The Experts below are selected from a list of 110823 Experts worldwide ranked by ideXlab platform
Andrei Tokmakoff - One of the best experts on this subject based on the ideXlab platform.
-
studying protein protein binding through t jump induced dissociation transient 2d ir Spectroscopy of insulin dimer
Journal of Physical Chemistry B, 2016Co-Authors: Xinxing Zhang, Chunte Sam Peng, Kevin C Jones, Carlos R Baiz, Ann Fitzpatrick, Chijui Feng, Andrei TokmakoffAbstract:Insulin homodimer associates through the coupled folding and binding of two partially disordered monomers. We aim to understand this dynamics by observing insulin dimer dissociation initiated with a nanosecond temperature jump using transient Two-Dimensional Infrared Spectroscopy (2D IR) of amide I vibrations. With the help of equilibrium FTIR and 2D IR spectra, and through a systematic study of the dependence of dissociation kinetics on temperature and insulin concentration, we are able to decompose and analyze the spectral evolution associated with different secondary structures. We find that the dissociation under all conditions is characterized by two processes whose influence on the kinetics varies with temperature: the unfolding of the β sheet at the dimer interface observed as exponential kinetics between 250 and 1000 μs and nonexponential kinetics between 5 and 150 μs that we attribute to monomer disordering. Microscopic reversibility arguments lead us to conclude that dimer association requires s...
-
computational amide i 2d ir Spectroscopy as a probe of protein structure and dynamics
Annual Review of Physical Chemistry, 2016Co-Authors: Mike Reppert, Andrei TokmakoffAbstract:Two-Dimensional Infrared Spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the Spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments an...
-
distinguishing gramicidin d conformers through two dimensional Infrared Spectroscopy of vibrational excitons
Journal of Chemical Physics, 2015Co-Authors: Paul Stevenson, Andrei TokmakoffAbstract:Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D Infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.
-
water vibrations have strongly mixed intra and intermolecular character
Nature Chemistry, 2013Co-Authors: Andrei Tokmakoff, Krupa Ramasesha, Luigi De Marco, Aritra MandalAbstract:Liquid water has the unique ability to mediate ultrafast energy transfer and relaxation in aqueous chemical reactions. Ultrafast broadband Two-Dimensional Infrared Spectroscopy that probes vibrations spanning the mid-Infrared region with sub-70-femtosecond time resolution now provides evidence for highly intertwined intra- and intermolecular vibrations in water that act to efficiently dissipate vibrational energy.
-
coherent two dimensional Infrared Spectroscopy quantitative analysis of protein secondary structure in solution
Analyst, 2012Co-Authors: Carlos R Baiz, Chunte Sam Peng, Kevin C Jones, Mike Reppert, Andrei TokmakoffAbstract:We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent Two-Dimensional Infrared (2DIR) Spectroscopy of backbone amide I vibrations (1550–1720 cm−1). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured Two-Dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional Infrared absorption of the proteins in the library.
Jianping Wang - One of the best experts on this subject based on the ideXlab platform.
-
ultrafast vibrational energy transfer through the covalent bond and intra and intermolecular hydrogen bonds in a supramolecular dimer by two dimensional Infrared Spectroscopy
Journal of Physical Chemistry B, 2020Co-Authors: Xueqian Dong, Pengyun Yu, Juan Zhao, Sumin Wang, Fan Yang, Lizhu Wu, Chenho Tung, Jianping WangAbstract:: In this work, the structural fluctuations and vibrational energy transfer dynamics in a supramolecular homodimer model, which is composed of 2-(9-anthracene)ureido-6-(1-undecyl)-4[1H]-pyrimidinone (UPAn) with quadruple intermolecular and single intramolecular hydrogen bonds (HBs), have been examined using ultrafast Two-Dimensional Infrared (2D IR) and steady-state IR spectroscopies. A less structurally fluctuating intermolecular HB is found between the pyrimidinone C═O and ureido N-H groups. However, a larger structurally fluctuating intramolecular HB is suggested by the equilibrium and dynamical line-shape measurements of the ureido C═O stretch. Further, dynamical time-dependent 2D IR diagonal and off-diagonal signals show that intra- and intermolecular vibrational energy transfer processes occur on the picosecond timescale, where the latter is more efficient due to intermolecular hydrogen bonding interaction and through-space interaction.
-
ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two dimensional Infrared Spectroscopy
Journal of Chemical Physics, 2019Co-Authors: Xuan Zheng, Jianping WangAbstract:In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear Infrared and nonlinear Two-Dimensional Infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these delocalized C=N stretching modes, acting as an efficient vibrational energy transfer channel. This work reasonably connects the experimentally observed IR signature to a specific g-CN structure and also provides the first report on the ultrafast intramolecular processes of such carbon nitride systems. The obtained results are fundamentally important for understanding the molecular mechanisms of such carbon-nitride based functional materials.
-
ultrafast intramolecular vibrational energy transfer in carbon nitride hydrocolloid examined by femtosecond two dimensional Infrared Spectroscopy
Journal of Chemical Physics, 2019Co-Authors: Xuan Zheng, Pengyun Yu, Jianping WangAbstract:In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear Infrared and nonlinear Two-Dimensional Infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these delocalized C=N stretching modes, acting as an efficient vibrational energy transfer channel. This work reasonably connects the experimentally observed IR signature to a specific g-CN structure and also provides the first report on the ultrafast intramolecular processes of such carbon nitride systems. The obtained results are fundamentally important for understanding the molecular mechanisms of such carbon-nitride based functional materials.In this work, ultrafast vibrational and structural processes in a graphitic carbon nitride hydrocolloid system were studied using a combination of linear Infrared and nonlinear Two-Dimensional Infrared (2D IR) spectroscopies. The experimentally observed three IR line shapes in the C=N stretching vibration frequency region were analyzed and attributed to the rigid and conjugated molecular frame of the prepared g-CN molecular species, which is believed to be a dimeric tris-s-triazine, as well as attributed to insignificant solvent influence on the delocalized C=N vibrations. Vibrational transition density cubes were also computed for the proposed g-CN dimer, confirming the heterocyclic C=N stretching nature of the three IR absorption peaks. Intramolecular vibrational energy transfer dynamics and spectral diffusion of the g-CN system were characterized by examining a series of time-dependent 2D IR spectra. A picosecond intramolecular vibrational energy redistribution process was found to occur among these de...
-
central metal effect on intramolecular vibrational energy transfer of m co 5br m mn re probed by two dimensional Infrared Spectroscopy
Physical Chemistry Chemical Physics, 2018Co-Authors: Fan Yang, Juan Zhao, Xueqian Dong, Minjun Feng, Jianping WangAbstract:Vibrational energy transfer in transition metal complexes with flexible structures in condensed phases is of central importance to catalytical chemistry processes. In this work, two molecules with different metal atoms, M(CO)5Br (where M = Mn, Re), were used as model systems, and their axial and radial carbonyl stretching modes as Infrared probes. The central-metal effect on intramolecular vibrational energy redistribution (IVR) in M(CO)5Br was investigated in polar and nonpolar solvents. The linear Infrared (IR) peak splitting between carbonyl vibrations increases as the metal atom changes from Mn to Re. The waiting-time dependent Two-Dimensional Infrared diagonal- and off-diagonal peak amplitudes reveal a faster IVR process in Re(CO)5Br than in Mn(CO)5Br. With the aid of density functional theory (DFT) calculations, the central-metal effect on IVR time linearly correlates with the vibrational coupling strength between the two involved modes. In addition, the polar solvent is found to accelerate the IVR process by affecting the anharmonic vibrational potentials of a solute vibration mode.
-
efficient intramolecular vibrational excitonic energy transfer in ru3 co 12 cluster revealed by two dimensional Infrared Spectroscopy
Journal of Physical Chemistry B, 2018Co-Authors: Xueqian Dong, Juan Zhao, Fan Yang, Jianping WangAbstract:Trinuclear transition-metal carbonyl complex dodecacarbonyl triruthenium (Ru3(CO)12) is considered as one of the paradigms in cluster chemistry, which plays an important role in photocatalysis, photoenergy conversion, and synthetic chemistry. Due to structural symmetry (D3h point group), 12 carbonyl (C≡O) groups in the Ru3(CO)12 complex contribute to mainly three excitonic carbonyl stretching modes: E′ (radial), A2″ (axial), and E′ (axial). In this work, efficient intramolecular vibrational energy redistribution (IVR) processes among the three modes in this Ru–CO complex were observed to occur on the time scale of tens of picoseconds. The IVR processes were characterized in detail using a kinetic model and fitting to the waiting-time-dependent diagonal and off-diagonal signals of ultrafast Two-Dimensional Infrared Spectroscopy. In addition, the diagonal anharmonicities of the three C≡O stretching modes were determined to be quite close to one another, and the coupling-induced cross peaks were invariant be...
Martin T Zanni - One of the best experts on this subject based on the ideXlab platform.
-
amyloid found in human cataracts with two dimensional Infrared Spectroscopy
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Ariel M Alperstein, Joshua S Ostrander, Tianqi O Zhang, Martin T ZanniAbstract:UV light and other factors damage crystallin proteins in the eye lens, resulting in cataracts that scatter light and affect vision. Little information exists about protein structures within these disease-causing aggregates. We examined postmortem lens tissue from individuals with and without cataracts using 2D Infrared (2DIR) Spectroscopy. Amyloid β-sheet secondary structure was detected in cataract lenses along with denatured structures. No amyloid structures were found in lenses from juveniles, but mature lenses with no cataract diagnosis also contained amyloid, indicating that amyloid structures begin forming before diagnosis. Light scatters more strongly in regions with amyloid structure, and UV light induces amyloid β-sheet structures, linking the presence of amyloid structures to disease pathology. Establishing that age-related cataracts involve amyloid structures gives molecular insight into a common human affliction and provides a possible structural target for pharmaceuticals as an alternative to surgery.
-
a free energy barrier caused by the refolding of an oligomeric intermediate controls the lag time of amyloid formation by hiapp
Journal of the American Chemical Society, 2017Co-Authors: Arnaldo L Serrano, Justin P Lomont, Daniel P Raleigh, Martin T ZanniAbstract:Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and Two-Dimensional Infrared Spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F23G24A25I26L27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of ...
-
energy transfer between coherently delocalized states in thin films of the explosive pentaerythritol tetranitrate petn revealed by two dimensional Infrared Spectroscopy
Journal of Physical Chemistry B, 2017Co-Authors: Joshua S Ostrander, Martin T Zanni, Robert Knepper, Alexander S Tappan, Jeffery Kay, Darcie FarrowAbstract:Pentaerythritol tetranitrate (PETN) is a common secondary explosive and has been used extensively to study shock initiation and energy propagation in energetic materials. We report 2D IR measurements of PETN thin films that resolve vibrational energy transfer and relaxation mechanisms. Ultrafast anisotropy measurements reveal a sub-500 fs reorientation of transition dipoles in thin films of vapor-deposited PETN that is absent in solution measurements, consistent with intermolecular energy transfer. The anisotropy is frequency dependent, suggesting spectrally heterogeneous vibrational relaxation. Cross peaks are observed in 2D IR spectra that resolve a specific energy transfer pathway with a 2 ps time scale. Transition dipole coupling calculations of the nitrate ester groups in the crystal lattice predict that the intermolecular couplings are as large or larger than the intramolecular couplings. The calculations match well with the experimental frequencies and the anisotropy, leading us to conclude that th...
-
Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy
2017Co-Authors: Huong T. Kratochvil, Michał Maj, Kimberly Matulef, Alvin W. Annen, Jared Ostmeyer, Eduardo Perozo, Benoît Roux, Francis I. Valiyaveetil, Martin T ZanniAbstract:The interplay between the intracellular gate and the selectivity filter underlies the structural basis for gating in potassium ion channels. Using a combination of protein semisynthesis, Two-Dimensional Infrared (2D IR) Spectroscopy, and molecular dynamics (MD) simulations, we probe the ion occupancy at the S1 binding site in the constricted state of the selectivity filter of the KcsA channel when the intracellular gate is open and closed. The 2D IR spectra resolve two features, whose relative intensities depend on the state of the intracellular gate. By matching the experiment to calculated 2D IR spectra of structures predicted by MD simulations, we identify the two features as corresponding to states with S1 occupied or unoccupied by K+. We learn that S1 is >70% occupied when the intracellular gate is closed and
-
Energy Transfer Between Coherently Delocalized States in Thin Films of the Explosive Pentaerythritol Tetranitrate (PETN) Revealed by Two-Dimensional Infrared Spectroscopy
2017Co-Authors: Joshua S. Ostrander, Martin T Zanni, Robert Knepper, Alexander S Tappan, Jeffrey J. Kay, Darcie A. FarrowAbstract:Pentaerythritol tetranitrate (PETN) is a common secondary explosive and has been used extensively to study shock initiation and energy propagation in energetic materials. We report 2D IR measurements of PETN thin films that resolve vibrational energy transfer and relaxation mechanisms. Ultrafast anisotropy measurements reveal a sub-500 fs reorientation of transition dipoles in thin films of vapor-deposited PETN that is absent in solution measurements, consistent with intermolecular energy transfer. The anisotropy is frequency dependent, suggesting spectrally heterogeneous vibrational relaxation. Cross peaks are observed in 2D IR spectra that resolve a specific energy transfer pathway with a 2 ps time scale. Transition dipole coupling calculations of the nitrate ester groups in the crystal lattice predict that the intermolecular couplings are as large or larger than the intramolecular couplings. The calculations match well with the experimental frequencies and the anisotropy, leading us to conclude that the observed cross peak is measuring energy transfer between two eigenstates that are extended over multiple PETN molecules. Measurements of the transition dipole strength indicate that these vibrational modes are coherently delocalized over at least 15–30 molecules. We discuss the implications of vibrational relaxation between coherently delocalized eigenstates for mechanisms relevant to explosives
Kiran Sankar Maiti - One of the best experts on this subject based on the ideXlab platform.
-
ultrafast vibrational coupling between c h and c o band of cyclic amide 2 pyrrolidinone revealed by 2dir Spectroscopy
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2020Co-Authors: Kiran Sankar MaitiAbstract:Abstract Coupling between C H and C O vibrational modes play an essential role on determination of biological structure and dynamics. However, due to the weakness of the C H absorption and strong absorption of the C O vibrational band make such experiments less straightforward than those with transitions of nearly the same strength. In this communication the characteristics of the C H and C O coupling has been studied using dual frequency two dimensional Infrared Spectroscopy. 2-Pyrrolidinone has been used as a model molecule of biological system. The coherent and incoherent couplings between C H and C O vibrational bands have been observed. The cross peaks dynamics have been discussed and time constant of the cross peak intensity has been calculated.
-
broadband two dimensional Infrared Spectroscopy of cyclic amide 2 pyrrolidinone
Physical Chemistry Chemical Physics, 2015Co-Authors: Kiran Sankar MaitiAbstract:In the past one-and-a-half decade there has been a significant methodological and technological development of two dimensional Infrared (2DIR) Spectroscopy, which unfolds many underlying physical and chemical processes of complex molecules, especially for biological molecules. Due to the extreme technical difficulties and non-uniform performance of ultrafast laser, so far, the method has been mostly applied to a small spectral region. A rather simple experimental methodology is presented here which is able to cover a broad spectral range from 1500 cm−1 to 3500 cm−1 to explore the molecular structure of cyclic amide, 2-Pyrrolidinone, via the time-resolved coupling of CO, CH and NH stretch vibrations. The signature of the coherent as well as incoherent coupling has been found. The amide-I band is incoherently coupled to CH and NH stretch vibrations and acts as an acceptor mode for vibrational energy relaxation from CH and NH stretch vibrations.
H S Chung - One of the best experts on this subject based on the ideXlab platform.
-
amide i two dimensional Infrared Spectroscopy of proteins
Accounts of Chemical Research, 2008Co-Authors: Ziad Ganim, Adam W Smith, H S Chung, Lauren P Deflores, Kevin C Jones, Andrei TokmakoffAbstract:We review Two-Dimensional Infrared (2D IR) Spectroscopy of the amide I protein backbone vibration. Amide I modes are known for secondary structural sensitivity derived from their protein-wide delocalization. However, amide I FTIR spectra often display little variation for different proteins due to the broad and featureless line shape that arises from different structural motifs. 2D IR offers increased structural resolution by spreading the spectra over a second frequency dimension to reveal Two-Dimensional line shapes and cross-peaks. In addition, it carries picosecond time resolution, making it an excellent choice for understanding protein dynamics. In 2D IR spectra, cross peaks arise from anharmonic coupling between vibrations. For example, the spectra of ordered antiparallel beta sheets shows a cross peak between the strong nu perpendicular mode at approximately 1620 cm(-1) and the weaker nu parallel mode at approximately 1680 cm(-1). In proteins with beta-sheet content, disorder spreads the cross peaks into ridges, which gives rise to a "Z"-shaped contour profile. 2D IR spectra of alpha helices show a flattened "figure-8" line shape, and random coils give rise to unstructured, diagonally elongated bands. A distinguishing quality of 2D IR is the availability of accurate structure-based models to calculate spectra from atomistic structures and MD simulations. The amide I region is relatively isolated from other protein vibrations, which allows the spectra to be described by coupled anharmonic local amide I vibrations at each peptide unit. One of the most exciting applications of 2D IR is to study protein unfolding dynamics. While 2D IR has been used to study equilibrium structural changes, it has the time resolution to probe all changes resulting from photoinitiated dynamics. Transient 2D IR has been used to probe downhill protein unfolding and hydrogen bond dynamics in peptides. Because 2D IR spectra can be calculated from folding MD simulations, opportunities arise for making rigorous connections. By introduction of isotope labels, amide I 2D IR spectra can probe site-specific structure with picosecond time resolution. This has been used to reveal local information about picosecond fluctuations and disorder in beta hairpins and peptides. Multimode 2D IR Spectroscopy has been used to correlate the structure sensitivity of amide I with amide II to report on solvent accessibility and structural stability in proteins.
-
two dimensional Infrared Spectroscopy of antiparallel beta sheet secondary structure
Journal of the American Chemical Society, 2004Co-Authors: Jasper Knoester, Andrei Tokmakoff, N Demirdoven, C M Cheatum, H S Chung, Munira KhalilAbstract:We investigate the sensitivity of femtosecond Fourier transform Two-Dimensional Infrared Spectroscopy to protein secondary structure with a study of antiparallel β-sheets. The results show that 2D IR Spectroscopy is more sensitive to structural differences between proteins than traditional Infrared Spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational Spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel β-sheet. In the proteins with antiparallel β-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from...
-
two dimensional Infrared Spectroscopy of antiparallel beta sheet secondary structure
Journal of the American Chemical Society, 2004Co-Authors: Jasper Knoester, Andrei Tokmakoff, N Demirdoven, C M Cheatum, H S Chung, Munira KhalilAbstract:We investigate the sensitivity of femtosecond Fourier transform Two-Dimensional Infrared Spectroscopy to protein secondary structure with a study of antiparallel β-sheets. The results show that 2D ...
