Efficient and reliable calculation of rice-ramsperger—kassel-marcus unimolecular reaction rate constants for biopolymers: Modification of beyer-swinehart algorithm for degenerate vibrations

Moon, Jeong Hee; Sun, Meiling; Kim, Myoung Soo

doi:10.1016/j.jasms.2007.03.012

Cited by 15 publications

(15 citation statements)

References 29 publications

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“…In Figure 2, the peak patterns for a 2 , b 2 , a 5 -NH 3 , d 5 , and a 7 in the 193 nm PD spectrum recorded with 3 kV cell voltage are compared with those in the voltage-off spectrum. It can be seen that post-cell peaks are stronger than in-cell peaks for a 2 , b 2 , and a 5 -NH 3 , while the opposite is the case for a 7 . In the case of d 5 , post-cell peak is nearly absent.…”

Section: Resultsmentioning

confidence: 88%

“…That is, the statistical dissociation rate constants to a n ϩ 1 and b n for substance P ions were calculated by RRKM-QET as if each of them occurred via a hypothetical one-step reaction. The software reported previously [5][6][7] was used in the calculation. The software also calculates the internal energy distribution for a precursor ion at a specified temperature.…”

Section: Resultsmentioning

confidence: 99%

“…The main reasons for such a lack of fundamental understanding are experimental and computational difficulties to get structural, mechanistic, and kinetic data for large polyatomic systems consisting of more than 100 atoms. In this regard, it is to be mentioned that we recently developed a systematic method to calculate sequence-specific statistical (Rice-Ramsperger-KasselMarcus, RRKM) rate constants for dissociations of peptide and protein ions [5][6][7].The most popular method to activate a peptide ion and hence to induce its dissociation is the collisionally activated dissociation (CAD) [8 -12]. The kinetic energy of a peptide ion is an important factor affecting the CAD spectral pattern.…”

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confidence: 99%

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Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: A statistical interpretation

Yoon

Chung

Kim

2008

J. Am. Soc. Mass Spectrom.

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Time-evolution of product ion signals in ultraviolet photodissociation (UV-PD) of singly protonated peptides with an arginine at the N-terminus was investigated by using a tandem time-of-flight mass spectrometer equipped with a cell floated at high voltage. Observation of different time-evolution patterns for different product ion types-an apparently nonstatistical behavior-could be explained within the statistical framework by invoking consecutive formation of some product ions and broad internal energy distributions for precursor ions. a n ϩ 1 and b n ions were taken as the primary product ions from this type of peptide ions. Spectral characteristics in post-source decay, UV-PD, and collisionally activated dissociation at low and high kinetic energies could be explained via rough statistical calculation of rate constants. Specifically, the striking characteristics in high-energy CAD and UV-PD-dominance of a n and d n formed via a n ϩ 1-were not due to the peculiarity of the excitation processes themselves, but due to quenching of the b n channels caused by the presence of arginine. ( T andem mass spectrometry has been widely used for identification and sequence determination of polypeptides and proteins [1][2][3]. In spite of extensive studies made so far, fundamental understanding on the dissociation of activated peptide ions observed by tandem mass spectrometry is still lacking. This is in contrast with the case of the dissociation of small polyatomic ions, for which nearly quantitative theoretical description and even prediction are possible [4]. The main reasons for such a lack of fundamental understanding are experimental and computational difficulties to get structural, mechanistic, and kinetic data for large polyatomic systems consisting of more than 100 atoms. In this regard, it is to be mentioned that we recently developed a systematic method to calculate sequence-specific statistical (Rice-Ramsperger-KasselMarcus, RRKM) rate constants for dissociations of peptide and protein ions [5][6][7].The most popular method to activate a peptide ion and hence to induce its dissociation is the collisionally activated dissociation (CAD) [8 -12]. The kinetic energy of a peptide ion is an important factor affecting the CAD spectral pattern. Hence, CAD of a peptide ion is classified into two categories, low (around 100 eV) and high (higher than 1 keV) energy regimes. In the lowenergy CAD [11], which is typically done with triple quadrupole ion trap and ion cyclotron resonance mass spectrometers, a peptide ion gains sufficient energy for dissociation usually via multiple collisions, each collision supplying rather small amounts of internal energy through vibrational excitation. Most of the product ions are b and y types (see Scheme 1) formed via rearrangement reactions.Presence of arginine, proline and aspartic acid residues and the charge state of a peptide ion are known to affect the relative intensities of these product ions. The "mobile proton" model [13,14] has been devised to explain this. In the high-energy CA...

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Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: A statistical interpretation

Yoon

Chung

Kim

2008

J. Am. Soc. Mass Spectrom.

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“…A brief account is as follows. k(E) and the internal energy distribution (P 0 (E)) at specified values of E 0 , ⌬S ‡ , and T were calculated by the method reported previously [19,20]. k tot (E) and P 0 (E) calculated for [HF 6 ϩ H] ϩ with E 0 ϭ 0.55 eV, ⌬S ‡ ϭ Ϫ35.2 eu (1 eu ϭ 4.184 J K Ϫ1 mol Ϫ1 ), and T ϭ 369 K are shown in Figure 2.…”

Section: Computationalmentioning

confidence: 99%

“…the critical energy (E 0 ) and entropy (⌬S ‡ ). A systematic method to calculate k(E) for peptide ions is available [19,20]. Regardless, rigorous RRKM analysis of tandem mass spectral data for peptide ions is a formidable problem because many competing and consecutive reactions participate [21], requiring more than one set of (E 0 , ⌬S ‡ ) for the kinetic analysis.…”

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confidence: 99%

Time-resolved photodissociation study of singly protonated peptides with a histidine residue generated by matrix-assisted laser desorption ionization: Dissociation rate constant and internal temperature

Yoon

Moon

Kim

2009

J. Am. Soc. Mass Spectrom.

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Product ion yields in post-source decay and time-resolved photodissociation at 193 and 266 nm were measured for some peptide ions with a histidine residue ([HF 6 ϩ H] ϩ , [F 6 H ϩ H] ϩ , and [F 3 HF 3 ϩ H] ϩ ) formed by matrix-assisted laser desorption ionization (MALDI). Compared with similar data for peptide ions without any basic residue reported previously, significant reduction in dissociation efficiency was observed. Internal temperatures (T) of the peptide ions and their dissociation kinetic parameters-the critical energy (E 0 ) and entropy (⌬S ‡ )-were determined by the method reported previously. Slight decreases in E 0 , ⌬S ‡ , and T were responsible for the histidine effect-reduction in dissociation rate constant. Regardless of the presence of the residue, ⌬S ‡ was far more negative than previous quantum chemical results. Based on this, we propose the existence of transition structures in which the nitrogen atoms in the histidine residue or at the N-terminus coordinate to the reaction centers. Reduction in T in the presence of a histidine residue could not be explained based on popular models for ion formation in MALDI, such as the gas-phase proton transfer model. T andem mass spectral information-list of product ions formed from a precursor ion and their relative intensities-is tremendously useful for peptide and protein sequencing [1]. Pioneering studies on the product ion species formed from protonated peptides generated by fast atom bombardment and the mechanistic explanations for their formation were made by Martin and Biemann [2]. Extensive investigations followed [3][4][5], which were made mostly for protonated peptides generated by matrix-assisted laser desorption ionization (MALDI) [6] and electrospray ionization (ESI) [7]. For small model peptide ions, investigations beyond simple mechanistic interpretation have been reported, such as the quantum chemical search for reaction paths [8 -10]. However, there has not been much study on kinetics of peptide ion dissociation [11].Tandem mass spectral patterns for protonated peptides are affected by factors, such as the charge state, the number of arginine residue, and the energy regime [2,3,12,13]. For singly protonated peptides-these will be called peptide ions from now on-without an arginine residue, b and y types (see reference [2] for product ion symbols) are the major product ions regardless of the energy regime. Oxazolone pathways [4, 8 -10] have been proposed to explain their formation, which consist of the migration of the additional proton to an amide nitrogen, rate-determining cleavage of the protonated amide bond via a five-membered ring transition structure, formation of a proton-bound dimer of an oxazolone derivative and a smaller peptide, and its breakup. For peptide ions with an arginine residue, b/y channels (rearrangement) are dominant in the lowenergy regime [3], such as in low-energy collisionally activated dissociation (CAD) and post-source decay (PSD). In the high-energy regime, such as in highenergy CAD [2] and ultraviolet p...

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Controlling Light‐Induced Proton Transfer from the GFP Chromophore

et al. 2021

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Green Fluorescent Protein (GFP) is known to undergo excited‐state proton transfer (ESPT). Formation of a short H‐bond favors ultrafast ESPT in GFP‐like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light‐induced proton transfer from the GFP chromophore in hydrogen‐bonded complexes with two anionic proton acceptors, I− and deprotonated trichloroacetic acid (TCA−). We address the role of the strong H‐bond and the quantum mechanical proton‐density distribution in the excited state, which determines the proton‐transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton‐transfer probability and it can become strongly wavelength dependent. The proton‐transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high‐level ab initio calculations, we show that light‐induced proton transfer takes place in S1, revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H‐bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S1, depending on the quantum‐density distribution upon vibrational excitation. We also show that the S1 potential‐energy surface, and hence excited‐state proton transfer, can be controlled by altering the chromophore microenvironment.

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Efficient and reliable calculation of rice-ramsperger—kassel-marcus unimolecular reaction rate constants for biopolymers: Modification of beyer-swinehart algorithm for degenerate vibrations

Cited by 15 publications

References 29 publications

Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: A statistical interpretation

Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: A statistical interpretation

Time-resolved photodissociation study of singly protonated peptides with a histidine residue generated by matrix-assisted laser desorption ionization: Dissociation rate constant and internal temperature

Controlling Light‐Induced Proton Transfer from the GFP Chromophore

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