Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 13 de 13
Filter
Add more filters










Publication year range
1.
J Mol Model ; 29(2): 42, 2023 Jan 18.
Article in English | MEDLINE | ID: mdl-36653546

ABSTRACT

CONTEXT: The reactivity of graphene oxide (GO) with amines is related to the ring-opening of the epoxy groups in its basal surface, as addressed experimentally. Therefore, discussing the hydroxyl/epoxy ratio for GO is relevant to improve the characterization of such material. As the adsorption of Methylene Blue into GO is related to a graphene derivative's oxidation degree (OD), we combined adsorption experimental information and theoretical data to estimate the hydroxyl/epoxy ratio. The theoretical data were compared to the experimental adsorption of Methylene Blue and Indigo Carmine into GO synthesized in our department. Our results show GO systems with hydroxyl/epoxy ratios equal to 0.7, 0.8, and 0.9 are the most representative in which the most coherent model corresponds to OH/EP=0.8 for our GO previously synthesized. METHODS: The GO-MODEL software was developed in the present work to obtain cartesian coordinates of GO systems. We investigated 204 systems comprising models with 486 carbon atoms with the GFN2-xTB semiempirical quantum method. The supramolecular arrangements were constructed with the recently developed UD-APARM program.

2.
J Mol Model ; 27(4): 101, 2021 Mar 04.
Article in English | MEDLINE | ID: mdl-33660108

ABSTRACT

Thiosemicarbazones (TSCs) encompasses a class of compounds relevant in the pharmacological context. Their specific applicability varies in function of the appropriated chemical modification and their binding to different transition metals. In the present work, we apply current standards functionals, B3LYP and B97D, with triple zeta basis set quality, 6-311++G(d,p), to investigate the relative stability of the various possible spatial arrangements for 2-acetylthiophene and 2-acetylthiophene-N1-phenyl thiosemicarbazones, denoted ATTSC and ATTSC-Ph, respectively. The relative stability of neutral and deprotonated species at ethanol described by an implicit solvent model was investigated. For ATTSC, the relative Gibbs energy changed significantly upon deprotonation, and for ATTSC-Ph, a novel global minimum was identified. Based on the present study, deprotonation determines population in condensed-media. Such information, valid for ATTSC and ATTSC-Ph, can be crucial in studying other thiosemicarbazones.

3.
ACS Omega ; 5(10): 5013-5025, 2020 Mar 17.
Article in English | MEDLINE | ID: mdl-32201787

ABSTRACT

Parameters comprising the relative position and relative rotation of molecules can be evaluated when the principal axes of inertia of the entities in a supramolecular association are employed as reference. Such information applies to the characterization and identification of experimental and theoretical nonbonded systems. The parameters are relevant to geometric comparison (for theory and experiment) and, for instance, to monitoring structures by theoretical simulations. This work introduces a software developed to obtain such parameters through the discussion of some intriguing host-guest systems, the ferrocene/cucurbit[7]uril and ferrocenyl azide/ß-cyclodextrin. The ideas within this contribution naturally apply to the study of other nonbonded associations beyond host-guest chemistry. A modified version of the software discussed herein serves to obtain user-defined spatial arrangements for two nonbonded entities. Therefore, with a given geometry, for instance, from X-ray data, the parameters can be derived, and with the parameters, from a theoretical perspective, a spatial arrangement can be obtained.

4.
J Phys Chem A ; 121(14): 2839-2846, 2017 Apr 13.
Article in English | MEDLINE | ID: mdl-28328211

ABSTRACT

In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for l-quebrachitol isomer, previously studied in our group, are reported with the aim of investigating in more detail the water solvent effect on the prediction of 1H NMR spectra. In order to include explicit water molecules, 20 water-l-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute. The solvated solute optimized geometries were then used in B3LYP/6-311+G(2d,p) NMR calculations with PCM-water. The inclusion of explicit solvent in the B3LYP NMR calculations resulted in large changes in the 1H NMR profiles. We found a remarkable improvement in the agreement with experimental NMR profiles when the explicit hydrated l-quebrachitol structure is used in B3LYP 1H NMR calculations, yielding a mean absolute error (MAE) of only 0.07 ppm, much lower than reported previously for the gas phase optimized structure (MAE = 0.11 ppm). In addition, a very improved match between theoretical and experimental 1H NMR spectrum measured in D2O was achieved with the new hydrated optimized l-quebrachitol structure, showing that a fine-tuning of the theoretical NMR spectra can be accomplished once solvent effects are properly considered.

5.
J Mol Graph Model ; 62: 11-17, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26340534

ABSTRACT

Thermodynamic properties for ß-cyclodextrin-Sertraline inclusion process was calculated at the density functional theory (DFT) level using the PBE0 functional with 6-31G(d,p), 6-31++G(d,p) and 6-311++G(2df,p) basis sets. Electron correlation was evaluated through Møller-Plesset second-order perturbation theory (MP2). The standard statistical thermodynamic approach was used to assess the entropic contribution to the Gibbs free energy value. According to our results, inclusion of hydration waters to describe the reactants and products in the complex formation reaction model is crucial in order to reproduce the experimental data and seems very coherent with basics thermodynamics yielding good agreement with experiment.


Subject(s)
Antidepressive Agents/chemistry , Sertraline/chemistry , beta-Cyclodextrins/chemistry , Carbohydrate Conformation , Computer Simulation , Entropy , Models, Molecular , Quantum Theory , Water/chemistry
6.
J Phys Chem B ; 118(1): 81-93, 2014 Jan 09.
Article in English | MEDLINE | ID: mdl-24321011

ABSTRACT

Me-ß-cyclodextrin (Me-ßCD) and HP-ß-cyclodextrin (HP-ßCD) inclusion complexes with isoniazid (INH) were prepared with the aim of modulating the physicochemical and biopharmaceutical properties of the guest molecule, a well-known antibuberculosis drug. The architectures of the complexes were initially proposed according to NMR data Job plot and ROESY followed by density functional theory (DFT) calculations of (1)H NMR spectra using the PBE1PBE functional and 6-31G(d,p) basis set, including the water solvent effect with the polarizable continuum model (PCM), for various inclusion modes, providing support for the experimental proposal. An analysis of the (1)H NMR chemical shift values for the isoniazid (H6',8' and H5',9') and cyclodextrins (H3,5) C(1)H hydrogens, which are known to be very adequately described by the DFT methodology, revealed them to be extremely useful, promptly confirming the inclusion complex formation. An included mode which describes Me-ßCD partially enclosing the hydrazide group of the INH is predicted as the most favorable supramolecular structure that can be used to explain the physicochemical properties of the encapsulated drug. Antibacterial activity was also evaluated, and the results indicated the inclusion complexes are a potential strategy for tuberculosis treatment.


Subject(s)
Anti-Bacterial Agents/pharmacology , Inclusion Bodies/chemistry , Isoniazid/pharmacology , Mycobacterium tuberculosis/drug effects , beta-Cyclodextrins/pharmacology , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Calorimetry, Differential Scanning , Dose-Response Relationship, Drug , Isoniazid/chemistry , Magnetic Resonance Spectroscopy , Microbial Sensitivity Tests , Protons , Quantum Theory , Structure-Activity Relationship , beta-Cyclodextrins/chemistry
7.
Magn Reson Chem ; 50(9): 608-14, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22865668

ABSTRACT

Density functional theory (DFT) calculations of (1) H NMR chemical shifts for l-quebrachitol isomers were performed using the B3LYP functional employing the 6-31G(d,p) and 6-311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP-calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental (1) H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP (1) H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O-methyl-inositol isomers, the l-quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical (1) H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies.


Subject(s)
Inositol/analogs & derivatives , Quantum Theory , Carbohydrate Conformation , Inositol/chemistry , Magnetic Resonance Spectroscopy/standards , Protons , Reference Standards , Stereoisomerism
8.
Phys Chem Chem Phys ; 14(6): 1934-44, 2012 Feb 14.
Article in English | MEDLINE | ID: mdl-22234498

ABSTRACT

The size, shape and surface chemistry of nanoparticles play an important role in cellular interaction. Thus, the main objective of the present study was the determination of the ß-cyclodextrin (ß-CD) self-assembly thermodynamic parameters and its structure, aiming to use these assemblies as a possible controlled drug release system. Light scattering measurements led us to obtain the ß-CD's critical aggregation concentration (cac) values, and consequently the thermodynamic parameters of the ß-CD spontaneous self-assembly in aqueous solution: Δ(agg)G(o) = -16.31 kJ mol(-1), Δ(agg)H(o) = -26.48 kJ mol(-1) and TΔ(agg)S(o) = -10.53 kJ mol(-1) at 298.15 K. Size distribution of the self-assembled nanoparticles below and above cac was 1.5 nm and 60-120 nm, respectively. The number of ß-CD molecules per cluster and the second virial coefficient were identified through Debye's plot and molecular dynamic simulations proposed the three-fold assembly for this system below cac. Ampicillin (AMP) was used as a drug model in order to investigate the key role of the guest molecule in the self-assembly process and the ß-CD:AMP supramolecular system was studied in solution, aiming to determine the structure of the supramolecular aggregate. Results obtained in solution indicated that the ß-CD's cac was not affected by adding AMP. Moreover, different complex stoichiometries were identified by nuclear magnetic resonance and isothermal titration calorimetry experiments.


Subject(s)
Ampicillin/chemistry , beta-Cyclodextrins/chemistry , Calorimetry , Drug Carriers/chemistry , Light , Molecular Dynamics Simulation , Nanoparticles/chemistry , Scattering, Radiation , Thermodynamics , Time Factors , Water/chemistry
9.
Magn Reson Chem ; 49(12): 763-7, 2011 Dec.
Article in English | MEDLINE | ID: mdl-22095853

ABSTRACT

The present study shows that a hydrogen bond between the OH group and the fluorine atom is not involved in the (1h)J(FH) spin-spin coupling transmission either for 4-bromo-2-fluorophenol or 2-fluorophenol. In fact, according to a quantum theory of atoms in molecules analysis, no bond critical point is found between O-H and F moieties. The nature of the transmission mechanism of the Fermi contact term of the (1h)J(FH) spin-spin coupling is studied by analyzing canonical molecular orbitals (see J. Phys. Chem. A 2010, 114, 1044), and it is observed that virtual orbitals play only a quite minor role in its transmission. This is typical of a Fermi contact term transmitted mainly through exchange interactions owing to the overlap of proximate electronic clouds; therefore, it is suggested to identify them as (nTS)J(FH) coupling where n stands for the number of formal bonds separating the coupling nuclei. In the cases studied in this work is n = 4. Results presented in this work could provide an interesting rationalization for different experimental signs known in the current literature for proximate J(FH) couplings.


Subject(s)
Electrons , Phenols/chemistry , Acetonitriles/chemistry , Chemistry, Physical , Cyclohexanes/chemistry , Hydrogen Bonding , Magnetic Resonance Spectroscopy/methods , Models, Molecular , Quantum Theory , Thermodynamics
10.
Org Lett ; 12(23): 5458-61, 2010 Dec 03.
Article in English | MEDLINE | ID: mdl-21043479

ABSTRACT

Two synthetic epoxide derivatives, important intermediates in organic synthesis, were obtained from L-quebrachitol, and their conformations were proposed based on spectroscopic analysis. Density functional theory (DFT) calculations of infrared and NMR spectra were shown to be reliable enough for organic chemistry applications. The observed structures were determined with the aid of the DFT spectroscopic data, stressing the relevance and utility of combined experimental/theoretical studies and also the usefulness of the (13)C NMR B3LYP/6-31G(d,p) calculations.

11.
J Phys Chem B ; 113(29): 9762-9, 2009 Jul 23.
Article in English | MEDLINE | ID: mdl-19603839

ABSTRACT

Empty linear associations accounting for three alpha-CD units and their corresponding pseudorotaxanes have been studied by means of long length molecular dynamics (MD) simulations in a vacuum and in aqueous solution. Results from MD for empty sequences lead to a quite stable arrangement formed by three mutually perpendicular cyclodextrin (CD) units named here as 3P. In such a spatial arrangement, the van der Waals term in the force field is pronounced, accounting for almost 40% of the association energy, which ensures the noticeable stability of the 3P association even in aqueous media. In addition, it can be stated that only the presence of the oligomer forces the CD units to acquire an almost linear association. Mutually perpendicular-based arrangements are the most favorable spatial disposition in aqueous media. We believe this work is the first step toward a more ambitious study including very large CD sequences, aiming to understand the association process in aqueous solution at a molecular level.


Subject(s)
Computer Simulation , Ethylene Glycols/chemistry , Models, Chemical , Rotaxanes/chemistry , alpha-Cyclodextrins/chemistry , Carbohydrate Conformation , Solutions , Thermodynamics , Water/chemistry
12.
J Phys Chem A ; 111(48): 12127-35, 2007 Dec 06.
Article in English | MEDLINE | ID: mdl-17997539

ABSTRACT

In this article we carried out a comprehensive investigation of true minima on the potential energy surface (PES) for the alpha-cyclodextrin molecule using ab initio Hartree-Fock (HF) and density functional theory (DFT) quantum chemical methods, employing basis sets ranging from 6-31 G(d,p) to 6-311++G(2d,2p) triple-zeta quality. Thermodynamic quantities and the solvent effect were evaluated at the DFT level of theory. We believe that the most relevant conformers present on the multidimensional PES were sampled in our work, using an adequate treatment of electron correlation effects to describe the intramolecular hydrogen bonds that are present in cyclodextrin species. We present new structures not reported so far and discuss, in detail, the relevance of the DFT gas-phase equilibrium structures for the experimental and theoretical studies involving cyclodextrins and corresponding inclusion complexes, in the condensed phase. In addition, among the various true minimum energy structures located on the DFT PES, the preferred structures in the gas phase and aqueous media, needed to be used as representative minima on the PES in further studies involving the interaction of alpha-cyclodextrin with other species, were unambiguously identified.


Subject(s)
Quantum Theory , alpha-Cyclodextrins/chemistry , Algorithms , Models, Chemical , Models, Molecular , Molecular Conformation , Phase Transition , Thermodynamics
13.
J Phys Chem A ; 109(14): 3209-19, 2005 Apr 14.
Article in English | MEDLINE | ID: mdl-16833650

ABSTRACT

The molecular structure, stabilization energy, and thermodynamic properties of the plausible modes of the interaction for the three possible alpha-cyclodextrin (alpha-CD) dimers (head-to-head, tail-to-tail, and head-to-tail) with a water cluster were obtained using quantum chemical methods for the first time. Nine distinct spatial arrangements were investigated. The head-to-head mode of interaction with water is preferred by more than 10 kcal.mol(-1) (BLYP/6-31G(d,p)//PM3 Gibbs free energy difference value at room temperature) in relation to the next stable structure, with a water dimer structure placed inside each cavity and cyclic water tetramers surrounding each tail end. The inter alpha-CD hydrogen bonds play a major role to stabilize the dimeric structures, with no water tetramer being found between the two alpha-CD subunits for the preferred global minimum structure. Therefore, a theoretical model aimed to describe the behavior of alpha-CD dimer, or their inclusion complexes, in the aqueous media should take into account this preference for binding of the water molecules.


Subject(s)
Models, Molecular , alpha-Cyclodextrins/chemistry , Computer Simulation , Dimerization , Thermodynamics
SELECTION OF CITATIONS
SEARCH DETAIL
...