minhaeng cho - Academia.edu (original) (raw)

Papers by minhaeng cho

The Journal of Physical Chemistry Letters, 2014

The influence of nanoconfinement on water structure is studied with time- and frequency-resolved ... more The influence of nanoconfinement on water structure is studied with time- and frequency-resolved vibrational spectroscopy of hydrazoic acid (HN3) encapsulated in reverse micelle. The azido stretch mode of HN3 is found to be a promising infrared probe for studying the structure and local hydrogen-bond environment of confined and interfacial water in reverse micelle due to its narrow spectral bandwidth and large transition dipole moment. The results show a clear separation between the core and shell spectral components, making it advantageous over the previously studied infrared probes. The measured vibrational lifetimes appear to be substantially different for the interfacial and bulk-like environments but show no remarkable size dependency, which indicates that water structures around this IR probe are distinctively different in the core and shell regions. The influence of local hydrogen bond network in the first and higher solvation shells on the vibrational dynamics of HN3 is further discussed.

The journal of physical chemistry. B, Jan 13, 2014

Vibrational spectroscopy has provided incisive information on the structure of biological molecul... more Vibrational spectroscopy has provided incisive information on the structure of biological molecules. Here, using a molecular dynamics simulation method, infrared vibrational circular dichroism and vibrational optical rotatory dispersion spectra of a right-handed α-helix in the terahertz (THz) frequency range are calculated. Both the autocorrelation function of an electric dipole moment and the cross-correlation function of electric and magnetic dipole moments of the α-helix are calculated and Fourier-transformed to obtain THz absorption and optical activity spectra, which reveal characteristic features of the helical polypeptide structure. The anharmonicity and delocalized nature of the low-frequency modes in the THz frequency domain are taken into account to obtain statistically convergent results on the THz optical activity spectra. In addition, the magnitude of the THz vibrational optical activity signal of the α-helix is directly compared with those of typical, previously studie...

The Journal of Physical Chemistry B, 2008

Beta-azidoalanine dipeptide 1 was synthesized, and its azido stretching vibration in H2O and dime... more Beta-azidoalanine dipeptide 1 was synthesized, and its azido stretching vibration in H2O and dimethyl sulfoxide (DMSO) was studied by using Fourier transform (FT) IR spectroscopy. The dipole strength of the azido stretch mode is found to be about 19 and 5 times larger than those of the CN and SCN stretch modes, respectively, which have been used as local environmental IR sensors. The azido stretch band in H2O is blue-shifted by about 14 cm(-1) in comparison to that in DMSO, indicative of its sensitivity to the electrostatic environment. To test the utility of beta-azidoalanine as an IR probe of the local electrostatic environment in proteins, azidopeptide 4 was prepared by its incorporation into Abeta(16-22) peptide of the Alzheimer's disease amyloid beta-protein at position Ala21. The amide I IR spectrum of 4 in D2O suggests that the azidopeptide thus modified forms in-register beta-sheets in aggregates as observed for normal Abeta(16-22). The azido peak frequency of 4 in aggregates is almost identical to that in DMSO, indicating that the azido group is not exposed to water but to the hydrophobic environment. We believe that beta-azidoalanine will be used as an effective IR probe for providing site-specific information about the local electrostatic environments of proteins.

The Journal of Physical Chemistry B, 2009

Synthesis of Compounds General. 1 H and 13 C NMR spectra were recorded on a Bruker Avance 500 NMR... more Synthesis of Compounds General. 1 H and 13 C NMR spectra were recorded on a Bruker Avance 500 NMR spectrometer. Chemical shifts (δ) and coupling constants (J) are reported in parts per million (ppm) and hertz (Hz), respectively. 1 H NMR spectra are referenced to TMS (tetramethylsilane in DMSO-d 6) as an internal standard. 13 C NMR spectra are referenced to solvent (13 C: DMSO-d 6 , δ 39.50 ppm) as an internal standard. 31 P NMR spectra are referenced to phosphoric acid as an external standard (100% phosphoric acid in the inner tube and CDCl 3 in the outer tube; 31 P: H 3 PO 4 , δ 0.0018 ppm). High-resolution mass spectra (HRMS) were recorded on a JEOL JMS-AX505WA or JMS-600W mass spectrometer using fast atom bombardment (FAB) or chemical ionization (CI) techniques, respectively. Thinlayer chromatography (TLC) was performed on silica gel 60 F 254 precoated plates (0.25 mm thickness, Merck, Darmstadt). Flash chromatography was carried out on silica gel 60 (230−400 mesh, Merck). Reagent-grade chemicals were purchased from Aldrich, Fluka, and TCI and used as received unless otherwise specified.

The Journal of Physical Chemistry B, 2005

Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrost... more Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrostatic potential around intramolecular peptide bonds and induce amide I mode frequency shifts in polypeptides. By carrying out a series of quantum chemistry calculation studies of various ionic di- and tripeptides as well as dipeptides of 20 different amino acids, these internal field effects on vibrational properties are theoretically investigated. The amide I local and normal mode frequencies and dipole and rotational strengths determining IR and vibrational circular dichroism intensities, respectively, are found to depend on the polar nature of side chains, whereas the vibrational coupling strength weakly does so. The empirical correction and fragment analysis methods were used to theoretically calculate the amide I local mode frequencies and dipole and rotational strengths. These values were directly compared with ab initio and density functional theory calculation results, and the agreements were found to be quantitative.

The Journal of Physical Chemistry B, 2004

Chain length and site dependencies of amide I local mode frequencies of R-helical polyalanines ar... more Chain length and site dependencies of amide I local mode frequencies of R-helical polyalanines are theoretically studied by carrying out semiempirical quantum chemistry calculations. A theoretical model that can be used to quantitatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed. Using this theoretical model and performing molecular dynamics simulation of an R-helical polyalanine in liquid water, we investigate conformational fluctuation and hydrogen-bonding dynamics by monitoring amide I frequency fluctuations. The instantaneous normal-mode analysis method is used to obtain densities of states of the one-and two-exciton bands and to quantitatively investigate the extent of delocalization of the instantaneous amide I normal modes. Also, by introducing a novel concept of the so-called weighted phase-correlation factor, the symmetric natures of the delocalized amide I normal modes are elucidated, and it is also shown that there is no unique way to classify any given amide I normal mode of the R-helical polyalanine in liquid water to be either A-mode-like or E 1-mode-like. From the ensembleaveraged dipole strength spectrum and density of one-exciton states, the amide I infrared absorption spectrum is numerically calculated and its asymmetric line shape is theoretically described. Considering both transitions from the ground state to one-exciton states and those from one-exciton states to two-exciton states, we calculate the two-dimensional IR pump-probe spectra and directly compare them with recent experimental results. A brief discussion on the cross-peaks previously observed in the two-dimensional difference spectrum is presented.

The Journal of Physical Chemistry A, 2011

Coherent two-dimensional optical spectroscopy based on a heterodyne-detected stimulated photon ec... more Coherent two-dimensional optical spectroscopy based on a heterodyne-detected stimulated photon echo measurement technique requires four ultrashort pulses whose pulse-to-pulse delay times, wavevectors, and frequencies are experimentally controllable variables. In addition, the polarization directions of the four radiations can also be arbitrarily adjusted. We show that the polarization-angle-scanning two-dimensional spectroscopy can be of effective use to selectively suppress either all the diagonal peaks or a cross-peak in a given two-dimensional spectrum. Theoretical relationships between the transition dipole vectors of a given pair of coupled modes or quantum transitions and the polarization angle configuration making the corresponding cross-peak vanish are established. Here, to shed light into the underlying principles of the polarization-angle-scanning two-dimensional spectroscopy, we considered the amide I vibrations of various isotope-labeled dipeptide conformers and show that one can selectively suppress a cross-peak by properly controlling the polarization angle of a chosen beam among them. Once the relative directions of the amide I transition dipole vectors are determined using the polarization-angle-scanning technique theoretically proposed here, they can serve as a set of constraints for determining structures of model peptides. The present work demonstrates that the polarization-controlled two-dimensional vibrational or electronic spectroscopy can provide invaluable information on intricate details of molecular structures.

Proteins: Structure, Function, and Bioinformatics, 2012

Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of a... more Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.

The Journal of Chemical Physics, 1999

ABSTRACT

The Journal of Chemical Physics, 2007

Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studyi... more Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studying biomolecular and chemical reaction dynamics of chiral molecules. Only recently, the two-dimensional ͑2D͒ circularly polarized photon echo ͑CP-PE͒ spectroscopy of polypeptides and a photosynthetic light-harvesting complex were discussed, where the beam configuration was specifically controlled in such a way to eliminate the quadrupole contribution to the CP-PE signal. In this paper, we generalize the CP-PE spectroscopy by including the transition quadrupole contributions from peptide amide I vibrational transition and chlorophyll electronic transition. By using a density functional theory calculation method, the corresponding amide I vibrational and chlorophyll Q y electronic transition quadrupole tensor elements are determined. Amplitude of nonlinear optical transition pathway involving a quadrupole transition is found to be comparable to those of magnetic dipole terms for two different cases considered, i.e., dipeptides and photosynthetic antenna complex. However, due to the rotational averaging factors, the overall quadrupole contribution is an order of magnitude smaller than the magnetic dipole contribution. This suggests that the conventional 2D photon echo method and experimental scheme can be directly used to measure the 2D CP-PE signal from proteins and molecular complexes and that the 2D CP-PE signal is mainly dictated by the magnetic dipole contribution.

The Journal of Chemical Physics, 2007

The phosphorylation effect on the small peptide conformation in water has not been clearly unders... more The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and beta-sheet conformations. The additional band at 1598 cm(-1) in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37 degrees C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1 kJ/mol and -51.2 J/K mol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.

The Journal of Chemical Physics, 2004

The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoreti... more The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.

The Journal of Chemical Physics, 2004

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution... more By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.

The Journal of Chemical Physics, 2012

Small infrared probe molecules have been widely used to study local electrostatic environment in ... more Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.

Chemical Physics, 2013

Ultrafast two-dimensional infrared (2DIR) and IR pump-probe (PP) spectroscopy was used to study t... more Ultrafast two-dimensional infrared (2DIR) and IR pump-probe (PP) spectroscopy was used to study the intermolecular vibrational energy transfer process from the excited state of asymmetric stretching vibration of HN 3 to the overtone band of CO stretching vibration of solvent methanol. A series of timeresolved 2DIR spectra indicate an intermolecular vibrational excitation transfer between the two modes, since the corresponding cross peaks appear at longer waiting times (>20 ps). However, detailed analyses of temperature-dependent FTIR, dispersed IR PP, and 2DIR spectra showed that the vibrational relaxation of the azido stretch mode and its energy transfer to solvent methanol CO stretch overtone mode involve not only heat dissipation directly to the solvent bath modes but also production of transient intermediate states. The present experimental work demonstrates that ultrafast nonlinear IR spectroscopy is quite useful to shed light into the complicated vibrational relaxation dynamics of H-bonded solute-solvent systems.

Scientific Reports, 2017

Quantum spectroscopy and imaging with undetected idler photons have been demonstrated by measurin... more Quantum spectroscopy and imaging with undetected idler photons have been demonstrated by measuring one-photon interference between the corresponding entangled signal fields from two spontaneous parametric down conversion (SPDC) crystals. In this Report, we present a new quantum optical measurement scheme utilizing three SPDC crystals in a cascading arrangement; here, neither the detection of the idler photons which interact with materials of interest nor their conjugate signal photons which do not interact with the sample is required. The coherence of signal beams in a single photon W-type path-entangled state is induced and modulated by indistinguishabilities of the idler beams and crucially the quantum vacuum fields. As a result, the optical properties of materials or objects interacting with the idler beam from the first SPDC crystal can be measured by detecting second-order interference between the signal beams generated by the other two SPDC crystals further down the set-up. Th...

The Journal of Physical Chemistry Letters, 2014

The influence of nanoconfinement on water structure is studied with time- and frequency-resolved ... more The influence of nanoconfinement on water structure is studied with time- and frequency-resolved vibrational spectroscopy of hydrazoic acid (HN3) encapsulated in reverse micelle. The azido stretch mode of HN3 is found to be a promising infrared probe for studying the structure and local hydrogen-bond environment of confined and interfacial water in reverse micelle due to its narrow spectral bandwidth and large transition dipole moment. The results show a clear separation between the core and shell spectral components, making it advantageous over the previously studied infrared probes. The measured vibrational lifetimes appear to be substantially different for the interfacial and bulk-like environments but show no remarkable size dependency, which indicates that water structures around this IR probe are distinctively different in the core and shell regions. The influence of local hydrogen bond network in the first and higher solvation shells on the vibrational dynamics of HN3 is further discussed.

The journal of physical chemistry. B, Jan 13, 2014

Vibrational spectroscopy has provided incisive information on the structure of biological molecul... more Vibrational spectroscopy has provided incisive information on the structure of biological molecules. Here, using a molecular dynamics simulation method, infrared vibrational circular dichroism and vibrational optical rotatory dispersion spectra of a right-handed α-helix in the terahertz (THz) frequency range are calculated. Both the autocorrelation function of an electric dipole moment and the cross-correlation function of electric and magnetic dipole moments of the α-helix are calculated and Fourier-transformed to obtain THz absorption and optical activity spectra, which reveal characteristic features of the helical polypeptide structure. The anharmonicity and delocalized nature of the low-frequency modes in the THz frequency domain are taken into account to obtain statistically convergent results on the THz optical activity spectra. In addition, the magnitude of the THz vibrational optical activity signal of the α-helix is directly compared with those of typical, previously studie...

The Journal of Physical Chemistry B, 2008

Beta-azidoalanine dipeptide 1 was synthesized, and its azido stretching vibration in H2O and dime... more Beta-azidoalanine dipeptide 1 was synthesized, and its azido stretching vibration in H2O and dimethyl sulfoxide (DMSO) was studied by using Fourier transform (FT) IR spectroscopy. The dipole strength of the azido stretch mode is found to be about 19 and 5 times larger than those of the CN and SCN stretch modes, respectively, which have been used as local environmental IR sensors. The azido stretch band in H2O is blue-shifted by about 14 cm(-1) in comparison to that in DMSO, indicative of its sensitivity to the electrostatic environment. To test the utility of beta-azidoalanine as an IR probe of the local electrostatic environment in proteins, azidopeptide 4 was prepared by its incorporation into Abeta(16-22) peptide of the Alzheimer's disease amyloid beta-protein at position Ala21. The amide I IR spectrum of 4 in D2O suggests that the azidopeptide thus modified forms in-register beta-sheets in aggregates as observed for normal Abeta(16-22). The azido peak frequency of 4 in aggregates is almost identical to that in DMSO, indicating that the azido group is not exposed to water but to the hydrophobic environment. We believe that beta-azidoalanine will be used as an effective IR probe for providing site-specific information about the local electrostatic environments of proteins.

The Journal of Physical Chemistry B, 2009

Synthesis of Compounds General. 1 H and 13 C NMR spectra were recorded on a Bruker Avance 500 NMR... more Synthesis of Compounds General. 1 H and 13 C NMR spectra were recorded on a Bruker Avance 500 NMR spectrometer. Chemical shifts (δ) and coupling constants (J) are reported in parts per million (ppm) and hertz (Hz), respectively. 1 H NMR spectra are referenced to TMS (tetramethylsilane in DMSO-d 6) as an internal standard. 13 C NMR spectra are referenced to solvent (13 C: DMSO-d 6 , δ 39.50 ppm) as an internal standard. 31 P NMR spectra are referenced to phosphoric acid as an external standard (100% phosphoric acid in the inner tube and CDCl 3 in the outer tube; 31 P: H 3 PO 4 , δ 0.0018 ppm). High-resolution mass spectra (HRMS) were recorded on a JEOL JMS-AX505WA or JMS-600W mass spectrometer using fast atom bombardment (FAB) or chemical ionization (CI) techniques, respectively. Thinlayer chromatography (TLC) was performed on silica gel 60 F 254 precoated plates (0.25 mm thickness, Merck, Darmstadt). Flash chromatography was carried out on silica gel 60 (230−400 mesh, Merck). Reagent-grade chemicals were purchased from Aldrich, Fluka, and TCI and used as received unless otherwise specified.

The Journal of Physical Chemistry B, 2005

Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrost... more Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrostatic potential around intramolecular peptide bonds and induce amide I mode frequency shifts in polypeptides. By carrying out a series of quantum chemistry calculation studies of various ionic di- and tripeptides as well as dipeptides of 20 different amino acids, these internal field effects on vibrational properties are theoretically investigated. The amide I local and normal mode frequencies and dipole and rotational strengths determining IR and vibrational circular dichroism intensities, respectively, are found to depend on the polar nature of side chains, whereas the vibrational coupling strength weakly does so. The empirical correction and fragment analysis methods were used to theoretically calculate the amide I local mode frequencies and dipole and rotational strengths. These values were directly compared with ab initio and density functional theory calculation results, and the agreements were found to be quantitative.

The Journal of Physical Chemistry B, 2004

Chain length and site dependencies of amide I local mode frequencies of R-helical polyalanines ar... more Chain length and site dependencies of amide I local mode frequencies of R-helical polyalanines are theoretically studied by carrying out semiempirical quantum chemistry calculations. A theoretical model that can be used to quantitatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed. Using this theoretical model and performing molecular dynamics simulation of an R-helical polyalanine in liquid water, we investigate conformational fluctuation and hydrogen-bonding dynamics by monitoring amide I frequency fluctuations. The instantaneous normal-mode analysis method is used to obtain densities of states of the one-and two-exciton bands and to quantitatively investigate the extent of delocalization of the instantaneous amide I normal modes. Also, by introducing a novel concept of the so-called weighted phase-correlation factor, the symmetric natures of the delocalized amide I normal modes are elucidated, and it is also shown that there is no unique way to classify any given amide I normal mode of the R-helical polyalanine in liquid water to be either A-mode-like or E 1-mode-like. From the ensembleaveraged dipole strength spectrum and density of one-exciton states, the amide I infrared absorption spectrum is numerically calculated and its asymmetric line shape is theoretically described. Considering both transitions from the ground state to one-exciton states and those from one-exciton states to two-exciton states, we calculate the two-dimensional IR pump-probe spectra and directly compare them with recent experimental results. A brief discussion on the cross-peaks previously observed in the two-dimensional difference spectrum is presented.

The Journal of Physical Chemistry A, 2011

Coherent two-dimensional optical spectroscopy based on a heterodyne-detected stimulated photon ec... more Coherent two-dimensional optical spectroscopy based on a heterodyne-detected stimulated photon echo measurement technique requires four ultrashort pulses whose pulse-to-pulse delay times, wavevectors, and frequencies are experimentally controllable variables. In addition, the polarization directions of the four radiations can also be arbitrarily adjusted. We show that the polarization-angle-scanning two-dimensional spectroscopy can be of effective use to selectively suppress either all the diagonal peaks or a cross-peak in a given two-dimensional spectrum. Theoretical relationships between the transition dipole vectors of a given pair of coupled modes or quantum transitions and the polarization angle configuration making the corresponding cross-peak vanish are established. Here, to shed light into the underlying principles of the polarization-angle-scanning two-dimensional spectroscopy, we considered the amide I vibrations of various isotope-labeled dipeptide conformers and show that one can selectively suppress a cross-peak by properly controlling the polarization angle of a chosen beam among them. Once the relative directions of the amide I transition dipole vectors are determined using the polarization-angle-scanning technique theoretically proposed here, they can serve as a set of constraints for determining structures of model peptides. The present work demonstrates that the polarization-controlled two-dimensional vibrational or electronic spectroscopy can provide invaluable information on intricate details of molecular structures.

Proteins: Structure, Function, and Bioinformatics, 2012

Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of a... more Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.

The Journal of Chemical Physics, 1999

ABSTRACT

The Journal of Chemical Physics, 2007

Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studyi... more Time-resolved nonlinear optical activity measurement spectroscopy can be a useful tool for studying biomolecular and chemical reaction dynamics of chiral molecules. Only recently, the two-dimensional ͑2D͒ circularly polarized photon echo ͑CP-PE͒ spectroscopy of polypeptides and a photosynthetic light-harvesting complex were discussed, where the beam configuration was specifically controlled in such a way to eliminate the quadrupole contribution to the CP-PE signal. In this paper, we generalize the CP-PE spectroscopy by including the transition quadrupole contributions from peptide amide I vibrational transition and chlorophyll electronic transition. By using a density functional theory calculation method, the corresponding amide I vibrational and chlorophyll Q y electronic transition quadrupole tensor elements are determined. Amplitude of nonlinear optical transition pathway involving a quadrupole transition is found to be comparable to those of magnetic dipole terms for two different cases considered, i.e., dipeptides and photosynthetic antenna complex. However, due to the rotational averaging factors, the overall quadrupole contribution is an order of magnitude smaller than the magnetic dipole contribution. This suggests that the conventional 2D photon echo method and experimental scheme can be directly used to measure the 2D CP-PE signal from proteins and molecular complexes and that the 2D CP-PE signal is mainly dictated by the magnetic dipole contribution.

The Journal of Chemical Physics, 2007

The phosphorylation effect on the small peptide conformation in water has not been clearly unders... more The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and beta-sheet conformations. The additional band at 1598 cm(-1) in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37 degrees C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1 kJ/mol and -51.2 J/K mol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.

The Journal of Chemical Physics, 2004

The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoreti... more The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.

The Journal of Chemical Physics, 2004

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution... more By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.

The Journal of Chemical Physics, 2012

Small infrared probe molecules have been widely used to study local electrostatic environment in ... more Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.

Chemical Physics, 2013

Ultrafast two-dimensional infrared (2DIR) and IR pump-probe (PP) spectroscopy was used to study t... more Ultrafast two-dimensional infrared (2DIR) and IR pump-probe (PP) spectroscopy was used to study the intermolecular vibrational energy transfer process from the excited state of asymmetric stretching vibration of HN 3 to the overtone band of CO stretching vibration of solvent methanol. A series of timeresolved 2DIR spectra indicate an intermolecular vibrational excitation transfer between the two modes, since the corresponding cross peaks appear at longer waiting times (>20 ps). However, detailed analyses of temperature-dependent FTIR, dispersed IR PP, and 2DIR spectra showed that the vibrational relaxation of the azido stretch mode and its energy transfer to solvent methanol CO stretch overtone mode involve not only heat dissipation directly to the solvent bath modes but also production of transient intermediate states. The present experimental work demonstrates that ultrafast nonlinear IR spectroscopy is quite useful to shed light into the complicated vibrational relaxation dynamics of H-bonded solute-solvent systems.

Scientific Reports, 2017

Quantum spectroscopy and imaging with undetected idler photons have been demonstrated by measurin... more Quantum spectroscopy and imaging with undetected idler photons have been demonstrated by measuring one-photon interference between the corresponding entangled signal fields from two spontaneous parametric down conversion (SPDC) crystals. In this Report, we present a new quantum optical measurement scheme utilizing three SPDC crystals in a cascading arrangement; here, neither the detection of the idler photons which interact with materials of interest nor their conjugate signal photons which do not interact with the sample is required. The coherence of signal beams in a single photon W-type path-entangled state is induced and modulated by indistinguishabilities of the idler beams and crucially the quantum vacuum fields. As a result, the optical properties of materials or objects interacting with the idler beam from the first SPDC crystal can be measured by detecting second-order interference between the signal beams generated by the other two SPDC crystals further down the set-up. Th...