Kevin Range
Lock Haven University of Pennsylvania, Chemistry, Faculty Member
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Research Interests: Computer Science, Algorithms, Chemistry, Computational Chemistry, Benchmarking, and 15 moreMedicine, Computer Simulation, Biopolymers, Acknowledgement, Phase transition, Citation, CHEMICAL SCIENCES, Download, Phosphates, Energy Transfer, Gas Phase, Molecule, Affinities, Permission, and binding sites
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Research Interests: Thermodynamics, Chemistry, Inorganic Chemistry, Water, Density-functional theory, and 15 moreMedicine, Magnesium, Density Functional Theory, Metal Complexes, Ligand Binding, Metal, Enzyme, Phosphates, Metal ion, Molecular Conformation, Ligands, Biochemistry and cell biology, Ribozyme, Binding affinity, and protonation
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<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.©... more
<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.© The Author 2005. Published by Oxford University Press. All rights reserved Here, is the number of site-bound ions and Δ is the corresponding change in . Note: .
<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.©... more
<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.© The Author 2005. Published by Oxford University Press. All rights reserved The human genome consists of ∼3 × 10 bp, two copies of which are contained in the nucleus of each somatic cell. The distance between the base pairs is ∼3.4 Å, leading to a total length of = 2.04 m. The radius of gyration, including excluded volume effects, can be estimated () as , where is the persistence length, taken here to be 500 Å, leading to a value of 3.34 × 10 m.
We present results illuminating some of the major chemical processes in the vapor deposition of ZnO nanowires. The analysis of our deposition experiments indicates that carbon dioxide is a major oxidizing agent rather than carbon monoxide... more
We present results illuminating some of the major chemical processes in the vapor deposition of ZnO nanowires. The analysis of our deposition experiments indicates that carbon dioxide is a major oxidizing agent rather than carbon monoxide as previously ...
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Research Interests: Computer Graphics, Thermodynamics, Chemistry, Computational Chemistry, Quantum Theory, and 14 moreQuantum Mechanics, Medicine, Molecular Mechanics, Solvation, Molecular, Computer Software, Quantum, Density Functional Theory, THEORETICAL AND COMPUTATIONAL CHEMISTRY, Potential Energy Surface, Reaction Mechanism, Database, Static Electricity, and Biochemistry and cell biology
<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.©... more
<b>Copyright information:</b>Taken from "The contribution of phosphate–phosphate repulsions to the free energy of DNA bending"Nucleic Acids Research 2005;33(4):1257-1268.Published online 1 Mar 2005PMCID:PMC552960.© The Author 2005. Published by Oxford University Press. All rights reserved Red points are intra-strand repulsions, blue points are inter-strand repulsions. See and for the definitions of ε′ and ′. Data beyond 30 Å are not shown to better illustrate the deviations at short range; beyond 30 Å the ε′ values are all very close to that of bulk water (ε = 80).
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Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Links to the 3 articles that cite this article, as of the time of this article download • Access to high... more
Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Links to the 3 articles that cite this article, as of the time of this article download • Access to high resolution figures • Links to articles and content related to this article • Copyright permission to reproduce figures and/or text from this article
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Research Interests: Computer Graphics, Thermodynamics, Quantum Theory, Quantum Mechanics, Molecular Mechanics, and 9 moreMolecular, Computer Software, Density Functional Theory, THEORETICAL AND COMPUTATIONAL CHEMISTRY, Potential Energy Surface, Reaction Mechanism, Database, Static Electricity, and Biochemistry and cell biology
In this work density functional calculations and continuum solvation methods are applied to various biomolecular systems spanning a wide range of sizes. Gas phase calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level of... more
In this work density functional calculations and continuum solvation methods are applied to various biomolecular systems spanning a wide range of sizes. Gas phase calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level of theory are used in conjunction with extensive experimental data collected by collaborators to derive a comprehensive infrared spectral fingerprint of redox active tyrosine. This same level of theory, which we denote as QCRNA, in combination with various continuum solvation methods, is used to characterize the structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas-phase and in solution. In related work, various multilevel methods and density functionals are benchmarked against experimental proton affinities and gas phase basicities. These benchmark results are then used to predict proton affinities and gas phase basicities of molecules important in the study of biological phosphoryl transfer for which experimental data are not available. Finally, a Green's function approach based on a linear-scaling smooth conductor-like screening model of continuum solvation is combined with Monte-Carlo sampling of counterion condensation to make an estimate of the contribution of phosphate-phosphate repulsions to the free energy of DNA bending.
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DNA bending,is important,for the packaging,of genetic material, regulation of gene expression and inter- action of nucleic acids with proteins. Consequently, it is of considerable,interest to quantify,the energetic factors that must,be... more
DNA bending,is important,for the packaging,of genetic material, regulation of gene expression and inter- action of nucleic acids with proteins. Consequently, it is of considerable,interest to quantify,the energetic factors that must,be overcome,to induce,bending,of DNA, such as base stacking and phosphate– phosphate repulsions. In the present work, the elec- trostatic,contribution,of,phosphate–phosphate repulsions,to the free energy,of bending,DNA is examined,for 71 bp,linear,and,bent-form,model structures. The
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Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed... more
Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonia...
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Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron transfer rate are not well understood. To develop a more detailed... more
Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence, we have performed 14N and 15N electron spin echo envelope modulation (ESEEM) measurements on tyrosyl radical, generated either in polycrystalline tyrosinate or in its 15N-labeled isotopomer, by UV photolysis. 14N-ESEEM was also performed on tyrosyl radical generated in tyrosine-containing pentapeptide samples. Simulation of the 14N- and 15N-tyrosyl radical ESEEM measurements yielded no significant isotropic hyperfine splitting to the amine or amide nitrogen; the amplitude of the anisotropic, nitrogen hyperfine coupling (0.21 MHz) was consistent with a dipole-dipole distance of 3.0 A. Density functional theory was used to calculate the isotropic and anisotropic hyperfine couplings to the amino nitrogen in four different tyrosyl radical conformers. Comparison with the simulated data suggested that the lowest energy radical conformer, generated in tyrosine at pH 11, has a 76 degrees Calpha-Cbeta-C1&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-C2&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; ring and a -73 degrees C-Calpha-Cbeta-C1&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; backbone dihedral angle. In addition, the magnitude, orientation, and asymmetry of the nuclear quadrupole coupling tensor were derived from analysis of the tyrosyl radical 14N-ESEEM. The simulations showed differences in the coupling and orientation of the nuclear quadrupole tensor, when the tyrosinate and pentapeptide samples were compared. These results suggest sequence- or conformation-induced changes in the ionic character of the NH bond in different tyrosine-containing peptides.
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Benchmark quantum calculations of proton affinities and gas-phase basicities of molecules relevant to biochemical processes, particularly acid/base catalysis, are presented and compared for a variety of multilevel and density functional... more
Benchmark quantum calculations of proton affinities and gas-phase basicities of molecules relevant to biochemical processes, particularly acid/base catalysis, are presented and compared for a variety of multilevel and density functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes, including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states and provides a benchmark database for development of next-generation semiempirical and approximate density functional quantum models and parametrization of methods to predict pK(a) values and relative solvation energies.
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Proton-coupled electron-transfer reactions are central to enzymatic mechanism in many proteins. In several enzymes, essential electron-transfer reactions involve oxidation and reduction of tyrosine side chains. For these redox-active... more
Proton-coupled electron-transfer reactions are central to enzymatic mechanism in many proteins. In several enzymes, essential electron-transfer reactions involve oxidation and reduction of tyrosine side chains. For these redox-active tyrosines, proton transfer couples with electron transfer, because the phenolic pKA of the tyrosine is altered by changes in the tyrosine redox state. To develop an experimentally tractable peptide system in which the effect of proton and electron coupling can be investigated, we have designed a novel amino acid sequence that contains one tyrosine residue. The tyrosine can be oxidized by ultraviolet photolysis or electrochemical methods and has a potential cross-strand interaction with a histidine residue. NMR spectroscopy shows that the peptide forms a beta-hairpin with several interstrand dipolar contacts between the histidine and tyrosine side chains. The effect of the cross-strand interaction was probed by electron paramagnetic resonance and electrochemistry. The data are consistent with an increase in histidine pKA when the tyrosine is oxidized; the effect of this thermodynamic coupling is to increase tyrosyl radical yield at low pH. The coupling mechanism is attributed to an interstrand pi-cation interaction, which stabilizes the tyrosyl radical. A similar interaction between histidine and tyrosine in enzymes provides a regulatory mechanism for enzymatic electron-transfer reactions.
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Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed... more
Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions
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Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes, including prostaglandin H synthase, galactose oxidase, ribonucleotide reductase, and photosystem II. Magnetic resonance and vibrational... more
Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes, including prostaglandin H synthase, galactose oxidase, ribonucleotide reductase, and photosystem II. Magnetic resonance and vibrational spectroscopy provide methods with which to study the structures of redox-active amino acids in proteins. In this report, ultraviolet photolysis was used to generate tyrosyl radicals from polycrystalline tyrosinate or dipeptides, and the structure of the radical was investigated with EPR and reaction-induced FT-IR spectroscopy at 77 K. Photolysis at 77 K is expected to generate a neutral tyrosyl radical through oxidation of the aromatic ring. EPR and FT-IR results obtained from (13)C-labeled tyrosine were consistent with that expectation. Surprisingly, labeling of the tyrosyl amino group with (15)N also resulted in isotope-shifted bands in the photolysis spectrum. The force constant of a NH deformation mode increased when the tyrosyl radical was generated. These data suggest an interaction between the pi system of the tyrosyl radical and the amino group. In spectra acquired from the dipeptides, evidence for a sequence-dependent interaction between the tyrosyl radical and the amide bond of the dipeptide was also obtained. We postulate that perturbation of the amino or the amide/imide groups may occur through a spin polarization mechanism, which is indirectly detected as a change in NH force constant. This conclusion is supported by density functional calculations, which suggest a conformationally sensitive delocalization of spin density onto the amino and carboxylate groups of the tyrosyl radical. These experiments provide a step toward a detailed spectral interpretation for protein-based tyrosyl radicals.
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Used mini lightsticks will fluoresce when inserted in a UV laser beam, making it easy to demonstrate that light of the same color is produced in both fluorescence and chemiluminescence. The chemiluminescence (CL) spectrum and the... more
Used mini lightsticks will fluoresce when inserted in a UV laser beam, making it easy to demonstrate that light of the same color is produced in both fluorescence and chemiluminescence. The chemiluminescence (CL) spectrum and the laser-induced fluorescence (LIF) spectrum obtained from a red mini lightstick are presented and compared, and strong similarity is noted: both spectra show peaks at