Hydrogen Bonding in Water Clusters:  Pair and Many-Body Interactions from Symmetry-Adapted Perturbation Theory

Milet, Anne; Moszyński, Robert; Wormer, Paul E. S.; Avoird, Ad van der

doi:10.1021/jp990773d

Cited by 102 publications

(111 citation statements)

References 119 publications

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“…Ab initio studies of interaction energies and reconfiguration barriers in water clusters suggest many-body energies can be quite significant (53).…”

Section: Figmentioning

confidence: 99%

Three-body interactions improve the prediction of rate and mechanism in protein folding models

Ejtehadi

Avall

Plotkin

2004

Proc. Natl. Acad. Sci. U.S.A.

113

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Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained C ␣ -model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go -like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is Ϸ20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin inhibitor than in the other proteins studied.U nderstanding the nature of the interactions that stabilize protein structures and govern protein folding mechanisms is a fundamental problem in molecular biology (1-6) that has applies to structure and function prediction (7-10) as well as rational enzyme design (11). Regarding folding mechanisms, protein folding has long been known to be a cooperative process, at least for smaller single-domain proteins (12). Experimental scenarios that lack a first-order-like folding barrier are rare (13), often in contrast to simulation results. There are other discrepancies between simulation and experiment. For example, although the experimental folding rates for a typical set of 18 two-state, single-domain proteins (given in Materials and Methods) span about six orders of magnitude, simulations of coarsegrained models of the same proteins have rates that vary by about a factor of 100, a discrepancy of four orders of magnitude.How does one then quantify the sources of the barrier that controls the folding rate? The folding barrier is the residual of an incomplete cancellation of large and opposing energetic and entropic contributions, with the relative smallness of the barrier allowing folding to occur on biological time scales (14,15). Among the important energetic contributions that drive folding are solventmediated hydrophobic forces (16), which are known to be weaker on short-length scales, or low concentrations of apolar side-chains (17), a scenario likely to be present when the protein is unfolded. Hence, the solvent-averaged potential governing folding almost certainly contains a nonadditive, many-body component, and several models have been proposed to capture this effect (18-27). The folding free-energy barrier increases as the nonadditivity of interactions is increased (20,21,23,25) because of the decreased energetic correlation between the native conformation and conformations that may be geometrically similar to it.Experimental values give a measure of the strength of native interactions involving a particular amino acid (residue) in the transition state (28), thus quantifying a residue's importance in folding. However the values obtained from simulations of coarsegrained protein models generally do not correlate well with the experimentally determined values. Model proteins are c...

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“…Ab initio studies of interaction energies and reconfiguration barriers in water clusters suggest many-body energies can be quite significant (53).…”

Section: Figmentioning

confidence: 99%

Three-body interactions improve the prediction of rate and mechanism in protein folding models

Ejtehadi

Avall

Plotkin

2004

Proc. Natl. Acad. Sci. U.S.A.

113

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“…The latter operation is the inversion with respect to the dimer center of mass. This PI group is denoted by G 16 . Note, parenthetically, that reflection in the mirror plane of the equilibrium structure is equivalent to (12)* ≡ (12) E*.…”

Section: Theory and Computational Detailsmentioning

confidence: 99%

“…Note, parenthetically, that reflection in the mirror plane of the equilibrium structure is equivalent to (12)* ≡ (12) E*. The VRT levels of the water dimer are labeled by the irreducible representations (irreps) of G 16 Figure 3. The bifurcation (donor) tunneling causes no splitting, but leads to a shift of the E symmetry levels and an opposite shift of the levels of A and B symmetry.…”

Section: Theory and Computational Detailsmentioning

confidence: 99%

“…For the radial basis Φ n (R), we use a contracted sinc function discrete variable representation (DVR). 47,48 The basis is adapted to the symmetry group G 16 and the eigenvectors of the Hamiltonian are computed separately for each irrep. The small, off-diagonal Coriolis coupling is neglected, which makes K an exact quantum number.…”

Section: Theory and Computational Detailsmentioning

confidence: 99%

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Vibrations, Tunneling, and Transition Dipole Moments in the Water Dimer

Smit¹,

Groenenboom²,

Wormer³

et al. 2001

J. Phys. Chem. A

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101

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“…So we see that starting from one of these six equilibrium structures one ultimately visits six equivalent minima through a cyclic process of singlehydrogen u-d flips. Since the energy barrier that has to be overcome by a single flip is rather low, about 80 cm −1 , 20,45,46,50,51,55 this rearrangement mechanism gives rise to large tunneling splittings.…”

Section: Theorymentioning

confidence: 99%

Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

Avoird

Szalewicz

2008

The Journal of Chemical Physics

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The torsional levels of ͑H 2 O͒ 3 and ͑D 2 O͒ 3 were calculated in a restricted dimensionality ͑three-dimensional͒ model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very accurate water dimer levels, also reproduce the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT͑ASP-W͒III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.

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Hydrogen Bonding in Water Clusters: Pair and Many-Body Interactions from Symmetry-Adapted Perturbation Theory

Cited by 102 publications

References 119 publications

Three-body interactions improve the prediction of rate and mechanism in protein folding models

Three-body interactions improve the prediction of rate and mechanism in protein folding models

Vibrations, Tunneling, and Transition Dipole Moments in the Water Dimer

Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

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