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  • 1.
    Erdtman, Edvin
    et al.
    Örebro University, School of Science and Technology.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University Ireland (NUI) Galway, Galway, Ireland.
    Computational insights into the mechanism of porphobilinogen synthase2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 50, p. 16860-16870Article in journal (Refereed)
    Abstract [en]

    Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

  • 2. Li, Xin
    et al.
    Rinkevicius, Zilvinas
    Tu, Yaoquan
    Örebro University, School of Science and Technology.
    Tian, He
    Ågren, Hans
    Nuclear magnetic shielding of 113Cd(II) ion in aqua solution: a combined molecular dynamics/density functional theory study2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, p. 11347-11352Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the 113Cd(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium−water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in 113Cd NMR experiments, due to the mutual cancelation between individual relativistic corrections.

  • 3. Li, Xin
    et al.
    Rinkevicius, Zilvinas
    Tu, Yaoquan
    Örebro University, School of Science and Technology.
    Tian, He
    Ågren, Hans
    Paramagnetic Perturbation of the 19F NMR Chemical Shift in Fluorinated Cysteine by O2: A Theoretical Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, p. 10916-10922Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the 19F NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O2 partial pressure. Molecular dynamics simulations are carried out to determine the dominant structures of O2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of 19F chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the 19F NMR chemical shifts, where the Fermi contact interaction plays the key role. The O2-induced paramagnetic 19F chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling 19F NMR chemical shifts in the presence of paramagnetic agents in an aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including 1H, 13C, 15N, and 19F is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

  • 4.
    Matxain, Jon M.
    et al.
    Euskal Herriko Unibertsitatea.
    Padro, Daniel
    Euskal Herriko Unibertsitatea.
    Ristilä, Mikael
    Örebro University, School of Science and Technology.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology.
    Evidence of High dot OH Radical Quenching Efficiency by Vitamin B-62009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 29, p. 9629-9632Article in journal (Refereed)
    Abstract [en]

    Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of the utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. Previous theoretical calculations have shown a high reactivity of pyridoxine toward hydroxyl radicals, where the latter preferably abstract H from either carbon of the two methanol substituents (C8 or C9). In this study, we have explored the reactivity of pyridoxine toward further hydroxyl radicals, considering as the first step the H abstraction from either C8 or C9, also including addition reactions and cyclization. Many of the reactions display similar ΔG, and hence, the quenching of hydroxyl radicals by pyridoxine may undergo different pathways leading to a mix of products. In addition, we observe that pyridoxine, under high hydroxyl radical concentrations, may scavenge up to eight radicals, supporting its observed high antioxidant activity.

  • 5.
    Musa, Klefah A. K.
    et al.
    Örebro University, School of Science and Technology.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology.
    Photodegradation Mechanism of Nonsteroidal Anti-Inflammatory Drugs Containing Thiophene Moieties: Suprofen and Tiaprofenic Acid2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 32, p. 11306-11313Article in journal (Refereed)
    Abstract [en]

    The photodegradation of nonsteroid anti-inflammatory drugs suprofen, 2-[4-(2-thienoyl)phenyl]propionic acid, and tiaprofenic acid, 2-(5-benzoyl-2-thienyl)propanoic acid, is studied by means of density functional theory. Besides the redox properties of the neutral species, we report on absorption spectra and degradation pathways involving excitation, intersystem crossing to the T-1 state. and spontaneous decarboxylation of the deprotonated species of each drug. The energetics and properties of the suprofen and tiaprofenic acid systems are found to be very similar to those of the highly photolabile benzyl analogue ketoprofen. Mechanisms leading to the formation of a closed-shell decarboxylated ethyl species, as well as peroxyl radicals capable of initiating lipid peroxidation reactions, are discussed.

  • 6.
    Musa, Klefah A. K.
    et al.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical assessment of naphazoline redoxchemistry and photochemistry2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 15, p. 3977-3981Article in journal (Refereed)
    Abstract [en]

    The imidazoline derivative naphazoline (2-(1-naphtylmethyl)-2-imidazoline) is an α2-adrenergic agonist used as non-prescription eye and nasal preparations. Besides its functionality in generating vascoconstriction and decongestion in the patient, the toxicity, ROS generating capability, and recently also possible antioxidant capacity of the compound have been reported in the literature. In the current work the structural and electronic features of the drug are explored, using computational chemical tools. Electron affinities, ionization potentials, and excitation energies are reported, as well as charge and spin distributions of various forms of the drug. The difference in photochemical behavior between the protonated and unprotonated (basic) species is explained by the molecular orbital distributions, allowing for efficient excitation quenching in the basic structure but clear naphthalene to imidazolene charge transfer upon HOMO→ LUMO excitation in the protonated form, enabling larger intersystem crossing capability to the imidazole localized excited triplet and a resulting higher singlet oxygen quantum yield.

  • 7.
    Musa, Klefah A. K.
    et al.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical Study of Ibuprofen Phototoxicity2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 46, p. 13345-13352Article in journal (Refereed)
    Abstract [en]

    The photochemical properties and degradation of the common nonsteroid anti-inflammatory drug ibuprofen is studied by means of hybrid density functional theory. Computed energies and properties of various species show that the deprotonated form dominates at physiological pH, and that the species will not be able to decarboxylate from a singlet excited state. Instead, decarboxylation will occur, with very high efficiency, provided the deprotonated compound can undergo intersystem crossing from an excited singlet to its excited triplet state. In the triplet state, the C−C bond connecting the carboxyl group is elongated, and the CO2 moiety detaches with a free energy barrier of less than 0.5 kcal/mol. Depending on the local environment, the decarboxylated product can then either be quenched through intersystem crossing (involving the possible formation of singlet oxygen) and protonation, or serve as an efficient source for superoxide anions and the formation of a peroxyl radical that will initiate lipid peroxidation.

  • 8.
    Ristilä, Mikael
    et al.
    Örebro University, Department of Natural Sciences.
    Matxain, Jon M.
    Strid, Åke
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    pH-dependent electronic and spectroscopic properties of pyridoxine (vitamin B6)2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 33, p. 16774-16780Article in journal (Refereed)
    Abstract [en]

    The key electronic and spectroscopic properties of vitamin B6 (pyridoxine) and some of its main charged and protonated/deprotonated species are explored using hybrid density functional theory (DFT) methods including polarized solvation models. It is found that the dominant species at low pH is the N1-protonated form and, at high pH, the O3¢-deprotonated compound. Computed and experimental UV-spectra for these species (experimental spectra recorded at pH 1.7 and 11.1, respectively) show a very close resemblance. At pH 4.3, the protonated species dominates, but with onset of the zwitterionic oxo form which is also the dominant species at neutral pH. The computational studies furthermore show that neither a polarized continuum model of the polar aqueous solvent or explicit hydrogen bonding through additional water molecules are sufficient to describe accurately the spectrum at physiological pH. Instead, Na+ and Cl- counterions were required to give a blue-shift of approximately 0.15 eV.

  • 9.
    Róg, Tomasz
    et al.
    Department of Physics, Tampere University of Technology, Temrpere, Finland.
    Martinez-Seara, Hector
    Department of Physical Chemistry, Barcelona University, Spain.
    Munck, Nana
    VTT Technical Research Centre of Finland, Espoo, Finland.
    Oresic, Matej
    VTT Technical Research Centre of Finland, Espoo, Finland.
    Karttunen, Mikko
    Department of Applied Mathematics, UniVersity of Western Ontario, London (ON), Canada.
    Vattulainen, Ilpo
    Department of Physics, Tampere University of Technology, Temrpere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense M, Denmark; Helsinki University of Technology, Finland.
    Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 11, p. 3413-3422Article in journal (Refereed)
    Abstract [en]

    Mitochondrial membranes are unique in many ways. Unlike other cellular membranes, they are comprised of two membranes instead of just one, and cardiolipins, one of the abundant lipid species in mitochondrial membranes, are not found in significant amounts elsewhere in the cell. Among other aspects, the exceptional nature of cardiolipins is characterized by their small charged head group connected to typically four hydrocarbon chains. In this work, we present atomic-scale molecular dynamics simulations of the inner mitochondrial membrane modeled as a mixture of cardiolipins (CLs), phosphatidylcholines (PCs), and phosphatidylethanolamines (PEs). For comparison, we also consider pure one-component bilayers and mixed PC-PE, PC-CL, and PE-CL membranes. We find that the influence of CLs on membrane properties depends strongly on membrane composition. This is highlighted by studies of the stability of CL-containing membranes, which indicate that the interactions of CL in ternary lipid bilayers cannot be deduced from the corresponding ones in binary membranes. Moreover, while the membrane properties in the hydrocarbon region are only weakly affected by CLs, the changes at the membrane-water interface turn out to be prominent. The effects at the interface are most evident in membrane properties related to hydrogen bonding and the binding phenomena associated with electrostatic interactions.

  • 10. Schyman, Patric
    et al.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology.
    Laaksonen, Aatto
    Hydrogen Abstraction from Deoxyribose by a Neighboring 3 '-Uracil Peroxyl Radical2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 18, p. 6574-6578Article in journal (Refereed)
    Abstract [en]

    Theoretical examination of the reactivity of the uracil-5-peroxyl radical when abstracting a hydrogen atom from a neighboring 5'-deoxyribose in 5'-ApU-5-peroxyl-3' has been performed using density functional theory with the MPWB1K functional. Halogenated uracils are often used as radiosensitizers in DNA since the reactive uracil-5-yl radical is formed upon radiation and is known to create strand break and alkali-labile sites. Under aerobic conditions, such as in the cell, it has been proposed that the uracil-5-peroxyl radical is formed and would be the damaging agent. Our results show low reactivity for the uracil-5-peroxyl radical, determined by calculating the activation and reaction energies for the plausible hydrogen abstraction sites C1', C2' and C3' of the neighboring 5'-deoxyribose. These findings support the hypothesis that hydrogen abstraction primarily occurs by the uracil-5-yl radical, also under aerobic conditions, prior to formation of the peroxyl radical.

  • 11. Sebastian, Eider San
    et al.
    Matxain, Jon M.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Stote, Roland H.
    Dejaegere, Annick
    Cossio, Fernando P.
    Lopez, Xabier
    Metal ion dependent adhesion sites in integrins: A Combined DFT and QMC Study on Mn2+2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 30, p. 9099-9103Article in journal (Refereed)
    Abstract [en]

    The theoretical study of relative energies of different spin states of Mn2+ has been carried out for the isolated cation and for structures in which the cation is coordinated to ligands that represent the first coordination shell in a protein environment that contains a metal ion dependent adhesion site (MIDAS, found in the ligand binding domain of protein LFA-1). The calculations determine whether the ligand field generated by a prototype protein environment affects the relative energies between high, intermediate, and low spin states. Geometry optimizations and vibrational frequency calculations were carried out at the B3LYP/SKBJ+* level of theory. Single point calculations were performed at the B3LYP/6-311++G(2df,2p) and diffusion monte carlo (DMC) levels for the refinement of the electronic energies. These calculations reveal important differences in the relative energies between high/low spin complexes obtained by B3LYP and DMC and show that although both DFT and DMC show similar trends, a higher level method such as DMC is necessary for a quantitative description of the interactions between Mn2+ and its natural ligands. (G)s of acetate-type ligand binding reactions were calculated that show that the higher the spin of the manganese complex, the lower the affinity for the ligand.

  • 12. Tejero, Ismael
    et al.
    Gonzalez-Lafont, Angels
    Lluch, José M.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 20, p. 5684-5693Article in journal (Refereed)
    Abstract [en]

    The OH-radical-induced mechanism of lipid peroxidation, involving hydrogen abstraction followed by O2 addition, is explored using the kinetically corrected hybrid density functional MPWB1K in conjunction with the MG3S basis set and a polarized continuum model to mimic the membrane interior. Using a small nonadiene model of linoleic acid, it is found that hydrogen abstraction preferentially occurs at the mono-allylic methylene groups at the ends of the conjugated segment rather than at the central bis-allylic carbon, in disagreement with experimental data. Using a full linoleic acid, however, abstraction is correctly predicted to occur at the central carbon, giving a pentadienyl radical. The Gibbs free energy for abstraction at the central C11 is 8 kcal/mol, compared to 9 kcal/mol at the end points (giving an allyl radical). Subsequent oxygen addition will occur at one of the terminal atoms of the pentadienyl radical fragment, giving a localized peroxy radical and a conjugated butadiene fragment, but is associated with rather high free energy barriers and low exergonicity at the CPCM-MPWB1K/MG3S level. The ZPE-corrected potential energy surfaces obtained without solvent effects, on the other hand, display considerably lower barriers and more exergonic reactions.

  • 13.
    Tian, Boxue
    et al.
    National University of Ireland, Galway, Ireland.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A.
    National University of Ireland, Galway, Ireland.
    Catalytic roles of active-site residues in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase: an ONIOM/DFT study2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 8, p. 1918-1926Article in journal (Refereed)
    Abstract [en]

    The catalytic mechanism of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) oxygenase (MHPCO) has been systematically studied using DFT and ONIOM(DFT:MM) methods. MHPCO catalyzes the hydroxylation and subsequent ring-opening of the aromatic substrate MHPC to give the aliphatic product R-(N-acetylaminomethylene)succinic acid (AAMS). Our calculations show that the active-site residues Arg211 and Tyr223 have a minor effect on the reaction, while the peptide bond of Pro295-Ala296, the side chain of Tyr82 and several crystal water molecules affect the reaction energy profile considerably. Both DFT and ONIOM calculations show that the ring-opening pathway B, in which an epoxy transition state is formed, is more favored than the direct C2-C3 cleavage pathway A. Different QM/MM partitioning schemes have been used to study the enzymatic reaction, and the results show that both the reaction barriers for the hydroxylation and the ring-opening pathways are sensitive to the QM/MM partitioning.

  • 14.
    Wang, Ran
    et al.
    Inst Chem Phys, Sch Sci, Beijing Inst Technol, Beijing, Peoples R China.
    Zhang, Ru Bo
    Inst Chem Phys, Sch Sci, Beijing Inst Technol, Beijing, Peoples R China.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology. Sch Chem, Natl Univ Ireland, Galway, Ireland.
    The fate of H atom adducts to 3'-Uridine Monophosphate2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 29, p. 9617-9621Article in journal (Refereed)
    Abstract [en]

    The stabilities of the adducts deriving from H free radical addition to the O2, O4, and C5 positions of 3'-uridine monophosphate (3'UMP) are studied by the hybrid density functional B3LYP approach. Upon H atom addition at the O2 position, a concerted low-barrier proton-transfer process will initially occur, followed by the potential ruptures of the N-glycosidic or beta-phosphate bonds. The rupture barriers are strongly influenced by the rotational configuration of the phosphate group at the 3' terminal, and are influenced by bulk solvation effects. The O4-H adduct has the highest thermal stability, as the localization of the unpaired electron does not enable cleavage of either the C1'-N1 or the C3'-O(P) bonds. For the most stable adduct, with H atom added to the C5 position, the rate-controlled step is the H2'a abstraction by the C6 radical site, after which the subsequent strand rupture reactions proceed with low barriers. The main unpaired electron densities are presented for the transient species. Combined with previous results, it is concluded that the H atom adducts are more facile to drive the strand scission rather than N-glycosidic bond ruptures within the nucleic acid bases.

  • 15.
    Wu, Min
    et al.
    Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A
    Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
    Photochemical reaction mechanism of UV-B-induced monomerization of UVR8 dimers as the first signaling event in UV-B-regulated gene expression in plants2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, p. 951-965Article in journal (Refereed)
    Abstract [en]

    The Arabidopsis thaliana UV RESISTANCE LOCUS8 (UVR8) protein has been identified to specifically mediate photomorphogenic UV-B responses by acting as a UV-B photoreceptor. The dimeric structure of the UVR8 protein dissociates into signaling–active monomers upon UV-B exposure, and the monomers rapidly interact with downstream signaling components to regulate gene expression. UVR8 monomers revert to dimers in the absence of UV-B radiation, thereby reversing transcription activation. UVR8 amino acid residues W233 and W285 have been identified to play critical roles in the UVR8 dimer for the response to UV-B irradiation. In the present work, the photo-reaction mechanism for UVR8 monomerization is explored using quantum chemical cluster calculations, and evaluated by molecular dynamics simulations using the wild type UVR8 dimer and novel force field parameters developed for intermediate radicals formed in the photochemical process. Three different models are investigated, which show that the preferred mechanism for UVR8 monomerization involves electron transfer from residue W233 to W285 and onwards to R338 initiated by UV-B irradiation, coupled to simultaneous proton transfer from W233 to D129 leading to the formation of protonated D129, a deprotonated W233 radical and a neutral R338 radical.. Due to the formation of the neutral R338 radical, salt bridges involving this residue are disrupted together with the concomitant interruption of several other key salt bridges R286-D96, R286-D107, R338-D44, R354-E43 and R354-E53. The resulting large decrease in protein-protein interaction energy arising from this sequence of events lead to the monomerization of the UVR8 dimer. The mechanism presented is in accord with all experimental data available to date.

  • 16.
    Zhang, Qiong
    et al.
    AlbaNova Univ Ctr, Dept Theoret Chem, Royal Inst Technol, Stockholm, Sweden; Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Tu, Yaoquan
    Örebro University, School of Science and Technology.
    Tian, He
    Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Zhao, Yanli
    Dept Chem, Northwestern Univ, Evanston IL, USA.
    Stoddart, Fraser J.
    Dept Chem, Northwestern Univ, Evanston IL, USA.
    Ågren, Hans
    AlbaNova Univ Ctr, Dept Theoret Chem, Royal Inst Technol, Stockholm, Sweden; Adv Mat Lab, E China Univ Sci & Technol, Shanghai, Peoples R China; Inst Fine Chem, E China Univ Sci & Technol, Shanghai, Peoples R China.
    Working mechanism for a redox switchable molecular machine based on cyclodextrin: a free energy profiles approach2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 19, p. 6561-6566Article in journal (Refereed)
    Abstract [en]

    This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.

  • 17. Zhang, Ru bo
    et al.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Effects of OH radical addition on proton transfer in the guanine-cytosine base pair2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 23, p. 6571-6576Article in journal (Refereed)
    Abstract [en]

    Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.

  • 18. Zhao, Ke
    et al.
    Tu, Yaoquan
    Örebro University, School of Science and Technology.
    Luo, Yi
    Molecular dynamics and quantum chemistry study on conformations and optical properties of hydrogen bonded dipolar merocyanine dyes2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 30, p. 10271-10276Article in journal (Refereed)
    Abstract [en]

    An earlier proposed strategy to orient two merocyanine dyes in the desirable head-to-tail parallel fashion through multiple hydrogen bonds has been examined by molecular dynamics simulations and quantum chemical calculations. Two different merocyanine dyes dissolved in chloroform solution under various conditions are simulated by molecular dynamics. It is found that two dipolar units can be well connected through various numbers of hydrogen bonds. Although the probability to form the desirable head-to-tail dimer is unfortunately small even under strong poling electric field and low temperature, the formation of unwanted antiparallel structure has been effectively reduced. Typical hydrogen bonded dimers obtained from molecular dynamics simulations have been studied by hybrid density functional calculations. It is found that only the most probable complex can lead to the optical absorption spectrum that is in close agreement with the corresponding experiments. Calculated results for dipole moments of ground and charge transfer states, as well as first hyperpolarizabilities, of three typical complexes have also been provided.

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