Cluster-model DFT simulations of the infrared spectra of triazine-based molecular crystals

2018 ◽  
Vol 20 (32) ◽  
pp. 20779-20784 ◽  
Author(s):  
Xiaohong Yuan ◽  
Kun Luo ◽  
Nan Liu ◽  
Xueqiang Ji ◽  
Chao Liu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Ir Spectra ◽  
Infrared Spectra ◽  
Cluster Model ◽  
Molecular Crystals ◽  
Dft Simulations ◽  
Independent Molecules ◽  
Model Approach

A cluster-model approach is developed to simulate the IR spectra of triazine-based molecular crystals, and the distinct hydrogen-bonding environments of the crystallographically independent molecules can be clearly revealed.

scholarly journals A study of the ir spectra of the copigments of malvin chloride with organic acids

2001 ◽  
Vol 66 (7) ◽  
pp. 451-462 ◽  
Author(s):  
Jasmina Dimitric-Markovic ◽  
Ubavka Mioc ◽  
Jelisavetam Baranac ◽  
Zoran Nedic
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Organic Acids ◽  
Ir Spectra ◽  
Infrared Spectra ◽  
Molecular Structures ◽  
Oxonium Ions ◽  
Hydroxy Groups ◽  
Formed Hydrogen

The infrared spectra of the copigments of malvin with several organic acids: caffeic, ferulic, sinapic, chlorogenic, and tannic, were analyzed in order to elucidate the bonding of the molecules in the copigments. It was established that copigmentation is realized through hydrogen bonding between malvin molecules and the acids under study. The infrared spectra reveal that two groups of hydrogen bonds are formed, which include interactions of different molecular structures: hydroxy groups (bands around 3500 cm-1) and oxonium ions of the molecules (bands below 3000 cm-1). The formed hydrogen bonds were found to be of different strengths. The strengths of the hydrogen bonds were tentatively correlated with thermodynamic properties of the corresponding copigmentation reactions.

scholarly journals Theoretical Study of the Structures of 4-(2,3,5,6-Tetrafluoropyridyl)Diphenylphosphine Oxide and Tris(Pentafluorophenyl)Phosphine Oxide: Why Does the Crystal Structure of (Tetrafluoropyridyl)Diphenylphosphine Oxide Have Two Different P=O Bond Lengths?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2778
Author(s):  
Joseph R. Lane ◽  
Graham C. Saunders
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Phosphine Oxide ◽  
Density Functional ◽  
Lone Pair ◽  
Diphenylphosphine Oxide ◽  
Functional Theory ◽  
Weak Hydrogen Bonding ◽  
Independent Molecules ◽  
The Difference

The crystal structure of 4-(2,3,5,6-tetrafluoropyridyl)diphenylphosphine oxide (1) contains two independent molecules in the asymmetric unit. Although the molecules are virtually identical in all other aspects, the P=O bond distances differ by ca. 0.02 Å. In contrast, although tris(pentafluorophenyl)phosphine oxide (2) has a similar crystal structure, the P=O bond distances of the two independent molecules are identical. To investigate the reason for the difference, a density functional theory study was undertaken. Both structures comprise chains of molecules. The attraction between molecules of 1, which comprises lone pair–π, weak hydrogen bonding and C–H∙∙∙arene interactions, has energies of 70 and 71 kJ mol−1. The attraction between molecules of 2 comprises two lone pair–π interactions, and has energies of 99 and 100 kJ mol−1. There is weak hydrogen bonding between molecules of adjacent chains involving the oxygen atom of 1. For one molecule, this interaction is with a symmetry independent molecule, whereas for the other, it also occurs with a symmetry related molecule. This provides a reason for the difference in P=O distance. This interaction is not possible for 2, and so there is no difference between the P=O distances of 2.

The chemistry of aliphatic unconjugated nitramines. II. Intramolecular properties and crystal packing

1969 ◽  
Vol 22 (12) ◽  
pp. 2505 ◽  
Author(s):  
J Stals
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Packing ◽  
Dipole Moments ◽  
Molecular Crystals ◽  
Bond Orders ◽  
Bond Energies ◽  
Electric Dipole Moments ◽  
Charge Distributions ◽  
Hydrogen Bonding Interactions ◽  
Vb Structures

The VESCF(BJ)-MO electric dipole moments, molecular ionization potentials, electronic bond energies, charge distributions, and bond orders for nitramide, N-methylnitramine, and s- and as-N,N- dimethylnitramines are reported. The packing of nitramide, RDX, and HNX in their molecular crystals is rationalized in terms of electrostatic and hydrogen-bonding interactions. Simple VB structures do not readily predict their calculated MO charge distributions and bond orders.

3-n-Butyl-2-methoxy-1-benzothieno[3,2-d]pyrimidin-4(3H)-one

2006 ◽  
Vol 62 (4) ◽  
pp. o1319-o1320 ◽  
Author(s):  
Min-Hui Cao ◽  
Sheng-Zhen Xu ◽  
Yang-Gen Hu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Benzene Ring ◽  
Title Compound ◽  
Thiophene Ring ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Compound C ◽  
Π Stacking ◽  
Independent Molecules

The title compound, C15H16N2O2S, contains a five-membered thiophene ring fused to a benzene ring and a substituted pyrimidinone ring. All three rings in each of the independent molecules of the asymmetric unit lie in approximately the same plane. The crystal structure is stabilized by intermolecular C—H...O hydrogen bonding and π–π stacking interactions.

Hydrogen bonding and conformation in cis- and trans-2-alkoxy-3-hydroxytetrahydrofurans

1968 ◽  
Vol 46 (1) ◽  
pp. 21-24 ◽  
Author(s):  
W. W. Zajac Jr. ◽  
F. Sweet ◽  
R. K. Brown
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectra ◽  
Hydroxyl Absorption ◽  
Cis And Trans ◽  
In Cis ◽  
Infrared Data ◽  
Hydrogen Bonded

Infrared spectra show both free and hydrogen bonded hydroxyl absorption in several trans-2-alkoxy-3-hydroxytetrahydrofurans. The extent of non-bonded hydroxyl is greater than that of bonded hydroxyl. Suggestions are made of possible conformations which might account for the infrared data.

Infrared spectra and hydrogen bonding of pentitols and pyranosides at 20 to 300 K

2000 ◽  
Vol 328 (3) ◽  
pp. 307-319 ◽  
Author(s):  
Mark Rozenberg ◽  
Aharon Loewenschuss ◽  
Yizhak Marcus
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectra

scholarly journals (S)-2-[(4-Fluorophenyl)formamido]-3-phenylpropanoic acid

IUCrData ◽  
2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Kathleen S. Lee ◽  
Luke Turner ◽  
Cynthia B. Powell ◽  
Eric W. Reinheimer
Keyword(s):  
Hydrogen Bonding ◽  
Title Compound ◽  
Phenyl Ring ◽  
Room Temperature ◽  
Solid Phase ◽  
Independent Molecule ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Compound C ◽  
Independent Molecules

The title compound, C16H14FNO3, was synthesized via solid phase methods; it exhibits monoclinic (P21) symmetry at room temperature. The two independent molecules that comprise the asymmetric unit display distinct torsion angles of 173.2 (2) and 72.6 (2)° along the central sp 3 C—N bond. In the crystal, hydrogen bonding through N—H...O contacts couples the asymmetric unit molecules into pairs that align in layers extending parallel to (100) via additional O—H...O interactions. The phenyl ring of one independent molecule was found to be disordered over two sets of sites in a 0.55 (3):0.45 (3) ratio.

scholarly journals Crystal structures of salts of bedaquiline

2020 ◽  
Vol 76 (11) ◽  
pp. 1010-1023
Author(s):  
Mercy Okezue ◽  
Daniel Smith ◽  
Matthias Zeller ◽  
Stephen R. Byrn ◽  
Pamela Smith ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Water Molecule ◽  
Salt Water ◽  
Sodium Ethoxide ◽  
New Drugs ◽  
Free Base ◽  
Dimethylamino Group ◽  
Patent Literature ◽  
Independent Molecules ◽  
Hydrogen Bonded

Bedaquiline [systematic name: 1-(6-bromo-2-methoxyquinolin-3-yl)-4-(dimethylamino)-2-(naphthalen-1-yl)-1-phenylbutan-2-ol, C32H31BrN2O2] is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt {systematic name: [4-(6-bromo-2-methoxyquinolin-3-yl)-3-hydroxy-3-(naphthalen-1-yl)-4-phenylbutyl]dimethylazanium 3-carboxyprop-2-enoate, C32H32BrN2O2 +·C4H3O4 −}, and about a dozen other salts of bedaquiline have been described in patent literature, but none have so far been structurally described. In a first communication, we present the crystal structure of bedaquilinium fumarate and of two new benzoate salts, as well as that of a degradation product of the reaction of bedaquilinium fumarate with sodium ethoxide, 3-benzyl-6-bromo-2-methoxyquinoline, C17H14BrNO. The fumarate and benzoate salts both feature cations monoprotonated at the dimethylamino group. The much less basic quinoline N atom remains unprotonated. Both salts feature a 1:1 cation-to-anion ratio, with the fumarate being present as monoanionic hydrofumarate. The conformations of the cations are compared to that of free base bedaquiline and with each other. The flexible backbone of the bedaquiline structure leads to a landscape of conformations with little commonalities between the bedaquiline entities in the various structures. The conformations are distinctively different for the two independent molecules of the free base, the two independent molecules of the hydrofumarate salt, and the one unique cation of the benzoate salt. Packing of the salts is dominated by hydrogen bonding. Hydrogen-bonding motifs, as well as the larger hydrogen-bonded entities within the salts, are quite similar for the salts, despite the vastly differing conformations of the cations, and both the hydrofumarate and the benzoate structure feature chains of hydrogen-bonded anions that are surrounded by and hydrogen bonded to the larger bedaquilinium cations, leading to infinite broad ribbons of anions, cations, and (for the benzoate salt) water molecules. The benzoate salt was isolated in two forms: as a 1.17-hydrate (C32H32BrN2O2 +·C7H5O2 −·1.166H2O), obtained from acetone or propanol solution, with one fully occupied water molecule tightly integrated into the hydrogen-bonding network of anions and cations, and one partially occupied water molecule [refined occupancy 16.6 (7)%], only loosely hydrogen bonded to the quinoline N atom. The second form is an acetonitrile solvate (C32H32BrN2O2 +·C7H5O2 −·0.742CH3CN·H2O), in which the partially occupied water molecule is replaced by a 74.2 (7)%-occupied acetonitrile molecule. The partial occupancy induces disorder for the benzoate phenyl ring. The acetonitrile solvate is unstable in atmosphere and converts into a form not distinguishable by powder XRD from the 1.17-hydrate.

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