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  • 1. Bastos, Erick L.
    et al.
    Farahani, Pooria
    Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
    Bechara, Etelvino J. H.
    Baader, Wilhelm J.
    Four‐membered cyclic peroxides: Carriers of chemical energy2017In: Journal of Physical Organic Chemistry, ISSN 0894-3230, E-ISSN 1099-1395, Vol. 30, no 9, article id e3725Article, review/survey (Refereed)
    Abstract [en]

    Four‐membered cyclic peroxides are high‐energy compounds often associated tocold light emission, but whose chemical and biological roles are still matters ofdebate. The often‐dangerous synthesis of 1,2‐dioxetanes, achieved around 50 yearsago, has been mastered over the years to a point where some derivatives are commerciallyavailable. This fact does not imply that 1,2‐dioxetanes can be convenientlyprepared in the gram scale or that the synthesis of analogous 1,2‐dioxetanones andthe elusive 1,2‐dioxetanedione are simple. Important questions on the mechanism ofchemiluminescence and bioluminescence reactions are under experimental and theoreticalscrutiny. The available data have contributed to relate structural and mediumeffects to the quantum efficiency of these compounds to produce excited states.Consequently, such peroxides have been suggested to produce biologically relevantelectronically excited species in vivo in the absence of light. The connection of thishypothesis with melanin‐mediated photodamage in the dark has renewed the interestin such cyclic peroxides. This reviewgives some insight on the synthesis, chemiluminescencemechanism, and biological relevance of 1,2‐dioxetanes, 1,2‐dioxetanones,and 1,2‐dioxetanedione and provides practical protocols for those interested inengaging this field.

  • 2.
    Farahani, Pooria
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical Studies of Solvent Effect on Normal Mode Analysis and Thermodynamic Properties of Zigzag (5, 0) Carbon Nanotube2011In: Fullerenes, nanotubes, and carbon nanostructures (Print), ISSN 1536-383X, E-ISSN 1536-4046, Vol. 19, p. 469-482Article in journal (Refereed)
    Abstract [en]

    Normal mode analysis is an important tool for studying the structure and dynamicsof nanosized systems. The vibrational frequencies obtained can be used to relateobserved spectra to the details of the molecular structure, dynamics and other thermodynamicproperties. It is important to understand the energetic, stability-dependentphysical properties of zigzag (5, 0) carbon nanotube. In this study we have employedsemi-empirical, DFT, molecular mechanic methods. Our results show that the processof introducing (5, 0) carbon nanotube to different dielectrics is energetically comparablein maximum energy; with increasing the dielectric, the energy declines and thestability increases. AM1and PM3 have the same results in the semi-empirical methodand have good agreement relative to each other.

  • 3.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Baader, Wilhelm J.
    Unimolecular Decomposition Mechanism of 1,2-Dioxetanedione: Concerted or Biradical? That is the Question!2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, p. 1189-1194Article in journal (Refereed)
    Abstract [en]

    Determination of the ground- and excited-stateunimolecular decomposition mechanisms of 1,2-dioxetanedionegives a level of insight into bimolecular decomposition reactionsof this kind for which some experimental results are reported.Although a few studies have put some effort to describe abiradical mechanism of this decomposition, there is still no systematic study that proves an existence of a biradical character.In the present study, state-of-the-art high-level multistatemulticonfigurational reference second-order perturbation theorycalculations are performed to describe the reaction mechanismof 1,2-dioxetanedione in detail. The calculations indicate that thedecomposition of this four-membered ring peroxide containingtwo carbonyl carbon atoms occurs in concerted but notsimultaneous fashion, so-called “merged”, contrary to the caseof unimolecular 1,2-dioxetane and 1,2-dioxetanone decompositions where biradical reaction pathways have been calculated. Atthe TS of the ground-state surface, the system enters an entropic trapping region, where four singlet and four triplet manifoldsare degenerated, which can lead to the formation of triplet and singlet excited biradical species. However, these excited specieshave to overcome a second activation barrier for C−C bond cleavage for excited product formation, whereas the ground-stateenergy surface possesses only one TS. Thus our calculations indicate that the unimolecular decomposition of 1,2-dioxetanedioneshould not lead to efficient excited-state formation, in agreement with the lack of direct emission from the peroxyoxalate reaction.

  • 4. Farahani, Pooria
    et al.
    Lundberg, Marcus
    Karlsson, Hans
    Ab initio quantum mechanical calculation of the reaction probability forthe Cl þ PH2Cl ! ClPH2 þ Cl reaction2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed)
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantummolecular dynamics simulations have been performed to study the prototype reactionCl þ PH2Cl ! ClPH2 þ Cl, using one and two-dimensional models. A potential energy surface, showingan energy well for a transition complex, was generated using ab initio electronic structure calculations.The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensionalmodel displays involved resonance structures in the reaction probability. The reaction rate is almosttwo orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energeticerrors in the potential energy surface is estimated to affect the rate by only a factor of two. Thisshows that for these types of reactions it is more important to increase the dimensionality of the modelingthan to increase the accuracy of the electronic structure calculation.

  • 5. Farahani, Pooria
    et al.
    Lundberg, Marcus
    Lindh, Roland
    Roca-Sanjuan, Daniel
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 6. Farahani, Pooria
    et al.
    Maeda, Satoshi
    Francisco, Joseph S.
    Lundberg, Marcus
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, p. 181-190Article in journal (Refereed)
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state ((2)sigma(+)) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (10(8) s(-1)M(-1) at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (10(9) s(-1)M(-1)), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2-3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

  • 7.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Oliveira, Marcelo
    Fdez. Galvan, Ignacio
    Baader, Wilhelm J.
    A combined theoretical and experimental study onthe mechanism of spiro-adamantyl-1,2-dioxetanone decomposition2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, p. 17462-17472Article in journal (Refereed)
    Abstract [en]

    1,2-Dioxetanones have been considered as model compounds for bioluminescence processes. Theunimolecular decomposition of these prototypes leads mainly to the formation of triplet excited stateswhereas in the catalysed decomposition of these peroxides singlet states are formed preferentially.Notwithstanding, these cyclic peroxides are important models to understand the general principles ofchemiexcitation as they can be synthesised, purified and characterised. We report here results ofexperimental and theoretical approaches to investigating the decomposition mechanism of spiroadamantyl-1,2-dioxetanone. The activation parameters in the unimolecular decomposition of thisderivative have been determined by isothermal kinetic measurements (30–70 C) and thechemiluminescence activation energy calculated from the correlation of emission intensities. Theactivation energy for peroxide decomposition proved to be considerably lower than thechemiluminescence activation energy indicating the existence of different reaction pathways for groundand excited state formation. These experimental results are compared with the calculations at thecomplete active space second-order perturbation theory (CASPT2), which reveal a two-step biradicalmechanism starting by weak peroxide bond breakage followed by carbon–carbon elongation. Thetheoretical findings also indicate different transition state energies on the excited and ground statesurfaces during the C–C bond cleavage in agreement with the experimental activation parameters.

  • 8.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Aquilante, Francesco
    A Two-Scale Approach to Electron Correlationin Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, p. 1609-1617Article in journal (Refereed)
    Abstract [en]

    We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environmentis meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposedscheme represent a hierarchical approach to the electroncorrelation problem, where two molecular scales aretreated each by means of the most suitable level of theory.

  • 9.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Frances-Monerris, Antonio
    Fdez. Galvan, Ignacio
    Lindh, Roland
    Liu, Ya-Jun
    Advances in computationalphotochemistry and chemiluminescenceof biological and nanotechnologicalmolecules2017In: Photochemistry / [ed] Elisa Fasani and Angelo Albini, Royal Society of Chemistry, 2017, 44, p. 16-60Chapter in book (Refereed)
    Abstract [en]

    Recent advances (2014–2015) in computational photochemistry and chemiluminescencederive from the development of theory and from the application of state-of-the-art andnew methodology to challenging electronic-structure problems. Method developmentshave mainly focused, first, on the improvement of approximate and cheap methods toprovide a better description of non-adiabatic processes, second, on the modification ofaccurate methods in order to decrease the computation time and, finally, on dynamicsapproaches able to provide information that can be directly compared with experimentaldata, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methodshave given rise to relevant findings in distinct fields of the excited-state chemistry.We brieflysummarise, in this chapter, the achievements on photochemical mechanisms andchemically-induced excited-state phenomena of interest in biology and nanotechnology.

  • 10.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

    Determining the ground and excited-statedecomposition mechanisms of 1,2-dioxetane is essential tounderstand the chemiluminescence and bioluminescencephenomena. Several experimental and theoretical studies hasbeen performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.;Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111,8013−8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O−O′ andC−C′ bond dissociations. New high-level multistate multiconfigurational reference second-order perturbation theory calculations and ab initio molecular dynamics simulations at constant temperature are performed in the present study, which provide further details on the mechanisms and allow to rationalize further experimental observations. In particular, the new results explain the high ratio of triplet to singlet dissociation products.

  • 11.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vacher, Morgane
    Valentini, Alssio
    Frutos, Luis M.
    Fdez. Galvan, Ignacio
    Karlsson, Hans
    Lindh, Roland
    How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield ofDioxetane?2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, p. 3790-3794Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence is the emission of light as aresult of a nonadiabatic chemical reaction. The present work isconcerned with understanding the yield of chemiluminescence,in particular how it dramatically increases upon methylation of1,2-dioxetane. Both ground-state and nonadiabatic dynamics(including singlet excited states) of the decomposition reactionof various methyl-substituted dioxetanes have been simulated.Methyl-substitution leads to a significant increase in thedissociation time scale. The rotation around the O−C−C−Odihedral angle is slowed; thus, the molecular system stayslonger in the “entropic trap” region. A simple kinetic model isproposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the designof efficient chemiluminescent systems in medical, environmental, and industrial applications.

  • 12.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yagoobi Nia, Narges
    Sabzyan, Hassan
    Zendehdel, Mahmoud
    Oftadeh, Mohsen
    A combined computational and experimental study of the [Co(bpy)3]2+/3+ complexesas one-electron outer-sphere redox couplesin dye-sensitized solar cell electrolyte media2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, p. 11481-11491Article in journal (Refereed)
    Abstract [en]

    A combined experimental and computational investigation conducted to understand the nature of theinteractions between cobalt II/III redox mediators ([Co(bpy)3]2+/3+) and their impact on the performanceof the corresponding dye-sensitized solar cells (DSCs) is reported. The fully optimized equilibriumstructures of cobalt(II/III)-tris-bipyridine complexes in the gas phase and acetonitrile solvent are obtainedby the density functional B3LYP method using LanL2DZ and 6-31G(d,p) basis sets. The harmonicvibrational frequencies, infrared intensities and Raman scattering activities of the complexes are alsocalculated. The scaled computational vibrational wavenumbers show very good agreement with theexperimental values. Calculations of the electronic properties of the complexes are also performed atthe TD-B3LYP/6-31G(p,d)[LanL2DZ] level of theory. Detailed interpretations of the infrared and Ramanspectra of the complexes in different phases are reported. Detailed atomic orbital coefficients of thefrontier molecular orbitals and their major contributions to electronic excitations of the complexes arealso reported. These results are in good agreement with the experimental electrochemical values.Marcus diagram is derived for the electron transfer reaction Co(II) + D35+ - Co(III) + D35 using theCo–N bond length as a reaction coordinate.

  • 13.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zendehdel, Mahmoud
    Yaghoobi Nia, Narges
    Nasr-Esfahani, Mojtaba
    Karbaschi, Mohamad Reza
    A combined computational and experimental study on the hydrogen bonding with chloride ion in a crab-claw like site of a new chromium Schiff base complex2016In: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 44, p. 150-161Article in journal (Refereed)
    Abstract [en]

    A combined experimental and computational study to understand the nature of the hydrogen bonding ina crab-claw site of a new synthesized chromium Schiff base complex is reported. The fully optimizedequilibrium structures of the Cr(III) complex in the presence and absence of chloride ion are obtainedat the B3LYP functional in conjunction with LanL2DZ basis set. The crystal structure of the chromiumSchiff base complex consists of [CrL2]+ cation, in which L is a tridentate Schiff base ligand with full nameof N-(2-(2-hydroxyethylamino)ethyl)5-methoxysalicylideneimine, and a chloride anion, in the asymmetricunit. The chromium(III) cation possesses a distorted octahedral geometry, coordinated with four nitrogenand two phenoxo oxygen atoms derived from two chelate Schiff base ligands. The harmonicvibrational frequencies, infrared intensities and Raman scattering activities of the complexes are alsoreported. The scaled computational geometry and vibrational wavenumbers are in very good agreementwith the experimental values of single crystal X-ray diffraction and FT-IR, respectively. The electronicproperties calculations of the complexes are also performed at the TD-B3LYP/LanL2DZ level of theory.The spectroscopic excitation parameters obtained for frontier molecular orbitals of the complexes arereported as well. These findings are in good agreement with the experimental UV–Vis diffuse-reflectancespectroscopy. Parabolic diagrams are derived for the chloride insertion and hydrogen bonding in thecrab-claw site with the average optimized H H distances of the effective hydrogen atoms in the crabclawsite as reaction coordinate.

  • 14. Giussani, Angelo
    et al.
    Farahani, Pooria
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Martinez-Munoz, Daniel
    Lundberg, Marcus
    Lindh, Roland
    Roca-Sanjuan, Daniel
    Molecular Basis of the Chemiluminescence Mechanism of Luminol2019In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed)
    Abstract [en]

    Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

1 - 14 of 14
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