Arvi Rauk - Academia.edu (original) (raw)
Papers by Arvi Rauk
Journal of the Chemical Society, Chemical Communications, 1993
The long-wavelength Cotton effect (CE) of the nitroamine chromophore is very sensitive to structu... more The long-wavelength Cotton effect (CE) of the nitroamine chromophore is very sensitive to structural non-planarity and helicity; the sign of this CE for N-nitroaziridines has the same connection with the intrinsic chirality of the chromophore as in the case of N-acyl-, N-nitroso-aziridines and aziridinones.
The Journal of Physical Chemistry, 1993
After considering all possible connectivities for structural isomers of molecular formula ClO[sub... more After considering all possible connectivities for structural isomers of molecular formula ClO[sub 3] on the doublet ROHF/6-31 G(d) potential energy surface, four minimum energy structures were identified and studied further at some or all of the ROHF, UHF, CIS, UMP2, RMP2, and QCISD(T) levels of theory using various basis sets ranging in quality from 6-31 G(d) to 6-311+G(3df). Among the four ClO[sub 3] isomers (and alternative electronic states for two of them), only the ground state ([sup 2]A[sub 1]) C[sub 3[nu]] structure was found to be stable at all correlated levels of theory. In particular, the isomers with connectivities ClOOO and OClOO are found to be unstable at the RMP2 and QCISD(T) levels of theory (6-31G(d) basis set). The implications of these results to the chemistry of stratospheric ozone depletion are discussed. In addition, predictions of a variety of physical properties of C[sub 3[nu]] ClO[sub 3] ([sup 2]A[sub 1]) were made, including vibrational spectra and thermochemical tabulations based on G2 energy data. 41 refs., 4 figs., 6 tabs.
ChemInform, 1995
ABSTRACT Optical resolution of 2,5-dimethyl-Δ3-pyrroline 2 has been carried out via diastereomeri... more ABSTRACT Optical resolution of 2,5-dimethyl-Δ3-pyrroline 2 has been carried out via diastereomeric salts with (+)- and (−)-10-camphorsulfonic acid. The absolute configuration of enantiomers 2 is determined and a possibility of their application in asymmetric synthesis is shown.
The Journal of Physical Chemistry A, 2004
... Eight reactions in water were analyzed: H atom reacting with methanol, ethanol, 2-propanol, m... more ... Eight reactions in water were analyzed: H atom reacting with methanol, ethanol, 2-propanol, methanediol and ethylene glycol; and methanethiol reacting with the radicals, methyl, hydroxymethyl, and 2-hydroxy-2-propyl. The ...
The Journal of Physical Chemistry A, 2004
... 24 The structure and stability of the peroxy product, CH 3 SCH 2 OO • (3 • ), have been studi... more ... 24 The structure and stability of the peroxy product, CH 3 SCH 2 OO • (3 • ), have been studied by McKee by using high-level calculations, (QCISD(T)/6-31+G(2df, p)//MP2/6-31G(d)). 35 The O 2 binding energy was reported to be 112 kJ mol -1 . We have determined the ...
The Journal of Physical Chemistry A, 2005
A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-,... more A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.
The Journal of Physical Chemistry A, 2005
A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namel... more A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namely, N-formylmethioninamide 1, has been carried out by quantum chemical computations. Geometries of the coordination modes obtained at the B3LYP/6-31G(d) level of theory are discussed in the context of copper coordination by the peptide backbone and the S atom of a methionine residue in peptides with special emphasis on Met35 of the amyloid-beta peptide (Abeta) of Alzheimer's disease. The relative binding free energies in the gas phase, DeltaG(g), are calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level of theory, and the solvation affects are included by means of the COSMO model to obtain the relative binding energies in solution, DeltaG(aq). A free energy of binding, DeltaG(aq) = -19.4 kJ mol(-1), relative to aqueous Cu(II) and the free peptide is found for the most stable Cu(II)/Met complex, 12. The most stable Cu(I)/Met complex, 23, is bound by -15.6 kJ mol(-1) relative to the separated species. The reduction potential relative to the standard hydrogen electrode is estimated to be E degrees (12/23) = 0.41 V. On the basis of these results, the participation of Met35 as a low affinity binding site of Cu(II) in Abeta, and its role in the redox chemistry underlying Alzheimer's disease is discussed.
Mendeleev Communications, 1994
Journal of the American Chemical Society, 1975
Rotatory strengths of twisted ethylene, nonplanar 1,3-butadiene, and the chiral 2and 3-methylcycl... more Rotatory strengths of twisted ethylene, nonplanar 1,3-butadiene, and the chiral 2and 3-methylcyclohexanones are computed directly from wave functions obtained by the following molecular orbital methods, CND0/2, INDO, ODIN, and RHF-LCAO-MO-SCF. Several approaches, including limited single-excitation CI and the electron-hole potential method are used to improve the description of the excited states. It is found that where configurational mixing is small, ordinary ab initio SCF calculations yield the correct sign of rotation for all the systems studied. The semiempirical methods give unpredictable results but the nonempirical approximate method, ODIN, with improved virtual orbitals yields values which in most cases agree well with values obtained by the RHF-SCF method. In none of the systems studied is origin dependence of (il d j ) (Am/ i ) a problem if it is evaluated from the nonempirically derived wave functions. (+)-2-Methylcyclohexanone is predicted to have the R absolute configuration contrary to the accepted assignment based on the octant rule.
Journal of the American Chemical Society, 1996
CASSCF and CASPT2N/6-31G* calculations have been performed on the opening of bicyclo [n. 1.0] alk... more CASSCF and CASPT2N/6-31G* calculations have been performed on the opening of bicyclo [n. 1.0] alkanones, n= 1-3 (1-3), to the corresponding 2-cycloalkanone-1, 3-diyls (4-6). In agreement with the failure to observe 1, 4-dimethylbicyclo [2.1. 0] pentan-5-one (2b) ...
Journal of the American Chemical Society, 1994
The C2H7+ potential energy surface was characterized by high-level ab initio calculations. The ef... more The C2H7+ potential energy surface was characterized by high-level ab initio calculations. The effects of electron correlation on geometries and relative energies are substantial. At MP4(SDTQ)/6-311G**//MP2(full)/ 6-31G**, the global minimum is the C-C protonated structure 1,4.4 kcal/mol (corrected to 298 K) more stable than the C-H protonated form 3. The proton affinity of ethane to give 1 (142.5 kcal/mol) is 12.5 kcal/mol greater than that of methane (130 kcal/mol). Methane adds to the methyl cation, leading to 1 without activation energy. Barriers for intramolecular hydrogen interchange are lower than the dissociation energy into the ethyl cation and hydrogen, consistent with the experimental observation that deuterium scrambling is faster than dissociation. C2H7+ loses H2 by 1,l-elimination in an endothermic (10.6 kcal/mol) process. Three frequencies deduced experimentally for C2H7+ correspond to those computed for 1, but neither 2, the H2-rotated C-H protonated form, nor 3 can explain the other set of experimental spectral data. Complexes between H2 and bridged C2H5+ were located, but they are too weakly bonded to be detected experimentally.
Journal of the American Chemical Society, 1981
The carbocations 1,5-and 1,6-dimethylcyclododecyl are postulated to have a p-hydrido-bridged stru... more The carbocations 1,5-and 1,6-dimethylcyclododecyl are postulated to have a p-hydrido-bridged structure. This assignment is based on the observation of a single very high-field hydrogen in the 'H NMR, anomalously low coupling constants involving this hydrogen, and very small isotope perturbation shifts using Saunders' criterion for equilibrating and resonance structural distinction. Both positional and conformational isomerization is possible in these bridged ions, but no evidence for cis-trans isomerization was found. The p-hydrido bridging is best treated as an "open" three-center, two-electron resonance system involving a single potential minimum for the bridged hydrogen. The bridging hydrogen is not electrophilic, and the bridged ions cannot be prepared by protonating the central bond of decalins nor can the p-hydrogen be removed as a proton. Numerous theoretical calculations have been performed and correlated with the experimental data.
Journal of the American Chemical Society, 1981
ABSTRACT
Journal of the American Chemical Society, 1996
Journal of Physical Organic Chemistry, 2004
ABSTRACT Ab initio calculations at the B3LYP/6-31G(d) and CBS-RAD level were carried out to inves... more ABSTRACT Ab initio calculations at the B3LYP/6-31G(d) and CBS-RAD level were carried out to investigate the reaction of αC-centered peroxy radicals of neutral, non-zwitterionic glycine and alanine (AH), and as residues in model peptides, N-formylglycinamide and N-formylalaninamide (PH). Bond dissociation enthalpies (BDEs) were calculated for the αC—O (D), O—O (DOO) and O—H (DOH) bonds of glycine and alanine peroxy radicals (AOO, POO) and hydroperoxides (AOOH, POOH). The predicted BDEs at 298 K, in kJ mol−1 are AOO(Gly), D = 70; AOO(Ala), D = 69; POO(Gly), D = 89; POO(Ala), D = 86; AOOH(Gly), D = 237, DOO = 203, DOH = 371; AOOH(Ala), D = 234, DOO = 195, DOH = 368; POOH(Gly), D = 266, DOO = 207, DOH = 380; POOH(Ala), D = 264, DOO = 208, DOH=383. Values of BDE of the peptides in β-sheet peptide conformations were also estimated by constraining the Ramachandran dihedral angles, Φ and Ψ to, values of −150° and +150°: (S)-POO(Gly), D = 99; (R)-POO(Gly), D = 78; (S)-POO(Ala), D = 88; (R)-POO(Ala), D = 83; (S)-POOH(Gly), D = 258, DOO = 195, DOH = 362; (R)-POOH(Gly), D = 278, DOO = 217, DOH = 404; (S)- POOH(Ala), D = 240, DOO = 192, DOH = 355; (R)-POOH(Ala), D = 270, DOO = 204, DOH = 390. The reactions of αC-peroxy radicals, POO, and αC-alkoxy radicals, PO, were studied in detail. Copyright © 2004 John Wiley & Sons, Ltd.
The Journal of Organic Chemistry, 1998
Ab initio methods have been employed to study the oxidation of the CH bonds in homo-(1a-d) and he... more Ab initio methods have been employed to study the oxidation of the CH bonds in homo-(1a-d) and heterosubstituted alkanes (2a-d, 3a,b) by the parent dioxirane as a model for the dioxirane oxidation of proteins. The study involved methane (1a), ethane (1b), propane (1c), isobutane (1d), methylamine (2a), methanol (2b), ethanol (2c), acetaldehyde (2d), glycolaldehyde (3a), and a peptide model, N-formylglycine amide (3b). Geometries were optimized at DFT (B3LYP) and MP2 levels of theory using 6-31G* and 6-311+G** basis sets. Stationary points were characterized by vibrational frequency analysis. Final energies for the oxidation of 1a were obtained at the MP4-(SDTQ)/6-311+G** and QCISD(T)/6-311+G** levels. A new mechanism of the oxidation reconciling the apparently contradictory experimental data was found. The reaction proceeds via a highly polar asynchronous transition state, which is common for either concerted oxygen insertion into the CH bond and formation of a radical pair (alkyl radical + R-hydroxyalkoxyl radical). These channels appear at a bifurcation point on the potential energy surface after the common transition state, which corresponds to formation of the new O-H bond, and ruptures of the C-H bond in the substrate and of the O-O bond in the dioxirane. The B3LYP theoretical model gives substantial hydride transfer character to the transition state and describes adequately the selectivity of the oxidation of hydrocarbons, alcohols, 1,2-diols, and leucine derivatives. The agreement with experimental data is further improved by taking into account the influence of a dielectric medium (IPCM model). The electrophilicity of dioxiranes in the oxidations of CH bonds implies that side groups of protected amino acids and proteins are more probable points for the attack of these oxidants than the weak R-CH bonds. It is of interest that selectivities of dioxirane oxidation are incorrectly predicted by the MP2 method, which overestimates the proton-transfer character of the transition state. S0022-3263(98)
The Journal of Organic Chemistry, 1997
... Edward Bures, Patrick G. Spinazzé, Giovanna Beese, Ian R. Hunt, Christine Rogers, and Brian A... more ... Edward Bures, Patrick G. Spinazzé, Giovanna Beese, Ian R. Hunt, Christine Rogers, and Brian A. Keay*. Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4. J. Org. Chem. , 1997, 62 (25), pp 8741 ...
The Journal of Organic Chemistry, 1998
Ab initio methods have been employed to study the conformational behavior and chiroptical propert... more Ab initio methods have been employed to study the conformational behavior and chiroptical properties of acyclic, structurally related aldehydes, ketenes, and diazoalkanes of the type MeCHRCH=XY. The study involved aldehydes 1, 4, and 7 (XY = O, R = H, Me, Et, correspondingly), ketenes (1-alken-1-ones) 2, 5, and 8 (XY = CO, R = H, Me, Et), and 1-diazoalkanes 3, 6, and 9 (XY = NN, R = H, Me, Et). Geometries were optimized at the B3LYP/6-31G level, stationary points were characterized by vibrational frequency analysis, and final energies of 7-9 were obtained at the B3LYP/6-311+G//B3LYP/6-31G level. The chiroptical properties were calculated by the CIS/6-31+G method. It was found that rotational barriers of the functional group (CHXY) about the CC bond are lowered in the following order: aldehydes (1.5-2.1 kcal mol(-1)) > ketenes (1.3-1.6) > diazoalkanes (0.5-0.7). A conformer with the C=X bond eclipsed by an alpha-hydrogen is the global minimum of the ketenes and diazoalkanes, unlike the aldehydes where eclipsing by an alpha-alkyl group is preferred over a hydrogen. In all three classes of compounds, the optical rotational strength of the n-pi transition is greatest for conformers with the dihedral angle, CCCX, in the range 80-100 degrees. Within this range, the signs of the n-pi rotational strengths for the ketenes and diazoalkanes are opposite to ones for the aldehydes. As a whole, the torsional dependencies of the n-pi rotational strength of the ketene and diazo chromophores can be explained within the framework of a model of "through-bond" perturbation. CD spectra of (S)-alpha-methyl-substituted butanal (7), 1-penten-1-one (8), and 1-diazobutane (9) were obtained experimentally. The calculated chiroptical properties of equilibrium mixtures of conformers of compounds 7-9 are in agreement with experimental data.
Journal of Molecular Structure, 1997
ABSTRACT Infrared absorption and vibrational circular dichroism (VCD) spectra of d(CGCGCGCG)·d(CG... more ABSTRACT Infrared absorption and vibrational circular dichroism (VCD) spectra of d(CGCGCGCG)·d(CGCGCGCG) and d(CGTATACG)·d(CGTATACG), free and complexed with the intercalating drug daunorubicin, are presented as examples of a series of similar deoxyoctanucleotides with varying base sequences. The spectra are qualitatively interpreted on the basis of previous assignments and on ab initio calculations of the nucleic acid bases and base pairs.
Journal of the Chemical Society, Chemical Communications, 1993
The long-wavelength Cotton effect (CE) of the nitroamine chromophore is very sensitive to structu... more The long-wavelength Cotton effect (CE) of the nitroamine chromophore is very sensitive to structural non-planarity and helicity; the sign of this CE for N-nitroaziridines has the same connection with the intrinsic chirality of the chromophore as in the case of N-acyl-, N-nitroso-aziridines and aziridinones.
The Journal of Physical Chemistry, 1993
After considering all possible connectivities for structural isomers of molecular formula ClO[sub... more After considering all possible connectivities for structural isomers of molecular formula ClO[sub 3] on the doublet ROHF/6-31 G(d) potential energy surface, four minimum energy structures were identified and studied further at some or all of the ROHF, UHF, CIS, UMP2, RMP2, and QCISD(T) levels of theory using various basis sets ranging in quality from 6-31 G(d) to 6-311+G(3df). Among the four ClO[sub 3] isomers (and alternative electronic states for two of them), only the ground state ([sup 2]A[sub 1]) C[sub 3[nu]] structure was found to be stable at all correlated levels of theory. In particular, the isomers with connectivities ClOOO and OClOO are found to be unstable at the RMP2 and QCISD(T) levels of theory (6-31G(d) basis set). The implications of these results to the chemistry of stratospheric ozone depletion are discussed. In addition, predictions of a variety of physical properties of C[sub 3[nu]] ClO[sub 3] ([sup 2]A[sub 1]) were made, including vibrational spectra and thermochemical tabulations based on G2 energy data. 41 refs., 4 figs., 6 tabs.
ChemInform, 1995
ABSTRACT Optical resolution of 2,5-dimethyl-Δ3-pyrroline 2 has been carried out via diastereomeri... more ABSTRACT Optical resolution of 2,5-dimethyl-Δ3-pyrroline 2 has been carried out via diastereomeric salts with (+)- and (−)-10-camphorsulfonic acid. The absolute configuration of enantiomers 2 is determined and a possibility of their application in asymmetric synthesis is shown.
The Journal of Physical Chemistry A, 2004
... Eight reactions in water were analyzed: H atom reacting with methanol, ethanol, 2-propanol, m... more ... Eight reactions in water were analyzed: H atom reacting with methanol, ethanol, 2-propanol, methanediol and ethylene glycol; and methanethiol reacting with the radicals, methyl, hydroxymethyl, and 2-hydroxy-2-propyl. The ...
The Journal of Physical Chemistry A, 2004
... 24 The structure and stability of the peroxy product, CH 3 SCH 2 OO • (3 • ), have been studi... more ... 24 The structure and stability of the peroxy product, CH 3 SCH 2 OO • (3 • ), have been studied by McKee by using high-level calculations, (QCISD(T)/6-31+G(2df, p)//MP2/6-31G(d)). 35 The O 2 binding energy was reported to be 112 kJ mol -1 . We have determined the ...
The Journal of Physical Chemistry A, 2005
A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-,... more A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.
The Journal of Physical Chemistry A, 2005
A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namel... more A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namely, N-formylmethioninamide 1, has been carried out by quantum chemical computations. Geometries of the coordination modes obtained at the B3LYP/6-31G(d) level of theory are discussed in the context of copper coordination by the peptide backbone and the S atom of a methionine residue in peptides with special emphasis on Met35 of the amyloid-beta peptide (Abeta) of Alzheimer's disease. The relative binding free energies in the gas phase, DeltaG(g), are calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level of theory, and the solvation affects are included by means of the COSMO model to obtain the relative binding energies in solution, DeltaG(aq). A free energy of binding, DeltaG(aq) = -19.4 kJ mol(-1), relative to aqueous Cu(II) and the free peptide is found for the most stable Cu(II)/Met complex, 12. The most stable Cu(I)/Met complex, 23, is bound by -15.6 kJ mol(-1) relative to the separated species. The reduction potential relative to the standard hydrogen electrode is estimated to be E degrees (12/23) = 0.41 V. On the basis of these results, the participation of Met35 as a low affinity binding site of Cu(II) in Abeta, and its role in the redox chemistry underlying Alzheimer's disease is discussed.
Mendeleev Communications, 1994
Journal of the American Chemical Society, 1975
Rotatory strengths of twisted ethylene, nonplanar 1,3-butadiene, and the chiral 2and 3-methylcycl... more Rotatory strengths of twisted ethylene, nonplanar 1,3-butadiene, and the chiral 2and 3-methylcyclohexanones are computed directly from wave functions obtained by the following molecular orbital methods, CND0/2, INDO, ODIN, and RHF-LCAO-MO-SCF. Several approaches, including limited single-excitation CI and the electron-hole potential method are used to improve the description of the excited states. It is found that where configurational mixing is small, ordinary ab initio SCF calculations yield the correct sign of rotation for all the systems studied. The semiempirical methods give unpredictable results but the nonempirical approximate method, ODIN, with improved virtual orbitals yields values which in most cases agree well with values obtained by the RHF-SCF method. In none of the systems studied is origin dependence of (il d j ) (Am/ i ) a problem if it is evaluated from the nonempirically derived wave functions. (+)-2-Methylcyclohexanone is predicted to have the R absolute configuration contrary to the accepted assignment based on the octant rule.
Journal of the American Chemical Society, 1996
CASSCF and CASPT2N/6-31G* calculations have been performed on the opening of bicyclo [n. 1.0] alk... more CASSCF and CASPT2N/6-31G* calculations have been performed on the opening of bicyclo [n. 1.0] alkanones, n= 1-3 (1-3), to the corresponding 2-cycloalkanone-1, 3-diyls (4-6). In agreement with the failure to observe 1, 4-dimethylbicyclo [2.1. 0] pentan-5-one (2b) ...
Journal of the American Chemical Society, 1994
The C2H7+ potential energy surface was characterized by high-level ab initio calculations. The ef... more The C2H7+ potential energy surface was characterized by high-level ab initio calculations. The effects of electron correlation on geometries and relative energies are substantial. At MP4(SDTQ)/6-311G**//MP2(full)/ 6-31G**, the global minimum is the C-C protonated structure 1,4.4 kcal/mol (corrected to 298 K) more stable than the C-H protonated form 3. The proton affinity of ethane to give 1 (142.5 kcal/mol) is 12.5 kcal/mol greater than that of methane (130 kcal/mol). Methane adds to the methyl cation, leading to 1 without activation energy. Barriers for intramolecular hydrogen interchange are lower than the dissociation energy into the ethyl cation and hydrogen, consistent with the experimental observation that deuterium scrambling is faster than dissociation. C2H7+ loses H2 by 1,l-elimination in an endothermic (10.6 kcal/mol) process. Three frequencies deduced experimentally for C2H7+ correspond to those computed for 1, but neither 2, the H2-rotated C-H protonated form, nor 3 can explain the other set of experimental spectral data. Complexes between H2 and bridged C2H5+ were located, but they are too weakly bonded to be detected experimentally.
Journal of the American Chemical Society, 1981
The carbocations 1,5-and 1,6-dimethylcyclododecyl are postulated to have a p-hydrido-bridged stru... more The carbocations 1,5-and 1,6-dimethylcyclododecyl are postulated to have a p-hydrido-bridged structure. This assignment is based on the observation of a single very high-field hydrogen in the 'H NMR, anomalously low coupling constants involving this hydrogen, and very small isotope perturbation shifts using Saunders' criterion for equilibrating and resonance structural distinction. Both positional and conformational isomerization is possible in these bridged ions, but no evidence for cis-trans isomerization was found. The p-hydrido bridging is best treated as an "open" three-center, two-electron resonance system involving a single potential minimum for the bridged hydrogen. The bridging hydrogen is not electrophilic, and the bridged ions cannot be prepared by protonating the central bond of decalins nor can the p-hydrogen be removed as a proton. Numerous theoretical calculations have been performed and correlated with the experimental data.
Journal of the American Chemical Society, 1981
ABSTRACT
Journal of the American Chemical Society, 1996
Journal of Physical Organic Chemistry, 2004
ABSTRACT Ab initio calculations at the B3LYP/6-31G(d) and CBS-RAD level were carried out to inves... more ABSTRACT Ab initio calculations at the B3LYP/6-31G(d) and CBS-RAD level were carried out to investigate the reaction of αC-centered peroxy radicals of neutral, non-zwitterionic glycine and alanine (AH), and as residues in model peptides, N-formylglycinamide and N-formylalaninamide (PH). Bond dissociation enthalpies (BDEs) were calculated for the αC—O (D), O—O (DOO) and O—H (DOH) bonds of glycine and alanine peroxy radicals (AOO, POO) and hydroperoxides (AOOH, POOH). The predicted BDEs at 298 K, in kJ mol−1 are AOO(Gly), D = 70; AOO(Ala), D = 69; POO(Gly), D = 89; POO(Ala), D = 86; AOOH(Gly), D = 237, DOO = 203, DOH = 371; AOOH(Ala), D = 234, DOO = 195, DOH = 368; POOH(Gly), D = 266, DOO = 207, DOH = 380; POOH(Ala), D = 264, DOO = 208, DOH=383. Values of BDE of the peptides in β-sheet peptide conformations were also estimated by constraining the Ramachandran dihedral angles, Φ and Ψ to, values of −150° and +150°: (S)-POO(Gly), D = 99; (R)-POO(Gly), D = 78; (S)-POO(Ala), D = 88; (R)-POO(Ala), D = 83; (S)-POOH(Gly), D = 258, DOO = 195, DOH = 362; (R)-POOH(Gly), D = 278, DOO = 217, DOH = 404; (S)- POOH(Ala), D = 240, DOO = 192, DOH = 355; (R)-POOH(Ala), D = 270, DOO = 204, DOH = 390. The reactions of αC-peroxy radicals, POO, and αC-alkoxy radicals, PO, were studied in detail. Copyright © 2004 John Wiley & Sons, Ltd.
The Journal of Organic Chemistry, 1998
Ab initio methods have been employed to study the oxidation of the CH bonds in homo-(1a-d) and he... more Ab initio methods have been employed to study the oxidation of the CH bonds in homo-(1a-d) and heterosubstituted alkanes (2a-d, 3a,b) by the parent dioxirane as a model for the dioxirane oxidation of proteins. The study involved methane (1a), ethane (1b), propane (1c), isobutane (1d), methylamine (2a), methanol (2b), ethanol (2c), acetaldehyde (2d), glycolaldehyde (3a), and a peptide model, N-formylglycine amide (3b). Geometries were optimized at DFT (B3LYP) and MP2 levels of theory using 6-31G* and 6-311+G** basis sets. Stationary points were characterized by vibrational frequency analysis. Final energies for the oxidation of 1a were obtained at the MP4-(SDTQ)/6-311+G** and QCISD(T)/6-311+G** levels. A new mechanism of the oxidation reconciling the apparently contradictory experimental data was found. The reaction proceeds via a highly polar asynchronous transition state, which is common for either concerted oxygen insertion into the CH bond and formation of a radical pair (alkyl radical + R-hydroxyalkoxyl radical). These channels appear at a bifurcation point on the potential energy surface after the common transition state, which corresponds to formation of the new O-H bond, and ruptures of the C-H bond in the substrate and of the O-O bond in the dioxirane. The B3LYP theoretical model gives substantial hydride transfer character to the transition state and describes adequately the selectivity of the oxidation of hydrocarbons, alcohols, 1,2-diols, and leucine derivatives. The agreement with experimental data is further improved by taking into account the influence of a dielectric medium (IPCM model). The electrophilicity of dioxiranes in the oxidations of CH bonds implies that side groups of protected amino acids and proteins are more probable points for the attack of these oxidants than the weak R-CH bonds. It is of interest that selectivities of dioxirane oxidation are incorrectly predicted by the MP2 method, which overestimates the proton-transfer character of the transition state. S0022-3263(98)
The Journal of Organic Chemistry, 1997
... Edward Bures, Patrick G. Spinazzé, Giovanna Beese, Ian R. Hunt, Christine Rogers, and Brian A... more ... Edward Bures, Patrick G. Spinazzé, Giovanna Beese, Ian R. Hunt, Christine Rogers, and Brian A. Keay*. Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4. J. Org. Chem. , 1997, 62 (25), pp 8741 ...
The Journal of Organic Chemistry, 1998
Ab initio methods have been employed to study the conformational behavior and chiroptical propert... more Ab initio methods have been employed to study the conformational behavior and chiroptical properties of acyclic, structurally related aldehydes, ketenes, and diazoalkanes of the type MeCHRCH=XY. The study involved aldehydes 1, 4, and 7 (XY = O, R = H, Me, Et, correspondingly), ketenes (1-alken-1-ones) 2, 5, and 8 (XY = CO, R = H, Me, Et), and 1-diazoalkanes 3, 6, and 9 (XY = NN, R = H, Me, Et). Geometries were optimized at the B3LYP/6-31G level, stationary points were characterized by vibrational frequency analysis, and final energies of 7-9 were obtained at the B3LYP/6-311+G//B3LYP/6-31G level. The chiroptical properties were calculated by the CIS/6-31+G method. It was found that rotational barriers of the functional group (CHXY) about the CC bond are lowered in the following order: aldehydes (1.5-2.1 kcal mol(-1)) > ketenes (1.3-1.6) > diazoalkanes (0.5-0.7). A conformer with the C=X bond eclipsed by an alpha-hydrogen is the global minimum of the ketenes and diazoalkanes, unlike the aldehydes where eclipsing by an alpha-alkyl group is preferred over a hydrogen. In all three classes of compounds, the optical rotational strength of the n-pi transition is greatest for conformers with the dihedral angle, CCCX, in the range 80-100 degrees. Within this range, the signs of the n-pi rotational strengths for the ketenes and diazoalkanes are opposite to ones for the aldehydes. As a whole, the torsional dependencies of the n-pi rotational strength of the ketene and diazo chromophores can be explained within the framework of a model of "through-bond" perturbation. CD spectra of (S)-alpha-methyl-substituted butanal (7), 1-penten-1-one (8), and 1-diazobutane (9) were obtained experimentally. The calculated chiroptical properties of equilibrium mixtures of conformers of compounds 7-9 are in agreement with experimental data.
Journal of Molecular Structure, 1997
ABSTRACT Infrared absorption and vibrational circular dichroism (VCD) spectra of d(CGCGCGCG)·d(CG... more ABSTRACT Infrared absorption and vibrational circular dichroism (VCD) spectra of d(CGCGCGCG)·d(CGCGCGCG) and d(CGTATACG)·d(CGTATACG), free and complexed with the intercalating drug daunorubicin, are presented as examples of a series of similar deoxyoctanucleotides with varying base sequences. The spectra are qualitatively interpreted on the basis of previous assignments and on ab initio calculations of the nucleic acid bases and base pairs.