scholarly journals Automating the IRC Analysis within Eyringpy

2021 ◽  
Author(s):  
Alan Quintal ◽  
Eugenia Dzib ◽  
Filiberto Ortíz ◽  
Pablo Jaque ◽  
Albeiro Restrepo Cossio ◽  
...  
Keyword(s):  
Chemical Property ◽  
Human Error ◽  
Dipole Moments ◽  
Reaction Force ◽  
Chemical Properties ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Data Set ◽  
Wiberg Bond Indices ◽  
Input Format

To analyze the evolution of a chemical property along the reaction path, we have to extract all the necessary information from a set of electronic structure computations. However, this process is time-consuming and prone to human error. Here we introduce IRC-Analysis, a new extension in Eyringpy, to monitor the evolution of chemical properties along the intrinsic reaction coordinate, including complete reaction force analysis. IRC-Analysis collects the entire data set for each point on the reaction coordinate, eliminating human error in data capture and allowing the study of several chemical reactions in seconds, regardless of the complexity of the systems. Eyringpy has a simple input format, and no programming skills are required. A tracer has been included to visualize the evolution of a given chemical property along the reaction coordinate. Several properties can be analyzed at the same time. This version can analysis the evolution of bond distances and angles, Wiberg bond indices, natural charges, dipole moments, and orbital energies (and related properties).

scholarly journals The reaction force: Three key points along an intrinsic reaction coordinate

2005 ◽  
Vol 117 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Peter Politzer ◽  
Alejandro Toro-Labbé ◽  
Soledad Gutiérrez-Oliva ◽  
Bárbara Herrera ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Reaction Force ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Key Points

scholarly journals New Insight into the Chloroacetanilide Herbicide Degradation Mechanism through a Nucleophilic Attack of Hydrogen Sulfide

2018 ◽  
Vol 19 (10) ◽  
pp. 2864 ◽  
Author(s):  
José Mora ◽  
Cristian Cervantes ◽  
Edgar Marquez
Keyword(s):  
Hydrogen Sulfide ◽  
Reaction Mechanism ◽  
Activation Barrier ◽  
Degradation Mechanism ◽  
Reaction Force ◽  
Transition States ◽  
Reaction Coordinate ◽  
Basis Sets ◽  
Nucleophilic Attack ◽  
Intrinsic Reaction Coordinate

The nucleophilic attack of hydrogen sulfide (HS−) on six different chloroacetanilide herbicides was evaluated theoretically using the dispersion-corrected hybrid functional wB97XD and the 6-311++G(2d,2p) Pople basis sets. The six evaluated substrates were propachlor (A), alachlor (B), metolachlor (C), tioacetanilide (D), β-anilide (E), and methylene (F). Three possible mechanisms were considered: (a) bimolecular nucleophilic substitution (SN2) reaction mechanism, (b) oxygen assistance, and (c) nitrogen assistance. Mechanisms based on O- and N-assistance were discarded due to a very high activation barrier in comparison with the corresponding SN2 mechanism, with the exception of compound F. The N-assistance mechanism for compound F had a free activation energy of 23.52 kcal/mol, which was close to the value for the corresponding SN2 mechanism (23.94 kcal/mol), as these two mechanisms could occur in parallel reactions with almost 50% of each one. In compounds A to D, an important electron-withdrawing effect of the C=O and C=S groups was seen, and consequently, the activation free energies in these SN2 reactions were smaller, with a value of approximately 18 kcal/mol. Instead, compounds E and F, which have a CH2 group in the β-position, presented a higher activation free energy (≈22 kcal/mol). Good agreement was found between experimental and theoretical values for all cases, and a reaction force analysis was performed on the intrinsic reaction coordinate profile in order to gain more details about the reaction mechanism. Finally, from the natural bond orbital (NBO) analysis, it was possible to evaluate the electronic reorganization through the reaction pathway where all the transition states were early in nature in the reaction coordinate (δBav < 50%); the transition states corresponding to compounds A to D turned out to be more synchronous than those for compounds E and F.

scholarly journals On the 3D → 2D Isomerization of Hexaborane(12)

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 28-38
Author(s):  
Josep M. Oliva-Enrich ◽  
Ibon Alkorta ◽  
José Elguero ◽  
Maxime Ferrer ◽  
José I. Burgos
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Transition States ◽  
Three Dimensional ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Limiting Factor ◽  
Two Dimensional ◽  
Axis Of Rotation

By following the intrinsic reaction coordinate connecting transition states with energy minima on the potential energy surface, we have determined the reaction steps connecting three-dimensional hexaborane(12) with unknown planar two-dimensional hexaborane(12). In an effort to predict the potential synthesis of finite planar borane molecules, we found that the reaction limiting factor stems from the breaking of the central boron-boron bond perpendicular to the C2 axis of rotation in three-dimensional hexaborane(12).

scholarly journals Optimization of the sampling scheme for maps of physical and chemical properties estimated by kriging

2013 ◽  
Vol 37 (5) ◽  
pp. 1128-1135 ◽  
Author(s):  
Gener Tadeu Pereira ◽  
Zigomar Menezes de Souza ◽  
Daniel De Bortoli Teixeira ◽  
Rafael Montanari ◽  
José Marques Júnior
Keyword(s):  
Soil Properties ◽  
Chemical Property ◽  
Chemical Properties ◽  
Sampling Scheme ◽  
Optimal Sampling ◽  
Sampling Schemes ◽  
Medium Scale ◽  
Chemical Soil ◽  
Physical And Chemical Property ◽  
Physical And Chemical

The sampling scheme is essential in the investigation of the spatial variability of soil properties in Soil Science studies. The high costs of sampling schemes optimized with additional sampling points for each physical and chemical soil property, prevent their use in precision agriculture. The purpose of this study was to obtain an optimal sampling scheme for physical and chemical property sets and investigate its effect on the quality of soil sampling. Soil was sampled on a 42-ha area, with 206 geo-referenced points arranged in a regular grid spaced 50 m from each other, in a depth range of 0.00-0.20 m. In order to obtain an optimal sampling scheme for every physical and chemical property, a sample grid, a medium-scale variogram and the extended Spatial Simulated Annealing (SSA) method were used to minimize kriging variance. The optimization procedure was validated by constructing maps of relative improvement comparing the sample configuration before and after the process. A greater concentration of recommended points in specific areas (NW-SE direction) was observed, which also reflects a greater estimate variance at these locations. The addition of optimal samples, for specific regions, increased the accuracy up to 2 % for chemical and 1 % for physical properties. The use of a sample grid and medium-scale variogram, as previous information for the conception of additional sampling schemes, was very promising to determine the locations of these additional points for all physical and chemical soil properties, enhancing the accuracy of kriging estimates of the physical-chemical properties.

scholarly journals COMPUTER CODES OF GEOCHEMICAL MODELING USED TO WATER-ROCK INTERACTION SIMPLE AND COMPLEX SYSTEMS

2019 ◽  
Vol 16 (32) ◽  
pp. 108-118
Author(s):  
Marcos Antônio KLUNK ◽  
Sudipta DASGUPTA ◽  
Mohuli DAS ◽  
Paulo Roberto WANDER
Keyword(s):  
Complex Systems ◽  
Geochemical Modeling ◽  
Chemical Properties ◽  
Coupled Transport ◽  
Burial History ◽  
Batch Mode ◽  
Data Set ◽  
Rock Interaction ◽  
Geochemical Reactions ◽  
Geochemical Models

The numerical modeling of transport and reaction was used for the understanding of the evolution of the diagenetic processes and their importance in the characterization and prediction of oil reservoir quality. Geochemical models are represented by numerical equations based on the physical-chemical properties of minerals. There are many software’s available in the market to simulate systems and geochemical reactions. The codes are divided into three distinct categories: coupled transport of reaction, modeling speciation, and batch mode according to the numerical method. Simple systems have clear connections between inputs and outputs. Complex systems have multiple factors that provide a probability distribution of data inputs that interact in specific functions. The outputs produced as a result are therefore impossible to predict with complete accuracy. Several research groups tried to develop numerical codes for geochemical modeling. The critical factors for the use of these systems are (i) verification of the simulation results with empirical data set and (ii) sensitivity analysis of these results, for the construction of general models which provide a predictive character. This last factor is particularly important as it establishes the qualitative and quantitative impact of each parameter in the simulations. Thus, with a complete numerical model diagenetic, it is possible to perform various simulations modifying one or the other parameter to test the sensitivity in the construction of these different geological scenarios. This set includes mineral composition and texture, the composition of fluids, paragenetic sequence, and burial history. This work brings fundamental concepts related to this topic as well as an analysis of commercial software available.

Reaction mechanism of 1,2-hydrogen migration of hydrogen peroxide

1990 ◽  
Vol 68 (5) ◽  
pp. 666-673 ◽  
Author(s):  
Enric Bosch ◽  
José M. Lluch ◽  
Juan Bertrán
Keyword(s):  
Hydrogen Peroxide ◽  
Reaction Mechanism ◽  
Water Molecule ◽  
Energy Barrier ◽  
Electron Distribution ◽  
Reaction Path ◽  
Bifunctional Catalyst ◽  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Hydrogen Migration

The 1,2-hydrogen migration of hydrogen peroxide has been investigated by abinitio methods and the Intrinsic Reaction Coordinate (IRC) has been constructed. An analysis of the evolution of the electron distribution along the reaction path has shown that the shifting hydrogen behaves as a proton. This transferring proton polarizes the O—O bond of the hydrogen peroxide that becomes broken at the transition state. If a water molecule is allowed to participate in the reaction, the energy barrier is noticeably lowered, this water molecule acting as a bifunctional catalyst. Keywords: 1,2-hydrogen migration, hydrogen peroxide, proton transfer, bifunctional catalyst, Intrinsic Reaction Coordinate.

ChemInform Abstract: Intrinsic Reaction Coordinate: Calculation, Bifurcation, and Automated Search

ChemInform ◽  
2016 ◽  
Vol 47 (4) ◽  
pp. no-no
Author(s):  
Satoshi Maeda ◽  
Yu Harabuchi ◽  
Yuriko Ono ◽  
Tetsuya Taketsugu ◽  
Keiji Morokuma
Keyword(s):  
Reaction Coordinate ◽  
Intrinsic Reaction Coordinate ◽  
Intrinsic Reaction Coordinate Calculation ◽  
Automated Search

Capillary Gas-Chromatographic Retention Behavior and Physico-Chemical Properties of Underivatized Equine Estrogens

1995 ◽  
Vol 60 (5) ◽  
pp. 813-819 ◽  
Author(s):  
Jasmina Novakovic ◽  
Eva Tvrzická ◽  
Václav Všetečka ◽  
Vladimír Pouzar ◽  
Ladislav Feltl
Keyword(s):  
Dipole Moments ◽  
Chemical Properties ◽  
Retention Indices ◽  
Chromatographic Retention ◽  
Retention Behavior ◽  
Kováts Retention Indices ◽  
Physico Chemical ◽  
In Series ◽  
Mixed Stationary Phase ◽  
Equine Estrogens

The capillary gas-chromatographic retention behavior of six underivatized equine estrogens (estrone, equilin, equilenin and their corresponding 17α-diols) on a mixed stationary phase (non-polar CP-Sil 5 CB and slightly polar CP-Sil 19 CB capillary columns coupled in series) was characterized by their Kovats retention indices and steroid numbers. In order to find whether a correlation exists between the chromatographic retention and some physico-chemical properties of the compounds, their octanol-water partition coefficients and dipole moments were measured. No straightforward correlation was observed between the physico-chemical properties and the retention behavior, which suggests that the GC separation of equine estrogens is governed by some specific electron donor-electron acceptor interactions of a chemical nature.

scholarly journals Two years of near real-time chemical composition of submicron aerosols in the region of Paris using an Aerosol Chemical Speciation Monitor (ACSM) and a multi-wavelength Aethalometer

2015 ◽  
Vol 15 (6) ◽  
pp. 2985-3005 ◽  
Author(s):  
J.-E. Petit ◽  
O. Favez ◽  
J. Sciare ◽  
V. Crenn ◽  
R. Sarda-Estève ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Real Time ◽  
Chemical Speciation ◽  
Chemical Properties ◽  
Temporal Variations ◽  
Mitigation Strategies ◽  
Chemical Information ◽  
Data Set ◽  
Pollution Episodes

Abstract. Aerosol mass spectrometer (AMS) measurements have been successfully used towards a better understanding of non-refractory submicron (PM1) aerosol chemical properties based on short-term campaigns. The recently developed Aerosol Chemical Speciation Monitor (ACSM) has been designed to deliver quite similar artifact-free chemical information but for low cost, and to perform robust monitoring over long-term periods. When deployed in parallel with real-time black carbon (BC) measurements, the combined data set allows for a quasi-comprehensive description of the whole PM1 fraction in near real time. Here we present 2-year long ACSM and BC data sets, between mid-2011 and mid-2013, obtained at the French atmospheric SIRTA supersite that is representative of background PM levels of the region of Paris. This large data set shows intense and time-limited (a few hours) pollution events observed during wintertime in the region of Paris, pointing to local carbonaceous emissions (mainly combustion sources). A non-parametric wind regression analysis was performed on this 2-year data set for the major PM1 constituents (organic matter, nitrate, sulfate and source apportioned BC) and ammonia in order to better refine their geographical origins and assess local/regional/advected contributions whose information is mandatory for efficient mitigation strategies. While ammonium sulfate typically shows a clear advected pattern, ammonium nitrate partially displays a similar feature, but, less expectedly, it also exhibits a significant contribution of regional and local emissions. The contribution of regional background organic aerosols (OA) is significant in spring and summer, while a more pronounced local origin is evidenced during wintertime, whose pattern is also observed for BC originating from domestic wood burning. Using time-resolved ACSM and BC information, seasonally differentiated weekly diurnal profiles of these constituents were investigated and helped to identify the main parameters controlling their temporal variations (sources, meteorological parameters). Finally, a careful investigation of all the major pollution episodes observed over the region of Paris between 2011 and 2013 was performed and classified in terms of chemical composition and the BC-to-sulfate ratio used here as a proxy of the local/regional/advected contribution of PM. In conclusion, these first 2-year quality-controlled measurements of ACSM clearly demonstrate their great potential to monitor on a long-term basis aerosol sources and their geographical origin and provide strategic information in near real time during pollution episodes. They also support the capacity of the ACSM to be proposed as a robust and credible alternative to filter-based sampling techniques for long-term monitoring strategies.

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