Simulating the Relaxation Dynamics of Microwave-Driven Zeolites

Combariza, Aldo F.; Sullivan, E.P.A.; Auerbach, Scott M.; Blanco, Cristian

doi:10.1021/jp0524680

Cited by 7 publications

(6 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…130 In interesting follow-up work on zeolite microwave heating, Combariza et al performed NEMD simulations on relaxation of ionic and dipolar phases in FAU-type zeolites, finding bi-exponential relaxation. 133 Fast-decay times were found to increase with an increase in the initial temperature difference between microwave-heated ions/dipoles and the equilibrium system. Kinetic-energy correlation functions were also found to show strong bi-exponential behaviour, indicative of a two-step heating mechanism with initial, efficient energy transfer mediated by strongly anharmonic zeolite-guest forces, followed by a slower process dominated by weaker coupling amongst normal modes in the zeolite framework.…”

Section: Heatingmentioning

confidence: 96%

“…Kinetic-energy correlation functions were also found to show strong bi-exponential behaviour, indicative of a two-step heating mechanism with initial, efficient energy transfer mediated by strongly anharmonic zeolite-guest forces, followed by a slower process dominated by weaker coupling amongst normal modes in the zeolite framework. 133 Jobic et al carried out further NEMD simulation of microwave heating in silicalites, along with quasielastic neutron scattering measurements, finding selective heating of methanol, but little heating of benzene. 134 Effective translational and rotational temperatures were extracted from experimental, and rotational temperatures were found to significantly exceed translational ones at high microwave power, in accord with NEMD, 134 giving microscopic proof for athermal effects in microwave-driven nanopores as suggested in earlier pure-NEMD work.…”

Section: Heatingmentioning

confidence: 99%

“…134 Effective translational and rotational temperatures were extracted from experimental, and rotational temperatures were found to significantly exceed translational ones at high microwave power, in accord with NEMD, 134 giving microscopic proof for athermal effects in microwave-driven nanopores as suggested in earlier pure-NEMD work. 130,133…”

Section: Heatingmentioning

confidence: 99%

See 2 more Smart Citations

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

English

Waldron

2015

Phys. Chem. Chem. Phys.

222

216

View full text Add to dashboard Cite

In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.

show abstract

Section: Heatingmentioning

confidence: 96%

Section: Heatingmentioning

confidence: 99%

See 1 more Smart Citation

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

English

Waldron

2015

Phys. Chem. Chem. Phys.

222

216

View full text Add to dashboard Cite

show abstract

“…The awe-inspiring development of computational performance in the last decades has open the door to a new way of doing science, which is usually referred as computational experimentation or in silico experimentation. [1][2][3] In general, an in silico experiment begins by modeling a real system using solid theoretical physical principles, followed by the simulation of the system through computer programmed mathematical algorithms. [3][4][5] In this work, we use a hybrid ab initio/mechano-statistical technique to study the features of biological macromolecules, proteins, and their interactions with low molecular weight chemical species, called ligands.…”

Section: Introductionmentioning

confidence: 99%

Ligand-Protein Interactions: A Hybrid ab initio/Molecular Mechanics Computational Study

Yr¹,

Álvarez²,

Combariza³

2019

Preprint

View full text Add to dashboard Cite

The enzymes Cyclooxygenase (COX) or prostaglandin-endoperoxide synthase (PTGS) are important in the synthesis of prostaglandins, which are the main mediating chemi- cals at inflammatory processes. The body produces two highly homologous COX isoforms, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2). COX-1 is involved in the pro- duction of prostaglandins which take part in physiological processes such as: protection of the gastric epithelium, maintenance of renal flow, platelet aggregation, neutrophil mi- gration and also expressed in the vascular endothelium; Meanwhile COX-2 is inducible by proinflammatory stimuli. To counteract the symptoms of inflammation, nowadays is very frequent the use of nonsteroidal antiinflammatory drugs (NSAIDs); These drugs in addi- tion to other benefits, can also cause side effects on people’s health (cardiovascular and respiratory problems, in the nervous system, among others). Due to the above, it is neces- sary to accelerate the investigations that allow to know in more detail the mechanisms of action that involve the use of natural plant products as pharmacological agents. In the pre- sent research, computational techniques are used, especially those based on the Molecular Docking Method to know the proteinligand interaction in systems of biological interest. It was possible to determine the structure-activity relationship in inflammatory processes involving the participation of a number of secondary plant metabolites such as luteolin, galangin, kaempferol, apigenin, morine and quercetin on the inactivation of the enzyme cyclooxygenase (COX-1 and COX -2). In the COX-1 / ligand coupling it was found that apigenin was the ligand which showed the lowest coupling energy with a value of -8.88, whereas quercetin showed the highest value (-6.65); for the coupling COX-2 / ligand the apigenin also showed the lowest energy value (-8.93), while kaempferol showed the highest value (-7.51). This shows that apigenin is the ligand with the best stability within the active site of both enzymes. On the other hand, quercetin showed the highest relative selectivity with a protein-ligand selectivity index (PLSI) of 1.17, while kaempferol showed an PLSI of 0.91. Taking into account the parameters of stability and selectivity we can say that of all the ligands used, quercetin would be the ideal to block COX-2.

show abstract

“…The awe-inspiring development of computational performance in the last decades has open the door to a new way of doing science, which is usually referred as computational experimentation or in silico experimentation. [1][2][3] In general, an in silico experiment begins by modeling a real system using solid theoretical physical principles, followed by the simulation of the system through computer programmed mathematical algorithms. [3][4][5] In this work, we use a hybrid ab initio/mechanical-statistical technique to study the features of biological macromolecules, proteins, and their interactions with low molecular weight chemical species, called ligands.…”

Section: Introductionmentioning

confidence: 99%

Ligand-Protein Interactions: A Hybrid ab initio/Molecular Mechanics Computational Study

Perez¹,

Alvarez²,

Combariza³

2019

Preprint

View full text Add to dashboard Cite

Cyclooxygenases (COX), or prostaglandin endoperoxide synthases (PTGS), are key enzimes in the synthesis of prostaglandins, which are chemical species critical in mediating inflammatory processes. There are two highly homologous COX isoforms: COX-1 and COX-2. COX-1 is involved in the production of prostaglandins, chemical compuounds that take part in physiological processes such as: protection of the gastric epithelium, maintenance of renal flow, platelet aggregation, neutrophil migration and, also, are expressed in the vascular endothelium. Meanwhile, COX-2 is induced by proinflammatory stimuli. It is very frequent the use of nonsteroidal antiinflammatory drugs (NSAIDs) to counteract the symptoms of inflammatory processes. These drugs, in addition to its benefits, can cause side effects on people’s health, such as cardiovascular and respiratory problems, among others. In the past years, it has been recognized the potential of plants secondary metabolites as pharmacological agents, prompting the need for investigations that shed light into its mechanism of action. In this work we have applied computational techniques, based on quantum chemistry and mechanical statistics, to study the protein-ligand interaction involving COX’s and secondary metabolites from natural sources. Our aim is to determine the structure activity interplay in processes involving the participation of secondary plant metabolites such as luteolin, galangin, kaempferol, apigenin, morine and quercetin on the inactivation of COX’s. From molecular docking analysis, we have extracted the energetics of the COX-(1,2)/metabolite coupling. By defining energy based factors, we have determined a procedure that predicts the chemical species with highest stability and selectivity towards inactivation of COX-2 over COX-1. The results are discussed with regard to conformational features of the selected ligands and its intermolecular strong/weak interactions inside the active-sites of the COX’s hosts.

show abstract

Simulating the Relaxation Dynamics of Microwave-Driven Zeolites

Cited by 7 publications

References 35 publications

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

Ligand-Protein Interactions: A Hybrid ab initio/Molecular Mechanics Computational Study

Ligand-Protein Interactions: A Hybrid ab initio/Molecular Mechanics Computational Study

Contact Info

Product

Resources

About