Excited States in Single-Stranded and i-Motif DNA with Silver Ions.

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT.

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Stability of Dibromo-Dipyrromethene Complexes Coordinated with B, Zn, and Cd in Solutions of Various Acidities.

The spectral luminescent properties of dipyrromethenates halogenated with bromine on both ends of the long axis and coordinated using boron fluoride, zinc, or cadmium in neutral ethanol and acidified with hydrochloric acid solutions were studied. The constants of the acid-base equilibrium of the complexes in the proton-donor solvents in the ground and excited states was determined. The mechanisms of complex protonation were discussed, depending on the structure of the compounds. The electronic structures of the neutral and protonated compounds were modeled and analyzed based on the quantum-chemical method. The structures and spectral-luminescence properties were calculated using the SMD model of ethanol solvent using the TD-DFT theory with the B3LYP functional and the composite def2-SVP/def2-TZVP/def2-TZVPP_ECP basis sets, depending on the atomic number of the elements.

Exploring Dyson's Orbitals and Their Electron Binding Energies for Conceptualizing Excited States from Response Methodology.

The molecular orbital (MO) concept is a useful tool, which relates the molecular ground-state energy with the energies (and occupations) of the individual orbitals. However, analysis of the excited states from linear response computations is performed in terms of the initial state MOs or some other forms of orbitals, e.g., natural or natural transition orbitals. Because these orbitals lack the respective energies, they do not allow developing a consistent orbital picture of the excited states. Herein, we argue that Dyson's orbitals enable description of the response states compatible with the concepts of molecular orbital theory. The Dyson orbitals and their energies obtained by mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for the response ground state are remarkably similar to the canonical MOs obtained by the usual DFT calculation. For excited states, the Dyson orbitals provide a chemically sensible picture of the electronic transitions, thus bridging the chasm between orbital theory and response computations.

Exciton Absorption and Luminescence in i-Motif DNA.

We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.

Unique Nanomechanical Properties of Diamond-Lonsdaleite Biphases: Combined Experimental and Theoretical Consideration of Popigai Impact Diamonds.

For the first time, lonsdaleite-rich impact diamonds from one of the largest Popigai impact crater (Northern Siberia) with a high concentration of structural defects are investigated under hydrostatic compression up to 25 GPa. It is found that, depending on the nature of a sample, the bulk modulus for lonsdaleite experimentally obtained by X-ray diffraction in diamond-anvil cells is systematically lower and equal to 93.3-100.5% of the average values of the bulk moduli of a diamond matrix. Density functional theory calculations reveal possible coexistence of a number of diamond/lonsdaleite and twin diamond biphases. Among the different mutual configurations, separate inclusions of one lonsdaleite (001) plane per four diamond (111) demonstrate the lowest energy per carbon atom, suggesting a favorable formation of single-layer lonsdaleite (001) fragments inserted in the diamond matrix. Calculated formation energies and experimental diamond (311) and lonsdaleite (331) powder X-ray diffraction patterns indicate that all biphases could be formed under high-temperature, high-pressure conditions. Following the equation of states, the bulk modulus of the diamond (111)/lonsdaleite (001) biphase is the largest one among all bulk moduli, including pristine diamond and lonsdaleite.

Inheritance of Photochromic Properties of Nitro-Substituted and Halogenated Spiropyrans Containing the Pyrrolidino[60]fullerene.

The photophysical and isomerization properties of hybrid molecular compounds that consist of photochromic nitro-substituted and halogenated spiropyran derivatives bonded to the surface of the [60]fullerene cage through the pyrrolidine bridge were investigated using various functionals and basis sets of TD-DFT and semiempirical quantum-chemical approaches. The role of nπ* states formed by the lone pairs of substituents in changing of the electronic structure and photochromic properties of spiropyran derivatives was evaluated. The Sππ(spiropyran) → intermediate nπ* states → Sππ(merocyanine) channel for phototransformation of the hybrid compound containing a nitro-substituted spiropyran moiety was established and compared with similar systems of halogenated spiropyrans attached to the [60]fullerene bulk where photoinduced isomerization does not process due to high probability of internal conversion from the excited electronic state localized on the spiropyran fragment to the states of the pyrrolidino[60]fullerene.

Luminescence Solvato- and Vapochromism of Alkynyl-Phosphine Copper Clusters.

The reaction of [Cu(NCMe)4][PF6] with aromatic acetylenes HC2R and triphosphine 1,1,1-tris(diphenylphosphino)methane in the presence of NEt3 results in the formation of hexanuclear Cu(I) clusters with the general formula [Cu6(C2R)4{(PPh2)3CH}2][PF6]2 (R = 4-X-C6H4 (1-5) and C5H4N (6); X = NMe2 (1), OMe (2), H (3), Ph (4), CF3 (5)). The structural motif of the complexes studied consists of a Cu6 metal core supported by two phosphine ligands and stabilized by σ- and π-coordination of the alkynyl fragments (together with coordination of pyridine nitrogen atoms in cluster 6). The solid state structures of complexes 2-6 were determined by single crystal XRD analysis. The structures of the complexes in solution were elucidated by (1)H, (31)P, (1)H-(1)H COSY NMR spectroscopy, and ESI mass spectrometry. Clusters 1-6 exhibit moderately strong phosphorescence in the solid state with quantum yields up to 17%. Complexes 1-5 were found to form solvates (acetone, acetonitrile) in the solid state. The coordination of loosely bound solvent molecules strongly affects emission characteristics and leads to solvato- and vapochromic behavior of the clusters. Thus, solvent-free and acetonitrile solvated forms of 3 demonstrate contrasting emission in orange (615 nm) and blue (475 nm) regions, respectively. The computational studies show that alkynyl-centered IL transitions mixed with those of MLCT between the Cu6 metal core and the ligand environment play a dominant role in the formation of excited states and can be considerably modulated by weakly coordinating solvent molecules leading to luminescence vapochromism.

Development and application of effective pairwise potentials for UO2(n+), NpO2(n+), PuO2(n+), and AmO2(n+) (n = 1, 2) ions with water.

Intra- and intermolecular force field parameters for the interaction of actinyl ions (AnO2(n+), where, An = U, Np, Pu, Am and n = 1, 2) with water have been developed using quantum mechanical calculations. Water was modeled with the extended simple point charge potential (SPC/E). The resulting force field consists of a simple form in which intermolecular interactions are modeled with pairwise Lennard-Jones functions plus partial charge terms. Intramolecular bond stretching and angle bending are treated with harmonic functions. The new potentials were used to carry out extensive molecular dynamics simulations for each hydrated ion. Computed bond lengths, bond angles and coordination numbers agree well with known values and previous simulations. Hydration free energies, computed from molecular dynamics simulations as well as from quantum simulations with a solvation model, were in reasonable agreement with estimated experimental values.

Absorption spectra of estradiol and tryptophan constructed by the statistical and elongation methods.

The statistical quantum chemical/molecular dynamical method is developed and employed to reproduce optical spectra. This technique includes quantum-mechanical calculations on energy states and photophysical properties of molecular conformers obtained during molecular dynamical simulation. Polycyclic organic molecule estradiol surrounded by solvent particles and protein structure including tryptophan fragment under thermodynamical conditions are considered. A wide absorption spectrum over several excited electronic states of estradiol is constructed. First longwave absorption band of tryptophan-cage mini protein is built involving the elongation method. These statistical spectra reflect the main features of the corresponding experimental ones.