Song Geng

Sichuan University, Hua-yang, Sichuan, China

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Publications (5)18.93 Total impact

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    ABSTRACT: We have made an extensive theoretical exploration of gas-phase N-alkylamino cation affinities (NAAMCA), including amino cation affinities (AMCA) and N-dimethylamino cation affinities (NDMAMCA), of neutral maingroup-element hydrides (MEH) of Groups 15-17 and Periods 2-4 in the Periodic Table by using G2(+)M method. Some similarities and differences are found between NAAMCA and the corresponding alkyl cation affinities (ACA) of HnX. Our calculations show that the AMCA and NDMAMCA are systematically lower than the corresponding proton affinities (PA) for HnX. In general, there is no linear correlation between NAAMCA and PA of HnX. Instead, the correlations only exist within the central elements X in Period 2, or Periods 3-4, which is significantly different from the reasonable correlations between ACA and PA for all HnX. NAAMCA(HnX) are weaker than NAAMCA(Hn-1X-) by more than 700 kJ/mol, and generally stronger than ACA(HnX) with three exceptions, H2ONR2+(R = H, Me) and HFNH2+. These new findings can be rationalized by the negative hyperconjugation and Pauli repulsion.
    No preview · Article · Apr 2014 · The Journal of Physical Chemistry A
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    ABSTRACT: Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation.
    Full-text · Article · May 2012 · Nucleic Acids Research
  • Song Geng · Yi Ren · Ning-Bew Wong · Wai-Kee Li
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    ABSTRACT: The gas-phase N-alkyl-amino-cation affinities (NAACA) of archetypal anionic main-group element hydrides across the Periodic Table have been investigated by means of a modified G2(+) scheme. The reactions studied include R(2)NB → R(2)N(+) + B(-) (R = H, Me; B = XH(n), n = 0-3; X = F, Cl, Br, O, S, Se, N, P, As, C, Si, Ge). Our calculations indicate that the reasonable linear correlations between NAACA and proton affinities (PA) only exist within the Period 2 anions, including H(3)C(-), H(2)N(-), HO(-), and F(-), or the anions within Periods 3-4 in the Periodic Table, which is significantly different from the alkyl cation affinities, where there is a reasonable correlation between the computed alkyl cation affinity and PA values of the set of anionic main-group element hydrides. The interesting differences can be ascribed to the generalized anomeric effect induced by n(N) → σ*(X-H) negative hyperconjugation found in R(2)NXH(n), with central atom X belonging to Groups 14-16 (X = O, S, Se, N, P, As, C, Si, Ge).
    No preview · Article · Mar 2012 · The Journal of Physical Chemistry A
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    ABSTRACT: The anionic S(N)2 reactions at neutral nitrogen, Nu(-) + NR(2)Cl → NR(2)Nu + Cl(-) (R = H, Me; Nu = F, Cl, Br, OH, SH, SeH, NH(2), PH(2), AsH(2)) have been systematically studied computationally at the modified G2(+) level. Two reaction mechanisms, inversion and retention of configuration, have been investigated. The main purposes of this work are to explore the reactivity trend of anions toward NR(2)Cl (R = H, Me), the steric effect on the potential energy surfaces, and the leaving ability of the anion in S(N)2@N reactions. Our calculations indicate that the complexation energies are determined by the gas basicity (GB) of the nucleophile and the electronegativity (EN) of the attacking atom, and the overall reaction barrier in the inversion pathway is basically controlled by the GB value of the nucleophile. The retention pathway in the reactions of NR(2)Cl with Nu(-) (Nu = F, Cl, Br, OH, SH, SeH) is energetically unfavorable due to the barriers being larger than those in the inversion pathway by more than 120 kJ mol(-1). Activation strain model analyses show that a higher deformation energy and a weaker interaction between deformed reactants lead to higher overall barriers in the reactions of NMe(2)Cl than those in the reactions of NH(2)Cl. Our studies on the reverse process of the title reactions suggest that the leaving ability of the anion in the gas phase anionic S(N)2@N reactions is mainly determined by the strength of the N-LG bond, which is related to the negative hyperconjugation inherent in NR(2)Nu (R = H, Me; Nu = HO, HS, HSe, NH(2), PH(2), AsH(2)).
    No preview · Article · Dec 2011 · The Journal of Physical Chemistry A
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    ABSTRACT: The detailed reaction mechanism for the water-assisted hydrolysis of isocyanic acid, HNCO + (n + 1) H(2)O → CO(2) + NH(3) + nH(2)O (n = 0-6), taking place in the gas phase, has been investigated. All structures were optimized and characterized at the MP2/6-31 + G level of theory, and then re-optimized at MP2/6-311++G. The seven explicit water molecules participating in the hydrolysis can be divided into two groups, one directly involved in the proton relay, and the other located in the vicinity of the substrate playing the cooperative role by engaging in hydrogen-bonding to HN = C = O. Two possible reaction pathways, the addition of water molecule across the C = N bond or across the C = O bond, are discussed, and the former is proved to be more favorable energetically. Our calculations suggest that, in the most kinetically favorable pathway for the titled hydrolysis, three water molecules are directly participating in the hydrogen transfer via an eight-membered cyclic transition state, while the other four water molecules catalyze the hydrolysis of HN = C = O by forming three eight-membered cooperative loops near the substrate. This strain-free hydrogen-bond network leads to the best estimated rate-determining activation energy of 24.9 kJ mol(-1) at 600 K, in excellent agreement with the gas-phase kinetic experimental result, 25.8 kJ mol(-1).
    No preview · Article · Dec 2010 · Journal of Molecular Modeling