Search filters

List of works by Andrei Tokmakoff

5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex

scientific article published on 14 January 2020

A lattice model for the interpretation of oligonucleotide hybridization experiments

scientific article published on 01 May 2019

A molecular interpretation of 2D IR protein folding experiments with Markov state models

scientific article (publication date: 18 March 2014)

A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy ⬇️

scientific article published on 01 April 2012

Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins ⬇️

scientific article published on December 27, 2012

Amide I two-dimensional infrared spectroscopy of proteins

scientific article published on 21 February 2008

Amide I two-dimensional infrared spectroscopy of β-hairpin peptides

scientific article published on 01 January 2007

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions

scientific article

Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity

scientific article published in March 2009

Anharmonic Vibrational Modes of Nucleic Acid Bases Revealed by 2D IR Spectroscopy

article

Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy

scientific article

Broadband 2D IR spectroscopy reveals dominant asymmetric H5O2+ proton hydration structures in acid solutions

scientific article published on 30 July 2018

Characterization of spectral diffusion from two-dimensional line shapes

scientific article published on 01 August 2006

Chemistry. Shining light on the rapidly evolving structure of water

scientific article published on 01 July 2007

Coherent two-dimensional infrared spectroscopy: quantitative analysis of protein secondary structure in solution.

scientific article

Collective Hydrogen Bond Reorganization in Water Studied with Temperature-Dependent Ultrafast Infrared Spectroscopy ⬇️

scientific article published on March 18, 2011

Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy

scientific article published on 01 May 2014

Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy.

scientific article

Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics.

scientific article

Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.

scientific article

Cooperative cold denaturation: the case of the C-terminal domain of ribosomal protein L9.

scientific article

Correction to "Length-Dependent Melting Kinetics of Short DNA Oligonucleotides Using Temperature-Jump IR Spectroscopy"

scientific article published on 28 February 2019

Correction: Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

scientific article published on 5 July 2017

Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy

scientific article published on 15 November 2002

Crossover from hydrogen to chemical bonding

scientific article published on 01 January 2021

Crystallization of Enantiomerically Pure Proteins from Quasi-Racemic Mixtures: Structure Determination by X-Ray Diffraction of Isotope-Labeled Ester Insulin and Human Insulin

scientific article

DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site

scientific article published on 22 September 2020

Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

scientific article published on 01 September 2020

Delocalization and stretch-bend mixing of the HOH bend in liquid water.

scientific article published in August 2017

Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy

scientific article published on 13 October 2021

Differences in the Vibrational Dynamics of H(2)O and D(2)O: Observation of Symmetric and Antisymmetric Stretching Vibrations in Heavy Water.

scientific article

Direct Observation of Activated Kinetics and Downhill Dynamics in DNA Dehybridization.

scientific article published on 5 March 2018

Direct Observation of Ion Pairing in Aqueous Nitric Acid Using 2D Infrared Spectroscopy

scientific article published on 20 December 2018

Direct observation of ground-state lactam–lactim tautomerization using temperature-jump transient 2D IR spectroscopy ⬇️

scientific article published on May 20, 2013

Direct observation of intermolecular interactions mediated by hydrogen bonding

scientific article published on 01 July 2014

Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch

scientific article

Dispersion compensation with optical materials for compression of intense sub-100-fs mid-infrared pulses

scientific article published on 01 March 2002

Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons.

scientific article

Efficient Total Chemical Synthesis of (13) C=(18) O Isotopomers of Human Insulin for Isotope-Edited FTIR.

scientific article

Electric field fluctuations drive vibrational dephasing in water

scientific article published on 01 October 2005

Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment ⬇️

scientific article published on April 7, 2013

Entropic barriers in the kinetics of aqueous proton transfer

scientific article published on 01 July 2019

Experimental Evidence of Fermi Resonances in Isotopically Dilute Water from Ultrafast Broadband IR Spectroscopy ⬇️

scientific article published on May 16, 2013

Fluorescence-Encoded Infrared Spectroscopy: Ultrafast Vibrational Spectroscopy on Small Ensembles of Molecules in Solution

scientific article published on 09 April 2019

Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy.

scientific article

Fourier Transform Fluorescence-Encoded Infrared Spectroscopy.

scientific article

Heterodyne-detected dispersed vibrational echo spectroscopy

scientific article

High-Level VSCF/VCI Calculations Decode the Vibrational Spectrum of the Aqueous Proton

scientific article published on 13 August 2019

Hydrogen bonds in liquid water are broken only fleetingly

scientific article

IR spectral assignments for the hydrated excess proton in liquid water.

scientific article

Identification of Lactam–Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy ⬇️

scientific article published on October 24, 2012

Identifying Residual Structure in Intrinsically Disordered Systems: A 2D IR Spectroscopic Study of the GVGXPGVG Peptide ⬇️

scientific article published on March 7, 2012

Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding

scientific article published on 09 June 2020

Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

scientific article

Interplay of Ion-Water and Water-Water Interactions within the Hydration Shells of Nitrate and Carbonate Directly Probed with 2D IR Spectroscopy

scientific article

Isotope-enriched protein standards for computational amide I spectroscopy

scientific article published on March 2015

Length-Dependent Melting Kinetics of Short DNA Oligonucleotides Using Temperature-Jump IR Spectroscopy

scientific article published on 22 January 2019

Local and collective reaction coordinates in the transport of the aqueous hydroxide ion

scientific article published on 07 April 2014

Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D(2)O

scientific article published on 01 February 2005

Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations.

scientific article published in September 2010

Molecular modeling and assignment of IR spectra of the hydrated excess proton in isotopically dilute water.

scientific article

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

scientific article published on 01 November 2006

Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics

scientific article published in November 2006

Nanosecond time scale dynamics of pseudo-nematic domains in the isotropic phase of liquid crystals

Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions

scholarly article

Obtaining absorptive line shapes in two-dimensional infrared vibrational correlation spectra

scientific article published on 30 January 2003

Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA

scientific article published on 05 February 2020

Phonon-assisted exciton relaxation dynamics for a (6,5)-enriched DNA-wrapped single-walled carbon nanotube sample

article

Picosecond Proton Transfer Kinetics in Water Revealed with Ultrafast IR Spectroscopy.

scientific article published on 16 February 2018

Picosecond infrared vibrational photon echoes in a liquid and glass using a free electron laser

scientific article published on 01 May 1993

Polarizable molecules in the vibrational spectroscopy of water

scientific article

Preface: Special Topic on Biological Water

Probing Local Structural Events in β-Hairpin Unfolding with Transient Nonlinear Infrared Spectroscopy

scientific article published on 01 January 2007

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

scientific article published in December 2008

Proton transfer in concentrated aqueous hydroxide visualized using ultrafast infrared spectroscopy.

scientific article published on 11 February 2011

Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala

scientific article published on 01 June 2018

Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

scientific article published on 13 October 2016

Residual Native Structure in a Thermally Denatured β-Hairpin

scientific article published on 01 September 2005

Revealing the Dynamical Role of Co-Solvents in the Coupled Folding and Dimerization of Insulin

scientific article published on 13 May 2020

Robust excitons inhabit soft supramolecular nanotubes

scientific article

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport

scientific article published on 01 December 2015

Role of water in electron-initiated processes and radical chemistry: issues and scientific advances

scientific article

Sequence-Dependent Mechanism of DNA Oligonucleotide Dehybridization Resolved through Infrared Spectroscopy

scientific article published on 12 August 2016

Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy

scientific article published on 01 May 2004

Single-shot two-dimensional infrared spectroscopy

scientific article published in January 2007

Single-shot two-dimensional spectrometer

scientific article published in January 2006

Single-stage MHz mid-IR OPA using LiGaSand a fiber laser pump source

scientific article published on 01 March 2018

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

scientific article published in December 2011

Source for ultrafast continuum infrared and terahertz radiation

scientific article

Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra.

scientific article

Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling

scientific article

Structural information from two-dimensional fifth-order Raman spectroscopy

Structural rearrangements in water viewed through two-dimensional infrared spectroscopy.

scientific article published on September 2009

Studying Protein-Protein Binding through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer.

scientific article

Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2'-deoxycytidine

scientific article

Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating

scientific article published on 09 September 2020

Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy

scientific article

Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface

scientific article published in July 2008

The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes ofN-Methylacetamide†

article

The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study.

scientific article published on August 2017

Time-resolved measurements of an ion channel conformational change driven by a membrane phase transition.

scientific article published on 25 September 2017

Transient 2D IR spectroscopy of ubiquitin unfolding dynamics

scientific article

Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics

scientific article

Transient two-dimensional spectroscopy with linear absorption corrections applied to temperature-jump two-dimensional infrared

article

Two-Photon-Excited Fluorescence-Encoded Infrared Spectroscopy

scientific article published on 14 November 2016

Two-dimensional Fourier transform spectroscopy in the pump-probe geometry

scientific article published on 01 October 2007

Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity

scientific article

Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure

scientific article

Two-dimensional line-shape analysis of photon-echo signal

article

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

scientific article published on 01 August 2011

Ultrafast 2D IR microscopy

scientific article

Ultrafast 2D IR spectroscopy of the excess proton in liquid water

scientific article

Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes.

scientific article

Ultrafast Hydrogen-Bond Dynamics in the Infrared Spectroscopy of Water ⬇️

scientific article published on September 19, 2003

Ultrafast N-H vibrational dynamics of cyclic doubly hydrogen-bonded homo- and heterodimers.

scientific article published on 27 September 2008

Upconversion multichannel infrared spectrometer

scientific article published on 01 July 2005

Vibrational Probe of Aqueous Electrolytes - The Field is Not Enough

scientific article published on 20 July 2020

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

scientific article published on 29 June 2020

Vibrational anharmonicities revealed by coherent two-dimensional infrared spectroscopy

scientific article published on 01 March 2001

Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy

scientific article

Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

scientific article published in November 2015

Vibrational excitons in ionophores: experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels

scientific article published on 18 November 2011

Visualization and characterization of the infrared active amide I vibrations of proteins

scientific article published on 01 February 2006

Visualizing KcsA conformational changes upon ion binding by infrared spectroscopy and atomistic modeling

scientific article published on 25 April 2015

Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange two-dimensional infrared spectroscopy.

scientific article

Water vibrations have strongly mixed intra- and intermolecular character

scientific article published on 22 September 2013

Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability

scientific article published on 7 December 2015

Paulina is supported by:

About Paulina

Help