Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides
Optimal structures and intramolecular web of H-bonds of cytidinc, undine, thymidine, 1heir deoxyribo-analogues and some O5'-, O3'-deutero derivatives were studied by means of MNDOl H semiempirical quantum-chemical method. Effect of the intramolecular H-bonda on the slereochemical structure...
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Інститут молекулярної біології і генетики НАН України
1998
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nasplib_isofts_kiev_ua-123456789-1554382025-02-09T09:55:46Z Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides Внутрішньомолекулярні водневі зв'язки та структурна нежорсткісті піримідинових нуклеозидів Внутримолекулярные водородные связи и структурная нежесткость пиримидинових нуклеозидов Mishchuk, Y.R. Hovorun, D.M. Optimal structures and intramolecular web of H-bonds of cytidinc, undine, thymidine, 1heir deoxyribo-analogues and some O5'-, O3'-deutero derivatives were studied by means of MNDOl H semiempirical quantum-chemical method. Effect of the intramolecular H-bonda on the slereochemical structure of nucleosides (particularly, on the stabilization of anti conformation), on the physico-chemical characteristics of nucleoside molecules (heat of formation, dipolc moment, first adiabatic ionization potential and the charge distribution), and on the dynamical characteristics of pyrimidine nucieosides (barriers of the interconvertion, frequencies of the torsional vibrations) was elucidated. The intramolecular 11-bonds in polynudeolides and their influence on the nucleic acid architecture, and nonlinear dynamic properties arc discussed. Оптимізовані структури цитидину, уридину і тимідину, їхніх дезоксирибо-аналогів та деяких О5', О3'-депротонованих похідних отримані за допомогою напівемпіричного квантовохімічного методу MNDO/H. Виявлено сітки внутрішньомолекулярних водневих зв'язків піримідинових нуклеозидів та вивчено їхній вплив на. стереохімічну структуру молекул (зокрема, на стабільність anti-конформації), фізико-хімічіні параметри /теплоту утворення, дипольний момент, потенціал, іонізації та розподіл зарядів), а також на динамічні характеристики піримідинових нуклеозидів (бар'єри інтер конверсії, частоти торсійних коливань). Обговорюється присутність внушріишьомолекулярних водневих зв'язків у полі нуклеоіпидах та їхнє значения у формуванні, структури та нелінійної динаміки нуклеїнових кислот. Оптимизированные структуры цитидина, уридина и тимидина, их дезоксирибо аналогов и некоторых О5'-, О3’ -депротонированных производных получены с помощью полуэмпирического квантовохиминеского метода. MNDO/H. Обнаружены сетки внутримолекулярных водородных связей пиримидиновых нуклеозидов и исследовано их влияние на стереохимическую структуру молекул с в частности, на стабильность anti-конформации), физико-химические параметры (теплоту образования, дипольный момент, потенциал ионизации и распределение зарядов), а также на. динамические характеристики пиримидииовых пуклеозидов (барьеры интерконверсии, частоты торсионых колебании). Обсуждается наличие внутримолекулярных водородных связей в полинуклеотидах и их значение в формировании структуры и нелинейной динамики нуклеиновых кислот. 1998 Article Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides / Y.R. Mishchuk, D.M. Hovorun // Биополимеры и клетка. — 1998. — Т. 14, № 4. — С. 360-370. — Бібліогр.: 36 назв. — англ. 0233-7657 DOI: http://dx.doi.org/10.7124/bc.0004E0 https://nasplib.isofts.kiev.ua/handle/123456789/155438 en Биополимеры и клетка application/pdf Інститут молекулярної біології і генетики НАН України |
| institution |
Digital Library of Periodicals of National Academy of Sciences of Ukraine |
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DSpace DC |
| language |
English |
| description |
Optimal structures and intramolecular web of H-bonds of cytidinc, undine, thymidine, 1heir deoxyribo-analogues and some O5'-, O3'-deutero derivatives were studied by means of MNDOl H semiempirical quantum-chemical method. Effect of the intramolecular H-bonda on the slereochemical structure of nucleosides (particularly, on the stabilization of anti conformation), on the physico-chemical characteristics of nucleoside molecules (heat of formation, dipolc moment, first adiabatic ionization potential and the charge distribution), and on the dynamical characteristics of pyrimidine nucieosides (barriers of the interconvertion, frequencies of the torsional vibrations) was elucidated. The intramolecular 11-bonds in polynudeolides and their influence on the nucleic acid architecture, and nonlinear dynamic properties arc discussed. |
| format |
Article |
| author |
Mishchuk, Y.R. Hovorun, D.M. |
| spellingShingle |
Mishchuk, Y.R. Hovorun, D.M. Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides Биополимеры и клетка |
| author_facet |
Mishchuk, Y.R. Hovorun, D.M. |
| author_sort |
Mishchuk, Y.R. |
| title |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| title_short |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| title_full |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| title_fullStr |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| title_full_unstemmed |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| title_sort |
intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides |
| publisher |
Інститут молекулярної біології і генетики НАН України |
| publishDate |
1998 |
| url |
https://nasplib.isofts.kiev.ua/handle/123456789/155438 |
| citation_txt |
Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides / Y.R. Mishchuk, D.M. Hovorun // Биополимеры и клетка. — 1998. — Т. 14, № 4. — С. 360-370. — Бібліогр.: 36 назв. — англ. |
| series |
Биополимеры и клетка |
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I S S N 0 2 3 3 - 7 6 5 7 . б и о п о л и м е р ы и к л е т к а . 1 9 9 8 . Т . 1 4 . № 4
Intramolecular hydrogen bonds and structural
nonrigidity of pyrimidine nucleosides
Yanina R. Mishchuk, Dmytro M. Hovorun
Institute of M o l e c u l a r B i o l o g y a n d G e n e t i c s of U k r a i n i a n N a t i o n a l A c a d e m y of S c i e n c e s
1 5 0 vul. Z a b o l o t n o h o , 2 5 2 1 4 3 K y i v , U k r a i n e
Optimal structures and intramolecular web of H-bonds of cytidinc, uridine, thymidine, their deoxyribo-
analogues and some 05'-, О У -deuie.ro derivatives were studied by means of MNDO/H semiempirical
quantum-chemical method. Effect of the intramolecular H-bonds on the stereochemical structure of
nucleosides (particularly, on the stabilization of ant і conformation), on the physico-chemical characteristics
of nucleoside molecules (heat of formation, dipole moment, first adiabatic ionization potential and the
charge distribution), and on the dynamical characteristics of pyrimidine nucleosides (barriers of the
inierconvertion, frequencies of the torsional vibrations) was elucidated. The intramolecular II bonds in
polynucleotides and their influence on the nucleic acid architecture and nonlinear dynamic properties are
discussed.
Introduction. Nucleoside molecules exhibit many pos
sibilities as model objects for biophysical inves
tigations [] ]. The structure of isolated nucleoside
molecule is complicated and nonrigid [2, 3 ]. Pyri
midine nucleosides have in particular a higher barr ier
of rotation around glycoside bond as purine ones.
While it is possible for pyrimidines to adopt the syri
conformations, it is slerically difficult and rarely
observed in nature (see [4—6 | and references there)
and leads to the preferring of a/z/^-conformation o:f
sugar. The optimal conformation of pyrimidine nuc
leoside is determined by the dipole-dipole inter
actions, torsion rigidity of glycoside C l ' N l bond and
steric h indrances . But there are additional inter
actions between the base residue and the sugar
moiety contributing in stabilization of the nucleoside
molecule in certain conformation.
Effect of such interactions was found in some
cases. For example, Emerson and Sundaral ingam [7 |
in their study of d ihydrour id ine 3'-monophosphate
hemihydrate pointed out that puckering of the base
could influence the ribose puckering due to inter
actions of the C6 methylene proton with the ribose
Van Lier, Smits and Buck [4 | in quantum-chemical
study of te t rahydrofuryl - l - (5-methylcytos ine) explain
© Ya. R. MIS H CI I UK, l>. M. H O V O R U N , 1998
its unusually high anti-syn transition barrier in terms
of an electronic effect of the / ;a /Yv-substi luted methyl
group on the and C2 ' methylene fragment through the
carbonyl C2 group.
Moreover, the hydrogen bonds (H-bonds) in
volving atoms of the base residue and the sugar
moiety were supposed in several s tudies, such as
N M R i n v e s t i g a t i o n s of m o n o n u c l e o t i d e s [ 8 ]
( 0 2 H . . . 0 2 ) , crystallographic refinement of tRNA |9J
( 0 2 T I . . . 0 2 , C 6 H . . . 0 5 ' ) , r e f i n e m e n t of cy t id ine
crystal s tructure [101 ( C 6 H . . . 0 5 ' ) , PM3 [11 I and
C N D O / 2 [12] semiempirical quantum chemical calcu
lations ( C 6 H . . . 0 5 ) . Ts ' o [13] in NMR investigation
of poly(U) also assumed the contribution of hydrogen
bonding in interactions of C6H proton with the
nearby ribose oxygen.
The possibility of participation of CH groups in
H-bonds in nucleic acid consti tuents was supported
by the experimental [14, 15] and theoretical [12, .16]
investigations. It also is known that the existence of
С-Н. . . 0 H-bond interactions in the nucleic acid
polymers have a strong influence on their molecular
structure [12, 16 |.
The present s tudy was under taken to elucidate
by means of M N D O / H semiempirical quantum-che
mical calculation method, what kinds of intramo
lecular H-bonds are in pyrimidine nucleosides and
what is the influence of these H-bonds on the
360
http://-deuie.ro
parameters of structural пол rigidity and dynamics of
the nucleosides
Methods. M N D O / H semiempirical quantum-che
mical calculation method was shown to be useful for
the investigation of the stereochemical nonrigidity of
nucleotide bases [17] and in calculation of the
parameters of hydrogen bonds [18] . It slightly un
derestimates the values of geometric and energetical
characteristics of nucleotide base nonplanari ty effects
[1 ], allowing о consider more precisely many of
phenomena having been earlier neglecting.
The structure, 1R spectra and some physico-
chemical properties of pyrimidine nucleosides were
calculated with full optimization of all geometric
parameters with the gradient norm < 0 . 0 1 . Starting
geometries were obtained by the composition of fully
optimized structures of components: nucleotide bases
[191 and ribose (deoxyribose) molecules. Optimi
zation of the structures of all pyrimidine nucleosides
were started from anli-conformation of the sugar
moiety with respect to base residue. Intramolecular
H-bond enthalpies were obtained by comparing of two
different heais of formation of the nucleoside mole
cule which were calculated in cases «with» and
«without» intramolecular H-bonds . For more details
of calculations see [17, 19] .
Results and Discussion. The resulting lowesi
energy structures of calculated pyrimidine nucleosides
cytidine (Cyd) , uridine (Urd) , thymidine (Thd) and
their deoxynbo-analogues (dCyd, dUrd , dThd res
pectively) are shown in Figure. All the pyrimidine
nucleoside sugar moieties are in an//-conformation
with respect to the base residues and in gauche-
gauche conformation a rcund C 4 ' - C 5 ' bond. This is in
accordance with the results of previous molecular
modelling | 51 , so as semiempirical quantum-chemica
MNDO [4 1 and C N D O / 2 [12] calculations in which
the preference of this conformation for pyrimidine
nucleosides was shown. In Figure, calculated values of
the x ( 0 4 C J N1C2 dihedral angle) , which charac
terizes the art//-conformation, are exhibited. As one
can see, x is somewhat higher in ribonucieosides than
in deoxyribomjclcosides. Besides, in cytidine nuc
leosides x values are obviously higher than in uridine
and thymidine ones.
In the structures shown in the Figure the cal
culated intramolecular H-bonds a re presented forming
the special web around the each nucleoside molecule
We have found three common types of intramolecular
H-bonds in pyrimidine nucleosides: H-bonds in
volving atoms of the base residue and the sugar
moiety, H-bonds between the base fragment atoms
and H-bonds between the furanose ring atoms. The
geometric and energetical parameters of the calculated
INTRAMOLECULAR H Y D R O G E N B O N D S O F PYRIMIDINE N U C L E O S I D E S
intramolecular H-bonds are presented in Table 1. For
comparison, the intramolecular H-bonds of the dif
f e r e n t o r g a n i c c o m p o u n d s h a v e e n e r g i e s
2 - И 0 kcal /mol [20] . It must be noted that all intra
molecular H-bonds , except N 4 H ' . . . N 3 (here and
below — H' is the proton of < C N H 2 fragment ot the
Cyt base residue involved in the N H . . . 0 inter-
molecular H-bond upon Gua:Cyt Watson-Crick base
pairing and H " is the ano ther aminoproton) (in Cyd
and dCyd) and C 6 H . . . 0 5 ' , are considered in isolated
pyrimidine nucleosides for the first time.
T h e bifurcated intramolecular H-bonds in organic
chemistry are known to be mutually affected [20, 21 [.
In nucleosides, the web of the intramolecular H-
bonds include not only bifurcated, but also the
H-bonds which are competitors in formation of nuc
leoside conformation (for example, H-bonds with
C6H and C 2 = 0 2 groups) (Figure) . This is because
they demonstra te pronounced cooperative effect: all
H-bonds a re mutually weakened by 0.29, 0.60 and
0.80 kcal/mol for Cyd, Urd and Thd respectively,
and these values a re much higher for dCyd, dUrd and
dThd : 1Л0, 2.10 and 2.16 kcal /mol respectively.
Result ing enthalpy of all intramolecular H-bonds are
18.07 and 14.32 kcal /mol for Cyd and dCyd, 19.21
and 15.64 kcal /mol for Urd and dUrd , 18.97 and
15.41 kcal/mol for Thd and d T h d .
Our results exhibit the influence of the intra
molecular H-bonds on the physico-chemical charac
teristics of the nucleosides: heat of formation, dipole
moment , first adiabatic ionization potential and the
fundamental vibration frequencies — some of these
parameters are shown in Table 2.
T h e data presented in Table 3 demonst ra te the
most prominent structural peculiarities of the nuc
leosides and the effect of the intramolecular H-bonds
on the conformation and mutual orientation of their
structural fragments.
Intramolecular H-bonds between the base residue
and the sugar moiety and nonrigidity of the pyrimidine
nucleoside, CI 'H . . . 02=C2 i n t r a m o l e c u l a r
H-b о n d. Earlier at tention have not been put on the
role of С Г Н group in the hydrogen bonding between
base residue and sugar moieties in nucleosides. There
were assumptions about the participation of С2=02 in
the Fl-bond but they were concerned with 0 2 ' H group
in pyrimidine nucleosides [4, 8, 9 ] .
Recently we studied the effect of N1 methylation
of pyrimidine nucleotide bases on their structural
nonrigidity 122]. The re the intramolecular H-bond
between С2=02 and C1H of methyl group have been
found (in agreement with further ab initio inves
tigations [23]) which serve us as the model for the
С Г Н . . . 0 2 = С 2 interaction in nucleosides. The exist-
361
MISHCMUK. Ya. R , H O V O R U N I) M.
Thd, Z= 136.8° dThd.X-m.O"
(TIM 136.9°) (dUrd, Z=133.5°)
F u l l y o p t i m i z e d b y M N D O / H s t r u c t u r e s of p y r i m i d i n e n u c l e o s i d e s wi th the ne twork of the i n t r a m o l e c u l a r h y d r o g e n b o n d s {% is the
0 4 ' C 1 ' N 1 C 2 d i h e d r a l a n g l e )
362
ence of C T H . . . 0 2 = C 2 H-bond can be evidenced by
diffuse low frequency band — satellite of fundamental
stretching vibration of С Г Н centered at ~ 2785 cm"1
in the nucleosides IR spectra [24] .
The enthalpies of the С Г Н . . . 0 2 intramolecular
H-bond was shown (Table 1) to be of the same order
of value HI uridine and thymidine nucleosides, but
INTRAMOLECULAR H Y D R O G E N B O N D S OF F'YRIMIDJNE NUCLEOSIDES
they are by 0 . K H 0 . 1 6 kca l /mol smaller in cytidine
ones: 3.47 kcal /mol (Cyd) and 3.57 kcal /mol (Urd
and T h d ) ; 3.67 kcal /mol (dCyd) and 3.83 kcal/mol
(dUrd and d T h d ) . Besides, one can see that in
r i b o n u c l e o s i d e s С Г Н . . . 0 2 H - b o n d s a r e by
0.20-^0.26 kcal /mol weaker than in their deoxyribo-
analogues. These tendencies a re in accordance with
Table I
Energetic and geometric characteristics of intramolecular hydrogen bonds in Cyd, Urd, Thd and their deoxyribo-analogues
x H-bond АН. В Enthalpy, kcal /mol Distance И В , A Angle A H B i.degrers.)
Cvd
(1С y d
Urd
dUrd
T h d
d'l'hd
363
MISHCHUK Ya. R., H O V O R U N D. M.
Table 2
Some physico-chemical characteristics and frequencies of torsional vibrations of pyrimidine nucleosides in cases «with» (H*Q) and
«wiihout» (H = 0) intramolecular hydrogen bonds
Table 3
Structural perturbation of pyrimidine ribo- and. deoxyribonucleosides in cases «with» (H * 0) and <<without»(// = 0) intramolecular
hydrogen bonds (the data, obtained from О UP Molecular Modelling Package)
364
the peculiarities of the base residue orientation: larger
values of x (Figure) and Н Г С Г Ш C 2 dihedral angles
(Table 3) correspond to molecules having weaker
C 1 H . . . 0 2 H-bonds .
On the other s ide ; accordingly to our data in
Cyd, Urd and Thd the 0 2 ' . . . 0 2 distances are respec
tively 3.57 A, 3.70 A and 3.82 A and 0 2 H 0 2 angles
values are 113% 108° and 116°. Such interaction of
0 2 ' H with C2==02 can reduce the energy of nucleo
side not more than by 0.35 kcal /mol . This fact is in
agreement with the same conclusion of Young and
Kallenbach (25 J that 0 2 H is unlikely to be involved
in H-bond with base atoms because of the poor
stereochemical fit.
I n t r a m о I e с u 1 a r H-b о n d s i n v o
l v i n g C6H g r o u p a n d t h e s u g a r
m o i e t y о x у g e r s. Earlier, assumptions have
been made about the interaction of C6H pyrimidine
group with ribose oxygens in the experimental studies
[7, 10, 26—28 |. We have found two bifurcated
intramolecular H-bonds with the C6H group partici
pation in pyrimidine nucleosides: C 6 H . . . 0 5 ' and
C6H. . . 04 ' (Figure, Table 1).
From the data in Table 1 one can see, that the
enthalpies of C 6 H . . . 0 5 H-bond in Thd and dThd
(3.98 and 3.49 k c a l / m o l respec t ive ly) a r e by
0.29 : 0.51 kcal/mol smaller than in other nucleosides
correlating with the larger C 6 H . . . 0 5 ' H-bond lengths.
The PM3 calculated H . . . 0 5 ' distances [11] show the
same tendency: 1.851 A in p d T is larger than 1.836 A
in pdC. Accordingly to results of C N D O / 2 calculation
[12] the C6FL. .05 ' H-bond in Urd is not weaker than
2 kcal/mol — it is the contribution of this H-bond to
the energy of gauche-gauche conformation of nuc
leoside. Further stabilization of such conformation in
polynucleotides was predicted due to the streng
thening of C 6 H . . . 0 5 ' H-bond when 0 5 ' belongs to
P0 4 ~ | 12 ] , It may be the reason for a number of
studies concerning the C 6 H . . . 0 5 ' intramolecular H-
bond interactions in nucleotides (see [6—9, 11, 12.
25, 26] and bibliography there) .
The intramolecular H-bond C 6 H . . . 0 4 ' have not
been found in above mentioned studies. In thymidine
nucleosides the largest enthalpies of C 6 H . . . 0 4 ' H-
bond are observed (Table 1), so the intramolecular
H-bonds involving C6H group in Thd and dThd have
the closer to each other enthalpy values (AE = 0.63
and 0.55 kcal/mol respectively) than other nucleo
sides (ДЕ = 1.06 4-1.34 kca l /mol ) . Besides, in r ibo-
nucleosides C 6 H . . . 0 5 ' a n d C 6 H . . . 0 4 ' a r e by
0.41 4-0.58 kcal/mol s t ronger than corresponding H~
bonds in dcoxynucleosides. These features of the
H-bond network of nucleosides have reflections in
INTRAMOLECULAR H Y D R O G E N B O N D S OP PYRIMIDINE NUCLEOSIDES
their s tructures: larger values of % (Figure) and
Н Г С Г Ы 1 С 2 angles (Table 3) are observed in mole
cules with weaker С Г Н . . . 0 2 H-bonds and stronger
C 6 H . . . 0 5 ' and C 6 H . . . 0 4 ' H-bonds .
From the Table 3 one can conclude, that the
neglecting of the intramolecular H-bonds results in
the essential changes in the dihedral angle values of
nuc leos ides , especially consis t ing with glycoside
N 1 C 1 ' bond, that reach 19° for nonhydrogen atoms
and 90° for protons. T h u s , intramolecular H-bonds
involving atoms of the base res idue and the sugar
moiety ( C 1 H . . . 0 2 , C 6 H . . . 0 4 ' and С6И. . . 05 ' ) put the
important contribution in the stabilization of anti-
c o n f o r m a t i o n of p y r i m i d i n e n u c l e o s i d e s (and
C 6 H . . . 0 5 ' H-bond addit ionally support also gauche-
gauche conformation [12]) .
T h e intramolecular H-bonds between the base
residue and the sugar moiety also affect the dynamics
of pyrimidine nucleosides, particularly the torsion
motion. In the Table 2 we have compared the
calculated frequencies of torsion (libration) vibrations
( w r ) in nucleosides in cases «with»(H 0) and «wit-
hout» (H = 0) intramolecular H-bonds . According to
our results , these low frequency torsional vibrations
are not only anharmonical but also anisotropic: the
direction of decreasing of the Н Г С Г Ы 1 С 2 dihedral
angle value of nucleoside is preferred.
Intramolecular H-bonds and structural nonrigi-
dity of the base residues. In the optimized structures
of Cyd, Urd , Thd and their deoxyribo-analogues the
intramolecular H-bonds between the base residue
atoms are observed: N4H ' . . .N3 H-bond in cytosine
and N 3 H . . . 0 2 , N 3 H . . . 0 4 in uracil and thymine bases
(Figure, Table 1).
Cytidine r ibo- and deoxyribonucleosides have the
weaker N 4 H 4 . . N 3 H-bond (2.92 and 2.76 kcal/mol
respectively) in comparison with isolated Cyt nucleo
tide base, where such H-bond have the enthalpy
2.99 kcal /mol [18] . Existence of the N4H ' . . ,N3 H-
bond in anomalous nucleoside 6-azaCyd was fixed
experimentally by means of PMR spectroscopy [29] .
In Ura, the calculated enthalpy of N3H. . . 02
intramolecular H-bond (1.94 kcal /mol [18]) is smal
ler than and of N 3 H . . . 0 4 H-bond (2.22 kcal/mol
[18]) , while in Urd and dUrd N 3 H . . . 0 2 H-bond is
somewhat stronger than N 3 H . . . 0 4 (Table 1) — it
must be due to the sugar moiety presence and its
H-bonding with the base, but the mechanism of this
effect is ra ther complicated.
The base residues of Cyd, Urd and Thd nucleo
sides and their deoxyribo-analogues all have slightly
puckering base r ings, in accordance with the data of
the previous quantum-chemical structural investiga
t ions of free nuc l eo t i de b a s e s [ 1 9 ] . Maximal
365
MISHCHI.'K Vi; \l, MOVOkllM I). M
deviat ions from planar i ty a re observed for the
N1C1 glycoside bond region of the pyrimidine nuc
leoside base rings with dihedral angle values not more
than 2,6°, 3.7°, 3.6° for Cyd, Urd , Thd and 3.7 C , 5.9%
6.1° for dCyd, dUrd and dThd respectively. It would
be noted that the neglecting of the intramolecular
H-bonds in the base residues results in increasing of
the base ring puckering: corresponding dihedral angle
reach the values 11.7% 9.6°, 9.3° for Cyd, Urd, Thd
and 8.0°, 6.5°, 7.1° for dCyd, dUrd , dThd respec
tively. Such behavior of the base rings upon the
influence of intramolecular H-bonds shows that in the
nucleosides the bases are also stereochemically non-
rigid fragments 119].
The cytosine base in the nucleoside has the
asymmetrically pyramidal aminogroup, so as Cyt in
the isolated state [19, 3 0 ] . T h e N 4 H 4 . . N 3 intramo
lecular H-bond affects the parameters of > C N H ,
fragment pyramidali ty (Table 3) . T h e character of
potential energy hypersurface which determines ste
reochemical nonrigidity of Cyt base remains almost
unchanged [31 j . T h e base residues with aminogroups
in nucleosides are usually considered as planar rigid
structures [3, 7, 9—12] . In contrast with this appro
ach, our data evidenced that the planar inversion
barrier of > C N H 2 fragment of Cyt residue in nucle
oside is LI (Cyd) —1.2 (dCyd) times higher than in
free Cyt (0.15 kcal /mol [32]) and consist 0.17 and
0.18 kcal /mol respectively. These data exhibit parti
cularly that the р/г-соп jugation of lone electron pair
of N4 with ^-e lect ron system of the base ring reduce
upon the transition from nucleotide base to nuc
leoside.
T h e internal rotation barr iers of the > CNH : ,
fragment mainly decrease in nucleosides in com
p a r i s o n w i t h f r e e C y t a n d c o n s i s t 3 . 3 7 ,
10.56 kcal/mol for Cyd and 2.33, 10.46 kcal /mol for
dCyd (3.72, 10.47 kcal /mol for Cyt [17]) for rotation
to the N3 atom and C5H bond respectively. T h e
intermediate state with two aminoprotons turned to
the N3 atom (with planar base ring and plane
symmetrical location of protons) is stabilized by the
bifurcated pair of int ramolecular N 4 H ' . . . N 3 and
N4H" . . .N3 H-bonds with the resulting enthalpy 3.59
and 3.55 kcal/mol for Cyd and dCyd respectively.
The internal rotation of aminogroup is the dipole
active process, transit ion dipole moment (~ 0.8 D)
lies in the ring plane in 90° with respect to C4N4
bond.
Intramolecular H-bonds and nonrigidity of the
sugar moiety. Analysis of a number of crystal struc
tures of nucleosides shows that furanose ring is
usually nonplanar conformationally nonrigid molecule
[2] . Theoretical studies and several NMR experi
ments show for furanose two preferred ring puckering
conformations, C2 ' -endo and СЗ ' -endo , with almost
equal energy and 2—5 kcal /mol barrier of inter-
conversion through 0 4 ' - e n d o intermediate confor
mation (see [5, 6 ] and bibliography there) .
According to our data , all energy differences
between C2 ' -endo , СЗ ' -endo and 0 4 ' - e n d o confor
mations of furanose ring in the pyrimidine nucleo
sides are find to be not more than 0.95 kcal/mol. This
fact is in agreement with the results of the Levitt and
Warshel 133 ] on the force field calculation of ener
getic profile of furanose ring in nucleosides, where
such energy differences including repuckering barrier
consist not more than 0.60 kca l /mol .
In pyrimidine nucleosides with either C2 ' -endo
or СЗ ' -endo sugar puckering modes the ribose atoms
are involved into О З Н . . . 0 2 ' H-bonds , while the
2 ' -deoxyr ibose a toms form C 4 ' H . . 0 3 H-bonds ,
which are more than 1.5 times weaker than the
0 3 H . . . 0 2 ' in ribose (Figure, Tab le 1). In spite the
fact that in crystal s t ructures of some nucleoside
derivatives [27] 0 2 ' H . . . 0 3 ' intramolecular H-bond
occurs more frequently than 0 3 ' H . . . 0 2 \ in free
pyrimidine nucleosides the fully optimized confor
m a t i o n w i t h 0 2 Н . . . О З ' H - b o n d is
4.00-^5.95 kcal /mol higher in energy than confor
mation shown in Figure.
T h e intramolecular H-bonds involving the sugar
moiety atoms reduce the furanose ring puckering
parameters (Table 3) and cause the essentially free
interconvertion at room temperatures . Increase of
dihedral angle values, which characterized the fura
nose ring puckering, is observed when the amplitude
of torsion motions around glycoside C l ' N l bond
increase. This is due to the weakness of the base
residue-sugar H-bonds caused by the torsion motions.
Other studies using AMI and PM3 semiempirical
quantum-chemical methods [11] , in which the full
optimization process involve calculation of hydrogen
bonding interactions between all accessible atoms,
also show the unusually small values of the sugar
puckering parameters . Influence of intramolecular
H-bonds results in decrease of the interconvertion
barr ier of furanose ring in pyrimidine nucleosides.
05- and 03'-deprotonated nucleoside molecules.
We have modelled the charge situation in nucleotides
and polynucleotides (polyanions) by deprotonalion of
Cyd and dCyd molecules at 0 5 ' and 0 3 sites. This
was done in order to elucidate the effect of negative
charged phosphate groups on the stereochemical non
rigidity and intramolecular H-bond web parameters of
nucleosides.
It was found that the change of the charge state
of nucleoside molecule by the deprotonation of its
366
sugar moiety does nol destroy the intramolecular
H-bond web. The deprotonation results in essential
perturbation of the balance of intramolecular H-bonds
in nucleoside (Table 4) and increasing of their
cooperativity (Л = - 2 . 1 0 4 3.64 kca l /mol) . In the nuc
leosides deprotonated at the 0 5 ' site C 6 H . . . 0 5 '
H-bond becomes much stronger, that results in the
weakness of С Г Н . . . 0 2 and other H-bonds (Table 4) .
This is in accordance with the predicted in [12]
strengthening of C 6 H . . . 0 5 ' H-bond when 0 5 ' belongs
to P0 4 ~. In the case of 0 3 ' deprotonation site
C 6 H . . . 0 5 ' becomes weaker (Table 4) because of the
turning of 0 5 proton to C6H (Table 5 ) , which
reduces the interaction of 0 5 ' atom with C6H group.
The data in Table 5 describe the changes of most
prominent structural parameters — dihedral angles in
case of neglecting of intramolecular H-bonds in the
anions under discussion.
The structural per turbat ion of cytidine nucleo
sides under the deprotonation can be considered
particularly by comparison of % values of anions:
INTRAMOLECULAR H Y D R O G E N B O N D S OF PYRIMIDINE NUCLEOSIDES
134.6° (Cyd C ) 5/~), 133.6° ( d C y d 0 5 ) , 140.1° ( C y d 0 , / )
and 121.2° ( d C y d 0 3 ) with corresponding angles in
Cyd and dCyd (Figure) . T h e deprotonation of the
sugar moiety affects also the stereochemical non-
rigidity of the base res idue in nucleoside molecule. In
Cyd" and dCyd~ the aminogroups become more pyra
midal, the base ring puckering parameters decrease
(Table 5 ) , their p lanar inversion barriers are 1.7
(Cyd - ) —1.8 (dCyd") times higher and the internal
anisotropic rotation barr iers a re reduced by 20—
40 %. These effects can be explained particularly by
the reducing of ря-conjugation in the base residue
upon the influence of the surplus negative charge in
the sugar moiety. T h e reverse is also true: possible
mtermolecular interactions which change the struc
tural and dynamic properties of the base, especially
in the vicinity of < C N H 2 fragment a t tachment , cause
the changes in charge distribution in the sugar
moiety.
Thus the local change of the charge state of
polynucleotide, for example, in the protein-nucleic
Table 4
Energetic and geometric characteristics of intramolecular hydrogen bonds in deprotonated Cyd and dCyd (Cydos ~, Cydoy~, dCydos'
dCydoy anions)
С у c l o y
d C y d o . v
С у d o r "
d C y d o . v
367
MISHfHl/K Ya. R., HOVORUN D. M.
Perturbation of geometric structure of deprotonated Cyd and dCyd in cases «with» (H ф 0) and « without» (H**0) all intramolecular
hydrogen bonds (data from the О UP Molecular Modelling Package)
acid recognition processes, can affect its structural
and dynamical properties, particularly the local curva
ture | 341 , through the dis turbance of p7r-conjugatior
of base residue.
Transformation of the intramolecular H-bond web
in polynucleotides. T h e intramolecular CI Т І . . . 0 2 ' .
C6H6 . . . 04 ' , C 6 H 6 . . . 0 5 ' H-bonds are expected to be
also in polynucleotides because there the pyrimidine
base and sugar a re in anгг-conformation | 4 , 6 ].
Moreover, the C 6 H . . . 0 5 ' H-bond in the polynuc
leotide structures [9, 25 | is predicted to be streng
thened when 0 5 ' belongs to P 0 4 ~ [12 J. It seems to be-
likely that 0 2 T I groups in polynucleotides are invol
ved in H-bond with 3 ' - P 0 4 ~ group (directly or thro
ugh water molecules) [35 | and with 0 4 ' of neighbour
furanose ring along the polynucleotide s t rand [9, 25.
36 j .
Indeed, ii is known that poly(dT) and poly(dU)
don' t form single s t rand helical s t ructure and on the
same conditions that poly(rT) poly(rU) does (see [6 j
and bibliography there) . And study of CD spectra
leads 'TVо 113 I to the conclusion that poly(rC) single
s t rands have more secondary s tructure (stacking)
than poly (dC) in the same conditions. Hydrogen
bonding of 0 2 ' H groups with 3 'phosphate and neig
hbour furanose can successfully explain such relative
stability of RNA s t rands with respect to DNA ones.
Conclusions. The structural and dynamical pro
perties of pyrimidine nucleosides are shown at first to
be formed with participation of the web of cooperative
i n t r a m o l e c u l a r H - b o n d s wi th e n t h a l p i e s ~ 2—
4 kcal /mol . Involving of any site of the nucleoside
into intermolecular hydrogen bonding (Watson-Crick
pairing, specific solvent, crystal packing and so on)
can per turb its intramolecular H-bond web that
results in changes of structural and dynamical para
meters of nucleoside.
Pyrimidine nucleosides, their base residues and
sugar moieties are stereochemically nonrigid struc
tures . The aminogroup pyramidali ty and plane inver
sion barr ier increase in nucleoside in comparison with
the nucleotide base and these parameters also depend
on the charge situation on the sugar moiety. The
intramolecular H-bonds effect the stereochemical
structure of nucleosides, conformation and mutual
orientation of their fragments, particularly, intra
molecular H-bonds involving atoms of the base resi
due and sugar moiety put the important contribution
in the stabilization of a/i/z-conformation of pyrimidine
nucleosides.
Intramolecular H-bonds affect the physico-che
mical characteristics of pyrimidine nucleosides (heat
of formation, dipole moment, first adiabatic ionization
potential and the charge dis t r ibut ion) , and they also
368
can change the dynamical characteristics of nucleo
side: barriers of the base residue and the sugar
moiety interconvertion, frequencies of the torsional
vibrations in nucleoside
Intramolecular H-bonds in polynucleotides take
part in the formation of the nucleic acid architecture
and nonlinear dynamic propert ies. Local change of the
charge distribution in the sugar region of polynuc
leotide, for example, in the protein-nucleic acid
recognition processes, can affect its structural and
dynamical properties through the dis turbance of prr
conjugation of base residue.
Taking into ассошії of the intramolecular H-
bonds is important for the NMR and IR spectra
interpretation, for molecular modelling, for the eluci
dation of mechanisms of structural and dynamic
changes under molecular recognition processes.
Я. P. Міщук, Д. М. Говорун
В н у т р і ш н ь о м о л е к у . ч я р н і в о д н е в і з в ' я з к и та с т р у к т у р н а
н е ж о р с т к і с т і . п і р и м і д и н о в и х н у к л е о з и д і в
Р е з ю м е
Оптимізовані структури цшпидину, уридину і тимідину, їхніх
дезоксирибо-аналогів та деяких 05'~, ОЗ'-депротонованих по
хідних отримані за допомогою напівемпіричного квантово-
хімічного методу MNDO/H. Виявлено сітки внутрішньомо-
лекулярних водневих зв'язків піримідинових нуклеозидів та
вивчено їхній вплив на. стереохімічну структуру молекул
(зокрема, на стабільність anti-конформації), фізико-хімічін
параметри /теплоту утворення, дипольний момент, потен
ціал, іонізації та розподіл зарядів), а також на. динамічні
характеристики піримідинових нуклеозидів (бар'єри інтер
конверсії, частоти торсійних коливань). Обговорюється при
сутність внушріишьомолекулярних водневих зв'язків у полі
нуклеоіпидах та їхнє значения у формуванні, структури то
нелінійної динаміки нуклеїнових кислот.
Я. Р. Мши,ук, Д. Л. Говорун
В н у т р и м о л е к у л я р н ы е в о д о р о д н ы е с в я з и и с т р у к т у р н а я
н е ж е с т к о с т ь п и р и м и д и н о в и х п у к л е о з и д о в
Р е з ю м е
Оптимизированные структуры цитидина, уридина и тим иди-
на, их дезоксирибо аналогов и некоторых 05'-, 03 -депротони-
рованных производных получены с помощью полуэмпирического
квантовохиминеского метода. MNDO/H. Обнаружены сетки
внутримолекулярных водородных связей пиоимидиновых пук
леозидов и исследовано их влияние на стереохимическую стру
ктуру молекул с в частности, на стабильность anti-конформа
нии), физико-химические параметры (теплоту образования,
дипольный момент, потоп циал ионизации и распределение
зарядов), а также на. динамические характеристики пирими-
дииовых пуклеозидов (барьеры интерконверсии, частоты тор-
аюииых колебании). Обсуждается наличие внутримолекуляр
ных водородных связей в колинуклеотидах и их значение в
формировании структуры и нелинейной динамики нуклеиновых
кислот.
INTRAMOLECULAR H Y D R O G E N B O N D S O F PYRIMIDINE NUCLEOSIDES
R E F E R E N C E S
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of n u c l e o s i d e m o l e c u l a r g e o m e t r i e s in t erms of four p a r a m e t e r s
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369
MlSHCl-Шк Ya. R., HOVORUN D U.
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