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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]

When calculating electric field gradients (EFGs), relativistic and electron correlation effects are crucial for obtaining accurate results, and the commonly used density functional methods produce unsatisfactory results, especially for heavy elements and/or strongly correlated systems. In this work, a stand-alone program is presented, which enables calculation of EFGs from the molecular orbitals supplied by an external high accuracy quantum chemical calculation and includes relativistic effects through the exact two-component (X2C) formalism and efficient local approximations to it. Application to BiN and BiP molecules shows that a high precision can be achieved in the calculation of nuclear quadrupole coupling constants of 209Bi by combining advanced ab initio methods with the X2C approach. For seventeen iron compounds, the Mössbauer nuclear quadrupole splittings (NQS) of 57Fe calculated using a double-hybrid functional method are in very good agreement with the experimental values. It is shown that, for strongly correlated molecules, the double-hybrid functionals are much more accurate than the commonly used hybrid functionals. The computer program developed in this study furnishes a useful utility for obtaining EFGs and related nuclear properties with high accuracy. [ABSTRACT FROM AUTHOR]

The optimization of the quantum efficiency of single-molecule light-driven rotary motors typically relies on chemical modifications. While, in isolated conditions, computational methods have been frequently used to design more efficient motors, the role played by the solvent environment has not been satisfactorily investigated. In this study, we used multiscale nonadiabatic molecular dynamics simulations of the working cycle of a 2-stroke photon-only molecular rotary motor. The results, which display dynamics consistent with the available transient spectroscopy measurements, predict a considerable decrease in the isomerisation quantum efficiency in methanol solution with respect to the gas phase. The origin of such a decrease is traced back to the ability of the motor to establish hydrogen bonds with solvent molecules. The analysis suggests that a modified motor with a reduced ability to form hydrogen bonds will display increased quantum efficiency, therefore extending the set of engineering rules available for designing light-driven rotary motors. Increasing the rotational efficiency of single-molecule light-driven rotary motors often relies on chemical modifications aimed at eliminating the factors that hinder rotation. Using multiscale nonadiabatic simulations, the authors investigate the transient conformations assumed by the motor molecule during its operation in a solvent and examine possibilities for enhancing the motor's efficiency by blocking certain solvent-solute interactions that restrain successful completion of the rotational movement. [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]

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]

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]

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]

The rational engineering of photoresponsive materials, e.g., light-driven molecular motors, is a challenging task. Here, we use structure-related design rules to prepare a prototype molecular rotary motor capable of completing an entire revolution using, exclusively, the sequential absorption of two photons; i.e., a photon-only two-stroke motor. The mechanism of rotation is then characterised using a combination of non-adiabatic dynamics simulations and transient absorption spectroscopy measurements. The results show that the rotor moiety rotates axially relative to the stator and produces, within a few picoseconds at ambient T, an intermediate with the same helicity as the starting structure. We discuss how such properties, that include a 0.25 quantum efficiency, can help overcome the operational limitations of the classical overcrowded alkene designs. Improving the efficiency of light-driven molecular rotary motors is a challenging task. Here, the authors combine theoretical modeling, synthesis and spectroscopy to prepare a prototype molecular motor capable of avoiding inefficient thermally activated motion; thus offering prospects to implement a 2-stroke photon-only molecular motor. [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 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]

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]

The analytic derivative algorithm for the effective contact densities obtained by the exact two-component (X2C) relativistic Hamiltonian is extended to the local approximations to X2C to achieve a higher computational efficiency without losing accuracy. The new algorithm has been implemented in a standalone program, which can utilize the molecular orbitals from state-of-the-art ab initio or density functional theory (DFT) calculations by other quantum chemistry programs in connection with various relativistic Hamiltonians. With the help of the utility program, the effective contact densities as well as the related Mössbauer isomer shifts can be studied by various advanced single-reference and multi-reference ab initio methods as long as the canonical or natural orbitals are available. Using the developed algorithm, the effective contact densities and the Mössbauer isomer shifts in a series of iron compounds and in HgFn (n = 1, 2, 4, and 6) molecules were studied. The obtained results show that (1) adequate account of the static electron correlation significantly improves the agreement of the theoretical 57Fe effective contact densities with the experimental isomer shifts, and (2) the non-monotonous changes of the effective contact density in a series of HgFn compounds are caused by the increasing screening effect due to shrinking of the Hg 5d orbitals. [ABSTRACT FROM AUTHOR]

Time-resolved photoelectron spectra during the photochemical ring-opening reaction of 1,3-cyclohexadiene (CHD) are modeled by an ensemble density functional theory (eDFT) method. The computational methodology employed in this work is capable of correctly describing the multi-reference effects arising in the ground and excited electronic states of molecules, which is important for the correct description of the ring-opening reaction of CHD. The geometries of molecular species along the non-adiabatic molecular dynamics (NAMD) trajectories reported in a previous study of the CHD photochemical ring-opening were used in this work to calculate the ionization energies and the respective Dyson orbitals for all possible ionization channels. The obtained theoretical time-resolved spectra display decay characteristics in a reasonable agreement with the experimental observations; i.e., the decay (and rise) of the most mechanistically significant signals occurs on the timescale of 100–150 fs. This is very different from the excited state population decay characteristics (τS1 = 234 ± 8 fs) obtained in the previous NAMD study. The difference between the population decay and the decay of the photoelectron signal intensity is traced back to the geometric transformation that the molecule undergoes during the photoreaction. This demonstrates the importance of including the geometric information in interpretation of the experimental observations. [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]

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]

Photodecomposition of cyclopropanone is investigated by static quantum chemical calculations and non-adiabatic molecular dynamics (NAMD) simulations. The quantum chemical calculations are carried out by an ensemble density functional theory (eDFT) method capable of delivering high quality results for the ground and excited electronic states of molecules with dissociating bonds. In the NAMD simulations, this method is combined with a novel trajectory surface hopping (TSH) methodology derived from the exact factorization of the electronic-nuclear wavefunction. An ultrafast biexponential decay of the S1 state of cyclopropanone is predicted, where the short (ca. 30 fs) decay time is due to the trajectories reaching the conical intersection (CI) seam on the first approach and the long (ca. 120 fs) decay time is due to recrossing of the CI seam. The experimentally observed dependence of the dissociation (C3H4O* → C2H4 + CO) quantum yield on the excitation wavelength is correctly reproduced by the NAMD simulations. The dependence is explained by the necessity to excite certain vibrational normal modes (e.g., a ring stretching mode with the frequency of 769 cm−1) to break a lateral C–C bond remaining intact at the geometries of the CI seam. [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]