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1.
Phys Chem Chem Phys ; 19(21): 13860-13867, 2017 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-28513675

RESUMO

A complete state-averaged active space self-consistent field (SA-CASSCF) calculation by means of the SA-CASSCF(18,14)-in-BP86 Miller-Manby embedding approach was performed to explore the ground and excited electronic states of the trans-[RuCl(NO)(NH3)4]2+ complex. Insights into the NO photodissociation mechanism and Ru-NO bonding properties are provided. In addition, spin-orbit (SO) interactions were taken into account to describe and characterize the spin-forbidden transitions observed at the low-energy regions of the trans-[RuCl(NO)(NH3)4]2+ UV-Vis spectrum. The SA-CASSCF(18,14)-in-BP86 electronic spectrum is in great agreement with the experimental data of Schreiner [Schreiner et al., Inorg. Chem., 1972, 11, 880].

2.
Rapid Commun Mass Spectrom ; 27(7): 816-24, 2013 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-23495028

RESUMO

RATIONALE: The use of quinonoid compounds against tropical diseases and as antitumor agents has prompted the search for new naturally occurring and synthetic derivatives. Among these quinonoid compounds, lapachol and its isomers (α- and ß-lapachone) serve as models for the synthesis of new compounds with biological activity, and the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis as a tool to elucidate and characterize these products has furnished important information about these compounds. METHODS: ESI-MS/MS analysis under collision-induced dissociation conditions was used to describe the fragmentation mechanisms for protonated 1,4-naphthoquinone, 1,2-naphthoquinone, α-lapachone, and ß-lapachone. The B3LYP/6-31+G(d,p) model was used to obtain proton affinities, gas-phase basicities, and molecular electrostatic potential maps, thus indicating the probable protonation sites. Fragmentation pathways were suggested on the basis of the relative enthalpies of the product ions. RESULTS: The ESI-MS signals of the cationized molecules of ortho quinonoid compounds were more intense than those of the protonated molecule. Formation of the major product ions with m/z 187 from protonated α- and ß-lapachone has been attributed to a retro-Diels-Alder (RDA) reaction. CONCLUSIONS: MS/MS studies on lapachol isomers (α- and ß-lapachone) will facilitate the interpretation of the liquid chromatography (LC)-MS/MS analysis of new metabolites. MS/MS data on the 1,4-naphthoquinone, 1,2-naphthoquinone, α-lapachone and ß-lapachone core will help characterize new derivatives from in vitro/in vivo metabolism studies in complex matrices. The product ions revealed the major fragmentation mechanisms and these ions will serve as diagnostic ions to identify each studied compound.


Assuntos
Naftoquinonas/química , Espectrometria de Massas por Ionização por Electrospray/métodos , Espectrometria de Massas em Tandem/métodos , Gases/química , Modelos Moleculares
3.
Langmuir ; 28(19): 7407-16, 2012 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-22530971

RESUMO

Tribocharged polymers display macroscopically patterned positive and negative domains, verifying the fractal geometry of electrostatic mosaics previously detected by electric probe microscopy. Excess charge on contacting polyethylene (PE) and polytetrafluoroethylene (PTFE) follows the triboelectric series but with one caveat: net charge is the arithmetic sum of patterned positive and negative charges, as opposed to the usual assumption of uniform but opposite signal charging on each surface. Extraction with n-hexane preferentially removes positive charges from PTFE, while 1,1-difluoroethane and ethanol largely remove both positive and negative charges. Using suitable analytical techniques (electron energy-loss spectral imaging, infrared microspectrophotometry and carbonization/colorimetry) and theoretical calculations, the positive species were identified as hydrocarbocations and the negative species were identified as fluorocarbanions. A comprehensive model is presented for PTFE tribocharging with PE: mechanochemical chain homolytic rupture is followed by electron transfer from hydrocarbon free radicals to the more electronegative fluorocarbon radicals. Polymer ions self-assemble according to Flory-Huggins theory, thus forming the experimentally observed macroscopic patterns. These results show that tribocharging can only be understood by considering the complex chemical events triggered by mechanical action, coupled to well-established physicochemical concepts. Patterned polymers can be cut and mounted to make macroscopic electrets and multipoles.

4.
J Phys Chem A ; 115(45): 12780-8, 2011 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-21714561

RESUMO

Mass spectrometry analysis of 2-(acylamino)-1,4-naphthoquinone derivatives was carried out using electrospray ionization ion source in combination with tandem mass spectrometry. Protonated molecules were dissociated by application of the collision-induced dissociation (CID), and the protonation sites were suggested on the basis of the HOMO, molecular electrostatic potential map (MEP), proton affinity, and Fukui functions calculated by B3LYP/6-31+G(d,p). The main fragmentation mechanisms undergone by the protonated ions were elucidated on the basis of energy, geometry, and topology analysis of equilibrium geometries. Compounds exhibiting only aliphatic hydrogens at the lateral chain undergo interesting ketene elimination. On the other hand, only the benzoylium ion formation is detected for 2-benzoylamino-1,4-naphthoquinone. The bonds geometric and atoms in molecules parameters give evidence that acidic hydrogen atoms play an important role in the fragmentation pathways.


Assuntos
Naftoquinonas/análise , Teoria Quântica , Espectrometria de Massas , Estrutura Molecular
5.
J Phys Chem A ; 115(21): 5453-60, 2011 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-21561138

RESUMO

Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(•-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q+15](-) was described as being a reaction between the solvent system and the radical anion, Q(•-). The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.


Assuntos
Naftoquinonas/química , Teoria Quântica , Ânions/síntese química , Ânions/química , Eletroquímica , Radicais Livres/síntese química , Radicais Livres/química , Gases/síntese química , Gases/química , Estrutura Molecular , Naftoquinonas/síntese química , Soluções , Espectrometria de Massas por Ionização por Electrospray , Estereoisomerismo
6.
J Mol Model ; 27(5): 148, 2021 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-33942180

RESUMO

Carbon monoxide (CO) exerts various protective effects on the body. Drugs known as CORMs (CO-releasing molecules) can continuously release small doses of CO into diseased tissues and cells. Transition metals interact strongly with the carbonyl group, and coordination compounds bearing carbonyl groups are a promising class of CORMs. This study investigates the octahedral coordination of Fe2+ and Fe3+ compounds with carbonyl groups (to give Fen+[CO]6) and subsequent substitutions with Cl-, Br-, NH3, and H2O, to understand how these ligands interfere in the M-CO bond. The geometry optimization calculations were performed with the methods BP86 and B3LYP and the atomic basis set def2-TZVP. The molecular orbitals and the properties derived from the electronic density based on QTAIM were analyzed. Coordination with ligands increased the influence of the metal atomic basin on the Fe-C bond, especially for the Fe2+ compounds, and the Cl- and Br- ligands led to lower local ionization energies at the Fe-C bonds. Trans effects were also observed in the QTAIM real functions: Fe-C bond distances were shorter when C was in trans position to a ligand.

7.
Rapid Commun Mass Spectrom ; 24(14): 2101-8, 2010 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-20552691

RESUMO

Electrospray ionization mass spectrometric analysis of lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) was accomplished in order to elucidate the gas-phase dissociation reactions of this important biologically active natural product. The occurrence of protonated and cationized species in the positive mode and of deprotonated species in the negative mode was explored by means of collision-induced dissociation (CID) experiments. For the protonated molecule, the H(2)O and C(4)H(8) losses occur by two competitive channels. For the deprotonated molecule, the even-electron rule is not conserved, and the radicalar species are eliminated by formation of distonic anions. The fragmentation mechanism for each ion was suggested on the basis of computational thermochemistry. Atomic charges, relative energies, and frontier orbitals were employed aiming at a better understanding of the gas-phase reactivity of lapachol. Potential energy surfaces for fragmentation reactions were obtained by the B3LYP/6-31+G(d,p) model.


Assuntos
Naftoquinonas/química , Modelos Químicos , Transição de Fase , Espectrometria de Massas por Ionização por Electrospray/métodos
8.
Dalton Trans ; 49(48): 17457-17471, 2020 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-33216076

RESUMO

This perspective focuses on the crucial role that energy decomposition schemes play in elucidating the physical nature of non-covalent interactions in supramolecular systems, particularly from the point of view of host-guest systems stabilized by non-covalent interactions, which are fundamental to molecular recognition. The findings reported here reveal the robustness and practical application of methods such as EDA-NOCV in rationalizing molecular recognition situations in systems such as calixarenes, cyclophanes and other box-shaped hosts, capable of incorporating different chemical species as anions and PAHs. We expect that the discussed cases in this perspective can be viewed as an initial assessment for the multidimensional nature of the weak interactions underlying supramolecular aggregations, which can be recognized in a plethora of different structures constantly synthesized and characterized by chemists around the world.

9.
Inorg Chem ; 48(11): 4692-700, 2009 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-19402621

RESUMO

Three novel polymetallic ruthenium (III) meso-tetra(4-pyridyl)porphyrins containing peripheral "RuCl(3)(dppb)" moieties have been prepared and characterized. The X-ray structure of the tetraruthenated {NiTPyP[RuCl(3)(dppb)](4)} porphyrin complex crystallizes in the triclinic space group P1. This structure is discussed and compared with the crystal data for the mer-[RuCl(3)(dppb)(py)]. The {TPyP[RuCl(3)(dppb)](4)} and {CoTPyP[RuCl(3)(dppb)](4)} porphyrins were used to obtain electrogenerated films on ITO and glass carbon electrode surfaces, respectively. Such tetraruthenated porphyrins form films of a mixed-valence species {TPyP[Ru(dppb)](4)(muCl(3))(2)}(2n)(4n2+) and {CoTPyP[Ru(dppb)](4)(muCl(3))(2)}(2n)(4n2+) on the electrode surface. The modified electrode with {CoTPyP[RuCl(3)(dppb)](4)} is very stable and can be used to detect organic substrates such as catechol.


Assuntos
Compostos Organometálicos/química , Fosfinas/química , Porfirinas/química , Rutênio/química , Cristalografia por Raios X , Eletrodos , Substâncias Macromoleculares/síntese química , Substâncias Macromoleculares/química , Modelos Moleculares , Conformação Molecular , Compostos Organometálicos/síntese química
10.
J Mol Model ; 25(1): 11, 2019 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-30607601

RESUMO

Ruthenophanes have been recognized as potential candidates to the design of electrically conducting polymers, particularly due to their electrochemical, structural, and spectroscopic properties. The comprehension and rationalization of the metal-ligand interaction is fundamental to pave the way for future applications as the design of new conducting materials. For that reason, this investigation sheds light on the electronic details behind the cation-π interactions present in ruthenophanes by using [Ru(η6-C16H16)(NH3)3]2+ as a model. Zeroth-order symmetry-adapted perturbation theory (SAPT0) shows the interaction Ru(II)-[2.2]paracyclophane with a predominant covalent character. However, the hapticity analysis of [2.2]paracyclophane shows only two predominantly covalent Ru-C bonds, as highlighted by the total energy density, H(r), in the bond critical point (BCP) obtained from quantum theory of atoms in molecules (QTAIM) method, and by second-order stabilization energy, ΔE(2), related to the processes: π C-C → dσ or dπ Ru, achieved in the natural bond orbital (NBO) method. The other two Ru-C chemical bonds show a largely electrostatic character, as can be visualized from the delocalization index, DI, between the electron basins in the electron localization function (ELF) method. Remarkably, the interacting quantum atoms (IQA) method showed practically the same value of the total interaction energy, E[Formula: see text], between Ru and these C atoms and, then, corroborates the hapticity four of the ligand: [2.2]paracyclophane. Source function distribution presents a correlation with the electronic interactions between different groups in [Ru(η6-C16H16)(NH3)3]2+. Graphical Abstract The nature of the interactions between [Ru(NH3)3]2+ and [2.2]paracyclophane in [Ru(η6-C16H16)(NH3)3]2+ was investigated with different methods of energy decomposition and electron density analysis. This interaction has a predominantly covalent character. It was possible to observe that some Ru-C interactions have a larger covalent character, in contrast for other that are mainly ionic.

11.
J Phys Chem A ; 112(17): 4060-6, 2008 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-18380497

RESUMO

The knowledge of thermochemical parameters such as the enthalpy of formation, gas-phase basicity, and proton affinity may be the key to understanding molecular reactivity. The obtention of these thermochemical parameters by theoretical chemical models may be advantageous when experimental measurements are difficult to accomplish. The development of ab initio composite models represents a major advance in the obtention of these thermochemical parameters, but these methods do not always lead to accurate values. Aiming at achieving a comparison between the ab initio models and the hybrid models based on the density functional theory (DFT), we have studied gamma-butyrolactone and 2-pyrrolidinone with a goal of obtaining high-quality thermochemical parameters using the composite chemical models G2, G2MP2, MP2, G3, CBS-Q, CBS-4, and CBS-QB3; the DFT methods B3LYP, B3P86, PW91PW91, mPW1PW, and B98; and the basis sets 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d), 6-311+G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ. Values obtained for the enthalpies of formation, proton affinity, and gas-phase basicity of the two target molecules were compared to the experimental data reported in the literature. The best results were achieved with the use of DFT models, and the B3LYP method led to the most accurate data.

12.
J Phys Chem A ; 112(46): 11784-800, 2008 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-18942810

RESUMO

A computational study of the isomers of tetrafluorinated [2.2]cyclophanes persubstituted in one ring, namely F4-[2.2]paracyclophane (4), F4-anti-[2.2]metacyclophane (5a), F4-syn-[2.2]metacyclophane (5b), and F4-[2.2]metaparacyclophane (6a and 6b), was carried out. The effects of fluorination on the geometries, relative energies, local and global aromaticity, and strain energies of the bridges and rings were investigated. An analysis of the electron density by B3PW91/6-31+G(d,p), B3LYP/6-31+G(d,p), and MP2/6-31+G(d,p) was carried out using the natural bond orbitals (NBO), natural steric analysis (NSA), and atoms in molecules (AIM) methods. The analysis of frontier molecular orbitals (MOs) was also employed. The results indicated that the molecular structure of [2.2]paracyclophane is the most affected by the fluorination. Isodesmic reactions showed that the fluorinated rings are more strained than the nonfluorinated ones. The NICS, HOMA, and PDI criteria evidenced that the fluorination affects the aromaticity of both the fluorinated and the nonfluorinated rings. The NBO and NSA analyses gave an indication that the fluorination increases not only the number of through-space interactions but also their magnitude. The AIM analysis suggested that the through-space interactions are restricted to the F4-[2.2]metacyclophanes. In addition, the atomic properties, computed over the atomic basins, gave evidence that not only the substitution, but also the position of the bridges could affect the atomic charges, the first atomic moments, and the atomic volumes.

13.
J Phys Chem A ; 112(46): 11731-43, 2008 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-18942818

RESUMO

The nature of the interactions between the platinum cluster Pt4 and the adsorbates (*)H, (*)OH, and H2O, as well as the influence of these adsorbates on the electronic structure of the Pt4 cluster, was investigated by density functional theory (B3LYP, B3PW91, and BP86) together with the effective core potential MWB for the platinum atoms, and 6-311++G(d,p) and aug-cc-pVTZ basis set for the H and O atoms. Identification of the optimal spin multiplicity state and the preferential adsorption sites were also evaluated. Adsorption changes the cluster geometry significantly, but the relaxation effects on the adsorption energy are negligible. The adsorbates bind preferentially atop of the cluster, where high bonding energies were observed for the radical species. Adsorption is followed by a charge transfer from the Pt4 cluster toward radical adsorbates, but this charge transfer occurs in a reversed way when the adsorbate is H2O. In contrast with water, adsorption of the radicals (*)H and (*)OH on platinum causes a remarkable re-distribution of the spin density, characterized by a spin density sharing between the (*)H and (*)OH radicals and the cluster. The covalent character of the cluster-adsorbate interactions, determined by electron density topological analysis, reveals that the Pt4-H interaction is completely covalent, Pt4-OH is partially covalent, and Pt4-H2O is almost noncovalent.

14.
J Mass Spectrom ; 42(10): 1279-86, 2007 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17902100

RESUMO

Diketopiperazines (DKPs) corresponding to cyclic dipeptides have been reported to exhibit antimicrobial, antitumor, antimutagenic and antiviral properties. These compounds are commonly isolated from microorganisms and sponges and from a variety of tissues and body fluids. In this work, we used electrospray ionization tandem mass spectrometry (ESI-MS/MS) to investigate the fragmentation of a series of DKPs previously isolated from Aspergillus fumigatus, which exhibit the same structural core. Loss of CO directly from the protonated molecule was found to be a fragmentation process common to all the compounds analyzed. However, our results revealed a series of ions that are diagnostic for the substituents at C(4) and C(9). In order to rationalize the differences in the fragmentation pathways of substituted and nonsubstituted DKPs, the relative Gibbs energies (DeltaG) of the product ions and intermediate ions were estimated using the B3LYP/6-31 + + G(d,p) model. The data reported here can be used for the structural elucidation of DKPs from low sample amounts, as an alternative to NMR.


Assuntos
Aspergillus fumigatus/química , Dicetopiperazinas/química , Espectrometria de Massas por Ionização por Electrospray/métodos , Espectrometria de Massas em Tandem/métodos , Estrutura Molecular
15.
J Chem Theory Comput ; 13(7): 3228-3235, 2017 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-28590736

RESUMO

Ozone and its sulfur-substituted isomers are studied by means of the Breathing Orbital Valence Bond ab initio method, with the objective of estimating their controversial diradical characters. The calculated weights of the various VB structures and their individual diabatic energies are found to be consistent with each other. All 1,3-dipoles can be described in terms of three major VB structures, one diradical and two zwitterionic ones, out of the six structures, forming a complete basis. Ozone has a rather large diradical character, estimated to 44%-49%. SOO and SOS are even more diradicalar, whereas SSO and especially OSO are better described as closed-shell zwitterions. Moreover, the description of 1,3-dipoles, in terms of the three major structures, yields VB weights in full agreement with simple chemical wisdom, i.e., a diradical weight of 33% when the three structures are quasi-degenerate, and a smaller (larger) value when the diradical structure is higher (lower) in energy than the zwitterionic ones. Therefore, the VB-calculated weight of the diradical structure of a molecule qualifies itself as a quantitative measure of diradical character, and not only as an indicator of tendencies. Other definitions of the diradical character, based on molecular orbital/configuration interaction methods, are discussed.

16.
ChemistryOpen ; 6(3): 410-416, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28638774

RESUMO

We have analyzed structure, stability, and Ru-NO bonding of the trans-[RuCl(NO)(NH3)4]2+ complex by using relativistic density functional theory. First, we focus on the bond dissociation energies associated with the three canonical dissociation modes leading to [RuCl(NH3)4]++NO+, [RuCl(NH3)4]2++NO, and [RuCl(NH3)4]3++NO-. The main objective is to understand the Ru-NO+ bonding mechanism in the conceptual framework of Kohn-Sham molecular orbital theory in combination with a quantitative energy decomposition analysis. In our analyses, we have addressed the importance of the synergism between Ru-NO+ σ-donation and π-backdonation as well as the so-called negative trans influence of the Cl- ligand on the Ru-NO bond. For completeness, the Ru-NO+ bonding mechanism is compared with that of the corresponding Ru-CO bond.

17.
J Phys Chem B ; 110(42): 21287-98, 2006 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-17048958

RESUMO

The non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are an important class of drugs employed in anti-HIV chemotherapy. TIBO compounds, which belong to the NNRTIs class, are potent inhibitors of the HIV-1 reverse transcriptase enzyme (HIV-1 RT). However, mutations in the amino acids present in the active site of these inhibitors limit their clinical use. In this work, the intermolecular interactions taking place between compounds of the TIBO family and Y181 (C181), K101, and Y188 amino acids are investigated. For this purpose the coordinates of three RT crystalline structures complexed with TIBO were taken from PDB database, and were analyzed by means of the B3LYP/6-31+G(d,p) model. The natural bond orbital (NBO) and atoms in molecules (AIM) methods indicate that not only does the Y181C mutation lead to loss of favorable interactions between the TIBO side chains and tyrosine, but it also affects the interaction between the inhibitor and K101 and Y188. Results also revealed that the interaction between TIBO and K101 is stabilized by N-H...O and N-H...S hydrogen bonds. This is the first time that the presence of the latter hydrogen bond (N-H...S) is reported to play an important role in the stabilization of the interaction between TIBO and K101. In addition the NBO and natural population analyses (NPA) indicate that the 8 Cl-TIBO inhibitor presents a more effective interaction with the Y181, K101, and Y188 than that of 9 Cl-TIBO.


Assuntos
Benzodiazepinas/química , Transcriptase Reversa do HIV/química , Imidazóis/química , Inibidores da Transcriptase Reversa/química , Aminoácidos , Fármacos Anti-HIV/química , Sítios de Ligação/genética , Transcriptase Reversa do HIV/antagonistas & inibidores , Ligação de Hidrogênio , Mutação , Especificidade por Substrato
18.
J Mol Model ; 22(11): 276, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27783233

RESUMO

In this computational study the interaction of NO., NO+, and NO- with H2O: [NO--H2O]., 1 ., [NO--H2O]+, 1 + , and [NO--H2O]-, 1 - was analysed. The optimized geometries indicate that the relative position of NO and H2O depends on the total charge: (ON.--H-OH), (NO---H-OH), and (ON+--OH2). Moreover, atomic spin density along with frontier molecular orbitals help to identify the preferred reduction or oxidation sites on the nitric oxide. Thus, quantum theory of atoms in molecules (QTAIM), electron localization function (ELF), and natural bond-bond polarizability (NBBP) methods aid to quantify the electron delocalization level between NO and H2O, 1 + > 1 . > 1 - , and show the predominantly ionic, and covalent character to inter-molecular, and intra-molecular chemical bonds, respectively. Furthermore, the natural bond orbital (NBO) and localized molecular orbital energy decomposition analysis (LMO-EDA) methods enable energy analyses of the interaction between NO and H2O in the complexes 1 ., 1 + , and 1 - . Where, the first method showed that the interaction between the natural bond orbitals in 1 - is more favorable, than in 1 + , and less in 1 ., however, the second method designates that the total interaction energy is lower for 1 + in relation to 1 - and 1 ., due mainly to the electrostatic component. As a final point, analysis of the electrostatic potential surfaces provides a clear and direct explanation for the relative position of the monomers. It also shows that the predominant Coulombic attraction between H2O and the charged NO+, and NO- compounds will be stronger in relation to the neutral NO.. Graphical abstract ᅟ.

19.
J Comput Chem ; 22(15): 1817-1829, 2001 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-12116413

RESUMO

TIBO (Tetrahydro-imidazo[4,5,1-jk][1,4]-benzodiazepin-2-one) and nevirapine (11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-6-one) are models for two classes of nonnucleoside inhibitors of the HIV-1 virus reverse transcriptase (NNRTI). This work presents the parameterization of compounds belonging to these two classes in the Cornell et al. force field through ab initio and semiempirical methods. The new parameters were used in the conformational analysis for TIBO R82913, TIBO R79882, and nevirapine. Various conformational search protocols were tested and the pseudosystematic method SUMM led to the best results. A better understanding of the distribution of conformers was obtained through clustering techniques in the data reduction stages. It was possible to reproduce various experimental data such as the crystallographic structures of the isolated or reverse transcriptase-complexed (RT) molecules. The proton-proton coupling constants (\documentclass{article}\pagestyle{empty}\begin{document}$\,J^{3}_{\mathrm{HH}}$\end{document}) obtained for TIBO through NMR were also reproduced. Cremer and Pople puckering parameters enabled a precise description of both the conformation of the seven-membered rings and the relative position of the substituents on them. These parameters also demonstrated the efficiency and precision of the two-stage clustering method. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1817-1829, 2001

20.
J Mol Model ; 20(7): 2332, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24965933

RESUMO

Interactions between an inhibitor and amino acids from a binding pocket could help not only to understand the nature of these interactions, but also to support the design of new inhibitors. In this paper, we explore the key interaction between a second generation non-nucleoside reverse transcriptase inhibitor (NNRTI), GW420867X, and HIV-1 RT amino acid Lys101 (K101), by quantum mechanical methods. The neutral, protonated, and zwitterionic complexes of GW420867X-K101 were studied. The interaction energies were determined by SCS-MP2/def2-cc-pVQZ, and the electron density was analyzed by natural bond orbital (NBO), atoms in molecules (AIM) and reduced gradient analysis. A large increase in the interaction was observed with the tautomerization of neutral or neutral protonated species. The monomers interact by two medium-strength hydrogen bonds, one partially covalent and another noncovalent. There are some van der Waals intramolecular interactions that are topologically unstable. The nature of the intermolecular interactions was also analyzed using quantitative molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) based on dispersion-corrected density functional theory (DFT) at BLYP-D/TZ2P.


Assuntos
Fármacos Anti-HIV/farmacologia , Transcriptase Reversa do HIV/antagonistas & inibidores , Quinoxalinas/farmacologia , Inibidores da Transcriptase Reversa/farmacologia , Fármacos Anti-HIV/química , Fármacos Anti-HIV/metabolismo , Sítios de Ligação , Elétrons , Transcriptase Reversa do HIV/química , Transcriptase Reversa do HIV/metabolismo , Concentração de Íons de Hidrogênio , Ligantes , Lisina , Simulação de Acoplamento Molecular , Estrutura Molecular , Ligação Proteica , Conformação Proteica , Teoria Quântica , Quinoxalinas/química , Quinoxalinas/metabolismo , Inibidores da Transcriptase Reversa/química , Inibidores da Transcriptase Reversa/metabolismo
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