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  • 151.
    Nilsson, Johan O.
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Leetmaa, Mikael
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Vekilova, Olga Yu.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala, Sweden.
    Simak, Sergei I.
    Skorodumova, Natalia V.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala, Sweden.
    Oxygen diffusion in ceria doped with rare-earth elements2017Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, s. 13723-13730Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We examine the effects of the dopant type and the dopant distribution on the ion diffusion in ceria doped with rare-earth elements (Pr, Nd, Pm, Sm, Eu, and Gd). Diffusion is simulated by means of a Kinetic Monte Carlo method using input transition rates derived from diffusion barriers calculated in the framework of density functional theory (DFT). Based on diffusion simulations, we discuss the characteristics of the dopants in terms of the diffusion barriers, and study oxygen ion trajectories for different dopants and distributions. Our simulations show a trend of increasing ion diffusivity with increasing atomic number for all distributions.

  • 152.
    Ning, Zhijun
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Molnár, Mátyás
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Chen, Yun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Friberg, Peter
    Gan, Liming
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Fu, Ying
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Role of surface ligands in optical properties of colloidal CdSe/CdS quantum dots2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 13, s. 5848-5854Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In order to study the role of surface ligands in determining optical properties of colloidal quantum dots (QDs), we have selectively fabricated and studied CdSe/CdS core-shell QDs with strongly confined electron and hole states attached with commonly used surface ligands. Optical properties, viz. absorption and fluorescence of these QDs, are characterized from which salient changes have been observed for different ligand substitutions which, through theoretical analysis, can be associated with electronic structure properties of the QD-ligand composite systems, in particular localization of wave functions of electrons and holes in the QDs and the band matching of the HOMO-LUMO gap of the ligands. The findings can be utilized to facilitate the understanding and optimization of properties of QD biomarkers with functionalizing surface ligands for targeting cellular objects.

  • 153. Nisar, Jawad
    et al.
    Pathak, Biswarup
    Wang, Baochang
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik.
    Kang, Tae Won
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik.
    Hole mediated coupling in Sr2Nb2O7 for visible light photocatalysis2012Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, nr 14, s. 4891-4897Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The band gap reduction and effective utilization of visible solar light are possible by introducing the anionic hole-hole mediated coupling in Sr2Nb2O7. By using the first principles calculations, we have investigated the mono-and co-anionic doping (S, N and C) in layered perovskite Sr2Nb2O7 for the visible-light photocatalysis. Our electronic structure and optical absorption study shows that the mono- (N and S) and co-anionic doped (N-N and C-S) Sr2Nb2O7 systems are promising materials for the visible light photocatalysis. The calculated binding energies show that if the hole-hole mediated coupling could be introduced, the co-doped systems would be more stable than their respective mono-doped systems. Optical absorption curves indicate that doping S, (N-N) and (C-S) in Sr2Nb2O7 can harvest a longer wavelength of the visible light spectrum as compared to the pure Sr2Nb2O7 for efficient photocatalysis.

  • 154.
    Niskanen, Johannes
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Li, Cui
    Monti, Susanna
    Carravetta, Vincenzo
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 1, s. 244-254Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

  • 155.
    Norman, Patrick
    Linköping University, Sweden.
    A perspective on nonresonant and resonant electronic response theory for time-dependent molecular properties2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 46, s. 20519-20535Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The development of electronic response theory in quantum chemistry has been reviewed, starting from the early 1970's and reaching the current state-of-the-art. The general theory has been applied to the calculation of a large number of spectroscopic parameters over the years, and it has been implemented for the majority of standard electronic structure methods. Two formulations of response theory, the Ehrenfest expectation value and the quasi-energy derivative formulation, have turned into leading alternatives for the derivation of computationally tractable expressions of response functions, and they are here reviewed with an attempt to, as far as possible, leave out technical details. A set of four steps are identified as common in derivations of response functions, and the two formulations are compared along this series of steps. Particular emphasis is given to the situation when the oscillation of the weak external electromagnetic field is in resonance with a transition frequency of the system. The formation of physically sound response functions in resonance regions of the spectrum is discussed in light of the causality condition and the Kramers-Kronig relations, and it is achieved in wave function theory by means of the introduction of relaxation parameters in a manner that mimics what one sees in density matrix theory. As a working example, equations are illustrated by their application to a two-state model for para-nitroaniline including the ground and the lowest charge-transfer state in the electric dipole approximation.

  • 156.
    Norman, Patrick
    et al.
    Linköping University, Sweden.
    Parello, J.
    Polavarapu, P. L.
    Linares, M.
    Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 34, s. 21866-21879Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.

  • 157.
    Notley, Shannon M.
    et al.
    KTH, Tidigare Institutioner, Fiber- och polymerteknologi.
    Biggs, S.
    Craig, V. S. J.
    Wågberg, Lars
    KTH, Tidigare Institutioner, Fiber- och polymerteknologi.
    Adsorbed layer structure of a weak polyelectrolyte studied by colloidal probe microscopy and QCM-D as a function of pH and ionic strength2004Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, nr 9, s. 2379-2386Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The adsorbed layer structure of a weak polyelectrolyte poly(2-vinylpyridine), on silica and mica, has been studied using colloidal probe microscopy (CPM) and the quartz crystal microbalance (QCM-D). The adsorbed layer structure was found to be highly dependent on both the solution conditions from which it was adsorbed and the molecular weight. Conditions were altered to favour both flat adsorbed layers and the development of significant steric layers. The structural reconformation of the large steric layer was furthermore studied as a function of pH. The equilibrium interaction force, measured using CPM as a function of surface separation, was used to determine the relative extension of the polyelectrolyte away from the interface. At low pH (3.2) and high ionic strength, the adsorbed polyelectrolyte molecules adopt a highly extended conformation; as the pH is increased (to 4.6 then to 5.5) the polymer chains collapse progressively towards the interface. Reversal of this pH cycle causes a re-protonation of the adsorbed polymers and highlights the finite timescale for this process to occur. The kinetics of this process was measured from the amount of trapped solvent within the polyelectrolyte layer as determined from the QCM-D. Upon decrease in pH, the adsorbed chains swell before partially collapsing. We propose that this is due to cross-linking of the polymer in the protonated state. Furthermore, the combination of techniques used in this study, namely optical reflectometry, CPM and QCM-D, allows the determination of the solvent content of the adsorbed film of polyelectrolyte as well as the extension of the polymer from the interface as a function of pH.

  • 158. Oliynyk, Vitaliy
    et al.
    Mille, Christian
    Ng, Jovice B. S.
    von Ballmoos, Christoph
    Corkery, Robert W.
    KTH, Skolan för kemivetenskap (CHE), Kemi.
    Bergström, Lennart
    Selective and ATP-driven transport of ions across supported membranes into nanoporous carriers using gramicidin A and ATP synthase2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 8, s. 2733-2740Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report a robust and versatile membrane protein based system for selective uptake and release of ions from nanoporous particles sealed with ion-tight lipid bilayers of various compositions that is driven by the addition of ATP or a chemical potential gradient. We have successfully incorporated both a passive ion channel-type peptide (gramicidin A) and a more complex primary sodium ion transporter (ATP synthase) into the supported lipid bilayers on solid nanoporous silica particles. Protein-mediated controlled release/uptake of sodium ions across the ion-tight lipid bilayer seal from or into the nanoporous silica carrier was imaged in real time using a confocal laser scanning microscope and the intensity changes were quantified. ATP-driven transport of sodium ions across the supported lipid bilayer against a chemical gradient was demonstrated. The possibility of designing durable carriers with tight lipid membranes, containing membrane proteins for selective ion uptake and release, offers new possibilities for functional studies of single or cascading membrane protein systems and could also be used as biomimetic microreactors for controlled synthesis of inorganic multicomponent materials.

  • 159. Onthong, U.
    et al.
    Megyes, T.
    Bako, I.
    Radnai, T.
    Grosz, T.
    Hermansson, Kersti
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Probst, M.
    X-ray and neutron diffraction studies and molecular dynamics simulations of liquid DMSO2004Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, nr 9, s. 2136-2144Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Liquid DMSO has been investigated by means of X-ray and neutron diffraction, quantum-chemical calculations and molecular dynamics (MD) simulations. A new analytical all-atom pair potential for DMSO-DMSO interactions was developed from quantum-chemical calculations and employed in the simulations. The MD-derived total structure function agrees favourably with those obtained from the X-ray and neutron diffraction experiments. An analysis of the local structure shows a rather unstructured liquid with a slight preference for antiparallel ordering of the S-O dipoles.

  • 160.
    Oostenrijk, Bart
    et al.
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Barreiro, Dario
    Univ Autonoma Madrid, Dept Quim, Modulo 13, E-28049 Madrid, Spain..
    Walsh, Noelle
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Sankari, Anna
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Månsson, Erik P.
    DESY, Attosecond Sci Grp, Photon Sci Div, Schenefeld, Germany..
    Maclot, Sylvain
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biomedicinsk fysik och röntgenfysik. Department of Physics, Lund University, Box 118, Lund, 22100, Sweden.
    Sorensen, Stacey L.
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Diaz-Tendero, Sergio
    Univ Autonoma Madrid, Dept Quim, Modulo 13, E-28049 Madrid, Spain.;Univ Autonoma Madrid, IFIMAC, E-28049 Madrid, Spain.;Univ Autonoma Madrid, IAdChem, E-28049 Madrid, Spain..
    Gisselbrecht, Mathieu
    Lund Univ, Dept Phys, Box 118, S-22100 Lund, Sweden..
    Fission of charged nano-hydrated ammonia clusters - microscopic insights into the nucleation processes2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 46, s. 25749-25762Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    While largely studied on the macroscopic scale, the dynamics leading to nucleation and fission processes in atmospheric aerosols are still poorly understood at the molecular level. Here, we present a joint experimental-theoretical study of a model system consisting of hydrogen-bonded ammonia and water molecules. Experimentally, the clusters were produced via adiabatic co-expansion. Double ionization ionic products were prepared using synchrotron radiation and analyzed with coincidence mass- and 3D momentum spectroscopy. Calculations were carried out using ab initio molecular dynamics to understand the fragmentation within the first similar to 500 fs. Further exploration of the potential energy surfaces was performed at a DFT level of theory to gain information on the energetics of the processes. Water was identified as an efficient nano-droplet stabilizer, and is found to have a significant effect even at low water content. On the molecular level, the stabilizing role of water can be related to an increase in the dissociation energy between ammonia molecules and the water enriched environment at the cluster surface. Furthermore, our results support the role of ammonium as a charge carrier in the solution, preferentially bound to surrounding ammonia molecules, which can influence the atmospheric nucleation process.

  • 161.
    Paloncýová, Markéta
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Ameloot, Marcel
    Hasselt Univ, Biomed Res Inst, Agoralaan Bldg C, B-3590 Diepenbeek, Belgium..
    Knippenberg, Stefan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 14, s. 7594-7604Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Characterization of the membrane phases is a crucial task in cell biology. Cells differ in composition of the lipids and consequently in adopted phases. The phases can be discriminated based upon lipid ordering and molecular diffusion and their identification could be used for characterization of cell membranes. Here we used molecular dynamics (MD) simulations to study the behavior of the fluorescent reporter molecule diphenylhexatriene (DPH) in different lipid phases - liquid disordered (L-d), liquid ordered (L-o), and solid ordered (S-o) composed of phosphatidylcholines (L-d and S-o) or a sphingomyelin/cholesterol (SM/Chol) mixture (L-o). To the best of our knowledge, this is the first simulation of DPH in L-o SM/Chol and S-o DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the L-o phase we observed a significant fraction of DPH positioned in between membrane leaflets, which agrees with experimental findings, but which has not been observed in previous MD simulations of DPH in phosphatidylcholine membranes. Further, we calculated rotational autocorrelation functions (ROTACF) from our MD simulations in order to model the time-resolved fluorescence anisotropy decay. We observed that order parameters P-2 and P-4 are sufficient to fully describe the orientation distribution of DPH. We analyzed the ROTACFs by a so-called general model for the time-resolved fluorescence anisotropy [W. van der Meer et al., Biophys. J., 1984, 46, 515] and observed an overestimation of P-4. We suggest a rescaling of the recovered P-4 yielding an orientation distribution of DPH close to the one observed in our MD simulations.

  • 162. Pasti, Igor A.
    et al.
    Baljozovic, Milos R.
    Granda-Marulanda, Laura P.
    Skorodumova, Natalia V.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Flerskalig materialmodellering.
    Bimetallic dimers adsorbed on a defect-free MgO(001) surface: bonding, structure and reactivity2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 15, s. 9666-9679Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A large number of computational studies have been devoted to the investigation of monometallic clusters supported by MgO. However, in practice, catalysis shows that multicomponent catalytic systems often win in catalytic performance over single component systems. In this study, the geometrical and electronic structure, stability and chemisorption properties of M1M2 metal dimers (M1, M2 = Ru, Rh, Pd, Ir, Pt) supported by defect free MgO(001) have been investigated in the framework of density functional theory. The oxygen sites of MgO(001) are the preferred adsorption sites for all the studied clusters, the majority of them adsorbing parallel to the surface with metal atoms attached to two surface oxygen atoms. The energetics of M1M2 + MgO(001) formation shows that the adsorption complexes are stable and benefit from metal-oxygen and metal-metal interaction. The chemisorption properties of Pd and Pt atoms in PdM2 and PtM2 dimers are studied using CO as a probe molecule. A linear relationship between the CO chemisorption and the d-band center position of the reacting atom in the dimer is observed, extending the d-band center model to the case of highly under-coordinated metal atoms supported by a non-conductive material.

  • 163.
    Pasti, Igor A.
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Univ Belgrade, Fac Phys Chem, Studentski Trg 12-16, Belgrade 11158, Serbia.
    Johansson, Börje
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala Univ, Dept Phys & Astron, Box 516, S-75120 Uppsala, Sweden..
    Skorodumova, Natalia V.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala Univ, Dept Phys & Astron, Box 516, S-75120 Uppsala, Sweden..
    Tunable reactivity of supported single metal atoms by impurity engineering of the MgO(001) support2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 9, s. 6337-6346Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Development of novel materials may often require a rational use of high price components, like noble metals, in combination with the possibility to tune their properties in a desirable way. Here we present a theoretical DFT study of Au and Pd single atoms supported by doped MgO(001). By introducing B, C and N impurities into the MgO(001) surface, the interaction between the surface and the supported metal adatoms can be adjusted. Impurity atoms act as strong binding sites for Au and Pd adatoms and can help to produce highly dispersed metal particles. The reactivity of metal atoms supported by doped MgO(001), as probed by CO, is altered compared to their counterparts on pristine MgO(001). We find that Pd atoms on doped MgO(001) are less reactive than on perfect MgO(001). In contrast, Au adatoms bind CO much more strongly when placed on doped MgO(001). In the case of Au on N-doped MgO(001) we find that charge redistribution between the metal atom and impurity takes place even when not in direct contact, which enhances the interaction of Au with CO. The presented results suggest possible ways for optimizing the reactivity of oxide supported metal catalysts through impurity engineering.

  • 164. Pasti, Igor A.
    et al.
    Jovanovic, Aleksandar
    Dobrota, Ana S.
    Mentus, Slavko V.
    Johansson, Börje
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala University, Sweden.
    Skorodumova, Natalia V.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala University, Sweden.
    Atomic adsorption on graphene with a single vacancy: systematic DFT study through the periodic table of elements2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 2, s. 858-865Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vacancies in graphene present sites of altered chemical reactivity and open possibilities to tune graphene properties by defect engineering. The understanding of chemical reactivity of such defects is essential for successful implementation of carbon materials in advanced technologies. We report the results of a systematic DFT study of atomic adsorption on graphene with a single vacancy for the elements of rows 1-6 of the periodic table of elements (PTE), excluding lanthanides. The calculations have been performed using the PBE, long-range dispersion interaction-corrected PBE (PBE+D2 and PBE+D3) and non-local vdW-DF2 functionals. We find that most elements strongly bind to the vacancy, except for the elements of groups 11 and 12, and noble gases, for which the contribution of dispersion interaction to bonding is most significant. The strength of the interaction with the vacancy correlates with the cohesive energy of the elements in their stable phases: the higher the cohesive energy is, the stronger bonding to the vacancy can be expected. As most atoms can be trapped at the SV site we have calculated the potentials of dissolution and found that in most cases the metals adsorbed at the vacancy are more "noble" than they are in their corresponding stable phases.

  • 165. Pašti, I. A.
    et al.
    Skorodumova, Natalia
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Flerskalig materialmodellering. Uppsala University, Sweden.
    Structural, electronic, magnetic and chemical properties of B-, C- and N-doped MgO(001) surfaces2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 1, s. 426-435Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Doping of simple oxide materials can give rise to new exciting physical and chemical properties and open new perspectives for a variety of possible applications. Here we use density functional theory calculations to investigate the B-, C- and N-doped MgO(001) surfaces. We have found that the investigated dopants induce magnetization of the system amounting to 3, 2 and 1 μB for B, C and N, respectively. The dopants are found to be in the X2- state and tend to segregate to the surface. These impurity sites also present the centers of altered chemical reactivity. We probe the chemisorption properties of the doped MgO(001) surfaces with the CO molecule and atomic O. The adsorption of CO is much stronger on B- and C-doped MgO(001) compared to pure MgO(001) as the impurity sites serve as potent electron donors. The situation is similar to the case of atomic oxygen, for which we find the adsorption energy of -8.78 eV on B-doped MgO(001). The surface reactivity changes locally around the dopant atom, which is mainly restricted to its first coordination shell. The presented results suggest doped MgO as a versatile multifunctional material with possible use as an adsorbent or a catalyst.

  • 166. Peach, M. J. G.
    et al.
    Helgaker, T.
    Salek, Pawel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi.
    Keal, T. W.
    Lutnaes, O. B.
    Tozer, D. J.
    Handy, N. C.
    Assessment of a Coulomb-attenuated exchange-correlation energy functional2005Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 8, nr 5Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The recently proposed CAM-B3LYP exchange-correlation energy functional, based on a partitioning of the r(12)(-1) operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties. Rydberg and charge transfer excitation energies and static electronic polarisabilities are notably improved over the standard B3LYP functional; classical reaction barriers also improve. Ionisation potentials, bond lengths, NMR shielding constants and indirect spin-spin coupling constants are comparable with the two functionals. CAM-B3LYP atomisation energies and diatomic harmonic vibrational wavenumbers are less accurate than those of B3LYP. Future research directions are outlined.

  • 167.
    Persson, Gustav
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Sandén, Tor
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Sandberg, AnnSofi
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Widengren, Jerker
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Fluorescence cross-correlation spectroscopy of a pH-sensitive ratiometric dye for molecular proton exchange studies2009Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, nr 21, s. 4410-4418Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fluorescence fluctuation analysis of individual pH-sensitive fluorophores has recently proven to be a useful approach for biomolecular proton exchange studies. In this work, dual-color fluorescence cross-correlation spectroscopy (FCCS) is demonstrated on a ratiometric pH-sensitive dye, for which both the excitation and emission spectra shift as a function of pH. In the FCCS measurements, the fluorescence signal from the predominant emission wavelength range of the protonated form of the dye is cross-correlated with that of the deprotonated form. Two lasers are used alternatingly to excite predominantly the protonated and the deprotonated form of the dye. The alternating excitation modulation scheme is combined with detection gating, and is based on a recently developed concept that allows extraction of correlation data for all correlation times regardless of the chosen modulation period. The scheme can thus be applied without concern for the time-scales of the molecular dynamic processes to be studied. By this combined discrimination based on both excitation and emission, spectral cross-talk is dramatically reduced and a very distinct and unambiguous anticorrelation can be recorded in the correlation curves as a consequence of the proton exchange. The strong discrimination power makes the approach applicable also to ratiometric dyes with less pronounced spectral shifts. It should also be useful in combination with ratiometric dyes sensitive to other ambient conditions and ions, such as the biologically very important calcium ion.

  • 168.
    Petrov, Oleg
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi. KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    Furo, Istvan
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi. KTH, Skolan för kemivetenskap (CHE), Centra, Centrum för Industriell NMR-teknik.
    A study of freezing-melting hysteresis of water in different porous materials: Part II: surfactant-templated silicas2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 36, s. 16358-16365Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The freezing-melting hysteresis of water in mesoporous silicas MCM-48, MCM-41 and SBA-16 has been studied by NMR cryoporometry. The hysteresis in MCM-48 was found to exhibit nearly parallel branches, matching type H1 hysteresis that had been observed earlier in controlled pore glass. The same type of hysteresis is observed in two of three different-sized MCM-41 under study (a pore diameter of 3.6 and 3 nm), superimposed with a secondary, extremely broad, type H3 hysteresis. No hysteresis was found in the smallest MCM-41 with a pore diameter < 3 nm. Finally, water in SBA-16 exhibits type H2 hysteresis with the freezing branch being essentially steeper than the melting one, which is attributed to a pore blockage upon freezing, similar to what we observed earlier in Vycor porous glass. The data were analyzed using the model of curvature-dependent metastability of a solid phase upon melting; the validity of this model has been discussed.

  • 169.
    Pilkington, Georgia A.
    et al.
    School of Chemistry, University of Bristol.
    Thormann, Esben
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Claesson, Per M.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Fuge, Gareth M.
    School of Chemistry, University of Bristol.
    Fox, Oliver J. L.
    School of Chemistry, University of Bristol.
    Ashfold, Michael N. R.
    School of Chemistry, University of Bristol.
    Leese, Hannah
    Dept of Chemical Engineering, University of Bath, UK.
    Mattia, Davide
    Dept of Chemical Engineering, University of Bath, UK.
    Briscoe, Wuge H.
    School of Chemistry, University of Bristol.
    Amontonian frictional behaviour of nanostructured surfaces2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, s. 9318-9326Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    With nanotextured surfaces and interfaces increasingly being encountered in technological and biomedical applications, there is a need for a better understanding of frictional properties involving such surfaces. Here we report friction measurements of several nanostructured surfaces using an Atomic Force Microscope (AFM). These nanostructured surfaces provide well defined model systems on which we have tested the applicability of Amontons' laws of friction. Our results show that Amontonian behaviour is observed with each of the surfaces studied. However, no correlation has been found between measured friction and various surface roughness parameters such as average surface roughness (Ra) and root mean squared (rms) roughness. Instead, we propose that the friction coefficient may be decomposed into two contributions, i.e., μ = μ0 + μg, with the intrinsic friction coefficient μ0 accounting for the chemical nature of the surfaces and the geometric friction coefficient μg for the presence of nanotextures. We have found a possible correlation between μg and the average local slope of the surface nanotextures.

  • 170.
    Ploss, Moritz A.
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Maskinkonstruktion (Inst.).
    Rutland, Mark W.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Glavatskih, Sergei
    KTH, Skolan för industriell teknik och management (ITM), Maskinkonstruktion (Inst.).
    Influence of electric potential on the apparent viscosity of an ionic liquid: facts and artifacts2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 38, s. 26609-26615Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    According to recent findings, the steady shear viscosity of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([Emim][Tf2N]) decreases significantly under the influence of electric potential. This implies a causal connection between nanoscale ordering at the electrified interface and a macroscopic change of transport properties. To study this phenomenon in more detail, we reproduced the above-mentioned measurements; however, we find no evidence that the viscosity of [Emim][Tf2N] is a function of electric potential. Additionally, our results show that steady shear measurements can lead to artifacts that, at first glance, may appear to be potential-induced changes in viscosity. We demonstrate that the artifacts result from a sliding electrical contact at the working electrode of the electrochemical cell and we suggest to consider our findings for future viscosity measurements of ionic liquids.

  • 171. Ren, H.
    et al.
    Zhang, G.
    Lin, N.
    Deng, L.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Huang, F.
    Strong Fermi level pinning induces a high rectification ratio and negative differential resistance in hydrogen bonding bridged single cytidine pair junctions2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 38, s. 26586-26594Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We propose a high performance single molecule rectifier by sandwiching a deoxycytidine base pair between gold electrodes. The conductance of the single base pair junction can be controlled by its protonation status, with ON/OFF ratios between the protonated (pCC) and deprotonated (CC) junctions of 3-5 orders of magnitude. In the conducting pCC state, we observed a high rectification ratio of two orders of magnitude at bias voltage values around 0.1 V. This rectification ratio surpasses most of the theoretical designs for single molecular rectifiers, while the low working voltage implies significant energy efficiency. Negative differential resistance (NDR) was also witnessed in the protonated state, with a peak to valley ratio of 24. Both the rectifying and NDR effects originate from strong Fermi level pinning effects. The electronic performance offers these single base pair junctions potential applications as a unimolecular rectifier or switch with an NDR effect. The current-voltage response is unique compared with those of the reported canonical A-T and G-C pairs, and provides the possibility to be used for i-motif DNA structure recognition or sequencing. © 2016 the Owner Societies.

  • 172.
    Riihimäki, Eva-Stina
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Oorganisk kemi.
    Manuel Martinez, Jose
    Physical Chemistry Department, University of Seville.
    Kloo, Lars A.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Oorganisk kemi.
    Structural effects of Cu(II)-coordination in the octapeptide region of the human prion protein2008Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, nr 18, s. 2488-2495Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The copper-binding ability of the prion protein is thought to be central to its function. The structural effects of copper coordination in the octapeptide region of the human prion protein have been investigated by molecular dynamics simulations. Simulations were performed with the apo state, in order to investigate the behavior of the region without copper ions, as well as with the octapeptide region in the presence of copper ions. While the structure of the apo state is greatly influenced by the interaction between the rings in the histidine, tryptophan and proline residues, the region shows evidence of highly ordered coordination sites in the presence of copper ions. The position of the tryptophan indole ring is stabilized by cation-pi interactions. Two stable orientations of the indole ring with respect to the equatorial coordination plane of copper were observed, which showed that the indole ring can reside on both sides of the coordination plane. The interaction with the indole ring was found to occur without a mediating axial water molecule.

  • 173.
    Rinkevicius, Zilvinas
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rosal Sandberg, Jaime Axel
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Non-linear optical properties of molecules in heterogeneous environments: a quadratic density functional/molecular mechanics response theory2014Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 19, s. 8981-8989Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems - such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.

  • 174. Rizzo, Antonio
    et al.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ab initio study of the circular intensity difference in electric-field-induced second harmonic generation of chiral natural amino acids2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 4, s. 1198-1207Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a systematic computational study of circular intensity difference (CID) in electric-field-induced second harmonic generation (EFISHG) of some representative chiral natural amino acids (Alanine, Arginine, Aspartic Acid, Cysteine and Tryptophan), taking into account the electric-dipole, electric-quadrupole and magnetic-dipole interactions. The calculations are performed by applying cubic response theory at both Hartree-Fock and Density Functional theory levels, the latter with the popular Becke-three parameters, Lee, Yang and Parr (B3LYP) functional. Special focus is given to the basis set, electron correlation and origin dependence of the properties. The full set of molecular parameters defined by Lam and Thirunamachandran in their reference theoretical paper published in 1982 [J. Chem. Phys., 1982, 77, 3810] is obtained and discussed. This permits the prediction of the CID observable for different possible experimental setups.

  • 175. Ruiz, Jesus Alvarez
    et al.
    Kivimaki, Antti
    Stankiewicz, Marek
    Garcia, Emilio Melero
    Coreno, Marcello
    Ali, Sahangir
    Koperski, Jaroslaw
    Rachlew, Elisabeth
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Atom- och molekylfysik.
    Vall-Ilosera i Serrano, Gemma
    Feyer, Vitaliy
    Tuckett, Richard
    VUV photon induced fluorescence study of SF5CF32006Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 8, nr 44, s. 5199-5206Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The interaction of SF5CF3 with vacuum-UV radiation has been investigated by photon induced fluorescence spectroscopy. Total fluorescence yield and dispersed fluorescence spectra of SF5CF3 were recorded in the 200-1000 nm fluorescence window. In all cases, the fluorescence spectra resemble those of CF3X (X H, F, Cl, and Br) molecules. At photon energies below 20 eV, the emission is attributed to the excited CF3 and CF2 fragments. The threshold for the CF3 emission is 10.2 +/- 0.2 eV, giving an upper limit estimate for the SF5-CF3 bond dissociation energy of 3.9 +/- 0.3 eV. The excitation functions of the CF3 and CF2 emissions were measured in the photon energy range 13.6-27.0 eV. The resonant structures observed in SF5CF3 are attributed to electronic transitions from valence to Rydberg orbitals, following similar assignments in CF3X molecules. The photoabsorption spectrum of SF5CF3 shows features at the same energies, indicating a strong contribution from Rydberg excitations.

  • 176. Rupp, Caroline J.
    et al.
    Chakraborty, Sudip
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM).
    Baierle, Rogerio J.
    The effect of impurities in ultra-thin hydrogenated silicene and germanene: a first principles study2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 34, s. 22210-22216Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Spin polarized density functional theory within the GGA-PBE and HSE06 approach for the exchange correlation term has been used to investigate the stability and electronic properties of nitrogen and boron impurities in single layers of silicane and germanane. We have observed that these impurities have lower formation energies in silicane and germanane when compared to their counterparts in graphane. We have also noticed that the adsorption of H atoms in the vicinity of defects stabilizes the system. In addition, we have shown that the electronic properties of silicane and germanane can be tuned when N and B are incorporated in the Si and Ge network. N-doping and B-doping give rise to n-type and p-type semiconductor properties. However, the adsorption of H atoms quenches the doping effects.

  • 177. Saidi, W. A.
    et al.
    Norman, Patrick
    Linköping University, Sweden.
    Spectroscopic signatures of topological and diatom-vacancy defects in single-walled carbon nanotubes2014Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 4, s. 1479-1486Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The optical properties, including UV-vis spectra and resonance Raman profiles, of pristine and defected single-walled carbon nanotubes (SWCNTs) are computed using state-of-the-art time-dependent density functional theory (TDDFT) as implemented using the Liouville-Lanczos approach to linear-response TDDFT. The CNT defects were of the form of Stone-Wales and diatom-vacancies. Our results are in very good agreement with experimental results where defects were introduced into a part of defect-free CNTs. In particular, we show that the first and second π-π* excitation energies are barely shifted due to the defects and associated with a relatively small reduction in the maxima of the absorption bands. In contrast, the resonance Raman spectra show close to an order of magnitude reduction in intensities, offering a means to distinguish between pristine and defected SWCNTs even at low defect concentrations.

  • 178.
    Salek, Pawel
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Baev, A.
    Gel'mukhanov, Faris
    KTH, Tidigare Institutioner, Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Dynamical properties of X-ray Raman scattering2003Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 5, nr 1, s. 1-11Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This paper reviews theory for resonant X-ray scattering, emphasizing the dynamical aspects related to the nuclear motion during the scattering process. Various features of the theory are illustrated by simulations on small molecules in the gaseous phase. After the introduction de ning the X-ray Raman scattering process, we briefly describe some central concepts of its theory: the Raman law, the time hierarchy of X-ray scattering and the generalized Kramers-Heisenberg relation. We then go into some detail of various theoretical aspects of the process: transition moments and light polarization, time-dependent formulation and wave packets. We review two aspects of recent experimental focus: Doppler effects and generalized Franck-Condon factors. In the last part of the paper we discuss X-ray Raman scattering of dissociative core excited states, and the intriguing concept of a duration time for the scattering. We address dissociative resonant photoemission from first principles, with particular emphasis on the conditions for observing so-called atomic peaks and atomic holes. The atomic holes are the results of continuum continuum interference effects between the atomic and molecular channels which may act destructively under certain conditions. We demonstrate that the resonant contribution and the evolution of the atomic peaks can be subject to strong dynamical suppression caused by nuclear motion. In general, the molecular geometry dependence of the electronic transition moments can change the scattering cross section quite dramatically. This is exemplified here by an unusual spectral flattening for the B state of N-2, and by a breakdown of the spectator versus participator classification in a part of the non-radiative resonant photoemission spectrum of HF. The notion of a duration time in resonant X-ray scattering is put forward as a powerful concept for predicting and understanding qualitative aspects of many of the effects or processes treated in this paper. The role of the pulse shape for short pulse X-ray excitation is also discussed.

  • 179.
    Sanchez-de-Armas, Rocio
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ahlquist, Mårten S. G.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    On the nature of hydrogen bonds to platinum(II): Which interaction can predict their strength?2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 2, s. 812-816Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The interaction between hydrogen bond donors and platinum has been analysed. Our results point to an interaction that can be entirely predicted from the d(z2) orbital energy of the platinum centre indicating strong charge transfer, with significant dispersion contribution to the bonding, very different from classical hydrogen bonds.

  • 180. Sardar, Samim
    et al.
    Sarkar, Soumik
    Myint, Myo Tay Zar
    Al-Harthi, Salim
    Dutta, Joydeep
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Funktionella material, FNM.
    Pal, Samir Kumar
    Role of Central Metal Ion in Hematoporphyrin-Functionalized Titania in Solar Energy Conversion Dynamics2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 42, s. 18562-18570Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, we have investigated the efficacy of electron transfer processes in hematoporphyrin (HP) and iron hematoporphyrin ((Fe) HP) sensitized titania as potential materials for capturing and storing solar energy. Steady-state and picosecond-resolved fluorescence studies show the efficient photoinduced electron transfer processes in hematoporphyrin-TiO2 (HP-TiO2) and Fe(III)-hematoporphyrin-TiO2 (Fe(III)HP-TiO2) nanohybrids, which reveal the role of central metal ions in electron transfer processes. The bidentate covalent attachment of HP onto TiO2 particulates is confirmed by FTIR, Raman scattering and X-ray photoelectron spectroscopy (XPS) studies. The iron oxidation states and the attachment of iron to porphyrin through pyrrole nitrogen atoms were investigated by cyclic voltammetry and FTIR studies, respectively. We also investigated the potential application of HP-TiO2 and Fe(III)HP-TiO2 nanohybrids for the photodegradation of a model organic pollutant methylene blue (MB) in aqueous solution under wavelength dependent light irradiation. To further investigate the role of iron oxidation states in electron transfer processes, photocurrent measurements were done by using Fe(III) and Fe(II) ions in porphyrin. This work demonstrates the role of central metal ions in fundamental electron transfer processes in porphyrin sensitized titania and their implications for dye-sensitized device performance.

  • 181.
    Sarman, Sten
    et al.
    Stockholm Univ, Dept Mat & Environm Chem, Arrhenius Lab, S-10691 Stockholm, Sweden..
    Wang, Yong-Lei
    Stockholm Univ, Dept Mat & Environm Chem, Arrhenius Lab, S-10691 Stockholm, Sweden.;Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Rohlmann, Patrick
    KTH, Skolan för industriell teknik och management (ITM), Maskinkonstruktion (Inst.).
    Glavatskih, Sergei
    KTH, Skolan för industriell teknik och management (ITM), Maskinkonstruktion (Inst.), Maskinkonstruktion (Avd.).
    Laaksonen, Aatto
    Stockholm Univ, Dept Mat & Environm Chem, Arrhenius Lab, S-10691 Stockholm, Sweden.;Uppsala Univ, Dept Chem, Angstrom Lab, Box 538, S-75121 Uppsala, Sweden..
    Rheology of phosphonium ionic liquids: a molecular dynamics and experimental study2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 15, s. 10193-10203Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have studied the rheological behavior of the ionic liquid trihexyl(tetradecyl)phosphonium bis(mandelato)borate, [P-66614][BMB], and compared it with that of another ionic liquid, namely trihexyl(tetradecyl)phosphonium chloride, [P-66614][Cl]. The non-halogenated [P-66614][BMB] has been selected as it is known to provide enhanced lubrication performance and is, consequently, of technological importance. The ionic liquid [P-66614][Cl], despite its relatively simple anion, exhibits viscosities very similar to those of [P-66614][BMB], making it an excellent reference fluid for the modeling study. The viscosities of the ionic liquids have been obtained by equilibrium atomistic simulations using the Green-Kubo relation, and by performing nonequilibrium shear flow simulations. The influence of the simulation system size and a reduction of the atomic charges on the viscosities of the ionic liquids are systematically studied. The atomic charges are reduced to mimic the temperature dependent charge transfer and polarization effects. It has been found that scaling the point charges with factors between 0.60 and 0.80 from full ion charges can provide reliable viscosities of [P-66614][BMB], consistent with the experimentally measured viscosities within the studied temperature interval from 373 to 463 K. The viscosities of [P-66614][Cl] have been obtained with scaling factors between 0.80 and 1.0 reflecting the lower polarizability and charge transfer effects of the chloride anion.

  • 182. Schio, Luca
    et al.
    Li, Cui
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. CNR, IPCF, Inst Chem Phys Proc, Italy.
    Monti, Susanna
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. CNR, ICCOM, Inst Chem Organometall Cpds, Italy.
    Salen, Peter
    Yatsyna, Vasyl
    Feifel, Raimund
    Alagia, Michele
    Richter, Robert
    Falcinelli, Stefano
    Stranges, Stefano
    Zhaunerchyk, Vitali
    Carravetta, Vincenzo
    NEXAFS and XPS studies of nitrosyl chloride2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 14, s. 9040-9048Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The electronic structure of nitrosyl chloride (ClNO) has been investigated in the gas phase by X-ray Photoelectron (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy at the Cl 2p, Cl 2s, N 1s and O 1s edges in a combined experimental and theoretical study. The theoretical calculations at different levels of approximation predict ionization potential values in good agreement with the experimental data and allow us to assign the main features of the absorption spectra. An unexpected failure of the density functional model is, however, observed in the calculation of the Cl 2s binding energy, which is related to a large self-interaction error. Largely different photoabsorption cross-section patterns are experimentally observed in core excitations from the investigated quantum shells (n = 1, 2). This finding is confirmed by the oscillator strength distributions calculated at different absorption edges; in the case of the n = 2 shell the bands below the threshold are extremely weak and most of the absorption intensity is due to excitations in the continuum.

  • 183.
    Selvaraj, Sudarson
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Al3+ induced planarization, conformational arrest and metallochromic shift in a pyrimidine dione dye: insight from integrated hybrid quantum-classical calculations2012Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, nr 7, s. 2339-2345Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In order to explore the possibilities of simulating metallochromism by modern molecular modeling, we apply a sequential hybrid quantum-classical approach to a prototype metallochromic system-the Al3+ ion and pyrimidinedione (PY) dye complex. The complex shows several structural features with relevance for the metallochromism: the PY dye exhibits conformers with dynamical transitions between twisted structures, which are inhibited by the addition of the metal ion leading to planarization and a conformational arrest: the Al3+ ion behaves like a structure-modifier for both intra and intermolecular degrees of freedom and with respect to the intermolecular solvation shell structure. The sequential approach that we have employed uses DFT/MM molecular dynamics for structure modeling and TDDFT/PCM for property modeling. The computed metallochromic shift between PY and the Al(PY)(3+) complex in DMSO solvent is obtained in excellent agreement with experiment. The results infer optimism for future use of such modeling techniques to design metallochromic indicators.

  • 184. Shah, Faiz Ullah
    et al.
    Glavatskih, Sergei
    Luleå University of Technology, Division of Machine Elements.
    MacFarlane, Douglas R.
    Somers, Anthony
    Forsyth, Maria
    Antzutkin, Oleg N.
    Novel halogen-free chelated orthoborate-phosphonium ionic liquids: synthesis and tribophysical properties2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 28, s. 12865-12873Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report on the synthesis, characterisation, and physical and tribological properties of halogen-free ionic liquids based on various chelated orthoborate anions with different phosphonium cations, both without halogen atoms in their structure. Important physical properties of the ILs including glass transition temperatures, density, viscosity and ionic conductivity were measured and are reported here. All of these new halogen-free orthoborate ionic liquids (hf-BILs) are hydrophobic and hydrolytically stable liquids at room temperature. As lubricants, these hf-BILs exhibit considerably better antiwear and friction reducing properties under boundary lubrication conditions for steel-aluminium contacts as compared with fully formulated (15W-50 grade) engine oil. Being halogen free these hf-BILs offer a more environmentally benign alternative to ILs being currently developed for lubricant applications.

  • 185. Shukla, V.
    et al.
    Araujo, R. B.
    Jena, N. K.
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik.
    Borophene's tryst with stability: Exploring 2D hydrogen boride as an electrode for rechargeable batteries2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 34, s. 22008-22016Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Graphene's emergence can be viewed as a positive upheaval in 2D materials research. Along the same line, the realization of a related elemental 2D material, borophene, is another breakthrough. To circumvent the stability issues of borophene, which is reported to have been synthesized on metallic substrates under extreme conditions, hydrogenation of borophene (otherwise called as borophane or hydrogen boride or boron hydride) has been a plausible solution, but only proposed computationally. A recent report (H. Nishino, T. Fujita, N. T. Cuong, S. Tominaka, M. Miyauchi, S. Iimura, A. Hirata, N. Umezawa, S. Okada, E. Nishibori, A. Fujino, T. Fujimori, S. Ito, J. Nakamura, H. Hosono and T. Kondo, J. Am. Chem. Soc., 2017, 139(39), 13761-13769) brings to fore its experimental realization. Our current study delves into the possibilities of employing this intriguing 2D hydrogen boride as anodes in Li/Na ion batteries. Using first-principles density functional theory methods, we computed relevant properties such as the ion (Li/Na) adsorption behavior, the possible pathways of ionic diffusion with the estimation of barriers as well as the theoretical specific capacities and average voltages to uniquely demonstrate that this material is of particular significance for battery applications. It is noted that the use of hydrogen boride leads to a high specific capacity of 861.78 mA h g-1 for Li ions, which is remarkably higher than the value reported in relation to its computationally predicted structure. Furthermore, Na ion intercalation leads to negative voltage profiles, implying the unsuitability of 2D hydrogen boride for this particular ion. Our findings are timely and pertinent towards adding insightful details relevant to the progress of applications of 2D materials for energy storage.

  • 186.
    Shukla, Vivekanand
    et al.
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Grigoriev, Anton
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Jena, Naresh K.
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik.
    Strain controlled electronic and transport anisotropies in two-dimensional borophene sheets2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 35, s. 22952-22960Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Two recent reports on realization of an elemental 2D analogue of graphene:borophene (Science, 2015, 350, 1513-1516; Nat. Chem., 2016, 8, 563-568) focus on the inherent anisotropy and directional dependence of the electronic properties of borophene polymorphs. Achieving stable 2D borophene structures may lead to some degree of strain in the system because of the substrate-lattice mismatch. We use first principles density functional theory (DFT) calculations to study the structural, electronic and transport properties of (12) and -borophene polymorphs. We verified the directional dependency and found the tunable anisotropic behavior of the transport properties in these two polymorphs. We find that strain as low as 6% brings remarkable changes in the properties of these two structures. We further investigate current-voltage (I-V) characteristics in the low bias regime after applying a strain to see how the anisotropy of the current is affected. Such observations like the sizeable tuning of transport and I-V characteristics at the expense of minimal strain suggest the suitability of 2D borophene for futuristic device applications.

  • 187.
    Singh, Deobrat
    et al.
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Panda, Pritam Kumar
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Mishra, Yogendra Kumar
    Univ Southern Denmark, NanoSYD, Mads Clausen Inst, Alsion 2, Odense, Denmark..
    Ahuja, Rajeev
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Condensed Matter Theory Grp, Box 516, SE-75120 Uppsala, Sweden..
    Van der Waals induced molecular recognition of canonical DNA nucleobases on a 2D GaS monolayer2020Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 22, nr 12, s. 6706-6715Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present study, we systematically investigated the adsorption mechanism of canonical DNA nucleobases and their two nucleobase pairs on a single-layer gallium sulfide (GaS) substrate using DFT+D3 methods. The GaS substrate has chemical interactions with molecules 0.02 |e| 0.11 |e| from molecules to the monolayer GaS surface. Due to the chemical interactions of adenine, cytosine, guanine, and thymine on the monolayer GaS surface, the work function is decreased by 0.69, 0.60, 0.97, and 0.20 eV, respectively. It is displayed that the bandgap of the monolayer GaS sheet can be significantly affected as induced molecular electronic states tend to appear near the Fermi level region due to chemical and physisorption mechanism. We have also investigated the transport properties of DNA nucleobases, namely, AT and GC pair molecules on the GaS surface, which shows significant reduction in the zero-bias transmission spectra. Moreover, with and without DNA nucleobases, namely, AT and GC pair molecules' absorptions on the GaS surface, clearly expressed in terms of distinct current signals, can be observed as ON and OFF states for this device. The distinctive nucleobase adsorption energies and different I-V responses may serve as potential probes for the selective detection of nucleobase molecules in imminent DNA sequencing applications based on a monolayer GaS surface.

  • 188. Sirtl, T.
    et al.
    Jelic, J.
    Meyer, J.
    Das, K.
    Heckl, W. M.
    Moritz, W.
    Rundgren, John
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Materialteori.
    Schmittel, M.
    Reuter, K.
    Lackinger, M.
    Adsorption structure determination of a large polyaromatic trithiolate on Cu(111): Combination of LEED-I(V) and DFT-vdW2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 26, s. 11054-11060Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The adsorption geometry of 1,3,5-tris(4-mercaptophenyl)benzene (TMB) on Cu(111) is determined with high precision using two independent methods, experimentally by quantitative low energy electron diffraction (LEED-I(V)) and theoretically by dispersion corrected density functional theory (DFT-vdW). Structural refinement using both methods consistently results in similar adsorption sites and geometries. Thereby a level of confidence is reached that allows deduction of subtle structural details such as molecular deformations or relaxations of copper substrate atoms.

  • 189. Sjodin, M.
    et al.
    Ghanem, R.
    Polivka, T.
    Pan, J.
    Styring, S.
    Sun, Licheng C.
    Sundstrom, V.
    Hammarstrom, L.
    Tuning proton coupled electron transfer from tyrosine: A competition between concerted and step-wise mechanisms2004Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, nr 20, s. 4851-4858Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The intra-molecular, proton-coupled electron transfer from a tyrosine residue to covalently linked tris-bipyridine ruthenium(III) complexes in aqueous solution (Ru-III-TyrOH --> Ru-II-TyrO(.) + H+) is studied in two complexes. The Ru-III-TyrOH state is generated by laser flash-induced photo-oxidation in the presence of the electron acceptor methyl viologen. The reaction is shown to follow either a concerted electron transfer-deprotonation (CEP) mechanism or a step-wise mechanism with electron transfer followed by deprotonation (ETPT). The CEP is characterised by a pH-dependent rate constant, a large reorganisation energy (lambda = 1.4 eV at pH = 7) and a significant kinetic isotope effect: k(H)/k(D) = 1.5-3. We can explain the pH-dependence and the high lambda by the pH-dependent DeltaGdegrees' for proton release to bulk water, and by the additional reorganisation energy associated with the proton transfer coordinate (both internal and solvent), respectively. In the calculation of lambda from the temperature dependent rate constant, correction is made for the large entropy increase of the reaction (TDeltaS(rxn) approximate to0.41 eV at pH = 7 and T = 298 K). The step-wise ETPT mechanism on the other hand shows a pH-independent rate, a lower reorganisation energy and no kinetic isotope effect. We propose that our complexes can be used as models to understand proton-coupled electron transfer in radical proteins. We show that the mechanism can be switched between CEP and ETPT by tuning the reaction pH and the electrochemical potential of the Ru-III/II oxidant. With a low driving force for the overall reaction the energy conservative CEP mechanism may dominate, in spite of the higher reorganisation energy as compared to ETPT.

  • 190. Sjöqvist, J.
    et al.
    González-Cano, R. C.
    López Navarrete, J. T.
    Casado, J.
    Ruiz Delgado, M. C.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes2014Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 45, s. 24841-24852Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra has been investigated, both experimentally and theoretically.

  • 191. Sjöqvist, J.
    et al.
    Linares, M.
    Lindgren, M.
    Norman, Patrick
    Linköping University, Sweden.
    Molecular dynamics effects on luminescence properties of oligothiophene derivatives: A molecular mechanics-response theory study based on the CHARMM force field and density functional theory2011Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, nr 39, s. 17532-17542Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    CHARMM force field parameter values for a class of oligothiophene derivatives have been derived with reference to density functional theory/B3LYP potential energy surfaces. The force field parametrization of these luminescent conjugated polyelectrolytes includes the electronic ground state as well as the strongly light absorbing first excited state. In conjunction with quantum chemical response theory calculations of transition state properties, a molecular dynamical model of the Stokes shift is obtained. The theoretical model is benchmarked against experimental data recorded at room temperature which refer to sodium salts of p-HTAA and p-FTAA with distilled water as a solvent. For p-HTAA the theoretically predicted Stokes shift of 112 nm is in good agreement with the experimental result of 124 nm, given the approximations about exciton localization that were introduced to obtain a force field for the excited state. This journal is © the Owner Societies.

  • 192.
    Skoglund, Sara
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap. Stockholm University, Sweden.
    Blomberg, Eva
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap. RISE Research Institutes of Sweden, Division Bioscience and Materials, Sweden.
    Odnevall Wallinder, Inger
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Grillo, Isabelle
    Pedersen, Jan Skov
    Bergström, L. Magnus
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap. Uppsala University, Uppsala, Sweden.
    A novel explanation for the enhanced colloidal stability of silver nanoparticles in the presence of an oppositely charged surfactant2017Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, nr 41, s. 28037-28043Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structural behavior in aqueous mixtures of negatively charged silver nanoparticles (Ag NPs) together with the cationic surfactants cetyltrimethylammonium bromide (CTAB) and dodecyltrimethylammonium chloride (DTAC), respectively, has been investigated using SANS and SAXS. From our SANS data analysis we are able to conclude that the surfactants self-assemble into micellar clusters surrounding the Ag NPs. We are able to quantify our results by means of fitting experimental SANS data with a model based on cluster formation of micelles with very good agreement. Based on our experimental results, we propose a novel mechanism for the stabilization of negatively charged Ag NPs in a solution of positively charged surfactants in which cluster formation of micelles in the vicinity of the particles prevents the particles from aggregating. Complementary SAXS and DLS measurements further support this novel way of explaining stabilization of small hydrophilic nanoparticles in surfactant-containing solutions.

  • 193.
    Spah, Alexander
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Pathak, Harshad
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Kim, Kyung Hwan
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Perakis, Fivos
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Mariedahl, Daniel
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Amann-Winkel, Katrin
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Sellberg, Jonas A.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biomedicinsk fysik och röntgenfysik.
    Lee, Jae Hyuk
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Kim, Sangsoo
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Park, Jaehyun
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Nam, Ki Hyun
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Katayama, Tetsuo
    Japan Synchrotron Radiat Res Inst, Kouto 1-1-1, Sayo, Hyogo 6795198, Japan..
    Nilsson, Anders
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Apparent power-law behavior of water's isothermal compressibility and correlation length upon supercooling2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 1, s. 26-31Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The isothermal compressibility and correlation length of supercooled water obtained from small-angle X-ray scattering (SAXS) were analyzed by fits based on an apparent power-law in the temperature range from 280 K down to the temperature of maximum compressibility at 229 K. Although the increase in thermodynamic response functions is not towards a critical point, it is still possible to obtain an apparent power law all the way to the maximum values with best-fit exponents of gamma = 0.40 +/- 0.01 for the isothermal compressibility and nu = 0.26 +/- 0.03 for the correlation length. The ratio between these exponents is close to a value of approximate to 0.5, as expected for a critical point, indicating the proximity of a potential second critical point. Comparison of gamma obtained from experiment with molecular dynamics simulations on the iAMOEBA water model shows that it would be located at pressures in the neighborhood of 1 kbar. The high value and sharpness of the compressibility maximum observed in the experiment are not reproduced by any of the existing classical water models, thus inviting further development of simulation models of water.

  • 194. Steindal, Arnfinn Hykkerud
    et al.
    Beerepoot, Maarten T. P.
    Ringholm, Magnus
    Holmgaard List, Nanna
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ruud, Kenneth
    Kongsted, Jacob
    Olsen, Jogvan Magnus Haugaard
    Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 40, s. 28339-28352Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA) properties can be studied by evaluating single residues of the response functions. The PE approach includes mutual polarization effects between the quantum and classical parts of the system through induced dipoles that are determined self-consistently with respect to the electronic density. The applicability of our approach is demonstrated by calculating MPA strengths up to four-photon absorption for the green fluorescent protein. We show how the size of the quantum region, as well as the treatment of the border between the quantum and classical regions, is crucial in order to obtain reliable MPA predictions.

  • 195.
    Sthoer, Adrien
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi.
    Hladilkova, Jana
    Lund Univ, Sweden.
    Lund, Mikael
    Lund Univ Sweden.
    Tyrode, Eric
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi.
    Molecular insight into carboxylic acid-alkali metal cations interactions: reversed affinities and ion-pair formation revealed by non-linear optics and simulations2019Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 21, s. 11329-11344Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Specific interactions between the carboxylic acid moiety and the monovalent salts CsCl, NaCl, and LiCl, have been investigated in Langmuir monolayers using vibrational sum frequency spectroscopy (VSFS) and complemented with coarse grained and all-atom molecular dynamics simulations. By exploiting VSFS's intrinsic surface specificity, an emphasis was made on targeting headgroup vibrations of both its charged and uncharged forms as well as water molecules in the interfacial layer. The degree of deprotonation of the monolayer as a function of cation concentration and pH was experimentally determined and theoretically rationalized. Starting from 100 mM, the surface charge was overestimated by the Gouy-Chapman model and varied depending on the identity of the cation, highlighting the appearance of ion specific effects. Agreement could be found using a modified Poisson-Boltzmann model that takes into account steric effects, with a fitted effective ion-size compatible with the hydrated ion diameters. The relative affinity of the cations to the carboxylic acid moiety was pH dependent: at pH 4.5 they arranged in the order Cs+ 4 Na+ 4 Li+, but fully reversed (Li+ 4 Na+ 4 Cs+) at pH 9. Simulations yielded microscopic insight into the origin of this behavior, with the cations showing contrasting interaction preferences for either the uncharged carboxylic acid or the charged carboxylate. Sum frequency spectra also provided evidence that all cations remained hydrated when interacting with the charged headgroup, forming solvent-separated or solvent-shared ion pairs. However, for the specific case of 1 M Li+ at pH 9, contact ion pairs were formed. Finally, the remarkable effect of trace metal multivalent cations in the interpretation of experiments is briefly discussed. The results provide exciting new insights into the complex interactions of alkali metal cations with the biophysically relevant carboxylic acid moiety.

  • 196. Sun, Bing
    et al.
    Mindemark, Jonas
    Morozov, Evgeny V.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Costa, Luciano T.
    Bergman, Martin
    Johansson, Patrik
    Fang, Yuan
    Furo, Istvan
    Brandell, Daniel
    Ion transport in polycarbonate based solid polymer electrolytes: experimental and computational investigations2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 14, s. 9504-9513Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with epsilon-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li+ and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li+-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.

  • 197.
    Sun, Lu
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hede, Thomas
    Stockholm University.
    Tu, Yaoquan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Leck, Caroline
    Stockholm University.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Molecular Dynamics Simulations Reveal the Assembly Mechanism of Polysaccharides in Marine Aerosols2014Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, nr 47, s. 25935-25941Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    The high Arctic marine environment has recently detected polymer gels in atmospheric aerosol particles and cloud water originating from the surface microlayer of the open leads within the pack ice area. These polysaccharide molecules are water insoluble but water solvated, highly surface-active and highly hydrated (99% water). In order to add to the understanding and to complement missing laboratory characterization of marine polymer gels we have in this work performed an atomistic study of the assembly process and interfacial properties of polysaccharides. Our study reveals a number of salient features of the microscopic process behind polysaccharide assembly into nanogels. With three- and four-repeating units the polysaccharides assemble into a cluster in 50 ns. The aggregates grow quicker by absorbing one or two polymers each time, depending on the unit length and the type of inter-bridging cation. Although both the hydrophobic and hydrophilic domains are contracted, the latter dominates distinctly upon the contraction of solvent accessible surface areas. The establishment of inter-chain hydrogen-bonds is the key to the assembly while ionic bridges can further promote aggregation. During the assembly of the more bent four-unit polymers, intra-chain hydrogen bonds are significantly diminished by Ca2+. Meanwhile, the percentage of Ca2+ acting as an ionic bridge is more eminent, highlighting the significance of Ca2+ ions for longer-chain polysaccharides. The aggregates are able to enhance surface tension more in the presence of Ca2+ than in the presence of Na+ owing to their more compact structure. These conclusions all demonstrate that studies of the present kind provide insight into the self-assembly process and interfacial properties of marine gels. We hope this understanding will keep up the interest in the complex and the fascinating relationship between marine microbiology, atmospheric aerosols, clouds and climate.

  • 198.
    Sun, Lu
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tu, Yaoquan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Origin of Ion Selectivity at the Air/Water Interface2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 6, s. 4311-4318Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Among many characteristics of ions, their capability to accumulate at air/water interfaces is a particular issue that has been the subject of much research attention. For example, the accumulation of halide anions (Cl-, Br-, I-) at the water surface is of great importance to heterogeneous reactions that are of environmental concern. However, the actual mechanism that drives anions towards the air/water interface remains unclear. In this work, we have performed atomistic simulations using polarizable models to mimic ionic behavior under atmospheric conditions. We find that larger anions are abundant at the water surface and that the cations are pulled closer to the surface by the counterions. We propose that polarization effects stabilize the anions with large radii when approaching the surface. This energetically more favorable situation is caused by the fact that the more polarized anions at the surface attract water molecules more strongly. Of relevance is also the ordering of the surface water molecules with their hydrogen atoms pointing outwards which induce an external electronic field that leads to a different surface behavior of anions and cations. The water-water interaction is weakened by the distinct water-ion attraction, a point contradicting the proposition that F- is a kosmotrope. The simulation results thus allow us to obtain a more holistic understanding of the interfacial properties of ionic solutions and atmospheric aerosols.

  • 199.
    Sun, Weiwei
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Li, Yunguo
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Zhu, Li
    Ma, Yanming
    Di Marco, Igor
    Johansson, Börje
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Korzhavyi, Pavel
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Gluing together metallic and covalent layers to form Ru2C under ambient conditions2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 15, s. 9730-9736Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ru2C has recently been synthesised at high pressure and high temperature, and was assumed to have a structure with space group P (3) over bar m1. However, subsequent theoretical work has revealed that this structure is unstable under ambient conditions, which motivated us to look for the stable structure. In this work, we explore the structures of Ru2C by using an unbiased swarm structure searching algorithm. The structures with R3m and R (3) over barm symmetries have been found to be lower in energy than the P (3) over bar m1 structure, at the same time being dynamically stable under ambient conditions. These layered structures consist of alternating Ru bilayers and C monolayers in the R3m structure, and alternating Ru tetra-layers and C bilayers in the R (3) over barm structure. The C layers are more evenly distributed and more covalently bound to the Ru layers in the R3m structure than in the R (3) over barm structure. Instead, in the R (3) over barm structure there exists more Ru-Ru metallic bonding, which has a crucial role in diminishing the hardness of this material. Our findings should stimulate further explorations of the structures and properties of the heavy transition metal carbides and nitrides, potentially leading to industrial applications.

  • 200.
    Svärd, Michael
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemiteknik. Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Devi, K. Renuka
    Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Khamar, Dikshitkumar
    Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Mealey, Donal
    Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Cheuk, Dominic
    Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Zeglinski, Jacek
    Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Rasmuson, Åke C.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemiteknik. Univ Limerick, Bernal Inst, Dept Chem & Environm Sci, Synth & Solid State Pharmaceut Ctr, Castletroy, Ireland..
    Solute clustering in undersaturated solutions systematic dependence on time, temperature and concentration2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 22, s. 15550-15559Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular clustering and solvent-solute interactions in isopropanol solutions of fenoxycarb have been thoroughly and systematically investigated by dynamic light scattering, small-angle X-ray scattering, and nanoparticle tracking, supported by infrared spectroscopy and molecular dynamics simulations. The existence of molecular aggregates, clusters, ranging in size up to almost a micrometre is clearly recorded at undersaturated as well as supersaturated conditions by all three analysis techniques. The results systematically reveal that the cluster size increases with solute concentration and time at stagnant conditions. For most concentrations the time scale of cluster growth is of the order of days. In undersaturated solutions the size appears to eventually reach a maximum value, higher the higher the concentration. Below a certain concentration threshold clusters are significantly smaller. Clusters are found to be smaller in solutions pre-heated at a higher temperature, which offers a possible explanation for the so-called "history of solution'' effect. The cluster distribution is influenced by filtration through membranes with a pore size of 0.1 mm, offering an alternative explanation for the "foreign particle-catalysed nucleation'' effect. At moderate concentrations larger clusters appear to be sheared into smaller ones, but the original size distribution is rapidly re-established. At higher concentrations, although still well below solubility, the cluster size as well as solute concentration are strongly affected, suggesting that larger clusters contain at least a core of more organized molecules not able to pass through the filter.

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