1.1 980 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Jan Forsman author f70464c8-6a9d-4d0e-83e8-495078dbda87 Sture Nordholm author Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department The pair interaction between two charged colloidal particles, in the presence of a polyelectrolyte as well as simple salt, is analyzed theoretically. Of particular interest is the way in which such a combination of salts can be used to induce a strong, long-range attraction, with at most a minor free energy barrier. We show that the nature of the simple salt is highly relevant, i.e., 2:1, 1:1, and 1:2 salts generate quite different particle interaction free energies at the same overall ionic strength. We adopt several different theoretical levels of description. Defining simulations at the primitive model level with explicit simple salt as our reference, we invoke stepwise coarse-graining with careful evaluations of each approximation. Representing monovalent simple ions by the ionic screening they generate is one such simplification. In order to proceed further, with additional computational savings, we also develop a correlation-corrected classical density functional theory. We analyze the performance of this theory with explicit spherical particles as well as in a flat surface geometry, utilizing Derjaguin's approximation. The calculations are particularly fast in the latter case, facilitating computational savings of many (typically 5-7) orders of magnitude, compared to corresponding simulations with explicit salt. Yet, the predictions are remarkably accurate, and considering the crudeness of the model itself, the density functional theory is a very attractive alternative to simulations. https://portal.research.lu.se/en/publications/c0ff8f7c-c701-4619-aaa9-84cf659c1284 The American Chemical Society (ACS) 2012 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 2517065 000301038000006 84857823963 22320216 10.1021/la2045459 http://dx.doi.org/10.1021/la2045459 yes 28 9 4069 4079 https://www.scopus.com/pages/publications/84857823963 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) c0ff8f7c-c701-4619-aaa9-84cf659c1284 2016-04-01T09:53:30+02:00 2025-10-14T09:02:42+02:00 2016-04-01T09:53:30+02:00 1 info:srw/schema/1/mods-v3.3xml journalArticle published yes 5 Rui-Ping Huo author Xiang Zhang author Xu-Ri Huang author Jilai Li author 7f7558d1-7a25-4a0e-90e7-b564499f0edd Chia-Chung Sun author Computational Chemistry v1000659 department The mechanism and kinetics of the radical C-3(2) + C3H8 reaction have been investigated theoretically by direct ab initio kinetics over a wide temperature range. The potential energy surfaces have been constructed at the CCSD(T)/B3//UMP2/B1 levels of theory. The electron transfer was also analyzed by quasi-restricted orbital (QRO) in detail. It was shown that all these channels proceed exclusively via hydrogen abstraction. The overall ICVT/SCT rate constants are in agreement with the available experimental results. The prediction shows that the secondary hydrogen of C3H8 abstraction by C-3(2) radical is the major pathway at low temperatures (below 700 K), while as the temperature increases, the primary hydrogen of C3H8 abstraction becomes more important and more favorable. A negative temperature dependence of the rate constants for the reaction of C-3(2) + C3H8 was observed. The three-(k (3)) and four-parameter (k (4)) rate-temperature expressions were also provided within 243-2000 K to facilitate future experimental studies. https://portal.research.lu.se/en/publications/29be1532-b9b4-4a16-9c4b-3cd936fa3a32 Springer Science and Business Media B.V. 2013 eng C-2 Chemical kinetics Rate constant Variational transition-state theory Theoretical Chemistry (including Computational Chemistry) 1610-2940 3670077 000315349800005 84877148784 23108701 10.1007/s00894-012-1616-8 http://dx.doi.org/10.1007/s00894-012-1616-8 yes 19 3 1009 1018 https://www.scopus.com/pages/publications/84877148784 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 29be1532-b9b4-4a16-9c4b-3cd936fa3a32 2016-04-01T09:53:47+02:00 2025-10-14T12:21:44+02:00 2016-04-01T09:53:47+02:00 2 info:srw/schema/1/mods-v3.3xml journalArticle published yes 6 Claudio Greco author Alexey Silakov author Maurizio Bruschi author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Luca De Gioia author Wolfgang Lubitz author Computational Chemistry v1000659 department In the present contribution, we report a theoretical investigation of the magnetic properties of the dihydrogen-evolving enzyme [FeFe]-hydrogenase, based on both DFT models of the active site (the H-cluster, a Fe6S6 assembly including a binuclear portion directly involved in substrates binding), and QM/MM models of the whole enzyme. Antiferromagnetic coupling within the H-cluster has been treated using the broken-symmetry approach, along with the use of different density functionals. Results of g value calculations turned out to vary as a function of the level of theory and of the extension of the model. The choice of the broken-symmetry coupling scheme also had a significant influence on the calculated g values, for both the active-ready (H-ox) and the CO-inhibited (H-ox-CO) enzyme forms. However, hyper-fine coupling-constant calculations were found to provide more consistent results. This allowed us to show that the experimentally detected delocalization of an unpaired electron at the binuclear subcluster in Desulfovibrio desulfuricans Hox is compatible with a weak interaction between the catalytic centre and a low-weight exogenous ligand like a water molecule. https://portal.research.lu.se/en/publications/09a0d005-0e6e-4a34-a78f-1c3004f6a669 https://portal.research.lu.se/files/136742673/152_feh2ase_epr.pdf application/pdf 1744763 no John Wiley & Sons Inc. 2011 eng Computer chemistry Density functional calculations Magnetic properties EPR parameters calculation Quantum mechanics Enzymes Hydrogenases Hydrogen Theoretical Chemistry (including Computational Chemistry) 1099-0682 1868502 000288099000015 79951872903 10.1002/ejic.201001058 http://dx.doi.org/10.1002/ejic.201001058 yes 7 1043 1049 https://www.scopus.com/pages/publications/79951872903 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 09a0d005-0e6e-4a34-a78f-1c3004f6a669 2016-04-01T09:53:50+02:00 2025-10-14T12:01:14+02:00 2016-04-01T09:53:50+02:00 3 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 J Andersen author Jimmy Heimdal author 6a1606a2-c9f0-4efa-b7f0-454bb8f1bc2c R Wugt Larsen author MAX IV Laboratory v1000329 department 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. https://portal.research.lu.se/en/publications/20e3ad10-f331-4bb9-9957-948e8faacff6 https://portal.research.lu.se/files/1385160/8514695.pdf application/pdf 1412923 no American Institute of Physics (AIP) 2015 eng Theoretical Chemistry (including Computational Chemistry) 0021-9606 8504692 26671383 000367194300035 84951784349 26671383 10.1063/1.4937482 http://dx.doi.org/10.1063/1.4937482 yes 143 22 224315 https://www.scopus.com/pages/publications/84951784349 20e3ad10-f331-4bb9-9957-948e8faacff6 2016-04-01T09:55:02+02:00 2025-10-14T13:23:41+02:00 2016-04-01T09:55:02+02:00 4 info:srw/schema/1/mods-v3.3xml journalArticle published yes 11 Delphine B. Salvatore author Nicolas Duraffourg author Adrien Favier author Björn Persson author f0e05e45-b17f-4e1f-a15b-3840b8ba0dd4 Mikael Lund author 19146bd3-d347-4a94-93a8-1d1a11e3f988 Marie-Madeleine Delage author Robert Silvers author Harald Schwalbe author Thomas Croguennec author Said Bouhallab author Vincent Forge author Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department Understanding the driving forces governing protein assembly requires the characterization of interactions at molecular level. We focus on two homologous oppositely charged proteins, lysozyme and alpha-lactalbumin, which can assemble into microspheres. The assembly early steps were characterized through the identification of interacting surfaces monitored at residue level by NMR chemical shift perturbations by titrating one N-15-labeled protein with its unlabeled partner. While a-lactalbumin has a narrow interacting site, lysozyme has interacting sites scattered on a broad surface. The further assembly of these rather unspecific heterodimers into tetrarners leads to the establishment of well-defined interaction sites. Within the tetramers, most of the electrostatic charge patches on the protein surfaces are shielded. Then, hydrophobic interactions, which are possible because alpha-lactalbumin is in a partially folded state, become preponderant, leading to the formation of larger oligomers. This approach will be particularly useful for rationalizing the design of protein assemblies as nanoscale devices. https://portal.research.lu.se/en/publications/2d4971fe-c16a-4898-b4cd-f13cfc0c36a4 The American Chemical Society (ACS) 2011 eng Theoretical Chemistry (including Computational Chemistry) 1526-4602 2056826 000291499900029 79958842162 21545084 10.1021/bm200285e http://dx.doi.org/10.1021/bm200285e yes 12 6 2200 2210 https://www.scopus.com/pages/publications/79958842162 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 2d4971fe-c16a-4898-b4cd-f13cfc0c36a4 2016-04-01T09:56:02+02:00 2025-10-14T11:35:55+02:00 2016-04-01T09:56:02+02:00 5 info:srw/schema/1/mods-v3.3xml journalArticle published yes 1 Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department Rubus vikensis A. Pedersen ex G. Wendt (sect. Corylifolii) was recently described from a restricted area in north western Scania, Sweden. In this investigation, I show that the same species occurs also on the Onsala peninsula in northern Halland and on a single locality in the middle of Halland. It has 35 chromosomes in all parts of the distribution area. Moreover, I show by random amplified polymorphic DNA (RAPD) analysis that R. vikensis is a distinct and well-defined species, clearly separated from the morphologically similar R. wahlbergii, with which it shares the chromosome number. https://portal.research.lu.se/en/publications/24fbc521-ef89-4190-9bdb-abe372ec0242 https://portal.research.lu.se/files/1407764/8508883.pdf application/pdf 1593237 no Wiley-Blackwell 2010 eng Theoretical Chemistry (including Computational Chemistry) 0107-055X 1603641 000276465700017 77955977608 10.1111/j.1756-1051.2009.00663.x http://dx.doi.org/10.1111/j.1756-1051.2009.00663.x yes 28 2 246 250 https://www.scopus.com/pages/publications/77955977608 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 24fbc521-ef89-4190-9bdb-abe372ec0242 2016-04-01T09:56:35+02:00 2025-10-14T10:31:59+02:00 2016-04-01T09:56:35+02:00 6 info:srw/schema/1/mods-v3.3xml journalArticle published yes 6 Sung-Yup Kim author Nitin Kumar author Petter Persson author 3341f36c-9984-4201-ab1c-4807affbaeae Jorge Sofo author Adri C. T. van Duin author James D. Kubicki author Computational Chemistry v1000659 department NanoLund: Centre for Nanoscience v1000190 department A new ReaxFF reactive force field has been developed to describe reactions in the Ti-O-H system. The ReaxFF force field parameters have been fitted to a quantum mechanical (QM) training set containing structures and energies related to bond dissociation energies, angle and dihedral distortions, and reactions between water and titanium dioxide, as well as experimental crystal structures, heats of formation, and bulk modulus data. Model configurations for the training set were based on DFT calculations on molecular clusters and periodic systems (both bulk crystals and surfaces). ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. ReaxFF also describes the relative energetics for rutile, brookite, and anatase. The results of ReaxFF match reasonably well with those of QM for water binding energies, surface energies, and H2O dissociation energy barriers. description, we have compared its performance against DFT/MD simulations for 1 and 3 monolayers of water interacting with a rutile (110) surface. We found agreement within a 10% error between the DFT/MD and ReaxFF water dissociation levels for both coverages. https://portal.research.lu.se/en/publications/b6599ae2-132e-456a-90a2-c19e5e7e6e71 The American Chemical Society (ACS) 2013 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 4170562 000321094100031 84879548063 23687907 10.1021/la4006983 http://dx.doi.org/10.1021/la4006983 yes 29 25 7838 7846 https://www.scopus.com/pages/publications/84879548063 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) b6599ae2-132e-456a-90a2-c19e5e7e6e71 2016-04-01T09:57:34+02:00 2025-10-14T09:31:10+02:00 2016-04-01T09:57:34+02:00 7 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Paulius Mikulskis author a13bc8cd-0dd4-4353-bc15-9e1b22f5b2d6 Samuel Genheden author bbfc8f53-f9d6-49ff-9926-38144c1c1d7c Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20-Å truncated spherical systems and only one intermediate state in the perturbations, we obtain an error of less than 4 kJ/mol for 54% of the studied relative affinities and a precision of 0.5 kJ/mol on average. However, only four of the proteins gave acceptable errors, correlations, and rankings. The results could be improved by using nine intermediate states in the simulations or including the entire protein in the simulations using periodic boundary conditions. However, 27 of the calculated affinities still gave errors of more than 4 kJ/mol, and for three of the proteins the results were not satisfactory. This shows that the performance of BAR calculations depends on the target protein and that several transformations gave poor results owing to limitations in the molecular-mechanics force field or the restricted sampling possible within a reasonable simulation time. Still, the BAR results are better than docking calculations for most of the proteins. https://portal.research.lu.se/en/publications/1870140e-48ec-45a6-b9d3-2167f9fbfc8e https://portal.research.lu.se/files/1434939/4699505.pdf application/pdf 638979 no The American Chemical Society (ACS) 2014 eng Theoretical Chemistry (including Computational Chemistry) 1549-960X 4699423 25264937 000343849600016 84908225639 25264937 10.1021/ci5004027 http://dx.doi.org/10.1021/ci5004027 54 10 2794 2806 https://www.scopus.com/pages/publications/84908225639 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 1870140e-48ec-45a6-b9d3-2167f9fbfc8e 2016-04-01T09:58:14+02:00 2025-10-14T12:55:57+02:00 2016-04-01T09:58:14+02:00 8 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Martin Turesson author Bo Jönsson author acad6398-af1f-4be3-8c0f-c7dbb066571d Christophe Labbez author Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department Effective pair potentials between charged colloids, obtained from Monte Carlo simulations of two single colloids in a closed cell at the primitive model level, are shown to reproduce accurately the structure of aqueous salt-free colloidal dispersions, as determined from full primitive model simulations by Linse et al. (Linse, P.; Lobaskin, V. Electrostatic Attraction and Phase Separation in Solutions of Like-Charged Colloidal Particles. Phys. Rev. Lett. 1999, 83, 4208). Excellent agreement is obtained even when ion-ion correlations are important and is in principle not limited to spherical particles, providing a potential route to coarse-grained colloidal interactions in more complex systems. https://portal.research.lu.se/en/publications/589458e5-3687-4bb0-90d2-f471383dcb0c The American Chemical Society (ACS) 2012 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 2495082 000301636900005 84858791098 22404737 10.1021/la3005008 http://dx.doi.org/10.1021/la3005008 yes 28 11 4926 4930 https://www.scopus.com/pages/publications/84858791098 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 589458e5-3687-4bb0-90d2-f471383dcb0c 2016-04-01T10:00:01+02:00 2025-10-14T11:08:39+02:00 2016-04-01T10:00:01+02:00 9 info:srw/schema/1/mods-v3.3xml journalArticle published yes 6 Martin Jarenmark author 33fecc52-5858-4709-82f2-f526fc224842 Lisa Fredin author c730cd68-077c-4814-92e5-8b5af47b0674 Joachim H J Hedberg author Isa Doverbratt author 8ef48fc2-b066-46cf-b2d9-0e2153255731 Petter Persson author 3341f36c-9984-4201-ab1c-4807affbaeae Maria Abrahamsson author Centre for Analysis and Synthesis v1000651 department Computational Chemistry v1000659 department We synthesized a new homoleptic, tris-bidentate complex [Ru(QPzH)3](2+) based on the novel biheteroaromatic, 8-(3-pyrazolyl)-quinoline ligand QPzH. The QPzH ligand was designed to reduce the distortions typically observed in complexes incorporating the 8-quinolinyl group into the ligand framework. This was indeed observed, and was also, as anticipated, found to facilitate the formation of tris-homoleptic Ru(II) complexes; [Ru(QPzH)3](2+) is the first reported tris-homoleptic complex with ligands based on the 8-quinolinyl group. The synthesis can either result in a statistical 3:1 mer/fac ratio of the complex, or, through controlled exposure to light, be tweaked to allow isolation of the pure mer isomer only. X-ray crystallography reveals three nonequivalent ligands, with significantly less strain than other quinoline-based bidentate ligands. The complex exhibits a nearly octahedral coordination geometry but shows large differences in bond lengths between the Ru core and the quinoline and pyrazoles, respectively. The Ru-N(pyrazole) bond distances are ∼2.04 Å, while the corresponding distances for Ru-N(quinoline) are ∼2.12 Å. Structural, photophysical, electrochemical, and theoretical characterization revealed a mer-Ru(II) complex with a low oxidation potential (0.57 V vs ferrocene(0/+)) attributed to the incorporation of the pyrazolyl group, a ground state absorption that is sensitive to the local environment of the complex, and a short-lived (3)MLCT excited state. https://portal.research.lu.se/en/publications/d6f716c1-28a0-4a1d-b20e-23ccde54af4f The American Chemical Society (ACS) 2014 eng Theoretical Chemistry (including Computational Chemistry) Chemical Sciences 1520-510X 4816214 000346544100017 25420224 84920181092 10.1021/ic502432c http://dx.doi.org/10.1021/ic502432c yes 53 24 12778 12790 https://www.scopus.com/pages/publications/84920181092 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039), Centre for Analysis and Synthesis (011001266) d6f716c1-28a0-4a1d-b20e-23ccde54af4f 2016-04-01T10:00:51+02:00 2025-10-14T13:16:42+02:00 2016-04-01T10:00:51+02:00 10 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Ryan Szparaga author d36d62ad-5649-450a-9f37-42431366fcd6 Clifford E Woodward author Jan Forsman author f70464c8-6a9d-4d0e-83e8-495078dbda87 Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department We use a combination of simulations and a simple theoretical approach to investigate interactions between neutral conducting surfaces, immersed in an electrolyte solution. The study is conducted at the primitive model level, which necessitates the use of multiple image reflections. Our approximate theory is based on a classical density functional formulation of Poisson-Boltzmann theory. The same approach can in principle also be imported to more advanced treatments, where ion correlations are accounted for. An important limiting result that guides our treatment of the image forces, is that the repulsive salt-induced interactions cancel the attractive zero frequency van der Waals attraction at long range. That is, at vanishing frequency, the van der Waals interaction between the conducting surfaces is, at large separations, perfectly screened by the intervening salt solution. The simulations are computationally intensive, due to a strong dependence upon the number of image reflections used, with especially poor convergence when an odd number of images is used. We demonstrate that our approximate density functional approach is remarkably accurate, even in the presence of a 2 : 1 salt, or when the surfaces preferentially adsorb one ion species. The former observation was rather unexpected, given the lack of ion correlations within our mean-field treatment, and is most likely due to a cancellation between two opposing effects, both of which are generated by ion correlations. https://portal.research.lu.se/en/publications/2b4ed179-1a89-4627-9019-614845e28efc https://portal.research.lu.se/files/27853153/manuscript_revised.pdf application/pdf 402694 no Royal Society of Chemistry 2015 eng Theoretical Chemistry (including Computational Chemistry) 1744-6848 5341020 25899056 000354449100008 84929377507 25899056 10.1039/c5sm00161g http://dx.doi.org/10.1039/c5sm00161g yes 11 20 4011 4021 https://www.scopus.com/pages/publications/84929377507 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 2b4ed179-1a89-4627-9019-614845e28efc 2016-04-01T10:00:53+02:00 2025-10-14T10:44:10+02:00 2016-04-01T10:00:53+02:00 11 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Clifford E. Woodward author Jan Forsman author f70464c8-6a9d-4d0e-83e8-495078dbda87 Computational Chemistry v1000659 department We use a continuum chain model and develop an analytical theory for the interaction between two spheres immersed in a fluid of ideal equilibrium polymers. The theory can be applied to both adsorbing and nonadsorbing spheres. Here we focus on two nonadsorbing spheres and determine the classical depletion interaction between them. Compact, and exact, results are derived for the asymptotic behavior of the depletion interaction, which has a Yukawa form. We show also that in the limit of large spheres (and large surface to surface separation) the Derjaguin approximation is valid. We compare our asymptotic expression with numerical solutions of an ideal equilibrium polymer fluid consisting of discrete chains. Our asymptotic approximation accurately predicts long-range interactions between small spheres. For large spheres it predicts the interaction very well over most of the separation range. We also consider a single sphere immersed in the polymer fluid and show how our results can be generalized to treat polydisperse polymer fluids, where the polydispersity is described by a Schulz-Flory distribution. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3494037] https://portal.research.lu.se/en/publications/05597c4c-c4b9-40fc-9880-553a370a3dee American Institute of Physics (AIP) 2010 eng Theoretical Chemistry (including Computational Chemistry) 0021-9606 1720441 000283359300063 78049231898 10.1063/1.3494037 http://dx.doi.org/10.1063/1.3494037 yes 133 15 154902 https://www.scopus.com/pages/publications/78049231898 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 05597c4c-c4b9-40fc-9880-553a370a3dee 2016-04-01T11:10:00+02:00 2025-10-14T12:29:22+02:00 2016-04-01T11:10:00+02:00 12 info:srw/schema/1/mods-v3.3xml journalArticle published yes 6 Mo Segad author 2f1d15fc-f638-4469-b46c-4d97299d8bfb S. Hanski author Ulf Olsson author 28005704-c79e-44ad-b7ee-1f6911bd89fb J. Ruokolainen author Torbjörn Åkesson author 5f078d78-6bd8-4ba1-8fa8-af73c2dd5e51 Bo Jönsson author acad6398-af1f-4be3-8c0f-c7dbb066571d Computational Chemistry v1000659 department Physical Chemistry v1000657 department Aqueous dispersions of pure sodium and calcium smectite clays with platelet sizes on the order of a few hundred nanometers were characterized using a combination of cryo-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). With monovalent sodium counterions the clay is dispersed as individual platelets, as seen by cryo-TEM, that order into a nematic phase. From SAXS a one-dimensional swelling of the day in water is observed with the characteristic spacing h(s) = delta/phi(c), where h(s) is the separation between the platelets, delta = 1 nm is the effective platelet thickness, and phi(c) is the clay volume fraction in the sample. In calcium montmorillonite, on the other hand, cryo-TEM images dearly show the presence of tactoids, where the platelets have aggregated into stacks with a periodic spacing of 2 nm. From imaging a large number of tactoids the distribution function f(N) far the number of platelets per tactoid was estimated, and the average number (N) approximate to 10. The characteristic 2 nm spacing as well as the small number of platelets per tactoid was also confirmed by SAXS. The present study demonstrates that cryo-TEM, with carefully prepared specimen, is a very useful technique to characterize clay dispersions, particularly in aggregated systems. https://portal.research.lu.se/en/publications/93e58ec2-3224-43cd-be66-9f0961bd67d4 The American Chemical Society (ACS) 2012 eng Physical Chemistry (including Surface- and Colloid Chemistry) Theoretical Chemistry (including Computational Chemistry) 1932-7447 2587529 000302336700046 84859576029 10.1021/jp300531y http://dx.doi.org/10.1021/jp300531y yes 116 13 7596 7601 https://www.scopus.com/pages/publications/84859576029 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039), Physical Chemistry 1 (S) (011001006) 93e58ec2-3224-43cd-be66-9f0961bd67d4 2016-04-01T11:11:06+02:00 2025-10-14T09:49:05+02:00 2016-04-01T11:11:06+02:00 13 info:srw/schema/1/mods-v3.3xml journalArticle published yes 13 Yizhu Liu author bd6e0613-f6dd-4387-b3f2-23f15a8c847e Kasper Kjaer author 5cc7e6b4-a36c-4cdf-94d4-a75b7ebb8cd6 Lisa Fredin author c730cd68-077c-4814-92e5-8b5af47b0674 Pavel Chabera author 94f7a4f7-289e-4307-bd63-afebb3843c76 Tobias Harlang author 035b7f8b-b209-44a2-a78e-53d0316c0737 Sophie Canton author 22d4da3a-1c36-4352-8bef-65b17c9eb535 Sven Lidin author f168024b-7e7a-40ac-a7f1-6bf9b221282a Jianxin Zhang author 1dc1c6d2-875a-45e3-b0a0-075406569aa7 Reiner Lomoth author Karl-Erik Bergquist author ed7e933d-999c-48c7-807c-a266b5f60baa Petter Persson author 3341f36c-9984-4201-ab1c-4807affbaeae Kenneth Wärnmark author 63bb2681-7203-403e-9314-ef67d2920685 Villy Sundström author 0eb7753e-1078-4253-a557-e64af206033a Centre for Analysis and Synthesis v1000651 department Chemical Physics v1000658 department Computational Chemistry v1000659 department Department of Chemistry v1000647 department NanoLund: Centre for Nanoscience v1000190 department Lund Laser Centre, LLC v1000184 department Strongly σ-donating N-heterocyclic carbenes (NHCs) have revived research interest in the catalytic chemistry of iron, and are now also starting to bring the photochemistry and photophysics of this abundant element into a new era. In this work, The efficient synthesis of a heteroleptic Fe(II) complex (1) is based on sequentially furnishing the Fe(II) center with the benchmark 2,2'-bipyridine (bpy) ligand and the more strongly σ-donating mesoionic ligand, 4,4'-bis(1,2,3-triazol-5-ylidene) (btz). Complex 1 was comprehensively characterized by electrochemistry, static and ultrafast spectroscopy, and quantum chemical calculations and compared to [Fe(bpy)3 ](PF6 )2 and (TBA)2 [Fe(bpy)(CN)4 ]. Heteroleptic complex 1 extends the absorption spectrum towards longer wavelengths compared to a previously synthesized homoleptic Fe(II) NHC complex. The combination of the mesoionic nature of btz and the heteroleptic structure effectively destabilizes the metal-centered (MC) states relative to the triplet metal-to-ligand charge transfer ((3) MLCT) state in 1, rendering it a lifetime of 13 ps, the longest to date of a photochemically stable Fe(II) complex. Deactivation of the (3) MLCT state is proposed to proceed via the (3) MC state that strongly couples with the singlet ground state. https://portal.research.lu.se/en/publications/3ed9a5f0-c307-4fd0-9bc2-e9a9cb0aef8c Wiley-Blackwell 2015 eng Theoretical Chemistry (including Computational Chemistry) Chemical Sciences Atom and Molecular Physics and Optics 1521-3765 4908360 25504660 000350116200019 25504660 84922988358 10.1002/chem.201405184 http://dx.doi.org/10.1002/chem.201405184 yes 21 9 3628 3639 https://www.scopus.com/pages/publications/84922988358 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039), Centre for Analysis and Synthesis (011001266), Chemical Physics (S) (011001060), Department of Chemistry (011001220) 3ed9a5f0-c307-4fd0-9bc2-e9a9cb0aef8c 2016-04-01T11:12:34+02:00 2026-05-29T11:56:49+02:00 2016-04-01T11:12:34+02:00 14 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Sophie Sumner author Pär Söderhjelm author 45ebbdaa-83be-4617-b881-8d2a64c0e7ef Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have examined the effect of geometry optimisation on energies calculated with the quantum-mechanical (QM) cluster, the combined QM and molecular-mechanics (QM/MM), the big-QM approaches (very large single-point QM calculations taken from QM/MM-optimised structures, including all atoms within 4.5 Å of the minimal active site, all buried charged groups in the protein, and truncations moved at least three residues away from the active site). We study a simple proton-transfer reaction between His-79 and Cys-546 in the active site of [Ni,Fe] hydrogenase and optimise QM systems of 50 different sizes (56–362 atoms). Geometries optimised with QM/MM are stable and reliable, whereas QM-cluster optimisations give larger changes in the structures and sometimes lead to large distortions in the active site if some hydrogen-bond partners to the metal ligands are omitted. Keeping 2–3 atoms for each truncated residue (rather than one) fixed in the optimisation improves the results, but does not solve all problems for the QM-cluster optimisations. QM-cluster energies in vacuum and a continuum solvent are insensitive to the geometry optimisations with a mean absolute change upon the optimisations of only 4–7 kJ/mol. This shows that geometry optimisations do not decrease the dependence of QM-cluster energies on how the QM system is selected – there is still a ~60 kJ/mol difference between calculations in which groups have been added to the QM system according to their distance to the active site or based on QM/MM free-energy components. QM/MM energies do not show such a difference, but they converge rather slowly with respect to the size of the QM system, although the convergence is improved by moving truncations away from the active site. The big-QM energies are stable over the 50 different optimised structures, 57±1 kJ/mol, although some smaller trends can be discerned. This shows that both QM-cluster geometries and energies should be interpreted with caution. Instead, we recommend QM/MM for geometry optimisations and energies calculated by the big-QM approach. https://portal.research.lu.se/en/publications/72f549fa-57fb-4919-b8e5-347e32b61807 https://portal.research.lu.se/files/2491818/4226432.pdf application/pdf 734864 no The American Chemical Society (ACS) 2013 eng Quantum mechanical cluster calculations QM/MM geometry optimisation density-functional theory [Ni Fe] hydrogenase. Theoretical Chemistry (including Computational Chemistry) 1549-9618 4226429 000330096800035 84884185644 26592409 10.1021/ct400339c http://dx.doi.org/10.1021/ct400339c yes 9 9 4205 4214 https://www.scopus.com/pages/publications/84884185644 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 72f549fa-57fb-4919-b8e5-347e32b61807 2016-04-01T11:14:00+02:00 2025-10-14T10:31:32+02:00 2016-04-01T11:14:00+02:00 15 info:srw/schema/1/mods-v3.3xml journalArticle published yes 1 Jan Forsman author f70464c8-6a9d-4d0e-83e8-495078dbda87 Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department The main question addressed in this work is as follows: Under pure electrosorption conditions, that is, disregarding nonelectrostatic effects, how does the net adsorption of a polyelectrolyte at an oppositely charged surface respond to the addition of simple salt? Previous simulations and mean-field calculations have suggested that the polymers will desorb. However, we will demonstrate that an increased adsorption also is possible, even for pure electrosorption, at low and intermediate levels of salt. As this is a correlation-driven effect, mean field approaches will fail to capture it. Using simulations, one will in general need to simulate large systems and relatively long polymers. Also important is the presence of a proper bulk solution, with a finite and well-defined polyelectrolyte concentration. We have performed a theoretical study of polyelectrolyte adsorption, assuming screened Coulomb interactions between monomers; that is, the salt is implicit. This work focuses on the effects from ionic screening and polymer length. Specifically, the adsorption at a weakly charged colloidal particle, with a diameter of 200 nm, is monitored for various salt concentrations, in the presence of highly charged chains. Using simulations, we investigate polymers with two different degrees of polymerization: 40 and 160, respectively. These simulations are complemented by predictions from classical polymer density functional theory, utilizing a recently developed correlation-correction (Forsman, J.; Nordholm, S. Langmuir, in press). The agreement with corresponding simulations is semiquantitative, and because the calculations run many orders of magnitude faster than the simulations, longer and more realistic polymers could be studied with this approach. However, switching off the correlation-correction leads to a mean-field theory, which fails to even qualitatively reproduce the simulated response to screening. https://portal.research.lu.se/en/publications/2dc0cad9-a9c5-488f-a04b-89c6a3121576 The American Chemical Society (ACS) 2012 eng Theoretical Chemistry (including Computational Chemistry) http://www.ncbi.nlm.nih.gov/pubmed/22360456?dopt=Abstract yes 0743-7463 2432551 000301636900029 22360456 84858780439 22360456 10.1021/la3000735 http://dx.doi.org/10.1021/la3000735 yes 28 11 5138 5150 https://www.scopus.com/pages/publications/84858780439 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 2dc0cad9-a9c5-488f-a04b-89c6a3121576 2016-04-01T11:14:05+02:00 2025-10-14T10:16:02+02:00 2016-04-01T11:14:05+02:00 16 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Martin Srnec author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Lubomir Rulisek author Computational Chemistry v1000659 department The key step in the reaction mechanism of multicopper oxidases (MCOs)-the cleavage of the O-O bond in O-2-has been investigated using combined quantum mechanical and molecular mechanical (QM/MM) methods. This process represents a reaction pathway from the peroxy intermediate after it accepts one electron from the nearby type-1 Cu site to the experimentally-observed native intermediate, which is the only fully oxidised catalytically relevant state in MCOs. Scans of the QM(DFT)/MM potential energy surface have allowed us to obtain estimates of the activation energies. Furthermore, vacuum calculations on a smaller model of the active site have allowed us to estimate the entropy contributions to the barrier height and to obtain further insight into the reaction by comparing the small cluster model with the QM/MM model, which includes the entire protein. Owing to the complicated electronic structure of these low-spin exchange coupled systems, multireference quantum chemical calculations at the complete-active space second-order perturbation theory (CASPT2) were used in an attempt to benchmark the barrier heights obtained at the DFT(B3LYP) level. Our best estimate of the activation barrier is Delta G = 60-65 kJ mol(-1), in good agreement with the experimental barrier of similar to 55 kJ mol(-1), which can be inferred from the experimental rate constant of k > 350 s(-1). It has also been shown that the reaction involves protonation of the O-2 moiety before bond cleavage. The proton likely comes from a nearby carboxylate residue which was recently suggested by the experiments. https://portal.research.lu.se/en/publications/cf0cd0de-7c7c-4d6a-aedc-ffae9bb6d59f https://portal.research.lu.se/files/2497019/2300268.pdf application/pdf 11880306 no Royal Society of Chemistry 2011 eng Theoretical Chemistry (including Computational Chemistry) 1364-5498 1773882 000285361500003 79952261204 10.1039/c004476h http://dx.doi.org/10.1039/c004476h yes 148 41 53 https://www.scopus.com/pages/publications/79952261204 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) cf0cd0de-7c7c-4d6a-aedc-ffae9bb6d59f 2016-04-01T11:14:13+02:00 2025-10-14T12:17:24+02:00 2016-04-01T11:14:13+02:00 17 info:srw/schema/1/mods-v3.3xml journalArticle published yes 4 Chris H. J. Evers author Thorbjorn Andersson author Mikael Lund author 19146bd3-d347-4a94-93a8-1d1a11e3f988 Marie Skepö author ed8299e4-0e9d-4dbb-9a76-3471cc6d5614 Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department In this Monte Carlo simulation study we use mesoscopic modeling to show that beta-casein, an unstructured milk protein, adsorbs to surfaces not only due to direct electrostatic and hydrophobic interactions but also due to structural rearrangement and charge regulation due to proton uptake and release. beta-casein acts as an amphiphilic chameleon, changing properties according to the chemical environment, and binding is observed to both positively and negatively charged surfaces. The binding mechanisms, however, are fundamentally different. A detailed, per-residue-level analysis shows that the adsorption process is controlled by a few very specific regions of the protein and that these change dramatically with pH. Caseins, being the most abundant proteins in milk, are crucial for the properties of fermented dairy products, such as nutrition, texture, and viscosity, but may also influence adhesion to packaging materials. The latter leads to product losses of about 10%, leading to economical and environmental problems. https://portal.research.lu.se/en/publications/307baa66-5067-42ff-bd38-4ef02e3c6c4f The American Chemical Society (ACS) 2012 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 3059327 000307479000021 84865179049 22783871 10.1021/la300892p http://dx.doi.org/10.1021/la300892p yes 28 32 11852 11858 https://www.scopus.com/pages/publications/84865179049 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 307baa66-5067-42ff-bd38-4ef02e3c6c4f 2016-04-01T11:14:17+02:00 2025-10-14T10:45:28+02:00 2016-04-01T11:14:17+02:00 18 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Jilai Li author 7f7558d1-7a25-4a0e-90e7-b564499f0edd Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department There are three families of mononuclear molybdenum enzymes that catalyze oxygen atom transfer (OAT) reactions, named after a typical example from each family, viz., dimethyl sulfoxide reductase (DMSOR), sulfite oxidase (SO), and xanthine oxidase (XO). These families differ in the construction of their active sites, with two molybdopterin groups in the DMSOR family, two oxy groups in the SO family, and a sulfido group in the XO family. We have employed density functional theory calculations on cluster models of the active sites to understand the selection of molybdenum ligands in the three enzyme families. Our calculations show that the DMSOR active site has a much stronger oxidative power than the other two sites, owing to the extra molybdopterin ligand. However, the active sites do not seem to have been constructed to make the OAT reaction as exergonic as possible, but instead to keep the reaction free energy close to zero (to avoid excessive loss of energy), thereby making the reoxidation (SO and XO) or rereduction of the active sites (DMSOR) after the OAT reaction facile. We also show that active-site models of the three enzyme families can all catalyze the reduction of DMSO and that the DMSOR model does not give the lowest activation barrier. Likewise, all three models can catalyze the oxidation of sulfite, provided that the Coulombic repulsion between the substrate and the enzyme model can be overcome, but for this harder reaction, the SO model gives the lowest activation barrier, although the differences are not large. However, only the XO model can catalyze the oxidation of xanthine, owing to its sulfido ligand. https://portal.research.lu.se/en/publications/c82f6baf-c352-4fa2-b315-d66dfea82b0e https://portal.research.lu.se/files/2511708/5266650.pdf application/pdf 4012029 no The American Chemical Society (ACS) 2014 eng Theoretical Chemistry (including Computational Chemistry) 1520-510X 4820219 25372012 000345264100011 84911065420 25372012 10.1021/ic5010837 http://dx.doi.org/10.1021/ic5010837 yes 53 22 11913 11924 https://www.scopus.com/pages/publications/84911065420 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) c82f6baf-c352-4fa2-b315-d66dfea82b0e 2016-04-01T11:15:28+02:00 2025-10-14T10:36:41+02:00 2016-04-01T11:15:28+02:00 19 info:srw/schema/1/mods-v3.3xml journalArticle published yes 5 Michael G G Fuchs author Sebastian Dechert author Serhiy Demeshko author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Franc Meyer author Computational Chemistry v1000659 department A unique [2Fe-2S] cluster (1) with genuinely five-coordinate ferric ions has been synthesized and investigated both structurally and spectroscopically. The crystal structure of 1 as well as (1)H NMR data reveal that 2,6-bis(imidazol-2-yl)pyridine binds to the [2Fe-2S] core as a tridentate capping ligand. DFT calculations showing spin density on all coordinating atoms support this finding. Cluster 1 has also been characterized by Mössbauer and UV/vis spectroscopy, mass spectrometry, cyclic voltammetry, and magnetic susceptibility measurements. Significant spectroscopic properties that make 1 distinct from conventional [2Fe-2S] clusters include a rather small quadrupole splitting of 0.43 mm/s. https://portal.research.lu.se/en/publications/5758c6ec-4862-4a0a-8b3e-256592cfd97f https://portal.research.lu.se/files/136743023/142_franc_5co.pdf application/pdf 473869 no The American Chemical Society (ACS) 2010 eng Theoretical Chemistry (including Computational Chemistry) 1520-510X 1626434 000279211500014 20518488 77954135147 20518488 10.1021/ic902559n http://dx.doi.org/10.1021/ic902559n yes 49 13 5853 5858 https://www.scopus.com/pages/publications/77954135147 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039) 5758c6ec-4862-4a0a-8b3e-256592cfd97f 2016-04-01T11:15:34+02:00 2025-10-14T13:00:00+02:00 2016-04-01T11:15:34+02:00 20 1.1subject exact 10407subjectexact10407