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1.
J Chem Phys ; 152(16): 164702, 2020 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-32357765

RESUMO

We present results from molecular dynamics simulations coupled with enhanced sampling techniques on the adsorption and isomerization of glyoxal (GL) and methylglyoxal (MG) at the air/hydroxylated silica (α-Quartz) interface. GL and MG are two organic compounds present in the atmosphere as oxidation products of both biogenic and anthropogenic precursors. By adsorption and hydration on liquid droplets or wetted dust particles, they can enable aerosol growth in the atmosphere. Moreover, thanks to the different polar characters of their trans and cis conformers, GL and MG have been suggested as possible molecular switches capable of responding to changes in solvent polarity. Here, we show that the hydroxylated silica surface does not significantly catalyze the trans-to-cis isomerization, but it stabilizes the cis-isomers, indicating a higher interfacial cis/trans relative concentration compared to the gas phase. Moreover, adsorbed GL prefers to lie parallel on the silica surface, while adsorbed MG shows a tilted orientation. In particular, we report the aldehyde group pointing upward (downward) to the gas phase (to the silica surface) in trans-MG (cis-MG). These results will help in the rationalization of upcoming experimental and modeling work on the adsorption of ketonic compounds on dust aerosols, while it clarifies the catalytic role of the solid substrate surface in promoting conformational changes.

2.
J Phys Chem Lett ; : 3422-3429, 2020 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-32283032

RESUMO

Multiphase reactions of halide ions in aqueous solutions exposed to the atmosphere initiate the formation of molecular halogen compounds in the gas phase. Their photolysis leads to halogen atoms, which are catalytic sinks for ozone, making these processes relevant for the regional and global tropospheric ozone budget. The affinity of halide ions in aqueous solution for the liquid-gas interface, which may influence their reactivity with gaseous species, has been debated. Our study focuses on the surface properties of the bromide ion and its oxidation products. In situ X-ray photoelectron spectroscopy carried out on a liquid jet combined with classical and first-principles molecular dynamics calculations was used to investigate the interfacial depth profile of bromide, hypobromite, hypobromous acid, and bromate. The simulated core electron binding energies support the experimentally observed values, which follow a correlation with bromine oxidation state for the anion series. Bromide ions are homogeneously distributed in the solution. Hypobromous acid, a key species in the multiphase cycling of bromine, is the only species showing surface propensity, which suggests a more important role of the interface in multiphase bromine chemistry than thought so far.

3.
J Am Chem Soc ; 142(12): 5574-5582, 2020 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-32091211

RESUMO

Aqueous-phase processing of methylglyoxal (MG) has been suggested to play a key role in the formation of secondary organic aerosols and catalyze particle growth in the atmosphere. However, the details of these processes remain speculative owing to the lack of a complete description of the physicochemical behavior of MG on atmospheric aerosols. Here, the solvation and hydrolysis of MG at the air/liquid water interface is studied via classical and first-principles molecular dynamics simulations combined with free-energy methods. Our results reveal that the polarity of the water solvent catalyzed the trans-to-cis isomerization of MG at the air/liquid water interface relative to the gas phase. Despite the presence of a hydrophobic group, MG often solvates with both the ketone and methyl groups parallel to the water interface. Analysis of the instantaneous water surface reveals that when MG is in the trans state, the methyl group repels interfacial water to maintain the planarity of the molecule, indicating that lateral and temporal inhomogeneities of interfacial environments are important for fully characterizing the solvation of MG. The counterintuitive behavior of the hydrophobic group is ascribed to a tendency to maximize the number of hydrogen bonds between MG and interfacial water while minimizing the torsional free energy. This drives MG hydration, and our simulations indicate that the formation of MG diol is catalyzed at the air/liquid water interface compared to the gas phase and occurs through nucleophilic attack of water on the carbonyl carbon.

4.
J Am Chem Soc ; 140(16): 5535-5543, 2018 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-29619831

RESUMO

Conformational isomerism plays a central role in organic synthesis and biological processes; however, effective control of isomerization processes still remains challenging and elusive. Here, we propose a novel paradigm for conformational control of isomerization in the condensed phase, in which the polarity of the solvent determines the relative concentration of conformers at the interfacial and bulk regions. By the use of state-of-the-art molecular dynamics simulations of glyoxal in different solvents, we demonstrate that the isomerization process is dipole driven: the solvent favors conformational changes toward conformers having molecular dipoles that better match its polar character. Thus, the solvent polarity modulates the conformational change, stabilizing and selectively segregating in the bulk vs the interface one conformer with respect to the others. The findings in this paper have broader implications affecting systems involving compounds with conformers of different polarity. This work suggests novel mechanisms for tuning the catalytic activity of surfaces in conformationally controlled (photo)chemical reactions and for designing a new class of molecular switches that are active in different solvent environments.

5.
Biosens Bioelectron ; 100: 298-303, 2018 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-28942212

RESUMO

One of the main targets in current clinical oncology is the development of a cheap device capable of monitoring in real-time the concentration of a drug in the blood of a patient. This would allow fine-tuning the dosage according to the patient's metabolism, a key condition to reduce side effects. By using surface plasmon resonance and fluorescence spectroscopy we here show that short peptides designed in silico by a recently developed algorithm are capable of binding the anticancer drug irinotecan (CPT-11) with micromolar affinity. Importantly, the recognition takes place in the denaturating solution used in standard therapeutic drug monitoring to detach the drug from the proteins that are present in human plasma, and some of the peptides are capable of distinguishing CPT-11 from its metabolite SN-38. These results suggest that the in silico design of small artificial peptides is now a viable route for designing sensing units, opening a wide range of applications in diagnostic and clinical areas.


Assuntos
Antineoplásicos/metabolismo , Camptotecina/análogos & derivados , Monitoramento de Medicamentos/métodos , Peptídeos/metabolismo , Ressonância de Plasmônio de Superfície/métodos , Sequência de Aminoácidos , Antineoplásicos/sangue , Sítios de Ligação , Camptotecina/sangue , Camptotecina/metabolismo , Humanos , Irinotecano , Modelos Moleculares , Peptídeos/química , Ligação Proteica , Espectrometria de Fluorescência
6.
Nat Commun ; 8(1): 700, 2017 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-28951540

RESUMO

Oxidation of bromide in aqueous environments initiates the formation of molecular halogen compounds, which is important for the global tropospheric ozone budget. In the aqueous bulk, oxidation of bromide by ozone involves a [Br•OOO-] complex as intermediate. Here we report liquid jet X-ray photoelectron spectroscopy measurements that provide direct experimental evidence for the ozonide and establish its propensity for the solution-vapour interface. Theoretical calculations support these findings, showing that water stabilizes the ozonide and lowers the energy of the transition state at neutral pH. Kinetic experiments confirm the dominance of the heterogeneous oxidation route established by this precursor at low, atmospherically relevant ozone concentrations. Taken together, our results provide a strong case of different reaction kinetics and mechanisms of reactions occurring at the aqueous phase-vapour interface compared with the bulk aqueous phase.Heterogeneous oxidation of bromide in atmospheric aqueous environments has long been suspected to be accelerated at the interface between aqueous solution and air. Here, the authors provide spectroscopic, kinetic and theoretical evidence for a rate limiting, surface active ozonide formed at the interface.

7.
J Am Chem Soc ; 139(1): 27-30, 2017 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-28073251

RESUMO

Interfacial chemistry involving glyoxal at aerosol surfaces is postulated to catalyze aerosol growth. This chemistry remains speculative due to a lack of detailed information concerning the physicochemical behavior of glyoxal at the interface of atmospheric aerosols. Here, we report results from high-level electronic structure calculations as well as both classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at the air/liquid water interface. When compared to the gas phase, the trans to cis isomerization of glyoxal at the liquid water interface is found to be catalyzed; additionally, the trans conformation is selectively solvated within the bulk to a greater degree than is the cis conformation. These two processes, i.e., the catalytic effect at the water interface and the differentially selective solvation, act to enhance the concentration of the cis isomer of glyoxal at the water interface. This has important consequences for the interpretation of experiments and for the modeling of glyoxal chemistry both at the interface of water clouds and at aerosols. Broader implications of this work relate to describing the role of interfaces in selecting specific stereo molecular structures at interfacial environments.

8.
J Chem Phys ; 144(21): 214701, 2016 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-27276960

RESUMO

Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols.

9.
Proteins ; 84(9): 1312-20, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27253756

RESUMO

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/química , Algoritmos , Modelos Estatísticos , Simulação de Dinâmica Molecular , Ribonucleoproteína Nuclear Pequena U5/química , Sítios de Ligação , Humanos , Simulação de Acoplamento Molecular , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Estrutura Secundária de Proteína , Projetos de Pesquisa , Software , Solventes/química
10.
J Phys Chem B ; 119(41): 12963-9, 2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26398715

RESUMO

Short peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature.


Assuntos
Simulação de Dinâmica Molecular , Compostos Orgânicos/química , Peptídeos/química , Solventes/química , Algoritmos , Sequência de Aminoácidos , Termodinâmica
11.
Phys Chem Chem Phys ; 17(35): 22947-58, 2015 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-26266625

RESUMO

Predictive theoretical models for mesoscopic roughening of ice require improved understanding of attachment kinetics occurring at the ice-vapor interface. Here, we use classical molecular dynamics to explore the generality and mechanics of a transition from anisotropic to isotropic self-diffusivity on exposed prismatic surfaces. We find that self-diffusion parallel to the crystallographic a-axis is favored over the c-axis at sub-melt temperatures below about -35 °C, for three different representations of the water-water intermolecular potential. In the low-temperature anisotropic regime, diffusion results from interstitial admolecules encountering entropically distinct barriers to diffusion in the two in-plane directions. At higher temperatures, isotropic self-diffusion occurring deeper within the quasi-liquid layer becomes the dominant mechanism, owing to its larger energy of activation.

12.
J Phys Chem A ; 119(19): 4482-8, 2015 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-25642913

RESUMO

Surface level ozone destruction in polar environments may be initiated by oxidation of bromide ions by ozone, ultimately leading to Br2 production. Ab initio calculations are used to support the development of atmospheric chemistry models, but errors can occur in study of the bromide-ozone reaction due to inappropriate treatment of the many-electron species and the ionic nature of the reaction. In this work, a high level ab initio study is used to take into account the electronic correlation and the polarization effects. Our results show three possible pathways for the reaction. In particular, we find that this process, though endothermic on the singlet spin state surface, can be energetically feasible on the triplet surface. The triplet surface can be reached through photoexcitation of ozone or by the spin crossing of the potential energy surface. Because this process is known to occur in the dark, it may be that it occurs after intersystem crossing to a triplet surface. This paper also provides a starting point calibration for any future ab initio calculation studies of the bromide-ozone reaction, from the gas to the condensed phase.


Assuntos
Brometos/química , Íons/química , Ozônio/química , Atmosfera/química , Elétrons , Gases/química , Modelos Químicos , Processos Fotoquímicos , Água/química
13.
J Phys Chem A ; 118(35): 7535-47, 2014 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-24945503

RESUMO

A combined experimental and computational approach was used to study the spectroscopic properties of benzene at the ice-air interface at 253 and 77 K in comparison with its spectroscopic behavior in aqueous solutions. Benzene-contaminated ice samples were prepared either by shock-freezing of benzene aqueous solutions or by benzene vapor-deposition on pure ice grains and examined using UV diffuse reflectance and emission spectroscopies. Neither the absorption nor excitation nor emission spectra provided unambiguous evidence of benzene associates on the ice surface even at a higher surface coverage. Only a small increase in the fluorescence intensity in the region above 290 nm found experimentally might be associated with formation of benzene excimers perturbed by the interaction with the ice surface as shown by ADC(2) excited-state calculations. The benzene associates were found by MD simulations and ground-state DFT calculations, although not in the arrangement that corresponds to the excimer structures. Our experimental results clearly demonstrated that the energy of the S0 → S1 electronic transition of benzene is not markedly affected by the phase change or the microenvironment at the ice-air interface and its absorption is limited to the wavelengths below 268 nm. Neither benzene interactions with the water molecules of ice nor the formation of dimers and microcrystals at the air-ice interface thus causes any substantial bathochromic shift in its absorption spectrum. Such a critical evaluation of the photophysical properties of organic contaminants of snow and ice is essential for predictions and modeling of chemical processes occurring in polar regions.

14.
J Phys Chem A ; 118(6): 1052-66, 2014 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-24450495

RESUMO

The adsorption, mobility, and self-association of naphthalene (NPH) and 1-methylnaphthalene (1MN), two of the simplest polycyclic aromatic hydrocarbons (PAHs), at the surface of liquid water at 289 K were investigated using classical molecular dynamics (MD) simulations and free energy profile calculations across the water-vapor interface. Both NPH and 1MN, which exhibit a strong preference to be adsorbed at the water-vapor interface, are found to readily self-associate at the water surface, adopting mostly configurations with distinctly nonparallel arrangement of the two monomers. The additional methyl group of 1MN represents only a minor perturbation in terms of the hydration properties, interfacial orientation, and self-association with respect to NPH. Implications of the observed self-association behavior for fluorescence spectroscopy of NPH and 1MN in aqueous interfacial environment are discussed.


Assuntos
Simulação de Dinâmica Molecular , Movimento (Física) , Naftalenos/química , Vapor , Adsorção , Dimerização , Conformação Molecular , Termodinâmica , Vácuo
15.
Phys Chem Chem Phys ; 14(32): 11371-85, 2012 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-22801804

RESUMO

We present a molecular dynamics simulation study in which we determined the melting point of ice I(h) for the polarizable SWM4-NDP water model (Lamoureux et al., Chem. Phys. Lett., 2006, 418, 245-249) and compared the performance of several popular water force fields, both polarizable and nonpolarizable, in terms of melting temperature, stability and orientational structuring of ice. The simulations yield the melting temperature of SWM4-NDP ice as low as T(m) = 185 ± 10 K, despite the quadrupole moment of a SWM4-NDP water molecule being close to the experimental gas phase value. The results thus show that the dependence of T(m) on the molecular quadrupole, observed for the three- and four-site water models, is generally lost if polarization is explicitly included. The study also shows that adding polarizability to a planar three-charge water model increases orientational disorder in hexagonal ice. In addition, analysis of the tetrahedral order in bulk ice reveals a correlation between the pre-existing degree of orientational disorder in ice simulated using different polarizable and nonpolarizable models and the melting temperature of the models. Our findings thus suggest some new considerations regarding the role of polarization forces in a crystalline solid that may guide future development of reliable polarizable water models for ice.

16.
Phys Chem Chem Phys ; 13(44): 19960-9, 2011 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-21993291

RESUMO

We present an Arrhenius analysis of self-diffusion on the prismatic surface of ice calculated from molecular dynamics simulations. The six-site water model of Nada and van der Eerden was used in combination with a structure-based criterion for determining the number of liquid-like molecules in the quasi-liquid layer. Simulated temperatures range from 230 K-287 K, the latter being just below the melting temperature of the model, 289 K. Calculated surface diffusion coefficients agree with available experimental data to within quoted precision. Our results indicate a positive Arrhenius curvature, implying a change in the mechanism of self-diffusion from low to high temperature, with a concomitant increase in energy of activation from 29.1 kJ mol(-1) at low temperature to 53.8 kJ mol(-1) close to the melting point. In addition, we find that the surface self-diffusion is anisotropic at lower temperatures, transitioning to isotropic in the temperature range of 240-250 K. We also present a framework for self-diffusion in the quasi-liquid layer on ice that aims to explain these observations.

17.
J Phys Chem A ; 115(41): 11412-22, 2011 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-21882845

RESUMO

A combined experimental-computational approach was used to study the self-organization and microenvironment of 1-methylnaphthalene (1MN) deposited on the surface of artificial snow grains from vapors at 238 K. The specific surface area of this snow (1.1 × 10(4) cm(2) g(-1)), produced by spraying very fine droplets of pure water from a nebulizer into liquid nitrogen, was determined using valerophenone photochemistry to estimate the surface coverage by 1MN. Fluorescence spectroscopy at 77 K, in combination with molecular dynamics simulations, and density functional theory (DFT) and second-order coupled cluster (CC2) calculations, provided evidence for the occurrence of ground- and excited-state complexes (excimers) and other associates of 1MN on the snow grains' surface. Only weak excimer fluorescence was observed for a loading of 5 × 10(-6) mol kg(-1), which is ∼2-3 orders of magnitude below monolayer coverage. However, the results indicate that the formation of excimers is favored at higher surface loadings (>5 × 10(-5) mol kg(-1)), albeit still being below monolayer coverage. The calculations of excited states of monomer and associated moieties suggested that a parallel-displaced arrangement is responsible for the excimer emission observed experimentally, although some other associations, such as T-shape dimer structures, which do not provide excimer emission, can still be relatively abundant at this surface concentration. The hydrophobic 1MN molecules, deposited on the ice surface, which is covered by a relatively flexible quasi-liquid layer at 238 K, are then assumed to be capable of dynamic motion resulting in the formation of energetically preferred associations to some extent. The environmental implications of organic compounds' deposition on snow grains and ice are discussed.


Assuntos
Simulação de Dinâmica Molecular , Naftalenos/química , Teoria Quântica , Neve/química , Propriedades de Superfície
18.
J Phys Chem A ; 115(23): 5973-82, 2011 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-21452834

RESUMO

We use molecular dynamics simulations to determine the melting point of ice I(h) for the polarizable POL3 water force field (Dang, L. X. J. Chem. Phys.1992, 97, 2659). Simulations are performed on a slab of ice I(h) with two free surfaces at several different temperatures. The analysis of the time evolution of the total energy in the course of the simulations at the set of temperatures yields the melting point of the POL3 model to be T(m) = 180 ± 10 K. Moreover, the results of the simulations show that the degree of hydrogen-bond disorder occurring in the bulk of POL3 ice is larger (at the corresponding degree of undercooling) than in ice modeled by nonpolarizable water models. These results demonstrate that the POL3 water force field is rather a poor model for studying ice and ice-liquid or ice-vapor interfaces. While a number of polarizable water models have been developed over the past years, little is known about their performance in simulations of supercooled water and ice. This study thus highlights the need for testing of the existing polarizable water models over a broad range of temperatures, pressures, and phases, and developing a new polarizable water force field, reliable over larger areas of the phase diagram.

19.
J Phys Chem A ; 115(23): 5895-9, 2011 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-21319857

RESUMO

The water-air interface plays a critical role in many physical and chemical processes of the Earth's atmosphere. In particular, heavy halide ions are strongly involved in processes of fundamental importance in determining the prevalence of many atmospheric components through heterogeneous reactions at the water-air interface. In this work, molecular dynamics simulations are used to study the halide enhancements at the water-air interface in the case of mixtures of Cl(-), Br(-), and I(-) ions. The results show a pattern of enhancement directly correlated to the anion polarizability. This effect is explained in terms of the charge distribution across the slab resembling an electrical double layer. As a result, the anions with higher polarizability lower the system's potential energy by enhancing their presence at the interface.


Assuntos
Halogênios/química , Sódio/química , Água/química , Ar , Modelos Moleculares , Simulação de Dinâmica Molecular , Sais/química , Soluções
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