| 1. |
- Heimdal Nilsson, Elna, et al.
(författare)
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Tropospheric Photolysis Rates of the Acetaldehyde Isotopologues CD3CHO and CD3CDO Relative to CH3CHO Measured at the European Photoreactor Facility.
- 2015
-
Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 119:11, s. 2562-2567
-
Tidskriftsartikel (refereegranskat)abstract
- Acetaldehyde is a hazardous pollutant found in indoor and ambient air. Acetaldehyde photolysis is pressure- and wavelength-dependent with three distinct product channels. In this study, the photolysis rates of CH3CHO, CD3CDO, and CD3CHO are studied in natural tropospheric conditions using long path FTIR spectroscopy, at the European Photoreactor Facility (EUPHORE) in Valencia, Spain. The average relative photolysis rate as an average of four experiments for the fully deuterated isotopologue is jCH3CHO/jCD3CDO = 1.75 ± 0.04, and as a result of a single experiment jCH3CHO/jCD3CHO = 1.10 ± 0.10. These results, combined with our previous determination of jCH3CHO/jCH3CDO = 1.26 ± 0.03, provide mechanistic insight into the photodissociation dynamics of the photoexcited species. Despite the extensive isotopic scrambling in photoexcited acetaldehyde that has recently been reported, the position of the substitution has a clear effect on the relative photolysis rates.
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| 2. |
- Andersen, J, et al.
(författare)
-
Communication: THz absorption spectrum of the CO2-H2O complex: Observation and assignment of intermolecular van der Waals vibrations.
- 2014
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 140:9
-
Tidskriftsartikel (refereegranskat)abstract
- Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm(-1) from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm(-1) for the dissociation energy D0.
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| 3. |
- Andersen, J, et al.
(författare)
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Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes.
- 2015
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 143:22
-
Tidskriftsartikel (refereegranskat)abstract
- The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bond interaction evidenced by a significantly blue-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformational energy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins.
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| 4. |
- Andersen, J., et al.
(författare)
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The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol-water complexes
- 2015
-
Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 17:37, s. 23761-23769
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Tidskriftsartikel (refereegranskat)abstract
- The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with methanol and t-butanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic substitution of individual subunits enabled by a dual inlet deposition procedure provides for the first time unambiguous assignments of the intermolecular high-frequency out-of-plane and low-frequency in-plane donor OH librational modes for mixed alcohol-water complexes. The vibrational assignments confirm directly that water acts as the hydrogen bond donor in the most stable mixed complexes and the tertiary alcohol is a superior hydrogen bond acceptor. The class of large-amplitude donor OH librational motion is shown to account for up to 5.1 kJ mol(-1) of the destabilizing change of vibrational zero-point energy upon intermolecular OH center dot center dot center dot O hydrogen bond formation. The experimental findings are supported by complementary electronic structure calculations at the CCSD(T)-F12/aug-cc-pVTZ level of theory.
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| 5. |
- De Vico, Luca, et al.
(författare)
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The ozone ring closure as a test for multi-state multi-configurational second order perturbation theory (MS-CASPT2)
- 2008
-
Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 461:1-3, s. 136-141
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Tidskriftsartikel (refereegranskat)abstract
- The open and closed forms of ozone and the path connecting them through a transition state, in C-2v symmetry, are explored using the multi-state, multi-configurational second order perturbative method, MS-CASPT2. It is demonstrated that, by using an ANO-L triple-zeta basis set, it is possible to set up an active space able to describe the otherwise troublesome transition state region. Both a conical intersection and a near degeneracy region between the 1(1)A(1) and 2(1)A(1) states are located in the vicinity of the transition state. The relative position of the intersection and the transition state are discussed. (c) 2008 Elsevier B. V. All rights reserved.
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| 6. |
- Greco, Claudio, et al.
(författare)
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Structural insights into the active-ready form of [FeFe]-Hydrogenase and mechanistic details of its inhibition by carbon monoxide
- 2007
-
Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 46:18, s. 7256-7258
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Tidskriftsartikel (refereegranskat)abstract
- [FeFe]-Hydrogenases harbor a {2Fe3S} assembly bearing two CO and two CN- groups, a mu-CO ligand, and a vacant coordination site trans to the mu-CO group. Recent theoretical results obtained studying the isolated {2Fe3S} subsite indicated that one of the CN- ligands can easily move from the crystallographic position to the coordination site trans to the mu-CO group; such an isomerization would have a major impact on substrates and inhibitors binding regiochemistry and, consequently, on the catalytic mechanism. To shed light on this crucial issue, we have carried out hybrid QM/MM and free energy perturbation calculations on the whole enzyme, which demonstrate that the protein environment plays a crucial role and maintains the CN- group fixed in the position observed in the crystal structure; these results strongly support the hypothesis that the vacant coordination site trans to the mu-CO group has a crucial functional relevance both in the context of CO-mediated inhibition of the enzyme and in dihydrogen oxidation/evolution catalysis.
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| 7. |
- Heimdal, Jimmy
(författare)
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Calculations of accurate energies in proteins with QM/MM methods
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Accurate calculation of energies for protein reactions is a hard problem. There are many reasons for wanting to calculate these energies, e.g. ligand design and the study of enzyme reactions. There are two major problem involved in these kinds of calculations. First, the large number of local minima in proteins introduces uncertainties when studying single structures. Second, the size of proteins prohibits the use of accurate quantum mechanical (QM) methods. This forces us to either to study small QM models of the active site or to turn to combined QM and molecular mechanics (QM/MM) methods that incorporate the whole protein. This thesis deals with these two problems. In particular, the effect of active-site size is studied, as well as the importance of sampling. The first problem is studied by looking at the effect of varying the size of the QM region in both QM-only and QM/MM calculations. The effect of the surroundings is also tested. The second problem is addressed by studying methods to perform free-energy perturbation calculations at the QM/MM level. Approximate methods to obtain QM/MM free-energies are also developed and tested.
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| 8. |
- Heimdal, Jimmy, et al.
(författare)
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Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations.
- 2012
-
Ingår i: Physical chemistry chemical physics : PCCP. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 14:36, s. 12592-12604
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Tidskriftsartikel (refereegranskat)abstract
- Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined quantum mechanics and molecular mechanics (QM/MM) level, e.g. for enzyme reactions. Such calculations require extensive sampling of phase space, which typically is prohibitive with density-functional theory or ab initio methods. Therefore, such calculations have mostly been performed with semiempirical QM (SQM) methods, or by using a thermodynamic cycle involving sampling at the MM level and perturbations between the MM and QM/MM levels of theory. However, the latter perturbations typically have convergence problems, unless the QM system is kept fixed during the simulations, because the MM and QM/MM descriptions of the internal degrees of freedom inside the QM system are too dissimilar. We have studied whether the convergence of the MM → QM/MM perturbation can be improved by using a thoroughly parameterised force field or by using SQM/MM methods. As a test case we use the first half-reaction of haloalkane dehalogenase and the QM calculations are performed with the PBE, B3LYP, and TPSSH density-functional methods. We show that the convergence can be improved with a tailored force field, but only locally around the parameterised state. Simulations based on SQM/MM methods using the MNDO, AM1, PM3, RM1, PDDG-MNDO, and PDDG-PM3 Hamiltonians have slightly better convergence properties, but very long simulations are still needed (∼10 ns) and convergence is obtained only if electrostatic interactions between the QM system and the surroundings are ignored. This casts some doubts on the common practice to base QM/MM FEPs on semiempirical simulations without any reweighting of the trajectories.
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| 9. |
- Heimdal, Jimmy, et al.
(författare)
-
Protonation of the proximal histidine ligand in heme peroxidases.
- 2008
-
Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:8, s. 2501-2510
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Tidskriftsartikel (refereegranskat)abstract
- The heme peroxidases have a histidine group as the axial ligand of iron. This ligand forms a hydrogen bond to an aspartate carboxylate group by the other nitrogen atom in the side chain. The aspartate is not present in the globins and it has been suggested that it gives an imidazolate character to the histidine ligand. Quantum chemical calculations have indicated that the properties of the heme site strongly depend on the position of the proton in this hydrogen bond. Therefore, we have studied the location of this proton in all intermediates in the reaction mechanism, using a set of different quantum mechanical and combined experimental and computational methods. Quantum refinements of a crystal structure of the resting FeIII state in yeast cytochrome c peroxidase show that the geometric differences of the two states are so small that it cannot be unambiguously decided where the proton is in the crystal structure. Vacuum calculations indicate that the position of the proton is sensitive to the surroundings and to the side chains of the porphyrin ring. Combined quantum and molecular mechanics (QM/MM) calculations indicate that the proton prefers to reside on the His ligand in all states in the reaction mechanism of the peroxidases. QM/MM free energy perturbations confirm these results, but reduce the energy difference between the two states to 12-44 kJ/mol.
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| 10. |
- Heimdal, Jimmy, et al.
(författare)
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Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods.
- 2011
-
Ingår i: ChemPhysChem. - : Wiley. - 1439-7641 .- 1439-4235. ; 12:Online: 29 SEP 2011, s. 3337-3347
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Tidskriftsartikel (refereegranskat)abstract
- We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.
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| 11. |
- Heimdal, Jimmy, et al.
(författare)
-
The role of axial ligands for the structure and function of chlorophylls
- 2007
-
Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 1432-1327 .- 0949-8257. ; 12:1, s. 49-61
-
Tidskriftsartikel (refereegranskat)abstract
- We have studied the effect of axial ligation of chlorophyll and bacteriochlorophyll using density functional calculations. Eleven different axial ligands have been considered, including models of histidine, aspartate/glutamate, asparagine/glutamine, serine, tyrosine, methionine, water, the protein backbone, and phosphate. The native chlorophylls, as well as their cation and anion radical states and models of the reaction centres P680 and P700, have been studied and we have compared the geometries, binding energies, reduction potentials, and absorption spectra. Our results clearly show that the chlorophylls strongly prefer to be five-coordinate, in accordance with available crystal structures. The axial ligands decrease the reduction potentials, so they cannot explain the high potential of P680. They also redshift the Q band, but not enough to explain the occurrence of red chlorophylls. However, there is some relation between the axial ligands and their location in the various photosynthetic proteins. In particular, the intrinsic reduction potential of the second molecule in the electron transfer path is always lower than that of the third one, a feature that may prevent back-transfer of the electron.
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| 12. |
- Hu, LiHong, et al.
(författare)
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Do quantum mechanical energies calculated for small models of protein-active sites converge?
- 2009
-
Ingår i: Journal of physical chemistry. A. - : American Chemical Society (ACS). - 1520-5215 .- 1089-5639. ; 113:43, s. 11793-11800
-
Tidskriftsartikel (refereegranskat)abstract
- A common approach for the computational modeling of enzyme reactions is to study a rather small model of the active site (20-200 atoms) with quantum mechanical (QM) methods, modeling the rest of the surroundings by a featureless continuum with a dielectric constant of approximately 4. In this paper, we discuss how the residues included in the QM model should be selected and how many residues need to be included before reaction energies converge. As a test case, we use a proton-transfer reaction between a first-sphere cysteine ligand and a second-sphere histidine group in the active site of [Ni,Fe] hydrogenase. We show that it is not a good approach to add groups according to their distance to the active site. A better approach is to add groups according to their contributions to the QM/MM energy difference. However, the energies can still vary by up to 50 kJ/mol for QM systems of sizes up to 230 atoms. In fact, the QM-only approach is based on the hope that a large number of sizable contributions will cancel. Interactions with neutral groups are, in general, short-ranged, with net energy contributions of less than 4 kJ/mol at distances above 5 A from the active site. Interactions with charged groups are much more long-ranged, and interactions with buried charges 20 A from the active site can still contribute by 5 kJ/mol to the reaction energy. Thus, to accurately model the influence of the surroundings on enzyme reaction energies, a detailed and unbiased atomistic account of the surroundings needs to be included.
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| 13. |
- Hu, LiHong, et al.
(författare)
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Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.
- 2011
-
Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:Online September 28, 2011, s. 13111-13126
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Tidskriftsartikel (refereegranskat)abstract
- We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory.
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| 14. |
- Jensen, Kasper P., et al.
(författare)
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A comparison of the tetrapyrrole cofactors in nature and their tuning by axial ligands
- 2008
-
Ingår i: Computational modeling for homogeneous and enzymatic catalysis. - 9783527318438 ; , s. 27-56
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter illustrates how quantum chemical calculations can be used to elucidate structural and functional aspects of tetrapyrrole cofactors, focusing on porphyrins, cobalamins, coenzyme F430, and chlorophyll. A particular emphasis is put on the biochemical significance of axial ligands, which can tune the function of the tetrapyrroles. With the use of quantum chemical calculations, it is possible to draw important conclusions regarding aspects of tetrapyrroles that could not otherwise be accessed. The results show that the general reactivity is mainly determined by the metal and the tetrapyrrole ring system, whereas the electronic structure and reactivity are tuned by the choice of axial ligands, providing a unique insight into the design of cofactors in nature.
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| 15. |
- Kaukonen, Markus, et al.
(författare)
-
Proton transfer at metal sites in proteins studied by quantum mechanical free-energy perturbations
- 2008
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:6, s. 985-1001
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Tidskriftsartikel (refereegranskat)abstract
- Catalytic metal sites in enzymes frequently have second-sphere carboxylate groups that neutralize the charge of the site and share protons with first-sphere ligands. This gives rise to an ambiguity concerning the position of this proton, which has turned out to be hard to settle with experimental, as well as theoretical, methods. We study three such proton-transfer reactions in two proteins and show that, in [Ni,Fe] hydrogenase, the bridging Cys-546 ligand is deprotonated by His-79, whereas in oxidized copper nitrite reductase, the His-100 ligand is neutral and the copper-bound water molecule is deprotonated by Asp-98. We show that these reactions strongly depend on the electrostatic interactions with the surrounding protein and solvent, because there is a large change in the dipole moment of the active site (2-6 D). Neither vacuum quantum mechanical (QM) calculations with large models, a continuum solvent, or a Poisson-Boltzmann treatment of the surroundings, nor combined QM and molecular mechanics (QM/MM) optimizations give reliable estimates of the proton-transfer energies (mean absolute deviations of over 20 kJ/mol). Instead, QM/MM free-energy perturbations are needed to obtain reliable estimates of the reaction energies. These calculations also indicate what interactions and residues are important for the energy, showing how the quantum system may be systematically enlarged. With such a procedure, results with an uncertainty of similar to 10 kJ/mol can be obtained, provided that a proper QM method is used.
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| 16. |
- Kaukonen, Markus, et al.
(författare)
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QM/MM-PBSA method to estimate free energies for reactions in proteins
- 2008
-
Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:39, s. 12537-12548
-
Tidskriftsartikel (refereegranskat)abstract
- We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite. reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.
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| 17. |
- Kollipost, F, et al.
(författare)
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The effect of hydrogen bonding on torsional dynamics: A combined far-infrared jet and matrix isolation study of methanol dimer.
- 2014
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 141:17
-
Tidskriftsartikel (refereegranskat)abstract
- The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm(-1), blue-shifted by more than 300 cm(-1) relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed at ∼286 cm(-1). The experimental findings are held against harmonic predictions from local coupled-cluster methods with single and double excitations and a perturbative treatment of triple excitations [LCCSD(T)] and anharmonic. VPT2 corrections at canonical MP2 and density functional theory (DFT) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion.
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| 18. |
- Lindgren, Johan, et al.
(författare)
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Interpreting melanin-based coloration through deep time : A critical Review
- 2015
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : Royal Society of London. - 0962-8452 .- 1471-2954. ; 282:1813
-
Forskningsöversikt (refereegranskat)abstract
- Colour, derived primarily from melanin and/or carotenoid pigments, is integral to many aspects of behaviour in living vertebrates, including social signalling, sexual display and crypsis. Thus, identifying biochromes in extinct animals can shed light on the acquisition and evolution of these biological traits. Both eumelanin and melanin-containing cellular organelles (melanosomes) are preserved in fossils, but recognizing traces of ancient melanin-based coloration is fraught with interpretative ambiguity, especially when observations are based on morphological evidence alone. Assigning microbodies (or, more often reported, their ‘mouldic impressions’) as melanosome traces without adequately excluding a bacterial origin is also problematic because microbes are pervasive and intimately involved in organismal degradation. Additionally, some forms synthesize melanin. In this review, we survey both vertebrate and microbial melanization, and explore the conflicts influencing assessment of microbodies preserved in association with ancient animal soft tissues.We discuss the types of data used to interpret fossil melanosomes and evaluate whether these are sufficient for definitive diagnosis. Finally, we outline an integrated morphological and geochemical approach for detecting endogenous pigment remains and associated microstructures in multimillion-year-old fossils.
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| 19. |
- Lindgren, Johan, et al.
(författare)
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Molecular composition and ultrastructure of Jurassic paravian feathers
- 2015
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Feathers are amongst the most complex epidermal structures known, and they have a well-documented evolutionary trajectory across non-avian dinosaurs and basal birds. Moreover, melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. We therefore used sensitive molecular imaging, supported by multiple independent analytical tests, to demonstrate that the filamentous epidermal appendages in a new specimen of the Jurassic paravian Anchiornis comprise remnant eumelanosomes and fibril-like microstructures, preserved as endogenous eumelanin and authigenic calcium phosphate. These results provide novel insights into the early evolution of feathers at the sub-cellular level, and unequivocally determine that melanosomes can be preserved in fossil feathers.
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| 20. |
- Roger, Kevin, et al.
(författare)
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Controlling water evaporation through self-assembly
- 2016
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 113:37, s. 10275-10280
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Tidskriftsartikel (refereegranskat)abstract
- Water evaporation concerns all land-living organisms, as ambient air is dryer than their corresponding equilibrium humidity. Contrarily to plants, mammals are covered with a skin that not only hinders evaporation but also maintains its rate at a nearly constant value, independently of air humidity. Here, we show that simple amphiphiles/water systems reproduce this behavior, which suggests a common underlying mechanism originating from responding self-assembly structures. The composition and structure gradients arising from the evaporation process were characterized using optical microscopy, infrared microscopy, and smallangle X-ray scattering. We observed a thin and dry outer phase that responds to changes in air humidity by increasing its thickness as the air becomes dryer, which decreases its permeability to water, thus counterbalancing the increase in the evaporation driving force. This thin and dry outer phase therefore shields the systems from humidity variations. Such a feedback loop achieves a homeostatic regulation of water evaporation.
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| 21. |
- Vajda, Vivi, et al.
(författare)
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Molecular signatures of fossil leaves provideunexpected new evidence for extinct plant relationships
- 2017
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Ingår i: Nature Ecology and Evolution. - London : Springer Nature. - 2397-334X. ; 1, s. 1093-1099
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Tidskriftsartikel (refereegranskat)abstract
- Gene sequences form the primary basis for understanding the relationships among extant plant groups, but genetic data are unavailable from fossils to evaluate the affinities of extinct taxa. Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data. Our novel chemotaxonomic data also support the hypothesis that the extinct Nilssoniales and Bennettitales are closely allied, but only distantly related to Cycadales. The chemical signature of the cuticle of Czekanowskia (Leptostrobales) is strongly similar to that of Ginkgo leaves and supports a close evolutionary relationship between these groups. Finally, our results also reveal that the extinct putative araucariacean, Allocladus, when analysed through HCA, is grouped closer to Ginkgoales than to conifers. Thus, in the absence of modern relatives yielding molecular information, FTIR spectroscopy provides valuable proxy biochemical data complementing morphological characters to distinguish fossil taxa and to help elucidate extinct plant relationships.
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| 22. |
- Zhu, Qiushi, et al.
(författare)
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Correlating structure and electronic band-edge properties in organolead halide perovskites nanoparticles
- 2016
-
Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 18:22, s. 14933-14940
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Tidskriftsartikel (refereegranskat)abstract
- After having emerged as primary contenders in the race for highly efficient optoelectronics materials, organolead halide perovskites (OHLP) are now being investigated in the nanoscale regime as promising building blocks with unique properties. For example, unlike their bulk counterpart, quantum dots of OHLP are brightly luminescent, owing to large exciton binding energies that cannot be rationalized solely on the basis of quantum confinement. Here, we establish the direct correlation between the structure and the electronic band-edge properties of CH3NH3PbBr3 nanoparticles. Complementary structural and spectroscopic measurements probing long-range and local order reveal that lattice strain influences the nature of the valence band and modifies the subtle stereochemical activity of the Pb2+ lone-pair. More generally, this work demonstrates that the stereochemical activity of the lone-pair at the metal site is a specific physicochemical parameter coupled to composition, size and strain, which can be employed to engineer novel functionalities in OHLP nanomaterials.
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