1.1 981 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 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 7 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 8 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 9 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Thomas Rod author e7317b06-3ef9-4157-9d43-6061d7a7d6c2 Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We recently described a method to compute accurate quantum mechanical free energies [Rod, T. H.; Ryde, U. Phys. Rev. Lett. 2005, 94, `138302]. The method, which we term quantum mechanical thermodynamic cycle perturbation (QTCP), employs a molecular mechanics force field to sample phase space and, subsequently, a thermodynamic cycle to estimate QM/MM free energy changes. Here, we discuss the methodology in detail and test an approach based on a different thermodynamic cycle. We also show that a new way of treating hydrogen link atoms makes the free energy changes converge faster and that extrapolation to higher accuracy can be performed. We finally discuss the quantum mechanical free energy (QM/MMFE) method in the framework of the QTCP method. All methods considered are applied to the methylation of catecholate catalyzed by catechol O-methyltransferase. We compute the free energy barrier for the reaction by computing free energy changes in steps between fixed OM regions along a predetermined reaction pathway. Using the QTCP approach, an extrapolated activation free energy of 69 kJ/mol for the forward reaction and 90 kJ/mol for the reverse reaction are obtained at the level of the B3LYP functional and the 6-311++G(2d,2p) basis set. The value for the forward reaction is in excellent agreement with the experimental value of 75 kJ/mol. Results based on the QM/MM-FE method differ by less than 10 kJ/mol from those values, indicating that QM/MM-FE may be a fairly accurate and cheap alternative to calculate QM/MM free energy changes. Moreover, the results are compared to barriers obtained with a fixed molecular mechanics environment as well as with structures optimized in a vacuum. All the computed free energy barriers are well converged. A major approximation in the current implementation of the QTCP method is that the QM region is fixed. The approximation leads to well-converged free energy barriers, which has been a problem in similar studies. https://portal.research.lu.se/en/publications/e8f0bac8-de4a-49a2-99e2-0eea867c6cad The American Chemical Society (ACS) 2005 eng Theoretical Chemistry (including Computational Chemistry) 1549-9618 152684 000233260300019 33646508010 10.1021/ct0501102 http://dx.doi.org/10.1021/ct0501102 yes 1 6 1240 1251 https://www.scopus.com/pages/publications/33646508010 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) e8f0bac8-de4a-49a2-99e2-0eea867c6cad 2016-04-01T11:45:13+02:00 2025-10-14T09:46:30+02:00 2016-04-01T11:45:13+02:00 10 info:srw/schema/1/mods-v3.3xml journalArticle published yes 4 Andrei Broukhno author cd8cc465-8068-4602-8fa8-b37ec72298b2 Malek O Khan author Torbjörn Åkesson author 5f078d78-6bd8-4ba1-8fa8-af73c2dd5e51 Bo Jönsson author acad6398-af1f-4be3-8c0f-c7dbb066571d Computational Chemistry v1000659 department The force between two planar charged surfaces in the presence of polyampholytes (PAs) is investigated as a function of the surface separation. The model system contains PA molecules with zero net charge adsorbing onto the charged surfaces from a dilute surrounding solution without salt. We compare the results obtained on three levels of approximation: (i) polyampholytes moving in the mean field due to the counterions, i.e., in the Poisson-Boltzmann field, (ii) PAs in a self-consistent field generated by both counterions and PA monomers, and (iii) with all interactions treated explicitly. Either the amount of PA is kept constant for varying slit widths or chemical equilibrium with a bulk solution is considered. The PA adsorption and the surface force are found to strongly depend on the charge sequence along the chain. That is, polyampholytes with alternating charges do not adsorb, and their effect on the force is similar to that of neutral polymers. For PAs with long blocks oppositely-charged to the surfaces, however, the adsorption is more favorable and the monomer distribution for these blocks resembles that of polyelectrolytes. The counterions are in this case efficiently displaced from the surfaces, which leads to a significant extension of the electric double layer. Thus, our main conclusion is that adsorbing polyampholytes always increase the double layer repulsion between planar charged surfaces, and, the major cause for this phenomenon is the counterion redistribution. Yet, PA chains are capable of establishing "bridges" at short surface separations, but the resulting attraction can only slightly reduce the repulsive net pressure. The simplest approximation (i) is in principle only valid in the limit of zero PA density. At a finite concentration, it is sufficient, though essential, to include a linear correction to the Poisson-Boltzmann solution in order to accurately predict the interfacial force or the amount of PA in the slit at chemical equilibrium. https://portal.research.lu.se/en/publications/0ba24892-e73d-4438-8003-2d2938afea9c The American Chemical Society (ACS) 2002 eng Theoretical Chemistry (including Computational Chemistry) 0743-7463 331934 000177224400070 0037031449 10.1021/la020094l http://dx.doi.org/10.1021/la020094l yes 18 16 6429 6436 https://www.scopus.com/pages/publications/0037031449 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) 0ba24892-e73d-4438-8003-2d2938afea9c 2016-04-01T11:45:20+02:00 2025-10-14T10:59:47+02:00 2016-04-01T11:45:20+02:00 11 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Mikael Lund author 19146bd3-d347-4a94-93a8-1d1a11e3f988 Bo Jönsson author acad6398-af1f-4be3-8c0f-c7dbb066571d Clifford Woodward author Computational Chemistry v1000659 department Solvation of protein surface charges plays an important role for the protonation states of titratable surface groups and is routinely incorporated in low dielectric protein models using surface accessible areas. For many-body protein simulations, however, such dielectric boundary methods are rarely tractable and a greater level of simplification is desirable. In this work, we scrutinize how charges on a high dielectric surface are affected by the nonpolar interior core of the protein. A simple dielectric model, which models the interior as a low dielectric sphere, combined with Monte Carlo simulations, shows that for small, hydrophilic proteins the effect of the low dielectric interior is largely negligible and that the protein (and solution) can be approximated with a uniform high dielectric constant equal to that of the solvent. This is verified by estimates of titration curves and acidity constants for four different proteins (BPTI, calbindin D-9k, ribonuclease A, and turkey ovomucoid third domain) that all correlate well with experimental data. Furthermore, the high dielectric approximation follows as a natural consequence of the multipole expansion of the potential due to embedded protein charges in the presence of the low dielectric core region. (c) 2007 American Institute of Physics. https://portal.research.lu.se/en/publications/e448def7-55e1-43ed-92db-b9f9bf7ffd7e American Institute of Physics (AIP) 2007 eng Theoretical Chemistry (including Computational Chemistry) 0021-9606 648827 000247247400048 34250702227 10.1063/1.2741543 http://dx.doi.org/10.1063/1.2741543 yes 126 22 https://www.scopus.com/pages/publications/34250702227 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) e448def7-55e1-43ed-92db-b9f9bf7ffd7e 2016-04-01T11:45:24+02:00 2025-10-14T10:25:39+02:00 2016-04-01T11:45:24+02:00 12 info:srw/schema/1/mods-v3.3xml journalArticle published yes 4 Patrik Rydberg author e05ec3fa-2b37-4dea-b5fa-6c382315efd9 Lars Olsen author Per-Ola Norrby author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have developed force-field parameters for the hydrogen-abstraction transition state of aliphatic hydroxylation by cytochrome P450 using the Q2MM approach. The parametrization is based on quantum chemical (B3LYP) transition-state structures and Hessian matrices for 24 diverse substrate models (14 in the training set and 10 in the test set). The force field is intended to be applicable to any druglike molecule by the use of the general Amber force field (GAFF) for the substrates. The parameters reproduce the geometries within 0.1 angstrom and 1.2 degrees for bond lengths and angles, respectively, with no significant differences between the training and test sets. The Hessian matrix is also well reproduced with a correlation coefficient of 0.99. The parametrization is performed by the ideal iterative approach of Norrby and Liljefors, which we have implemented for the Amber software. https://portal.research.lu.se/en/publications/daf44db2-e503-4cb0-b4b6-779b388b394e https://portal.research.lu.se/files/136746349/101_p450forcefield.pdf application/pdf 922999 no The American Chemical Society (ACS) 2007 eng Theoretical Chemistry (including Computational Chemistry) 1549-9618 657319 000249454500012 35948961951 10.1021/ct700110f http://dx.doi.org/10.1021/ct700110f yes 3 5 1765 1773 https://www.scopus.com/pages/publications/35948961951 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) daf44db2-e503-4cb0-b4b6-779b388b394e 2016-04-01T11:45:45+02:00 2025-10-14T11:33:02+02:00 2016-04-01T11:45:45+02:00 13 info:srw/schema/1/mods-v3.3xml journalArticle published yes 5 Pär Söderhjelm author 45ebbdaa-83be-4617-b881-8d2a64c0e7ef Charlotte Husberg author Angela Strambi author Massimo Olivucci author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department We have developed automatic methods to calculate multipoles and anisotropic polarizabilities for all atoms and bond centers in a protein and to include such a model in the calculation of electronic properties at any level of quantum mechanical theory. This approach is applied for the calculation of the electronic spectra of retinal in rhodopsin at the CASPT2//CASSCF level (second-order multiconfigurational perturbation theory) for the wild-type protein, as well as two mutants and isorhodopsin in QM/MM structures based on two crystal structures. We also perform a detailed investigation of the importance and distance dependence of the multipoles and the polarizabilities for both the absolute and the relative absorption energies. It is shown that the model of the surrounding protein strongly influences the spectrum and that different models give widely different results. For example, the Amber 1994 and 2003 force fields give excitation energies that differ by up to 16 kJ/mol. For accurate excitation energies, multipoles up to quadrupoles and anisotropic polarizabilities are needed. However, interactions with residues more than 10 A from the chromophore can be treated with a standard polarizable force field without any dipoles or quadrupoles. https://portal.research.lu.se/en/publications/919a5777-96ad-4b91-902b-ce01917d0389 https://portal.research.lu.se/files/136744686/121_rhodopsin.pdf application/pdf 1432410 no The American Chemical Society (ACS) 2009 eng Theoretical Chemistry (including Computational Chemistry) 1549-9618 1404851 000264085600021 65349179259 26610229 10.1021/ct800459t http://dx.doi.org/10.1021/ct800459t yes 5 3 649 658 https://www.scopus.com/pages/publications/65349179259 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) 919a5777-96ad-4b91-902b-ce01917d0389 2016-04-01T11:46:40+02:00 2025-10-14T11:48:57+02:00 2016-04-01T11:46:40+02:00 14 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Jan Forsman author f70464c8-6a9d-4d0e-83e8-495078dbda87 CE Woodward author Computational Chemistry v1000659 department According to a recently developed density functional theory, athermal polymer solutions, in which the solvent particles are smaller than the monomers, may undergo a bulk fluid-fluid phase separation, driven by excluded volume effects. In recent work, we showed that an inert surface immersed in the dilute polymer phase can, in principle, be wetted by the condensed phase. However, we show here that the "prewetting transition" we assumed in our earlier studies is in fact a different type of surface transition. Rather than completely wet the surface at coexistence, the condensed phase layer which forms in the presence of the dilute bulk remains globally stable (and is finite in width) even as the bulk coexistence conditions are approached. Hence, the adsorbed phase inhibits complete wetting of the surface by the dilute phase. The surface transition is first order for the systems we study here and, for longer polymers, the surface phase coexistence line meets the bulk coexistence curve nontangentially to give rise to a lower transition point. For short polymers, we find that the surface transition can occur for a supercritical bulk. We develop a simple one-component thermal model, which displays analogous behavior at an adsorbing surface and provides us with some insight into the qualitative mechanisms responsible. https://portal.research.lu.se/en/publications/c9fda7d4-410c-4b4a-8546-4e91acb948d8 American Physical Society 2006 eng Theoretical Chemistry (including Computational Chemistry) 1539-3755 406998 000237951300054 33646867452 16802959 10.1103/PhysRevE.73.051803 http://dx.doi.org/10.1103/PhysRevE.73.051803 yes 73 5 https://www.scopus.com/pages/publications/33646867452 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) c9fda7d4-410c-4b4a-8546-4e91acb948d8 2016-04-01T11:46:43+02:00 2025-10-14T11:02:59+02:00 2016-04-01T11:46:43+02:00 15 info:srw/schema/1/mods-v3.3xml journalArticle published yes 4 T J Lee author Björn Roos author 7d3f3df5-ff3d-45ad-9dad-bf6cd3535f77 C E Dateo author M Rubio author Computational Chemistry v1000659 department The CCSD(T) method has been used to compute a highly accurate quartic force field and fundamental frequencies for all 16O and 18O isotopomers of the ozonide anion. The CCSD and CASPT2 methods have also been used to verify the reliability of the CCSD(T) fundamental frequencies. The computed fundamental frequencies are in agreement with gas-phase experiments, but disagree with matrix isolation experiments for the antisymmetric stretch, n3. CASPT2 calculations show that the antisymmetric part of the O3- potential surface is sensitive to the external environment. It is concluded that the antisymmetric stretch exhibits a significant matrix shift in the matrix isolation experiments and that the matrix environment is not representative of the gas-phase environment for ozonide anion. It is hoped that the theoretical data provided here will aid in the interpretation of future high-resolution gas-phase experiments. https://portal.research.lu.se/en/publications/8306a91e-b64c-47f7-a8b9-018db32244b2 Institute of Organic Chemistry and Biochemistry 2003 eng Theoretical Chemistry (including Computational Chemistry) 2192-6506 128771 000180883800011 0037250870 10.1135/cccc20030189 http://dx.doi.org/10.1135/cccc20030189 yes 68 1 189 201 https://www.scopus.com/pages/publications/0037250870 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) 8306a91e-b64c-47f7-a8b9-018db32244b2 2016-04-01T11:47:04+02:00 2025-10-14T11:23:29+02:00 2016-04-01T11:47:04+02:00 16 info:srw/schema/1/mods-v3.3xml journalArticle published yes 2 Kasper Jensen author ab4bdb39-c287-4029-af04-235d6be47f2d Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department Density functional calculations have been used to compare various geometric, electronic and functional properties of iron and cobalt porphyrin (Por) and corrin (Cor) species. The investigation is focussed on octahedral MII/III complexes (where M is the metal) with two axial imidazole ligands (as a model of b and c type cytochromes) or with one imidazole and one methyl ligand (as a model of methylcobalamin). However, we have also studied some five-coordinate MII complexes with an imidazole ligand and four-coordinate MI/II complexes without any axial ligands as models of other intermediates in the reaction cycle of coenzyme B12. The central cavity of the corrin ring is smaller than that of porphine. We show that the cavity of corrin is close to ideal for low-spin CoIII, CoII, and CoI with the axial ligands encountered in biology, whereas the cavity in porphine is better suited for intermediate-spin states. Therefore, the low-spin state of Co is strongly favoured in complexes with corrins, whereas there is a small energy difference between the various spin states in iron porphyrin species. There are no clear differences for the reduction potentials of the octahedral complexes, but [CoICor] is more easily formed (by at least 40 kJ mole-1) than [FeIPor]. Cobalt and corrin form a strong CoC bond that is more stable against hydrolysis than iron and porphine. Finally, FeII/III gives a much lower reorganisation energy than CoII/III; this is owing to the occupied dz2 orbital in CoII. Altogether, these results give some clues about how nature has chosen the tetrapyrrole rings and their central metal ion. https://portal.research.lu.se/en/publications/d4901b40-44d9-418f-869e-91e2e80009ca https://portal.research.lu.se/files/135490921/55_por_comp.pdf application/pdf 890049 no John Wiley & Sons Inc. 2003 eng Theoretical Chemistry (including Computational Chemistry) 1439-4227 128717 12740813 000182962700006 0038702224 10.1002/cbic.200200449 http://dx.doi.org/10.1002/cbic.200200449 yes 4 5 413 424 https://www.scopus.com/pages/publications/0038702224 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) d4901b40-44d9-418f-869e-91e2e80009ca 2016-04-01T11:47:27+02:00 2025-10-14T09:56:55+02:00 2016-04-01T11:47:27+02:00 17 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Lubomir Rulisek author 161aab1b-870a-4ad9-a6b1-4cf2af3a9859 E I Solomon author Ulf Ryde author 3257e3e5-5cf7-4f19-abb3-36356498cac3 Computational Chemistry v1000659 department The four-electron reduction of dioxygen to water in multicopper oxidases takes place in a trinuclear copper cluster, which is linked to a mononuclear blue copper site, where the substrates are oxidized. Recently, several intermediates in the catalytic cycle have been spectroscopically characterized, and two possible structural models have been suggested for both the peroxy and native intermediates, In this study, these spectroscopic results are complemented by hybrid quantum and molecular mechanical (QM/MM) calculations, taking advantage of recently available crystal structures with a full complement of copper ions. Thereby, we obtain optimized molecular structures for all of the Experimentally studied intermediates involved in the reductive cleavage of the O-2 molecule and energy profiles for individual reaction steps, This allows identification of the experimentally observed intermediates and further insight into the reaction mechanism that is probably relevant for the whole class of multicopper oxidases, We suggest that the peroxy intermediate contains an O-2(2-) ion, in which one oxygen atom bridges the type 2 copper ion and one of the type 3 copper ions, whereas the other one coordinates to the other type 3 copper ion, One-electron reduction of this intermediate triggers the cleavage of the O-O bond, which involves the uptake of a proton, The product of this cleavage is the observed native intermediate, which we suggest to contain a O-2 ion coordinated to all three of the copper ions in the center of the cluster. https://portal.research.lu.se/en/publications/5819617a-b12f-474b-bbcd-976c76e2a5d5 https://portal.research.lu.se/files/135493204/77_lacc.pdf application/pdf 3864445 no The American Chemical Society (ACS) 2005 eng Theoretical Chemistry (including Computational Chemistry) 1520-510X 152715 000231030900012 16060610 23844550273 10.1021/ic050092z http://dx.doi.org/10.1021/ic050092z yes 44 16 5612 5628 https://www.scopus.com/pages/publications/23844550273 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) 5819617a-b12f-474b-bbcd-976c76e2a5d5 2016-04-01T11:47:36+02:00 2025-10-14T11:09:08+02:00 2016-04-01T11:47:36+02:00 18 info:srw/schema/1/mods-v3.3xml journalArticle published yes 5 PB Coto author A Sinicropi author Luca De Vico author 83f6a50b-6192-445a-bb12-fb5529b87de4 N Ferre author M Olivucci author Computational Chemistry v1000659 department The branching plane associated with the conical intersection controlling the photochemical Z -> E isomerization reaction of rhodopsin has been mapped using a CASPT2//CASSCF/ AMBER quantum mechanics-molecular mechanics method. The nature of the derivative coupling and gradient difference vectors spanning the branching plane has been investigated, showing that the conical intersection is not only associated with the isomerization process but also to a charge transfer along the retinal backbone. Using a simple Landau-Zener model, the paper discusses the possible effects of the documented conical intersection topologies on the efficiency of the reactive process. It is argued that the peculiar shape of the conical intersection favours decay at structures that are geometrically displaced towards the photoproduct bathorhodopsin. https://portal.research.lu.se/en/publications/e30aa23b-1044-4dd3-b179-e66bb2ab7c1b Taylor & Francis 2006 eng Theoretical Chemistry (including Computational Chemistry) 1362-3028 411131 000236853100029 33645794978 10.1080/00268970500415865 http://dx.doi.org/10.1080/00268970500415865 yes 104 5-7 983 991 https://www.scopus.com/pages/publications/33645794978 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) e30aa23b-1044-4dd3-b179-e66bb2ab7c1b 2016-04-01T11:48:07+02:00 2025-10-14T11:18:19+02:00 2016-04-01T11:48:07+02:00 19 info:srw/schema/1/mods-v3.3xml journalArticle published yes 3 Anders Engdahl author 2de5faea-06cb-4dcf-bb60-ac5c4ee21802 Gunnar Karlström author 6fb98aa4-891c-4c2c-8735-3be59b672049 Bengt Nelander author 54dcf22b-872b-4abc-8b00-a2481dec561f MAX IV Laboratory v1000329 department Computational Chemistry v1000659 department Chemical Physics v1000658 department The water–hydroxyl radical complex was prepared by irradiating peroxy radicals in hydrogen-doped argon matrices. The low water content of the matrices made it possible to observe the fundamental bands of the complexed water molecule. The experimental results are compared with the results from ab initio calculations. The complex rotates around the O–O axis in the matrix. ©2003 American Institute of Physics. https://portal.research.lu.se/en/publications/b08518c6-b686-46a2-a577-824d9a5fdee3 American Institute of Physics (AIP) 2003 eng Atom and Molecular Physics and Optics Theoretical Chemistry (including Computational Chemistry) 0021-9606 128669 000182276100009 0037838958 10.1063/1.1563608 http://dx.doi.org/10.1063/1.1563608 yes 118 17 7797 7802 https://www.scopus.com/pages/publications/0037838958 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Chemical Physics (S) (011001060), Theoretical Chemistry (S) (011001039), Max-laboratory (011012005) b08518c6-b686-46a2-a577-824d9a5fdee3 2016-04-01T11:48:14+02:00 2026-09-21T10:05:46+02:00 2016-04-01T11:48:14+02:00 20 1.1subject exact 10407subjectexact10407