Home The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate
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The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate

  • Tebogo M. L. Mokoto ORCID logo , Andreas Lemmerer ORCID logo , Yasien Sayed ORCID logo and Mark G. Smith ORCID logo EMAIL logo
Published/Copyright: March 29, 2024

Abstract

2(C37H47N4O5·3(H2O), triclinic, P1 (no. 1), a = 11.6319(7) Å, b = 13.9452(7) Å, c = 24.1727(14) Å, α = 106.203°, β = 103.296°, γ = 90.777°, V = 3651.7(4) Å3, Z = 4, R gt(F) = 0.0682, wR ref(F 2) = 0.1899, T = 123 K.

CCDC no.: 2306133

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless plate
Size: 0.34 × 0.09 × 0.03 mm
Wavelength: CuKα radiation (1.54178 Å)
μ: 0.66 mm−1
Diffractometer, scan mode: Bruker D8 Venture photon, ω
θ max, completeness: 65.0°, >99 %
N(hkl)measured, N(hkl)unique, R int: 100,267, 24,878, 0.060
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 20,249
N(param)refined: 1720
Programs: Bruker [1], Shelx [2, 3], WinGX/Ortep [4], Mercury [5], Platon [6]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
C1A −0.2574 (5) 0.0790 (4) 0.3976 (3) 0.0274 (13)
C2A −0.2859 (6) 0.0726 (5) 0.3374 (3) 0.0340 (15)
C3A −0.4043 (6) 0.0465 (5) 0.3063 (3) 0.0429 (17)
H3A −0.426365 0.039566 0.264940 0.051*
C4A −0.4886 (6) 0.0308 (5) 0.3346 (3) 0.0402 (17)
H4A −0.568791 0.013306 0.312825 0.048*
C5A −0.4588 (6) 0.0398 (5) 0.3935 (4) 0.0423 (17)
H5A −0.518933 0.028435 0.412203 0.051*
C6A −0.3418 (6) 0.0656 (5) 0.4277 (3) 0.0368 (15)
C7A −0.3082 (8) 0.0779 (7) 0.4932 (4) 0.061 (2)
H7AA −0.237636 0.042368 0.502759 0.091*
H7AB −0.373840 0.050248 0.504738 0.091*
H7AC −0.291061 0.149307 0.514924 0.091*
C8A −0.1922 (7) 0.0921 (6) 0.3079 (3) 0.0475 (18)
H8AA −0.163098 0.163064 0.323212 0.071*
H8AB −0.225474 0.075001 0.264893 0.071*
H8AC −0.126402 0.050881 0.316119 0.071*
C9A −0.1001 (6) 0.1975 (5) 0.4615 (3) 0.0364 (15)
H9AA −0.106526 0.207614 0.502845 0.044*
H9AB −0.153813 0.241882 0.444312 0.044*
C10A 0.0267 (5) 0.2275 (5) 0.4623 (3) 0.0284 (13)
C11A 0.2089 (5) 0.1766 (5) 0.4320 (3) 0.0272 (13)
H11A 0.230445 0.250427 0.448590 0.033*
C12A 0.2895 (6) 0.1260 (5) 0.4728 (3) 0.0358 (15)
H12A 0.274184 0.052456 0.455183 0.043*
H12B 0.372873 0.144022 0.474117 0.043*
C13A 0.2748 (6) 0.1525 (5) 0.5352 (3) 0.0362 (15)
C14A 0.3441 (9) 0.2319 (6) 0.5796 (3) 0.057 (2)
H14A 0.402468 0.269728 0.570839 0.069*
C15A 0.3268 (13) 0.2554 (8) 0.6373 (4) 0.085 (4)
H15A 0.375064 0.308334 0.668014 0.102*
C16A 0.2426 (14) 0.2037 (11) 0.6493 (4) 0.091 (4)
H16A 0.229642 0.223273 0.688206 0.110*
C17A 0.1741 (10) 0.1231 (9) 0.6073 (4) 0.073 (3)
H17A 0.117508 0.085256 0.617226 0.088*
C18A 0.1905 (8) 0.0985 (7) 0.5489 (3) 0.052 (2)
H18A 0.143055 0.044247 0.518829 0.062*
C19A 0.2323 (5) 0.1441 (4) 0.3692 (2) 0.0242 (12)
H19A 0.314625 0.172209 0.373695 0.029*
C20A 0.1513 (5) 0.1875 (4) 0.3247 (2) 0.0251 (12)
H20A 0.068020 0.164896 0.320827 0.030*
H20B 0.159943 0.261522 0.340358 0.030*
C21A 0.1766 (5) 0.1577 (4) 0.2634 (2) 0.0246 (12)
H21A 0.177707 0.083184 0.249909 0.029*
C22A 0.2977 (5) 0.2058 (4) 0.2638 (2) 0.0257 (12)
H22A 0.294679 0.279456 0.274058 0.031*
H22B 0.359760 0.191008 0.295195 0.031*
C23A 0.3327 (5) 0.1698 (4) 0.2052 (3) 0.0254 (12)
C24A 0.3562 (5) 0.0697 (5) 0.1846 (3) 0.0306 (14)
H24A 0.346075 0.024393 0.206390 0.037*
C25A 0.3946 (6) 0.0356 (5) 0.1323 (3) 0.0321 (14)
H25A 0.411263 −0.032307 0.118752 0.038*
C26A 0.4081 (5) 0.1015 (5) 0.1005 (3) 0.0336 (15)
H26A 0.434222 0.078651 0.064942 0.040*
C27A 0.3842 (6) 0.1992 (5) 0.1196 (3) 0.0348 (15)
H27A 0.393023 0.243998 0.097331 0.042*
C28A 0.3465 (5) 0.2334 (5) 0.1727 (3) 0.0310 (14)
H28A 0.330416 0.301457 0.186054 0.037*
C29A 0.0134 (5) 0.1231 (5) 0.1741 (3) 0.0273 (13)
C30A −0.0600 (5) 0.1681 (4) 0.1276 (2) 0.0263 (13)
H30A −0.059042 0.241859 0.146225 0.032*
C31A −0.1890 (5) 0.1243 (5) 0.1062 (3) 0.0301 (14)
H31A −0.190827 0.050743 0.086684 0.036*
C32A −0.2425 (7) 0.1396 (8) 0.1592 (4) 0.064 (3)
H32A −0.196599 0.107033 0.187161 0.097*
H32B −0.324666 0.110072 0.145792 0.097*
H32C −0.240831 0.211432 0.178830 0.097*
C33A −0.2594 (6) 0.1721 (5) 0.0615 (4) 0.0469 (19)
H33A −0.258128 0.244311 0.080027 0.070*
H33B −0.341475 0.142393 0.048205 0.070*
H33C −0.224120 0.160452 0.027302 0.070*
C34A 0.0505 (5) 0.2321 (4) 0.0680 (3) 0.0279 (13)
C35A −0.0092 (7) 0.0504 (5) 0.0376 (3) 0.0386 (16)
H35A −0.082227 0.039490 0.005287 0.046*
H35B −0.013974 0.000691 0.059514 0.046*
C36A 0.0956 (7) 0.0360 (5) 0.0120 (3) 0.0427 (17)
H36A 0.085940 −0.030748 −0.017606 0.051*
H36B 0.167571 0.038814 0.043803 0.051*
C37A 0.1101 (7) 0.1155 (5) −0.0172 (3) 0.0429 (17)
H37A 0.188485 0.113498 −0.026746 0.052*
H37B 0.048320 0.102471 −0.054814 0.052*
N1A 0.0849 (4) 0.1591 (4) 0.4309 (2) 0.0269 (11)
H1A 0.046521 0.101336 0.408770 0.032*
N2A 0.0853 (4) 0.1878 (4) 0.2204 (2) 0.0246 (10)
H2A 0.077793 0.252146 0.225537 0.029*
N3A −0.0008 (4) 0.1527 (3) 0.0784 (2) 0.0259 (11)
N4A 0.1004 (5) 0.2144 (4) 0.0217 (2) 0.0342 (12)
O1A 0.0686 (4) 0.3123 (3) 0.49173 (19) 0.0363 (10)
O2A 0.0052 (4) 0.0321 (3) 0.16678 (19) 0.0363 (11)
O3A −0.1371 (4) 0.0970 (3) 0.42850 (18) 0.0295 (9)
O4A 0.2319 (4) 0.0391 (3) 0.34645 (18) 0.0283 (9)
H4AA 0.168678 0.011452 0.348090 0.043*
O5A 0.0499 (4) 0.3212 (3) 0.09908 (17) 0.0272 (9)
C1B 0.3082 (6) 0.7441 (5) 1.0764 (3) 0.0301 (14)
C2B 0.4222 (6) 0.7170 (5) 1.0929 (3) 0.0330 (14)
C3B 0.4768 (6) 0.7457 (5) 1.1535 (3) 0.0407 (16)
H3B 0.555765 0.730047 1.166654 0.049*
C4B 0.4173 (6) 0.7962 (5) 1.1942 (3) 0.0408 (16)
H4B 0.456835 0.816689 1.235136 0.049*
C5B 0.3025 (7) 0.8177 (5) 1.1772 (3) 0.0394 (16)
H5B 0.262439 0.850132 1.206458 0.047*
C7B 0.1194 (7) 0.8159 (6) 1.0970 (4) 0.0509 (19)
H7BA 0.119475 0.879269 1.086855 0.076*
H7BB 0.078760 0.821990 1.128924 0.076*
H7BC 0.078117 0.762079 1.061911 0.076*
C8B 0.4854 (6) 0.6578 (5) 1.0484 (3) 0.0417 (16)
H8BA 0.429848 0.634413 1.009295 0.063*
H8BB 0.516535 0.599983 1.060699 0.063*
H8BC 0.551078 0.700373 1.046360 0.063*
C9B 0.2809 (7) 0.7899 (6) 0.9882 (3) 0.0475 (18)
H9BA 0.368194 0.800942 0.996690 0.057*
H9BB 0.249710 0.854580 1.004784 0.057*
C10B 0.2311 (7) 0.7545 (6) 0.9232 (3) 0.0468 (18)
C11B 0.1049 (7) 0.6289 (6) 0.8387 (3) 0.0442 (17)
H11B 0.160028 0.649902 0.817150 0.053*
C12B 0.0968 (7) 0.5141 (6) 0.8225 (3) 0.0499 (19)
H12C 0.058406 0.493659 0.850449 0.060*
H12D 0.043769 0.487358 0.782278 0.060*
C13B 0.2102 (7) 0.4651 (6) 0.8230 (3) 0.0495 (19)
C14B 0.2052 (8) 0.3599 (7) 0.8122 (3) 0.061 (2)
H14B 0.131819 0.323687 0.806949 0.073*
C15B 0.3039 (9) 0.3101 (8) 0.8092 (4) 0.064 (2)
H15B 0.298340 0.239554 0.802510 0.077*
C16B 0.4096 (9) 0.3578 (8) 0.8155 (4) 0.069 (3)
H16B 0.477392 0.321372 0.812127 0.082*
C17B 0.4175 (10) 0.4599 (10) 0.8267 (6) 0.085 (3)
H17B 0.491732 0.495090 0.832360 0.102*
C18B 0.3183 (9) 0.5116 (8) 0.8299 (5) 0.070 (3)
H18B 0.325499 0.582183 0.837026 0.084*
C19B −0.0131 (7) 0.6705 (6) 0.8206 (3) 0.0467 (18)
H19B −0.001951 0.745235 0.836276 0.056*
C20B −0.1117 (7) 0.6336 (6) 0.8435 (3) 0.0462 (18)
H20C −0.079191 0.587802 0.866831 0.055*
H20D −0.174424 0.594476 0.809022 0.055*
C21B −0.1680 (6) 0.7167 (5) 0.8822 (3) 0.0405 (16)
H21B −0.103062 0.760287 0.914432 0.049*
C22B −0.2516 (7) 0.6738 (5) 0.9112 (3) 0.0406 (16)
H22C −0.325726 0.644785 0.880762 0.049*
H22D −0.214442 0.618518 0.925096 0.049*
C23B −0.2830 (6) 0.7491 (5) 0.9632 (3) 0.0381 (16)
C24B −0.2103 (7) 0.7690 (5) 1.0192 (3) 0.0433 (17)
H24B −0.140422 0.734738 1.024693 0.052*
C25B −0.2348 (8) 0.8366 (6) 1.0675 (4) 0.058 (2)
H25B −0.182601 0.848499 1.105697 0.070*
C26B −0.3348 (11) 0.8870 (7) 1.0604 (5) 0.073 (3)
H26B −0.353153 0.933523 1.093650 0.088*
C27B −0.4088 (9) 0.8692 (6) 1.0044 (6) 0.070 (3)
H27B −0.477728 0.904655 0.999219 0.084*
C28B −0.3840 (7) 0.8001 (6) 0.9553 (4) 0.055 (2)
H28B −0.435732 0.788274 0.916986 0.066*
C29B −0.2042 (6) 0.8771 (5) 0.8565 (3) 0.0421 (17)
C30B −0.2894 (7) 0.9252 (6) 0.8160 (3) 0.0475 (18)
H30B −0.328181 0.870438 0.779403 0.057*
C31B −0.2242 (9) 1.0004 (7) 0.7964 (4) 0.064 (2)
H31B −0.176332 1.051381 0.832646 0.077*
C32B −0.1411 (10) 0.9486 (9) 0.7604 (5) 0.083 (3)
H32D −0.078691 0.922368 0.785631 0.125*
H32E −0.105175 0.996534 0.745079 0.125*
H32F −0.185303 0.893232 0.727143 0.125*
C33B −0.3147 (10) 1.0551 (8) 0.7606 (5) 0.076 (3)
H33D −0.373821 1.005619 0.730218 0.114*
H33E −0.273114 1.093013 0.741479 0.114*
H33F −0.354283 1.101052 0.787551 0.114*
C34B −0.4791 (7) 0.9062 (6) 0.8401 (3) 0.0481 (18)
C35B −0.3505 (8) 1.0561 (6) 0.8964 (4) 0.061 (2)
H35C −0.313657 1.037577 0.932761 0.073*
H35D −0.292485 1.101429 0.889506 0.073*
C36B −0.4580 (9) 1.1066 (7) 0.9036 (4) 0.067 (3)
H36C −0.491437 1.127436 0.867652 0.081*
H36D −0.436667 1.167801 0.937794 0.081*
C37B −0.5500 (10) 1.0424 (7) 0.9134 (5) 0.071 (3)
H37C −0.626985 1.072284 0.907613 0.085*
H37D −0.527540 1.037690 0.954547 0.085*
C70C 0.2434 (6) 0.7924 (5) 1.1169 (3) 0.0363 (15)
N1B 0.1553 (6) 0.6732 (5) 0.9024 (3) 0.0466 (15)
H1B 0.134880 0.645389 0.927625 0.056*
N2B −0.2297 (5) 0.7785 (4) 0.8470 (2) 0.0366 (13)
H2B −0.289063 0.748556 0.816766 0.044*
N3B −0.3835 (6) 0.9660 (4) 0.8454 (3) 0.0475 (15)
N4B −0.5611 (7) 0.9405 (6) 0.8704 (3) 0.0607 (19)
O1B 0.2625 (5) 0.8017 (5) 0.8914 (3) 0.0655 (16)
O2B −0.1199 (5) 0.9261 (4) 0.8957 (3) 0.0609 (15)
O3B 0.2506 (4) 0.7185 (3) 1.0160 (2) 0.0381 (11)
O4B −0.0394 (5) 0.6433 (5) 0.7565 (2) 0.0567 (15)
H4BA −0.111248 0.649602 0.743054 0.085*
O5B −0.4959 (5) 0.8178 (4) 0.8054 (2) 0.0527 (13)
C1C 0.7794 (6) 0.3874 (4) 0.3873 (3) 0.0299 (14)
C2C 0.8495 (6) 0.4005 (4) 0.3502 (3) 0.0330 (14)
C3C 0.7957 (7) 0.3740 (5) 0.2896 (3) 0.0415 (17)
H3C 0.840774 0.380674 0.262508 0.050*
C4C 0.6777 (7) 0.3381 (6) 0.2683 (3) 0.0445 (18)
H4C 0.641237 0.323649 0.227101 0.053*
C5C 0.6132 (7) 0.3234 (5) 0.3066 (3) 0.0450 (18)
H5C 0.533063 0.296464 0.291164 0.054*
C6C 0.6620 (6) 0.3469 (5) 0.3674 (3) 0.0340 (15)
C7C 0.5926 (7) 0.3271 (6) 0.4081 (4) 0.0451 (17)
H7CA 0.552311 0.259451 0.391275 0.068*
H7CB 0.533522 0.376237 0.413001 0.068*
H7CC 0.646031 0.332469 0.446805 0.068*
C8C 0.9770 (7) 0.4403 (6) 0.3745 (4) 0.0488 (19)
H8CA 0.981812 0.509492 0.399764 0.073*
H8CB 1.013503 0.438829 0.341560 0.073*
H8CC 1.018892 0.398770 0.397956 0.073*
C9C 0.8040 (7) 0.5072 (5) 0.4805 (3) 0.0439 (17)
H9CA 0.716743 0.509046 0.472202 0.053*
H9CB 0.836589 0.560798 0.467476 0.053*
C10C 0.8542 (6) 0.5259 (5) 0.5465 (3) 0.0437 (17)
C11C 0.9874 (6) 0.4797 (6) 0.6266 (3) 0.0445 (18)
H11C 0.935433 0.519904 0.650371 0.053*
C12C 0.9984 (7) 0.3809 (6) 0.6422 (3) 0.0497 (19)
H12E 1.035503 0.334997 0.613367 0.060*
H12F 1.053719 0.394246 0.681870 0.060*
C13C 0.8871 (7) 0.3271 (7) 0.6434 (3) 0.050 (2)
C14C 0.8843 (9) 0.2249 (7) 0.6407 (4) 0.062 (2)
H14C 0.953199 0.190433 0.636708 0.075*
C15C 0.7865 (10) 0.1737 (9) 0.6437 (4) 0.072 (3)
H15C 0.788497 0.104817 0.641872 0.086*
C16C 0.6847 (10) 0.2207 (8) 0.6492 (4) 0.070 (3)
H16C 0.616200 0.185402 0.651364 0.084*
C17C 0.6851 (9) 0.3189 (9) 0.6515 (5) 0.075 (3)
H17C 0.614806 0.351845 0.654413 0.090*
C18C 0.7833 (8) 0.3723 (8) 0.6499 (4) 0.068 (2)
H18C 0.780462 0.441666 0.653190 0.082*
C19C 1.1020 (7) 0.5438 (6) 0.6402 (3) 0.0445 (18)
H19C 1.085048 0.602515 0.624398 0.053*
C20C 1.1991 (7) 0.4887 (6) 0.6140 (3) 0.0435 (17)
H20E 1.263156 0.480290 0.646797 0.052*
H20F 1.165437 0.420962 0.588367 0.052*
C21C 1.2528 (7) 0.5425 (5) 0.5774 (3) 0.0412 (16)
H21C 1.187492 0.550686 0.544442 0.049*
C22C 1.3448 (7) 0.4800 (5) 0.5497 (3) 0.0427 (17)
H22E 1.415691 0.481244 0.581825 0.051*
H22F 1.310906 0.409528 0.532155 0.051*
C23C 1.3827 (6) 0.5145 (5) 0.5031 (3) 0.0414 (17)
C24C 1.4825 (7) 0.5777 (6) 0.5168 (4) 0.0505 (19)
H24C 1.528579 0.599844 0.556678 0.061*
C25C 1.5172 (8) 0.6096 (7) 0.4740 (5) 0.060 (2)
H25C 1.585063 0.655752 0.484766 0.072*
C26C 1.4552 (9) 0.5757 (7) 0.4160 (5) 0.066 (3)
H26C 1.482771 0.594855 0.386247 0.080*
C27C 1.3503 (8) 0.5123 (7) 0.4003 (4) 0.060 (2)
H27C 1.304092 0.491321 0.360408 0.072*
C28C 1.3159 (7) 0.4813 (6) 0.4442 (3) 0.0428 (17)
H28C 1.246484 0.437200 0.434310 0.051*
C29C 1.2680 (8) 0.7282 (7) 0.6069 (4) 0.060 (2)
C30C 1.3423 (8) 0.8215 (6) 0.6525 (4) 0.057 (2)
H30C 1.386805 0.800296 0.687144 0.068*
C31C 1.2617 (10) 0.9014 (7) 0.6753 (5) 0.074 (3)
H31C 1.208379 0.916461 0.640425 0.088*
C32C 1.1843 (11) 0.8583 (9) 0.7086 (6) 0.093 (4)
H32G 1.137025 0.797639 0.681458 0.139*
H32H 1.131334 0.908298 0.722944 0.139*
H32I 1.235626 0.841884 0.742368 0.139*
C33C 1.3360 (12) 0.9981 (7) 0.7152 (5) 0.093 (4)
H33G 1.385861 0.985112 0.750544 0.139*
H33H 1.283206 1.049882 0.727307 0.139*
H33I 1.386383 1.021139 0.693271 0.139*
C34C 1.5372 (8) 0.8215 (6) 0.6331 (4) 0.055 (2)
C35C 1.3847 (10) 0.8933 (8) 0.5740 (5) 0.078 (3)
H35E 1.355085 0.837188 0.537434 0.093*
H35F 1.318365 0.935322 0.580674 0.093*
C36C 1.4831 (11) 0.9544 (9) 0.5666 (5) 0.087 (3)
H36E 1.454329 0.980197 0.532087 0.104*
H36F 1.509731 1.012538 0.602411 0.104*
C37C 1.5839 (11) 0.8935 (9) 0.5574 (5) 0.088 (4)
H37E 1.562506 0.843768 0.517664 0.105*
H37F 1.653345 0.937306 0.559416 0.105*
N1C 0.9280 (5) 0.4627 (4) 0.5635 (2) 0.0405 (14)
H1C 0.941901 0.409699 0.536798 0.049*
N2C 1.3069 (6) 0.6419 (4) 0.6138 (3) 0.0432 (14)
H2C 1.370275 0.645021 0.642484 0.052*
N3C 1.4271 (6) 0.8529 (5) 0.6256 (3) 0.0543 (17)
N4C 1.6133 (8) 0.8422 (6) 0.6032 (3) 0.074 (2)
O1C 0.8229 (5) 0.5992 (4) 0.5805 (2) 0.0593 (15)
O2C 1.1848 (8) 0.7356 (5) 0.5671 (4) 0.104 (3)
O3C 0.8330 (4) 0.4124 (3) 0.44826 (19) 0.0362 (10)
O4C 1.1479 (5) 0.5803 (4) 0.7040 (2) 0.0530 (14)
H4CA 1.098451 0.614936 0.719272 0.080*
O5C 1.5720 (6) 0.7737 (5) 0.6715 (3) 0.0666 (17)
C1D 1.3338 (5) 0.4176 (4) 0.0554 (3) 0.0287 (13)
C2D 1.3680 (5) 0.4683 (4) 0.1162 (3) 0.0296 (13)
C3D 1.4863 (6) 0.4685 (5) 0.1446 (3) 0.0387 (16)
H3D 1.512152 0.501745 0.185913 0.046*
C4D 1.5663 (6) 0.4224 (5) 0.1151 (4) 0.0416 (17)
H4D 1.646510 0.423357 0.135884 0.050*
C5D 1.5306 (6) 0.3742 (5) 0.0548 (3) 0.0411 (17)
H5D 1.587007 0.342511 0.034504 0.049*
C6D 1.4142 (6) 0.3713 (5) 0.0236 (3) 0.0342 (15)
C7D 1.3730 (8) 0.3212 (7) −0.0423 (3) 0.056 (2)
H7DA 1.309147 0.269129 −0.049814 0.084*
H7DB 1.439356 0.290701 −0.057293 0.084*
H7DC 1.343610 0.371088 −0.062508 0.084*
C8D 1.2805 (7) 0.5202 (5) 0.1485 (3) 0.0412 (16)
H8DA 1.259557 0.580296 0.136256 0.062*
H8DB 1.315615 0.539375 0.191378 0.062*
H8DC 1.209033 0.474857 0.139013 0.062*
C9D 1.1822 (6) 0.4871 (5) −0.0022 (3) 0.0334 (14)
H9DA 1.192424 0.464154 −0.043273 0.040*
H9DB 1.235749 0.548501 0.019276 0.040*
C10D 1.0563 (6) 0.5110 (4) −0.0039 (3) 0.0302 (14)
C11D 0.8728 (5) 0.4805 (4) 0.0245 (3) 0.0267 (13)
H11D 0.849934 0.537552 0.007951 0.032*
C12D 0.7950 (6) 0.3863 (5) −0.0175 (3) 0.0341 (14)
H12G 0.814016 0.329151 −0.001177 0.041*
H12H 0.710752 0.397606 −0.018607 0.041*
C13D 0.8104 (6) 0.3586 (5) −0.0799 (3) 0.0327 (14)
C14D 0.8944 (7) 0.2937 (5) −0.0962 (3) 0.0430 (17)
H14D 0.940703 0.265009 −0.068077 0.052*
C15D 0.9111 (7) 0.2706 (7) −0.1534 (4) 0.056 (2)
H15D 0.967011 0.224618 −0.164554 0.067*
C16D 0.8462 (8) 0.3144 (7) −0.1944 (3) 0.059 (2)
H16D 0.860013 0.300665 −0.232976 0.071*
C17D 0.7622 (8) 0.3776 (6) −0.1788 (3) 0.056 (2)
H17D 0.716400 0.406693 −0.206900 0.067*
C18D 0.7443 (7) 0.3991 (5) −0.1217 (3) 0.0441 (17)
H18D 0.685468 0.442526 −0.111309 0.053*
C19D 0.8487 (5) 0.5067 (4) 0.0864 (2) 0.0253 (12)
H19D 0.766623 0.529170 0.082087 0.030*
C20D 0.9306 (5) 0.5935 (4) 0.1316 (3) 0.0252 (12)
H20G 0.924515 0.652584 0.116365 0.030*
H20H 1.013455 0.575017 0.136018 0.030*
C21D 0.9027 (5) 0.6221 (4) 0.1927 (2) 0.0255 (12)
H21D 0.899401 0.559853 0.205343 0.031*
C22D 0.7848 (5) 0.6678 (4) 0.1930 (3) 0.0256 (12)
H22G 0.789095 0.731567 0.182807 0.031*
H22H 0.722180 0.621997 0.161484 0.031*
C23D 0.7488 (5) 0.6884 (4) 0.2507 (3) 0.0242 (12)
C24D 0.7258 (5) 0.6094 (5) 0.2727 (3) 0.0288 (13)
H24D 0.736248 0.543078 0.251349 0.035*
C25D 0.6885 (6) 0.6248 (5) 0.3245 (3) 0.0326 (14)
H25D 0.673616 0.569729 0.338538 0.039*
C26D 0.6729 (6) 0.7222 (5) 0.3561 (3) 0.0347 (15)
H26D 0.646326 0.734106 0.391594 0.042*
C28D 0.7346 (5) 0.7845 (5) 0.2839 (3) 0.0303 (14)
H28D 0.751838 0.839994 0.270733 0.036*
C29D 1.0635 (5) 0.6724 (4) 0.2841 (2) 0.0247 (13)
C30D 1.1398 (5) 0.7629 (4) 0.3312 (3) 0.0261 (13)
H30D 1.142096 0.818776 0.312994 0.031*
C31D 1.2671 (5) 0.7383 (5) 0.3529 (3) 0.0316 (14)
H31D 1.265673 0.684967 0.373115 0.038*
C32D 1.3199 (7) 0.6987 (9) 0.2997 (4) 0.067 (3)
H32J 1.278061 0.634008 0.275030 0.101*
H32K 1.404059 0.690003 0.313596 0.101*
H32L 1.311578 0.746421 0.276315 0.101*
C33D 1.3404 (7) 0.8310 (6) 0.3972 (4) 0.060 (2)
H33J 1.343021 0.883743 0.377750 0.089*
H33K 1.421213 0.814057 0.411470 0.089*
H33L 1.304229 0.854940 0.430841 0.089*
C34D 1.0301 (5) 0.8826 (4) 0.3895 (3) 0.0282 (13)
C35D 0.9622 (8) 0.8498 (6) 0.4735 (3) 0.0478 (18)
H35G 0.880796 0.852010 0.479441 0.057*
H35H 1.018273 0.878352 0.512695 0.057*
C36D 0.9854 (9) 0.7452 (7) 0.4483 (4) 0.059 (2)
H36G 1.001321 0.712624 0.480522 0.071*
H36H 0.912856 0.709902 0.418757 0.071*
C37D 1.0828 (8) 0.7324 (5) 0.4202 (3) 0.0457 (18)
H37G 1.080953 0.661052 0.397566 0.055*
H37H 1.158164 0.749826 0.451227 0.055*
27D 0.6965 (6) 0.8012 (5) 0.3351 (3) 0.0338 (14)
H 0.686248 0.867582 0.356393 0.041*
N1D 0.9975 (4) 0.4689 (4) 0.0259 (2) 0.0263 (11)
H1D 1.035946 0.432471 0.047358 0.032*
N2D 0.9958 (4) 0.6933 (3) 0.2370 (2) 0.0238 (10)
H2D 1.007533 0.752672 0.232296 0.029*
N3D 1.0797 (5) 0.7946 (4) 0.3798 (2) 0.0286 (11)
N4D 0.9751 (5) 0.9099 (4) 0.4346 (2) 0.0360 (13)
O1D 1.0139 (4) 0.5701 (3) −0.03185 (19) 0.0356 (10)
O2D 1.0664 (4) 0.5882 (3) 0.29168 (19) 0.0357 (11)
O3D 1.2142 (4) 0.4110 (3) 0.02649 (18) 0.0295 (9)
O4D 0.8489 (4) 0.4217 (3) 0.10907 (18) 0.0273 (9)
H4DA 0.914633 0.397179 0.110306 0.041*
O5D 1.0327 (4) 0.9418 (3) 0.35767 (18) 0.0279 (9)
O1W 0.7402 (3) 0.6491 (3) 0.68525 (12) 0.0674 (17)
H1WA 0.682483 0.687704 0.682447 0.101*
H1WB 0.757366 0.649105 0.722242 0.101*
O2W 0.1105 (3) 0.3976 (3) 0.22708 (13) 0.0439 (12)
H2WA 0.047949 0.426775 0.234593 0.066*
H2WB 0.150262 0.392714 0.261220 0.066*
O3W 0.3960 (3) 0.6383 (3) 0.73942 (13) 0.0577 (14)
H3WA 0.406452 0.694676 0.767557 0.087*
H3WB 0.463689 0.612506 0.745386 0.087*
O4W 0.9770 (4) 0.8959 (3) 0.22969 (16) 0.0443 (12)
H4WA 1.003928 0.923905 0.206608 0.066*
H4WC 0.974716 0.917373 0.266398 0.066*
O5W 0.5974 (3) 0.5375 (3) 0.73680 (13) 0.191 (7)
H5WA 0.651735 0.572288 0.729206 0.287*
H5WB 0.521659 0.549227 0.725132 0.287*
O6W 0.8625 (3) 0.7908 (3) 0.58660 (12) 0.195 (7)
H6WA 0.855942 0.854965 0.598074 0.292*
H6WB 0.918164 0.784987 0.567433 0.292*

1 Source of materials

All reagents are commercially sourced without the need of further purifications. Approximately 0.010 g of lopinavir (0.0159 mmol) was dissolved in 5 mL of methanol. The solution was left in a polytop vial to allow slow evaporation at temperatures between 10 and 15 °C for 24 h. Colourless needles were formed and were observed after 5 weeks.

2 Experimental details

The collection method involved ω-scans of 0.5° width. The data was reduced using SAINT-Plus version 6.02.6 software. Sadabs was then used to process the empirical absorption corrections [1]. The crystal structure was solved using Shelxt [2]. Hydrogen atoms were geometrically positioned and U iso(H) = 1.2U eq(C). All diagrams were prepared for publication using Ortep [4], WinGX [4], Mercury [5] Platon [6].

3 Comment

Lopinavir is a selective and potent protease inhibitor used for the treatment and management of HIV infections [7]. Lopinavir was crystallised as a hydrate with methanol. The figure illustrates the asymmetric unit of the molecule, this unit consists of two molecules of N-{5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl) butanamide and three molecules of water. All bond lengths and angles were as expected as reported by [8].

The secondary amine functional group is attached by a N2D–H2D⋯O4W bond to a water molecule, the bond length is recorded at 2.888 Å. Another secondary amine functional group is attached by a N2A–H2A⋯O2W bond to a water molecule with a bond length of 2.892 Å. The pyrimidinone moiety is attached by a C34–O5D⋯H4WC bond to a water molecule, the bond length was noted as 2.892 Å. These bond lengths are between 2.7 and 2.9 Å, according to [8] these bonds are considered moderate hydrogen bonds. Hydrates are crystal compounds that contain water in their crystal lattice [9]. The crystal structure synthesised is a hydrate, this is evident as there are three water molecules that interact with one another, but do not interact with the host molecule (lopinavir), making the crystal structure a trihydrate. The water molecules that interact with one another and those that interact with the host molecule are bifurcated hydrogen bond interactions. These water molecules are attached to one another by O5W–H5WB⋯O3W and O3W–H3WB⋯O5W bonds, both bond lengths 2.752 Å as well as O5W–H5WA⋯O1W bonds with a bond length of 2.949 Å.

Hydrates as well as cocrystals in general are found useful; they play a significant role in pharmaceutical drug design. These types of drugs are of key interest because water molecules are small and can form interactions as both hydrogen bond acceptors and donors. Hydrates are also considered non-toxic and are also able to form spontaneously [10].


Corresponding author: Mark G. Smith, Chemistry Department, University of South Africa, Unisa Science Campus, 28 Pioneer Avenue, Florida, Roodepoort, Gauteng, South Africa, E-mail:

Funding source: National Research Foundation (NRF)

Award Identifier / Grant number: Doctoral General Scholarship Grant number PMDS22071841801

Funding source: University of the Witwatersrand

Funding source: University of South Africa

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by the National Research Foundation (NRF) Doctoral General Scholarship Grant number PMDS22071841801, the University of the Witwatersrand and the University of South Africa.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2024-01-10
Accepted: 2024-02-29
Published Online: 2024-03-29
Published in Print: 2024-06-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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