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1.	Baev, Alexander, et al. (author) Theoretical Simulations of clamping levels in optical power limiting 2006 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207 .- 1520-5215. ; 110:42, s. 20912-20916 Journal article (peer-reviewed)abstract Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol-gel glass matrix. A clamping level of 2.5 mu J is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.
2.	Malysheva, Lyuba, et al. (author) Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling 2005 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106 .- 1520-5207. ; 109:34, s. 7788-7796 Journal article (peer-reviewed)abstract The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O)6H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.
3.	Abbas, Zareen, 1962, et al. (author) Monte Carlo Simulations of Salt Solutions: Exploring the Validity of Primitive Models 2009 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:17, s. 5905-5916 Journal article (peer-reviewed)abstract An extensive series of Monte Carlo (MC) simulations were performed in order to explore the validity of simple primitive models of electrolyte solutions and in particular the effect of ion size asymmetry on the bulk thermodynamic properties of real salt solutions. Ionic activity and osmotic coefficients were calculated for 1:1, 2:1, and 3:1 electrolytes by using the unrestricted primitive model (UPM); i.e., ions are considered as charged hard spheres of different sizes dissolved in a dielectric continuum. Mean ionic activity and osmotic coefficients calculated by the MC simulations were fitted simultaneously to the experimental data by adjusting only the cation radius while keeping the anion radius fixed at its crystallographic value. Ionic radii were further optimized by systematically varying the cation and anion radii at a fixed sum of ionic radii. The success of this approach is found to be highly salt specific. For example, experimental data (mean ionic activity and osmotic coefficients) of salts which are usually considered as dissociated such as HCl, HBr, LiCl, LiBr, LiClO4, and KOH were successfully fitted up to 1.9, 2.5, 1.9, 3, 2.5, and 4.5 M concentrations, respectively. In the case of partially dissociated salts such as NaCl, the successful fits were only obtained in a more restricted concentration range. Consistent sets of the best fitted cation radii were obtained for acids, alkali, and alkaline earth halides. A list of recommended ionic radii is also provided. The reliability of the optimized ionic radii was further tested in simulations of the osmotic coefficients of LiCl−NaCl−KCl salt mixtures. A very good agreement between the simulated and experimental data was obtained up to ionic strength of 4.5 M.
4.	Abdurrokhman, Iqbaal, 1991, et al. (author) Protic Ionic Liquids Based on the Alkyl-Imidazolium Cation: Effect of the Alkyl Chain Length on Structure and Dynamics 2019 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 123:18, s. 4044-4054 Journal article (peer-reviewed)abstract Protic ionic liquids are known to form extended hydrogen-bonded networks that can lead to properties different from those encountered in the aprotic analogous liquids, in particular with respect to the structure and transport behavior. In this context, the present paper focuses on a wide series of 1-alkyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquids, [HC n Im][TFSI], with the alkyl chain length (n) on the imidazolium cation varying from ethyl (n = 2) to dodecyl (n = 12). A combination of several methods, such as vibrational spectroscopy, wide-angle X-ray scattering (WAXS), broadband dielectric spectroscopy, and 1 H NMR spectroscopy, is used to understand the correlation between local cation-anion coordination, nature of nanosegregation, and transport properties. The results indicate the propensity of the -NH site on the cation to form stronger H-bonds with the anion as the alkyl chain length increases. In addition, the position and width of the scattering peak q 1 (or the pre-peak), resolved by WAXS and due to the nanosegregation of the polar from the nonpolar domains, are clearly dependent on the alkyl chain length. However, we find no evidence from pulsed-field gradient NMR of a proton motion decoupled from molecular diffusion, hypothesized to be facilitated by the longer N-H bonds localized in the segregated ionic domains. Finally, for all protic ionic liquids investigated, the ionic conductivity displays a Vogel-Fulcher-Tammann dependence on inverse temperature, with an activation energy E a that also depends on the alkyl chain length, although not strictly linearly.
5.	Acebes, S., et al. (author) Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases 2017 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 121:16, s. 3946-3954 Journal article (peer-reviewed)abstract Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.
6.	Acke, Filip, 1968, et al. (author) Role of adsorbed surface oxygen in the adsorption of NO on alkaline earth oxides and Pt-promoted CaO surfaces 1999 In: Journal of Physical Chemistry B Materials. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 103:6, s. 972-978 Journal article (peer-reviewed)abstract Adsorbed surface oxygens are formed on CaO, SrO, and BaO during exposure to N2O, and their presence is shown to affect the room-temperature NO adsorption. Information about the adsorbed intermediates is contained in the desorption products and in the desorption temperatures during the subsequent heating ramp in Ar. The presence of adsorbed oxygen species increases the total amount of adsorbed NO for CaO and BaO substrates, whereas for SrO the adsorbed intermediate is stabilized. Two NO desorption peaks are found for CaO and SrO, one at low and one at high temperature. The former is assigned to adsorbed NO, whereas the latter is assigned to adsorbed -NO2 and/or -NO3 species. NO adsorption as -NO2 and/or -NO3 species finds evidence in the corresponding O2 desorption. Only one NO desorption peak is found for BaO. This NO desorption peak disappears in the absence of preadsorbed surface oxygens. O2 desorption is observed, even in the absence of any preadsorbed surface oxygens, for CaO and SrO substrates. This suggests NO bond dissociation upon NO adsorption. The effect of the promotion of CaO by Pt has also been investigated. The respective desorption profiles are similar to those for the unpromoted CaO with preadsorbed surface oxygens, although the amounts are significantly increased.
7.	Acke, Filip, et al. (author) Study of the reduction and reoxidation of a CaO surface 1997 In: J Phys Chem B. - 1520-5207 .- 1520-6106. ; 101:33, s. 6484- Journal article (peer-reviewed)abstract The reduction of NO with CO and H2 is shown to comprise two basic reactions: a surface oxygen abstraction by the reducing agent and a reoxidation of the surface by NO. The former reaction step has been demonstrated by transient CO2 formation during CO exposure of oxidized CaO surfaces, while the latter was demonstrated by N2 and/or N2O transient formation during NO exposure of a prereduced CaO surface. It was shown that at low temperatures (between room temperature and 500 °C) both N2 and N2O were formed, but at temperatures above 500 °C only N2 was observed. The activation energies of the respective steps have been determined using temperature-programmed reaction experiments. The activation energy of the surface oxygen abstraction was determined to be 25 kcal/mol and is similar to the apparent activation energy of the overall reaction. The activation energy of the NO bond breakage was determined to be maximum 10 kcal/mol as measured by N2O formation. The importance of an N2O2- or N2O22- intermediate in the formation of N2O will be discussed, and the importance of N2O decomposition in forming N2 at temperatures above 500 °C will be compared with a N surface diffusion mechanism.
8.	Adebahr, J, et al. (author) Ion and solvent dynamics in gel electrolytes based on ethylene oxide grafted acrylate polymers 2002 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106 .- 1089-5647. ; 106:47, s. 12119-12123 Journal article (peer-reviewed)abstract Multinuclear pulsed field gradient NMR measurements and theological viscosity measurements were performed on three series of polymer gel electrolytes. The gels were based on a lithium salt electrolyte swollen into a copolymer matrix comprising an acrylate backbone and ethylene oxide side chains. In each series the side chains differed in length and number, but the acrylate-to-ethylene oxide ratio was kept constant. It was found that the self-diffusion coefficient of the cations was much lower than that of the anions, and that it decreased rapidly when the side chains got longer. In contrast, the self-diffusion coefficient of the anions was found to be independent of chain length. In the gel electrolytes, the diffusion coefficients of the solvent molecules are relatively constant despite an increased viscosity with increasing length of the side chains. However, in saltfree gels made for comparison, the diffusion coefficients of the solvent molecules decreased with, increasing length of the side chains, which is consistent with an increased viscosity.
9.	Agrell, H. G., et al. (author) Conductivity studies of nanostructured TiO2 films permeated with electrolyte 2004 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:33, s. 12388-12396 Journal article (peer-reviewed)abstract Charge transport in nanostructured TiO2 films permeated with an electrolyte was studied, using temperature-dependent conductivity and electron accumulation measurements. Two regions for charge transport were distinguished from the relationship between conductivity and electron concentration. In the first region (similar to1-20 electrons per TiO2 particle), the effective electron mobility is dependent on the electron concentration and values between 7 x 10(-4) and 78 x 10(-4) cm(2) V-1 s(-1) were determined. The activation energy of the mobility was similar to0.3 eV. The charge transport can be described with a trapping/detrapping model that involves localized band-gap states. In the second region (> 20 electrons per TiO2 particle), the effective electron mobility is independent of electron concentration and values of similar to150 x 10(-4) cm(2) V-1 s(-1) are calculated. The activation energy of mobility is in the range of 0-0.15 eV, depending on the electrolyte. Transport of electrons in the conduction band seems to be the most applicable model.
10.	Agzenai, Y, et al. (author) In Situ X-ray Polymerization: From Swollen Lamellae to Polymer-Surfactant Complexes 2014 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:4, s. 1159-1167 Journal article (peer-reviewed)abstract The influence of the monomer diallyldimethylammonium chloride (D) on the lamellar liquid crystal formed by the anionic surfactant aerosol OT (AOT) and water is investigated, determining the lamellar spacings by SAXS and the quadrupolar splittings by deuterium NMR, as a function of the D or AOT concentrations. The cationic monomer D induces a destabilization of the AOT lamellar structure such that, at a critical concentration higher than 5 wt %, macroscopic phase separation takes place. When the monomer, which is dissolved in the AOT lamellae, is polymerized in situ by X-ray initiation, a new collapsed lamellar phase appears, corresponding to the complexation of the surfactant with the resulting polymer. A theoretical model is employed to analyze the variation of the interactions between the AOT bilayers and the stability of the lamellar structure.
11.	Ahadi, Aylin, et al. (author) Three-Dimensional Simulation of Nanoindentation Response of Viral Capsids. Shape and Size Effects 2009 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 113:11, s. 3370-3378 Journal article (peer-reviewed)abstract The nanoindentation response of empty viral capsids is modeled using three-dimensional finite element analysis. Simulation with two different geometries, spherical and icosahedral, is performed using the finite element code Abaqus. The capsids are modeled as nonlinear Hookean elastic, and both small and large deformation analysis is performed. The Young's modulus is determined by calibrating the force-indentation curve to data from atomic force microscopy (AFM) experiments. Force-indentation curves for three different viral capsids are directly compared to experimental data. Predictions are made for two additional viral capsids. The results from the simulation showed a good agreement with AFM data. The paper demonstrates that over the entire range of virus sizes (or Foppl-von Karman numbers) spherical and icosahedral models yield different force responses. In particular, it is shown that capsids with dominantly spherical shape (for low Foppl-von Karman numbers) exhibit nearly linear relationship between force and indentation, which has been experimentally observed on the viral shell studies so far. However, we predict that capsids with significant faceting (for large Foppl-von Karman numbers) and thus more pronounced icosahedral shape will exhibit rather nonlinear deformation behavior.
12.	Ai, Yue-Jie, 1982-, et al. (author) Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase 2011 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982 Journal article (peer-reviewed)abstract Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
13.	Ai, Yue-Jie, et al. (author) Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA 2010 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102 Journal article (peer-reviewed)abstract The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
14.	Aidas, Kestutis, et al. (author) Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics 2013 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 2069-2080 Journal article (peer-reviewed)abstract Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.
15.	Ainalem, Marie-Louise, et al. (author) On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates To Penetrate POPC Model Biomembranes 2010 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:21, s. 7229-7244 Journal article (peer-reviewed)abstract Poly(amido amine) (PAMAM) dendrimers have previously been shown, as cationic condensing agents of DNA, to have high potential for nonviral gene delivery. This study addresses two key issues for gene delivery: the interaction of the biomembrane with (i) the condensing agent (the cationic PAMAM dendrimer) and (ii) the corresponding dendrimer/DNA aggregate. Using in situ null ellipsometry and neutron reflection, parallel experiments were carried out involving dendrimers or generations 2 (G2), 4 (G4), and 6 (G6). The study demonstrates that free dendrimers of all three generations were able to traverse supported palmitoyloleoylphosphatidylcholine (POPC) bilayers deposited on silica surfaces. The model biomembranes were elevated front the solid surfaces upon dendrimer penetration, which offers a promising new way to generate more realistic model biomembranes where the contact with the supporting surface is reduced and where aqueous cavities are present beneath the bilayer. The largest dendrimer (GO) induced partial bilayer destruction directly upon penetration, whereas the smaller dendrimers (G2 and G4) leave the bilayer intact, so we propose that lower generation dendrimers have greater potential as transfection mediators. In addition to the experimental observations, coarse-grained simulations on the interaction between generation 3 (03) dendrimers and POPC bilayers were performed in the absence and presence of a bilayer-supporting negatively charged surface that emulates the support. The simulations demonstrate that G3 is transported across free-standing POPC bilayers by direct penetration and not by endocytosis. The penetrability was, however, reduced in the presence of a surface, indicating that the membrane transport observed experimentally was not driven solely by the surface. The experimental reflection techniques were also applied to dendrimer/DNA aggregates of charge ratio = 0.5, and while G2/DNA and G4/DNA aggregates interact with POPC bilayers. G6/DNA displays no such interaction. These results indicate that, in contrast to free dendrimer molecules, dendrimer/DNA aggregates of low charge ratios are not able to traverse a membrane by direct penetration.
16.	Akhtar, Sultan, et al. (author) Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor 2010 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:41, s. 13255-13262 Journal article (peer-reviewed)abstract The present work provides the first real-space analysis of nanobead-DNA coil interactions. Immobilization of oligonucleotide-functionalized magnetic nanobeads in rolling circle amplified DNA-coils was studied by complex magnetization measurements and transmission electron microscopy (TEM), and a statistical analysis of the number of beads hybridized to the DNA-coils was performed. The average number of beads per DNAcoil using the results from both methods was found to be around 6 and slightly above 2 for samples with 40 and 130 nm beads, respectively. The TEM analysis supported an earlier hypothesis that 40 nm beads are preferably immobilized in the interior of DNA-coils whereas 130 nm beads, to a larger extent, are immobilized closer to the exterior of the coils. The methodology demonstrated in the present work should open up new possibilities for characterization of interactions of a large variety of functionalized nanoparticles with macromolecules, useful for gaining more fundamental understanding of such interactions as well as for optimizing a number of biosensor applications.
17.	Akinchina, Anna, et al. (author) Monte Carlo simulations of polyion-macroion complexes. 2. Polyion length and charge density dependence 2003 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:32, s. 8011-8021 Journal article (peer-reviewed)abstract The complexation between a polyion and an oppositely charged spherical macroion in the framework of the primitive model has been studied by the use of Monte Carlo simulations. The polyion length, linear charge density, and bare persistence length are varied systematically, while the properties of the macroion are kept constant. The polyion charge to macroion charge ratio is varied between 1/4 and 4. The structure of the complex is investigated by direct visualization; polyion bead complexation probability; loop, tail, and train characteristics; degree of overcharging; and tail joint probability functions. The strongest complexes are observed for flexible chains, where the polyion is folded around the macroion. In the case of fully flexible chains, a transition from a collapsed state to a fluctuating two-tail state and eventually to a one-tail state are observed as the chain length is increased. As the stiffness is increased, several complex structures, such as multiloop, single-loop, and solenoid arrangements, and finally a structure involving only a single contact between the polyion and the macroion occur. In particular, for long and highly charged polyions, a transition from the one-tail state to a two-tail state appears as the chain stiffness is increased. A discussion with recent theories and other simulation studies is also provided.
18.	Akke, Mikael, et al. (author) NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins 2023 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 127:3, s. 591-599 Research review (peer-reviewed)abstract Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale “breathing” motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
19.	Al-Manasir, Nodar, et al. (author) Effects of Temperature and pH on the Contraction and Aggregation of Microgels in Aqueous Suspensions 2009 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:32, s. 11115-11123 Journal article (peer-reviewed)abstract Chemically cross-linked poly(N-isopropylacrylamide) (PNIPAM) microgels and PNIPAM with different amounts of acrylic acid groups (PNIPAM-co-PAA) were synthesized and the temperature-induced aggregation behaviors of aqueous suspensions of these microgels were investigated mainly with the aid of dynamic light scattering (DLS) and turbidimetry. The DLS results show that the particles at all conditions shrink at temperatures up to approximately the lower critical solution temperature (LCST), but the relative contraction effect is larger for the microgels without acid groups or for microgels with added anionic surfactant (SDS). A significant depression of the cloud point is found in suspensions of PNIPAM with very low concentrations of SDS. The compression of the microgels cannot be traced from the turbidity results, but rather the values of the turbidity increase in this temperature interval. This phenomenon is discussed in the framework of a theoretical model. At temperatures above LCST, the size of the microgels without attached charged groups in a very dilute suspension is unaffected by temperature, while the charged particles (pH 7 and 11) continue to collapse with increasing temperature over the entire domain. In this temperature range, low-charged particles of higher concentration and particles containing acrylic acid groups at low pH (pH 2) aggregate, and macroscopic phase separation is approached at higher temperatures. This study demonstrates how the stabilization of microgels can be affected by factors such as polymer concentration, addition of ionic surfactant to particles without charged acid groups, amount of charged groups in the polymer, and pH.
20.	Al-Tikriti, Yassir, et al. (author) Drug-Eluting Polyacrylate Microgels : Loading and Release of Amitriptyline 2020 In: Journal of Physical Chemistry B. - : AMER CHEMICAL SOC. - 1520-6106 .- 1520-5207. ; 124:11, s. 2289-2304 Journal article (peer-reviewed)abstract We investigated the loading of an amphiphilic drug, amitriptyline hydrochloride (AMT), onto sodium polyacrylate hydrogels at low ionic strength and its release at high ionic strength. The purpose was to show how the self-assembling properties of the drug and the swelling of the gel network influenced the loading/release mechanisms and kinetics, important for the development of improved controlled-release systems for parenteral administration of amphiphilic drugs. Equilibrium studies showed that single microgels (similar to 100 mu m) in a large solution volume underwent a discrete transition between swollen and dense states at a critical drug concentration in the solution. For single macrogels in a small solution volume, the transition progressed gradually with increasing amount of added drug, with swollen and dense phases coexisting in the same gel; in a suspension of microgels, swollen and collapsed particles coexisted. Time-resolved micropipette-assisted microscopy studies showed that drug self-assemblies accumulated in a dense shell enclosing the swollen core during loading and that a dense core was surrounded by a swollen shell during release. The time evolution of the radius of single microgels was determined as functions of liquid flow rate, network size, and AMT concentration in the solution. Mass transport of AMT in the surrounding liquid, and in the dense shell, influenced the deswelling rate during loading. Mass transport in the swollen shell controlled the swelling rate during release. A steady-state kinetic model taking into account drug self-assembly, core-shell phase separation, and microgel volume changes was developed and found to be in semiquantitative agreement with the experimental loading and release data.
21.	Alarcon, H., et al. (author) Dye-sensitized solar cells based on nanocrystalline TiO2 films surface treated with Al3+ ions : Photovoltage and electron transport studies 2005 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 109:39, s. 18483-18490 Journal article (peer-reviewed)abstract Nanocrystalline TiO2 films, surface modified with Al3+, were manufactured by depositing a TiO2 suspension containing small amounts of aluminum nitrate or aluminum chloride onto conducting glass substrates, followed by drying, compression, and finally heating to 530 degrees C. Electrodes prepared with TiO2 nanoparticles coated with less than 0.3 wt % aluminum oxide with respect to TiO2 improved the efficiency of the dye sensitized solar cell. This amount corresponds to less than a monolayer of aluminum oxide. Thus, the Al ions terminate the TiO2 surface rather than form a distinct aluminum oxide layer. The aluminum ion surface treatment affects the solar cell in different ways: the potential of the conduction band is shifted, the electron lifetime is increased, and the electron transport is slower when aluminum ions are present between interconnected TiO2 particles.
22.	Alavi, Fatemeh Sadat, et al. (author) QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase 2017 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 121:51, s. 11427-11436 Journal article (peer-reviewed)abstract Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.
23.	Albèr, Cathrine, et al. (author) Hydration of Hyaluronan : Effects on Structural and Thermodynamic Properties 2015 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:11, s. 4211-4219 Journal article (peer-reviewed)abstract Hyaluronan (HA) is a frequently occurring biopolymer with a large variety of functions in nature. During the past 60 years, there have been numerous reports on structural and dynamic behavior of HA in water. Nevertheless, studies covering a wider concentration range are still lacking. In this work, we use isothermal scanning sorption calorimetry for the first time to investigate hydration-induced transitions in HA (sodium hyaluronate, 17 kDa). From this method, we obtain the sorption isotherm and the enthalpy and the entropy of hydration. Thermotropic events are evaluated by differential scanning calorimetry (DSC), and structure analysis is performed with X-ray scattering (SWAXS) and light and scanning electron microscopy. During isothermal hydration, HA exhibits a glass transition, followed by crystallization and subsequent dissolution of HA crystals and formation of a one-phase solution. Structural analysis reveals that the crystal may be indexed on an orthorhombic unit cell with space group P212121. Crystallization of HA was found to occur either through endothermic or exothermic processes, depending on the temperature and water content. We propose a mechanism of crystallization that explains this phenomenon based on the interplay between the hydrophobic effect and strengthening of hydrogen bonds during formation of crystals. The combined results were used to construct a binary phase diagram for the HA–water system.
24.	Ali, Ehesan, et al. (author) Influence of Solute-Solvent Hydrogen Bonding on Intramolecular Magnetic Exchange Interaction in Aminoxyl Diradicals : A QM/MM Broken-Symmetry DFT Study 2009 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:16, s. 5545-5548 Journal article (peer-reviewed)abstract We have investigated the effect of nitroxide radical-water hydrogen bonding (NO center dot center dot center dot center dot H2O) on the intramolecular magnetic exchange interaction (J) for biologically relevant aminoxyl diradicals. We adopt a combination of broken-symmetry density functional theory and the quantum mechanics/molecular mechanics (QM/MM) approach. We find that the presence of hydrogen bonding reorients the radical spin density on -NO center dot. This phenomenon reduces the effective distance between the two interacting localized spin centers that eventually increases the intramolecular magnetic exchange interaction. We have also investigated the functional variation of the magnetic exchange interaction, using various GGA (BLYP, PBE, HCTH407), meta-GGA (TPSS, VXSC), and hybrid (O3LYP, B3LYP, B3P86, B3PW91, and PBE0) functionals.
25.	Ali, Md. Ehesan, et al. (author) Electronic Structure, Spin-States, and Spin-Crossover Reaction of Heme-Related Fe-Porphyrins : A Theoretical Perspective 2012 In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:20, s. 5849-5859 Journal article (peer-reviewed)abstract The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).

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