1.1 976 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 LiHong Hu author 86e8d89d-f5e4-421e-8f60-8591dd2053ba Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have critically examined and compared various ways to obtain standard harmonic molecular mechanics (MM) force-field parameters for metal sites in proteins, using the 12 most common Zn2+ sites as test cases. We show that the parametrization of metal sites is hard to treat with automatic methods. The choice of method is a compromise between speed and accuracy and therefore depends on the intended use of the parameters. If the metal site is not of central interest in the investigation, for example, a structural metal far from the active site, a simple and fast parametrization is normally enough, using either a nonbonded model with restraints or a bonded parametrization based on the method of Seminario. On the other hand, if the metal site is of central interest in the investigation, a more accurate method is needed to give quantitative results, for example, the method by Norrby and Liljefors. The former methods are semiautomatic and can be performed in seconds, once a quantum mechanical (QM) geometry optimization and frequency calculation has been performed, whereas the latter method typically takes several days and requires significant human intervention. All approaches require a careful selection of the atom types used. For a nonbonded model, standard atom types can be used, whereas for a bonded model, it is normally wise to use special atom types for each metal ligand. For accurate results, new atom types for all atoms in the metal site can be used. Atomic charges should also be considered. Typically, QM restrained electrostatic potential charges are accurate and easy to obtain once the QM calculation is performed, and they allow for charge transfer within the complex. For negatively charged complexes, it should be checked that hydrogen atoms of the ligands get proper charges. Finally, water ligands pose severe problems for bonded models in force fields that ignore nonbonded interactions for atoms separated by two bonds. Complexes with a single water ligand can normally be accurately treated with a bonded potential, once it is ensured that the water H atoms have nonzero Lennard-Jones parameters. However, for metal sites with several water molecules, a nonbonded model with restraints (taken from the QM calculations) is more stable. https://portal.research.lu.se/en/publications/c87d4e32-28b2-498d-bcd6-860f3a854724 https://portal.research.lu.se/files/1246213/2338988.pdf application/pdf 986807 no The American Chemical Society (ACS) 2011 eng Theoretical Chemistry (including Computational Chemistry) 1549-9618 2160455 000293662500014 80051645750 26606619 10.1021/ct100725a http://dx.doi.org/10.1021/ct100725a yes 7 8 2452 2463 https://www.scopus.com/pages/publications/80051645750 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) c87d4e32-28b2-498d-bcd6-860f3a854724 2016-04-01T09:47:34+02:00 2025-10-14T11:07:29+02:00 2016-04-01T09:47:34+02:00 1 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 eSSENCE: The e-Science Collaboration v1001240 department We developed an analytical theory for the many-body potential of mean force (POMF) between N spheres immersed in a continuum chain fluid. The theory is almost exact for a T polymer solution in the protein limit (small particles, long polymers), where N-body effects are important. Polydispersity in polymer length according to a SchulzFlory distribution emerges naturally from our analysis, as does the transition to the monodisperse limit. The analytical expression for the POMF allows for computer simulations employing the complete N-body potential (i.e., without n-body truncation; n < N). These are compared with simulations of an explicit particle/polymer mixture. We show that the theory produces fluid structure in excellent agreement with the explicit model simulations even when the system is strongly fluctuating, e.g., at or near the spinodal region. We also demonstrate that other commonly used theoretical approaches, such as truncation of the POMF at the pair level or the Asakura Oosawa model, are extremely inaccurate for these systems. https://portal.research.lu.se/en/publications/08cf5d9c-3759-47a1-b830-17b72fd0dcd3 https://portal.research.lu.se/files/27852723/langlett.pdf application/pdf 417107 no The American Chemical Society (ACS) 2015 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 5201280 000348085900005 84921265921 25547161 10.1021/la5037184 http://dx.doi.org/10.1021/la5037184 yes 31 1 22 26 https://www.scopus.com/pages/publications/84921265921 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) 08cf5d9c-3759-47a1-b830-17b72fd0dcd3 2016-04-01T09:47:36+02:00 2025-10-14T12:39:41+02:00 2016-04-01T09:47:36+02:00 2 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Martin Trulsson author 6169ee6c-8851-4647-acc7-cf405f60b46a Bo Jönsson author acad6398-af1f-4be3-8c0f-c7dbb066571d Christophe Labbez author 31116218-904a-45ea-bd0c-2c544a1fd95a Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department Monte Carlo simulations show that charge-regulation alone can cause highly charged zirconium nanoparticles to adsorb to a similarly charged or neutral silica particle and thereby stabilizing the latter. This mechanism, referred to as halo stabilization, is quite general and applicable in a range of systems provided that pH, van der Waals forces, and dissociation constants of the charge-regulating particles are properly chosen. In our modeling we see an overall attraction at low volume fractions of nanoparticles, while at higher a repulsive barrier is created, stabilizing the microparticles and protecting them from aggregation. The charge-regulation mechanism also turns the silica surface from positively charged, without nanoparticles, to negatively charged in the presence of nanoparticles. https://portal.research.lu.se/en/publications/35485b97-19a9-460d-af01-90398b4cedc0 Royal Society of Chemistry 2013 eng Theoretical Chemistry (including Computational Chemistry) 1463-9084 3218618 000311963600017 23172156 84870914996 23172156 10.1039/c2cp42404e http://dx.doi.org/10.1039/c2cp42404e yes 15 2 541 545 https://www.scopus.com/pages/publications/84870914996 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) 35485b97-19a9-460d-af01-90398b4cedc0 2016-04-01T09:48:30+02:00 2025-10-14T12:32:14+02:00 2016-04-01T09:48:30+02:00 3 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 eSSENCE: The e-Science Collaboration v1001240 department We use a continuum chain model and develop an analytical theory for the interaction between many spheres immersed in a fluid of ideal polydisperse polymers. Assuming local spherical symmetry of the polymer field about each particle, combined with a local approximation, compact expressions are derived for the many-body interaction between the spheres. We use a mean-field approximation to investigate the fluid-fluid phase diagram for the mixture. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3685834] https://portal.research.lu.se/en/publications/06fafbf0-1ea4-4d7f-af22-a40e80547c83 American Institute of Physics (AIP) 2012 eng approximation theory many-body problems phase diagrams polymers Theoretical Chemistry (including Computational Chemistry) 0021-9606 2383319 000300944000039 84857850625 22380062 10.1063/1.3685834 http://dx.doi.org/10.1063/1.3685834 yes 136 8 https://www.scopus.com/pages/publications/84857850625 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) 06fafbf0-1ea4-4d7f-af22-a40e80547c83 2016-04-01T09:49:02+02:00 2025-10-14T12:35:39+02:00 2016-04-01T09:49:02+02:00 4 info:srw/schema/1/mods-v3.3xml journalArticle published yes 5 Jimmy Heimdal author 6a1606a2-c9f0-4efa-b7f0-454bb8f1bc2c Markus Kaukonen author e12132a4-d2ae-4269-9c67-c4b7712bab21 Martin Srnec author Lubomir Rulisek author 161aab1b-870a-4ad9-a6b1-4cf2af3a9859 Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department 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. https://portal.research.lu.se/en/publications/44ad90af-cba7-48ec-aaa6-1b8a782375d6 John Wiley & Sons Inc. 2011 eng Theoretical Chemistry (including Computational Chemistry) 1439-7641 2200935 000297693200029 21960467 82955229600 21960467 10.1002/cphc.201100339 http://dx.doi.org/10.1002/cphc.201100339 yes 12 Online: 29 SEP 2011 3337 3347 https://www.scopus.com/pages/publications/82955229600 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) 44ad90af-cba7-48ec-aaa6-1b8a782375d6 2016-04-01T09:51:00+02:00 2025-10-14T10:45:00+02:00 2016-04-01T09:51:00+02:00 5 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 6 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 7 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 8 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 9 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 10 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 11 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 12 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 13 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 14 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 15 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 16 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 LiHong Hu author 86e8d89d-f5e4-421e-8f60-8591dd2053ba Pär Söderhjelm author 45ebbdaa-83be-4617-b881-8d2a64c0e7ef Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimisation on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a second-sphere histidine residue in the active site of [Ni,Fe] hydrogenase, which has been shown to be very sensitive to the surroundings. We include in the QM calculations all residues within 4.5 Å of the active site, two capped residues on each side of the active-site residues, as well as all charged groups that are buried inside the protein, which for this enzyme includes three iron–sulphur clusters, in total 930 atoms. These calculations are performed at the BP86/def2-SV(P) level, but the energies are then extrapolated to the B3LYP/def2-TZVP level with a smaller QM system and zero-point energy, entropy, and thermal effects are added. We test three approaches to model the remaining atoms of the protein solvent, viz. by standard QM/MM approaches using either mechanical or electrostatic embedding, or by using a continuum solvation model for the large QM systems. Quite encouragingly, the three approaches give the same results within 13 kJ/mol and variations in the size of the QM system do not change the energies by more than 8 kJ/mol, provided that the QM/MM junctions are not moved closer to the QM system. The statistical precision for the average over ten snapshots is 1–3 kJ/mol. https://portal.research.lu.se/en/publications/a4cc32bc-e8c1-4859-8beb-13dfd346901f https://portal.research.lu.se/files/1496077/3412413.pdf application/pdf 543192 no The American Chemical Society (ACS) 2013 eng Quantum mechanical cluster calculations QM/MM calculations continuum solvation large quantum mechanical calculations proton transfer [Ni Fe] hydrogenase. Theoretical Chemistry (including Computational Chemistry) 1549-9618 3412412 000313378700064 84872130995 26589061 10.1021/ct3005003 http://dx.doi.org/10.1021/ct3005003 yes 9 640 649 https://www.scopus.com/pages/publications/84872130995 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) a4cc32bc-e8c1-4859-8beb-13dfd346901f 2016-04-01T10:02:00+02:00 2025-10-14T12:50:34+02:00 2016-04-01T10:02:00+02:00 17 info:srw/schema/1/mods-v3.3xml journalArticle published yes 4 Charlotte Gustavsson author 70563a02-8dea-4e60-966a-bbfdd3249a2f Joaquim Li author c31c4a7b-fe58-41c0-beb7-2f1df51b7d23 Karen J. Edler author Lennart Piculell author ba05325e-3755-4a99-a375-85b130756ee7 Physical Chemistry v1000657 department Computational Chemistry v1000659 department Water-insoluble films of oppositely charged polyionsurfactant ion complex salts (CS) are readily cast on solid surfaces from ethanolic solutions. The methodology introduces new possibilities to study and utilize more or less hydrated CS. Direct SAXS measurements show that the surface films are water-responsive and change their liquid crystalline structure in response to changes in the water activity of the environment. In addition to the classical micellar cubic and hexagonal phases, a rectangular ribbon phase and a hexagonal close-packed structure have now been detected for CS composed of cationic alkyltrimethylammonium surfactants with polyacrylate counterions. Added cosurfactants, decanol or the nonionic surfactant C12E5, yield additional lamellar and bicontinuous cubic structures. Images of the surfaces by optical and atomic force microscopy show that the films cover the surfaces well but have a more or less irregular surface topology, including craters of sizes ranging from a few to hundreds of micrometers. The results indicate possibilities to create a wealth of water-responsive structured CS films on solid surfaces. https://portal.research.lu.se/en/publications/8216acbd-908d-4ba9-bea4-98b3fb21cd7b The American Chemical Society (ACS) 2014 eng Theoretical Chemistry (including Computational Chemistry) Physical Chemistry (including Surface- and Colloid Chemistry) 0743-7463 5073027 000347744100009 84908285322 25264925 10.1021/la503210g http://dx.doi.org/10.1021/la503210g yes 30 42 12525 12531 https://www.scopus.com/pages/publications/84908285322 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) 8216acbd-908d-4ba9-bea4-98b3fb21cd7b 2016-04-01T10:02:03+02:00 2025-10-14T12:43:29+02:00 2016-04-01T10:02:03+02:00 18 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Victor Vysotskiy author 07a23015-41f3-4cdf-9d30-e5c310542824 Jonas Boström author 9cfe4295-5fae-41f5-84ff-26916d034c10 Valera Veryazov author 58fd57ab-ebb3-4246-8d3f-94e823ff02a0 Computational Chemistry v1000659 department eSSENCE: The e-Science Collaboration v1001240 department A parallel procedure for an effective optimization of relative position and orientation between two or more fragments has been implemented in the MOLCAS program package. By design, the procedure does not perturb the electronic structure of a system under the study. The original composite system is divided into frozen fragments and internal coordinates linking those fragments are the only optimized parameters. The procedure is capable to handle fully independent (no border atoms) fragments as well as fragments connected by covalent bonds. In the framework of the procedure, the optimization of relative position and orientation of the fragments are carried out in the internal "Z-matrix" coordinates using numerical derivatives. The total number of required single points energy evaluations scales with the number of fragments rather than with the total number of atoms in the system. The accuracy and the performance of the procedure have been studied by test calculations for a representative set of two- and three-fragment molecules with artificially distorted structures. The developed approach exhibits robust and smooth convergence to the reference optimal structures. As only a few internal coordinates are varied during the procedure, the proposed constrained fragment geometry optimization can be afforded even for high level ab initio methods like CCSD(T) and CASPT2. This capability has been demonstrated by applying the method to two larger cases, CCSD(T) and CASPT2 calculations on a positively charged benzene lithium complex and on the oxygen molecule interacting to iron porphyrin molecule, respectively. © 2013 Wiley Periodicals, Inc. https://portal.research.lu.se/en/publications/b6405f74-66fb-49d4-89c8-b2556bc70b91 John Wiley & Sons Inc. 2013 eng Theoretical Chemistry (including Computational Chemistry) 1096-987X 4066271 000325540200008 24006272 84885630229 10.1002/jcc.23428 http://dx.doi.org/10.1002/jcc.23428 yes 34 30 2657 2665 https://www.scopus.com/pages/publications/84885630229 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) b6405f74-66fb-49d4-89c8-b2556bc70b91 2016-04-01T10:04:49+02:00 2025-10-14T13:24:24+02:00 2016-04-01T10:04:49+02:00 19 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Samuel Genheden author bbfc8f53-f9d6-49ff-9926-38144c1c1d7c Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have studied whether the efficiency of alchemical free-energy calculations with the Bennett acceptance ratio method of protein-ligand binding energies can be improved by simulating only part of the protein. To this end, we solvated the full protein in a spherical droplet with a radius of 46 angstrom, surrounded by a vacuum. Then, we systematically reduced the size of the droplet and at the same time ignored protein residues that were outside the droplet. Radii of 40-15 angstrom were tested. Ten inhibitors of the blood clotting factor Xa were studied, and the results were compared to an earlier study in which the protein was solvated in a periodic box, showing complete agreement between the two sets of calculations within statistical uncertainty. We then show that the simulated system can be truncated down to 15 angstrom, without changing the calculated affinities by more than 0.5 kJ/mol on average (maximum difference of 1.4 kJ/mol). Moreover, we show that reducing the number of intermediate states in the calculations from eleven to three gave deviations that, on average, were only 0.5 kJ/mol (maximum of 1.4 kJ/mol). Together, these results show that truncation is an appropriate way to improve the efficiency of free-energy calculations for small mutations that preserve the net charge of the ligand. in fact, each calculation of a relative binding affinity requires only six simulations, each of which takes similar to 15 CPU h of computation on a single processor. https://portal.research.lu.se/en/publications/69813152-eee8-4181-9b20-66378d1e34bd https://portal.research.lu.se/files/1548525/3412387.pdf application/pdf 1467080 no The American Chemical Society (ACS) 2012 eng Theoretical Chemistry (including Computational Chemistry) 1549-9618 2574864 000302487700030 84859619156 26596755 10.1021/ct200853g http://dx.doi.org/10.1021/ct200853g yes 8 4 1449 1458 https://www.scopus.com/pages/publications/84859619156 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) 69813152-eee8-4181-9b20-66378d1e34bd 2016-04-01T10:05:10+02:00 2025-10-14T12:46:28+02:00 2016-04-01T10:05:10+02:00 20 1.1subject exact 10407subjectexact10407