Reaction Energy Values Research Articles

(2S)-2-(Difluoro(methoxy)methyl)pyrrolidine-1-sulfinyl fluoride as a new reagent in the Cl/F exchange reactions with aryl and alkyl sulfonyl chlorides

The reaction of (2S)-2-(difluoro(methoxy)methyl)pyrrolidine-1-sulfinyl fluoride with aryl, heteryl and alkyl sulfonyl chlorides provides a convenient synthetic route to sulfonyl fluorides. DFT calculations predict negative reaction energy values for the exchange reaction. The S-F bond energy is higher in the sulfonyl fluorides than that in sulfinyl fluorides.

DFT mechanistic study of [4+2] cycloaddition reactions of 1-methyl-1H-pyrrole-2,5-dione with furoic acid, anticancer Activity, molecular modeling and ADMET properties of new products from the Norcantharimide family substituted by a carboxylic acid

The [4+2] cycloaddition reactions of 1-methyl-1H-pyrrole-2,5-dione, with furan-2-carboxylic acid, 5-methylfuran-2-carboxylic acid and 5 -(hydroxymethyl)-furan-2-Carboxylic acid have been studied using various theoretical approaches at the M06/6–311++G(d,p) level of theory. Conceptual DFT (CDFT) analysis shows that 1-methyl-1H-pyrrole-2,5-dione behaves as an electrophile and furan-2-carboxylic acid, 5-methylfuran-2-carboxylic acid and 5 -(hydroxymethyl)-furan-2-Carboxylic acid act as nucleophiles. Furthermore, the regioselectivity has been explored from the Parr functions and Houk's rule. The studied DA reactions followed a one-step mechanism presenting a polar character where the formation of the new bonds takes place according to an asynchronous process. The activation and reaction energy values, extracted from the energetic profile plots, allow us to determine the most favorable reaction pathway. Moreover, the topology of the electronic localization function (ELF) in specific points of the intrinsic reaction coordinate profile (IRC) associated with the most favorable reaction pathway makes it possible to highlight a non-concerted two stages one-step molecular mechanism. The valorization of the anticancer activity of six products from the Norcantharimide family substituted by carboxylic acids has been carried out using molecular docking calculations. It has been shown, for the first time, that these products are efficient against breast cancer. Finally, the physicochemical properties and medicinal potential of these products were evaluated using the SwissADME online tool, revealing that they lack toxicity and their potential as promising drug candidates.

Effects of External Electric Field on the Hydrolysis of Cisplatin: A Density Functional Theory Approach

In this study, hydrolysis of the anticancer drug cis-PtCl2(NH3)2 complex in the absence and presence of external electric field (EEF) has been studied using quantum mechanical methods. The B3P86 functional and basis sets of 6-311G(d,p) and LANL2DZ for main group element and Pt atoms, respectively, have been employed in these calculations. Two typical reactions involved in the complex hydrolysis include the first and second hydrolysis processes. We have tried to show how the total energy, barrier energy, thermodynamic, and kinetic parameters of cisplatin hydrolysis have been affected by the external electric field. In addition, variations of the structural parameters have been illustrated in the absence and presence of EEF. The structural-properties correlations between these parameters and strength of EEF have been provided. In addition, the barrier energy and reaction energy values of hydrolysis processes have been calculated by applying the isodensity polarizable continuum model (IPCM) for aqueous phase.

A comparative experimental and density functional study of glucose adsorption and electrooxidation on the Au-graphene and Pt-graphene electrodes

At present, the graphene is covered on Cu foil with the 5 sccm hexane (C6H14) flow rate, 50 sccm hydrogen (H2) flow rate, and 20 min deposition time parameters by the CVD method. The graphene on the Cu foil is then covered onto few-layer ITO electrode. Furthermore, the Pt and Au metals are electrodeposited on graphene/ITO electrode with electrochemical method. These electrodes are characterized by Raman spectroscopy and Scanning Electron Microscopy-Energy Dispersive X-Ray analysis (SEM-EDX). The graphene structure is approved via Raman analysis. Au, Pt, and graphene network are openly visible from SEM results. In addition, glucose (C6H12O6) electrooxidation is investigated with cyclic voltammetry (CV), chronoamperometry (CA), and electrochemical impedance spectroscopy (EIS) measurements. As a result, Pt-graphene/ITO indicates the best C6H12O6 electrooxidation activity with 9.21 mA cm−2 specific activity (highly above the values reported in the literature). In all electrochemical measurements, Pt-graphene/ITO exhibits best electrocatalytic activity, stability, and resistance compared to the other electrodes. The adsorption of the C6H12O6 molecule is examined theoretically over metal atom (gold and platinum)-doped graphene surfaces using the density functional theory (DFT) method. The interaction between C6H12O6 molecule and OH adsorbed Pt-doped surface is stronger than that of OH adsorbed Au-doped graphene surface thermodynamically according to the reaction energy values.

Dual Bond Enhanced Multidimensional Constructed Composite Silicon Anode for High-Performance Lithium Ion Batteries.

The development of silicon-based anode materials is important for improving the energy density of current lithium ion batteries. However, there are still strong demands for these materials with better cycle stability and higher reversible capacity. Here, a kind of dual bond restricted MXene-Si-CNT composite anode materials with enhanced electrochemical performance is reported. These dual bonds have been clearly revealed by an X-ray photoelectron spectroscopy technique and also proven by theoretical calculations with spontaneous reaction energy values (-0.190 and -0.429 eV/atom for Ti-Si and C-Si bonds, respectively). The cycle stability of the composites, prepared by a facile ball-milling synthetic method, can obviously be improved because of the existence of these dual bonds and the multidimensional constructed architecture. The MXene-Si-CNT composite with 60 wt % silicon possesses the best overall performance, with ∼80% capacity retention after 200 cycles, and achieves 841 mAh g-1 at 2 A g-1. This approach demonstrates a promising strategy to exploit high-performance anode materials and lessens the immanent negative effect of silicon-based materials. Furthermore, it is significant to extend this method to other anode materials with serious volumetric change problems during the cycling process.

Molecular hydrogen formation in the interstellar medium: the role of polycyclic aromatic hydrocarbons analysed by the reaction force and activation strain model

The formation of H2 onto pyrene (from hydrogen atoms) was studied in the framework of the Eley–Rideal mechanism, which was fully analysed for all the adsorption sites of pyrene. The structural and electronic contributions to the activation energies were characterized through the reaction force and activation strain model (ASM). The reaction force indicates that the activation process of the hydrogen chemisorption is dominated by the structural rearrangements of reactants rather than by electronic reordering. Furthermore, the ASM shows that the structural rearrangements are driven by the approach of hydrogen to the pyrene surface, which generates a strong repulsive interaction. However, the changes in the geometry of the surface generate a minimal increase of the total energy, being negligible at the absorption sites at the edge of the surface. For that reason, the process is most kinetically favoured at the edge sites, which have lower activation energies (∼1–3 kcal mol–1) than the internal ones (∼6 kcal mol–1). On the other hand, the recombination of hydrogen atoms for the subsequent H2 formation is a barrier-less process, no matter the adsorption site of the carbonaceous surface. The ASM analysis shows that the attractive interactions take place at the beginning of the recombination process, they avoid that the energy barrier can be generated by structural distortions. Both the chemisorption and the abstraction of the adsorbed hydrogen atom by an incoming H atom, throughout the entire surface, are highly exoenergetic processes, with reaction energy values in the range of −12 to −36 kcal mol–1 and −84 to −60 kcal mol–1, respectively.

Theoretical study of chemisorption of hydrogen atoms on (5, 5) silicon carbide nanotubes with and without Stone-Wales defects

The adsorption of one hydrogen atom on the surface of (5, 5) single-walled silicon carbide nanotube (SiCNT) and (5, 5) SiCNTs with two types of Stone-Wales defects (labeled as SW1 and SW2) has been investigated employing density functional theory. The reaction energy values for the hydrogenation at various sites were obtained at the UB3LYP/6-31G∗ level. It is shown that hydrogen can chemically adsorb on carbon sites or silicon sites on pristine (5, 5) SiCNT, with the reaction energies ranging from −34.7 to −36.6kcal/mol. The introduction of a SW defect on the (5, 5) SiCNT shows an enhanced interaction of hydrogen with the defective SiCNTs compared to that with the pristine SiCNT. The computed reaction energies range from −39.9 to −67.9kcal/mol for (5, 5) SW1 and from −33.6 to −69.8kcal/mol for (5, 5) SW2 SiCNTs. Furthermore, the adsorption of two hydrogen atoms has also been explored. It is found that the system is more energetically favorable for both perfect and SW defective (5, 5) SiCNTs. The electronic properties analysis indicates that single hydrogen atom chemisorption can reduce the HOMO-LUMO gap of corresponding nanotubes, but not for double hydrogen chemisorbed SW defective nanotube.

Designing graphene as a new frustrated Lewis pair catalyst for hydrogen activation by co-doping.

Boron and nitrogen co-doped bilayer graphene (BN-G) and graphene ribbon (BN-GR) as Frustrated Lewis Pair (FLP) catalysts are investigated for hydrogen molecule activation. The nitrogen and boron atoms are separated as they are in different layers of BN-G/GR. Calculations show that this novel FLP catalyst is capable of activating hydrogen molecules. From the Bader charge, Mayer bond order, and the geometrical structures, it can be seen that the hydrogen molecules undergo heterolytic scission and have a late product-like transition state. More interestingly, the active sites are identified as being the carbon atoms around dopants for BN-G. The BN-G/GR catalysts deliver performances comparable to that of the reported FLP catalyst when considering their barrier and reaction energy values. The current work demonstrates the great potential of doped carbon catalysts as FLP catalysts and paves the way to nanostructured carbon catalyst applications in reactions by directly utilizing hydrogen molecules.

Evaluation and synthesis of AZT prodrugs with optimized chemical stabilities: experimental and theoretical analyses

The design of prodrugs of nucleoside reverse transcriptase inhibitors (NRTIs) constitutes a promising strategy to overcome several suboptimal pharmacotherapeutic properties of these kinds of drugs, among which zidovudine (AZT) is the most studied example. The chemical stability of prodrugs is a critical issue in the context of their pharmacotherapeutic performance since it constitutes a key event in the reconversion of the bioactive NRTIs. In this study, five prodrugs of AZT and lamivudine (3TC) were studied by means of DFT and classical molecular dynamics (MD) strategies in order to model the reaction coordinates involved in their chemical hydrolysis, and extend these conclusions to further structure rationalization of prodrugs. Therefore, the inclusion of explicit water molecules was found to be of great relevance to the mentioned reaction coordinates since it allowed a very good correlation between calculated reaction energy values and the corresponding hydrolysis constants. Based on these findings, three ester based prodrugs of AZT were designed, synthesized and evaluated regarding their chemical stability. These prodrugs exhibited optimized chemical stabilities when compared to the previously reported AZT prodrugs, which may result in an enhanced pharmacotherapeutic performance. In conclusion, the developed theoretical model provides a valuable assistance in the design and development of novel prodrugs of NTRIs with rationalized chemical stabilities.

Reaction pathways and transition states of the C-C and C-H bond cleavage in the aromatic pyrenemolecule - A Density Functional study

The activation and reaction energies of the C-C and C-H bonds cleavage in pyrene molecule are calculated applying the Density Functional Theory and 6-311G Gaussian basis. Different values for the energies result for the different bonds, depending on the location of the bond and the structure of the corresponding transition states. The C-C bond cleavage reactions include H atom migration, in many cases, leading to the formation of CH 2 groups and H-C≡C- acetylenic fragments. The activation energy values of the C-C reactions are greater than 190.00 kcal/mol for all bonds, those for the C-H bonds are greater than 160.00 kcal/mol. The reaction energy values for the C-C bonds range between 56.497 to 191.503 kcal/mol. As for the C-H cleavage reactions the activation energies range from 163.535 to 165.116 kcal/mol, the reaction energies are nearly constant, 117.500kcal/mol. The geometries of the transition states and reaction products are discussed too.

Reactivity of the interior surface of (5,5) single-walled carbon nanotubes with and without a Stone–Wales defect

The adsorption of hydrogen and fluorine atoms on the interior surface of defect-free and Stone–Wales defect armchair (5,5) single-walled carbon nanotubes were investigated using density functional theory. The reaction energy values for the hydrogenation and fluorination at all the possible unique sites were obtained at the UB3LYP/6-31G* level. The calculated reaction energy values were used to corroborate the reactivities of different sites on the interior surface of SWCNTs. The results indicate that for defect-free nanotube, endohedral adsorption is rather unfavorable both for hydrogen and fluorine. The computed exothermicities range from 4.8 to 13.4kcal/mol for hydrogenation and from 16.6 to 23.2kcal/mol for fluorination. However, the introduction of a SW defect on the (5,5) SWCNT improves the chemical reactivity of the interior surface of the defected tube. The computed exothermicities for the endohedral hydrogen and fluorine atoms are within the ranges of 7.0–33.4 and 18.5–41.8kcal/mol, respectively. The most exothermic and reactive site on the interior surface of SW defective (5,5) SWCNT is the C2 site shared by two seven-membered rings and one five-membered ring. This is different from the results reported on the reactivity of the exterior surface of SW defective nanotubes. The electronic and vibrational properties of the (5,5) SWCNTs with adsorption of hydrogen and fluorine atoms on the interior surface were also explored.

Surface Reactivity for Chlorination on Chlorinated (5,5) Armchair SWCNT: A Computational Approach

In the present work, we first attached one chlorine radical and then examined the site selectivity for the addition of a second chlorine radical on the external surface of (5,5) armchair single-walled carbon nanotubes (SWCNTs) of 9 and 15 carbon layers. Optimized geometries and energetics were determined using density functional theory (DFT), at the M06-2X/6-31G(d,p) level. Computed reaction energy values for second chlorination have been used to corroborate the prediction of the reactivities of different sites based on the electron density distribution in the singly occupied molecular orbital (SOMO), total spin density, the DFT based local reactivity descriptors (viz., Fukui function, local softness), and the average local ionization energy. Natural bond orbital (NBO) analysis was performed to confirm the covalent bonding between the chlorine and carbon of the SWCNT. The present study reveals that the first chlorine attached to the SWCNT behaves like an ortho- and para-director. The addition of a second chlorine on an already chlorinated SWCNT exhibits positional preference.

Reaction mechanism of hydrogenation and direct desulfurization routes of dibenzothiophene‐like compounds: A density functional theory study

AbstractReaction mechanisms of the two distinct routes, namely hydrogenation (HYD) and direct desulfurization (DDS), of dibenzothiophene (DBT)‐type compounds in hydrodesulfurization (HDS) process have been investigated by means of density functional theory (DFT). A series of methyl‐ and dimethyl‐compounds substituted at different positions in DBT were compared to get a deeper insight into the electronic effects of the alkyl position substitution. The Gibbs energy of reaction for each route and the CS bond energies were calculated. The calculations showed that HYD route is more exergonic than DDS route. Refractory compounds exhibited less reaction energy values and high CS bond stability. Full chemical structures in the energetic profile of HYD and DDS routes were identified. We proposed a reaction mechanism for each HDS route based on our theoretical calculations. According to our proposed mechanisms, the HYD reaction route is favored compared to DDS reaction route because energetic barriers are higher on the DDS route. The effect of methyl groups is clearly observed. Refractory compounds have higher activation and lower formation energies. This systematic study trough DFT method provides an important contribution in the field of HDS because the proposed mechanisms are related with some experimental observations. © 2012 Wiley Periodicals, Inc.

Computational Modeling of the Catalytic Mechanism of Human Placental Alkaline Phosphatase (PLAP)

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Quantum mechanical, molecular dynamics, and molecular docking techniques were applied to computationally model the catalytic mechanism of human placental AP (PLAP). Kinetic and thermodynamic evaluations were performed for each reaction step. The functional significances of the more important residues within the active site were analyzed. The role of the metal ion at the metal binding site M3 was also examined. The calculated activation and reaction energy and free energy values obtained suggested the nucleophilic attack of the Ser92 alkoxide on the phosphorus atom of the substrate would be the rate-limiting step of the catalytic hydrolysis of alkyl phosphate monoesters by PLAP. The reactivities of the wild-type M3-Mg enzyme and the M3-Zn protein were compared, and the main difference observed was a change in the coordination number of the M3 metal for the M3-Zn enzyme. This modification in the active site structure lowered the free energy profile for the second chemical step of the catalytic mechanism (hydrolysis of the covalent phosphoserine intermediate). Consequently, a greater stabilization of the phosphoseryl moiety resulted in a small increment in the activation free energy of the phosphoserine hydrolysis reaction. These computational results suggest that the activation of APs by magnesium at the M3 site is caused by the preference of Mg(2+) for octahedral coordination, which structurally stabilizes the active site into a catalytically most active conformation. The present theoretical results are in good agreement with previously reported experimental studies.

Ion [C5H5O]+ formation in the electron-impact mass spectra of 4-substituted N-(2-furylmethyl)anilines. Relative abundance prediction ability of the DFT calculations

Six 4-substituted N-(2-furylmethyl)anilines have been studied by electron ionization (EI) mass spectrometry. The heterolytic dissociation of the C–N bond of the molecular ions was proposed as the route to the main fragment ion in the mass spectra, [C5H5O]+ (m/z=81). Reaction energies for this process were calculated at UB3LYP/6-31G(d,p) and UHF/6-31G(d,p) levels of theory. DFT calculations produced reaction energy values that showed very good correlation with the logarithms of the peak intensity ratios for the [C5H5O]+ and [M]+ ions. Linear regression yielded an equation, which could be used to calculate the intensity ratio [C5H5O]+/[M]+, with an error <10%, from both the analogous ratio in a known mass spectrum and theoretical reaction energies.

Competitive Diels−Alder Reactions: Cyclopentadiene and Phospholes with Butadiene

Diene-dienophile competing Diels-Alder reaction pathways of cyclopentadiene, 1H-, 2H- and 3H-phospholes with butadiene were explored at the B3LYP level using 6-31G(d) and 6-311+G(d,p) basis sets, and at the CCSD(T)/6-31G(d)//B3LYP/6-31G(d) level. Activation barriers show that cyclopentadiene favors a diene rather than a dienophile conformation. Pathways 1 and 2 (A and B) corresponding to butadiene as the diene and dienophile are predicted to be highly competitive in the case of 1H-phosphole. Secondary orbital interactions and the preferable bispericyclic nature of transition states are responsible for the stability of endo transition states. The study indicates that some of the transition states are bispericyclic and most of them are highly asynchronous. The reactions require a lower activation energy when the conversion of weak C=P to C-P occurs in the case of 2H- and 3H-phospholes. The high stability of the products resulting via path 1 can be attributed to the less strain in the bicyclo[4.3.0]nonadiene skeleton compared to the norbornene derivatives obtained from path 2. Activation and reaction energy values for these Diels-Alder reaction pathways are compared with the values reported for the [4+2] cyclodimerizations of each of the reactants to examine the likelihood of cyclodimerizations along these pathways.

Pseudorotation Barriers of Biological Oxyphosphoranes: A Challenge for Simulations of Ribozyme Catalysis

Pseudorotation reactions of biologically relevant oxyphosphoranes were studied by using density functional and continuum solvation methods. A series of 16 pseudorotation reactions involving acyclic and cyclic oxyphosphoranes in neutral and monoanionic (singly deprotonated) forms were studied, in addition to pseudorotation of PF5. The effect of solvent was treated by using three different solvation models for comparison. The barriers to pseudorotation ranged from 1.5 to 8.1 kcal mol(-1) and were influenced systematically by charge state, apicophilicity of ligands, intramolecular hydrogen bonding, cyclic structure and solvation. Barriers to pseudorotation for monoanionic phosphoranes occur with the anionic oxo ligand as the pivotal atom, and are generally lower than for neutral phosphoranes. The OCH3 groups were observed to be more apicophilic than OH groups, and hence pseudorotations that involve axial OCH3/equatorial OH exchange had higher reaction and activation free energy values. Solvent generally lowered barriers relative to the gas-phase reactions. These results, together with isotope 18O exchange experiments, support the assertion that dianionic phosphoranes are not sufficiently long-lived to undergo pseudorotation. Comparison of the density functional results with those from several semiempirical quantum models highlight a challenge for new-generation hybrid quantum mechanical/molecular mechanical potentials for non-enzymatic and enzymatic phosphoryl transfer reactions: the reliable modeling of pseudorotation processes.

Atomistic simulation of the surface structure of wollastonite and adsorption phenomena relevant to flotation

Atomistic simulation techniques have been used to calculate the surface structure and stability of wollastonite crystal and its adsorption behaviour in the presence of molecular and dissociated water, and two widely used collector head group molecules of methanoic acid and methylamine. Seven predominant surfaces have been modelled and their calculated surface energies correspond well with their preferred morphological domination. Surfaces are identified having fourfold and threefold coordination of surface silicon. Threefold surface silicon are stabilized by addition of hydroxyl ion on them and proton on surface oxygen. Stable surfaces thus obtained are subjected to surface Ca 2+ replacement by 2H + by transforming 2O 2− to 2OH −. Surface energy and reaction energy values indicate wollastonite surface stabilized to a great extent by adsorbing water in dissociated form. The Ca 2+ replacement from the first few layers of the surface is energetically more favourable in acidic condition. Three Miller indexed surfaces terminating with fully coordinated silicon were reconstructed to make the surface free of lone oxygen, and these surface cuts were chosen to carry out simulation work for adsorption of molecules. A comparison of surface energies revealed that all the surfaces become stabilized in the presence of added molecules but the presence of methylamine decreases surface energy to lowest values. Adsorption of dissociated water is preferred by {100} and {102} surfaces, while {001} surface adsorbs methylamine strongly as the results show highly negative adsorption energies. In terms of pure molecule adsorption, the preferred adsorption sequence for all the surfaces is methylamine>methanoic acid>water. For {100} and {102} predominant surfaces, the difference in adsorption energy values is not much and we conclude that the collectors having long-chain hydrophobic alkyl chain, the two head group molecules considered, cannot render enough hydrophobicity due to inadequate adsorption on wollastonite. Thus the presence of activators/modifiers in actual wollastonite flotation practice is substantiated.

Atomistic simulation of the surface structure of wollastonite

Abstract Atomistic simulation techniques have been used to calculate the surface structure and stability of wollastonite crystal. Seven predominant surfaces have been modelled and their calculated surface energy corresponds well with their morphological domination. The surface energy, hydration energy and reaction energy values indicate wollastonite surfaces stabilized to great extent by adsorbing water in dissociated form. The Ca 2+ replacement from the first few layers of the surface is found to be energetically more favourable, elucidating high dissolution phenomena of wollastonite mineral.

Determination of reaction energy values for biological pyrite oxidation by calorimetry

The reaction energy values for pyrite oxidation by chemolithotrophic leaching bacteria (pure cultures of Thiobacillus ferrooxidans, Leptospirillum ferrooxidans, and mixed cultures of L. ferrooxidans and T. thiooxidans) were calorimetrically measured in batch experiments. The obtained data were compared with the nonconservative values for the corresponding abiotic processes that were calculated from standard enthalpies and chemical analyses of the leaching products. Due to the different abilities of the investigated species to oxidize the sulphur moiety of pyrite, the measured reaction energy values ranged from −1100 to −1600 kJ/mol with an accuracy of 4–16%. In samples with T. ferrooxidans and with the mixed cultures, no significant difference between the calorimetric and theoretical reaction energy values occurred. In contrast, pure cultures of L. ferrooxidans exhibited measured values which were up to 200 kJ/mol lower than the theoretical ones. It is highly unlikely that this difference may be explained by a higher energy conservation efficiency of L. ferrooxidans compared to the one of T. ferrooxidans or T. thiooxidans. Besides use in efficiency studies, the collected data can be used to determine the activity of leaching bacteria in natural biotopes by calorimetric measurements.