| 1. |
- Heimdal Nilsson, Elna, et al.
(författare)
-
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.
|
|
| 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.
|
|
| 3. |
- Andersen, J, et al.
(författare)
-
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.
|
|
| 4. |
- Andersen, J., et al.
(författare)
-
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
-
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.
|
|
| 5. |
- De Vico, Luca, et al.
(författare)
-
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
-
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.
|
|
| 6. |
- Greco, Claudio, et al.
(författare)
-
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
-
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.
|
|
| 7. |
- Heimdal, Jimmy
(författare)
-
Calculations of accurate energies in proteins with QM/MM methods
- 2010
-
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.
|
|
| 8. |
- Heimdal, Jimmy, et al.
(författare)
-
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
-
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.
|
|
| 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
-
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.
|
|
| 10. |
- Heimdal, Jimmy, et al.
(författare)
-
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
-
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.
|
|
