Chemical Physics Letters 436 (2007) 258–262

www.elsevier.com/locate/cplett

Triplet–singlet spin communication between DNA nucleotides

serves the basis for quantum computing
a,* b
Alexander A. Tulub , Vassily E. Stefanov
a
Department of Pure and Applied Mathematics, Computational Modeling Group, Saint-Petersburg State University, Universitetskaya
Embankment 7/9, 199034 Saint-Petersburg, Russian Federation
b
Department of Biology, Saint-Petersburg State University, Universitetskaya Embankment 7/9, 199034 Saint-Petersburg, Russian Federation

Received 9 November 2006

Available online 23 January 2007

Abstract

The nature of spin communication between DNA nucleotide pairs is discussed. The results are based on CIU (2 · 106 configurations,
6-311G** basis set) quantum chemistry computations at a constant temperature T = 310 K of complementary nucleotide pairs, guano-
sine–cytidine (G–C) and adenosine–thymidine (A–T) monophosphates, assembled into DNA fragments of different length. Calculations
reveal alternation of low energy triplet–singlet (T–S) potential energy surfaces (PESs), assigned to individual nucleotides. In a narrow
energy interval these PESs approach, showing repulsion and uncommon crossings. Complementary nucleotide pairing, a result of Wat-
son–Crick hydrogen bonding, produces a global minimum in total energy, coming from the unique crossing between two singlet by nat-
ure PESs strictly around 310 K. Interaction between non-complementary nucleotides reveals no minima and points rather to system
destabilization. Computations show that regularly organized DNA is a structure of similarly oriented spins along each of its two chains,
so that the resultant spin of the whole structure is equal to zero. Disordering in spin structure produces coherent effects, appearing in spin
flipping, which serves the basis for constructing DNA-based quantum computing.
 2007 Elsevier B.V. All rights reserved.

1. Introduction biological systems [9], operating in femtosecond-nanosec-

Initially, DNA computations are based on DNA and
molecular biology technologies [1,2]. Despite some advan-
tages [mostly thanks to highly developed parallelism, oper-
ating with a great number of four occurring in nature
nucleotides: adenosine (A), guanosine (G), cytidine (C),
and thymidine (T) monophosphates] over silicon-based
computing [1,3,4], conventional DNA computing repro-
duces the main features of classical Turing and von Neu-
mann machines and faces similar computational
problems currently existing in ‘computational complexity
theory’ and ‘exspace problem’. Most problems, associated
with classical computing, are eliminated in quantum com-
puting [5–8], which seems to be an integral part of most
*
Corresponding author.
E-mail address: clarisse@svs.ru (A.A. Tulub).
ond time intervals [10]. A switch between classical and
quantum DNA computing is in finding appropriate carri-
ers, providing signal communication between its nano-size
parts [11]. Classical DNA computing is based on Watson–
Crick (W–C) pairing/breaking rule [1], associated with
hydrogen bond making/rupturing between nucleotides, or
changing distance between stacked nucleotides of oppo-
sitely oriented DNA chains [1]. Both processes are rather
slow and do not provide desirable rate of signal processing.
Quantum computing uses fast operating signal carriers like
nuclear or electron spins, which are allowed to have two or
more different energy levels [5,7] commonly associated with
‘up’ and ‘down’ states [5,7].
Present Letter, aims at elucidating the nature of spin
communication in DNA W–C pairs and oppositely ori-
ented DNA chains. This communication – a result of mul-
tiple repulsions and crossings between singlet (S) and
triplet (T) potential energy surfaces, PESs – could serve

0009-2614/$ - see front matter  2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.cplett.2007.01.054
 A.A. Tulub, V.E. Stefanov / Chemical Physics Letters 436 (2007) 258–262
the basis for constructing DNA quantum computing, at the
heart of which is coherent electron spin flipping in DNA
nucleotides, occurring at W–C distances in a narrow tem-
perature interval around 310 K.
2. Model and methods of computations
Initially, W–C pairing was modeled with oppositely ori-
ented in space G and C nucleotides, 3 0 –5 0 and 5 0 –3 0 direc-
tions [12], Fig. 1. One of phosphate oxygens of each
nucleotide is blocked with methyl, mimicking the core of
other possibly joined intrachain nucleotides. The total
charge on each nucleotide is 1. G and C bases, guanine
and cytosine, respectively, lie practically in the same plane
(the deviation from plane symmetry does not exceed 0.15 Å
[12]) and initially are separated by 7.5 Å, the distance at
which no hydrogen bonding occurs.
In every computation run G and C were allowed to
approach at a step of 0.05 Å over a distance of 7.5 ‚
2.4 Å between nucleotide planes in a bath of 38 water mol-
ecules, surrounding both nucleotides on the periphery of
hydrophilic backbones, a region between C and G planes
excluded. On reaching the W–C distance, three hydrogen
bonds between G and C planes occur, Fig. 1 (dashed lines),
corresponding to conventional bond lengths r[HNH(C)–
O(G)] = 2.91 Å, r[N(C)–N(G)] = 2.95 Å, and r[O(C)–
HNH(G)] = 2.86 Å [13].
Computations use conventional configuration interac-
tion (unrestricted) CIU method (2 · 106 configurations, 6-
311G** basis set) at a constant human body temperature,
T = 310 K. The heating to this final temperature (the initial
temperature is 0 K) suggested a step-by-step procedure,
each step of 10 K per 1 ps. Subsequent cooling to 0 K
occurred in the reverse sequence with the same step. Such
a procedure at each step provides reaching thermodynamic
equilibrium between G and C subsystems and the water
bath. The distances and angles between the water mole-
cules meet the following limits: ROO 6 3.60 Å;
ROH 6 2.45 Å; /OHO 6 450 (ROO is the distance between
oxygens, ROHis that between the oxygen and hydrogen,
and /OHO the angle between two bonds, formed by a
hydrogen atom and two oxygen atoms). Computations
Fig. 1. Structure of C (left) and G (right) molecules, oriented in opposite
3 0 –5 0 and 5 0 –3 0 directions. W–C pairing occurs through three hydrogen
bonds (dashed lines) between N and O atoms. Oxygens are in red,
nitrogens in blue, carbons in grey, phosphorus in violet; small-size atoms
are hydrogens. (For interpretation of the references to color in this figure
legend, the reader is referred to the web version of this article.)
259
are carried out with NWCHEM 3.05 plus software on a
Compaq Alpha Workstation cluster [14]. To obtain reliable
statistics, computations included 25 independent runs
(T = 310 K), started from different randomly initiated
points within 7.5 ‚ 2.4 Å distance intervals between C
and G planes. The data were subsequently processed with
the root-mean-square technique of the Statistica-7-Release
software. The initial geometry of C and G was obtained
from the Protein Data Bank of the University of Califor-
nia. At every computational step the G–C geometry was
optimized over bond lengths, valence and torsion angles
to reach the minimum of total energy Etot.
Further, computations much similar in their routine,
dealt with other complementary/non-complementary
nucleotide pairs and their ensembles mimicking a real
DNA fragment, see Section 3.
Additionally, at W–C point (T = 310 K) we have carried
out quantum MD computations with the same basis set by
including only four lowest, preliminary obtained for this
point, S and T levels. The aim was to reveal spin density
redistribution between nucleotides over the time interval
of Dt = 3 ps.
3. Results
Fig. 2 shows the change of Etot on approaching C and G
planes in the distance interval 7.5 ‚ 2.4 Å. As a reference
(zero) point, Dr = 0.0, is taken the distance, corresponding
to W–C pairing at hydrogen bond distances, indicated in
Section 2. In a distance interval Dr = 3.5 ‚ 2.60 Å we
observe a slow increase in DEtot, then, in a distance interval
Dr = 2.60 ‚ 0.00 Å, a decrease in DEtot, the value reaches
its minimum at Dr = 0.0. Both intervals are marked by
energy oscillations, most pronounced (11.8 ‚ 12.9 kcal/
mol) in 3.0 ‚ 1.50 Å region. Below W–C, Dr < 0, we have
a dramatic increase in DEtot, caused by repulsion between
approaching C and G planes. Fig. 3 displays the lowest
Fig. 2. Change of Etot (kcal/mol) on approaching C and G nucleotides,
according to W–C pairing rule. The distance between C and G (Dr, Å) is
referred to that of a conventional W–C pair, assumed as a zero point [13].
260 A.A. Tulub, V.E. Stefanov / Chemical Physics Letters 436 (2007) 258–262
Fig. 3. The lowest in energy triplet (T) and singlet (S) states, correspond-
ing to G and C nucleotides on approaching each other with the formation
of G–C Watson–Crick (W–C) pair.
in energy PES projections on the DEtot  Dr plot. These
projections (curves) correspond, respectively to T and S
energy surfaces of G and C. Assignment to G or C is quite
natural because overlapping between nucleotide molecular
orbitals is weak and each nucleotide holds its individuality
in G–C pairing. The energies of T and S curves show the
following, descending in energy, order: E(TG) > E(SC) > E
(TC) > E(SG).
Trapped in a narrow energy interval 7.2 ‚ 30.5 kcal/mol
(Dr = 4.0 ‚ 0.90 Å), Fig. 3, these curves reveal dramatic
repulsion between TG and SC, TC and SG. The repulsion
is the evidence of ‘no crossing rule’ [15] between closely
approached PESs - the case of adiabatic treatment [15–
17], a conventional approach used in multiple quantum
chemistry computations of large systems, like ours. Diabat-
ically, the crossings are allowed in a very narrow space-
energy region, so-called conical intersections[18] between
different PESs. Adiabatically or diabatically treated, T
and S energy surfaces show tendency to be separated in
space due to difference in their symmetry, except for
pseudocrossings [18]. The effect results in diverging T and
S PESs in space and crossing appearance with other PESs,
often allowed by symmetry, in other space regions. This
picture is observed in our case, when, after being repulsed
from TG and TC, SC and SG curves begin to meet jDEtot
(SG)  DEtot (SC)j „ de 6 1.6 kcal/mol in Dr = 0.86 ‚
0.00 region, Fig. 3. At Dr = 0.00 we have the minimum in
de = 0.62 kcal/mol; in Dr < 0 SG and SC go practically
together, jDEtot (SG)  DEtot (SC)j 6 0.5 kcal/mol, reveal-
ing an increase in Etot, see above. When combined, SG
and SC curves of two regions, Dr > 0 and Dr < 0, form
the global minimum, corresponding to formation of a sta-
ble, W–C pair (Dr = 0.00), Fig. 3. TG and SC, TC and SG
repulsions result in appearing a crossing point between
TG and TC PESs at Dr = 0.24 Å, DEtot = 41.2 kcal/mol.
Unlike SG–SC crossing at r = 0.00, TG–TC crossing has
no minimum around Dr = 0.24 Å and thus is unstable.
The pseudocrossing between TC and SC at Dr = 1.81 Å
Fig. 4. The lowest in energy triplet (T) and singlet (S) states, correspond-
ing to non-complementary guanosine (G) and thymidine (T) nucleotides
on approaching each other in the same distance interval, see Fig. 3.
gives a local minimum, metastable by nature and broken
down by small perturbations of different origin, chemical
modifications of a remote site, e.g.
With no hydrogen bonding, as in the case of G–T non-
complementary pair, we observe a rather different picture,
Fig. 4. TG, ST, TT, and SG PESs appear to be turned in
space in such a way that their mutual repulsion does not
produce a desirable for stabilization minimum. SG–SC
crossing at a distance Dr = 0.44 Å from the imaginary
W–C point (for clarity it is reproduced from Fig. 3) gener-
ates a metastable state. TG–TT crossing at Dr = 1.32 Å has
no effect on stability, and G–T pair appears to be unstable,
the experimentally known fact [12]. A–T complementary
pairing reveals a picture almost identical to that of G–C
pairing. A–T complex is stable at W–C point; its stability
is due to appearance of a global minimum, a result of
SA–ST crossing. As anticipated, A–C complex is unstable,
the reasons for that are identical to those encountered in
G–T complex, Fig. 4.
4. Discussion
Though G–C pair around Dr = 0.00 has an overall S
state, its nature is rather intriguing. Being very close, SG
and SC states exchange their spin orientation from ‘up’ to
‘down’ and vice versa. This uniquely comes from spin den-
sity maps on each nucleotide, indicating rapid spin density
redistribution upon thermal nuclear movements,
s = 2 · 1013 s, around W–C point (MD computations,
T = 310 K). Time-dependent redistribution of spin density
reveals oscillatory nature, suggesting coherent in time
inversion of two spins, localized, respectively, on two com-
plementary nucleotides. The same is valid for other W–C
pairs and absolutely nontypical for non-W–C pairs.
The enlargement of the initial G–C system by consecu-
tive adding of A–T, and then C–G and T–A complemen-
tary nucleotide pairs, reveals no less intriguing picture,
Fig. 5. Computations show that oppositely oriented chains
 A.A. Tulub, V.E. Stefanov / Chemical Physics Letters 436 (2007) 258–262
(3 0 –5 0 , 5 0 –3 0 directions) forming a small DNA fragment,
G-A-C-T
| | | |, produce the state of oppositely oriented electron
C-T- G-A
spins. Totally, the state is singlet and comes from very spe-
cific fact that electrons within each chain have identical
spin orientation, Fig. 5. When paired, the resultant spin
on one chain is fully compensated by that on the other,
so the total spin equals to zero. Such an arrangement of
spins suggests that each spin is surrounded by oppositely
oriented ones. MD computations (four S and T lowest lev-
els from each complementary pair) of this fragment at
W–C point show some stabilization of spin flipping in time.
Specifically, we do not observe, as with a single W–C pair,
rapid spin exchange at s @ 2 · 1013 s caused by thermal
nuclear movements. Thus for G–C pair the energy of spin
G-A C-T
flipping corresponds to @0.62 kcal/mol, for | | and | |
C-T G-A
G-A-C-T
fragment it equals to @1.64 kcal/mol, and for | | | | frag-
C-T- G-A
ment it is 4.22 kcal/mol. The results come from compulsory
inversion of spin orientation within nucleotide strings of
spin ‘up’ and spin ‘down’ states in spin density matrice at
W–C point (T = 310 K), Fig. 5. One could anticipate that
alternate external field of appropriate value, depending
on the string length, applied, spins can change their direc-
tions thus producing coherent in time inversions. Specifi-
cally, in natural environment this field is produced by
Mg2+(H2O)2 water complex bound to a free oxygen of a
monophosphate bridge, which links riboses of a single
nucleotide string [19]. The case is that, when bound, Mg
complex can easily change its oxidation state,[19,20]
becoming a singly charged radical Mg+(H2O)2. Near this
oxidation state it shows small but very rapid fluctuations
in charge [20,21], cohered with opposite in sign charge fluc-
tuations on the bound nucleotide string. Such a device,
composed of Mg complex and nucleotide string, produce
cohered changes in energy, necessary for spin exchange.
It should be stressed separately that coherence in spin
flipping in single W–C pairs and oppositely oriented nucle-
otides is reached exactly around 310 K, when S curves
from oppositely oriented nucleotides come together,
Fig. 5. Spin arrangement in a DNA fragment, composed of four
complementary paired nucleotides. Dashed and solid lines indicate
intrachain spin coupling between oppositely directed chains.
261
Fig. 3. Below and above this temperature (±5 K) S curves
reveal significant energy gap of 5 kcal/mol and more, and,
what is most intriguing, these curves begin to separate, thus
manifesting decoherence in spin behavior in the vicinity of
W–C point. Spin operation in a very narrow temperature
interval around 310 K seems to be highly specific for bio-
logical molecules [22].
5. Conclusion
For computational purposes we need two spin-depen-
dent oscillators. They come from oppositely oriented nucle-
otides, which show weak tendency to spin density
overlapping. In single pairs there is a rapid exchange of
spins, maintaining the total wave function, WF, in S state
in the vicinity of W–C point. This exchange, which serves
the basis for constructing a spin-dependent computational
device, initially suggests diabatic behavior of the system,
composed of two parts – nucleotides, m and n. The time-
dependent WF of m (the same is valid for n) near W–C
point can be expressed in the form of (1).
    X    
d d ðdÞ ðdÞ d
 
W m ¼  m  m W m  e ½ið/n /m 
m n Wn
dt dt dt
m6¼n
ð1Þ
where /ðdÞ is the dynamic phase
m
Z t
/ðdÞ ðtÞ ¼ ð
h Þ 1
dt0 Em ½Rðt0 Þ ð2Þ
m
0
and hm j dtd j niB Im,n is the matrix element, linking m and n
parts
d
I m;n ¼ hm½RðtÞjrR jn½RðtÞi RðtÞ ð3Þ
dt
R(t) is the configuration parameter, showing the depen-
dence of W on the vector of nuclear coordinates. Diabati-
cally treated, Im,n is knowingly not equal to zero, thus
providing spin exchange between m and n parts, /ðdÞ m and
/ðdÞ
n are basically not equal, thus generating a dynamic
angular momentum between m and n spinors [23,24]. This
altering in time momentum, a result of coherent spin ex-
change between nucleotides, could be uniquely used in
quantum computations. We are a bit away from giving ex-
act engineer solution for such a device, but operating with
phase coherence is still a very promising idea for modulat-
ing entangled signal transfer [5].
In multinucleotide DNA fragments, Section 3, to pre-
serve their spin individuality, Fig. 5, nucleotides break
down their dynamic phase by replacing it with a topology
phase [16,25] – a result of twisting nucleotide strings into a
spiral at a step of 360, B-form of DNA [12]. According to
our computations [26], this twist comes from leveling
dynamic angular rotations, corresponding to S and T fre-
quencies, xS and xT, evolving in opposite directions on
the Bloch sphere at a ratio of 8/5. To initiate spin entangle-
ment we need to break (at least slightly) DNA spiral sym-
metry by applying external field, a Mg-device (Section 3),
262 A.A. Tulub, V.E. Stefanov / Chemical Physics Letters 436 (2007) 258–262
e.g. In this case, one anticipates coherent signal transfer
between nucleotides.
Acknowledgements
This Research is supported by the Ministery of Educa-
tion of Russian Federation (Grant RNP 2.1.1.4139) and
Nasa Ecology Program for providing access to necessary
computer resources.
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