ABSTRACT From the standpoint of models that use a polarizable continuum to represent the solvent ... more ABSTRACT From the standpoint of models that use a polarizable continuum to represent the solvent in studying the phenomenon of solvation, a systematic and detailed analysis is made of the influence of the cavity size and shape on calculated energies. The solute is represented by its ab initio wavefunction, and the electronic part of the solvation energy is calculated including terms that take into account electron correlation up to third order. The analysis shows the convenience of modeling the cavity according to considerations of homogeneity, which are based fundamentally on how the solute wavefunction is constructed, i.e., the basis set used.
ABSTRACT A nonequilibrium polarizable continuum model, proposed in a previous paper (J. Chem. Phy... more ABSTRACT A nonequilibrium polarizable continuum model, proposed in a previous paper (J. Chem. Phys. 1993, 98, 7375), is applied to the study, at CIS and CISD levels, of solvent effects on the electronic structure of the (1)(n, pi*) transition of formaldehyde. To obtain a proper description of the excited state properties in solution, the generalized density matrix must be employed. The effects of the electrostatic dielectric potential, dispersion, and the Stark term, as well as the specific solute-solvent interaction are analyzed. The contribution to the solvent shift from the dispersion component is of comparatively minor importance in the absorption process, but constitutes an appreciable fraction of the total shift in the emission process. The contribution of the Stark effect term is very small and may be neglected. Explicit addition of water molecules to the carbonyl compound is necessary to account for the observed blue shift.
In the last decades the search for environmentally friendlier solvents [1] has been accompanied o... more In the last decades the search for environmentally friendlier solvents [1] has been accompanied on the theoretical side by a renewed interest in the development of methods oriented to understanding and predicting how the structure, properties, and reactivity of molecules are affected by ...
A study of the competition between intra- and intermolecular hydrogen bonds and its influence on ... more A study of the competition between intra- and intermolecular hydrogen bonds and its influence on the stability of the Cys-Asn-Ser tripeptide in aqueous solution was performed by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a DFT-B3LYP/6-311+G(d) quantum treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In gas phase, the most stable structure adopts a C5 conformation. Somewhat higher in energy are found the PP(II) and C7eq structures. In solution, the stability order of the different conformers is reversed: the PP(II) structure becomes the most stable, and the C5 structure is strongly destabilized. The conformational equilibrium is shifted toward conformations in which the intramolecular hydrogen bonds (IHB) have been substituted with intermolecular hydrogen bonds with the water molecules. The solvent stabilizes extended structures without IHBs that are not stable in vacuum. The effect of the protonation state on the conformational equilibrium was also analyzed.
... ML Sánchez, ME MartÃn, I. Fdez. Galván, FJ Olivares del Valle, and MA Aguilar*. Dpto. QuÃmica... more ... ML Sánchez, ME MartÃn, I. Fdez. Galván, FJ Olivares del Valle, and MA Aguilar*. Dpto. QuÃmica-FÃsica, Universidad de Extremadura. Avda de Elvas s/n, 06071 Badajoz, Spain. J. Phys. Chem. B , 2002, 106 (18), pp 4813–4817. ...
A novel Conus peptide, conorfamide-Sr1, has been characterized. The sequence of the natural pepti... more A novel Conus peptide, conorfamide-Sr1, has been characterized. The sequence of the natural peptide was determined using standard Edman sequencing methods and mass spectrometry, and confirmed by chemical synthesis. The peptide has 12 amino acids and no cysteine residues. The following sequence was obtained: GPMGWVPVFYRF-NH(2). No other peptide from a vermivorous Atlantic Conus species has previously been characterized. Conorfamide-Sr1 belongs to the RFamide neuropeptide family, and is the first RFamide peptide to be found in any venom. The presence of conorfamide-Sr1 as a major peptide in Conus spurius venom suggests that Conus lineages in the Atlantic may have evolved novel Conus venom peptide families.
ABSTRACT From the standpoint of models that use a polarizable continuum to represent the solvent ... more ABSTRACT From the standpoint of models that use a polarizable continuum to represent the solvent in studying the phenomenon of solvation, a systematic and detailed analysis is made of the influence of the cavity size and shape on calculated energies. The solute is represented by its ab initio wavefunction, and the electronic part of the solvation energy is calculated including terms that take into account electron correlation up to third order. The analysis shows the convenience of modeling the cavity according to considerations of homogeneity, which are based fundamentally on how the solute wavefunction is constructed, i.e., the basis set used.
ABSTRACT A nonequilibrium polarizable continuum model, proposed in a previous paper (J. Chem. Phy... more ABSTRACT A nonequilibrium polarizable continuum model, proposed in a previous paper (J. Chem. Phys. 1993, 98, 7375), is applied to the study, at CIS and CISD levels, of solvent effects on the electronic structure of the (1)(n, pi*) transition of formaldehyde. To obtain a proper description of the excited state properties in solution, the generalized density matrix must be employed. The effects of the electrostatic dielectric potential, dispersion, and the Stark term, as well as the specific solute-solvent interaction are analyzed. The contribution to the solvent shift from the dispersion component is of comparatively minor importance in the absorption process, but constitutes an appreciable fraction of the total shift in the emission process. The contribution of the Stark effect term is very small and may be neglected. Explicit addition of water molecules to the carbonyl compound is necessary to account for the observed blue shift.
In the last decades the search for environmentally friendlier solvents [1] has been accompanied o... more In the last decades the search for environmentally friendlier solvents [1] has been accompanied on the theoretical side by a renewed interest in the development of methods oriented to understanding and predicting how the structure, properties, and reactivity of molecules are affected by ...
A study of the competition between intra- and intermolecular hydrogen bonds and its influence on ... more A study of the competition between intra- and intermolecular hydrogen bonds and its influence on the stability of the Cys-Asn-Ser tripeptide in aqueous solution was performed by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a DFT-B3LYP/6-311+G(d) quantum treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In gas phase, the most stable structure adopts a C5 conformation. Somewhat higher in energy are found the PP(II) and C7eq structures. In solution, the stability order of the different conformers is reversed: the PP(II) structure becomes the most stable, and the C5 structure is strongly destabilized. The conformational equilibrium is shifted toward conformations in which the intramolecular hydrogen bonds (IHB) have been substituted with intermolecular hydrogen bonds with the water molecules. The solvent stabilizes extended structures without IHBs that are not stable in vacuum. The effect of the protonation state on the conformational equilibrium was also analyzed.
... ML Sánchez, ME MartÃn, I. Fdez. Galván, FJ Olivares del Valle, and MA Aguilar*. Dpto. QuÃmica... more ... ML Sánchez, ME MartÃn, I. Fdez. Galván, FJ Olivares del Valle, and MA Aguilar*. Dpto. QuÃmica-FÃsica, Universidad de Extremadura. Avda de Elvas s/n, 06071 Badajoz, Spain. J. Phys. Chem. B , 2002, 106 (18), pp 4813–4817. ...
A novel Conus peptide, conorfamide-Sr1, has been characterized. The sequence of the natural pepti... more A novel Conus peptide, conorfamide-Sr1, has been characterized. The sequence of the natural peptide was determined using standard Edman sequencing methods and mass spectrometry, and confirmed by chemical synthesis. The peptide has 12 amino acids and no cysteine residues. The following sequence was obtained: GPMGWVPVFYRF-NH(2). No other peptide from a vermivorous Atlantic Conus species has previously been characterized. Conorfamide-Sr1 belongs to the RFamide neuropeptide family, and is the first RFamide peptide to be found in any venom. The presence of conorfamide-Sr1 as a major peptide in Conus spurius venom suggests that Conus lineages in the Atlantic may have evolved novel Conus venom peptide families.
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