Ab initio water

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Ab initio water

• Normally we use CM sampling for nuclear motions,
  we continue to do that in AIMD
• BUT, we allow the electrons to relax to whatever
  distribution is appropriate, thus allow for
  polarization of the electron cloud
• Note the dipole moment of water goes from about
  1.85 D in the gas phase to about 2.6 D in liquid
  water, so there can be a substantial
  redistribution of charge, and thats important
  for all of biophysics

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Ab initio water

• Free energy of liquid water on the basis of
  quasichemical theory and ab initio molecular
  dynamics
• D. Asthagiri, Lawrence R. Pratt, and J. D. Kress
• Theoretical Division, Los Alamos National
  Laboratory, Los Alamos, New Mexico 87545, USA

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RDFs
FIG. 1. Oxygen-oxygen radial density
distribution. The data were collected in bins of
width 0.05 Å. The current best experimental study
using the Advanced Light Source _at_24 experiment
ALS! is also shown. The PW91 run is at a
temperature of 334 K, the PBE run is at a
temperature of 337 K, and the rPBE run is at a
temperature of 314 K. The experiments are at 300
K.
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Compare methods
FIG. 2. Oxygen-oxygen radial density distribution
obtained by different groups using the BLYP
functional and the Car-Parrinello molecular
dynamics algorithm. The legend follows the same
code as in Table I, which also lists the stated
simulation temperature. Except for P96 which was
a 32 molecule simulation, all the results are for
a 64 molecule simulation.
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Free energies (1st time)
FIG. 6. Cluster variation of the hydration free
energy of water. The open circles give the
chemical contribution, RT ln x0. The open squares
give the packing contribution, 2RT ln p0. The
open triangles give the sum of outer-sphere
electrostatic and dispersion contributions. The
net free energy is shown by solid line.
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Water the saga continues

• Water an enduring mystery
• Yet another theory of liquid water structure
  raises questions about interdisciplinarity, drug
  design, astrobiology, molecular biology,
  geochemistry and more.
• Philip Ball, Nature v. 452 Mar 20, 2008

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Mysteries of Water, 2008

• Must waters enduring mystery merely induce
  despair in those who want to know how proteins
  fold and function, say, or how minerals dissolve
  or suspended particles clump together? No.
  Sometimes the details wont matter much,
  sometimes empirical knowledge and heuristics will
  suffice. Think of this puzzle more as an exercise
  in humility. Water reminds us of the dangers of
  doing science in silos, the risks of leaving
  apparently tidy explanations unexamined, the
  importance of not letting ubiquity lead to
  invisibility, and the recognition that new ways
  of studying the world can exacerbate as well as
  dispel confusion. -- Philip Ball, Nature
  commentary

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Ions in Water

• An ion in water exerts a large electrostatic
  force on neighboring water molecules
• That can distort the charge distribution,
  especially for multivalent ions
• Therefore a chemical treatment is often necessary

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Be2 in Water
Fig. 1. Structures representing the deprotonated
tetra-aquo cation, BeOH½H2Oþ3 , and the
aggregate formed by the coalescence of one such
unit and a Be½H2O2þ 4 , with explusion of
a water molecule.
Asthagiri and Pratt, CPL 371,613 (2003)
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Free energies for complexes
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Beck, et al, Our book, See syllabus
The PMV for Na is negative but for K is
positive, WHY?
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Other ions

• Many workers have looked at OH- and H in water
  as key chemical examples
• These are complex problems that we will go back
  to later
• These issues are at the heart of acid-base
  equilibria in aqueous solutions, and are still
  controversial!
• Transition metal ions Asthagiri et al JACS 126,
  1285 (2004)

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Ions in channels

• Ion channels are large membrane proteins which
  control the passive flow of ions into/out-of
  cells
• They can gate based on pH, ligands, voltage
• They often are selective, e.g. K vs. Na, very
  similar ions, how select?

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Example channels K
Doyle et al Science 280, 69 (1998)
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Cl- channel (transporter)
Dutzler et al Nature 415, 287 (2002)
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K channel selectivity

• K/Na Selectivity in K Channels and Valinomycin
  Over-coordination Versus Cavity-size constraints
• Sameer Varma, Dubravko Sabo and Susan B. Rempe
• JMB 376, 13 (2008)

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K channel and valinomycin
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K solvation in KcsA
Varma and Rempe, BJ 93,1093 (2007)
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DNA modeling

• ONETEP, Payne et al
• SIESTA, Spanish group including Ordejon, Artacho,
  Soler, etc.
• Using DFT, solve for the electronic ground state

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From a talk by M. Payne, also JCP 122, 084119
(2005)
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Using SIESTA
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Enzyme reactions
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