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  • 1. Adnan, Muhammad
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Hussain, Riaz
    Akhtar, Muhammad Nadeem
    Rashid, Muhammad Abid
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ayub, Khurshid
    Fine Tuning the Optoelectronic Properties of Triphenylamine Based Donor Molecules for Organic Solar Cells2017Ingår i: Zeitschrift fur physikalische Chemie (Munchen. 1991), ISSN 0942-9352, Vol. 231, nr 6, s. 1127-1139Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Geometrical parameters, electronic structures and photophysical properties of three new triphenylamine (TPA) and diphenylamine (DPA) based electron donor materials M1-M3 (for organic solar cells) have been investigated through density functional theory (DFT) methods at the B3LYP/6-31G(d) level of the theory. TPA and DPA are used as donor moieties due to their electron donating ability while benzothiazole, cyanide and cyanomethylacetate (CMA) moieties have been taken as acceptor moieties. The time dependent-DFT (TD-DFT) method has been employed [TD-B3LYP/6-31G (d)] for the computation of excited state properties in the gas phase and in solvent (chloroform). The polarization continuum model is applied for calculations in the solvent phase. The designed molecules exhibited broad absorption in the visible and near infra-red region of spectrum with respect to a reference molecule "R" of a similar class of compounds. Based on reorganization energies calculations, these materials could act as excellent hole transport materials.

  • 2. Andrew, Rhiann E.
    et al.
    Ferdani, Dominic W.
    Ohlin, C. Andre
    Chaplin, Adrian B.
    Coordination Induced Atropisomerism in an NHC-Based Rhodium Macrocycle2015Ingår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 34, nr 5, s. 913-917Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reversible interaction with carbon monoxide results in the onset of dynamic atropisomerism at 298 K in an otherwise static NHC-based rhodium pincer complex, [Rh(C boolean AND N boolean AND C-(CH2)(12))(CO)][BArF4] (1, ArF = 3,5-C6H3(CF3)(2)). The mechanism of this process has been comprehensively interrogated by a combination of variable-temperature NMR spectroscopy, IR spectroscopy, and computational modeling. In addition, a structural analogue of a high-energy symmetrical intermediate species-invoked in the process but not directly observed spectroscopically-has been prepared and characterized in solution and the solid-state.

  • 3. Ans, Muhammad
    et al.
    Iqbal, Javed
    Ahmad, Zahoor
    Muhammad, Shabbir
    Hussain, Riaz
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ayub, Khurshid
    Designing Three‐dimensional (3D) Non‐Fullerene Small Molecule Acceptors with Efficient Photovoltaic Parameters2018Ingår i: ChemistrySelect, ISSN 2365-6549, Vol. 3, nr 45, s. 12797-12804Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Three dimensional (3D) acceptor‐donor‐acceptor (A−D‐A) type small molecules (M1, M2, M3 and M4) are theoretically investigated for optoelectronic properties. The designed molecules contain spirobifluorene as core unit linked with end capped acceptors through four four thieno‐[3,2‐b]Thiophene (TT) units. The end capped acceptors are (3‐methyl‐2‐thioxothiazolidin‐4‐one) (M1), 2‐(2‐ethylidene‐5,6‐difluoro‐3‐oxo‐2,3‐dihydroinden‐1‐ylidene)malononitrile (M2), 2‐(3‐ethyl‐4‐oxothiazolidin‐2‐ylidine)malononitrile (M3) and 2‐(2‐ethylidene‐5,6‐dicyano‐3‐oxo‐2,3‐dihydroinden‐1‐ylidene)malononitrile (M4). The photovoltaic parameters of the designed molecules are compared with the recently reported reference compound R. Among all designed molecules, M4 is a low energy gap material (2.28 eV), broad absorption which is attributed to excellent communication between strong electron withdrawing end capped acceptors through extended conjugation. All newly designed molecules have lower binding energy as compared to reference molecule R which results in higher exciton dissociation in excited state. The reorganization energy calculations indicate good charge transfer ability of the designed molecules. M4 shows the lowest λe (0.0022) value with respect to the reference molecule R (0.034) which signifies its enhanced electronic transport behavior. The calculated open circuit voltages (Voc) ranges from 1.97 to 2.36 eV, 2.11 to 2.49 eV and 1.9 eV to 2.28 eV with respect to three different well known donor materials PTB7‐Th, PBDB−T and P3HT, respectively.

  • 4. Ans, Muhammad
    et al.
    Iqbal, Javed
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Saif, Muhammad Jawwad
    Ayub, Khurshid
    Opto-electronic properties of non-fullerene fused-undecacyclic electron acceptors for organic solar cells2019Ingår i: Computational materials science, ISSN 0927-0256, E-ISSN 1879-0801, Vol. 159, s. 150-159Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Due to limitations of fullerene based acceptor molecules for solar cell applications, research is recently diverted to explore non-fullerene acceptor molecules. In this regard, four new A-D-A type fused ring electron acceptor molecules (M1, M2, M3 and M4) are evaluated for their opto-electronic properties for transparent organic solar cells. These molecules contain strong electron donor undecacyclic linked with four different acceptor moieties, 2-(3-ethly-5-methylene-4-oxothiazolidin-2-yluidene)malononitrile (M1), 2-(5,6-dicyano-2-methylene-3-oxo -2,3-dihydroindene-1-ylidene)malononitrile (M2), 2-(5-methylene-6-oxo-tetrahydro-1H-cyclopenta-thiophene-4(5H)-ylidene)malononitrile (M3), and 3-ethyl-5-methylene-2-thioxothiazolidin-4-one (M4). The electronic and optical properties of these molecules are compared with the reference molecule R, which is recently reported as excellent non-fullerene based acceptor molecule. Among all molecules, M2 exhibits the maximum red shift where absorption appears 893.5 nm with B3LYP/6-31 + + G(d,p) level of theory due to highly extended conjugation between electron withdrawing end-capped acceptor moieties. The calculated Open circuit voltage (V-oc) of reference molecule R is 1.78 eV with donor polymer PTB7-Th while molecule M2 exhibits the V-oc value of 1.86 eV.

  • 5.
    Barzegar, Hamid Reza
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Gracia-Espino, Eduardo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sharifi, Tiva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Nitze, Florian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Wågberg, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Nitrogen Doping Mechanism in Small Diameter Single-Walled Carbon Nanotubes: Impact on Electronic Properties and Growth Selectivity2013Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, nr 48, s. 25805-25816Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nitrogen doping in carbon nanostructures has attracted interest for more than a decade, and recent implementation of such structures in energy conversion systems has boosted the interest even more. Despite numerous studies, the structural conformation and stability of nitrogen functionalities in small diameter single-walled carbon nanotubes (SWNTs), and the impact of these functionalities on the electronic and mechanical properties of the SWNTs, are incomplete. Here we report a detailed study on nitrogen doping in SWNTs with diameters in the range of 0.8?1.0 nm, with well-defined chirality. We show that the introduction of nitrogen in the carbon framework significantly alters the stability of certain tubes, opening for the possibility to selectively grow nitrogen-doped SWNTs with certain chirality and diameter. At low nitrogen concentration, pyridinic functionalities are readily incorporated and the tubular structure is well pertained. At higher concentrations, pyrrolic functionalities are formed, which leads to significant structural deformation of the nanotubes and hence a stop in growth of crystalline SWNTs. Raman spectroscopy is an important tool to understand guest atom doping and electronic charge transfer in SWNTs. By correlating the influence of defined nitrogen functionalities on the electronic properties of SWNTs with different chirality, we make precise interpretation of experimental Raman data. We show that the previous interpretation of the double-resonance G?-peak in many aspects is wrong and instead can be well-correlated to the type of nitrogen doping of SWNTs originating from the p- or n-doping nature of the nitrogen incorporation. Our results are supported by experimental and theoretical data.

  • 6. Das, Susanta
    et al.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry and Biochemistry, University of Texas at Arlington, United States.
    Major, Dan Thomas
    Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA2018Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, nr 3, s. 1695-1705Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

  • 7.
    Huang, Yang
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Analysis of NMR Spin-lattice Relaxation Dispersion on Complex Systems2015Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis focus on the analysis of spin-lattice NMRD relaxation profilesmeasured in various complex systems such as proteins, zeolites and ionicliquids. Proton, deuterium and fluoride T1-NMRD relaxation profiles wereobtained from a fast-field cycling (FFC) instrument. It is found that alsopossible to obtain NMRD profiles from the molecular dynamics (MD)simulation trajectories. NMRD Profiles were analyzed by using differentrelaxation models, such as the Solomon-Bloembergen-Morgan (SBM) theoryand the Stochastic Liouville (SL) theory.

    Paper I described the hydration of protein PrxV obtained from a MDsimulation, and compared with the picture emerges from an analysis byusing a generally accepted relaxation model [appendix C]. The result showsthat the information from NMRD analysis is an averaged picture of watermolecules with similar relaxation times; and the MD simulations containsinformation of all types of interested water molecules with differentresidence times.

    In paper II NMRD profiles have been used to characterize the hydration ofthe oxygen-evolving complex in state S1 of photosystem II. NMRDexperiments were performed on both intact protein samples and Mndepletedsamples, and characteristic dispersion difference were foundbetween 0.03 MHz to 1 MHz; approximately. Both the SBM theory and theSL theory have been used to explain this dispersion difference, and it isfound that this is due to a paramagnetic enhancement of 1-2 water moleculesnearby ~10 Å from the spin center of the Mn4CaO5 cluster. The result showsthe reorientation of the molecular cluster is in μs time interval. Whencompare these two theories, the SL theory presented a better interpretationbecause parameters obtained from the SBM theory shows they didn’t fulfilthe presupposed perturbation criterion (the Kubo term).

    Paper III deals with the water dynamics in the restricted/confined spaces inthe zeolite samples (H-ZSM-5 and NH4-ZSM-5) and obtained by proton anddeuterium spin-lattice NMRD profiles. The results show that the spin-latticeNMRD can be used to characterize various zeolites. The temperature has aweak effect on the relaxation rate R1, but the change of different counter ionsmay change the hydration and the translational diffusion pores and givedifferent R1.

    Proton and fluoride NMRD profiles and MD simulations were both used tostudy the dynamics of BMIM[PF6] in paper IV. Results indicate the reorientation of the molecules are in the ns time regime, and the effectivecorrelation time obtained from 1H and 19F are the same. From the MDsimulation it is found the reorientation of [PF6]- ions is much faster (in ps)compare with BMIM+ ion which moves in the ns time range.

    With previous results, the FFC NMRD profiles are indeed very informativetools to study the molecular dynamics of complex systems. The MDsimulation can be used as a complementary method to obtain detailedinformation. By combine these two methods, it provide a more colorfulpicture in the study of protein hydration and liquid molecular dynamics.

  • 8.
    Huang, Yang
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Siljebo, William
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Westlund, Per-Olof
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Water proton and deuterium spin-lattice relaxation in Zeolite ZSM-5 by fast field-cycling NMR relaxometry2015Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    The water dynamics in the confined space of the zeolite ZSM-5 has bee ninvestigated by means of the field dependence of 1H- and 2H- spin-lattice relaxation rates using a 1T Stelar FFC2000 fast field-cycling instrument. The NMRD analysis of  the experimental results indicates that the characteristic time dependence ( 50 ns to 1-2.4 μs) is due to water translational diffusion in narrow pores. The temperature dependence of the spin-lattice relaxation rates is weak.Zeolites with different counter ions( H+, NH4+ change the water hydration and the water translational diffusion in the pores drastically. The Zeolite-NH4+ slow down the water motion with a factor of 2.The NMRD profiles show somewhat stretched character and is described by two Lorenzian which indicates that the distribution of pore sizes is broaden.The water 1H and 2H spin lattice relaxation profiles give qualitatively information about water hydration in zeolites with different counter ions and is expected also to indicate structural changes of the zeolites. 

  • 9.
    Huang, Yang
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sparrman, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wang, Young-lei
    Laaksonen, Aatto
    Arrhenius Laboratory, Stockholm University, Sweden .
    Westlund, Per-Olof
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Analysis of proton/fluoride spin-lattice NMR dispersion experiment of an ionic liquid, BMIM[PF6] by using molecular dynamics simulations and relaxation theory2015Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Proton/Fluoride spin-lattice nuclear magnetic relaxation dispersion(NMRD) measurements of 1-Butyl-3-methylimidazolium-hexa fluorophosphate (BMIM[PF6])have been carried out using a 1T Stelar FFC2000 fast-field-cycling instrument at proton Larmor frequencies ranging from 10 kHz to 40 MHz and at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation modelbased on the inter- and intra-molecular dipole dipole relaxation mechanims. Using an atomic and a coarse-grained (CG)Molecular Dynamics (MD) simulations at temperature 323 K the relevant dipole-dipole correlation functions are calculated. The result indicate that the NMRD profiles can be rationalized using a combination of intra and inter molecular dipole-dipole couplings. However, both are mainly modulated by molecular reorientation whereas translation diffusion plays a minor role. The molecular reorientation dynamics  of BMIM[PF6] ,BMIM+ ion are in the nano secondtime regime whereas the reorientation of  [PF6]- is much faster and loses its correlation in the ps regime. The relaxation mechanism for  [PF6]- is H-F inter-molecular dipole-dipole coupling which is modulated by the reorientation of  the H-containing molecule.

  • 10. Irfan, Muhammad
    et al.
    Iqbal, Javed
    Sadaf, Sana
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Rana, Usman Ali
    Ud-din Khan, Salah
    Ayub, Khurshid
    Design of donor-acceptor-donor (D-A-D) type small molecule donor materials with efficient photovoltaic parameters2017Ingår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 117, nr 10, artikel-id e25363Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Four Donor-Acceptor-Donor (D-A-D) type of donor molecules (M1-M4) with triphenylamine (TPA) as donor moiety, thiophene as bridge, and thiazolothiazole as acceptor unit were designed and its photovoltaic parameters were equated with reference molecule R. DFT functional CAM-B3LYP/6-31G (d,p) was found best for geometry optimization and TD-CAM-B3LYP/6-31G (d,p) was found suitable for excited state calculations. Among designed donor molecules, M4 manifests suitable lowest band gap of 4.73 eV, frontier molecular orbital energy levels as well as distinctive broad absorption of 455.3 nm due to the stronger electron withdrawing group. The electron-withdrawing substituents contribute to red shifts of absorption spectra and better stabilities for designed molecules. The theoretically determined reorganization energies of designed donor molecules suggested excellent charge mobility property. The lower (e) values in comparison with (h) illustrated that these four donor materials would be ideal for electron transfer and M4 would be best amongst the investigated molecules with lowest (e) of 0.0177. Furthermore, the calculated Voc of M4 is 2.04 V with respect to PC60BM (phenyl-C61-butyric acid methyl ester). This study revealed that the designed donor materials are suitable and recommended for high performance organic solar cell devices.

  • 11. Johnson, Rene L.
    et al.
    Villa, Eric M.
    Ohlin, C. Andre
    Rustad, James R.
    Casey, William H.
    O-17 NMR and Computational Study of a Tetrasiliconiobate Ion, [H2+xSi4Nb16O56]((14-x)-)2011Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 17, nr 34, s. 9359-9367Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Rates of oxygen-isotope exchange were measured in the tetrasiliconiobate ion [H2+xSi4Nb16O56]((14-x)-) to better understand how large oxide ions interact with water. The molecule has 19 nonequivalent oxygen sites and is sufficiently complex to evaluate hypotheses derived from our previous work on smaller clusters. We want to examine the extent to which individual oxygen atoms react independently with particular attention given to the order of protonation of the various oxygen sites as the pH decreases from 13 to 6. As in our previous work, we find that the set of oxygen sites reacts at rates that vary over approximately 104 across the molecule at 6 < pH < 13 but with similar pH dependencies. There is NMR evidence of an intra-or intermolecular reaction at pH similar to 7, where new peaks began to slowly form without losing the O-17 isotopic tag, and at pH <= 6 these new peaks formed rapidly. The oxygen atoms bonded to silicon atoms began to isotopically exchange at pH 9 and below. The 17O NMR peak positions also vary considerably with pH for some, but not all, nonequivalent oxygen sites. This variation could be only partly accounted by electronic calculations, which indicate that oxygen atoms should shift similarly upon protonation. Instead, we see that some sites change enormously with pH, whereas other, similarly coordinated oxygen atoms are less affected, suggesting that either some protons are exchanging so rapidly that the oxygen sites are seeing an averaged charge, or that counterions are modulating the effect of the coordinated protons.

  • 12. Khalid, Muhammad
    et al.
    Ali, Muhammad
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Aslam, Muhammad
    Sumrra, Sajjad Hussain
    Khan, Muhammad Usman
    Raza, Nadeem
    Kumar, Naresh
    Imran, Muhammad
    Frontier molecular, natural bond orbital, UV-VIS spectral study, solvent influence on geometric parameters, vibrational frequencies and solvation energies of 8-hydroxyquinoline2017Ingår i: International Journal of Pharmaceutical Sciences and Research, ISSN 0975-8232, Vol. 8, nr 2, s. 457-469Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    N-heterocyclic compounds have extensive biological and pharmaceutical applications. 8-Hydroxyquinoline (8-HQ) also plays a significant role in many fields of life. The excellent biological significance of the 8-HQ prompted us to extend the DFT based studies. The frontier molecular orbitals (FMOs), UV-VIS and solvation model based studies remained unknown. Therefore, we intended to study the natural bond orbital, FMOs, UV-VIS, thermodynamic properties and medium influence on solvation energies, dipole moment, FTIR and FT-Raman using polarizable continuum model (PCM) and density-based solvation model (SMD). The electronic properties of molecule were calculated by M06-2X/6-31G (d,P) and B3LYP/6-31G (d,p) level of theories. The solvent influence on the geometric parameters, FT-IR and FT-Raman were studied by B3LYP /6-31G(d) method. A good correspondence is found between the optimized parameters and the reported X-ray data. Natural bond orbital reveals that the maximum stabilization energy reached up to 39.64kJ/mol which is responsible for extra stability of the molecule. In solvated 8-HQ, a significant medium effects on FT-IR and FT-Raman intensities is observed. The intensities enhanced from gas to solvent phase. The solvation free energies are found to be -28.710 and -39.456 kJ/mol in PCM and SMD models respectively. FMOs suggested that this molecule contain less hardness and larger softness values. These findings reveal that the molecule might be bioactive.

  • 13.
    Li, Yaozong
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Understanding molecular mechanisms of protein tyrosine kinases by molecular dynamics and free energy calculations2017Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Background: Insulin receptor kinase (IRK) and Insulin-like growth factor 1 receptor kinase (IGF-1RK) are two important members in the large class of tyrosine kinase receptors. They play pivotalroles in the regulation of glucose homeostasis, cell proliferation, differentiation, motility, andtransformation. Their dysfunctions are linked to diabetes, rheumatoid arthritis and many cancers.Although their regulatory mechanisms have been widely studied experimentally, the atomisticdetails are still poorly understood, especially for the influences caused by activation loop (A-loop)phosphorylation.Methods: Molecular dynamics (MD) and alchemical free energy simulations are carried out tounderstand mechanisms underlying the kinase proteins regulation and their thermodynamic basis.To capture a full picture about the entire kinase catalytic cycle, different functional steps areconsidered, i.e., conformational transition, substrate binding, phosphoryl transfer and productrelease. The effects of the A-loop phosphorylation on protein’s dynamics, structure, stability, andfree energy landscape are examined by various analysis methods, including principle componentanalysis (PCA), motion projection, dynamical network analysis and free energy perturbation.Results: The main findings are: 1) A-loop phosphorylation shifts the kinase conformationalpopulation to the active one by changing the electrostatic environments in the kinase apo form, 2)allosterically fine-tunes the orientation of the catalytic residues mediated by the >C-helix in thereactant and product binding states, and 3) thermodynamically favors the kinase catalysis presentedby a catalytic-cycle-mimic free energy landscape. An integrated view on the roles of A-loopphosphorylation in kinase allostery is developed by incorporating kinase’s dynamics, structuralinteractions, thermodynamics and free energy landscape. In addition, new soft-core potentials(Gaussian soft-core) and protocols are developed to conduct accurate and efficient alchemical freeenergy calculations.Conclusions: The entire catalytic cycle is examined by MD and free energy calculations andcomprehensive analyses are conducted. The findings from the studied kinases are general and canbe implemented to the other members in IRK family or even to more non-homologous familiesbecause of the conservation of the characteristic residues between their A-loop and >C-helix. Inaddition, the Gaussian soft-core potentials provide a new tool to perform alchemical free energycalculations in an efficient way.

  • 14.
    Li, Yaozong
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Univ Texas Arlington, Dept Chem & Biochem, Arlington, TX 76019 USA.
    Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation2017Ingår i: Chemical Science, ISSN 2041-6539, Vol. 8, nr 5, s. 3453-3464Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Despite the importance of kinases' catalytic activity regulation in cell signaling, detailed mechanisms underlying their activity regulation are poorly understood. Herein, using insulin-like growth factor 1 receptor kinase (IGF-1RK) as a model, the mechanisms of kinase regulation by its activation loop (A-loop) phosphorylation were investigated through molecular dynamics (MD) and alchemical free energy simulations. Analyses of the simulation results and free energy landscapes determined for the entire catalytic cycle of the kinase revealed that A-loop phosphorylation affects each step in the IGF-1RK catalytic cycle, including conformational change, substrate binding/product release and catalytic phosphoryl transfer. Specifically, the conformational equilibrium of the kinase is shifted by 13.2 kcal mol−1 to favor the active conformation after A-loop phosphorylation, which increases substrate binding affinity of the activated kinase. This free energy shift is achieved primarily viadestabilization of the inactive conformation. The free energy of the catalytic reaction is also changed by 3.3 kcal mol−1 after the phosphorylation and in the end, facilitates product release. Analyses of MD simulations showed that A-loop phosphorylation produces these energetic effects by perturbing the side chain interactions around each A-loop tyrosine. These interaction changes are propagated to the remainder of the kinase to modify the orientations and dynamics of the αC-helix and A-loop, and together yield the observed free energy changes. Since many protein kinases share similar interactions identified in this work, the mechanisms of kinase allostery and catalysis unraveled here can be applicable to them.

  • 15.
    Li, Yaozong
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Physical end-point extrapolatable soft-core potentials for efficient and accurate alchemical free energy calculationsManuskript (preprint) (Övrigt vetenskapligt)
  • 16.
    Lindström, Anton
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
    Edvinsson, Lotta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Andersson, C David
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Andersson, Ida E
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Raubacher, Florian
    Linusson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Postprocessing of docked protein-ligand complexes using implicit solvation models2011Ingår i: Journal of chemical information and modeling, ISSN 1549-960X (online), 1549-9596 (print), Vol. 51, nr 2, s. 267-282Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein−ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson−Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein−ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GBHCT+SA model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) Aq protein. These results indicate that the protocol for the postprocessing of docked protein−ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.

  • 17. Manzoor, Farah
    et al.
    Iqbal, Javed
    Zara, Zeenat
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mahr, Muhammad Shabir
    Ayub, Khurshid
    Theoretical Calculations of the Optical and Electronic Properties of Dithienosilole- and Dithiophene-Based Donor Materials for Organic Solar Cells2018Ingår i: ChemistrySelect, ISSN 2365-6549, Vol. 3, nr 5, s. 1593-1601Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Six Acceptor-Donor-Acceptor (A-D-A) types molecules with dimethyl dithieno[3, 2-b:2',3'-d]silole) -2,6-diyl (DTS) (M-1-M-3) and dimethyl cyclopenta [2, 1-b;3,4-b]-dithiophene (CPDT) (M-4-M-6) core flanged by different acceptor units through methylthiophene bridge are evaluated as donor materials for photovoltaic applications. The photovoltaic properties of M-1-M-3 and M-4-M-6 are compared with standard RaRc and R-b,R-d respectively. Geometry optimization was performed with CAM-B3LYP/6-31G (d) level of theory. TD-CAM-B3LYP has been employed for the estimation of excited state properties of the molecules. M-1, M-2, M-3 and M-4, M-5, M-6 symbolized suitable frontier molecular orbital's (FMO's) energy levels with broad absorption spectra. The electron withdrawing substituents impart red shift in absorption spectra along with good consistancy of designed donor molecules. Reorganization energies of donor molecules (M-1-M-6) showed ideal properties of charge mobility. M-1 and M-4 illustrated lowest le values as compared to lambda(h), thus dictated that designed donor molecules are of good choice for their electron donating ability. Furthermore, M-2 and M-6 demonstrated shortest Eg of 3.7 and 3.72 eV among HOMO and LUMO energy levels.

  • 18.
    Nam, Kwangho
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Karplus, Martin
    Insights into the origin of the high energy-conversion efficiency of F-1-ATPase2019Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, nr 32, s. 15924-15929Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Our understanding of the rotary-coupling mechanism of F-1-ATPase has been greatly enhanced in the last decade by advances in X-ray crystallography, single-molecular imaging, and theoretical models. Recently, Volkan-Kacso and Marcus [S. Volkan-Kacso, R. A. Marcus, Proc. Natl. Acad. Sci. U.S.A. 112, 14230 (2015)] presented an insightful thermodynamic model based on the Marcus reaction theory coupled with an elastic structural deformation term to explain the observed gamma-rotation angle dependence of the adenosine triphosphate (ATP)/ adenosine diphosphate (ADP) exchange rates of F-1-ATPase. Although the model is successful in correlating single-molecule data, it is not in agreement with the available theoretical results. We describe a revision of the model, which leads to consistency with the simulation results and other experimental data on the F-1-ATPase rotor compliance. Although the free energy liberated on ATP hydrolysis by F-1-ATPase is rapidly dissipated as heat and so cannot contribute directly to the rotation, we show how, nevertheless, F-1-ATPase functions near the maximum possible efficiency. This surprising result is a consequence of the differential binding of ATP and its hydrolysis products ADP and P-i along a well-defined pathway.

  • 19. Ohlin, C. Andre
    et al.
    Rustad, James R.
    Casey, William H.
    The energetics of isomerisation in Keggin-series aluminate cations2014Ingår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 43, nr 39, s. 14533-14536Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Electronic-structure calculations show that the e-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)(2)-(H2O))(12)](7+) is the thermodynamically favoured one. Direct interconversion between the epsilon- and delta-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)(56)(H2O)26](18+) ion are discussed.

  • 20.
    Ohlin, C. André
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pascual-Borràs, Magda
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Protonation and water exchange kinetics in sandwich polyoxometalates2018Ingår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 47, nr 38, s. 13602-13607Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Density functional theory is used to explore the locus and consequences of protonation in [Zn4(HO)2(PW9O34)2]10−. The results are used to explain recent observations regarding the contrasting pH effects on the water-ligand exchange in [Mn4(H2O)2(P2W15O56)2]16− and [Co4(H2O)2(P2W15O56)2]16−, and the general effect of protonation on solvent exchange in metal oxides is discussed.

  • 21. Phillips, Brian L.
    et al.
    Ohlin, C. Andre
    School of Chemistry, Monash University, Clayton, Australia.
    Vaughn, John
    Woerner, William
    Smart, Scott
    Subramanyam, Ravi
    Pan, Long
    Solid-State 27Al NMR Spectroscopy of the γ-Al13 Keggin Containing Al Coordinated by a Terminal Hydroxyl Ligand2016Ingår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 55, nr 23, s. 12270-12280Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report solid-state 27Al NMR spectroscopic results for the sulfate salt of the γ-Al13 Keggin cluster, γ-[AlO4Al12(OH)25(OH2)11][SO4]3·[H2O]14, that provide a spectroscopic signature for partial hydrolysis of this Keggin-type cluster. In 27Al multiple-quantum magic-angle spinning NMR spectra, all 13 Al positions of the cluster are at least partially resolved and assigned with the aid of density functional theory (DFT) calculations of the 27Al electric field gradients. The isotropic chemical shift of the single tetrahedral site, 75.7 ppm, is nearly identical to that reported for solutions from which the cluster crystallizes. Reflecting broadly similar coordination environments, the octahedral Al show mostly small variations in isotropic chemical shift (+7 to +11 ppm) and quadrupolar coupling constant (CQ; 6–7.5 MHz), except for one resonance that exhibits a much smaller CQ and another site with a larger value. DFT calculations show that deprotonation of a terminal water ligand, to form an η-OH group, causes a large reduction in the 27Al CQ, allowing assignment of a distinct, narrow peak for octahedral Al to this hydroxyl-terminated site. This result suggests a relationship between octahedral 27Al NMR line width and hydrolysis for solids prepared from Keggin-type clusters.

  • 22. Santos, Denys E. S.
    et al.
    Li, Danyang
    Ramstedt, Madeleine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gautrot, Julien E.
    Soares, Tereza A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Brazil.
    Conformational Dynamics and Responsiveness of Weak and Strong Polyelectrolyte Brushes: Atomistic Simulations of Poly(dimethyl aminoethyl methacrylate) and Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride)2019Ingår i: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 35, nr 14, s. 5037-5049Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The complex solution behavior of polymer brushes is key to control their properties, including for biomedical applications and catalysis. The swelling behavior of poly(dimethyl aminoethyl methacrylate) (PDMAEMA) and poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) (PMETAC) in response to changes in pH, solvent, and salt types has been investigated using atomistic molecular dynamics simulations. PDMAEMA and PMETAC have been selected as canonical models for weak and strong polyelectrolytes whose complex conformational behavior is particularly challenging for the development and validation of atomistic models. The GROMOS-derived atomic parameters reproduce the experimental swelling coefficients obtained from ellipsometry measurements for brushes of 5–15 nm thickness. The present atomistic models capture the protonated morphology of PDMAEMA, the swollen and collapsed conformations of PDMAEMA and PMETAC in good and bad solvents, and the salt-selective response of PMETAC. The modular nature of the molecular models allows for the simple extension of atomic parameters to a variety of polymers or copolymers.

  • 23. Sharma, Rupali
    et al.
    Zhang, Jie
    Ohlin, C. André
    Predicting O-17 NMR chemical shifts of polyoxometalates using density functional theory2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 11, s. 8235-8241Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have investigated the computation of O-17 NMR chemical shifts of a wide range of polyoxometalates using density functional theory. The effects of basis sets and exchange-correlation functionals are explored, and whereas pure DFT functionals generally predict the chemical shifts of terminal oxygen sites quite well, hybrid functionals are required for the prediction of accurate chemical shifts in conjunction with linear regression. By using PBE0/def2-tzvp//PBE0/cc-pvtz(H-Ar), lanl2dz(K-) we have computed the chemical shifts of 37 polyoxometalates, corresponding to 209 O-17 NMR signals. We also show that at this level of theory the protonation-induced pH dependence of the chemical shift of the triprotic hexaniobate Lindqvist anion, [HxNb6O19]((8-x)), can be reproduced, which suggests that hypotheses regarding loci of protonation can be confidently tested.

  • 24. Stich, Troy A.
    et al.
    Krzystek, J.
    Mercado, Brandon Q.
    McAlpin, J. Gregory
    Ohlin, C. Andre
    Olmstead, Marilyn M.
    Casey, William H.
    Britt, R. David
    Structural insights into [Co4O4(C5H5N)(4)(CH3CO2)(4)](+), a rare Co(IV)-containing cuboidal complex2013Ingår i: Polyhedron, ISSN 0277-5387, E-ISSN 1873-3719, Vol. 64, nr SI, s. 304-307Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report high-frequency (up to 219 GHz) and correspondingly high-field electron paramagnetic resonance spectra and X-ray crystal structure of [Co4O4(pyridine)(4)(acetate)(4)](+) ([Co4O4(py)(4)(OAc)(4)](+)) that serves as a structural and spectroscopic model of cobalt-oxide films that are capable of oxidizing water. These results are, in large part, consistent with those from our earlier, lower-frequency study and serve to benchmark future high-field studies on paramagnetic states of the catalyst film. (C) 2013 Published by Elsevier Ltd.

  • 25.
    Westlund, Per-Olof
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    A proton T1-nuclear magnetic resonance dispersion study of water motion in snowflakes and hexagonal ice2019Ingår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 117, nr 7-8, s. 960-967Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Snowflakes and ordinary hexagonal ice were studied measuring water proton spin–lattice relaxation rate R1(ωI)-nuclear magnetic resonance dispersion (NMRD) profiles at proton Larmor frequencies ranging from 1 to 30 MHz and at different temperatures ranging from −2◦C to −10◦C. The spin–spin relaxation rate 1/ 1/T2(ωI) was determined at a single Larmor frequency of 16.3 MHz. The high-field wing of the proton R1(ωI)-NMRD profile was characterised by two parameters: a correlation time τc which described the dipole–dipole spectral density, and the relaxation rate at low fields R max real (0) which was determined from T 2 . The correlation time τc depended on the dynamic model used. A rotation diffusion model yield approximatively 3μs at −3◦C to about 5μs at 10◦C, whereas for a more realistic six-site discrete exchange model, the correlation times decreased slightly to about 80% for the same temperature interval. Proton dipole–dipole interactions were divided into intramolecular and intermolecular contributions where the intermolecular contribution was about 0.4–0.8 × the intramolecular contribution. It was not possible to discriminate between the dynamic models or to detect ice/water interface effects by comparing the NMRD data from snowflakes with ordinary hexagonal ice data.

  • 26. Wheatley, James E.
    et al.
    Ohlin, C. Andre
    Chaplin, Adrian B.
    Solvent promoted reversible cyclometalation in a tethered NHC iridium complex2014Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, nr 6, s. 685-687Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reaction of [Ir(COD)(py-(IBu)-Bu-t)](+) (py-(IBu)-Bu-t = 3-tert-butyl-1-picolylimidazol-2-ylidene) with acetonitrile results in reversible intramolecular C-H bond activation of the NHC ligand and formation of [Ir(g(2):g 1-C8H13)(py-ItBu’)(NCMe)](+). Coordinated COD acts as an internal hydride acceptor and acetonitrile coordination offsets the otherwise unfavourable thermodynamics of the process.

  • 27. Zara, Zeenat
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Sadaf, Sana
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Designing Benzodithiophene-Based Donor Materials with Favorable Photovoltaic Parameters for Bulk Heterojunction Organic Solar Cells2017Ingår i: CHEMISTRYSELECT, ISSN 2365-6549, Vol. 2, nr 20, s. 5628-5639Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Computational study on four Acceptor-Donor-Acceptor (A-D-A) type of donor molecules namely, dimethyl cyanoacetate terthiophene di(methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDMTBDT) (M1), methylrhodanine terthiophene di (methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDMTBDT) (M2), dimethyl cyanoacetate terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDFMTBDT) (M3), and methylrhodanine terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDFMTBDT) (M4) was carried out and their photovoltaic properties were associated with methyl cyanoacetate terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DCAO3TBDT) (R1) and methylrhodanine terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DR3TBDT) (R2). For the geometry optimization DFT functional CAM B3LYP/6-31G(d) was found to be the best choice, hence TD-CAM B3LYP/631G(d) was opted for the calculation of excited state of the molecules. M3 and M4 represented appropriate frontier molecular orbital energy levels and broad absorption band. The reorganization energies of the designed molecules illustrated excellent charge mobility property. The lower le values as compared to lambda(i) illustrate that the designed donor molecules are better electron donors. M4 was found as champion molecules with the lowest le (0.01601) value. The Voc value of M3 and M4 are 2.74 eV and 2.63 eV respectively with respect to the energy levels of PC60BM (acceptor).

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