SM 1

Analytical and Bionalytical Chemistry

Electronic Supplementary Material

Stacked and continuous helical self-assemblies of guanosine

monophosphates detected by vibrational circular dichroism

Iryna Goncharova, Jana Novotná and Marie Urbanová

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Fig. S1 Noise traces (a), the baseline subtraction (b) and reproducibility of VCD spectra (c).

(a) VCD spectra obtained as an average of twelve 20 minute blocs of 3686 interferometric scans

(full line), noise traces obtained as relative standard deviation of averaged spectra (short dashed line)

of GMP at concentration 0.3 mol L-1 without K+ (black) and with K+, [K+]/[GMP] = 1/2 (blue), the

spectra were baseline corrected as described in panel (b)

(b) Spectra of the sample solution (full line) and spectra of solvents measured at the same condition

which were used as the baseline (long dashed line), arrow indicates the resulting spectrum obtained

by the baseline subtraction, the concentrations as in panel (a)

(c) VCD spectra of GMP at concentration 0.3 mol L-1 with K+, [K+]/[GMP] = 1/2, the different

sample preparations in the time interval of half year (colour lines), the averaged spectrum (black),

and relative standard deviation (short dashed line)

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Fig. S2 ECD spectra of sodium salt of guanosine monophosphate(GMP), guanosine diphosphate (GDP), and

triphosphate (GTP) in H2O at 2.10-4 (gray), 0.3 (black), and 0.7 mol L-1 (dashed)

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Fig. S3 ECD (Δε) and UV (ε) spectra of GMP (blue), GDP (green) and GTP (red) in aqueous solution at

concentration 0.3 mol L-1 with Na+ and K+. The ratio of additional ion/guanosine derivative was 1/2

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Tab. S1 Experimental parameters of VCD and IR absorption spectra of guanosine monophosphate (GMP), guanosine diphosphate (GDP),

and triphosphate (GTP) in H2O as function of concentration and additional metal cations

IR VCD

Compound Concentration Addedions Maximum Relative intensity FWHH Maximum Relative intensity “Markerpeak” Relative intensity Maximum Maximum

mol·L-1

ν(C=O), cm-1 ν(C=O), % ν(C=O), cm-1 C=C/C=N, cm-1 C=C/C=N, % position, cm-1 “Markerpeak”, % ν(C=O), cm-1 C=C/C=N, cm-1

GMP 0.3 - 1665 100 37 1578 100 1539 24 1657(-) -

0.7 - 1672 89 33 1580 58 1536 38 1688(-), 1665(-) -

0.3 Na+ 1670 94 30 1579 60 1536 34 1695(-), 1679(+)/1663(-) -

0.7 Na+ 1672 85 28 1587 52 1537 32 1694(-), 1680(+)/1666(-) 1591(+)/1576(-)

0.3 K+ 1670 109 24 1587 38 1535 76 1675(+)/1660(-) 1592(+)/1570(-)

0.7 K+ 1672 125 24 1590 38 1534 100 1677(+)/1663(-) 1592(+)/1569(-)

GDP 0.3 - 1665 100 36 1578 100 1538 21 1655(-) -

0.7 - 1667 83 38 1579 85 1537 19 1656(-) -

0.3 Na+ 1670 98 36 1579 68 1537 24 1676(+), 1654(-) 1596(+)/1576(-)

0.7 Na+ 1672 85 34 1579 63 1537 38 1681(+)/1666(-) 1596(+)/1580(-)

0.3 K+ 1669 132 25 1583 57 1535 108 1677(+)/1660(-) 1595(+)/1576(-)

0.7 K+ 1668 138 24 1590 51 1534 120 1677(+)/1663(-) 1578(+)/1564(-)

GTP 0.3 - 1665 100 38 1578 100 1538 11 1664(-) -

0.7 - 1667 94 38 1579 81 1538 21 1655(-) -

0.3 Na+ 1667 98 37 1578 94 1538 24 1657(-) -

0.7 Na+ 1668 80 38 1579 79 1538 24 1682(+), 1655(-) -

0.3 K+ 1667 98 36 1578 75 1537 11 1657(-) -

0.7 K+ 1670 108 30 1580 55 1536 44 1677(+)/1660(-) 1594(+)/1572(-)

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Fig. S4 Temperature-dependent ECD spectra of GMP at 0.5 mol L-1 in the presence of K+, the GMP/K+ ratio was

2/1. Numbers denote the temperature

Calculations of optical parameters by degenerate couplet oscillator method

In the degenerate couplet oscillator (DCO) method, the intrinsic chirality of each oscillator is omitted, i.e.,

the magnetic dipole transition moment for each oscillator is zero and optical activity originates in chiral

arrangement of the both transition moment [1-3]. When polar coordinates (Figure S3) are used, and assuming

that the two dipoles are of the same value, μ1 = μ2 = μ, the dipole strength D, the rotation strength R, Davydov’s

splitting V12, and the split frequencies ν± are given:

1 2jKC (1) 2

2 1 21 sin cosD (2) 2

0 1 2/ 2 sin cosR c R (3)

2

12 2 1 2 1 2 1 23sin cos 3sin sin cos cosV

R

(4)

12V (5) The magnitude of μ was obtained from the experimental molar absorptivity spectrum ε(ν) of the

corresponding absorption band by calculating the dipolar strength, D:

1 2

2D , where (6)

380.92 10 /D d (7)

Fig. S5 Polar coordinates used for DCO calculations

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Structural model of guanosine assemblies used for determination of optical parameters by degenerate couplet

oscillator calculation

We calculated the optical parameters (1)−(5) for three different structures. The data that determine the

geometry and the obtained value of the calculated parameters R+ and V12 are given in the Table S2.

1 Tetramer G4 without a central coordinated metal cation

The initial geometry of the cyclic tetramer, the G-quartet, was obtained from the previous studies of G-

quartets that have been performed by Setnicka and Novy [4,5], where the tetramer geometry was optimized at

the B3LYP/6-31G** level.

The calculated optical parameters of the tetramer by DCO correspond (Table S2) well to the sign for

previously calculated by DFT [5] and experimentally obtained terms of intensities and spectral patterns. The IR

bands were distinguished and vibration modes assigned on the basis of dynamic visualization of the normal

mode displacements using the HyperChem programs set. The most intense bands at 1710−1670 cm−1 were

assigned to the C=O modes mixed with a minor contribution of guanine skeletal ν(C=C). In the region below

these bands, there were significant contributions from aromatic ring vibrations, mostly ν(C=C) and ν(C=N). The

sugar vibrations contributed only weakly to the spectral region 1800−1400 cm−1. Thus, this spectral region

mainly reflects the G-ring vibrations. Our assignment of the vibration modes is consistent with results published

previously.

2 Octamer composed of two stacked G-quartets

We used the C4 symmetry octamer structure with the “head-to-tail” (H-T) configuration of the adjacent

tetramers and their mutual twist angle of 30°. The initial geometry of two stacked helical species was obtained

by the association of planar tetramers in octamer conformation placed at an appropriate distance. Cartesian

coordinates were used from crystallographic data for the H-T-oriented octamers in the dodecamer structure

[6].We also took into account the results of several theoretical studies of stacked tetramers in quadruplex

structure that had been performed previously [6-13]. The molecular model of the octamer was then optimized for

energy minimization by the MM (AMBER99) [14].

The magnitudes of μ were obtained from the experimental molar absorptivity spectrum ε(υ) for two

vibrational transitions localities in the C=O and C=N groups. The VCD spectrum was calculated from the

obtained rotational strengths R+ and R- at ν+ and ν- (Formula (3)) using a Lorenzian band shape and a half-width

of 5 cm-1.The obtained spectrum was in a good agreement with experimental results for the associates GMP,

GDP, and GTP with K+ ions.

3 Continuous helical assemblies

Structural modeling of continuous helical assembles was performed using the MM method (AMBER99

[14]) implemented in the HyperChem 8.03 software package (Hypercube, Inc.) for Windows. Some of the

geometrical parameters (guanosine-guanosine distance, position of the cations, and relative orientation of

guanosines) were kept within the values observed in the crystal structures obtained in the quadruplex structure

and the ribbons geometry of guanosine monophosphate [6-8,10-12].

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The calculation of the rotational strength was made by the model for the exciton states in a helical

arrangement of N identical chromophores when only next-neighbor interactions are considered [15,16]. Under

these conditions, we assumed that the directions of the transition dipole moments were along the chemical bonds

C=O and C=N and form the helix of transition moments. The signs of the rotational strength were in good

agreement with the experimental results in both the C=O and C=N regions. The concept of formation of helical

associates is further confirmed by the existing liquid crystal phase observed at higher concentrations of the

guanosine derivatives and/or K+ composed of helical associates as a build unit along with quadruplexes.

Tab. S2 Geometrical Parameters and Calculated Values that characterized the Self-Assembled Species

Self-associatingspecies Oscillators[a] θ1,deg φ1,deg θ2,deg φ2,deg R12, Å R+, *10 42 esu2cm2 V12, cm-1

Tetramer C61=O/ C62=O 90 89 110 10 4.09 -2.18 0.82

C=N31/ C=N32 90 26 122 74 8.07 -0.81 -0.14

Stacked helical(octamer) C61=O/ C62=O 90 24 95 294 4.70 -0.36 -2.93

C61=O/ C611=O 90 81 57 84 3.66 2.84 6.36

C=N31/ C=N32 90 22 92 68 7.84 -0.04 -0.18

C=N31/ C=N311 90 86 70 70 4.19 1.16 1.15

Continuous helical C61=O/ C62=O 90 -35 148 44 3.74 -3.92 4.36

C61=O/ C611=O 90 77 105 76 3.47 -1.86 5.37

C=N31/ C=N32 90 88 108 21 5.87 3.56 -6.32

C=N31/ C=N311 90 89 60 85 3.42 1.16 1.81

[a] Subscript numbering belongs to dipoles which are schematically depicted in Figure S4

Fig S6 Numbering of the guanosine units used for degenerate coupled oscillators

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