Sep 2005 - Jan 2012
Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
Field of study
- Physical Chemistry
Research Items (13)
The degree of chirality of protein backbone residues is used to enrich the Ramachandran Plot (RP), and create 3D chiral RPs with much more structural information. Detailed comparative analysis of the four classical RPs - general, glycine, proline and pre-proline - is provided, including statistical analysis of quantitative chirality distributions in the maps and in the secondary structures. Our results show that points with outlier chirality levels represent special transitional points in the folded protein such as α-helix kinks, twists of β-strands, and transition points between secondary structures. A protein chirality spectrum in which the degree of chirality of each residue is plotted against the sequence number explores these special points. Over 65,000 residues extracted from 200 high quality proteins are used for this study which shows that quantitative chirality is a general and useful structural parameter for proteins conformational studies.
- Sep 2017
Ramachandran plots (RPs) map the wealth of conformations of the polypeptide backbone and are widely used to characterize protein structures. A limitation of the RPs is that they are based solely on two dihedral angles for each amino acid residue, and provide therefore only a partial picture of the conformational richness of the protein. Here we extend the structural RP analysis of proteins from a 2D map to a 3D map by adding the quantitative degree of chirality – the Continuous Chirality Measure (CCM) – of the amino acid residue at each point in the RP. This measure encompasses all bond angles and bond lengths of an amino acid residue. We focus in this report on glycine (Gly) because, due to its flexibility, it occupies large portion of the 2D map, thus allowing a detailed study of the chirality measure; and in order to evaluate the justification of classically labeling Gly as the only achiral amino acid. We have analyzed in detail 4,366 Gly residues extracted from high resolution crystallographic data of 160 proteins. This analysis reveals not only that glycine is practically always conformationally chiral, but that upon comparing with the backbone of all amino acids, the quantitative chirality values of Gly are of similar magnitudes to those of the (chiral) amino acids. Structural trends and energetic considerations are discussed in detail. Generally we show that adding chirality to Ramachandran plots creates far more informative plots that highlight the sensitivity of the protein structure to minor conformational changes.
Gas-phase H9O4(+) has been considered an archetypal Eigen cation, H3O(+)(H2O)3. Yet ab initio molecular dynamics (AIMD) suggested that its infrared spectrum is explained by a linear-chain Zundel isomer, alone or in a mixture with the Eigen cation. Recently, hole-burning experiments suggested a single isomer, with a 2nd order vibrational perturbation theory (VPT2) spectrum agreeing with the Eigen cation. To resolve this discrepancy, we have extended both calculations to more advanced DFT functionals, better basis sets and dispersion correction. For Zundel-isomers, we find VPT2 anharmonic frequencies for 4 low-frequency modes involving the excess proton motion unreliable, including the 1750 cm(-1) band that is pivotal for differentiating between the two isomers. Because the analogous band of the H5O2(+) cation shows little effect of anharmonicity, we utilize the harmonic frequencies for these modes. With this caveat, both AIMD and VPT2 agree on the spectrum as originating from a Zundel isomer. VPT2 also shows that both isomers have the same spectrum in the high frequency region, so that the hole burning experiments should be extended to lower frequencies.
- Mar 2012
The 193 nm photodissociation dynamics of CH2CHCOCl in the gas phase has been examined with the technique of time-resolved Fourier transform infrared emission (TR-FTIR) spectroscopy. Vibrationally excited photofragments of CO (ν ⩽ 5), HCl (ν ⩽ 6), and C2H2 were observed and two photodissociation channels, the C-Cl fission channel and the HCl elimination channel have been identified. The vibrational and rotational state distributions of the photofragments CO and HCl have been acquired by analyzing their fully rotationally resolved ν→ν − 1 rovibrational progressions in the emission spectra, from which it has been firmly established that the mechanism involves production of HCl via the four-center molecular elimination of CH2CHCOCl after its internal conversion from the S1 state to the S0 state. In addition to the dominant C-Cl bond fission along the excited S1 state, the S1→S0 internal conversion has also been found to play an important role in the gas phase photolysis of CH2CHCOCl as manifested by the considerable yield of HCl.
By means of transient UV-visible absorption spectra/fluorescence spectra, combined with electronic structure calculations, the present work focuses on characterizing the photophysical and electronic properties of five PCBM-like C(60) derivatives (F1, F2, F3, F4, and F5) and understanding how these properties are expected to affect the photovoltaic performance of polymer solar cells (PSCs) with those molecules as acceptors. Spectral data reveal that the fluorescence quantum yields (Φ(F)) are enhanced and the triplet quantum yields (Φ(T)) are lowered for the five PCBM-like C(60) derivatives as compared to those of the pristine C(60), suggesting that functionalization of a C═C double bond perturbs the fullerene's π-system and breaks the I(h) symmetry of pristine C(60), which results in modifications of photophysical properties of the fullerene derivatives. PBEPBE/6-311G(d,p)//PBEPBE/6-31G(d) level of electronic structure calculations yields the HOMO-LUMO gaps and LUMO energies, showing that the electron-withdrawing effect induced by the side chain functional groups perturbs LUMO energies, from which different open circuit voltages V(oc) are resulted. The predicted V(oc) from our calculation agrees with previous experiment results. Basically, we found that functionalization of a C═C double bond sustains the fullerene structure and its electron affinitive properties. Adducted side chains contribute to adjust the HOMO-LUMO gap and LUMO levels of the acceptors to improve open circuit voltage. The results could provide fundamental insights for understanding how structural modifications influence the photovoltaic performance, which paves a way for guiding the synthesis of new fullerene derivatives with improved performance in polymer solar cells.
We present the structure-dependent nonlinear optical (NLO) properties of fully conjugated tri(perylene bisimides) (triPBIs) toward the understanding of the role of conformational flexibility and pi-electron conjugation in molecular NLO properties of model graphene-nanoribbon (GNR)-like molecules. In the present paper, we report the NLO absorption properties of the triPBIs in toluene excited at 532 nm with nanosecond laser pulses, where the observed transient excited state is determined to be a triplet and presented in the nonlinear process similar to the NLO properties that occur in C(60). As a result, the all-optical switching in both visible and near-infrared regions upon excitation at 532 nm was demonstrated, suggesting that the chemically synthesized model GNRs act well as smart all-optical switching devices without the need of external control. Furthermore, Raman spectral measurement was further used to characterize the conjugated structure properties of model compounds of functionalized graphene nanoribbons (F-GNRs), while the dispersion and splitting of the G-band and D-band in both frequency and intensity can help to distinguish the pi-conjugation and conformational flexibility of the two different triPBI isomers, showing the opportunity to tailor their optoelectronic properties by precisely controlling the edge orientation, edge width, and chemical termination of the edges in the synthesized F-GNRs.
The product channels and mechanisms of the C2HCl2+O2 reaction are investigated by step-scan time-resolved Fourier transform infrared emission spectroscopy and the G3MP2//B3LYP/6-311G(d,p) level of electronic structure calculations. Vibrationally excited products of HCl, CO, and CO2 are observed in the IR emission spectra and the product vibrational state distribution are determined which shows that HCl and CO are vibrationally excited with the nascent average vibrational energy estimated to be 59.8 and 51.8 kJ/mol respectively. In combination with the G3MP2//B3LYP/6-311G(d,p) calculations, the reaction mechanisms have been characterized and the energetically favorable reaction pathways have been suggested.
- Nov 2009
Time-resolved Fourier transform infrared absorption spectroscopy measurements and B3LYP/cc-pVDZ calculations have been conducted to characterize the reaction dynamics of a remarkable photoinduced 1,3-Cl sigmatropic rearrangement reaction upon 193 or 266 nm excitation of the model systems acryloyl chloride (CH(2)CHCOCl) and crotonyl chloride (CH(3)CHCHCOCl) in solution. The reaction is elucidated to follow nonadiabatic pathways via two rapid ISC processes, S(1) --> T(1) and T(1) --> S(0), and the S(1)/T(1) and T(1)/S(0) surface intersections are found to play significant roles leading to the nonadiabatic pathways. The S(1) --> T(1) --> S(0) reaction pathway involving the key participation of the T(1) state is the most favorable, corresponding to the lowest energy path. It is also suggested that the photoinduced 1,3-Cl migration reaction of RCHCHCOCl (R = H, CH(3)) proceeds through a stepwise mechanism involving radical dissociation-recombination, which is quite different from the generally assumed one-step concerted process for pericyclic reactions.
The environmentally important free radical reaction of chlorinated methyl CHCl2 with NO2 was investigated by step-scan time-resolved FTIR (TR-FTIR) emission spectroscopy. Vibrationally excited products of CHClO, NO, CO, and HCl are observed in the high-resolution IR emission spectra and three possible reaction channels are therefore elucidated. In particular, the product CO is newly detected and the product HCl is identified explicitly as a yield from the CHCl2+NO2 reaction, taking advantage of the sensitive detection of HCl and CO with TR-FTIR. These results are of particular interests to understand the related realistic chemical processes including atmospheric photochemistry, biofuel combustion, waste destruction, and smoking fire.
- Jan 2009
For the reaction of O((3)P) with propyne, the product channels and mechanisms are investigated both theoretically and experimentally. Theoretically, the CCSD(T)//B3LYP/6-311G(d,p) level of calculations are performed for both the triplet and singlet potential energy surfaces and the minimum energy crossing point between the two surfaces are located with the Newton-Lagrange method. The theoretical calculations show that the reaction occurs dominantly via the O-addition rather than the H-abstraction mechanism. The reaction starts with the O-addition to either of the triple bond carbon atoms forming triplet ketocarbene (3)CH(3)CCHO or (3)CH(3)COCH which can undergo decomposition, H-atom migration or intersystem crossing from which a variety of channels are open, including the adiabatic channels of CH(3)CCO + H (CH(2)CCHO + H), CH(3) + HCCO, CH(2)CH + HCO, CH(2)CO + CH(2), CH(3)CH + CO, and the nonadiabatic channels of C(2)H(4) + CO, C(2)H(2) + H(2) + CO, H(2) + H(2)CCCO. Experimentally, the CO channel is investigated with TR-FTIR emission spectroscopy. A complete detection of the CO product at each vibrationally excited level up to v = 5 is fulfilled, from which the vibrational energy disposal of CO is determined and found to consist with the statistical partition of the singlet C(2)H(4) + CO channel, but not with the triplet CH(3)CH + CO channel. In combination with the present calculation results, it is concluded that CO arises mainly from the singlet methylketene ((1)CH(3)CHCO) dissociation following the intersystem crossing of the triplet ketocarbene adduct ((3)CH(3)CCHO). Fast intersystem crossing via the minimum energy crossing point of the triplet and singlet surfaces is shown to play significant roles resulting into nonadiabatic pathways for this reaction. Moreover, other interesting questions are explored as to the site selectivity of O((3)P) atom being added to which carbon atom of the triple bond and different types of internal H-atom migrations including 1,2-H shift, 3,2-H shift, and 3,1-H shift involved in the reaction.
- Sep 2006
Eight exothermic product channels of the reaction of chlorinated vinyl radical (C2Cl3) with molecular oxygen (O2) have been investigated using ab initio quantum chemistry methods. The energetics of the reaction pathways were calculated at the second-order Moller-Plesset Gaussian-3 level of theory (G3MP2) using the B3LYP/6-311G(d) optimized geometries. It has been shown that the C2Cl3 + O2 reaction takes place via a barrierless addition to form the chlorinated vinylperoxy radical complex, which can decompose or isomerize to various products via the complicated mechanisms. Two major reaction routes were revealed, i.e., the three-member-ring reaction mechanism leading to ClCO + CCl2O, CO + CCl3O, CO2 + CCl3, Cl + (ClCO)2, etc., and the OO bond cleavage mechanism leading to O(3P) + C2Cl3O. The other mechanisms are shown to be unimportant. The results are validated by the calculations using the restricted coupled cluster theory [RCCSD(T)] with the complete basis set extrapolation. Variational transition state theory was employed to calculate the individual and total rate coefficients as a function of temperature and pressure (helium). The theoretical rate coefficients are in good agreement with the available experimental data. It was found that the total rate coefficients show strong negative temperature dependence in the range 200-2000 K. At room temperature (297 K), the total rate coefficients are shown to be nearly pressure independent over a wide range of helium pressures (1-10(9) Torr). The deactivation of the initial adduct, C2Cl3O2, is only significant at pressures higher than 1000 Torr. The three-member-ring reaction mechanism is always predominant over the OO bond cleavage.
Awards & Achievements (1)
Award · Jun 2013
Golda Meir Postdoc Fellowship