Competing Photocleavage on Boron and at the -Position in BODIPY Photocages.

BODIPY photocages (photocleavable protective groups) have stirred interest because they can release biologically active cargo upon visible light excitation. We conducted combined theoretical and experimental investigations on selected BODIPY photocages to elucidate the mechanism of the competing photocleavage at the boron and -position. Based on the computations, the former reaction involves elongation of the B-C bond, yielding a tight borenium cation and methyl anion.

Unveiling the electron-induced ionization cross sections and fragmentation mechanisms of 3,4-dihydro-2H-pyran.

The interactions of electrons with molecular systems under various conditions are essential to interdisciplinary research fields extending over the fundamental and applied sciences. In particular, investigating electron-induced ionization and dissociation of molecules may shed light on the radiation damage to living cells, the physicochemical processes in interstellar environments, and reaction mechanisms occurring in combustion or plasma. We have, therefore, studied electron-induced ionization and dissociation of the gas phase 3,4-dihydro-2H-pyran (DHP), a cyclic ether appearing to be a viable moiety for developing efficient clinical pharmacokinetics and revealing the mechanisms of biofuel combustion.

On SOCP-based disjunctive cuts for solving a class of integer bilevel nonlinear programs.

Unlabelled: We study a class of integer bilevel programs with second-order cone constraints at the upper-level and a convex-quadratic objective function and linear constraints at the lower-level. We develop disjunctive cuts (DCs) to separate bilevel-infeasible solutions using a second-order-cone-based cut-generating procedure. We propose DC separation strategies and consider several approaches for removing redundant disjunctions and normalization.

Time-resolved spectroscopic and computational study of the initial events in doxazosin photochemistry.

Doxazosin is a quinazoline derivative widely used in medicine as a drug. In this study, a combined experimental and computational approach based on the time-dependent density functional theory was used to elucidate the primary events following the photoexcitation of DOX upon interaction with light. The photophysical properties and photochemical reactivity of DOX were investigated by steady-state and time-resolved absorption and fluorescence spectroscopy.

Ultrafast Photoelimination of Nitrogen from Upper Excited States of Diazoalkanes and the Fate of Carbenes Formed in the Reaction.

The photochemical reactivity of diphenyldiazomethane and phenyl 1- and 2-adamantyl diazomethanes and , respectively, was investigated by transient absorption spectroscopy (TA). Photoelimination of N upon UV excitation takes place in the anti-Kasha ultrafast photochemical reaction from the upper excited singlet states to deliver singlet carbenes, which were, in the case of and , detected by fs-TA. The reactivity of the carbenes differs with respect to the substituent at the carbene center.

Core-shell excitation of isoxazole at the C, N, and O K-edges - an experimental NEXAFS and theoretical TD-DFT study.

The near-edge X-ray absorption fine structure (NEXAFS) spectra of the gas-phase isoxazole molecule have been measured by collecting total ion yields at the C, N, and O K-edges. The spectral structures have been interpreted using time-dependent density functional theory (TD-DFT) with the short-range corrected SRC2-BLYP exchange-correlation functional. Experimental and calculated energies of core excitations are generally in good agreement, and the nature of observed core-excitation transitions has been elucidated.

Frontier orbital stability of nitroxyl organic radicals probed by means of inner shell resonantly enhanced valence band photoelectron spectroscopy.

We have investigated the frontier orbitals of persistent organic radicals known as nitroxyls by resonant photoelectron spectroscopy (ResPES) under inner shell excitation. By means of this site-specific technique, we were able to disentangle the different atomic contributions to the outer valence molecular orbitals and examine several core-hole relaxation pathways involving the singly occupied molecular orbital (SOMO) localized on the nitroxyl group. To interpret the ResPES intensity trends, especially the strong enhancement of the SOMO ionized state at the N K-edge, we computed the Dyson spin orbitals (DSOs) pertaining to the transitions between the core-excited initial states and several of the singly ionized valence final states.

Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders.

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response.

Kinetics of chain reaction driven by proton-coupled electron transfer: α-hydroxyethyl radical and bromoacetate in buffered aqueous solutions.

We measured and computed the rate constants of the reaction between the α-hydroxyethyl radical (˙CH(CH3)OH) and bromoacetate (BrCH2CO2-) in the non-buffered (NB), as well as in the bicarbonate (HCO3-) and hydrogen phosphate (HPO42-) buffered aqueous solutions in the presence of ethanol. These complex multistep reactions are initiated by the proton-coupled electron transfer (PCET) which reduces BrCH2CO2- and incites its debromination. The PCET is followed by the step in which the resulting carboxymethyl radical propagates a radical chain reaction thus recovering ˙CH(CH3)OH and enhancing the debromination yields.

Vibrationally resolved valence and core photoionization and photoexcitation spectra of an electron-deficient trivalent boron compound: the case of catecholborane.

Compounds containing trivalent boron (TB) as the electron-deficient site(s) find numerous practical uses ranging from Lewis bases in organic synthesis to high-tech industry, with a number of novel applications anticipated. We present an experimental and theoretical study of the gas-phase valence photoionization (VUV-PES), core photoionization (XPS) and photoexcitation (NEXAFS) spectra of a representative TB compound catecholborane (CB). For modelling and assigning the spectra we used the ΔDFT and restricted single excitation space TD-DFT methods for the XPS and NEXAFS, and OVGF and EOM-CCSD for the VUV-PES.

Comparing the performances of various density functionals for modelling the mechanisms and kinetics of bimolecular free radical reactions in aqueous solution.

We carried out an investigation of the performances of 18 density functionals (DFs) for modelling the mechanisms and kinetics of the aqueous phase reactions between the α-hydroxyisopropyl radical and 9 organic substrates. The primary goal was to evaluate the applicability of density functional theory specifically in conjunction with the polarizable continuum model (DFT/PCM) for a fully implicit description of the aqueous environment. Accordingly, the solute is augmented with the explicit molecule(s) of the water solvent only when it is confirmed that the water participates in the reaction mechanism directly and not just as a potential donor or acceptor of additional hydrogen bonds.

Proton-coupled electron transfer is the dominant mechanism of reduction of haloacetates by the α-hydroxyethyl radical in aqueous media.

The reaction systems of α-hydroxyalkyl radicals with halogenated organics in aqueous solutions are uniquely suited for studying the fundamentally important proton-coupled electron transfer (PCET) mechanism in competition with alternatives such as substitution, hydrogen abstraction, halogen atom abstraction etc. We report experimental (steady state γ-radiolysis) and theoretical (density functional theory) studies of reactions of the α-hydroxyethyl radical (˙EtOH) with the four monohaloacetate anions (XAc-): fluoroacetate (FAc-), chloroacetate (ClAc-), bromoacetate (BrAc-) and iodoacetate (IAc-). The reactions are conducted in non-buffered and buffered (bicarbonate or phosphate) aqueous solutions of ethanol.

Characterisation of the electronic structure of galvinoxyl free radical by variable energy UPS, XPS and NEXAFS spectroscopy.

Insights into the electronic structure of galvinoxyl - a prototype persistent free radical species - are of interest to elucidate its attractive photophysical and magnetic properties and to pave way for a sensible design of novel applications. To this end, we study the photoionization and photoexcitation UPS, XPS and NEXAFS spectra of the gas-phase galvinoxyl in the valence and core (C 1s and O 1s) regions using synchrotron X-ray radiation. We observe significant variations of relative band intensities with photon energy for valence ionizations below 10 eV which are rationalized in terms of the properties of the corresponding valence molecular orbitals.

Decomposition methods for the two-stage stochastic Steiner tree problem.

A new algorithmic approach for solving the stochastic Steiner tree problem based on three procedures for computing lower bounds (dual ascent, Lagrangian relaxation, Benders decomposition) is introduced. Our method is derived from a new integer linear programming formulation, which is shown to be strongest among all known formulations. The resulting method, which relies on an interplay of the dual information retrieved from the respective dual procedures, computes upper and lower bounds and combines them with several rules for fixing variables in order to decrease the size of problem instances.

Reactions of 2-Propanol Radical with Halogenated Organics in Aqueous Solution: Theoretical Evidence for Proton-Coupled Electron Transfer and Competing Mechanisms.

The reactions of α-hydroxyalkyl radicals in aqueous medium are of interest because they exhibit a rich variety of fundamentally important competing mechanisms, such as proton-coupled electron transfer (PCET), hydrogen atom transfer, free radical substitutions, abstractions and additions, etc. We present a theoretical study of the mechanism and kinetics of the aqueous reactions of α-hydroxyisopropyl (2-propanol) radical with four halogenated organic substrates: iodoacetate (IAc), iodoacetamide (IAm), 5-bromouracil (5-BrU), and carbon tetrachloride (CCl). The reactions are studied using density functional theory (DFT) (M06-2X), and the solvent is modeled as a polarizable continuum, either without the explicit solvent molecules or with one added water molecule.

An experimental NEXAFS and computational TDDFT and ΔDFT study of the gas-phase core excitation spectra of nitroxide free radical TEMPO and its analogues.

Core-hole spectroscopy adds to the fundamental understanding of the electronic structure of stable nitroxide free radicals thus paving way for a sensible design of new analogues with desired functionalities. We study the gas-phase C 1s, N 1s and O 1s excitation spectra of three nitroxide free radicals - TEMPO and two of its amide-substituted analogues - using the experimental NEXAFS technique and the theoretical TDDFT and ΔDFT methods in the unrestricted setting. The short-range corrected SRC1-BLYP and SRC2-BLYP exchange-correlation functionals are used with TDDFT, and the standard B3LYP functional with ΔDFT.

The study of the electronic structure of some N-heterocyclic carbenes (NHCs) by variable energy photoelectron spectroscopy.

The photoionization of three N-heterocyclic carbenes (NHCs) has been studied in the valence and core regions using synchrotron radiation. We observed different variations in the relative band intensities with photon energy for the NHCs in the valence ionization region. This is due to the intra-ring interactions between the C=C bond, nitrogen and carbene lone pairs in the heterocyclic ring of NHCs.

Reliability of Density Functional and Perturbation Theories for Calculating Core-Ionization Spectra of Free Radicals.

The C 1s, N 1s, and O 1s ionization energies were calculated for the three stable nitroxide free radicals, viz., tempo and its two analogues, and compared to their most recent high-resolution core photoelectron spectra. We compare the performance of unrestricted and restricted open shell based ΔHF, ΔMP2, and ΔB3LYP methods.

Characterisation of the electronic structure of some stable nitroxyl radicals using variable energy photoelectron spectroscopy.

The photoionization of three stable nitroxyl radicals has been studied in the valence and core regions using synchrotron radiation. We observed different variations of the relative band intensities with the photon energy for two pyrrolidine nitroxyls (nitroxyl8 and nitroxyl9) in the valence ionization region. This is due to strong intramolecular interactions between the amide substituent and the ring π-orbital when present.

Non-radiative relaxation of UV photoexcited phenylalanine residues: probing the role of conical intersections by chemical substitution.

A conformation-selective photophysics study in phenylalanine model peptides, combining pump-probe gas phase experiments and excited state calculations, highlights for the first time the quenching properties of a primary amide group (through its nπ* excited state) along with the effect of vibrational energy that facilitates access to the conical intersection area.

An efficient buffer-mediated control between free radical substitution and proton-coupled electron transfer: dehalogenation of iodoethane by the α-hydroxyethyl radical in aqueous solution.

A remarkable buffer-mediated control between free-radical substitution (FRS) and proton-coupled electron transfer (PCET) is demonstrated for the reaction between iodoethane and the α-hydroxyethyl radical in neutral aqueous solution in the presence of bicarbonate or phosphate buffer. The reaction is initiated by the γ-radiolysis of the water solvent, and the products, either the iodine atom (FRS) or anion (PCET), are analysed using ion chromatographic and spectrophotometric techniques. A detailed insight into the mechanism is gained by employing density functional theory (M06-2X), Møller-Plesset perturbation treatment to the second order (MP2), and multireference methods (CASSCF/CASPT2).

Unraveling the mechanisms of nonradiative deactivation in model peptides following photoexcitation of a phenylalanine residue.

The mechanisms of nonradiative deactivation of a phenylalanine residue after near-UV photoexcitation have been investigated in an isolated peptide chain model (N-acetylphenylalaninylamide, NAPA) both experimentally and theoretically. Lifetime measurements at the origin of the first ππ* state of jet-cooled NAPA molecules have shown that (i) among the three most stable conformers of the molecule, the folded conformer NAPA B is ∼50-times shorter lived than the extended major conformer NAPA A and (ii) this lifetime is virtually insensitive to deuteration at the NH(2) and NH sites. Concurrent time-dependent density functional theory (TDDFT) based nonadiabatic dynamics simulations in the full dimensionality, carried out for the NAPA B conformer, provided direct insights on novel classes of ultrafast deactivation mechanisms, proceeding through several conical intersections and leading in fine to the ground state.

Photoinduced dynamics of formic acid monomers and dimers: the role of the double hydrogen bond.

Nonadiabatic dynamics in the framework of time-dependent density functional theory was used to simulate gas-phase relaxation dynamics of pairs of conformations of formic acid monomers (cis and trans FAM) and dimers (acyclic aFAD and cyclic cFAD). In the early phase of the excited state dynamics, elongation of the C═O bond and pyramidalization of the carbon atom is observed in both FAM and FAD. Subsequently, the photodynamics of FAM is shown to be dominated by fragmentation processes occurring mostly in the excited state and resulting in HCO and OH radicals.

QTL mapping using a memetic algorithm with modifications of BIC as fitness function.

The problem of locating quantitative trait loci (QTL) for experimental populations can be approached by multiple regression analysis. In this context variable selection using a modification of the Bayesian Information Criterion (mBIC) has been well established in the past. In this article a memetic algorithm (MA) is introduced to find the model which minimizes the selection criterion.

Quasiclassical trajectory calculations of hydrogen absorption in the (NaAlH4)2Ti system on a model analytical potential energy surface.

We performed a quasiclassical trajectory dynamics study on a model analytical 21-dimensional (7 active atoms) potential energy surface (PES) to examine in detail the mechanism of the hydrogen absorption in a simple (NaAlH(4))(2)Ti model system. The reaction involves a capture of H(2) by the Ti centre and formation of the (η(2)-H(2))Ti(NaAlH(3))(2) coordination complex containing the side-on bonded dihydrogen ligand. The calculated rate constant corresponds to a very fast capture of H(2) by the Ti coordination sphere without a demonstrable barrier.