1
|
Gómez S, Flórez E, Acelas N, Cappelli C, Hadad C, Restrepo A. Encapsulation of charged halogens by the 5 12 water cage. Phys Chem Chem Phys 2024; 26:15426-15436. [PMID: 38747303 DOI: 10.1039/d4cp01340a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.
Collapse
Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Elizabeth Flórez
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Nancy Acelas
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| |
Collapse
|
2
|
Gómez S, Gómez S, David J, Guerra D, Cappelli C, Restrepo A. Dissecting Bonding Interactions in Cysteine Dimers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248665. [PMID: 36557799 PMCID: PMC9786917 DOI: 10.3390/molecules27248665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.
Collapse
Affiliation(s)
- Santiago Gómez
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Jorge David
- Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300, Medellín 050022, Colombia
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Correspondence: (C.C.); (A.R.)
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia
- Correspondence: (C.C.); (A.R.)
| |
Collapse
|
3
|
Flórez E, Gómez S, Acelas N, Hadad C, Restrepo A. Microsolvation versus Encapsulation in Mono, Di, and Trivalent Cations. Chemphyschem 2022; 23:e202200456. [PMID: 35962558 DOI: 10.1002/cphc.202200456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Indexed: 01/05/2023]
Abstract
The effects of the formal charge in the stability and bonding of water cavities when solvating a cation are studied here using [X(H2 O)20 ]q+ clusters starting with the well known 512 isomer of (water)20 , placing a single mono, di, or trivalent Xq+ cation at the interior, and then optimizing and characterizing the resulting clusters. Highly correlated interaction and deformation energies are calculated using the CCSD(T)-DLPNO formalism. Bonding interactions are characterized using the tools provided by the quantum theory of atoms in molecules, natural bond orbitals, and non-covalent surfaces. Our results indicate that water to water hydrogen bonds are sensibly strengthened resulting in strong cooperative effects, which amount to ≈ 2 ${ \approx 2}$ kcal/mol per hydrogen bond in the bare cavity and to larger values for the systems including the cations. Approximate encapsulation, that is, surrounding the cation by a network of hydrogen bonds akin to the well known methane clathrate seems to be preferred by cations with smaller charge densities while microsolvation, that is, cluster structures having explicit X⋯O contacts seem to be preferred by cations with larger charge densities which severely deform the cavity.
Collapse
Affiliation(s)
- Elizabeth Flórez
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, 050026, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Nancy Acelas
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, 050026, Colombia
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| |
Collapse
|
4
|
Moreno N, Hadad CZ, Restrepo A. Microsolvation of electrons by a handful of ammonia molecules. J Chem Phys 2022; 157:134301. [PMID: 36209021 DOI: 10.1063/5.0107245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microsolvation of electrons in ammonia is studied here via anionic NH3 n - clusters with n = 2-6. Intensive samplings of the corresponding configurational spaces using second-order perturbation theory with extended basis sets uncover rich and complex energy landscapes, heavily populated by many local minima in tight energy windows as calculated from highly correlated coupled cluster methods. There is a marked energetical preference for structures that place the excess electron external to the molecular frame, effectively coordinating it with the three protons from a single ammonia molecule. Overall, as the clusters grow in size, the lowest energy dimer serves as the basic motif over which additional ammonia molecules are attached via unusually strong charge-assisted hydrogen bonds. This is a priori quite unexpected because, on electrostatic grounds, the excess electron would be expected to be in contact with as many protons as possible. Accordingly, a full quantum mechanical treatment of the bonding interactions under the tools provided by the quantum theory of atoms in molecules is carried out in order to dissect and understand the nature of intermolecular contacts. Vertical detachment energies reveal bound electrons even for n = 2.
Collapse
Affiliation(s)
- Norberto Moreno
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Cacier Z Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| |
Collapse
|
5
|
Correa E, Montaño D, Restrepo A. Cation ⋯anion bonding interactions in 1–Ethyl–3–Methylimidazolium based ionic liquids. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
6
|
Analysis of Conformational Preferences in Caffeine. Molecules 2022; 27:molecules27061937. [PMID: 35335301 PMCID: PMC8949453 DOI: 10.3390/molecules27061937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/10/2022] Open
Abstract
High level DLPNO−CCSD(T) electronic structure calculations with extended basis sets over B3LYP−D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C−H bond on the same plane of the aromatic system, leading to the C−H bonds eclipsing one carbonyl group, one heavily delocalized C−N bond constituent of the fused double ring aromatic system, and one C−H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional −CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.
Collapse
|
7
|
Bensberg M, Türtscher PL, Unsleber JP, Reiher M, Neugebauer J. Solvation Free Energies in Subsystem Density Functional Theory. J Chem Theory Comput 2022; 18:723-740. [PMID: 34985890 DOI: 10.1021/acs.jctc.1c00864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise the scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent. The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.
Collapse
Affiliation(s)
- Moritz Bensberg
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Paul L Türtscher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jan P Unsleber
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| |
Collapse
|
8
|
Florez E, Acelas N, Gomez S, Hadad C, Restrepo A. To be or not to be? that is the entropic, enthalpic, and molecular interaction dilemma in the formation of (water)20 clusters and methane clathrate. Chemphyschem 2021; 23:e202100716. [PMID: 34761856 DOI: 10.1002/cphc.202100716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2021] [Indexed: 11/09/2022]
Abstract
A detailed analysis under a comprehensive set of theoretical and computational tools of the thermodynamical factors and of the intermolecular interactions behind the stabilization of a well known set of (water)20 cavities and of the methane clathrate is offered in this work. Beyond the available reports of experimental characterization at extreme conditions of most of the systems studied here, all clusters should be amenable to experimental detection at 1 atm and moderate temperatures since 280 K marks the boundary at which, ignoring reaction paths, formation of all clusters is no longer spontaneous from the 20H2O → (H2O)20 and CH4 + 20H2O → CH4@512 processes. As a function of temperature, a complex interplay leading to the free energy of formation occurs between the destabilizing entropic contributions, mostly due to cluster vibrations, and the stabilizing enthalpic contributions, due to intermolecular interactions and the PV term, is best illustrated by the highly symmetric 512 cage consistently showing signs of stronger intermolecular bonding despite having smaller binding energy than the other clusters. A fluxional wall of attractive non-covalent interactions, arising because of the cumulative effect of a large number of tiny individual charge transfers to the interstitial region, plays a pivotal role stabilizing the CH4@512 clathrate.
Collapse
Affiliation(s)
- Elizabeth Florez
- Universidad de Medellín: Universidad de Medellin, Ciencias basicas, COLOMBIA
| | - Nancy Acelas
- Universidad de Medellín: Universidad de Medellin, Ciencias Basicas, COLOMBIA
| | - Sara Gomez
- Scuola Normale Superiore Classe di Scienze, Chemistry, ITALY
| | - Cacier Hadad
- Universidad de Antioquía: Universidad de Antioquia, Chemistry, COLOMBIA
| | - Albeiro Restrepo
- Universidad de Antioquia, Chemistry, AA 1226, 00000, Medellin, COLOMBIA
| |
Collapse
|
9
|
Rojas-Valencia N, Gómez S, Núñez-Zarur F, Cappelli C, Hadad C, Restrepo A. Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes. J Phys Chem B 2021; 125:10383-10391. [PMID: 34492187 DOI: 10.1021/acs.jpcb.1c06766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol-1 and yields a net stabilization of also ≈5 kJ mol-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system.
Collapse
Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia.,Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia.,Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300 Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
| |
Collapse
|
10
|
Uribe L, Gómez S, Giovannini T, Egidi F, Restrepo A. An efficient and robust procedure to calculate absorption spectra of aqueous charged species applied to NO 2. Phys Chem Chem Phys 2021; 23:14857-14872. [PMID: 34223573 DOI: 10.1039/d1cp00652e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accurate calculation of absorption spectra of aqueous NO2- requires rigorously sampling the quantum potential energy surfaces for microsolvation of NO2- with at least five explicit water molecules and embedding the resulting clusters in a continuum solvent accounting for the statistical weighted contributions of individual isomers. This method, which we address as ASCEC + PCM, introduces several desired features when compared against MD simulations derived QM/MM spectra: comparatively fewer explicit solvent molecules to be treated with expensive QM methods, the identification of equilibrium structures in the quantum PES to be used in further vibrational spectroscopy, and the unequivocal identification of cluster orbitals undergoing electronic transitions and charge transfer that originate the spectral bands.
Collapse
Affiliation(s)
- Lina Uribe
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Franco Egidi
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| |
Collapse
|
11
|
Gómez S, Rojas-Valencia N, Gómez SA, Cappelli C, Merino G, Restrepo A. A molecular twist on hydrophobicity. Chem Sci 2021; 12:9233-9245. [PMID: 34276953 PMCID: PMC8261874 DOI: 10.1039/d1sc02673a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
A thorough exploration of the molecular basis for hydrophobicity with a comprehensive set of theoretical tools and an extensive set of organic solvent S/water binary systems is discussed in this work. Without a single exception, regardless of the nature or structure of S, all quantum descriptors of bonding yield stabilizing S⋯water interactions, therefore, there is no evidence of repulsion and thus no reason for etymological hydrophobicity at the molecular level. Our results provide molecular insight behind the exclusion of S molecules by water, customarily invoked to explain phase separation and the formation of interfaces, in favor of a complex interplay between entropic, enthalpic, and dynamic factors. S⋯water interfaces are not just thin films separating the two phases; instead, they are non-isotropic regions with density gradients for each component whose macroscopic stability is provided by a large number of very weak dihydrogen contacts. We offer a definition of interface as the region in which the density of the components in the A/B binary system is not constant. At a fundamental level, our results contribute to better current understanding of hydrophobicity. Notwithstanding the very weak nature of individual contacts, it is the cumulative effect of a large number of interactions (green NCI surfaces) which provides macroscopic stability to the interfaces.![]()
Collapse
Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA Calle 70 No. 52-21 Medellín Colombia .,Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit AA 3300 Medellín Colombia
| | - Santiago A Gómez
- Instituto de Química, Universidad de Antioquia UdeA Calle 70 No. 52-21 Medellín Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida. Km 6 Antigua Carretera a Progreso. Apdo. Postal 73, Cordemex 97310 Mérida Yucatan Mexico
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA Calle 70 No. 52-21 Medellín Colombia
| |
Collapse
|
12
|
|
13
|
Towards a converged strategy for including microsolvation in reaction mechanism calculations. J Comput Aided Mol Des 2021; 35:473-492. [PMID: 33420644 DOI: 10.1007/s10822-020-00366-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/28/2020] [Indexed: 01/27/2023]
Abstract
A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pKa values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.
Collapse
|
14
|
Rojas-Valencia N, Gómez S, Guerra D, Restrepo A. A detailed look at the bonding interactions in the microsolvation of monoatomic cations. Phys Chem Chem Phys 2020; 22:13049-13061. [PMID: 32478372 DOI: 10.1039/d0cp00428f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Global and local descriptors of the properties of intermolecular bonding, formally derived from independent methodologies (QTAIM, NCI, NBO, density differences) afford a highly complex picture of the bonding interactions responsible for microsolvation of monoatomic cations. In all cases, the dominant factor dictating geometries and interaction strengths is the electrophilic power of the metal cation. The formal charge disrupts the hydrogen bonding network otherwise present in pristine water clusters, making the hydrogen bonds considerably stronger, even inducing some degree of covalency. All MO interactions are highly ionic, with strengths than in some cases approach that of the reference LiCl bond. Accumulation of electron density in the region connecting MO is observed, thus, ionic bonding in the microsolvation of monoatomic cations is not as simple as an electrostatic interaction between opposing charges.
Collapse
Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia. and Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| |
Collapse
|
15
|
|
16
|
Rojas-Valencia N, Gómez S, Montillo S, Manrique-Moreno M, Cappelli C, Hadad C, Restrepo A. Evolution of Bonding during the Insertion of Anionic Ibuprofen into Model Cell Membranes. J Phys Chem B 2019; 124:79-90. [DOI: 10.1021/acs.jpcb.9b09705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Sebastian Montillo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| |
Collapse
|
17
|
Abstract
A wide variety of descriptors of the evolution of bonding, rooted in the formalism of quantum mechanics, but otherwise conceptually and methodologically independent of each other (based on the quantum theory of atoms in molecules and natural bond orbitals), consistently indicate that in the mechanism of the salt-free Wittig reaction, regardless of the nature of the ylide, regardless of the nature of the transition state, and regardless of the positioning of the substituents around the reactive center, the degree of advance in the formation of the emerging C-C bond as early as at the transition state for the oxaphosphetane formation step is firmly tied to the stereochemistry of the final alkene. In addition to the fast evolution of the emerging C-C bond, very early in the reaction, a long range, weak interaction between a lone pair in the oxygen atom of the carbonyl group and an empty p orbital in the phosphorous atom, resulting from the polarization of the P═C bond in the ylide (nO → πP═C*), clamps the P═C and C═O bonds to the positions required for the subsequent formation of oxaphosphetanes, thus explaining the formation of cyclic intermediates rather than betaines. Each step of the Wittig reaction is a highly asynchronous process.
Collapse
Affiliation(s)
- Paola Farfán
- Instituto de Química , Universidad de Antioquia UdeA , Calle 70 No. 52-21 , 50037 Medellín , Colombia
| | - Sara Gómez
- Scuola Normale Superiore , Classe di Scienze , Piazza dei Cavalieri 7 , 56126 Pisa , Italy
| | - Albeiro Restrepo
- Instituto de Química , Universidad de Antioquia UdeA , Calle 70 No. 52-21 , 50037 Medellín , Colombia
| |
Collapse
|
18
|
Acelas N, Flórez E, Hadad C, Merino G, Restrepo A. A Comprehensive Picture of the Structures, Energies, and Bonding in [SO4(H2O)n]2–, n = 1–6. J Phys Chem A 2019; 123:8650-8656. [DOI: 10.1021/acs.jpca.9b07033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nancy Acelas
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Medellín, Colombia
| | - Elizabeth Flórez
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Medellín, Colombia
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52−21, Medellín, Colombia
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida Km 6 Antigua Carretera a Progreso. Apdo. Postal 73 Cordemex, 97310 Mérida, Yuc, México
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52−21, Medellín, Colombia
| |
Collapse
|
19
|
Ammonia borane dehydrogenation tendencies using Pt4, Au4, and Pt2Au2 clusters as catalysts. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
20
|
Jana G, Jha R, Pan S, Chattaraj PK. Microsolvation of lithium–phosphorus double helix: a DFT study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2462-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
|
Llano S, Gómez S, Londoño J, Restrepo A. Antioxidant activity of curcuminoids. Phys Chem Chem Phys 2019; 21:3752-3760. [PMID: 30702098 DOI: 10.1039/c8cp06708b] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An exploration of the antioxidant power of curcumin, demethoxycurcumin, and bisdemethoxycurcumin, three natural antioxidants found in Curcuma longa, is reported in this work. We exhaust all structural possibilities leading to intramolecular hydrogen bonding and evaluate 15 isomers in total. Calculations were carried out in the gas phase and in the presence of solvents (water, to mimic biological media, and ethanol, to reproduce experimental assays) following the hydrogen atom transfer (HAT) and single electron transfer (SET) mechanisms. CH3OH-O hydrogen bonds are directly related to the antioxidant power via both mechanisms. We provide evidence to explain the experimental observations and to understand the fundamental factors driving antioxidant activity from a molecular perspective. Noticeably, the solvent enhances the antioxidant power in every case. All structures considered here are predicted to have better antioxidant abilities than phenol, and come very close to or surpass vitamin E.
Collapse
Affiliation(s)
- Sandra Llano
- Departamento de Educación y Ciencias Básicas, Instituto Tecnológico Metropolitano, Calle 73 No. 76A-354, Medellín, Colombia
| | | | | | | |
Collapse
|
22
|
Coa JC, Cardona-Galeano W, Restrepo A. Fe3+chelating quinoline–hydrazone hybrids with proven cytotoxicity, leishmanicidal, and trypanocidal activities. Phys Chem Chem Phys 2018; 20:20382-20390. [DOI: 10.1039/c8cp04174a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Neglected tropical diseases cause great concern in developing countries where there are millions of reported infected humans. Our calculations support a direct relationship between biological activity and the Fe3+chelating ability of the shown set of quinoline–hydrazone hybrids.
Collapse
Affiliation(s)
- Juan Carlos Coa
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| | | | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| |
Collapse
|