3-D rendering of the bonding that is consistent with understanding of the bonding provided by using Lewis structures. [ABSTRACT FROM AUTHOR]

A QTAIM investigation of the torsion in both the clockwise and counter-clockwise directions about the π bonds of the retinal protonated Schiff base chromophore in the lowest electronically excited state provided a detailed description of the changing bonding topology that was sensitive to both the torsion and the direction of torsion. Analysis of the separate torsion calculations demonstrated a clear order of preferred bonding torsion in terms of principles of maximizing bonding. Unusual behavior of the bond ellipticity in the S 1 state was found for the two less favorable bonds for torsion and explained in terms of the presence of weak bonding interactions. [ABSTRACT FROM AUTHOR]

P53 protein is more frequently mutated in human tumours compared with the other proteins. While the majority of the p53 mutations, especially within its DNA-binding domain, lead to the loss of the wild-type function, there are accumulating data demonstrating that the p53 mutants gain tumour promoting activities; the latter triggers a revitalised interest in functional analysis of the p53 mutants. A systematic screening for p53 mutations in surgical materials from patients with glioma revealed a 378C>G mutation that creates a stop codon at the position of amino acid residue 126. The mutation eliminates the recognition site for the restriction endonuclease Sca I that allowed us to carry out RFLP analysis of DNA extracted from the clinical samples and suggests that this mutation is more frequent than is documented in the p53 databases. Both the ECV-304 and EJ cell lines, that probably originate from the bladder carcinoma T24 cell line, were confirmed to contain the homozygous 378C>G mutation but were shown to produce the p53 protein of expected full-length size detected by Western blotting. We provide evidence that the 378C>G mutation generates an alternative 3’ splice site (ss) which is more often used instead of the authentic upstream 3’ ss, driving the production of mRNA encoding the protein with the single amino acid deletion (p53ΔY126). Using endogenous expression, we demonstrated that the p53ΔY126 protein is nearly as active as the wild type protein in inducing the p21/Waf1 expression and apoptosis. [ABSTRACT FROM AUTHOR]

A quantum theory of atoms in molecules (QTAIM) and stress tensor analysis was applied to analyze intramolecular interactions influencing the photoisomerization dynamics of a light-driven rotary molecular motor. For selected nonadiabatic molecular dynamics trajectories characterized by markedly different S1 state lifetimes, the electron densities were obtained using the ensemble density functional theory method. The analysis revealed that torsional motion of the molecular motor blades from the Franck-Condon point to the S1 energy minimum and the S1/S0 conical intersection is controlled by two factors: greater numbers of intramolecular bonds before the hop-time and unusually strongly coupled bonds between the atoms of the rotor and the stator blades. This results in the effective stalling of the progress along the torsional path for an extended period of time. This finding suggests a possibility of chemical tuning of the speed of photoisomerization of molecular motors and related molecular switches by reshaping their molecular backbones to decrease or increase the degree of coupling and numbers of intramolecular bond critical points as revealed by the QTAIM/stress tensor analysis of the electron density. Additionally, the stress tensor scalar and vector analysis was found to provide new methods to follow the trajectories, and from this, new insight was gained into the behavior of the S1 state in the vicinity of the conical intersection. [ABSTRACT FROM AUTHOR]

Various types of interactions between halogen (X) and π moiety (X−π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X2 and CX4 (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X−π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Møller-Plesset second-order perturbation theory (MP2), and various flavors of density functional theory (DFT) methods, we study complexes of benzene (Bz) with halogen-containing molecules X2 and CX4 (X = Cl/Br) and analyze various components of the interaction energy using symmetry adapted perturbation theory (SAPT). As for the lowest energy conformers (S1), X2-Bz is found to have the T-shaped structure where the electropositive X atom-end of X2 is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX4-Bz has the stacked structure. In addition to this CX4-Bz (S1), other low energy conformers of X2-Bz (S2/S3) and CX4-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X2-Bz (S1), whereas the deviations are relatively small for CX4-Bz where the dispersion is more important. The halogen bond shows highly anisotropic electron density around halogen atoms and the DFT results are very sensitive to basis set. The unsatisfactory performance of many density functionals could be mainly due to less accurate exchange. This is evidenced from the good performance by the dispersion corrected hybrid and double hybrid functionals. B2GP-PLYP-D3 and PBE0-TS(Tkatchenko-Scheffler)/D3 are well suited to describe the X−π interactions adequately, close to the CCSD(T)/CBS binding energies (within ∼1 kJ/mol). This understanding would be useful to study diverse X−π interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers. [ABSTRACT FROM AUTHOR]

The utility of the QTAIM/stress tensor analysis method for characterizing the photoisomerization of light driven molecular rotary machines is investigated on the example of the torsion path in fluorene molecular motor. The scalar and vector descriptors of QTAIM/stress tensor reveal additional information on the bonding interactions between the rotating units of the motor, which cannot be obtained from the analysis of the ground and excited state potential energy surfaces. The topological features of the fluorene motor molecular graph display that, upon the photoexcitation a certain increase in the torsional stiffness of the rotating bond can be attributed to the increasing topological stability of the rotor carbon atom attached to the rotation axle. The established variations in the torsional stiffness of the rotating bond may cause transfer of certain fraction of the torsional energy to other internal degrees of freedom, such as the pyramidalization distortion. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

While rotary molecular switches based on neutral and cationic organic -systems have been reported, structurally homologous anionic switches providing complementary properties have not been prepared so far. Flere we report the design and preparation of a molecular switch mimicking the anionic p-HBDI chromophore of the green fluorescent protein. The investigation of the mechanism and dynamics of the E/Z switching function is carried out both computationally and experimentally. The data consistently support axial rotary motion occurring on a sub-picosecond time scale. Transient spectroscopy and trajectory simulations show that the nonadiabatic decay process occurs in the vicinity of a conical intersection (CInt) between a charge transfer state and a covalent/diradical state. Comparison of our anionic p-HBDI-like switch with the previously reported cationic N-alkyl indanylidene pyrrolinium switch mimicking visual pigments reveals that these similar systems translocate, upon vertical excitation, a similar net charge in the same axial direction. [ABSTRACT FROM AUTHOR]

Testing of pregnant women reveals weakening of neutrophil-mediated effector functions, such as reactive oxygen species generation. This study provides data confirming the phenomenon, gained through application of the flow cytometry technique. Key factors influencing neutrophil functional activity in blood plasma of pregnant women have not been detected so far. At the same time, concentration of ceruloplasmin – a copper-containing glycoprotein – is known to increase in blood significantly during pregnancy. We observed the negative correlation between ceruloplasmin concentration in blood plasma of pregnant women and the intensity of respiratory burst of neutrophils. Fractionation of plasma using gel-filtration revealed that ceruloplasmin-containing fraction demonstrated suppression of the respiratory burst reaction. Partial elimination of ceruloplasmin from the blood of pregnant women, performed with the help of specific antibodies and followed by immunoprecipitation, leads to an increased respiratory burst reaction. On the contrary, addition of ceruloplasmin to blood samples of healthy donors noticeably decreases the respiratory burst reaction. The results presented prove that change in ceruloplasmin level in plasma is necessary and sufficient for modulating the ability of neutrophils to produce reactive oxygen species during pregnancy. [ABSTRACT FROM PUBLISHER]

Variation of the precession K along the torsion C2-C6 BCP bond-path of fulvene for the S 0 (left panel) and S 1 (right panel) electronic states for a series of values of the torsion θ = 0.0° (Franck-Condon) to θ = 64.3° (conical intersection). Bond critical points (BCP s) are located at a distance = 0.0 a.u along the bond-path. • Determined the precessions K of the path-packets for the S 0 and S 1 states of fulvene. • The precessions K of the path-packets quantified the bond rigidity and flexibility. • An asymmetry is found for the S 1 state variation in the bond-path rigidity with torsion. • The S 1 state at torsion θ = 0.0° possesses maximum bond-rigidity along the entire bond. • The S 1 state possessed a higher degree of bond-anharmonicity than the S 0 state. Here we have determined the precessions K and K' of the { p , p ′} and { q , q ′} path-packets for the excited state deactivation reaction of fulvene in terms of bond-flexing, bond-torsion and bond-anharmonicity that includes the tendencies towards bond-path-rigidity and bond-path-flexibility. An asymmetry is found for the S 1 state resulting in an unpredictable variation in the direction of the bond-path-rigidity as a function of the torsion coordinate. Uniquely, the S 1 state at torsion θ = 0.0° possesses the possible maximum bond-path-rigidity, along the entire bond-path but then drops lower than for the S 0 state at the conical intersection indicating photo-excitation facilitates the torsion. [ABSTRACT FROM AUTHOR]

Simple Summary: Exosomes are nanoscale membrane extracellular vesicles that are involved in intercellular communication and signaling, and are a promising tool in biomedicine for drug delivery. Despite the progress in practical application and morphological characterization, information about their biomechanical properties is still scarce. The presence of non-membrane particles called exomeres with similar functions has recently been reported. We applied the atomic force microscopy technique to study the biomechanical properties of both types of particles in air and in liquid. We found a correlation between the biomechanical properties of the vesicles, their size, structure, and function. Our data provide useful information for a better understanding of the biomechanical characteristics of extracellular vesicles and non-membrane extracellular particles and their AFM detection. While extracellular vesicles (EVs) are extensively studied by various practical applications in biomedicine, there is still little information on their biomechanical properties due to their nanoscale size. We identified isolated blood plasma vesicles that carried on biomarkers associated with exosomes and exomeres and applied atomic force microscopy (AFM) to study them at single particle level in air and in liquid. Air measurements of exosomes revealed a mechanically indented internal cavity in which highly adhesive sites were located. In contrast, the highly adhesive sites of exomeres were located at the periphery and the observed diameter of the particles was ~35 nm. In liquid, the reversible deformation of the internal cavity of exosomes was observed and a slightly deformed lipid bi-layer was identified. In contrast, exomeres were not deformed and their observed diameter was ~16 nm. The difference in diameters might be associated with a higher sorption of water film in air. The parameters we revealed correlated with the well-known structure and function for exosomes and were observed for exomeres for the first time. Our data provide a new insight into the biomechanical properties of nanoparticles and positioned AFM as an exclusive source of in situ information about their biophysical characteristics. [ABSTRACT FROM AUTHOR]

Variations of the bond-path ellipticity ε profiles of the bond-path ( r ) of the torsional C2-C6 BCP corresponding to the (S 0 , S 1 , S 01) (left panel) (S 0 , S 2 , S 02) (right panel) electronic states at values of the torsion θ = 64.3° corresponding to the conical intersection (CI). The vertical dashed lines indicate the position of the BCP for each electronic state. • Present the S 0 → S 1 and S 0 → S 2 NTO densities for fulvene with 3-D next generation QTAIM. • Symmetrization of the S 0 → S 1 torsional BCP along bond-path found for the presence of a CI. • Corresponding NTO transition density S 0 → S 1 displays hindered BCP motion. • NTO density for S 0 → S 1 of the torsional BCP undergoes a large rearrangement at the CI. • Symmetrization effect absent for the S 0 → S 2 torsional BCP that lacks a CI. We present, for the first time, the S 0 → S 1 (S 01) and S 0 → S 2 (S 02) natural transition orbital (NTO) densities for fulvene, using the 3-D next generation QTAIM that can visualize and quantify the rearrangement of the charge density that occurs in response to the applied torsion and as a consequence of the preferred direction of electron density accumulation. A symmetrization of the position of the bond critical point (BCP) of the torsional C2-C6 BCP along the containing bond-path was determined to be characteristic of the presence of a conical intersection (CI) for the S 0 → S 1 (S 01) transition. [ABSTRACT FROM AUTHOR]

Next‐generation quantum theory of atoms in molecules was applied to analyze, along an entire bond path, intramolecular interactions known to influence the photoisomerization dynamics of a light‐driven rotary molecular motor. The 3D bond‐path framework set B0,1 constructed from the least and most preferred directions of electronic motion, provided new insights into the bonding leading to different S1 state lifetimes including the first quantification of covalent character of a closed‐shell intramolecular bond path. We undertook the first use of the stress tensor trajectory Tσ(s) analysis on selected nonadiabatic molecular dynamics trajectories with the electron densities obtained using the ensemble density functional theory method. The stress tensor Tσ(s) analysis was found to be well suited to follow the dynamics trajectories that included the S0 and S1 electronic states through the conical intersection and also provided to a new measure to assess the degree of purity of the axial bond rotation for the design of rotary molecular motors. [ABSTRACT FROM AUTHOR]

The conical intersections corresponding to the C─O and C─C ring opening were optimized and the reaction paths traversing these intersections were obtained. Investigation of the C─O ring opening revealed that when traversing the lowest energy conical intersection, the reaction path returns to the closed ring geometry. The C─O path traversing the intersection featuring torsion of terminal CH2 group however, led to a ring‐opened geometry, an H‐shift and the formation of acetaldehyde that can undergo further dissociation. The observation of different reaction paths was explained by the 3‐D paths from quantum theory of atoms in molecules (QTAIM) that defined the most preferred direction of electronic motion that precisely tracked the mechanisms of bond breaking and formation throughout the photo‐reactions. The size, orientation, and location of these most preferred 3‐D paths indicated the extent and direction of motion of atoms, bonds, and the degree of torsion or planarity of a bond indicating a predictive ability. [ABSTRACT FROM AUTHOR]

A balanced treatment of the covalent and ionic contributions to the ground and excited states originating from torsion about double bonds is known to be strongly dependent on the presence of dynamic electron correlation. We undertake an analysis of the minimum energy pathways corresponding to deactivation of the first excited singlet state of PSB3. In doing so we consider torsion about the three double bonds including other intramolecular degrees of freedom, such as the bond length alternation. The 3‐D bond‐path analysis provides a new 'bond‐localized orbital‐like' directional interpretation of bonding. Therefore, we present a more sophisticated method of determination of the degree of covalent and ionic contributions known to be responsible for altering the relative stability of the S1/S0 conical intersections. The results presented suggest that the commonly used simplified multi‐reference methodologies that often result in incorrect predictions for the excited state deactivation reaction mechanism. The bond‐path framework set B visualization of the spectrum of the chemical character (covalent–biradical‐ionic) displayed of each of the back‐bone bonds as well as the influence on neighboring bonds. The most preferred directions of accumulation of charge density, q‐ and q′‐paths along the backbone bond‐path (r) corresponding to the torsional C10‐N12 BCP for the S0 (top) and S1 (below) states at a value of the torsion q = 90.0°. [ABSTRACT FROM AUTHOR]

The factors underlying the experimentally observed branching ratio (70:30) of the (1,3‐cyclohexadiene) CHD → HT (1,3,5‐hexatriene) photochemical ring‐opening reaction are investigated. The ring‐opening reaction path is optimized by a high‐level multi‐reference DFT method and the density along the path is analyzed by the quantum theory of atoms in molecules (QTAIM) and stress tensor methods. The performed density analysis suggests that, in both S1 and S0 electronic states, there exists an attractive interaction between the ends of the fissile σ‐bond of CHD that steers the ring‐opening reaction predominantly in the direction of restoration of the ring. It is suggested that opening of the ring and formation of the reaction product (HT) can only be achieved when there is a sufficient persistent nuclear momentum in the direction of stretching of the fissile bond. As this orientation of the nuclear momentum vector can be expected relatively rare during the dynamics, this explains the observed low quantum yield of the ring‐opening reaction. Experimentally observed branching ratio (70:30) of the (1,3‐cyclohexadiene) CHD → HT (1,3,5‐hexatriene) photochemical ring‐opening reaction is investigated by first‐principles calculations and next‐generation quantum theory of atoms in molecules. It is suggested that opening of the ring and formation of the reaction product can only be achieved when there is a sufficient persistent nuclear momentum in the direction of stretching of the fissile bond. [ABSTRACT FROM AUTHOR]

A vector‐based representation of the chemical bond is introduced, which we refer to as the bond‐path framework set B = {p, q, r}, where p, q, and r represent 3 eigenvector‐following paths with corresponding lengths H*, H, and the familiar quantum theory of atoms in molecules (QTAIM) bond‐path length (BPL). The intended application of B is for molecules subjected to various types of reactions and distortions, including photoisomerization reactions, applied torsions θ, or normal modes of vibration. The lengths H* and H of the eigenvector‐following paths are constructed using the e1 and e2 Hessian eigenvectors, respectively, along the bond path, these corresponding to the least and most preferred directions of charge density accumulation. In particular, the paths p and q provide a vector representation of the scalar QTAIM ellipticity ε. The bond‐path framework set B is applied to the excited state deactivation of fulvene that involves distortions along various intramolecular degrees of freedom, such as the bond stretching/compression of bond‐length alternation and bond torsion distortions. We find that the H* and H lengths can differentiate between the ground and excited electronic states, in contrast to the QTAIM BPL. Five unique paths were presented for B= {(p0,p1), (q0,q1), r} for the ground and first excited states where the profile of the scaling factor, the ellipticity ε, reveals a large unexpected asymmetry for the excited state. A "next‐generation" quantum theory of atoms in molecules (QTAIM) is introduced to analyze all types of bonding in molecules subjected to various types of reactions and distortions, including photoisomerization reactions, applied torsions θ, or normal modes of vibration. The double‐bond isomerization of fulvene is used as test model for this "next‐generation" QTAIM approach. [ABSTRACT FROM AUTHOR]