scholarly journals Detection and identification of Criegee intermediates from the ozonolysis of biogenic and anthropogenic VOCs: comparison between experimental measurements and theoretical calculations

2017 ◽  
Vol 200 ◽  
pp. 559-578 ◽  
Author(s):  
Chiara Giorio ◽  
Steven J. Campbell ◽  
Maurizio Bruschi ◽  
Alexander T. Archibald ◽  
Markus Kalberer
Keyword(s):  
Density Functional ◽  
Spin Trap ◽  
Theoretical Calculations ◽  
Reaction System ◽  
Molecular Structures ◽  
Chemical Mechanism ◽  
Experimental Measurements ◽  
Reaction Products ◽  
Criegee Intermediates ◽  
Wide Range

Ozonolysis of alkenes is a key reaction in the atmosphere, playing an important role in determining the oxidising capacity of the atmosphere and acting as a source of compounds that can contribute to local photochemical “smog”. The reaction products of the initial step of alkene-ozonolysis are Criegee intermediates (CIs), which have for many decades eluded direct experimental detection because of their very short lifetime. We use an innovative experimental technique, stabilisation of CIs with spin traps and analysis with proton transfer reaction mass spectrometry, to measure the gas phase concentration of a series of CIs formed from the ozonolysis of a range of both biogenic and anthropogenic alkenes in flow tube experiments. Density functional theory (DFT) calculations were used to assess the stability of the CI-spin trap adducts and show that the reaction of the investigated CIs with the spin trap occurs very rapidly except for the large β-pinene CI. Our measurement method was used successfully to measure all the expected CIs, emphasising that this new technique is applicable to a wide range of CIs with different molecular structures that were previously unidentified experimentally. In addition, for the first time it was possible to study CIs simultaneously in an even more complex reaction system consisting of more than one olefinic precursor. Comparison between our new experimental measurements, calculations of stability of the CI-spin trap adducts and results from numerical modelling, using the master chemical mechanism (MCM), shows that our new method can be used for the quantification of CIs produced in situ in laboratory experiments.

First-Principles Studies of the Magnetic Properties of hcp Cr in Cr/Cu(111) and Cr/Ru(0001) Superlattices

2002 ◽  
Vol 721 ◽  
Author(s):  
G. Y. Guo
Keyword(s):  
First Principles ◽  
Density Functional ◽  
Recent Observation ◽  
Theoretical Calculations ◽  
Ferromagnetic State ◽  
Full Potential ◽  
Generalized Gradient ◽  
Plane Wave Method ◽  
Wide Range ◽  
Linearized Augmented Plane Wave

AbstractLatest first-principles density functional theoretical calculations using the generalized gradient approximation and highly accurate all-eleectron full-potential linearized augmented plane wave method, show that bulk hcp Cr would be a paramagnet and that no ferromagnetic state could be stabilized over a wide range of volume [1]. To understand the recent observation of the weakly ferromagnetic state of Cr in hcp Cr/Ru (0001) superlattices [2], the same theoretical calculations have been carried out for the hcp Cr3/Ru7 (0001) and hcp Cr3/fcc Cu6 (111) superlattices. The Cr/Ru superlattice is found to be ferromagnetic with a small magnetic moment of ∼0.31μB/Cr while in contrast, Cr/Cu superlattice is found to be nonmagnetic.

Interaction mechanisms and structural properties of B-, Si-doped C60 fullerenes with 1-formylpiperazine

2016 ◽  
Vol 39 (5-6) ◽  
Author(s):  
Cemal Parlak ◽  
Özgür Alver ◽  
Ponnadurai Ramasami
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Interaction Mechanism ◽  
Potential Interaction ◽  
Binding Energies ◽  
Molecular Structures ◽  
Interaction Mechanisms ◽  
Wide Range ◽  
Si Doped ◽  
Physical And Chemical

AbstractPiperazines and fullerene nanocages are versatile compounds. These are discussed in a wide range of academic work, especially in the field of medicine, and considered for various applications by the pharmaceutical industry. In the present research, the potential interaction mechanisms between B-, Si-doped C60 and 1-formylpiperazine (1-fp) were examined within the framework of density functional theory, along with their optimized molecular structures and electronic properties. The calculated binding energies and various other physical and chemical parameters of 1-fp found in this work in comparison with the Si- and B-doped fullerenes suggest that doping of fullerene nanocage leads to a strong interaction mechanism that alters the chemical and electronic properties of the investigated compounds. This finding can be used as a guide for their further applications.

scholarly journals Mesomorphic, Optical and DFT Aspects of Near to Room-Temperature Calamitic Liquid Crystal

Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1044
Author(s):  
Ayman A. Zaki ◽  
Mohamed Hagar ◽  
Rua B. Alnoman ◽  
Mariusz Jaremko ◽  
Abdul-Hamid Emwas ◽  
...  
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Theoretical Calculations ◽  
Fatty Acid Derivative ◽  
Molecular Structures ◽  
Resonance Spectroscopy ◽  
Scanning Calorimetry ◽  
Stable Conformer ◽  
Geometrical Isomers ◽  
Theoretical Approaches

A new liquid crystalline, optical material-based Schiff base core with a near to room-temperature mesophase, (4-methoxybenzylideneamino)phenyl oleate (I), was prepared from a natural fatty acid derivative, and its physical and chemical properties investigated by experimental and theoretical approaches. The molecular structure was confirmed by elemental analysis, FT-IR (Fourier-Transform-Infrared Spectroscopy) and NMR (nuclear magnetic resonance) spectroscopy. Optical and mesomorphic activities were characterized by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The results show that compound (I) exhibits an enantiotropic monomorphic phase comprising a smectic A phase within the near to room-temperature range. Ordinary and extraordinary refractive indices as well as birefringence with changeable temperatures were analyzed. Microscopic and macroscopic order parameters were also calculated. Theoretical density functional theory (DFT) calculations were carried out to estimate the geometrical molecular structures of the prepared compounds, and the DFT results were used to illustrate the mesomorphic results and optical characteristics in terms of their predicted data. Three geometrical isomers of the prepared compound were investigated to predict the most stable isomer. Many parameters were affected by the geometrical isomerism such as aspect ratio, planarity, and dipole moment. Thermal parameters of the theoretical calculations revealed that the highest co-planar aromatic core is the most stable conformer.

scholarly journals Hg2+-Promoted Spirolactam Hydrolysis Reaction: A Design Strategy for the Highly Selective Sensing of Hg2+ over other Metal Ions in Aqueous Media

Sensors ◽  
2019 ◽  
Vol 19 (1) ◽  
pp. 128 ◽  
Author(s):  
Mai Bay ◽  
Nguyen Hien ◽  
Subin Son ◽  
Nguyen Trinh ◽  
Nguyen Trung ◽  
...  
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Aqueous Media ◽  
Colorimetric Method ◽  
Hydrolysis Reaction ◽  
Experimental Investigations ◽  
Reaction Products ◽  
Before And After ◽  
Excitation Processes

A mercury sensor (N-(rhodamine-6G)lactam-ethylenediamine-4-dimethylamino-cinnamaldehyde—RLED) based on the Hg2+-promoted hydrolysis reaction has been designed and developed with a combination of theoretical calculations and experimental investigations. The interaction between RLED and Hg2+ goes through a fast-initial stage with formation of a 1:1 complex, followed by a slow hydrolysis process. The formation of durable intermediate complexes is due to quite a long hydrolysis reaction time. As a result, RLED can selectively detect Hg2+ in the presence of other metal ions, with a detection limit of 0.08 μM for the colorimetric method, and of 0.008 μM with the fluorescent method. In addition, the RLED sensor can work in a solution with a small amount of organic solvent, with a wide pH range from 5 to 10. The time-dependent density functional theory has been used for investigations of the excitation and de-excitation processes in RLED, intermediate complexes, and reaction products, thereby clarifying the changes in the fluorescence intensity before and after the RLED interacts with Hg2+ ions.

scholarly journals Atomic Structure, Electronic and Mechanical Properties of Pyrophyllite under Pressure: A First-Principles Study

Minerals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 778
Author(s):  
Xinzhan Qin ◽  
Jian Zhao ◽  
Jiamin Wang ◽  
Manchao He
Keyword(s):  
Mechanical Properties ◽  
High Pressure ◽  
Atomic Structure ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Electronic Density ◽  
Functional Theory ◽  
Wide Range ◽  
Pressure Transmission ◽  
Pressure Synthesis

Pyrophyllite is extensively used in the high-pressure synthesis industry as a pressure-transmitting medium because of its outstanding pressure transmission, machinability, and insulation. Therefore, the atomic structure, electronic, and mechanical behavior of pyrophyllite [Al4Si8O20(OH)4] under high pressure should be discussed deeply and systematically. In the present paper, the lattice parameters, bond length, the electronic density of states, band structure, elastic constants, and mechanical parameters of pyrophyllite are investigated using density functional theory (DFT) from a microscopic perspective. The pressure dependence of atomic structure, electronic, and mechanical properties of pyrophyllite is analyzed for a wide range of pressure (from 0 GPa to 13.87 GPa). Under high pressure, the major bond lengths and layer thicknesses decrease slightly, and mechanical properties are improved with increasing pressure. The calculated electronic and band structures show only a slight change with increasing pressure, implying that the effect of pressure on the electronic property of pyrophyllite is weak, and pyrophyllite still has good stability under high pressure. The theoretical calculations presented here clarify the electronic and mechanical properties of natural pyrophyllite that are difficult to obtain experimentally because of their small particle size.

scholarly journals Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

2015 ◽  
Vol 11 ◽  
pp. 1865-1875 ◽  
Author(s):  
Biljana M Šmit ◽  
Radoslav Z Pavlović ◽  
Dejan A Milenković ◽  
Zoran S Marković
Keyword(s):  
Density Functional Theory ◽  
Double Bond ◽  
Density Functional ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Reaction Products ◽  
Dft Methods ◽  
Functional Theory ◽  
H Nmr ◽  
Good Agreement

The mechanism and selectivity of a bicyclic hydantoin formation by selenium-induced cyclization are investigated. The proposed mechanism involves the intermediates formed by an electrophilic addition of the selenium reagent on a double bond of the starting 5-alkenylhydantoin prior the cyclization. These intermediates are readily converted into the more stable cyclic seleniranium cations. A key step of the mechanism is an intramolecular cyclization which is realized through an anti-attack of the internal nucleophile, the amidic nitrogen, to the seleniranium cation yielding the intermediate imidazolinium cations. Their deprotonation is followed by the formation of the fused bicyclic reaction products. Important intermediates and key transition states are studied by using density functional theory (DFT) methods. The pathways of the reaction are investigated in detail. There are two regioselective pathways related to 5-exo and 6-endo products. Theoretical calculations and the monitoring of the cyclization reaction using 1H NMR spectroscopy are in a good agreement with the proposed mechanism and are consistent with our experimental results. The preferred pathway for formation of 5-exo products is confirmed.

High-resolution electron spectroscopy and molecular structures of Cu–(2,2′-bipyridine) and Cu-(4,4′-bipyridine)

2013 ◽  
Vol 91 (7) ◽  
pp. 613-620 ◽  
Author(s):  
Xu Wang ◽  
Jung Sup Lee ◽  
Dong-Sheng Yang
Keyword(s):  
Ground State ◽  
Metal Binding ◽  
Electron Spectroscopy ◽  
Density Functional ◽  
Copper Complexes ◽  
Theoretical Calculations ◽  
Molecular Structures ◽  
Laser Vaporization ◽  
Binding Modes ◽  
Mp2 Calculations

Copper complexes of 2,2′-bipyridine (22BIPY) and 4,4′-bipyridine (44BIPY) were prepared in a laser-vaporization supersonic molecular beam source and identified by laser photoionization time-of-flight mass spectrometry. Electronic spectra and molecular structures were studied with pulsed-field ionization zero electron kinetic energy (ZEKE) electron spectroscopy, density functional theory (DFT) and second-order Møller–Plesset perturbation (MP2) calculations, and spectral simulations. Adiabatic ionization energies and metal–ligand and ligand-based vibrational frequencies of Cu–22BIPY and Cu–44BIPY were measured from the ZEKE spectra. Ground electronic states and molecular structures of the two complexes were determined by comparing the spectroscopic measurements with the theoretical calculations. The ground state of Cu–22BIPY ( 2 B1, C2v) has a planar bidentate structure with Cu binding to two nitrogen atoms and two pyridine molecules in the cis configuration. The ground state of Cu–44BIPY ( 2 A, C2) has a monodentate structure with Cu binding to one nitrogen and two pyridines in a twisted configuration. The ionization energy of Cu–22BIPY is considerably lower and its bond energy is much higher than that of Cu–44BIPY. The different ionization and dissociation energies are attributed to the distinct metal binding modes of the two complexes. It has been found that the DFT calculations yield the correct structures for the Cu–22BIPY complex, whereas the MP2 calculations produce the best structures for the Cu–44BIPY complex.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions ◽  
The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

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