J. Kubelka

发表

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein.

Regine Herbst-Irmer, Jan Kubelka, William A Eaton, 2005, Proceedings of the National Academy of Sciences of the United States of America.

The protein folding 'speed limit'.

J. Hofrichter, W. Eaton, J. Kubelka, 2004, Current opinion in structural biology.

Experimental tests of villin subdomain folding simulations.

J. Hofrichter, W. Eaton, J. Kubelka, 2003, Journal of molecular biology.

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

E. Henry, J. Hofrichter, W. Eaton, 2008, Proceedings of the National Academy of Sciences.

Sub-microsecond protein folding.

J. Hofrichter, W. Eaton, D. Davies, 2006, Journal of molecular biology.

Discrimination between Peptide 310- and α-Helices. Theoretical Analysis of the Impact of α-Methyl Substitution on Experimental Spectra

T. Keiderling, J. Kubelka, R. A. Silva, 2002 .

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

D. Liberles, J. Kubelka, J. Lai, 2012, Journal of molecular biology.

Differentiation of β-Sheet-Forming Structures: Ab Initio-Based Simulations of IR Absorption and Vibrational CD for Model Peptide and Protein β-Sheets

T. Keiderling, J. Kubelka, 2001 .

Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution

Johan A. Grahnen, D. Liberles, J. Kubelka, 2011, Journal of Molecular Evolution.

Multivariate analysis of spectral data with frequency shifts: application to temperature dependent infrared spectra of peptides and proteins.

J. Kubelka, 2013, Analytical chemistry.

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers

J. Kubelka, F. Bickelhaupt, F. Bickelhaupt, 2017, The journal of physical chemistry. A.

Supramolecular ssDNA templated porphyrin and metalloporphyrin nanoassemblies with tunable helicity.

Brian M. Leonard, Gevorg Sargsyan, J. Kubelka, 2014, Chemistry.

Hydrogen gas formation from the photolysis of rhenium hydrides - mechanistic and computational studies.

J. Kubelka, Jianqiang Huo, J. O. Hoberg, 2019, Dalton transactions.

Ligand induced circular dichroism and circularly polarized luminescence in CdSe quantum dots.

Brian M. Leonard, J. Kubelka, M. Balaz, 2013, ACS nano.

Solid Parahydrogen Infrared Matrix Isolation and Computational Studies of Lin-(C2H4)m Complexes.

David T. Anderson, J. Kubelka, David T Anderson, 2018, The journal of physical chemistry. A.

Isotope-edited infrared spectroscopy.

J. Kubelka, Ginka S. Buchner, 2012, Methods in molecular biology.

Chirality Inversion of CdSe and CdS Quantum Dots without Changing the Stereochemistry of the Capping Ligand.

Brian M. Leonard, Levente G. Pap, J. Kubelka, 2016, ACS nano.

CdSe Quantum Dots Functionalized with Chiral, Thiol-Free Carboxylic Acids: Unraveling Structural Requirements for Ligand-Induced Chirality.

Brian M. Leonard, J. Kubelka, M. Balaz, 2017, ACS nano.

Formation and helicity control of ssDNA templated porphyrin nanoassemblies.

Gevorg Sargsyan, J. Kubelka, M. Balaz, 2013, Chemical communications.

Quantitative Predictions and Experimental Validation of Liquid-Vapor Interfacial Tension in Binary and Ternary Mixtures of Alkanes Using Molecular Dynamics Simulations.

J. Kubelka, M. Piri, Reihaneh Toutouni, 2022, The journal of physical chemistry. B.

Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics

J. Kubelka, 2009, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Functional Nanoassemblies with Mirror-Image Chiroptical Properties Templated by a Single Homochiral DNA Strand

Brian M. Leonard, J. Kubelka, M. Balaz, 2020 .

Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

P. Bouř, T. Keiderling, J. Kubelka, 2002, Biopolymers.

Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory.

W. Welch, T. Keiderling, J. Kubelka, 2013, The journal of physical chemistry. B.

Vibrational Circular Dichroism of Biopolymers: Summary of Methods and Applications

T. Keiderling, J. Kubelka, J. Hilario, 2005 .

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution.

P. Bouř, T. Keiderling, J. Kubelka, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Temperature dependence of peptide carboxylic group IR spectra in the amide I′ region at neutral and acidic pH

J. Kubelka, B. A. Anderson, Ginka S. Kubelka, 2015 .

Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region.

J. Kubelka, B. A. Anderson, Alex Literati, 2015, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

Insight into the packing pattern of β2 fibrils: a model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy.

W. Welch, T. Keiderling, J. Kubelka, 2013, Biomacromolecules.

Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations.

W. Welch, T. Keiderling, J. Kubelka, 2013, The journal of physical chemistry. B.

DFT-based simulations of amide I' IR spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model.

W. Welch, J. Kubelka, 2012, The journal of physical chemistry. B.

DFT-based simulations of IR amide I' spectra for a small protein in solution. Comparison of explicit and empirical solvent models.

Johan A. Grahnen, J. Kubelka, Krista E. Amunson, 2010, Journal of Physical Chemistry B.

Quantum mechanical calculations of peptide vibrational force fields and spectral intensities

P. Bouř, T. Keiderling, J. Kubelka, 2009 .

Simulation of Vibrational Spectra of Large Molecules by Arbitrary Time Propagation.

P. Bouř, J. Kubelka, 2009, Journal of chemical theory and computation.

Cross-strand coupling of a beta-hairpin peptide stabilized with an Aib-Gly turn studied using isotope-edited IR spectroscopy.

Joohyun Kim, T. Keiderling, J. Kubelka, 2007, Journal of the American Chemical Society.

Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.

J. Kubelka, D. R. Turner, 2007, Journal of Physical Chemistry B.

Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures

P. Bouř, Joohyun Kim, T. Keiderling, 2006 .

Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water.

T. Keiderling, J. Kubelka, Rong Huang, 2005, Journal of Physical Chemistry B.

Nature of vibrational coupling in helical peptides: an isotopic labeling study.

T. Keiderling, J. Kubelka, R. A. Silva, 2004, Journal of the American Chemical Society.

Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution.

T. Keiderling, J. Kubelka, J. Hilario, 2003, Journal of the American Chemical Society.

The anomalous infrared amide I intensity distribution in (13)C isotopically labeled peptide beta-sheets comes from extended, multiple-stranded structures: an ab initio study.

T. Keiderling, J. Kubelka, J. and, 2001, Journal of the American Chemical Society.

Simulations of oligopeptide vibrational CD: Effects of isotopic labeling

P. Bouř, T. Keiderling, J. Kubelka, 2000, Biopolymers.

Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides.

C. Toniolo, F. Formaggio, M. Crisma, 2002, Biopolymers.

IR study of cross-strand coupling in a β-hairpin peptide using isotopic labels

T. Keiderling, J. Kubelka, V. Setnička, 2005 .

Temperature dependence of amino acid side chain IR absorptions in the amide I' region

J. Kubelka, B. A. Anderson, Alex Literati, 2014, Biopolymers.

Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy.

J. Kubelka, Ginka S. Kubelka, 2014, Journal of the American Chemical Society.

Temperature Effects on the Optical Path Length of Infrared Liquid Transmission Cells

J. Kubelka, B. A. Anderson, Krista E. Amunson, 2011, Applied spectroscopy.

DFT-Based Simulations of Ir Amide I’ Spectra for a Small Protein in Solution

Johan A. Grahnen, J. Kubelka, 2011 .

Simulations of the temperature dependence of amide I vibration.

P. Bouř, J. Kubelka, Jakub Kaminský, 2011, The journal of physical chemistry. A.

On the temperature dependence of amide I intensities of peptides in solution

J. Kubelka, P. Stawski, Krista E. Amunson, 2009 .

Beyond the nearest‐neighbor Zimm–Bragg model for helix‐coil transition in peptides

J. Kubelka, A. Murza, 2009, Biopolymers.

Site-specific unfolding thermodynamics of a helix-turn-helix protein.

J. Kubelka, Krista E. Amunson, Loren Ackels, 2008, Journal of the American Chemical Society.

On the temperature dependence of amide I frequencies of peptides in solution.

J. Kubelka, Krista E. Amunson, 2007, The journal of physical chemistry. B.

ChemInform Abstract: Chirality in Peptide Vibrations: ab initio Computational Studies of Length, Solvation, Hydrogen Bond, Dipole Coupling, and Isotope Effects on Vibrational CD.

P. Bouř, T. Keiderling, J. Kubelka, 2002 .

Spectroscopic characterization of selected β- sheet hairpin models

T. Keiderling, S. Gellman, F. Syud, 2002 .

Sequence, structure, and cooperativity in folding of elementary protein structural motifs

J. Kubelka, J. Lai, Ginka S. Kubelka, 2015, Proceedings of the National Academy of Sciences.

Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity.

J. Kubelka, Jakub Kaminský, O. Socha, 2021, The journal of physical chemistry. B.

Relationship between molecular charge distribution and wettability reversal efficiency of cationic surfactants on calcite surfaces

J. Kubelka, M. Piri, Shixun Bai, 2020 .

A positively charged calcite surface model for molecular dynamics studies of wettability alteration.

J. Kubelka, M. Piri, Shixun Bai, 2020, Journal of colloid and interface science.

Wettability reversal on oil-wet calcite surfaces: Experimental and computational investigations of the effect of the hydrophobic chain length of cationic surfactants.

J. Kubelka, M. Piri, Shixun Bai, 2022, Journal of colloid and interface science.

Effect of asphaltene structure on association and aggregation using molecular dynamics.

W. Welch, J. Kubelka, Lamia Goual, 2013, The journal of physical chemistry. B.

Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets.

T. Keiderling, J. Kubelka, 2001, Journal of the American Chemical Society.

Biophysical and structural considerations for protein sequence evolution

Johan A. Grahnen, Jan Kubelka, David A Liberles, 2011, BMC Evolutionary Biology.

A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution

Claudia C Weber, Peter B Chi, Dohyup Kim, 2018, Proteins.

Specificity of the initial collapse in the folding of the cold shock protein.

Jan Kubelka, Elisha Haas, E. Haas, 2006, Journal of molecular biology.

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

Frank Küster, Robert B Best, Benjamin Schuler, 2009, Proceedings of the National Academy of Sciences.

The N-terminal Domain Allosterically Regulates Cleavage and Activation of the Epithelial Sodium Channel*

N. Dokholyan, P. Kota, M. Gentzsch, 2014, The Journal of Biological Chemistry.

Epithelial Sodium Channel Regulates Cleavage and Activation of the The N-terminal Domain Allosterically Molecular Biophysics

N. Dokholyan, P. Kota, M. Gentzsch, 2014 .

Toward the Rational Design of Chemical Formulations for EOR from Carbonates: Molecular–Level Understanding of Carbonate Wettability and its Reversal by Surfactants and Ions

J. Kubelka, M. Piri, Shixun Bai, 2021, Day 4 Thu, November 18, 2021.

Surfactant-induced wettability reversal on oil-wet calcite surfaces: Experimentation and molecular dynamics simulations with scaled-charges.

J. Kubelka, M. Piri, Shixun Bai, 2021, Journal of colloid and interface science.

Effects of Surfactant Charge and Molecular Structure on Wettability Alteration of Calcite: Insights from Molecular Dynamics Simulations.

J. Kubelka, M. Piri, Shixun Bai, 2021, The journal of physical chemistry. B.

Liquid-Vapor Interfacial Tension in Alkane Mixtures: Improving Predictive Capabilities of Molecular Dynamics Simulations.

J. Kubelka, M. Piri, Reihaneh Toutouni, 2022, The journal of physical chemistry. B.

Wettability alteration by Smart Water multi-ion exchange in carbonates: A molecular dynamics simulation study

J. Kubelka, M. Piri, Shixun Bai, 2021, Journal of Molecular Liquids.

Wettability Reversal on Dolomite Surfaces by Divalent Ions and Surfactants: An Experimental and Molecular Dynamics Simulation Study.

J. Kubelka, M. Piri, Shixun Bai, 2021, Langmuir : the ACS journal of surfaces and colloids.

Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids

J. Kubelka, B. Francis, Kevin J. Watkins, 2017, Life.

Theoretical Study of Vibrationally Averaged Dipole Moments for the Ground and Excited C═O Stretching States of trans-Formic Acid.

David T. Anderson, P. Bouř, J. Kubelka, 2010, Journal of chemical theory and computation.

A Phylogenetic Analysis of Normal Modes Evolution in Enzymes and its Relationship to Enzyme Function

Jan Kubelka, David A. Liberles, D. Liberles, 2012 .

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

Jan Kubelka, Nicolae-Viorel Buchete, N. Buchete, 2011, Biochimica et biophysica acta.

T1BT* structural study of an anti-plasmodial peptide through NMR and molecular dynamics

J. Kubelka, G. Armstrong, T. Lehmann, 2013, Malaria Journal.

The Effect of Molecular Isomerism on the Induced Circular Dichroism of Cadmium Sulfide Quantum Dots

Brian M. Leonard, J. Kubelka, M. Balaz, 2021, Journal of Materials Chemistry C.

Experimental and Theoretical Investigation of the Geometry and Vibrational Frequencies of 1,2,3-Triazole, 1,2,4-Triazole, and Tetrazole Anions

J. Kubelka, A. A. El-Azhary, H. Suter, 1998 .

Determination of ultrafast protein folding rates from loop formation dynamics.

J. Hofrichter, W. Eaton, J. Kubelka, 2005, Journal of molecular biology.

Effect of Oil Carboxylate Hydrophobicity on Calcite Wettability and its Reversal by Cationic Surfactants: An Experimental and Molecular Dynamics Simulation Investigation

J. Kubelka, M. Piri, Julius Tetteh, 2023, Journal of Molecular Liquids.

Atomistic Molecular Dynamics Simulations of Surfactant-Induced Wettability Alteration in Crevices of Calcite Nanopores

J. Kubelka, M. Piri, Shixun Bai, 2020 .

Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data.

Jan Kubelka, William A Eaton, Victor Muñoz, 2008, The journal of physical chemistry. B.

Novel Use of a Static Modification of Two-Dimensional Correlation Analysis. Part I: Comparison of the Secondary Structure Sensitivity of Electronic Circular Dichroism, FT-IR, and Raman Spectra of Proteins

T. Keiderling, J. Kubelka, P. Pančoška, 1999 .

Novel Use of a Static Modification of Two-Dimensional Correlation Analysis. Part II: Hetero-Spectral Correlations of Protein Raman, FT-IR, and Circular Dichroism Spectra

T. Keiderling, J. Kubelka, P. Pančoška, 1999 .

Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration.

E. Henry, J. Hofrichter, W. Eaton, 2007, Journal of the American Chemical Society.

Unusual cold denaturation of a small protein domain.

J. Kubelka, Amy E. Reece, S. Niebling, 2012, Biochemistry.

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

J. Kubelka, Ginka S. Buchner, Ronan D. Murphy, 2011, Biochimica et biophysica acta.

Experimental and Theoretical Investigation of the Geometry and Vibrational Frequencies of

J. Kubelka, H. Suter, A. El-Azhary, 1998 .

Effect of Mutations on the Global and Site-Specific Stability and Folding of an Elementary Protein Structural Motif.

J. Kubelka, J. Lai, Ginka S. Kubelka, 2018, The journal of physical chemistry. B.

Ligand induced circular dichroism and circularly polarized luminescence in CdSe quantum dots.

Brian M. Leonard, J. Kubelka, M. Balaz, 2013, ACS nano.