Brian Wladkowski - Academia.edu (original) (raw)
Papers by Brian Wladkowski
The Journal of Physical Chemistry, 1995
Page 1. J. Phys. Chem. 1995, 99, 6273-6276 6273 Ribonuclease A Catalyzed Transphosphorylation: An... more Page 1. J. Phys. Chem. 1995, 99, 6273-6276 6273 Ribonuclease A Catalyzed Transphosphorylation: An ab Znitio Theoretical Study Brian D. Wladkowski,**+ Morris Krauss, and Walter J. Stevens Center for Advanced Research ...
J Am Chem Soc, 1994
... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In th... more ... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In the early part of this century Petrenko-Krit~chenko,~~ Backer and van Mels,15 as well as Davies et a1.16 reported interesting (13) Shaik, S. S. J. Am. Cbem. Soc. 1983, 105, 4358. ...
The Journal of Physical Chemistry, 1993
... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowsk... more ... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowski and John I. Brauman' Department of Chemistry, Stanford University, Stanford, California 94305-5080 Received: February 17, 1993; In Final Form: June 25, 19936 ...
The Journal of Physical Chemistry, 1994
... Brian D. Wladkowski ... The sp space of the [ 1 3 ~ 8 ~ 6 d 4 f , 8 ~ 6 ~ 4 d ] ( + ) basis i... more ... Brian D. Wladkowski ... The sp space of the [ 1 3 ~ 8 ~ 6 d 4 f , 8 ~ 6 ~ 4 d ] ( + ) basis is comprised of the uncontracted primitives of van D~ijneveldt.~~ For the diffuse orbitals constituting the (+) augmentations, the following exponents were employed, as derived by even-tempered ...
The Journal of Physical Chemistry, 1993
... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowsk... more ... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowski and John I. Brauman' Department of Chemistry, Stanford University, Stanford, California 94305-5080 Received: February 17, 1993; In Final Form: June 25, 19936 ...
The Journal of Physical Chemistry, 1995
Page 1. 4490 J. Phys. Chem. 1995,99, 4490-4500 Apicophilicities of Substituted Oxyphosphoranes: [... more Page 1. 4490 J. Phys. Chem. 1995,99, 4490-4500 Apicophilicities of Substituted Oxyphosphoranes: [P(OH)4X, PO-(OH)3X] Brian D. Wladkowski,*>+ Morris Krauss, and Walter J. Stevens Center for Advanced Research in Biotechnology ...
The Journal of Physical Chemistry A, 1998
Journal of the American Chemical Society, 1994
The detailed dynamics of sN2 reactions are not fully understood. Although various statistical rea... more The detailed dynamics of sN2 reactions are not fully understood. Although various statistical reaction rate theories, including Rice-Ramsperger-Kassel-Marcus (RRKM) theory, have been used to model the experimental kinetics and predict energies of activation for these reactions,I4 recent experimental and theoretical results suggest that certain sN2 reactions behave 'non~tatistically".~1~ These results raise important concerns regarding the use of statistical theories to model sN2 reaction kinetics.
Journal of the American Chemical Society, 1992
The direct competition between substitution (SN2) and elim-ination (E2) pathways for reactions of... more The direct competition between substitution (SN2) and elim-ination (E2) pathways for reactions of anionic nucleophiles with alkyl substrates is a fundamental problem. The factors that influence this competition in solution have been studied exten-sively;l-3 the results depend ...
Journal of the American Chemical Society, 1995
The transphosphorylation step in the enzyme-catalyzed hydrolysis of phosphate esters by Ribonucle... more The transphosphorylation step in the enzyme-catalyzed hydrolysis of phosphate esters by Ribonuclease A (RNase A) is explored using ab initio quantum chemical methods. For the first time, components found in the RNase A active site are included in the all-electron chemical model, made up of 2-hydroxyethyl methyl phosphate monoanion used as the substrate, and small model compounds used to mimic the three important residues, His-12, His-119, and Lys-41, found in the RNase A active site. The remainder of the immediate active site, including ten residues and six bound water molecules, is treated using effective fragment potentials (EFPs) incorporated directly into the Hamiltonian of the quantum system. The EFPs, derived from separate quantum calculations on individual components, are constructed to accurately represent the correct electrostatics and polarization fields of each component. High-resolution X-ray crystallographic data are used to assign the fixed relative positions of each component in the quantum and EFP regions. Characterization of the salient stationary points along the transphosphorylation reaction pathway at the RHF level using a 3-21+G(d) basis set reveals several low-barrier proton transfer steps between the substrate and the active site residues which allow transphosphorylation to occur with modest activation, consistent with the experimental data. Merller-Plesset perturbation theory ( M E ) and density functional theory methods utilizing a larger 6-3 l+G(d) basis are also used to explore the effects of electron correlation on the surface energetics. Consistent with expectations, the electrostatic field effects from the EFPs used to represent the non-participating parts of the active site are found to differentially stabilize certain structures along the reaction pathway.
Journal of the American Chemical Society, 1991
Journal of the American Chemical Society, 1993
The energy dependence of the branching ratio for the dissociation of a proton-transfer reaction i... more The energy dependence of the branching ratio for the dissociation of a proton-transfer reaction intermediate, [ (NC)~CHZ.CI-], has been observed in the gas phase using Fourier transform ion cyclotron resonance spectrometry.
Journal of the American Chemical Society, 1992
... product (k2) channels. Infrared multiple-photon (IRMP) activationI6 of the isolated and therm... more ... product (k2) channels. Infrared multiple-photon (IRMP) activationI6 of the isolated and thermalized complex A accesses a low-energy, low angular momentum regime1' (0-3 kcal mol-' above threshold). Chemical activation (CA ...
Journal of the American Chemical Society, 1997
ABSTRACT
Journal of the American Chemical Society, 1998
A joint X-ray crystallographic (1.3 Å resolution) and ab initio quantum mechanical analysis of a ... more A joint X-ray crystallographic (1.3 Å resolution) and ab initio quantum mechanical analysis of a uridine vanadate−ribonuclease A complex (UV−RNase A) is undertaken to probe specific aspects of the microscopic mechanism by which ribonuclease functions to catalyze the hydrolysis ...
Journal of the American Chemical Society, 1996
The potential energy surface for rotation of the exocyclic hydroxymethyl group of R-D-glucopyrano... more The potential energy surface for rotation of the exocyclic hydroxymethyl group of R-D-glucopyranose has been studied using ab initio quantum mechanical methods. Relevant stationary points, including for the first time rotational transition states, have been characterized by full geometry optimization using basis sets ranging in quality from 6-31G(d) to 6-311(2d,1p). Effects of dynamical electron correlation on both the geometric structures and the energy surface are also investigated using second-order Møller-Plesset perturbation theory (MP2) and density functional methods (BLYP). A total of six stationary points along the hydroxymethyl rotational surface, including three minima and three transition states, were identified. The effects of basis set augmentation and electron correlation on the relative energies are small; the relative energies for each stationary point vary by less than 5 kJ mol -1 for all levels of theory considered. Final energetic barriers to hydroxymethyl rotation ranged from 15 to 29 kJ mol -1 . Differences between these barriers and previously reported ab initio results on a carbohydrate model compound, 2-(hydroxymethyl)tetrahydropyran, as well as energies calculated using force field methods, are discussed.
Journal of the American Chemical Society, 1993
Determination of the contributions of competing pathways in ion-molecule reactions is a fundament... more Determination of the contributions of competing pathways in ion-molecule reactions is a fundamental problem. Ion-molecule reactions involving ambident nucleophiles represent a particularly interesting class of multichannel reactions. The factors that influence the inherent competition associated with reactions of ambident nucleophiles in solution have been studied extensively, since the neutral products can be easily distinguished.' In the gas phase, however, determination of the relative contributions of such competing pathways is extremely difficult, because only ionic species are dectected (Scheme I).
Journal of the American Chemical Society, 1994
... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In th... more ... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In the early part of this century Petrenko-Krit~chenko,~~ Backer and van Mels,15 as well as Davies et a1.16 reported interesting (13) Shaik, S. S. J. Am. Cbem. Soc. 1983, 105, 4358. ...
The Journal of Organic Chemistry, 1989
The Journal of Organic Chemistry, 1992
orously stirred overnight at room temperature and then diluted in methanol (2 mL). After filtrati... more orously stirred overnight at room temperature and then diluted in methanol (2 mL). After filtration over Celite 545, the filtrate was evaporated under vacuum, diluted in ether, and then dried over magnesium sulfate. Flash chromatography (elution with methylene chloride-ethyl acetate, 65:35) gave the methyl ester LTB4 12 (41 mg; 70%): [ a I m~ +4.6' (c 0.39, CCC); IR (NaCl film) 3400 (OH), 3000 (=CHI, 1730 (C=O), 1595 (C=C--c=C) cm-'; 'H NMR (300 MHz, CDClJ 6 6.47 (1 H, dd, J = 14.5 Hz, J = 11 Hz, HB), 6.3 (1 H, ddd, J = 15 Hz, J 10.5 Hz, J = 1 Hz, HlJ, 6.21 (1 H, dd, J = 14.5 Hz, J = 10.5 Hz, Hs), 6.07 (1 H, t, J = 11 Hz, H,), 5.77 (1 H, dd, J = 15 Hz, J = 6.3 Hz, HI'), 5.55 (1 H, m, J = 10.5 Hz, J = 7 Hz, H15), 5.54 (1 H, dd, J = 11 Hz, J = 9.5 Hz, He), 5.34 (1 H, m, J = 10.5 Hz, J = 7 Hz, H14), 4.57 (1 H, m, J = 9.5 Hz, Hs), 4.2 (1 H, q, J = 6.3 Hz, H12), 3.65 (3 H, s, OCH,), 2.33 (4 H,m, H4) and 2.02 (2 H, q,J = 6 Hz, Hie), 1.72-1.60 (5 H, m, aliphatics H and OH), 1.36-1.21 (7 H, m, aliphatics H and OH), 0.87 (3 H, t, J = 6.5 Hz, CH3-20).
The Journal of Physical Chemistry, 1995
Page 1. J. Phys. Chem. 1995, 99, 6273-6276 6273 Ribonuclease A Catalyzed Transphosphorylation: An... more Page 1. J. Phys. Chem. 1995, 99, 6273-6276 6273 Ribonuclease A Catalyzed Transphosphorylation: An ab Znitio Theoretical Study Brian D. Wladkowski,**+ Morris Krauss, and Walter J. Stevens Center for Advanced Research ...
J Am Chem Soc, 1994
... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In th... more ... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In the early part of this century Petrenko-Krit~chenko,~~ Backer and van Mels,15 as well as Davies et a1.16 reported interesting (13) Shaik, S. S. J. Am. Cbem. Soc. 1983, 105, 4358. ...
The Journal of Physical Chemistry, 1993
... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowsk... more ... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowski and John I. Brauman' Department of Chemistry, Stanford University, Stanford, California 94305-5080 Received: February 17, 1993; In Final Form: June 25, 19936 ...
The Journal of Physical Chemistry, 1994
... Brian D. Wladkowski ... The sp space of the [ 1 3 ~ 8 ~ 6 d 4 f , 8 ~ 6 ~ 4 d ] ( + ) basis i... more ... Brian D. Wladkowski ... The sp space of the [ 1 3 ~ 8 ~ 6 d 4 f , 8 ~ 6 ~ 4 d ] ( + ) basis is comprised of the uncontracted primitives of van D~ijneveldt.~~ For the diffuse orbitals constituting the (+) augmentations, the following exponents were employed, as derived by even-tempered ...
The Journal of Physical Chemistry, 1993
... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowsk... more ... Reactions: Experimental Support of the Marcus Theory Additivity Postulate+ Brian D. Wladkowski and John I. Brauman' Department of Chemistry, Stanford University, Stanford, California 94305-5080 Received: February 17, 1993; In Final Form: June 25, 19936 ...
The Journal of Physical Chemistry, 1995
Page 1. 4490 J. Phys. Chem. 1995,99, 4490-4500 Apicophilicities of Substituted Oxyphosphoranes: [... more Page 1. 4490 J. Phys. Chem. 1995,99, 4490-4500 Apicophilicities of Substituted Oxyphosphoranes: [P(OH)4X, PO-(OH)3X] Brian D. Wladkowski,*>+ Morris Krauss, and Walter J. Stevens Center for Advanced Research in Biotechnology ...
The Journal of Physical Chemistry A, 1998
Journal of the American Chemical Society, 1994
The detailed dynamics of sN2 reactions are not fully understood. Although various statistical rea... more The detailed dynamics of sN2 reactions are not fully understood. Although various statistical reaction rate theories, including Rice-Ramsperger-Kassel-Marcus (RRKM) theory, have been used to model the experimental kinetics and predict energies of activation for these reactions,I4 recent experimental and theoretical results suggest that certain sN2 reactions behave 'non~tatistically".~1~ These results raise important concerns regarding the use of statistical theories to model sN2 reaction kinetics.
Journal of the American Chemical Society, 1992
The direct competition between substitution (SN2) and elim-ination (E2) pathways for reactions of... more The direct competition between substitution (SN2) and elim-ination (E2) pathways for reactions of anionic nucleophiles with alkyl substrates is a fundamental problem. The factors that influence this competition in solution have been studied exten-sively;l-3 the results depend ...
Journal of the American Chemical Society, 1995
The transphosphorylation step in the enzyme-catalyzed hydrolysis of phosphate esters by Ribonucle... more The transphosphorylation step in the enzyme-catalyzed hydrolysis of phosphate esters by Ribonuclease A (RNase A) is explored using ab initio quantum chemical methods. For the first time, components found in the RNase A active site are included in the all-electron chemical model, made up of 2-hydroxyethyl methyl phosphate monoanion used as the substrate, and small model compounds used to mimic the three important residues, His-12, His-119, and Lys-41, found in the RNase A active site. The remainder of the immediate active site, including ten residues and six bound water molecules, is treated using effective fragment potentials (EFPs) incorporated directly into the Hamiltonian of the quantum system. The EFPs, derived from separate quantum calculations on individual components, are constructed to accurately represent the correct electrostatics and polarization fields of each component. High-resolution X-ray crystallographic data are used to assign the fixed relative positions of each component in the quantum and EFP regions. Characterization of the salient stationary points along the transphosphorylation reaction pathway at the RHF level using a 3-21+G(d) basis set reveals several low-barrier proton transfer steps between the substrate and the active site residues which allow transphosphorylation to occur with modest activation, consistent with the experimental data. Merller-Plesset perturbation theory ( M E ) and density functional theory methods utilizing a larger 6-3 l+G(d) basis are also used to explore the effects of electron correlation on the surface energetics. Consistent with expectations, the electrostatic field effects from the EFPs used to represent the non-participating parts of the active site are found to differentially stabilize certain structures along the reaction pathway.
Journal of the American Chemical Society, 1991
Journal of the American Chemical Society, 1993
The energy dependence of the branching ratio for the dissociation of a proton-transfer reaction i... more The energy dependence of the branching ratio for the dissociation of a proton-transfer reaction intermediate, [ (NC)~CHZ.CI-], has been observed in the gas phase using Fourier transform ion cyclotron resonance spectrometry.
Journal of the American Chemical Society, 1992
... product (k2) channels. Infrared multiple-photon (IRMP) activationI6 of the isolated and therm... more ... product (k2) channels. Infrared multiple-photon (IRMP) activationI6 of the isolated and thermalized complex A accesses a low-energy, low angular momentum regime1' (0-3 kcal mol-' above threshold). Chemical activation (CA ...
Journal of the American Chemical Society, 1997
ABSTRACT
Journal of the American Chemical Society, 1998
A joint X-ray crystallographic (1.3 Å resolution) and ab initio quantum mechanical analysis of a ... more A joint X-ray crystallographic (1.3 Å resolution) and ab initio quantum mechanical analysis of a uridine vanadate−ribonuclease A complex (UV−RNase A) is undertaken to probe specific aspects of the microscopic mechanism by which ribonuclease functions to catalyze the hydrolysis ...
Journal of the American Chemical Society, 1996
The potential energy surface for rotation of the exocyclic hydroxymethyl group of R-D-glucopyrano... more The potential energy surface for rotation of the exocyclic hydroxymethyl group of R-D-glucopyranose has been studied using ab initio quantum mechanical methods. Relevant stationary points, including for the first time rotational transition states, have been characterized by full geometry optimization using basis sets ranging in quality from 6-31G(d) to 6-311(2d,1p). Effects of dynamical electron correlation on both the geometric structures and the energy surface are also investigated using second-order Møller-Plesset perturbation theory (MP2) and density functional methods (BLYP). A total of six stationary points along the hydroxymethyl rotational surface, including three minima and three transition states, were identified. The effects of basis set augmentation and electron correlation on the relative energies are small; the relative energies for each stationary point vary by less than 5 kJ mol -1 for all levels of theory considered. Final energetic barriers to hydroxymethyl rotation ranged from 15 to 29 kJ mol -1 . Differences between these barriers and previously reported ab initio results on a carbohydrate model compound, 2-(hydroxymethyl)tetrahydropyran, as well as energies calculated using force field methods, are discussed.
Journal of the American Chemical Society, 1993
Determination of the contributions of competing pathways in ion-molecule reactions is a fundament... more Determination of the contributions of competing pathways in ion-molecule reactions is a fundamental problem. Ion-molecule reactions involving ambident nucleophiles represent a particularly interesting class of multichannel reactions. The factors that influence the inherent competition associated with reactions of ambident nucleophiles in solution have been studied extensively, since the neutral products can be easily distinguished.' In the gas phase, however, determination of the relative contributions of such competing pathways is extremely difficult, because only ionic species are dectected (Scheme I).
Journal of the American Chemical Society, 1994
... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In th... more ... with Chloride Ion Brian D. Wladkowski,t James L. Wilbur,* and John I. Brauman' ... In the early part of this century Petrenko-Krit~chenko,~~ Backer and van Mels,15 as well as Davies et a1.16 reported interesting (13) Shaik, S. S. J. Am. Cbem. Soc. 1983, 105, 4358. ...
The Journal of Organic Chemistry, 1989
The Journal of Organic Chemistry, 1992
orously stirred overnight at room temperature and then diluted in methanol (2 mL). After filtrati... more orously stirred overnight at room temperature and then diluted in methanol (2 mL). After filtration over Celite 545, the filtrate was evaporated under vacuum, diluted in ether, and then dried over magnesium sulfate. Flash chromatography (elution with methylene chloride-ethyl acetate, 65:35) gave the methyl ester LTB4 12 (41 mg; 70%): [ a I m~ +4.6' (c 0.39, CCC); IR (NaCl film) 3400 (OH), 3000 (=CHI, 1730 (C=O), 1595 (C=C--c=C) cm-'; 'H NMR (300 MHz, CDClJ 6 6.47 (1 H, dd, J = 14.5 Hz, J = 11 Hz, HB), 6.3 (1 H, ddd, J = 15 Hz, J 10.5 Hz, J = 1 Hz, HlJ, 6.21 (1 H, dd, J = 14.5 Hz, J = 10.5 Hz, Hs), 6.07 (1 H, t, J = 11 Hz, H,), 5.77 (1 H, dd, J = 15 Hz, J = 6.3 Hz, HI'), 5.55 (1 H, m, J = 10.5 Hz, J = 7 Hz, H15), 5.54 (1 H, dd, J = 11 Hz, J = 9.5 Hz, He), 5.34 (1 H, m, J = 10.5 Hz, J = 7 Hz, H14), 4.57 (1 H, m, J = 9.5 Hz, Hs), 4.2 (1 H, q, J = 6.3 Hz, H12), 3.65 (3 H, s, OCH,), 2.33 (4 H,m, H4) and 2.02 (2 H, q,J = 6 Hz, Hie), 1.72-1.60 (5 H, m, aliphatics H and OH), 1.36-1.21 (7 H, m, aliphatics H and OH), 0.87 (3 H, t, J = 6.5 Hz, CH3-20).