Study of the structure of molecular complexes

Clementi, E.; Barsotti, Riccardo; Fromm, Jacob E.; Watts, R. O.

doi:10.1007/bf00547251

Cited by 59 publications

(11 citation statements)

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“…It is also known, however, that some thermodynamic data may be reproduced poorly unless threebody corrections are included; hence in the rest of this paper we shall use tile Monte Carlo technique mainly to deal with structural predictions. Details on our computer programs and on specific Monte Carlo computations are available elsewhere for liquid water, {Lie Lie, et al, 1976) for water solutions containing ions {Clementi and Barsotti, 1976Barsotti, , 1978Fromm, et ai., 1975;Ctementi, 1980: Watts, et al, 1974.} and for chemical systems composed of water molecules, counterions, and nucleic acids (Clementi, 1981(Clementi, , 1983Clementi and Corongiu, 1979a, 1979h, 1979c, 1981a, 1981b, 1981c, 1982a, 1982b, 1982c.…”

Section: Computational Techniquesmentioning

confidence: 99%

Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

Clementi

Corongiu

1983

J Biol Phys

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ABSTRACT:The position and orientation of water molecules hydrating fragments of DNA in the B and Z conformations are analyzed with the help of computer simulations. Monte Carlo studies are carried out at room temperature, high relative humidity (500 ~ater/nolecule~ per pitch) and in " "--',the presence of counterons such as L1 Na and K . Differences In hydration patterns and in the counterionic structures were found by compairing B-DNA with Z-DNA double helices and B-DNA helices with different base-pair distributions. The present, extension of our similations to Z-DNA and to Li* and K" eounterions permits some general conelusions concerning nucleic acids in solution.

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Section: Computational Techniquesmentioning

confidence: 99%

Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

Clementi

Corongiu

1983

J Biol Phys

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“…For each pair of water molecules with oxygen atoms that fall within the given range of one another, all of the (16) electrostatic contributions and the single Lennard-Jones term [Eq. (5)] are included. The same potential range applies to the water-dipeptide interactions; that is, for each dipeptide atom, interactions are computed with all five centers in each water molecule that has its oxygen atom within 8 A.…”

Section: Rossky Karplus and Rahmanmentioning

confidence: 99%

A model for the simulation of an aqueous dipeptide solution

1979

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SynopsisA model for the simulation of a solution of an alanine dipeptide in water is presented that combines a previous model for bulk water (ST2) with that used in conformational energy studies on small molecules and proteins. The results of a pilot molecular dynamics study indicate that the model leads to reasonable solvent-solute interactions. No evidence is found for substantial changes in the structure or dynamics of the dipeptide in solution as compared to in uucuo. Furthermore, a t the elevated temperature examined, there appear to be no significant effects on the dynamics or intermolecular bonding of the water molecules in contact with the solute.

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“…71 Uncertainty in the coordination number is evinced from theoretical studies, with variations between 5.1 and 8.4 depending on the simulation techniques adopted. 56,60,67,68,[71][72][73][74][75][76][77] Thus, despite extensive efforts, a complete microscopic model of the hydration shell of the aqueous chloride ion and its dynamics is still being debated.…”

Section: Introductionmentioning

confidence: 99%

Linking electronic and molecular structure: insight into aqueous chloride solvation

Bernasconi

Hunt

2013

Phys. Chem. Chem. Phys.

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Aqueous chloride solutions are ubiquitous and diverse; systems include sea water, atmospheric droplets, geological processes and biological organisms. However, despite considerable effort, a complete microscopic model of the hydration shell, and local electronic structure of the aqueous chloride ion and its dynamics has not been established. In this work we employ ab initio molecular dynamics to study an aqueous chloride solution. In particular, local solvation events and the electronic structure around the chloride ion are interrogated. We employ the Effective Molecular Orbital (EMO) method which partitions the electronic structure into solute and solvent components while maintaining a rigorous quantum mechanical description of both. Movement of the chloride highest occupied molecular orbital (HOMO) energy within the valence band of water is revealed. The chloride ion has little impact on the average water electronic structure, however, locally the electronic effect of the chloride ion is significant. With the Hofmeister series in mind we find that the electronic effect of the chloride ion extends beyond the first solvation shell, but not beyond the edge of the second solvation shell. The chloride ion sits near the centre of the Hofmeister series because of an essential degeneracy between water-water and water-Cl H-bonding and because of a strong similarity in the water and chloride electronic structure. The chloride ion prefers to be symmetrically solvated by six H-bonding water molecules, however, the chloride HOMO energy and the coordination number oscillate in response to local fluctuations driven by the dynamics of the bulk water. A combined structural and electronic analysis has led to a distinction between two types of water molecule within the first solvation shell, those that H-bond to the chloride ion, and those that remain local (i.e. within the first solvation shell) but which H-bond to other water molecules. There are indications that these exhibit different dynamics with respect to residence times and rotational vs. translational motion.

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Study of the structure of molecular complexes

Cited by 59 publications

References 11 publications

Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

A model for the simulation of an aqueous dipeptide solution

Linking electronic and molecular structure: insight into aqueous chloride solvation

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