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1.
Philos Trans A Math Phys Eng Sci ; 378(2167): 20190450, 2020 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-32008445

RESUMEN

Here, a bioinspired strategy is used to prepare well-ordered nanotubular structures, as observed in animals and plants, such as gecko toe pads or corals. The nanotubes are obtained by templateless electropolymerization of thieno[3,4-b]thiophene-based monomers with various aromatic groups in an organic solvent (dichloromethane). The most interesting and robust structures were obtained with carbazole and pyrene substituents to the base monomer structure, since these groups participate significantly in the polymerization and also have strong π-stacking interactions. The addition of water to electropolymerization solvent significantly impacted the formation of nanotubes, as it caused the release of a significant amount of H2 and O2 bubbles, depending on the electropolymerization method. Identifying templateless approaches to vary nanotubular structures is very interesting, as these materials are sought-after for applications in water harvesting systems. This article is part of the theme issue 'Bioinspired materials and surfaces for green science and technology (part 3)'.


Asunto(s)
Electroquímica/métodos , Cloruro de Metilo/química , Nanotecnología/métodos , Nanotubos/química , Tiofenos/química , Biomimética , Carbazoles/química , Tecnología Química Verde , Hidrógeno/química , Sustancias Macromoleculares , Microscopía Electrónica de Rastreo , Compuestos Orgánicos , Oxígeno/química , Polímeros/química , Solventes/química , Propiedades de Superficie , Agua/química , Humectabilidad
2.
Artículo en Inglés | MEDLINE | ID: mdl-31941122

RESUMEN

Methyl chloride (CH3Cl) is presently understood to arise from biotic and abiotic processes in marine systems. However, the production of CH3Cl via photochemical processes has not been well studied. Here, we reported the production of CH3Cl from humic acid (HA) in sunlit saline water and the effects of the concentration of HA, chloride ions, ferric ions and pH were investigated. HA in aqueous chloride solutions or natural seawater were irradiated under an artificial light, and the amounts of CH3Cl were determined using a purge-and-trap and gas chromatography-mass spectrometry. CH3Cl was generated upon irradiation and its amount increased with increasing irradiation time and the light intensity. The formation of CH3Cl increased with an increase of HA concentration ranging from 2 mg L-1 to 20 mg L-1 and chloride ion concentration ranging from 0.02 mol L-1 to 0.5 mol L-1. The photochemical production of CH3Cl was pH-dependent, with the highest amount of CH3Cl generating near neutral conditions. Additionally, the generation of CH3Cl was inhibited by ferric ions. Finally, natural coastal seawater was irradiated under artificial light and the concentration of CH3Cl rose significantly. Our results suggest that the photochemical process of HA may be a source of CH3Cl in the marine environment.


Asunto(s)
Sustancias Húmicas/efectos de la radiación , Hierro/química , Cloruro de Metilo/química , Agua de Mar/química , Contaminantes Químicos del Agua/química , Concentración de Iones de Hidrógeno , Luz , Procesos Fotoquímicos , Salinidad
3.
J Chem Theory Comput ; 15(11): 6085-6096, 2019 Nov 12.
Artículo en Inglés | MEDLINE | ID: mdl-31545600

RESUMEN

We present a strategy to generate "concentrically local orbitals" for the purpose of decreasing the computational cost of wave function-in-density functional theory (WF-in-DFT) embedding. The concentric localization is performed for the virtual orbitals by first projecting the virtual space onto atomic orbitals centered on the embedded atoms. Using a one-particle operator, these projected orbitals are then taken as a starting point to iteratively span the virtual space, recursively creating virtual orbital "shells" with consecutively decreasing correlation energy recovery at each iteration. This process can be repeated to convergence, allowing for tunable accuracy. Assessment of the proposed scheme is performed by application to the potential energy diagram of the Menshutkin reaction of chloromethane and ammonia inside a segment of a carbon nanotube and the torsional potential of a simplified version of the retinal chromophore.


Asunto(s)
Teoría Funcional de la Densidad , Amoníaco/química , Cloruro de Metilo/química , Modelos Moleculares , Nanotubos de Carbono/química
4.
J Environ Qual ; 47(2): 254-262, 2018 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-29634809

RESUMEN

Chloromethane (CHCl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CHCl budget, and especially the CHCl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CHCl hydrogen and carbon and investigated bacterial diversity during CHCl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CHCl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 µg g dry wt. d for forest soil, from 0.1 to 0.9 µg g dry wt. d for grassland soil, and from 0.1 to 0.4 µg g dry wt. d for agricultural soil and increased with increasing temperature and CHCl supplementation. The measured mean stable hydrogen enrichment factor of CHCl of -50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CHCl degradation rates and ranged from -38 to -11‰. Bacterial community composition correlated with soil properties was independent from CHCl degradation or isotope enrichment. Nevertheless, increased abundance after CHCl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CHCl degradation, may play a role in the microbial CHCl sink in soil.


Asunto(s)
Cloruro de Metilo/química , Microbiología del Suelo , Agricultura , Isótopos , Suelo
5.
J Chem Phys ; 143(23): 234111, 2015 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-26696050

RESUMEN

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.


Asunto(s)
Cloruro de Metilo/química , Teoría Cuántica
6.
J Chem Phys ; 142(24): 244306, 2015 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-26133427

RESUMEN

Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.


Asunto(s)
Cloruro de Metilo/química , Teoría Cuántica , Vibración , Electrones , Termodinámica
7.
J Chem Phys ; 142(24): 244505, 2015 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-26133439

RESUMEN

The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.


Asunto(s)
Cianuros/química , Cloruro de Metilo/química , Teoría Cuántica , Agua/química , Modelos Moleculares , Conformación Molecular , Solventes/química , Electricidad Estática
8.
Biochim Biophys Acta ; 1850(5): 954-965, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25038480

RESUMEN

BACKGROUND: Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. SCOPE OF REVIEW: Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. MAJOR CONCLUSIONS: The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. GENERAL SIGNIFICANCE: As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics.


Asunto(s)
Simulación de Dinámica Molecular , Proteínas/química , Cloruros/química , Transferencia de Energía , Dicloruros de Etileno/química , Hidrolasas/química , Cinética , Cloruro de Metilo/química , Simulación de Dinámica Molecular/normas , Conformación Proteica , Pliegue de Proteína , Estabilidad Proteica , Desplegamiento Proteico , Estándares de Referencia , Relación Estructura-Actividad , Propiedades de Superficie , Termodinámica , Uracilo/química
9.
Phys Chem Chem Phys ; 16(48): 26658-71, 2014 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-25384675

RESUMEN

The formation of CH3Cl from (CH3)3SCl in various solvents has been studied based on M05/6-311+G(2d,p) DFT calculations to quantify the influence of the solvent on the stability of sulfonium cations. Four different pathways (one SN1, one backside and two frontside attacks for SN2) as well as the formation of different ion pairs (tripod, seesaw, and linear) are discussed to investigate the origin of the kinetic solvent effect (KSE) and the contribution of ion pairs to the overall reaction. Ion pairs are formed only in solvents with a permittivity ε lower than 28, but the reaction proceeds via a standard SN2 mechanism with a backside attack in all solvents. The formation of ion pairs does not change the order of the rate law, but it strongly influences the KSE, which can distinguish between reactions starting from free ions and those starting from ion pairs, in contrast to standard kinetic analysis.


Asunto(s)
Cloruro de Metilo/química , Sulfuros/química , Compuestos de Sulfonio/química , Iones/química , Cinética , Modelos Moleculares , Solventes/química
10.
J Org Chem ; 79(17): 7889-94, 2014 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-25105663

RESUMEN

Glycoside formation in organic synthesis is believed to occur along a reaction path involving an activated glycosyl donor with a covalent bond between the glycosyl moiety and the leaving group, followed by formation of contact ion pairs with the glycosyl moiety loosely bound to the leaving group, and eventually solvent-separated ion pairs with the glycosyl moiety and the leaving group being separated by solvent molecules. However, these ion pairs have never been experimentally observed. This study investigates the formation of the ion pairs from a covalent intermediate, 2,3,4,6-tetra-O-methyl-α-d-glucopyranosyl triflate, by means of computational chemistry. Geometry optimization of the ion pairs without solvent molecules resulted in re-formation of the covalent α- and ß-triflates but was successful when four solvent (dichloromethane) molecules were taken into account. The DFT(M06-2X) computations indicated interconversion between the α- and ß-covalent intermediates via the α- and ß-contact ion pairs and the solvent-separated ion pairs. The calculated activation Gibbs energy of this interconversion was quite small (10.4-13.5 kcal/mol). Conformational analyses of the ion pairs indicated that the oxacarbenium ion adopts (4)H3, (2)H3/E3, (2)H3/(2)S0, E3, (2,5)B, and B2,5 pyranosyl ring conformations, with the stability of the conformers being strongly dependent on the relative location of the counteranion.


Asunto(s)
Glicósidos/síntesis química , Iones/química , Cloruro de Metilo/química , Glicósidos/química , Cloruro de Metilo/análogos & derivados , Modelos Moleculares
11.
Chemosphere ; 111: 575-9, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24997968

RESUMEN

Chloromethane, accounting for approximately 16% of the tropospheric chlorine, is mainly coming from natural sources. However anthropogenic activities, such as combustion of biomass may contribute significantly as well. The present study focuses on the thermal solid state reaction between pectin, an important constituent of biomass, and chloride ions as found in alkali metal chlorides. The formation of chloromethane is evident with the amount formed being linear with respect to chloride if pectin is in great excess. Thus the reaction is explained as a pseudo first order SN2 reaction between the chloride ion and the methyl ester moiety in pectin. It is suggested that the polymeric nature of pectin plays an active role by an enhanced transport of halides along the carbohydrate chain. Optimal reaction temperature is around 210°C. At higher temperatures the yield of chloromethane decreases due to a thermal decomposition of the pectin. The possible influence of the type of cation is discussed.


Asunto(s)
Cloruros/química , Cloruro de Metilo/química , Pectinas/química , Biomasa , Cloro/química , Iones/química , Temperatura
12.
J Phys Chem B ; 118(24): 6456-65, 2014 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-24484473

RESUMEN

The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl4, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability.


Asunto(s)
Hidrocarburos Clorados/química , Tetracloruro de Carbono/química , Gases/química , Halógenos/química , Cloruro de Metilo/química , Modelos Moleculares , Teoría Cuántica , Electricidad Estática , Termodinámica
13.
J Chem Phys ; 140(5): 054109, 2014 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-24511924

RESUMEN

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.


Asunto(s)
Cloruros/química , Cloruro de Metilo/química , Teoría Cuántica , Solventes/química , Simulación por Computador , Iones , Soluciones
14.
J Phys Chem A ; 117(47): 12569-80, 2013 Nov 27.
Artículo en Inglés | MEDLINE | ID: mdl-24148008

RESUMEN

The microwave (4-20 GHz range) and infrared (HCl and DCl stretch ranges) spectra of six isotopic species of the CH3Cl-HCl hydrogen bond complex have been recorded for the first time and analyzed with the support of high level ab initio calculations (MP2 and CCSD(T) levels). Accurate molecular parameters, including rotational, quartic centrifugal distortion, and nuclear-quadrupole coupling constants, vibrational frequencies, and anharmonic coupling constants, are presented in this paper. These parameters have then been used to estimate the hydrogen bond geometry and confirm the strong coupling between intramolecular and low frequency intermolecular modes. Experimental and theoretical evidence, in agreement with each other, tend to point out a free rotation of the CH3Cl unit in the complex, emphasizing the very peculiar dynamical properties of a hydrogen bond and, consequently, the necessity of taking those effects into account to correctly model the intra- and intermolecular interactions.


Asunto(s)
Deuterio/química , Ácido Clorhídrico/química , Cloruro de Metilo/química , Termodinámica , Enlace de Hidrógeno , Estructura Molecular , Teoría Cuántica , Espectroscopía Infrarroja por Transformada de Fourier
15.
Artículo en Inglés | MEDLINE | ID: mdl-23912047

RESUMEN

The reactions of iron and manganese monoxide molecules (FeO, and MnO) with monochloromethane in solid argon have been studied by matrix isolation infrared spectroscopy and quantum chemistry calculations. When annealing, the reactions of FeO and MnO with CH3Cl first form the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes, which can isomerize to CH3MOCl (MMn, Fe) upon 300<λ<580 nm irradiation. The products were characterized by isotopic IR studies with CD3Cl and (13)CH3Cl and density functional calculations. Based on theoretical calculations, the OFe-(η(Cl)-CH3Cl) and OMn-(η(Cl)-CH3Cl) complexes have (5)A' and (6)A' ground state with Cs symmetry, respectively. The accurate CCSD(T) single point calculations illustrate the CH3MOCl isomerism are 13.8 and 3.1 kcal/mol lower in energy than the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes.


Asunto(s)
Compuestos Férricos/química , Compuestos de Manganeso/química , Cloruro de Metilo/química , Óxidos/química , Modelos Moleculares , Teoría Cuántica , Espectrofotometría Infrarroja
16.
J Mol Model ; 19(10): 4181-93, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23455925

RESUMEN

Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.


Asunto(s)
Cloro/química , Cloruro de Metilo/química , Contaminantes Atmosféricos/química , Simulación por Computador , Gases , Cinética , Modelos Químicos , Modelos Moleculares , Teoría Cuántica , Termodinámica
17.
J Mol Model ; 19(4): 1489-505, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-23239396

RESUMEN

Ab initio calculations at the G2 level were used in a theoretical description of the kinetics and mechanism of the hydrogen abstraction reactions from fluoro-, chloro- and bromomethane by chlorine atoms. The profiles of the potential energy surfaces show that mechanism of the reactions under investigation is complex and consists of two - in the case of CH3F+Cl - and of three elementary steps for CH3Cl+Cl and CH3Br+Cl. The heights of the energy barrier related to the H-abstraction are of 8-10 kJ mol(-1), the lowest value corresponds to CH3Cl+Cl and the highest one to CH3F+Cl. The rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The kinetic equations derived in this study[Formula: see text]and[Formula: see text]allow a description of the kinetics of the reactions under investigation in the temperature range of 200-3000 K. The kinetics of reactions of the entirely deuterated reactants were also included in the kinetic analysis. Results of ab initio calculations show that D-abstraction process is related with the energy barrier of 5 kJ mol(-1) higher than the H-abstraction from the corresponding non-deuterated reactant molecule. The derived analytical equations for the reactions, CD3X+Cl, CH2X+HCl and CD2X+DCl (X = F, Cl and Br) are a substantial supplement of the kinetic data necessary for the description and modeling of the processes of importance in the atmospheric chemistry.


Asunto(s)
Cloro/química , Hidrocarburos Bromados/química , Cloruro de Metilo/química , Modelos Químicos , Ozono/química , Atmósfera/química , Catálisis , Calentamiento Global , Hidrógeno/química , Cinética , Metano/química , Pérdida de Ozono , Temperatura , Termodinámica
18.
J Chem Phys ; 137(18): 184308, 2012 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-23163372

RESUMEN

High-energy electron transfer dissociation (HE-ETD) on collisions with alkali metal targets (Cs, K, and Na) was investigated for CH(3)X(+) (X = Cl, Br, and I) ions by a charge inversion mass spectrometry. Relative peak intensities of the negative ions formed via HE-ETD strongly depend on the precursor ions and the target alkali metals. The dependency is explained by the exothermicities of the respective dissociation processes. Peak shapes of the negative ions, especially of the X(-) ions, which comprise a triangle and a trapezoid, also strongly depend on the precursor ions and the target alkali metals. The trapezoidal part of the I(-) peak observed with the Na target is more dominant and much broader than that with the Cs target. This dependence on the targets shows an inverse relation between the peak width and the available energy, which corresponds to the exothermicity assuming formation of fragment pair in their ground internal states. From a comparison of the kinetic energy release value calculated from the trapezoidal shape of I(-) with the available energy of the near-resonant level on the CH(3)I potential energy curve reported by ab initio calculations, the trapezoidal part is attributed to the dissociation to CH(3) + I((2)P(3/2)) via the repulsive (3)Q(1) state of CH(3)I, which is not dominant in the photo-dissociation of CH(3)I. The observation of trapezoid shape of the CH(2)I(-) peak with the Cs target indicates spontaneous dissociation via repulsive potential from the (3)R(2) Rydberg state, although the correlation between the (3)R(2) Rydberg state and relevant repulsive states has not been reported by any theoretical calculation.


Asunto(s)
Electrones , Hidrocarburos Bromados/química , Hidrocarburos Yodados/química , Metales Alcalinos/química , Cloruro de Metilo/química , Teoría Cuántica , Cinética , Espectrometría de Masas
19.
J Phys Chem B ; 116(27): 7898-913, 2012 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-22690808

RESUMEN

Cryptophane-D is composed of two nonequivalent cyclotribenzylene caps bound together by three OCH2CH2O bridges in a syn arrangement. Host-guest complexes with chloroform and dichloromethane were investigated in solution by NMR spectroscopy. Variable temperature NMR (1)H and (13)C spectra showed effects of chemical exchange between the free and bound guest and of conformational exchange for the host, strongly and specifically affected by guest binding. We found in particular that the carbon-13 chemical shifts for the linkers connecting the two cyclotribenzylene units are very informative. The NMR results were supported by DFT calculations. The guest exchange was also studied quantitatively, either by EXSY measurements (for chloroform as guest) or by line-shape analysis (for dichloromethane as guest). In the case of chloroform guest, we also investigated cross-relaxation between the guest and host protons, as well as carbon-13 longitudinal relaxation and heteronuclear NOE at three different fields. The results were interpreted in terms of orientation and dynamics of the guest inside the host cavity. Putting together various types of evidence resulted in remarkably detailed insight into the process of molecular recognition of the two guests by cryptophane-D host.


Asunto(s)
Cloruro de Metilo/química , Compuestos Policíclicos/química , Teoría Cuántica , Cinética , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Conformación Molecular
20.
J Mol Model ; 18(10): 4625-38, 2012 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-22643975

RESUMEN

The nature and strength of halogen bonding in halo molecule-Lewis base complexes were studied in terms of molecular mechanics using our recently developed positive extra-point (PEP) approach, in which the σ-hole on the halogen atom is represented by an extra point of positive charge. The contributions of the σ-hole (i.e., positively charged extra point) and the halogen atom to the strength of this noncovalent interaction were clarified using the atomic parameter contribution to the molecular interaction (APCtMI) approach. The molecular mechanical results revealed that the halogen bond is electrostatic and van der Waals in nature, and its strength depends on three types of interaction: (1) the attractive electrostatic interaction between the σ-hole and the Lewis base, (2) the repulsive electrostatic interaction between the negative halogen atom and the Lewis base, and (3) the repulsive/attractive van der Waals interactions between the halogen atom and the Lewis base. The strength of the halogen bond increases with increasing σ-hole size (i.e., magnitude of the extra-point charge) and increasing halogen atom size. The van der Waals interaction's contribution to the halogen bond strength is most favorable in chloro complexes, whereas the electrostatic interaction is dominant in iodo complexes. The idea that the chloromethane molecule can form a halogen bond with a Lewis base was revisited in terms of quantum mechanics and molecular mechanics. Although chloromethane does produce a positive region along the C-Cl axis, basis set superposition error corrected second-order Møller-Plesset calculations showed that chloromethane-Lewis base complexes are unstable, producing halogen-Lewis base contacts longer than the sum of the van der Waals radii of the halogen and O/N atoms. Molecular mechanics using the APCtMI approach showed that electrostatic interactions between chloromethane and a Lewis base are unfavorable owing to the high negative charge on the chlorine atom, which overcomes the corresponding favorable van der Waals interactions.


Asunto(s)
Halógenos/química , Fenómenos Mecánicos , Modelos Moleculares , Benceno/química , Formaldehído/química , Cloruro de Metilo/química , Electricidad Estática , Termodinámica
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