| 1. |
- Engdahl, Anders, et al.
(författare)
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The water-hydroxyl radical complex: A matrix isolation study.
- 2003
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 118:17, s. 7797-7802
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Gagliardi, Laura, et al.
(författare)
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Local properties of quantum chemical systems : The LoProp approach
- 2004
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 121:10, s. 4494-4500
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Tidskriftsartikel (refereegranskat)abstract
- A new method is presented, which makes it possible to partition molecular properties like multipole moments and polarizabilities, into atomic and interatomic contributions. The method requires a subdivision of the atomic basis set into occupied and virtual basis functions for each atom in the molecular system. The localization procedure is organized into a series of orthogonalizations of the original basis set, which will have as a final result a localized orthonormal basis set. The new localization procedure is demonstrated to be stable with various basis sets, and to provide physically meaningful localized properties. Transferability of the methyl properties for the alkane series and of the carbon and hydrogen properties for the benzene, naphtalene, and anthracene series is demonstrated.
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| 3. |
- Hermida-Ramón, Jose Manuel, et al.
(författare)
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Analysis of the relative stability of cis-urocanic acid in condensed phase : The use of Langevin dipoles
- 2002
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 106:28, s. 7115-7120
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Tidskriftsartikel (refereegranskat)abstract
- A series of ab initio calculations employing a modified Langevin dipoles method to model neutral, cationic, and anionic cis-urocanic acid in human skin is presented. A comparison between the stability of the conformers in gas phase and in a condensed phase is performed. In particular, the energy barrier and transition state of the isomerization reaction of the anionic forms of cis-urocanic acid have been characterized. The modifications of the Langevin dipoles method, a procedure to obtain the required model parameters, and model verifications are presented. The latter include computing the water solvation energy and the free energy of the water dissociation.
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| 4. |
- Hermida-Ramon, J M, et al.
(författare)
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Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields
- 2003
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 24:2, s. 161-176
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Tidskriftsartikel (refereegranskat)abstract
- An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 161-176, 2003
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| 5. |
- Hermida-Ramón, Jose Manuel, et al.
(författare)
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On the influence of the basis set superposition error on calculated vibrational frequencies
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 190-195
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Tidskriftsartikel (refereegranskat)abstract
- The relation between the so called basis set superposition error and intramolecular vibrational frequencies calculated at the Hartree Fock SCF level of approximation was investigated. A linear conformation of HF dimer was chosen as test system for the investigation. It was found that the direct basis set superposition error for the studied system is rather small. It was further found that the shifts are mainly determined by the geometry parameters of the system
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| 6. |
- Hermida-Ramon, J M, et al.
(författare)
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Study of the hydronium ion in water. A combined quantum chemical and statistical mechanical treatment
- 2004
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Ingår i: Journal of molecular structure. Theochem. - : Elsevier BV. - 0166-1280. ; 712:1-3, s. 167-173
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Tidskriftsartikel (refereegranskat)abstract
- A combined quantum mechanical statistical mechanical method has been used to study the solvation of the hydronium ion in water. The system is divided in three parts, a quantum core (the ion), 89 classical water molecules and a dielectric continuum. The water molecules are represented using a polarizable potential. The first solvation shell of the ion consists of three water molecules linked by hydrogen bonds to the hydrogen atoms of the ion. The calculations show conformations where up to three water molecules directly interact with the oxygen of the ion. The intramolecular bond length in the ion increases by 0.080 a.u. and the angle decreases in 6.9degrees upon solvation relative to the gas phase value. (C) 2004 Elsevier B.V. All rights reserved.
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| 7. |
- Hermida-Ramon, J M, et al.
(författare)
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Study of the hydroxyl ion in water. A combined quantum chemical and statistical mechanical treatment.
- 2003
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 107:26, s. 5217-5222
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Tidskriftsartikel (refereegranskat)abstract
- A combined quantum mechanical-statistical mechanical method has been used to study the behavior of the hydroxyl ion in water. The system is divided into three parts, a quantum core (the ion), 89 classical water molecules, and a dielectric continuum. The water molecules are represented using a polarizable potential. The first solvation shell consists of four water molecules, two linked by hydrogen bonds to the oxygen of the ion and the other two linked to the hydrogen of the ion. The intermolecular distances obtained are in the same range as those in previous calculations. The intramolecular bond length in the ion decreases by 0.09 au upon solvation relative to the gas-phase value.
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| 8. |
- Karlström, Gunnar, et al.
(författare)
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Lattice model calculations of interactions between proteins and surface grafted polymers with tethered affinity ligands
- 2001
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Ingår i: Colloids and Surfaces B: Biointerfaces. - 1873-4367. ; 20:3, s. 245-256
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Tidskriftsartikel (refereegranskat)abstract
- Monte Carlo calculations of protein binding to affinity ligands tethered to a surface by polymers have been done and analyzed with statistical mechanical perturbation theory. The interaction of the polymers with the surface, the solvent and the protein has been varied. Different solution conditions of the polymers have been investigated, varying from collapsed polymer structures on a surface to structures extending out in the solution (athermic condition) or to mushroom like structures (hydrophobic polymers grafted on hydrophilic surface). The variation in binding of model proteins of different sizes and interactions with polymers has been studied. In general, smaller proteins bind better than larger proteins. Two types of polymer collapses have been studied. One type is due to increased polymer-surface attraction. The second type is due to increased polymer-self attraction. In the former case the binding, as a function of degree of collapse, decreases monotonically except for small proteins with attraction to the polymer. For collapses of the second type the loss of binding goes through a maximum except for large proteins.
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| 9. |
- Karlström, Gunnar, et al.
(författare)
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MOLCAS : a program package for computational chemistry
- 2003
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Ingår i: Computational materials science. - 0927-0256 .- 1879-0801. ; 28:2, s. 222-239
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Tidskriftsartikel (refereegranskat)abstract
- The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations. MOLCAS is especially adapted to treat systems with a complex electronic structure, where the simplest quantum chemical models do not work. These features together with the inclusion of relativistic effects makes it possible to treat with good accuracy systems including atoms from the entire periodic system. MOLCAS has effective methods for geometry optimization of equilibria, transition states, conical intersections, etc. This facilitates studies of excited state energy surfaces, spectroscopy, and photochemical processes.
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| 10. |
- Karlström, Gunnar
(författare)
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On the effective interaction between an ion and a hydrophobic particle in polar solvents. A step towards an understanding of the hofmeister effect?
- 2003
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084. ; 5:15, s. 3238-3246
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Tidskriftsartikel (refereegranskat)abstract
- It has been shown that the generally accepted assumption that hydrophobic molecules and ions repel each other in polar solvents is only valid for moderately polar solvents. When the dipole moment of the medium molecules is increased, then ions and hydrophobic particles start to attract each other. For particles with the size and dipole moment of a water molecule one can expect that the effective potential curve between the two types of particles is almost flat. This opens up for an explanation of the 114 years old unexplained Hofmeister effect.
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