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Yirong Mo

Publications and source records attributed to Yirong Mo.

17 recordsLinked to original sources
PubMed2007

How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs.

Amides↗
PubMed2006

Amine-hydrogen halide complexes: experimental electric dipole moments and a theoretical decomposition of dipole moments and binding energies.

The Stark effect has been observed in the rotational spectra of several gas-phase amine-hydrogen halide complexes and the following electric dipole moments have been determined: H(3)(15)N-H(35)Cl (4.05865 +/- 0.00095 D), (CH(3))(3)(15)N-H(35)Cl (7.128 +/- 0.012 D), H(3)(15)N-H(79)Br (4.2577 +/- 0.0022 D), and (CH(3))(3)(15)N-H(79)Br (8.397 +/- 0.014 D). Calculations of the binding energies and electric dipole moments for the full set of complexes R(n)()(CH(3))(3)(-)(n)()N-HX (n = 0-3; X = F, Cl, Br) at the MP2/aug-cc-pVDZ level are also reported. The block localized wave function (BLW) energy decomposition method has been used to partition the binding energies into contributions from electrostatic, exchange, distortion, polarization, and charge-transfer terms. Similarly, the calculated dipole moments have been decomposed into distortion, polarization, and charge-transfer components. The complexes studied range from hydrogen-bonded systems to proton-transferred ion pairs, and the total interaction energies vary from 7 to 17 kcal/mol across the series. The individual energy components show a much wider variation than this, but cancellation of terms accounts for the relatively narrow range of net binding energies. For both the hydrogen-bonded complexes and the proton-transferred ion pairs, the electrostatic and exchange terms have magnitudes that increase with the degree of proton transfer but are of opposite sign, leaving most of the net stabilization to arise from polarization and charge transfer. In all of the systems studied, the polarization terms contribute the most to the induced dipole moment, followed by smaller but still significant contributions from charge transfer. A significant contribution to the induced moment of the ion pairs also arises from distortion of the HX monomer.

Journal Article↗
PubMed2006

Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: mechanism of ammonia/ammonium transport.

Molecular dynamics (MD) simulations have been performed at the atomic level to study the ammonium/ammonia transport across the Escherichia coli AmtB membrane protein. Although ammonia primarily exists in the form of NH(4)(+) in aqueous solution, the recent X-ray structure determination of AmtB reveals that the ammonium/ammonia transporter proteins are ammonia-conducting channels rather than ammonium ion transporters [Khademi, S.; et al. Science 2004, 305, 1587; Zheng, L.; et al. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17090]. Our simulations showed that the entrance of NH(4)(+) into the periplasmic recruitment vestibule requires only 3.1 kcal/mol of energy. This is consistent with the X-ray crystal structure, where one NH(4)(+) is captured in the binding vestibule. In this vestibule, NH(4)(+) loses one water of hydration, but the loss is compensated by a hydrogen bond, first with the backbone carbonyl oxygen of Phe161 then with the hydroxyl group of Ser219, as well as the stabilizing pi-cation interactions with the aromatic rings of Trp148 and Phe107 in the AmtB protein. In the end of this recruitment vestibule, the phenyl ring of Phe107 dynamically switches to an open state. This is correlated with a slight rotation and shifting of the indole ring of Trp148, which eventually creates a slot for the initially buried carboxylate group of Asp160 to become exposed to the bulk solvent. A hydrogen bond wire between NH(4)(+) and the carboxylate group of Asp160 via two water molecules was observed. Thus, Asp160 is most likely the proton acceptor from NH(4)(+). This explains the high conservation of Asp160 in Amt proteins and why the D160A mutant would completely quench the activity of AmtB [Javelle, A.; et al. J. Biol. Chem. 2004, 279, 8530; Marini, A. M.; et al. Curr. Genet. 2006, 49, 364]. Once NH(4)(+) deprotonates, the phenyl ring of Phe215 rotates to open, and the subsequent passage of NH(3) through the channel is straightforward.

Ammonia↗
PubMed2006

Probing the nature of hydrogen bonds in DNA base pairs.

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

Base Pairing↗
PubMed2006

Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.

Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.

Chemistry, Physical↗
PubMed2006

An energetic measure of aromaticity and antiaromaticity based on the Pauling-Wheland resonance energies.

Various criteria based on geometric, energetic, magnetic, and electronic properties are employed to delineate aromatic and antiaromatic systems. The recently proposed block-localized wave function (BLW) method evaluates the original Pauling-Wheland adiabatic resonance energy (ARE), defined as the energy difference between the real conjugated system and the corresponding virtual most stable resonance structure. The BLW-derived ARE of benzene is 57.5 kcal mol(-1) with the 6-311+G** basis set. Kistiakowsky's historical experimental evaluation of the stabilization energy of benzene (36 kcal mol(-1)), based on heats of hydrogenation, seriously underestimates this quantity due to the neglect of the partially counterbalancing hyperconjugative stabilization of cyclohexene, employed as the reference olefin (three times) in Kistiakowsky's evaluation. Based instead on the bond-separation-energy reaction involving ethene, which has no hyperconjugation, as well as methane and ethane, the experimental resonance energy of benzene is found to be 65.0 kcal mol(-1). We derived the "extra cyclic resonance energy" (ECRE) to characterize and measure the extra stabilization (aromaticity) of conjugated rings. ECRE is the difference between the AREs of a fully cyclically conjugated compound and an appropriate model with corresponding, but interrupted (acyclic) conjugation. Based on 1,3,5-hexatriene, which also has three double bonds, the ECRE of benzene is 36.7 kcal mol(-1), whereas based on 1,3,5,7-octatetraene, which has three diene conjugations, the ECRE of benzene is 25.7 kcal mol(-1). Computations on a series of aromatic, nonaromatic, and antiaromatic five-membered rings validate the BLW-computed resonance energies (ARE). ECRE data on the five-membered rings (derived from comparisons with acyclic models) correlate well with nucleus-independent chemical shift (NICS) and other quantitative aromaticity criteria. The ARE of cyclobutadiene is almost the same as butadiene but is 10.5 kcal mol(-1) less than 1,3,5-hexatriene, which also has two diene conjugations. The instability and high reactivity of cyclobutadiene thus mainly result from the sigma-frame strain and the pi-pi Pauli repulsion.

Journal Article↗
PubMed2006

Why is the linking C-C bond in tetrahedranyltetrahedrane so short?

[structure: see text]. The block-localized wave function (BLW) method has been employed to probe the origin of the very short linking C-C bond (1.436 A) in tetrahedranyltetrahedrane. Computations show that the vicinal hyperconjugative interactions between the two tetrahedranyl groups is stronger than the conjugation in butadiene, and if there were no hyperconjugation effect, the bond distance would be 1.491 A. Thus, both the hybridization mode and hyperconjugative interactions contribute to the shortening of the central C-C bond in tetrahedranyltetrahedrane.

Butadienes↗
PubMed2005

Y-aromaticity: why is the trimethylenemethane dication more stable than the butadienyl dication?

[reactions: see text] Resonance energies of the trimethylenemethane dication (1) and the butadienyl dication (4) were evaluated using two independent computational methodologies to provide insight into the validity of Y-aromaticity. One methodology employed density functional theory calculations and examined the resonance contribution of the C=C double bond toward the double hydride abstraction enthalpies of methylpropene (6) and 2-butene (8), yielding 1 and 4, respectively. These resonance contributions by the double bond were determined by calculating the double hydride abstraction enthalpies of both the parallel and perpendicular conformations of vinylogues of 6 and 8, in which n = 1-4 vinyl units were inserted between the central carbon-carbon double bond and each of the reaction centers. Extrapolation of the resonance contribution in each vinylogue to n = 0 yielded the resonance contribution in the respective parent molecules. The second methodology employed an orbital deletion procedure (ODP), which effectively allowed us to examine the energies of individual resonance structures. The resonance energy of each dication is computed as the difference between the most stable resonance structure and that of the delocalized species. The two methodologies are in agreement, suggesting that the resonance energy of the trimethylenemethane dication is substantially greater than that of the butadienyl dication. The origin of this difference in resonance stabilization is discussed.

Journal Article↗
PubMed2005

Density functional study on dihydrogen activation at the H cluster in Fe-only hydrogenases.

Models simulating the catalytic diiron subcluster [FeFe](H) in Fe-only hydrogenases have often been designed for computational exploration of the catalytic mechanism of the formation and cleavage of dihydrogen. In this work, we extended the above models by explicitly considering the electron reservoir [4Fe-4S](H) which is linked to the diiron subcluster to form a whole H cluster ([6Fe-6S] = [4Fe-4S](H) + [FeFe](H)). Large-scale density functional theory (DFT) computations on the complete H cluster, together with simplified models in which the [4Fe-4S](H) subcluster is not directly involved in the reaction processes, have been performed to probe hydrogen activation on the Fe-only hydrogenases. A new intermediate state containing an Fe(p)...H...CN two-electron three-center bond is identified as a key player in the H2 formation/cleavage processes.

Binding Sites↗
PubMed2005

XMVB: a program for ab initio nonorthogonal valence bond computations.

An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available.

Journal Article↗
PubMed2005

Steric strain versus hyperconjugative stabilization in ethane congeners.

Rotation barriers in the group IVB ethane congeners H(3)X-YH(3) (X, Y = C, Si, Ge, Sn, Pb) have been systematically studied and deciphered using the ab initio valence bond theory in terms of the steric strain and hyperconjugation effect. Our results show that in all cases the rotation barriers are dominated by the steric repulsion whereas the hyperconjugative interaction between the X-H bond orbitals and the vicinal Y-H antibond orbitals (and vice versa) plays a secondary role, although indeed the hyperconjugation effect favors staggered structures. By the independent estimations of the hyperconjugative and steric interactions in the process of rotations, we found that the structural effect which mainly refers to the central X-Y bond relaxation makes a small contribution to the rotational barriers. Therefore, we conclude that both the rigid and fully relaxed rotations in the group IVB ethane congeners H(3)X-YH(3) observe the same mechanism which is governed by the conventional steric repulsion.

Journal Article↗
PubMed2004

Resonance effect in the allyl cation and anion: a revisit.

The interest over the magnitude of the conjugation effect in the allyl cation (1) and anion (2) has been revived recently by Barbour and Karty (J. Org. Chem. 2004, 69, 648-654), who derived the resonance energies of 20-22 and 17-18 kcal/mol for 1 and 2, respectively, using an empirical extrapolation approximation. This paper revisits the case by explicitly calculating the Pauling-Wheland resonance energy, which measures the stabilization from the most stable resonance structure to the delocalized energy-minimum state of a conjugated system, using our newly developed block-localized wave function (BLW) method. This BLW method has the geometrical optimization capability. The computations result in adiabatic resonance energies of 37 kcal/mol for 1 and 38 kcal/mol for 2. The significant disagreement between these values and Barbour and Karty's results originates from the neglect of structural and electronic variations in their derivation which are energy costing.

Journal Article↗
PubMed2004

Hyperconjugation effect in substituted methyl boranes: an orbital deletion procedure analysis.

The hyperconjugation effect in the substituted methyl boranes, XCH(2)BH(2) (X = H, CH(3), NH(2), PH(2), OH, SH, F, Cl, Br), has been quantitatively evaluated by using the orbital deletion procedure (ODP), where the p(pi) orbital on boron is deactivated. Except for the case of X = NH(2), which forms a three-membered ring, the magnitude of the hyperconjugative stabilization in all other substituted methylborane ranges from 6.8 to 3.4 kcal/mol. Significant structural changes are observed, particularly the shortening of the central B-C bond distance and the reducing of the corresponding XCB and HCB bond angles. In general, the strength of the hyperconjugative interaction between the occupied sigma(C-X) bond and the vacant p(pi) orbital on boron is correlated to the electronegativity of X, and the competition between the donation ability of the sigma(C-X) and the sigma(C-H) bonds determines the preference of the staggered or eclipsed structure as the energy minimum state. When the donation abilities of the C-X and C-H bonds are comparable, other factors such as electron correlation and steric effect may play elaborate roles in the geometrical propensity of the most stable structures.

Journal Article↗
PubMed2004

Charge transfer in the electron donor-acceptor complex BH3NH3.

As a simple yet strongly binding electron donor-acceptor (EDA) complex, BH(3)NH(3) serves as a good example to study the electron pair donor-acceptor complexes. We employed both the ab initio valence bond (VB) and block-localized wave function (BLW) methods to explore the electron transfer from NH(3) to BH(3). Conventionally, EDA complexes have been described by two diabatic states: one neutral state and one ionic charge-transferred state. Ab initio VB self-consistent field (VBSCF) computations generate the energy profiles of the two diabatic states together with the adiabatic (ground) state. Our calculations evidently demonstrated that the electron transfer between NH(3) and BH(3) falls in the abnormal regime where the reorganization energy is less than the exoergicity of the reaction. The nature of the NH(3)-BH(3) interaction is probed by an energy decomposition scheme based on the BLW method. We found that the variation of the charge-transfer energy with the donor-acceptor distance is insensitive to the computation levels and basis sets, but the estimation of the amount of electron transferred heavily depends on the population analysis procedures. The recent resurgence of interest in the nature of the rotation barrier in ethane prompted us to analyze the conformational change of BH(3)NH(3), which is an isoelectronic system with ethane. We found that the preference of the staggered structure over the eclipsed structure of BH(3)NH(3) is dominated by the Pauli exchange repulsion.

Journal Article↗
PubMed2004

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers.

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.

Catalysis↗
PubMed2002

Cation-pi interactions: an energy decomposition analysis and its implication in delta-opioid receptor-ligand binding.

The nature and strength of the cation-pi interaction in protein-ligand binding are modeled by considering a series of nonbonded complexes involving N-substituted piperidines and substituted monocylic aromatics that mimic the delta-opioid receptor-ligand binding. High-level ab initio quantum mechanical calculations confirm the importance of such cation-pi interactions, whose intermolecular interaction energy ranges from -6 to -12 kcal/mol. A better understanding of the electrostatics, polarization, and other intermolecular interactions is obtained by appropriately decomposing the total interaction energy into their individual components. The energy decomposition analysis is also useful for parametrizing existing molecular mechanics force fields that could then account for energetic contributions arising out of cation-pi interactions in biomolecules. The present results further provide a framework for interpreting experimental results from point mutation reported for the delta-opioid receptor.

Cations↗