Water Molecule Interactions

Hankins, D.E.; Moskowitz, Jules W.; Stillinger, Frank H.

doi:10.1063/1.1673986

Cited by 622 publications

(376 citation statements)

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“…The decomposition of the total interaction energy into clusters of multi-body expansion can be defined as follows [26,27]:…”

Section: Introductionmentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Selected conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of 162 analyzed tetramers both threeand four-body contributions are negligible except of d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal/mol. This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of the total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.Response to Reviewers: 1) I recommend to do a careful proofreading, there are many typos and some sentences are difficult to understand. Thank you. Careful proofreading was applied and text was modified accordingly.2) Page 3, Results and discussion Alltogether 162 dinucleotide steps were analyzed. The number of individual steps is variable, why is it so? Why there was 48 d(GpG) steps, but only 10 d(GpC) steps? What were the PDB codes of structures from which steps were chosen, and which steps (chain ID, res ID) were chosen? What was the resolution of these structures? This information could go to the Supplementary material.In supplementary material details related to analyzed structures are provided now. The differences in dinucleotide populations have strictly technical reason. Since in my previous work accepted for publication in Int.J.Quantum Chem. (DOI:10.1002/qua.22435) detailed analysis of d(GpG) steps were presented I have just included these data in this work. Consequently this dinucleotide is overrepresented. Since it constitutes its own class I do not think that such overrepresentation changes papers conclusions. On the other hand it is not necessary extending the number of other dinucleotide steps since the non-additivity is quite small and they were selected from broad range of data according to IIE and structural parameters diversities.3) Page 3, Results and discussion The numbers of steps are large enough to perform some statistical analysis of resulting energies. E.g. ANOVA could be performed to test whether the mean energies in dinucleotide steps differ significantly each from other. Also, is the distribution of energies for individual steps Gaussian or not? If not, some non-parametric ...

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“…The decomposition of the total interaction energy into clusters of multi-body expansion can be defined as follows [26,27]:…”

Section: Introductionmentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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“…The equilibrium structure of the water dimer was predicted by ab initio calculations [39][40][41][42] and experimentally determined in 1974 by microwave spectroscopy. 1 In 1977 it was shown by the now classical work of Dyke and co-workers 2,43 that the six-dimensional intermolecular potential surface of the water dimer has eight equivalentpermutationally distinct-global minima and that this dimer may tunnel between the eight equivalent equilibrium structures.…”

Section: Tunneling and Vibrations In The Water Dimermentioning

confidence: 99%

Water pair potential of near spectroscopic accuracy. II. Vibration–rotation–tunneling levels of the water dimer

Groenenboom

Wormer

Avoird

et al. 2000

The Journal of Chemical Physics

118

167

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Nearly exact six-dimensional quantum calculations of the vibration-rotation-tunneling ͑VRT͒ levels of the water dimer for values of the rotational quantum numbers J and K р2 show that the SAPT-5s water pair potential presented in the preceding paper ͑paper I͒ gives a good representation of the experimental high-resolution far-infrared spectrum of the water dimer. After analyzing the sensitivity of the transition frequencies with respect to the linear parameters in the potential we could further improve this potential by using only one of the experimentally determined tunneling splittings of the ground state in (H 2 O) 2 . The accuracy of the resulting water pair potential, SAPT-5st, is established by comparison with the spectroscopic data of both (H 2 O) 2 and (D 2 O) 2 : ground and excited state tunneling splittings and rotational constants, as well as the frequencies of the intermolecular vibrations.

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“…Considerable efforts are invested in developing linear scaling or O(N ) methods. 14,15 The fragmentation methods have a fairly long history [16][17][18][19][20][21][22] and now it is an active area of research. 13, 23-32 a) Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, in order to realize linear scaling, approximations have been proposed for the time-consuming ESP calculation in FMO 34,37 and other methods. 10 The fragment self-consistent procedure employed in FMO has been used in somewhat different forms in other methods, 18,19,9,38,39 while the many-body expansion of the energy is conceptually related to the theory of intermolecular interactions 16 or the density expansion method. 20 Over the past decade, the FMO method has become one of the most extensively developed fragmentation methods for the calculation of accurate chemical properties, such as the total energy, the dipole moment, and the interaction energy between fragments in large systems.…”

Section: Introductionmentioning

confidence: 99%

Fully analytic energy gradient in the fragment molecular orbital method

Brorsen¹,

Fedorov²

2011

The Journal of Chemical Physics

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The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H 2 O) 64 , alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO selfconsistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes. KeywordsPolymers, Electrostatics, Chemical bonds, Proteins, Density functional theory Disciplines Chemistry CommentsThe following article appeared in Journal of Chemical Physics 134 (2011) The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H 2 O) 64 , alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO self-consistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes.

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Water Molecule Interactions

Cited by 622 publications

References 20 publications

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Water pair potential of near spectroscopic accuracy. II. Vibration–rotation–tunneling levels of the water dimer

Fully analytic energy gradient in the fragment molecular orbital method

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