Carina Pamies - Academia.edu (original) (raw)
Papers by Carina Pamies
La preservación de biomateriales es un tema de vital importancia en las industrias alimentaria, c... more La preservación de biomateriales es un tema de vital importancia en las industrias alimentaria, cosmética y farmacéutica. Durante el secado y almacenamiento de estos biomateriales ocurren reacciones de deterioro, como las de Maillard, que afectan a las propiedades organolépticas de los alimentos y a las propiedades funcionales de las proteínas. La estabilización a menudo se logra incorporando estos materiales a soluciones de azúcares amorfos. Profundizar en el conocimiento del mecanismo por el cual estos azúcares son capaces de estabilizar y proteger biomoléculas lábiles ha motivado el desarrollo de este trabajo de tesis. Para el logro de este objetivo, se utilizaron diferentes métodos teóricos. En el Capítulo I se introducen brevemente los antecedentes históricos acerca del origen del interés por parte de la comunidad científica en los carbohidratos como agentes bioprotectores. Se presentan además a los disacáridos trehalosa, sacarosa y maltosa, los cuales serán el objeto de estudi...
ChemPhysChem
Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In... more Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group −NHR, and the replacement of the whole −NH2 group (R=H, F, CH3 and COCH3). Through our dispersion‐corrected density functional theory computations, we explain which covalent modification will show the best self‐assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N−H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group not...
Chemphyschem : a European journal of chemical physics and physical chemistry, 2021
Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in ... more Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl - and N-H⋅⋅⋅Cl - bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together...
Journal of Molecular Modeling, 2017
The nature of non-covalent interactions in selfassembling systems is a topic that has aroused gre... more The nature of non-covalent interactions in selfassembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a variety of molecular aggregates of CA are examined using three different DFT functionals (B3LYP, B3LYP-D3, and ω-B97XD) in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Herein, a step by step aggregation path is proposed and the origin of cooperative effects is also examined. It is shown that a greater cooperativity is not always associated with a greater binding energy, and the greatest cooperative effect occurs with highly directional hydrogen bonds. The intramolecular charge transfers play a key role in this effect.
ChemistrySelect, 2017
Protein-polyphenols interactions are of greatest interest in several fields like food technology ... more Protein-polyphenols interactions are of greatest interest in several fields like food technology and leather industry. Also, it is thought that these interactions are responsible for the undesired phenomenon of colloidal turbidity. However, there is sparse information about the molecular implications leading to this phenomenon. In this study, Molecular Dynamic (MD) simulations in conjunction with the analysis of the topology of the electron density are used to study protein/polyphenol interactions in a model system which consists of a ternary mixture of water, the flavonoids Catechin and Procianidin B3 and proline pentapeptides. After 50 ns of simulation, root mean square deviation, root mean square fluctuation and number of hydrogen bonds were calculated. Information about the intermolecular interactions that drive the assembly of colloidal complexes has been obtained by the analysis of the electron charge density. Results show the formation of a stable adduct, with a very complex network of conventional and nonconventional hydrogen bonds. This study has also shown the significance of C-H•••O and C-H•••p interactions in the phenomenon of colloidal turbidity.
Theoretical Chemistry Accounts, 2016
charge density descriptors were used to evaluate the aromaticity of M in each complex. Results sh... more charge density descriptors were used to evaluate the aromaticity of M in each complex. Results show that the hydrogen and halogen (XBs) bond interactions, which direct the self-assembly process in these complexes, are anti-cooperative. Binding energies decrease in the following order: M/ (CA) n > M/(TCA) n > M/(CABr) n > M/(CACl) n (for all values of n). Brominated CA arises as a potential compound to self-assembly with M via XBs. Keywords Cyanuric acid • Supramolecular • Molecular building blocks • Hydrogen bond • Halogen bond Published as part of the special collection of articles "CHITEL 2015-Torino-Italy".
The Journal of Physical Chemistry A, 2010
Density functional theory (DFT) and atoms in molecules theory (AIM) were used to study the charac... more Density functional theory (DFT) and atoms in molecules theory (AIM) were used to study the characteristic of the noncovalent interactions in complexes formed between Lewis bases (NH 3 , H 2 O, and H 2 S) and Lewis acids (ClF, BrF, IF, BrCl, ICl, and IBr). In order to compare halogen and hydrogen bonds interactions, this study included hydrogen complexes formed by some Lewis bases and HF, HCl, and HBr Lewis acids. Ab initio, wave functions were generated at B3LYP/6-311++G(d,p) level with optimized structures at the same level. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of halogen interactions in Lewis complexes. The main purpose of the present work is to provide an answer to the following questions: (a) why can electronegative atoms such as halogens act as bridges between two other electronegative atoms? Can a study based on the electron charge density answer this question? Considering this, we had performed a profound study of halogen complexes in the framework of the AIM theory. A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. We had also explored the concentration and depletion of the charge density, displayed by the Laplacian topology, in the interaction zone and in the X-Y halogen donor bond. From the atomic properties, it was generally observed that the two halogen atoms gain electron population in response to its own intrinsic nature. Because of this fact, both atoms are energetically stabilized.
Biophysical Chemistry
Molecular interactions between proteins and polyphenols are responsible for many natural phenomen... more Molecular interactions between proteins and polyphenols are responsible for many natural phenomena like colloidal turbidity, astringency, denaturation of enzymes and leather tanning. Although these phenomena are well known, there are open questions about the specific interactions involved in the complexation process. In this work, Molecular Dynamic (MD) simulations and the topology of the electron density analysis were used to study the interactions between the flavonoid procyanidin C1 and a collagen fragment solvated in water. Root mean square deviation; root mean square fluctuation and hydrogen bonds occupancy were examined after 50 ns. The interactions were also analyzed by means of the quantum theory of atoms in molecules. Our results show that the main interactions are hydrogen bonds between -OH groups of the polyphenol and CO groups of the peptide bond. Stacking interactions between proline rings and phenol rings, that is CH⋯π hydrogen bonds, also stabilize the dynamic structure of the complex.
Structural Chemistry, 2016
In this work, electronic structure calculations and Molecular Dynamics (MD) simulations were perf... more In this work, electronic structure calculations and Molecular Dynamics (MD) simulations were performed in order to carry out a static and dynamic study of disaccharides, trehalose, sucrose and maltose. These three disaccharides share the same chemical formula and the same number of OH groups; however, it has been widely shown that trehalose has a superior ability to protect biological structures. In order to contribute to the understanding of the factors that determine this ability of trehalose, in this work a comparative study of the three disaccharides in gas phase and dilute aqueous solution is performed. A detailed analysis of hydrogen bonds (HBs) was carried out using Quantum Theory of Atoms In Molecules (QTAIM) on wave functions obtained at B3LYP/6-311++G** level. Besides, stereoelectronic effects were examined by Natural Bond Orbital (NBO) analysis. In addition, the intra- and intermolecular HB interactions in MD runs of infinitely dilute aqueous solution of sugars have been monitored. Results show that the three disaccharides form a significant number of HBs of C-H∙∙∙O type, mainly in trehalose. An intermolecular bond of this type determines the conformational rigidity of trehalose in solution which contributes to stabilize a clam shell conformation as the one observed in the crystal. In this disaccharide, hydrogen bonds are more labile, showing a quickly exchange of the water molecules that form these HBs. This fact slows down ice formation and could be the explanation for trehalose capabilities as a cryoprotectant.
Physical Chemistry Chemical Physics
Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters.... more Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters. Its triazine ring is also superior to the melamine one for capturing anions as well as cations.
Physical Chemistry Chemical Physics
Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters.... more Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters. Its triazine ring is also superior to the melamine one for capturing anions as well as cations.
La preservación de biomateriales es un tema de vital importancia en las industrias alimentaria, c... more La preservación de biomateriales es un tema de vital importancia en las industrias alimentaria, cosmética y farmacéutica. Durante el secado y almacenamiento de estos biomateriales ocurren reacciones de deterioro, como las de Maillard, que afectan a las propiedades organolépticas de los alimentos y a las propiedades funcionales de las proteínas. La estabilización a menudo se logra incorporando estos materiales a soluciones de azúcares amorfos. Profundizar en el conocimiento del mecanismo por el cual estos azúcares son capaces de estabilizar y proteger biomoléculas lábiles ha motivado el desarrollo de este trabajo de tesis. Para el logro de este objetivo, se utilizaron diferentes métodos teóricos. En el Capítulo I se introducen brevemente los antecedentes históricos acerca del origen del interés por parte de la comunidad científica en los carbohidratos como agentes bioprotectores. Se presentan además a los disacáridos trehalosa, sacarosa y maltosa, los cuales serán el objeto de estudi...
ChemPhysChem
Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In... more Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group −NHR, and the replacement of the whole −NH2 group (R=H, F, CH3 and COCH3). Through our dispersion‐corrected density functional theory computations, we explain which covalent modification will show the best self‐assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N−H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group not...
Chemphyschem : a European journal of chemical physics and physical chemistry, 2021
Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in ... more Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl - and N-H⋅⋅⋅Cl - bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together...
Journal of Molecular Modeling, 2017
The nature of non-covalent interactions in selfassembling systems is a topic that has aroused gre... more The nature of non-covalent interactions in selfassembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a variety of molecular aggregates of CA are examined using three different DFT functionals (B3LYP, B3LYP-D3, and ω-B97XD) in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Herein, a step by step aggregation path is proposed and the origin of cooperative effects is also examined. It is shown that a greater cooperativity is not always associated with a greater binding energy, and the greatest cooperative effect occurs with highly directional hydrogen bonds. The intramolecular charge transfers play a key role in this effect.
ChemistrySelect, 2017
Protein-polyphenols interactions are of greatest interest in several fields like food technology ... more Protein-polyphenols interactions are of greatest interest in several fields like food technology and leather industry. Also, it is thought that these interactions are responsible for the undesired phenomenon of colloidal turbidity. However, there is sparse information about the molecular implications leading to this phenomenon. In this study, Molecular Dynamic (MD) simulations in conjunction with the analysis of the topology of the electron density are used to study protein/polyphenol interactions in a model system which consists of a ternary mixture of water, the flavonoids Catechin and Procianidin B3 and proline pentapeptides. After 50 ns of simulation, root mean square deviation, root mean square fluctuation and number of hydrogen bonds were calculated. Information about the intermolecular interactions that drive the assembly of colloidal complexes has been obtained by the analysis of the electron charge density. Results show the formation of a stable adduct, with a very complex network of conventional and nonconventional hydrogen bonds. This study has also shown the significance of C-H•••O and C-H•••p interactions in the phenomenon of colloidal turbidity.
Theoretical Chemistry Accounts, 2016
charge density descriptors were used to evaluate the aromaticity of M in each complex. Results sh... more charge density descriptors were used to evaluate the aromaticity of M in each complex. Results show that the hydrogen and halogen (XBs) bond interactions, which direct the self-assembly process in these complexes, are anti-cooperative. Binding energies decrease in the following order: M/ (CA) n > M/(TCA) n > M/(CABr) n > M/(CACl) n (for all values of n). Brominated CA arises as a potential compound to self-assembly with M via XBs. Keywords Cyanuric acid • Supramolecular • Molecular building blocks • Hydrogen bond • Halogen bond Published as part of the special collection of articles "CHITEL 2015-Torino-Italy".
The Journal of Physical Chemistry A, 2010
Density functional theory (DFT) and atoms in molecules theory (AIM) were used to study the charac... more Density functional theory (DFT) and atoms in molecules theory (AIM) were used to study the characteristic of the noncovalent interactions in complexes formed between Lewis bases (NH 3 , H 2 O, and H 2 S) and Lewis acids (ClF, BrF, IF, BrCl, ICl, and IBr). In order to compare halogen and hydrogen bonds interactions, this study included hydrogen complexes formed by some Lewis bases and HF, HCl, and HBr Lewis acids. Ab initio, wave functions were generated at B3LYP/6-311++G(d,p) level with optimized structures at the same level. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of halogen interactions in Lewis complexes. The main purpose of the present work is to provide an answer to the following questions: (a) why can electronegative atoms such as halogens act as bridges between two other electronegative atoms? Can a study based on the electron charge density answer this question? Considering this, we had performed a profound study of halogen complexes in the framework of the AIM theory. A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. We had also explored the concentration and depletion of the charge density, displayed by the Laplacian topology, in the interaction zone and in the X-Y halogen donor bond. From the atomic properties, it was generally observed that the two halogen atoms gain electron population in response to its own intrinsic nature. Because of this fact, both atoms are energetically stabilized.
Biophysical Chemistry
Molecular interactions between proteins and polyphenols are responsible for many natural phenomen... more Molecular interactions between proteins and polyphenols are responsible for many natural phenomena like colloidal turbidity, astringency, denaturation of enzymes and leather tanning. Although these phenomena are well known, there are open questions about the specific interactions involved in the complexation process. In this work, Molecular Dynamic (MD) simulations and the topology of the electron density analysis were used to study the interactions between the flavonoid procyanidin C1 and a collagen fragment solvated in water. Root mean square deviation; root mean square fluctuation and hydrogen bonds occupancy were examined after 50 ns. The interactions were also analyzed by means of the quantum theory of atoms in molecules. Our results show that the main interactions are hydrogen bonds between -OH groups of the polyphenol and CO groups of the peptide bond. Stacking interactions between proline rings and phenol rings, that is CH⋯π hydrogen bonds, also stabilize the dynamic structure of the complex.
Structural Chemistry, 2016
In this work, electronic structure calculations and Molecular Dynamics (MD) simulations were perf... more In this work, electronic structure calculations and Molecular Dynamics (MD) simulations were performed in order to carry out a static and dynamic study of disaccharides, trehalose, sucrose and maltose. These three disaccharides share the same chemical formula and the same number of OH groups; however, it has been widely shown that trehalose has a superior ability to protect biological structures. In order to contribute to the understanding of the factors that determine this ability of trehalose, in this work a comparative study of the three disaccharides in gas phase and dilute aqueous solution is performed. A detailed analysis of hydrogen bonds (HBs) was carried out using Quantum Theory of Atoms In Molecules (QTAIM) on wave functions obtained at B3LYP/6-311++G** level. Besides, stereoelectronic effects were examined by Natural Bond Orbital (NBO) analysis. In addition, the intra- and intermolecular HB interactions in MD runs of infinitely dilute aqueous solution of sugars have been monitored. Results show that the three disaccharides form a significant number of HBs of C-H∙∙∙O type, mainly in trehalose. An intermolecular bond of this type determines the conformational rigidity of trehalose in solution which contributes to stabilize a clam shell conformation as the one observed in the crystal. In this disaccharide, hydrogen bonds are more labile, showing a quickly exchange of the water molecules that form these HBs. This fact slows down ice formation and could be the explanation for trehalose capabilities as a cryoprotectant.
Physical Chemistry Chemical Physics
Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters.... more Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters. Its triazine ring is also superior to the melamine one for capturing anions as well as cations.
Physical Chemistry Chemical Physics
Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters.... more Cyanuric acid is shown to be the best supramolecular building block to obtain cage-like clusters. Its triazine ring is also superior to the melamine one for capturing anions as well as cations.