A self-consistent microscopic theory of

hydrogen bond melting with application to

poly(dG)⋅poly(dC)
Cite as: J. Chem. Phys. 80, 6291 (1984); https://doi.org/10.1063/1.446732
Submitted: 21 November 1983 . Accepted: 13 March 1984 . Published Online: 04 June 1998

Y. Gao, K. V. Devi-Prasad, and E. W. Prohofsky

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J. Chem. Phys. 80, 6291 (1984); https://doi.org/10.1063/1.446732 80, 6291

© 1984 American Institute of Physics.

A self-consistent microscopic theory of hydrogen bond melting with
application to poly (dG)·poly{dC)
Y. Gao, K. V. Devi-Prasad, and E. W. Prohofsky
Department of Physics, Purdue University, West Lafayette, Indiana 47907

(Received 21 November1983; accepted for publication 13 March 1984)

In this paper we develop a modified self-consistent phonon approximation model which displays
effects which indicate melting. The model is applied to hydrogen bond melting of poly
(dG )·poly(dC )and predicts melting at 340 K. The calculation has no parameters adjusted to fit the
melting, the hydrogen bond potentials are adjusted to fit data at room temperature.

I. INTRODUCTION In this paper we use the formalisrn of self-consistent

Experimental observations on double helical DNA do
indicate that the vibrational excitations are phonons. At low
frequencies where the distinction between phonon and other
type modes is more important evidence has now accumulat-
ed which is only consistent with the existence of phonon-like
modes. Low frequency Raman scattering has been carried
out by Urabe et aU from 10-300 cm -1 and modes in this
region are observed to have quasimomentum conservation
selection rules, i.e., scattering occurs only when the change
in wave vector for the incident and scattered optical waves is
parallel to the helix axis. This indicates that the modes are
phonon (SCPA) theory to explicitly determine the effective
force constant and how they change with temperature based
on an assumed Morse potential. We have found that by a
suitable modification ofSCPA we calculate behavior which
we believe can be interpreted as helix melting.
II. THE SELF-CONSISTENT PHONON APPROXIMATION
The SCPA has been explored in a large number of pub-
lications. An extensive review tutorial article has been writ-

~~
phonons which propagate along the helix and have a quasi- .03 ~06 Poly (dT) •
Poly (dA)
mornentum along the helix. These same modes were also .02

II
observed to strongly obey phonon selection rules2 having to .01
do with the polarization of the incident and scattered waves. o l .052-j
I I 1
Fc~
Urabe and Tominaga3 have also observed the mode soften- .03 Poly(dG) .
Poly (dC)
ing associated with the A to B conformation change as pre- .02
dicted by phonon calculations4 and in quantitative agree-
ment with more recent calculations. s Urabe and Tominaga6 gc:
o
.0 I

0
I I I I I
e~
have also observed a broad phonon mode centered at 85 if .03 Poly(dAG)' Poly(dCTI
cm - I which they note seems to involve hydrogen bond mo- =
.. .02
tion and behave anomalously as the temperature approaches
the helix melting temperature. Such a band was predicted
~ .0 I
; 0 I I !
k~
based on phonon calculations7 and its involvement in the .:::: .03 Poly (dAC) . Poly (dGT)

melting suggested. Figure 1 reprints 8 a graph of the ampli- ~ .02

..:
tude of average H-bond stretch frequency for the phonon
modes having large coherent H-bond stretch. The cluster of
~ .0 I
Ii; 0
.....071
I I
~~
modes for different composition DNA indicates that a o .03 Poly (dAT)' Poly (dATI
Z
broadband centered about 85 cm - 1 would be seen in random al .02
sequence DNA. The results seen by Urabe et al., have been
verified independently by Lindsay et al. 9
:I: .0 I

2 0
I I I I I I I I
~ .03

~~
In addition to the low frequency Raman work, bulk Poly(dGC)' Poly(dGC)
acoustic modes in fibers,IO·11 local mode resonances l2 and .02
microwave absorption 13 have all been observed and the ob-
servations are in agreement with phonon calculation predic-
.0 I
o
30 4() lIO eo
t I,
70 eo
II [
90 100 110 120 130 140 IlIO 160 170 180 190
i
tions.I4-16 All the calculations referred to have used force
Frequency (cm- I )
constants which have been refined to experimental observa-
tions. 14,17 These force constants would be effective force con- FIG. 1. Hydrogen bond stretch modes for various DNA polymers. The bars
stants as they are determined from data taken at tempera- represent the amplitude ofH-bond stretch averaged over the H bonds in the
particular polymer. These amplitUdes are per phonon where the amplitude
tures greater than zero Kelvin. is normalized to one phonon per unit cell. For N cells these amplitudes
should be mUltiplied by N - 1/2. The location of the bars on the frequency
scale indicate the frequency of the mode. Only coherent stretch modes, i.e.,
those in which the stretch is in phase on each H bond are displayed. This
.IThis work supported in part by a grant from Indiana Elks Purdue Cancer calculation used H-bond force constants determined from the Lippincott-
Research Committee. Schroeder model.

J. Chern. Phys. 80 (12). 15June 1984 0021-9606/64/126291-08$02.10 © 1984 American Institute of Physics 6291
6292 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting

ten by Werthammer l8 which also contains references to ear- (V(r ikjv )0 = exp(¥>ikjv:VV)V(Rij + d kv )· (12)
lier work. In this section we describe the theory in a
The stationary condition of the free energy requires that
condensed development which leads to the particular forms
we use in later sections. ~=O. (13)
Consider a periodic system with the repeat unit labeled arPikjv
by Ri and the equilibrium position of an atom in the unit by By direct differentiation of Eq. (7) we find that
d k • The dynamic displacement of the atom is defined as
rPikjv = (VVV(rikjv)O
(1)
= exp( - !Dikjv:VV)VVV(Rij + dkv ). (14)
where rik is the position of the atom and Ri and dk may
depend on the temperature. If we know from experimental Using a Fourier transformation
observation that the resulting vibrational solutions will be
phonon-like solutions we can define an effective Hamilton-
A.. . =-l-fd
'i'lk J v-(2'l7f
3
q
e- !D,k,jv:qq

ian quadratic in the displacements which will give phonon-

like solutions. We define the effective Hamiltonian Ho as xf d 3 uVVV(R ij + dkv + u)e iq. U

(2)
f d 3 ue -!U'DikJ~'UVVV(Rij + d kv + u)
where Uikjv =Uik - Ujv and the force constants rPikjv is to be (15)
determined self-consistantly. Mk is the mass of atom k and
Uik is the velocity of atom ik.
Since the material considered is at finite temperature The inverse of Dik,jV is taken in the three-dimensional space.
and we are interested in temperature dependent effects we The effective force constants thus obtained can be dia-
use the free energy Fwhich is defined as gonalized in a unit cell subspace to provide the frequency
F = -,B -Ilog Tr{ exp( -,BH) J, (3) spectrum
where H is the true Hamiltonian and,B = (KT) -I. For the
model Hamiltonian, we define the free energy as
Fo = -,B -Ilog Tr{ exp( - ,BHo)). (4) where
The thermal average (Jo of any operator (J is
thv(k)= 1 I e-lk'R'J I !(c5;;,c5 kk ' -c5il c5 kv )
«(J )o=Tr{ (Je -IIH O)/Tr{ e -IIH o). (5) ~MkMvRi-Rj tk'lv'
Then X (c5j ;" c5 vk , - c5j.lc5",; )rPrk',fv" (17)

F - Fo = -,B - I log( exp [1 -illdte - iHot.::1 VeiHot ] ) 0 •

The model free energy can then be diagonalized to

(6) Fo =,B - I Ilog{ 2 sinh [VJw,dk)] ). (18)

.<,k
The .::1 V is the difference between the real and the model From Eq. (4),
Hamiltonians
~ -
aFo _I( ) =ID
4 U,k,jvU,kjv 0-4 ikjv' (19)
.::1V=H-Ho·
V',k.Jl'
If the rPikjv 's are selected properly, (.::1 V) 6 will be small and it
Carrying out the differentiation,
is possible to expand the difference between F and Fo in pow-
ers of (.::1 V) o. The first order approximation gives 1 1
D ikjv = - I - - ctanh [!,Bw.< (k)]
N k,.< 2li.I.«k)
F-Fo + (.::1 V)o. (7)
For simplicity we will assume that the true Hamiltonian in- X {[~kA(k)elkoR' - ~v.«k)elk'RJ] xc.c.},
cludes only two body interactions ~ JM:
(20)
V(rl, ... rN)=!IV(rikjv)' (8)
ik,jv where N is the number of unit cells in the crystal and C.C.
Then stands for complex conjugates. Equations (15H17) and (20)
then form a self-consistent loop.
(.::1 V)o =!I (V(rikjv)O -! I !Dikjv:rPikjv' (9) One can get a phenomenological insight into the work-
ikJv ik,jv
ings ofSCPA by inspecting Eq. (15) It is seen that the effec-
where the correlation tensor is defined as tive force constant is not the force constant at the potential
==
D ikjv (Uikjv Uikjv) o. (10) minimum but is an averaged force constant, averaged over
the extent of the likely displacements as determined by the
The first part can be expanded in a Taylor series:
correlation tensor which in tum is determined by the level of
(V(rikjv)O = (exp(uikjv·V)oV(Rij + dkv )' (11) thermal excitations. The effective force constant is deter-
The phonon-like behavior ofuikjv further simplifies Eq. (11): mined by the self-consistent oscillator amplitudes.

J. Chern. Phys., Vol. 80, No. 12, 15 June 1984

 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting 6293

III. MODIFIED SCPA
The SCPA is a phenomenologically appealing ap-
proach but has a number of problems which arise due to its
inability to incorporate thermal expansion and deal correct-
ly with odd power terms in the potential expanded about
equilibrium. Since the term exp[ - J-l 21W ] is symmetric in J-l
all odd terms necessarily cancel in the integral of Eq. (15).
This problem was recognized and led to the "improved self-
consistent phonon approximation or ISP. 19 This improve-
ment introduced the odd terms into the free energy in some
level of approximation and improved the agreement between
calculated and observed properties at high temperatures.
The ISP also failed as T approached melting temperatures
valence chemical bonds and consist of force constant for
bond stretch, angle bends, torsions, and out of plane bends,
etc. We have defined these terms in earlier papers. 20 These
force constants are defined with respect to displacements
which are internal, i.e., fixed to lines between pairs of atoms,
angles between pairs of chemical bonds, etc. We define these
internal coordinates as 'TIn where n labels the unit cell. The
dynamic solution is simpler in mass weighted Cartesian co-
ordinates (MWC) Sn. The internal coordinates can be writ-
ten in terms of the MWC coordinates by the definition of a B
matrix previously described 20 as
(22)
m= ~ 00

due to the approximate handling of the odd power terms.

where B::' is the transformation matrix from the (n + m)th
We have chosen to explore a different modification of
unit in MWC to the nth in internal coordinates. Because of
the approach which retains the simple phenomenological
the helical symmetry of DNA,
features of the SCPA but specifically introduces an effective
thermal expansion. We do this by simply shifting the origin B':" =B~(RT)n, (23)
of the displacement J-l from the potential minimum to a self- where R is the rotational part of the screw operation of the
consistent thermal mean position. This shift in origin is done helix and B ~ is the B matrix for the zeroth unit cell. We will
in the integral of Eq. (15) and leads to incorporation of odd subsequently drop the superscript (0). The potential may be
power terms in a way that does not introduce an infinite written in terms of the valence force constants as
series of terms. We feel such an approach is in keeping with
the spirit of an effective oscillatory solution that results from 2V= (24)
self-consistent calculations. We explored a number of ways m, n = - co

of determining the mean position based on thermodynamic The force constant matricesF depend only on the separation
weighting of the displacements most of which turned out to of units (m) because of helical symmetry. Define an orthogo-
involve very clumsy and lengthy calculations as subroutines nal transformation
in our self-consistent solutions. The simplest formulation for (25)
finding the mean position involved the classical condition
that at the classical turnaround point all the oscillator ener- Combining Eqs. (22)-(25) we can get the potential expression
gy is in potential energy. This indicates that the near and far in MWC:
turnaround points are at the same value of potential energy. 00

The oscillator would then be described by harmonic dis- 2V = Ln,j,kS',.,+j(R Ty B fFnBkR kS ',.,+n+k'
m,
(26)
placements from a point midway between the classical turn-
around points and we defined this midpoint as the origin of From symmetry considerations the solutions form bands
the displacement parameter J-l. This led to a simple integral which differ along the bands by having different phase shift
in determining the effective force constant. from one unit to the next. We incorporate this phase shift 8
The displacement weight function is exp[ - J-l 2 /2D ] into the problem by defining the Fourier transformed varia-
and we define a classical amplitude J-l( T) as the half-width of bles
that function. The mean equilibrium position Rij + du for
a given T is specified by the condition
S~ = _l_Il7 dO X (O)e - in(). (27)
.[iii -17

V[Rij +dM +u(T)] = V[Rij +dM -u(T)]. (21) By substitution of Eq. (27) into Eq. (26) we get

IV. APPLICATION TO POLY (dG}·POLY(dC). 2V= J~l7dOX+(O)B +(O)F(O)B(8)X(O), (28)

The formalism ofSCPA was developed for a crystalline where
solid in which the symmetry operations were translations. In
L
00

dealing with the DNA helix one is in a one dimensional heli- B(O)= BnRne-in(), (29)
cal system where the symmetry operations are screw axis n= - 00

operations. The differences are mostly superficial, the suces-

sion of screw operations is isomorphic to a one dimensional (30)
m= - 00

succession of translation operations. However, the formal-
ism does have to be altered to reflect the difference. In DNA
we are also dealing with a large number of atoms in a unit
cell, all in different symmetry sites. This necessitates the use
of a valence force field approximation to separate the large
force constants as distinct from nonbonded force costants.
The valence force constants are correlated to the concept of
From group theory the overall secular determinant breaks
down into diagonal blocks for each value of 0 and these can
be solved independently from
det[B+(O)F(O)B(O)-A(O)I] =0. (31)
The eigenvalue A (0) is 0)2 for the vibrational modes and the
eigenvectors can be found from the unitary transformation

J. Chern. Phys., Vol. 80, No. 12, 15 June 1984

6294 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting
that diagonalizes the first term ofEq. (31). This then defines
the normal vibrational modes of the model DNA helix. If
one assumes these solutions in the SCPA then the correla-
tion tensor of Eq. (20) will be given by
Dmk,nY
1
=-2 L J1T-1T dO 2w,,(O)
1T"
1 ctanh [ ~w,,(O)
2
1 ]
X{[ ~ ekA.(O)e
imll
- ~ ey,,(O)e inli
] Xc.c.},
where m and n specify the unit cells, k and v specify particu-
lar atom displacement components within the cell, w(O) are
the frequencies from Eq. (31), ekA. are the components of the
eigenvectors associated with band A also from Eq. (31), Mk
and My are the masses of atoms k and v, and C.c. stands for
the complex conjugate of the terms in the preceding square
brackets. In all the vibrational modes that are important to
the H-bond melting w varies little with 0 and as does ekA. (0).
This is because the modes are optical modes with relatively
little dispersion. To simplify the further calculations we treat
the modes in the Einstein approximation. We assume
w(O) = w(O) and e(O) = e(O), i.e., values at zone centers and
the integration over 0 is then trivial and Eq. (32) reduces to
D mk. nv = L ~tanhH (Jw,,)
" 2w"
x{[~kA. -~v"]Xc.c.}.
.JM; ~ the initial value of the tensor D by use ofEq. (33). The effec-
The values of the force constants F (Eq. (24) used are
those that have been determined by refinining an initial set to
experimental Raman 21 and Brillouin 14 scattering observa-
tions. Since the experimental data was taken at room tem-
perature and the force constants were fitted to that data
these force constants are the effective force constants at
room temperature. They are what would arise as the ¢ , s with
D determined at room temperature. As long as the physical
conditions are unchanged there is no need to further correct
these force constants. However, if we wish to explore varia-
tions in temperature we must use the MSPA formalism to
calculate the temperature dependence of these force con-
stants. A boundary condition on such a calculation is that
the calculated effective force constants agree with the fitted
values at room temperature. As the bulk of the valence po-
tentials are much stiffer than those for H bonds we assume
that the variation in effective force constant with tempera-
ture over the range of interest is small for all force constants
except those associated with the H bonds. We will apply the
formalism of MSP A to these force constants holding all oth-
er force constants fixed.
The set offorce constants used have base stacking inter-
actions included. These were introduced to fit the acoustic
velocity measurements. 14 They are significant in maintain-
ing equilibrium structure of the double helix. The calculated
displacement and therefore also D contains the effects of
these stacking forces. They are included in the calculation
which ultimately leads to the onset of melting. The assump-
tion here is that since they are mostly electrostatic or van der
Waals-like in character they vary less with small changes in
distance than the H bonds and therefore their renormaliza-
J. Chern. Phys., Vol. 80, No. 12, 15 June 1984
tion for correlated motion alters these nonbonded effective
force constant very little.
In keeping with the model calculations on a simpler
system 22 we approximate the true potential for the H bonds
as a Morse potential. This was done for calculational conve-
nience. The Morse potential does introduce a phenomeno-
logically correct nonlinear behavior into the potential. We
(32) refined the parameters Vo, a, and Ro ofthe Morse potential
to fit the observed separation of H bonds and to also fit the
experimentally observed dynamic behavior at room tem-
peratures. The heavy atom separation of the three H bonds
was taken from, x-ray data and the dynamic behavior refers
to fitting room temperature force constants so as to give an
H-bond stretch mode at the observed 85 cm- 1 frequency.
We believe that with parameters chosen in this way the
Morse potential can be made to fairly accurately represent
the true potentials of the three H bonds. The fitted param-
eters for the three H-bond potentials are listed in Table I.
The variable in the Morse potential is the heavy atom-heavy
atom distance and assumes that the hydrogen atom achieves
equilibrium rapidly compared to all other motions in the
problem.
An initial solution of the vibrational modes from solu-
tion of Eq. (31) is achieved using the refined force constants
and H-bond force constants chosen by use of the Lippincott
Schroeder relations. 23 These frequencies wand eigenvector
(33) projections on the H-bond coordinates eare used to evaluate
tive force constants for the H bonds are then calculated using
Eqs. (21) and (15). These values of effective force constants
for the H bonds are substituted into Eq. (31) and the whole
procedure is iterated until selfconsistency is achieved. It was
necessary to modify this approach somewhat as the subrou-
tine for the calculation of eigenvalues and eigenvectors, Eq.
(31) was set up initially in a way that did not faithfully repro-
duce the Dxx and Dzz components of the H-bond correlation
tensor. The z direction is parallel to the helix axis. The x
direction is along the C2 symmetry axis for the helix back-
bone and the y axis is the third orthogonal direction and is
roughly parallel to the direction of the H bonds. The values
calculated for Dxx and Dzz were too large compared to the
Dyy component. The problem arose due to an idiosyncracy
in the definition of harmonic coordinates and harmonic
force constants. To simplify the calculation we used the
faithfully calculated vlaues of the Dyy component and as-
sumed Dxx = Dyy = Dzz , i.e., tr(D) = 3Dyy . The trace of D
relates to the total correlated motion which stretches the
hydrogen bond and is the parameter important in Eq. (21).
In the iteration scheme we define a divergence L1 and
continue the iteration until
TABLE I. The Morse potential parameters for the three H bonds.
Bond N(I)HN(3) N(2)HO(2) N(4)HO(6)
0.03mdynA 0.07 mdyn A 0.072 mdynA
1.4 A ~I 1.9IA~' 1.92 A ~I
2.7236 A 2.5401 A 2.5278A
 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting 6295

.:i = abs[ L det[D - Do]] <0.0001, (34)

Hbonds det[Do]
where D is the latest values for the correlation tensor and Do
are the values from the previous iteration. We also compared
values of .:i with previous step values .:io and watched for
instability for which.:i / .:io > 1. The first solution was carried
out at T = 293 K. The frequencies and values of RT were
fitted to 85 cm - I and the x-ray values of H-bond distance.
After self-consistency was established the procedure was re-
peated until self-consistency was established at each tem-
perature for temperatures at 10 K intervals. No parameters
were altered after the initial fittings of Vo's, a's, and Ro's at
T = 293 K. At 340 K no self-consistent solution was found.
The results of this calculation is displayed in Figs. 2-5.
Figure 2 shows the values of the three H-bond thermal ex-
panded heavy atom heavy atom distance as a function of
temperature. It is clear that an instability occurs at :::::: 340 K.
The H-bond adjacent to the major groove "melts" first ra-
pidly followed by the other two bonds. The value of the effec-
tive stretch force constants for the three H bonds are shown
as a function of temperature in Fig. 3. The frequency of two
vibrational modes are shown as a function of temperature in
Fig. 4. These modes were selected for display as they have
the character of H-bond stretch modes i.e., they involve
large coherent beating of one strand of the helix against the
other. These modes are the largest contributors to the H-
bond correlation tensors. The values of Vo and a of the three
Morse potentials were chosen to have the higher frequency
mode match the experimentally observed line at 85 cm - 1 at
room temperature. Figure 4 shows the values of the compo-
nent of the correlation tensor Dyy as a function of tempera-
ture for the three H bonds. Again the onset of the instability
is clearly displayed in this figure.
At temperatures where D is large the atom displace-
ment varies over a large range of instantaneous values of the
force constants, the force and the motion can be expected to
be very nonharmonic. The frequencies displayed in Fig. 4
would be very much broadened at the higher temperatures
and could be broadened to the point of contributing to a
central feature.
V. DISCUSSION
A number of assumptions and approximations have
been made in the above calculations. The principal assump-
tion in the formalism is that the thermal expansion l9 can be
incorporated into the theory as we have done. Another im-
portant assumption is that the model can be applied to DNA
in the first place, i.e., that the excitations of the helix can be
described as phonons in an effective harmonic approxima-
tion. It is also an assumption that the bulk of the force con-
stants do not have to be renormalized over the temperature
range considered that only the hydrogen bond constants
change significantly. In addition, we have employed an Ein-
stein approximation for the dispersion of the optical modes
and we have inferred the three dimensional behavior of the
hydrogen bond displacement by extrapolating from the dis-
placement of one component. The particular form and para-
metrization of the bare Morse potentials are also approxima-
tions. The reasonability of all these assumptions has been
discussed at various places in this paper. With these assump-
tions one calculates behavior which reproduces the behavior

3.100

3.060 I
I
I
I
I
3.000 I
I
I FIG. 2. The mean distance between end heavy
I atoms (thermal expansion) for the three H
I bonds as a function of temperature. The solid
I line is for the central or N( l)-H- N(3) bond, the
I short dash line is for the O(6)-H-N(4) bond ad-
" jacent the major groove, and the long dash line
is the N(2)-H-O(2) bond adjacent the minor
groove. The curve is plotted as a succession of
2.900 straight segments between calculated points.
The kinks are simply the position of the calcu-
lated points.

2.860

2.«m;-----~r-----_r------~----~------._----~
280.0 s.eo.O 330.0 3110.0 360.0
T (IN Kl
J. Chern. Phys., Vol. 80, No. 12, 15 June 1984
6296 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting

.3000

.2&00

.2000

~
z
>-
c FIG. 3. The effective force constants for the
x .1&00 three H bonds as a function of temperature. The
z.... lines refer to the same bonds as in Fig. 2.

u.
.1IJOO

.0500
--
.OOOO~-------'--------'-------~--------r--------r------~
290.0 300.0 310.0 320.0 330.0 SIIO.O 3&0.0
T (IN K)
expected at the H-bond melting and at temperatures close to nates between pairs of atoms could be defined and particular
the observed melting. restoring forces postulated. It is the breakdown of this set of
The entire formalism of MSPA is based on a set of as- assumptions that we associate with the breakdown of the
sumptions which are only true for a solid. That is coordi- solid structure. A more correct analysis of the melting of a

80.00

8&.00
-..--..
-..--..
-"-"-..
---..
80.00
-"-"-..

-- --"-.. -..
.....
"-
"- ,
FIG. 4. The frequencies for two zone center
phonons as a function of temperature. The up-
::;'1&.00 per frequency was used to fit Vo and a to the
frequency of an observed Raman line. S The two
chosen have large components of H-bond mo-
tion.
70.00

8&.00

m.oo~------r------'------~------.-------'------'
290.0 300.0 310.0 320.0 330.0 sqO.O 350.0
T (IN K)
J. Chem. Phys., Vol. 80, No. 12, 15 June 1984
 Gao, Devi-Prasad, and Prohofsky: Microscopic theory of hydrogen bond melting 6297

.1800

.11fOO
I
I

-
LU

~
g
.1200

1
1
1
1
I
I
I

1
a:: .1000 FIG. 5. The correlation tensor D for each H

-
:z
,,"
""I
/
I bond as a function of temperature. The lines re-
fer to the same bonds as in Fig. 2.

-
""')

c .0800

- --
.,," "
.,,'" ."..,-
.,,'" .........
."..,-
/"

--:::.---
----
----
... ......... .........

.0800
--
.~4-------~------~------~----~~----~-------,
290.0 SOD.O 310.0 320.0 330.0 sqo.O 360.0
T (IN K)

solid would calculate the free energy of the solid and com-
pare it with the free energy of the melted state to determine
when melting occurs. The free energy of solid phase can be
calculated using MSPA as can be seen from Eq. (4). One can
also get a crude idea of the behavior of the solid free energy
from the parameters already calculated.
The parameter D is associated with mean squared mo-
tion of certain variables. Thus increase in D indicates an
increase in kinetic energy and by the effect of softening effec-
tive force constants a decrease in binding energy. Therefore
i,ncreases in D indicate increases in the free energy of the
solid. A large increase in D will cause a large increase in free
energy and if this increase is large enough it will certainly
cause the free energy of the solid to exceed that of the melted
state. It is possible that the solid free energy becomes greater
than that of the melted state at temperatures below the onset
of the instabilities in our theory and in such a case melting
would occur at the lower temperature. The instability we
calculate is than an upper limit to the melting temperature
and it can be calculated without recourse to an ability to
calculate the free energy of the melted state. The agreement
of the onset of instability with the observed melting tempera-
ture would argue that the free energy of the solid is signifi-
cantly below that of the melted state until the onset of the
solid instability. It would be nice if this is in fact correct for
then the onset of melting will be wholly determined by the
state of the solid DNA helix which would simplify the mech-
anisms that control the dynamic behavior of DNA.
It is difficult to compare the result of this analysis, in
which salt concentration, degree of hydration, loop entropy,
base mismatch, etc. are not explicitly dealt with to the ob-
served melting behavior which is known to depend on such
factors. The effect of salt and hydration does enter our calcu-
lations implicitly. The calculation has nonbonded forces
which effect the normal mode solutions and therefore effect
the parameter D. These nonbonded forces do vary consider-
ably with environmental effects such as salt concentration.
The force constants used were derived by fitting the acoustic
velocity in fibers l4 and should therefore represent a low salt
situation. At 19.5 mM ofNa+ concentration the reported 24
melting temperature is 360 K, which compares very favor-
ably to the value of 340 K we calculate. It would be of inter-
est to vary these nonbonded forces in a way consistent with
altered salt concentration and determine the sensitivity of
the melting temperature to such effects. From a preliminary
analysis it does seem to have the correct qualitative behavior.
It is also possible to incorporate some of the other macro-
scopic factors such as loops etc., into this formalism by using
a phonon spectrum which includes local modes associated
with such effects. IS Such extensions of this simple model can
then be compared to observations to determine the useful-
ness and limitations of the approach.
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