Daniel Severance
Yale University, Chemistry, Alumnus
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Abstract The fully optimized transition states for hydrogen abstraction from methane by formaldehyde and acetaldehyde have been computed using UMP2/6-31G(d)//6-31G(d) calculations. The geometry of the formaldehyde/methane transition state... more
Abstract The fully optimized transition states for hydrogen abstraction from methane by formaldehyde and acetaldehyde have been computed using UMP2/6-31G(d)//6-31G(d) calculations. The geometry of the formaldehyde/methane transition state matches well with the geometry obtained previously using the 3-21G basis set, but the energy is lowered somewhat (18.7 versus 22 kcal/mol, respectively). Approach of the methane trans-periplanar (i.e. anti) to the acetaldehyde methyl group leads to a transition state similar to that for formaldehyde (saddle point at 17.9 kcal/mol). Approach syn to the methyl group leads to a modest variation in both the saddle point geometry and energy (19.1 kcal/mol), both attributed to unfavorable steric interactions in this trajectory.
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An all atom model of benzene has been developed and tested. It was used in potential of mean force (PMF, free energy vs benzene center-center distance) calculations to determine the K$\sb{a}$ for benzene dimers in water and chloroform. It... more
An all atom model of benzene has been developed and tested. It was used in potential of mean force (PMF, free energy vs benzene center-center distance) calculations to determine the K$\sb{a}$ for benzene dimers in water and chloroform. It was found that the free energy minimum in all solvents corresponds to a T-shaped benzene dimer, not pi-stacked, even in water. The OPLS parameters for butyrolactam and succinimide were used to investigate the experimental preference of lactam dimerization over imide dimerization. By computing the free energy difference between the 3 possible, the experimental trends were reproduced and was further shown to be due to bad secondary coulombic interactions. Furthermore, the higher binding of imides to adenine relative to lactams was also reproduced and explained. Potential functions for the ground state and two transition states of dimethylacetamide (DMA) were developed and used to study solvation effects on the barrier to rotation. It was found that in the gas phase, the two transition states differ by about 4 kcal/mol, but in solution they become nearly isoenergetic. The results in carbon tetrachloride show a much smaller solvent effect than previous experimental data. The Claisen rearrangement is studied using the ab initio minimum energy reaction path and charges fit to the electrostatic potential surface. The solvent stabilization is 3.85 kcal/mol, and is shown to result from enhanced water hydrogen bonding in the transition state. The effects of molecular shape are also discussed
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... 5307-5363. (3) Bauld, N. L. Aduances in Electron Transfer Chemistry; Mariano. P. M., Ed.; JAI Press: Greenwich, CT, 1992; Vol. 2, pp 1-66. (4) Steams, R. A.; Ortiz de Montellano. PRJ Am. Chem. Soc. ... Chem. Soc. 1990, 112, (IO)... more
... 5307-5363. (3) Bauld, N. L. Aduances in Electron Transfer Chemistry; Mariano. P. M., Ed.; JAI Press: Greenwich, CT, 1992; Vol. 2, pp 1-66. (4) Steams, R. A.; Ortiz de Montellano. PRJ Am. Chem. Soc. ... Chem. Soc. 1990, 112, (IO) Calhoun, GC; Schuster, GBJ Am. Chem. Soc. ...
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Results A. Photochemistry of exo-Benzobicyclo [2.2. 2] octen-2-yl Chloride (exo-BBCl). Synthesis. The title compound was prepared by the reaction sequence given in eq 2.6 The exo and endo isomers are formed in a 5545 ratio and were... more
Results A. Photochemistry of exo-Benzobicyclo [2.2. 2] octen-2-yl Chloride (exo-BBCl). Synthesis. The title compound was prepared by the reaction sequence given in eq 2.6 The exo and endo isomers are formed in a 5545 ratio and were separated by preparative GLC. ...
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ABSTRACT
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Research Interests: Engineering, Chemistry, Monte Carlo Simulation, Chemical Physics, Very Low Frequency Electromagnetics, and 14 moreElectron Transfer, Time of Flight, Physical sciences, Van Der Waals, Electron Density, Hydrogen Bond, CHEMICAL SCIENCES, Ionization, Ionization Potential, Chemical Reaction, Benzene, Aqueous Solution, Molecule, and Mass Spectrometer
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A combination of quantum and statistical mechanics is being used to probe the origins of solvent effects on the kinetics of organic reactions. Ab initio molecular orbital calculations provide gas-phase reaction paths and partial charges... more
A combination of quantum and statistical mechanics is being used to probe the origins of solvent effects on the kinetics of organic reactions. Ab initio molecular orbital calculations provide gas-phase reaction paths and partial charges for the reacting systems. The reaction paths are then followed by Monte Carlo simulations in periodic cells containing hundreds of solvent molecules, and the changes in Gibbs free energies of solvation are obtained. Results are provided for several prototypical pericyclic reactions : Diels–Alder cycloadditions for methyl vinyl ketone with cyclopentadiene and the dimerization of cyclopentadiene, the Claisen rearrangement of allyl vinyl ether, and the electrocyclic ring opening of cyclopropanones to oxyallyls. Detailed insights are obtained on issues such as the acceleration of the Diels–Alder reactions and Claisen rearrangement in water, and the electronic nature of oxyallyls.
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Adsorption of Sulfur Containing Molecules on Gold: The ... Effect of Oxidation on Monolayer Formation and Stability ... Robin L. Garrell,"" Janice E. Chadwick: Daniel L. Severance3 Nora A. McDonald3 and David C. Myles*,*... more
Adsorption of Sulfur Containing Molecules on Gold: The ... Effect of Oxidation on Monolayer Formation and Stability ... Robin L. Garrell,"" Janice E. Chadwick: Daniel L. Severance3 Nora A. McDonald3 and David C. Myles*,* ... Contribution from the Department of Chemistry ...
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Monte Carlo statistical mechanics simulations have been carried out for Cl− and Na+ in clusters of 1–14 water molecules. OPLS potential functions were used including the TIP4P model of water that do not include explicit polarization... more
Monte Carlo statistical mechanics simulations have been carried out for Cl− and Na+ in clusters of 1–14 water molecules. OPLS potential functions were used including the TIP4P model of water that do not include explicit polarization effects. In contrast to a prior report with the same potential functions, the computed enthalpies of binding for Cl− are shown to agree closely with experimental data, while the values for Na+ are about 10% too exothermic. The latter discrepancy is largely removed by using Aqvist’s Na+ parameters with TIP3P water. Moreover, the structures of the clusters show the expected nonspherical distribution of water molecules.
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Intermolecular potential functions have been developed for urea. Ab initio 6–31G(d) calculations were performed on urea-water complexes to obtain interaction energies and hydrogen-bond lengths that were used in developing the partial... more
Intermolecular potential functions have been developed for urea. Ab initio 6–31G(d) calculations were performed on urea-water complexes to obtain interaction energies and hydrogen-bond lengths that were used in developing the partial charges for the OPLS model. An important test was made by computing through Monte Carlo simulations the difference in chloroform/water partition coefficients for urea and acetamide, Δ log P. The accord between the computed result from statistical perturbation theory for TIP4P water and OPLS chloroform (2.0 ± 0.1 ) and the experimental value (1.9) is excellent. The computed absolute free energy of hydration of acetamide (-9.5 ± 0.4 kcal/mol) also matches the experimental data at 25 °C (-9.68 kcal/mol). These facts provide confidence in the computed value of −13.6 ± 0.4 kcal/mol for the absolute free energy of hydration of urea, an experimentally unavailable result. The water structure around urea and acetamide was also characterized; the average numbers of solute-water hydrogen bonds are 5 for urea and 3–4 for acetamide.
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... Chem. SOC. 1990, 11 2, 4168-4114 Aromatic-Aromatic Interactions: Free Energy Profiles for the ... Interactions between aromatic rings are emerging as significant elements that can influence the stereochemistry of organic... more
... Chem. SOC. 1990, 11 2, 4168-4114 Aromatic-Aromatic Interactions: Free Energy Profiles for the ... Interactions between aromatic rings are emerging as significant elements that can influence the stereochemistry of organic re-actions,' binding affinities in host-guest chemistry? ...
Research Interests: Chemistry, Data Analysis, Monte Carlo Simulation, Face to Face, Icon, and 14 moreFree Energy, CHEMICAL SCIENCES, Mathematical Model, Altmetrics, Benzene, ICON, Aqueous Solution, Experimental Data, Physical Properties, Organic Compound, Thermodynamic Properties, Monte Carlo Method, The American, and Chloroform
The association of benzene with itself, urea, guanidinium ion, and tetramethylammonium ion has been studied in water via Monte Carlo statistical mechanics simulations. Benzene dimerization in chloroform and liquid benzene have also been... more
The association of benzene with itself, urea, guanidinium ion, and tetramethylammonium ion has been studied in water via Monte Carlo statistical mechanics simulations. Benzene dimerization in chloroform and liquid benzene have also been considered as well as the association of urea with naphthalene in water. Calculations of potentials of mean force predict complexes to exist in each case at contact separations. The energetics and optimal structures for the gas-phase complexes have also been characterized. Differences with the solution structures are discussed along with general implications for host-guest chemistry.
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ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full... more
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
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An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely... more
An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Abstract The fully optimized transition states for hydrogen abstraction from methane by formaldehyde and acetaldehyde have been computed using UMP2/6-31G(d)//6-31G(d) calculations. The geometry of the formaldehyde/methane transition state... more
Abstract The fully optimized transition states for hydrogen abstraction from methane by formaldehyde and acetaldehyde have been computed using UMP2/6-31G(d)//6-31G(d) calculations. The geometry of the formaldehyde/methane transition state matches well with the geometry obtained previously using the 3-21G basis set, but the energy is lowered somewhat (18.7 versus 22 kcal/mol, respectively). Approach of the methane trans-periplanar (i.e. anti) to the acetaldehyde methyl group leads to a transition state similar to that for formaldehyde (saddle point at 17.9 kcal/mol). Approach syn to the methyl group leads to a modest variation in both the saddle point geometry and energy (19.1 kcal/mol), both attributed to unfavorable steric interactions in this trajectory.
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EZH2 (enhancer of zeste homologue 2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2) that catalyzes the methylation of lysine 27 of histone H3 (H3K27). Dysregulation of EZH2 activity is associated with several human... more
EZH2 (enhancer of zeste homologue 2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2) that catalyzes the methylation of lysine 27 of histone H3 (H3K27). Dysregulation of EZH2 activity is associated with several human cancers and therefore EZH2 inhibition has emerged as a promising therapeutic target. Several small molecule EZH2 inhibitors with different chemotypes have been reported in the literature, many of which use a bicyclic heteroaryl core. Herein, we report the design and synthesis of EZH2 inhibitors containing an indoline core. Partial saturation of an indole to an indoline provided lead compounds with nanomolar activity against EZH2, while also improving solubility and oxidative metabolic stability.
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Adsorption of Sulfur Containing Molecules on Gold: The ... Effect of Oxidation on Monolayer Formation and Stability ... Robin L. Garrell,"" Janice E. Chadwick: Daniel L. Severance3 Nora A. McDonald3 and David C. Myles*,*... more
Adsorption of Sulfur Containing Molecules on Gold: The ... Effect of Oxidation on Monolayer Formation and Stability ... Robin L. Garrell,"" Janice E. Chadwick: Daniel L. Severance3 Nora A. McDonald3 and David C. Myles*,* ... Contribution from the Department of Chemistry ...
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Knowledge Bank. Search Knowledge Bank. Advanced Search. Home. About the Knowledge Bank Go. Browse. Communities & Collections. Issue Date. ...
... Erin M. Duffy, Daniel L. Severance, and William L. Jorgensen* Contribution from the Department of Chemistry, Yale University, New Haven, Connecticut ... Benson's prescription was followed with estimated barriers of 0 and... more
... Erin M. Duffy, Daniel L. Severance, and William L. Jorgensen* Contribution from the Department of Chemistry, Yale University, New Haven, Connecticut ... Benson's prescription was followed with estimated barriers of 0 and 1.8 kcal/mol for the N-methyl rotations in the ground and ...
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... 5307-5363. (3) Bauld, N. L. Aduances in Electron Transfer Chemistry; Mariano. P. M., Ed.; JAI Press: Greenwich, CT, 1992; Vol. 2, pp 1-66. (4) Steams, R. A.; Ortiz de Montellano. PRJ Am. Chem. Soc. ... Chem. Soc. 1990, 112, (IO)... more
... 5307-5363. (3) Bauld, N. L. Aduances in Electron Transfer Chemistry; Mariano. P. M., Ed.; JAI Press: Greenwich, CT, 1992; Vol. 2, pp 1-66. (4) Steams, R. A.; Ortiz de Montellano. PRJ Am. Chem. Soc. ... Chem. Soc. 1990, 112, (IO) Calhoun, GC; Schuster, GBJ Am. Chem. Soc. ...
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Spectroscopic measurements of C6H6-(CH3OH) sub n clusters are reported with an eye toward comparison with those on C6H6-(H2O) sub n; a variety of vibronic level arguments are used to constrain the geometries of the C6H6-(CH3OH) sub n... more
Spectroscopic measurements of C6H6-(CH3OH) sub n clusters are reported with an eye toward comparison with those on C6H6-(H2O) sub n; a variety of vibronic level arguments are used to constrain the geometries of the C6H6-(CH3OH) sub n clusters. The 1:1 and 1:2 clusters possess vibronic level features which are very similar to their aqueous counterparts. The 1:1 cluster places the methanol molecule in a pi hydrogen-bonded configuration on or near the sixfold axis of benzene. The spectral characteristics of the 1:2 cluster are consistent with both methanol molecules residing on the same side of the benzene ring as a methanol dimer. Higher C6H6-(CH3OH) sub n clusters show distinct differences from corresponding C6H6-(H2O) sub n clusters. The methanol molecules in the 1:3 cluster show the strongest hydrogen bonding to the pi cloud of any of the clusters and attach to benzene in such a way as to strongly break the sixfold symmetry of its pi cloud. The 1:4 clusters are at most only very weakly hydrogen bonded to the pi cloud, break benzene's sixfold symmetry moderately well, and possess strong activity in a VLF intermolecular mode.
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Mixed clusters of C 6H 6 and H 2O type of C 6H 6(H 2O) n where n = 1-5 have been studied using one-color resonance-enhanced two-photon ionization coupled with time-of-flight mass spectrometric detection. The 1:1 complex is seen to have... more
Mixed clusters of C 6H 6 and H 2O type of C 6H 6(H 2O) n where n = 1-5 have been studied using one-color resonance-enhanced two-photon ionization coupled with time-of-flight mass spectrometric detection. The 1:1 complex is seen to have an electronically forbidden origin with intensity at least 1000 times less than that at 6 10. The H 2O molecule thus lies on the sixfold axis of benzene and is undergoing free radical rotation about this axis. The blue-shift and high-efficiency of fragmentation of the 1:1 complex argue for hydrogen bonding of the H 2O molecule to the benzene π cloud. The 1:2 complex induces a strong origin with intensity 14% of that at 6 10. The rotational band contour yields a geometry in which the two water molecules bind to benzene on one side of the benzene ring, with a H 2OH 2O separation close to that in the water dimer. Higher 1: n clusters show spectra which suggest structures involving a network of hydrogen bonded water molecules building up away from the benzene ring, consistent with a microscopic immiscibility of C 6H 6 and H 2O.