10 research outputs found

    SN2 Reactions with an Ambident Nucleophile: A Benchmark Ab Initio Study of the CN-+ CH3Y [Y = F, Cl, Br, and I] Systems

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    We characterize the Walden-inversion, front-side attack, and double-inversion SN2 pathways leading to Y- + CH3CN/CH3NC and the product channels of proton abstraction (HCN/HNC + CH2Y-), hydride-ion substitution (H- + YH2CCN/YH2CNC), halogen abstraction (YCN-/YNC- + CH3 and YCN/YNC + CH3-), and YHCN-/YHNC- complex formation (YHCN-/YHNC- + 1CH2) of the CN- + CH3Y [Y = F, Cl, Br, and I] reactions. Benchmark structures and frequencies are computed at the CCSD(T)-F12b/aug-cc-pVTZ level of theory, and a composite approach is employed to obtain relative energies with sub-chemical accuracy considering (a) basis-set effects up to aug-cc-pVQZ, (b) post-CCSD(T) correlation up to CCSDT(Q), (c) core correlation, (d) relativistic effects, and (e) zero-point energy corrections. C-C bond formation is both thermodynamically and kinetically more preferred than N-C bond formation, though the kinetic preference is less significant. Walden inversion proceeds via low or submerged barriers (12.1/17.9(F), 0.0/4.3(Cl), -3.9/0.1(Br), and -5.8/-1.8(I) kcal/mol for C-C/N-C bond formation), front-side attack and double inversion have high barriers (30-64 kcal/mol), the latter is the lower-energy retention pathway, and the non-SN2 electronic ground-state product channels are endothermic (ΔH0 = 31-92 kcal/mol). © 2022 The Authors. Published by American Chemical Society

    Large and multi scale mechanistic modeling of Diels-Alder reactions

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    The [4+2] cycloaddition reaction between conjugated dienes and substituted alkenes is known as the Diels-Alder (DA) reaction, in honor of two German chemists, Otto Diels and Kurt Alder, who first reported this marvelous chemical transformation. The DA reaction is one of the most popular reactions in organic chemistry, allowing for the regio- and stereospecific establishment of six-membered rings with up to four stereogenic centers. This pericyclic reaction has found many applications in areas as diverse as natural products chemistry, polymer chemistry, and agrochemistry. Over the past decades, the mechanism of the Diels-Alder (DA) reaction has been the subject of numerous studies, dealing with questions as diverse as the mechanistic pathway, the synchronicity, the use of catalysts, the effect of solvents and salts, etc. On the other hand, as an example, fullerenes (and particularly [60] fullerene) have been found to act as good dienophiles in DA reactions to the extent that many functionalized fullerenes with interesting applications are still synthesized by reacting C60 with dienes. However, despite the very abundant literature about the mechanism of the DA reaction, some pertinent questions have been still pending, including, without being restricted to, the prediction of transition state (TS) geometries and the modeling of DA reactions involving large systems, such as those of C60 fullerene. It must be emphasized that TSs are not easy to predict and the main reason is that many existing algorithms require that the search is initiated from a good starting point (guess TS), which must be very similar to the actual TS. This problem is even more difficult when many TSs are to be located as may be the case in large-scale studies. Moreover, due to the large size of the C60 molecule, the usage of accurate high-level computational methods in the investigation of its reactivity towards dienes is computationally costly, implying the need to find the best threshold between accuracy and computational cost. Therefore, the present study was carried out to contribute to solving the problems of large-scale prediction of DA transition state geometries and the multi-scale modeling of C60 fullerene DA reactions. To address the first problem (large-scale prediction of TSs), we have developed a python program named “AMADAR”, which predicts an unlimited number of DA transition states, using only the SMILES strings of the cycloadducts. AMADAR is customizable and allows for the description of intramolecular DA reactions as well as systems resulting in competing paths. In addition, The AMADAR tool contains two separate modules that perform reaction force analyses and atomic decomposition of energy derivatives from the predicted Intrinsic Reaction Coordinates (IRC) paths. The performance of AMADAR was assessed using 2000 DA cycloadducts and showed a success rate of ~ 95%. Most of the errors were due to basis set inconsistencies or convergence issues that we are still working on. Furthermore, a set of 150 IRC paths generated by the AMADAR program were analyzed to get insight into the (a)synchronicity of DA reactions. This investigation confirmed that the reaction force constant (second derivatives of the system energy with respect to the reaction coordinate) was a good indicator of synchronicity in DA reactions. A close inspection of the profile of has enabled us to propose an alternative classification of DA reactions based on their synchronicity degree, in terms of (quasi)-synchronous, moderate asynchronous, asynchronous, and likely two-steps DA reactions. Natural population analyses seemed to indicate that the global maximum of the reaction force constant could be identified with the formation of all the bonds in the reaction site. Finally, the atomic resolution of energy derivatives suggested that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each C-C bond. A striking mechanistic difference between synchronous and asynchronous DA reactions emerging from this study is that, in asynchronous reactions, the driving and retarding forces are mainly caused by the fast and slow-forming bonds (elementary process) respectively, while in the case of synchronous ones both elementary processes retard and drive the process concomitantly and equivalently. Regarding the DA reaction of C60 fullerene that was considered to illustrate the problem of multiscale modeling, we have constructed 12 ONIOM2 and 10 ONIOM3 models combining five semi-empirical methods (AM1, PM3, PM3MM, PDDG, PM6) and the LDA(SVWN) functional in conjunction with the B3LYP/6-31G(d) level. Then, their accuracy and efficiency were assessed in comparison with the pure B3LYP/6-31G(d) level considering first the DA reaction between C60 and cyclopentadiene whose experimental data are available. Further, different DFT functionals were employed in place of the B3LYP functional to describe the higher-layer of the best ONIOM partition, and the results obtained were compared to experimental data. At this step, the ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model, where the higher layer encompasses the diene and pyracyclene portion of C60, was found to provide the best tradeoff between accuracy and cost, with respect to experimental data. This model showed errors lower than 2.6 and 2.0 kcal/mol for the estimation of the activation and reaction enthalpies respectively. We have also demonstrated, by comparing several ONIOM2(DFT/6-31G(d): SVWN/STO-3G) models, the importance of dispersion corrections in the accurate estimation of reaction and activation energies. Finally, we have considered a set of 21 dienes, including anthracene, 1,3-butadiene, 1,3-cyclopentadiene, furan, thiophene, selenothiophene, pyrrole and their mono-cyano and hydroxyl derivatives to get insight into the DA reaction of C60 using the best ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model. For a given diene and its derivatives, the analysis of frontier molecular orbitals provides a consistent explanation for the substituent effect on the activation barrier. It revealed that electron-donating (withdrawing) groups such as -OH (–CN) cut down on the activation barrier of the reaction by lowering (extending) of the HOMOdiene – LUMOC60 gap and consequently enhancing (weakening) the interaction between the two reactants. Further, the decomposition of the activation energy into the strain and interaction components suggested that, for a given diene, electron-donating groups (here –OH) diminish the height of the activation barrier not only by favoring the attractive interaction between the diene and C60, but also by reducing the strain energy of the system; the opposite effect is observed for electron-withdrawing groups (here –CN). In contrast with some previous findings on typical DA reactions, we could not infer any general rule applicable to the entire dataset for the prediction of activation energies because the latter does not correlate well with either of the TS polarity, electrophilicity of the diene, or the reaction energy.Thesis (MSc) -- Faculty of Science, Chemistry, 202

    Predicting and Understanding Binding Affinities of Synthetic Anion Receptors

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    Anion receptors are molecules that can recognise and bind anions. They have applications in organocatalysis, anion sensing and the removal of anions from wastewater. Some anion receptors are also able to transport anions across cell membranes and show promise for the treatment of diseases such as cystic fibrosis and cancer. As such, it is of interest to develop computational methods that can reliably predict the physicochemical properties and anion binding affinities of these molecules. However, efforts to computationally model these molecules are hampered by the sheer size of typical receptors, making them too expensive to treat using accurate quantum chemical methods. Whilst efficient approximations such as local-correlation methods have been developed, the broader accuracy of these methods, particularly in their application to ionic non-covalent systems remains unclear. To address this gap, this thesis has carried out an extensive validation of local-correlation methods, and economical density functional theory (DFT) methods for receptors with different binding motifs. Additionally, multiscale models have also been examined with the view to extending the scope of these methods to model very large anion receptors. DFT methods giving good agreement with highly accurate calculations at a fraction of the cost were identified. The use of semiempirical methods combined with DFT in a multiscale model for calculating anion binding affinities lead to unexpectedly large errors with modest savings of computational time, while some "three-fold corrected" methods show promise in reducing the cost of geometry optimisations of large receptors. These validated protocols were subsequently applied to investigate the structure-binding relationships of a wide range of dual-hydrogen bonding receptors. Notably, different receptor motifs were found to have different conformational preferences, which could explain why experimentally, thioureas, thiosquaramides and croconamides show weaker chloride binding affinities than would be expected based on their acidity. The results suggest that pre-organising anion receptors in the conformer that facilitates hydrogen bond formation could be a promising strategy for the development of anion receptors. It is envisaged that these findings will aid in the design and screening of novel anion receptors with increased binding affinity and selectivity

    Laser Pulses

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    This book discusses aspects of laser pulses generation, characterization, and practical applications. Some new achievements in theory, experiments, and design are demonstrated. The introductive chapter shortly overviews the physical principles of pulsed lasers operation with pulse durations from seconds to yoctoseconds. A theory of mode-locking, based on the optical noise concept, is discussed. With this approximation, all paradoxes of ultrashort laser pulse formation have been explained. The book includes examples of very delicate laser operation in biomedical areas and extremely high power systems used for material processing and water purification. We hope this book will be useful for engineers and managers, for professors and students, and for those who are interested in laser science and technologies

    The structure and rheological properties of liquified natural gas gelled with water and methanol clathrates

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    Thesis. 1977. Ph.D.--Massachusetts Institute of Technology. Dept. of Chemical Engineering.Microfiche copy available in Archives and Science.Bibliography : leaves 414-426.by Lucile M. Shanes.Ph.D

    Rare Earth Elements analysis to identify anthropogenic signatures at Valle del Serpis (Spain) Neolithic settlements

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    Due to their particular geochemical properties and stability Rare Earth Elements (REE) can act as a ‘fingerprint’ for soils, and as a consequence have been employed in a variety of different archaeological scenarios in order to identify past human activities.In this study, for the first time, we apply REE signatures in different Spanish Neolithic settlements, all located in the Valle del Serpis region. More than 100 Neolithic settlements have been identified in this area, and most of these open sites are characterised by dark brown strata that are in contrast with the light brown soils of the valley. These dark brown deposits are usually covered by paleosols and have been interpreted as markers of anthropogenic activities. However, in order to demonstrate whether these strata are anthropogenic or natural features requires a better understand-ing of soil development processes. A total of fifty samples were taken across six different sites, and from each site the sam-pling was carried out at different depths through 3m deep sections. Four sites are clearly associated with archaeological findings (sites BF, LP, PB and AC); another one is from a natural section near the Neolithic site of Mas d’Is (MD) and has been radiocarbon dated to the beginning of the Holocene (7751-7611 cal BC); and the last corresponds to a place of uncertain attribution (BK). Major, minor and trace elements including REE were determined using XRF and ICP- MS, with Principal Components Analysis (PCA) used to statistically analyze these data. Results were then compared with the strata soil properties analysed by XRD and particle size analysis, and cross-referenced with archaeological data to aid interpretation. The results demonstrate that REE analyses provide significant details regarding anthropogenic activities and strata development history, and in this instance confirm and elaborate on the archaeological interpretation that these dark brown deposits are evidence of a region-wide agricultural system in the Neolithic Valle del Serpis

    The source of the building stones from the Sagunto Castle archaeological area and its surroundings

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    A multidisciplinary study was carried out on the building stones of the masonries belonging to the Castle of Sagunto (Valencia, Spain), an important historical and archeological complex, characterized by several construction phases from the Roman Period to the Modern Ages. For the first time, the stones of the Sagunto Castle have been analysed to determine their chemical, mineralogical and petrographic features, the main physical and mechanical properties, and to understand their decay, use and recycling dynamics in the different building during the entire occupational period. Geochemical and mineralogical analyses employing X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry (ICP-MS) and X-ray diffraction (XRD) were carried out together with optical and electronic microscope analysis to observe the stone macro- and micro-structures. The collected data were processed by Principal Component Analysis (PCA) to highlight differences among the studied structures. The results show that the stones employed to build Sagunto`s structures during the different historical periods are related to a specific quarried area located nearby Sagunto Castle hill and differences between the studied samples are mostly related to the conservation state of the buildings. Therefore, geochemical analyses confirm the origin of the raw materials, while petrographic and physical analyses have been useful to evaluate the conservation state of the studied Sagunto Castle structures
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