T. Haack et al. / Bioorg. Med. Chem. 13 (2005) 4425–4433
4431
1
assumption that the correlation time s is equal for all
J = 3.3 Hz, H300), 7.54 (1H, d, J = 3.3 Hz, H400);
H
c
molecular internuclear vectors the distance ratios can
be obtained directly from the ratio of the cross-peak
intensities:
NMR (DMSO-d ): d 9.19 (1H, d, J = 2.6 Hz, H ), 7.73
6
5
(1H, dd, J = 2.6 and 9.2 Hz, H ), 8.33 (1H, d,
J = 9.2 Hz, H ), 4.87 (2H, s, H ), 4.01 (3H, s, OCH ),
7
1
1
8
11
3
8
.44 (1H, d, J = 4.7 Hz, H2 ), 7.32 (1H, d, J = 4.7 Hz,
0
1
=6
r
ij=rki ¼ ðaki=aijÞ
H3 ), 8.65 (1H, s, H6
7.99 (1H, d, J = 3.2 Hz, H400); C NMR (CDCl ): d
156.6 (C ), 149.9 (C ), 106.2 (C ), 163.4 (C ), 125.2
(C ), 126.6 (C ), 126.6 and 121.9 (C , C ), 36.7 (C ),
0 0), 8.20 (1H, d, J = 3.2 Hz, H 00),
3
1
3
This equation, provided rki is known, allows one to
obtain the unknown distance r . The distance r(H ,
H ) estimated with this method is an apparent distance
3
ij
8
1
4
5
6
1
1
7 8 9 10 11
due to the magnetic equivalence of the methylene
protons and mainly reflects the distance between H8
and the nearest H11 hydrogen. For all compounds 2–5
56.7 (OCH ), 149.7 (C ), 145.0 and 131.9 (C4 , C5 ),
0 0 0
3 6
148.1 (C2
0
), 125.4 (C3
0), 144.2 (C300), 122.5 (C400).
1
˚
the H –H distance of 2.41 A as determined by the mod-
7
Compound 5: H NMR (CDCl ): d 7.32 (1H, d,
8
3
elling calculations was chosen as the reference distance.
J = 2.6 Hz, H ), 7.67 (1H, dd, J = 2.6 and 9.2 Hz, H ),
5
7
8.23 (1H, d, J = 9.2 Hz, H ), 4.95 (2H, s, H ), 3.96
(3H, s, OCH ), 8.55 (2H, s, H
8 11
0 0), 8.05 (1H, s, H200),
2 ,6
The steady state NOE difference experiments were car-
ried out by acquiring both on- and off-resonance spectra
using a 75 dB attenuation of the decoupling power. This
experiment was employed to investigate the spatial dis-
position of the five-membered rings with respect to the
3
7.27 (1H, d, J = 1.6 Hz, H 00), 7.49 (1H, d, J = 1.6 Hz,
4
1
H500); H NMR (DMSO-d ): d 7.26 (1H, d, J = 2.6 Hz,
6
H ), 7.85 (1H, dd, J = 2.6 and 9.1 Hz, H ), 8.62 (1H,
d, J = 9.1 Hz, H ), 5.04 (2H, s, H ), 3.97 (3H, s,
5
7
8
11
), 8.32 (1H, s, H200), 7.25
phthalazine moiety. As the T values of the hydrogens
1
OCH ), 8.69 (2H, s, H
3 2 ,6
(1H, d, J = 1.4 Hz, H 00), 7.88 (1H, d, J = 1.4 Hz, H500);
4
0
0
on five-membered rings are rather long (5–9 s), an irra-
diation time of 30–40 s was used to reach with certainty
the steady state and detect also very small NOE
enhancements.
1
3
C NMR (C D /CD OD 1:1): d 156.2 (C ), 150.3
6
6
3
1
(C ), 102.9 (C ), 164.2 (C ), 126.1 (C ), 127.1 (C ),
126.1 and 123.5 (C , C ), 34.4 (C ), 56.0 (OCH ),
4
5
6
7
8
9
10
11
3
147.8 (C2
0
0
), 134.5 (C
0
0
), 143.9 (C4
0
), 138.3 (C200),
,6
3 ,5
The NMR spectra of compounds 2–5 were obtained in
CDCl and DMSO-d solutions.
130.0 (C400), 120.9 (C500).
.3. Computer simulations
All simulations were performed with InsightII/Discov-
3
6
4
1
Compound 2: H NMR (CDCl ): d 8.49 (1H, d,
3
J = 2.6 Hz, H ), 7.68 (1H, dd, J = 2.6 and 9.2 Hz, H ),
.23 (1H, d, J = 9.2 Hz, H ), 4.96 (2H, s, H ), 4.04
5
7
1
2
13
8
er, using the consistent valence force field CVFF
8
11
0 0), 8.27 (1H, s, H300),
(
3H, s, OCH ), 8.55 (2H, s, H
3
with a Morse potential for the bonded atoms. The initial
geometries, generated through the available library frag-
ments, were fully minimised up to an energy gradient
2 ,6
.23 (1H, s, H500); H NMR (DMSO-d ): d 7.96 (1H, d,
1
9
J = 2.6 Hz, H ), 7.87 (1H, dd, J = 2.6 and 9.2 Hz, H ),
6
5
7
ꢀ
3
ꢀ1 ꢀ1
˚
lower than 10 kcal mol A . The molecular dynam-
8
.63 (1H, d, J = 9.2 Hz, H ), 5.07 (2H, s, H ), 3.97
8
11
0 0), 8.49 (1H, s, H300),
(
3H, s, OCH ), 8.69 (2H, s, H
3
ics simulations at 300 K were performed (i) in vacuo, (ii)
into an effective dielectric medium mimicking water
using a distance-dependent dielectric constant and (iii)
in the explicit presence of the solvent, using a large num-
2 ,6
.38 (1H, s, H500); C NMR (DMSO-d ): d 156.8 (C ),
6 1
1
3
9
1
49.4 (C ), 104.7 (C ), 163.4 (C ), 126.0 (C ), 127.8
7
4
5
6
(
(
(
C ), 123.3 and 123.2 (C , C ), 34.4 (C ), 56.9
8
9
10
11
ꢀ
3
OCH ), 147.9 (C
3
0
0
), 133.8 (C ), 143.9 (C4
0 0
3 ,5
0
), 146.3
ber of water molecules at a density of 1 g cm with peri-
odic boundary conditions. The temperature was
controlled through the Berendsen thermostat, and the
dynamical equations were integrated through the Verlet
algorithm with a timestep of 1 fs. After an initial equil-
ibration of 30 ps, the data collection was carried out
for 500 ps, and a large number of instantaneous struc-
tures was optimised in search of the global energy min-
ima. These geometries were subjected to a systematic
dihedral search, first by changing the dihedral angles de-
2 ,6
C300), 154.1 (C500).
1
Compound 3: H NMR (CDCl ): d 9.36 (1H, d,
3
J = 2.6 Hz, H ), 7.61 (1H, dd, J = 2.6 and 9.2 Hz, H ),
.18 (1H, d, J = 9.2 Hz, H ), 4.95 (2H, s, H ), 4.08
8 11
5
7
8
(
3H, s, OCH ), 8.53 (2H, s, H
3
0
0
), 8.06 (1H, d,
H
2 ,6
1
J = 3.3 Hz, H300), 7.50 (1H, d, J = 3.3 Hz, H400);
NMR (DMSO-d ): d 9.22 (1H, d, J = 2.4 Hz, H ), 7.82
6
5
(
J = 9.2 Hz, H ), 5.04 (2H, s, H ), 4.05 (3H, s, OCH ),
1H, dd, J = 2.4 and 9.2 Hz, H ), 8.56 (1H, d,
7
fined by atoms C –C –C –C and C –C –C –C5 (U
0
0
0
8
11
3
9 1 11 4 1 11 4
8
(
.67 (2H, s, H2
0
0
), 8.19 (1H, d, J = 3.3 Hz, H 00), 7.96
and W, respectively), for a total of 1369 conformations,
and then by changing the P dihedral angle around the
bond connecting the five-membered ring to the phthal-
azine nucleus defined by atoms X200–X100–C –C
10
,6
3
1
3
1H, d, J = 3.3 Hz, H400); C NMR (CDCl ): d 155.3
3
(
1
C ), 150.2 (C ), 106.8 (C ), 163.8 (C ), 125.7 (C ),
25.6 (C ), 126.9 and 122.3 (C , C ), 34.7 (C ), 56.7
1
4
5
6
7
8
9
10
11
4
(
(
OCH ), 148.1 (C
3
C300), 122.9 (C400).
0
0
), 134.4 (C ), 143.6 (C4
0 0
3 ,5
0
), 144.7
(X = N or C; see Scheme 1), for a total of 73 conforma-
tions. The geometries sampled in the MD runs were ana-
lysed through the pair distribution function g (r) (or
2 ,6
ij
1
Compound 4: H NMR (CDCl ): d 9.33 (1H, d,
PDF for short). This function gives the probability den-
sity of finding atoms j at a distance comprised between r
and r + dr from atoms i, and is defined as
g (r) = dhN (r)i/q Æ dV(r). Here, dhN (r)iis the average
3
J = 2.6 Hz, H ), 7.50 (1H, dd, J = 2.6 and 9.2 Hz, H ),
7
5
7
.94 (1H, d, J = 9.2 Hz, H ), 4.81 (2H, s, H ), 4.06
8 11
(3H, s, OCH ), 8.31 (1H, d, J = 4.9 Hz, H2
d, J = 4.9 Hz, H3
0
0
), 7.07 (1H,
), 8.09 (1H, d,
3
ij
ij
j
ij
0
), 8.62 (1H, s, H6
number of times the j atoms are comprised in a spherical