scholarly journals Cocrystal trimorphism as a consequence of the orthogonality of halogen- and hydrogen-bonds synthons

2019 ◽  
Vol 55 (93) ◽  
pp. 14066-14069
Author(s):  
Filip Topić ◽  
Katarina Lisac ◽  
Mihails Arhangelskis ◽  
Kari Rissanen ◽  
Dominik Cinčić ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Critical Role ◽  
Molecular Crystals

Trimorphic cocrystals, i.e. multi-component molecular crystals with three polymorphic structures, are exceedingly rare. First example of a trimorphic halogen-bonded cocrystal, reported here, shows a critical role for the interaction orthogonality.

scholarly journals X-ray Crystallographic Study of Ranaconitine

2011 ◽  
Vol 6 (11) ◽  
pp. 1934578X1100601
Author(s):  
Yang Li ◽  
Jun-Hui Zhou ◽  
Gui-Jun Han ◽  
Min-Juan Wang ◽  
Wen-Ji Sun ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Critical Role ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Crystallographic Study ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The crystal structure of natural diterpenoid alkaloid ranaconitine isolated from Aconitum sinomontanum Nakai has been determined by single crystal X-ray diffraction analysis. The crystal presents a monoclinic system, space group C2 with Z = 4, unit cell dimensions a = 30.972(19) Å, b = 7.688(5) Å, and c = 19.632(12) Å. Moreover, the intermolecular O–H···O hydrogen bonds and weak π-π interactions play a critical role in expanding the dimensionality.

Hydrogen-Bonded Three-Dimensional Molecular Architectures Featuring Carboxylate - Imidazole - Zinc Triad Systems

2002 ◽  
Vol 55 (11) ◽  
pp. 741 ◽  
Author(s):  
Jin-Hua Yang ◽  
Shao-Liang Zheng ◽  
Jun Tao ◽  
Gao-Feng Liu ◽  
Xiao-Ming Chen
Keyword(s):  
Hydrogen Bonds ◽  
Critical Role ◽  
Three Dimensional ◽  
Water Molecules ◽  
Molecular Architecture ◽  
Lattice Water ◽  
Carboxylate Oxygen ◽  
Polymeric Chains ◽  
Molecular Architectures ◽  
Hydrogen Bonded

Two complexes, [Zn(Him)2(mpa)] (1) and [Zn(Him)2(tpa)]·H2O (2) (Him = imidazole, mpa = m-phthalate, and tpa = terephthalate), have been prepared and structurally characterized, revealing two different three-dimensional hydrogen-bonded molecular architectures. Each features [Zn(Him)2(dicarboxylate)] zigzag polymeric chains and intermolecular N–H…O hydrogen bonds between the uncoordinated Him nitrogen atoms and carboxylate oxygen atoms that are similar to the carboxylate–histidine–zinc triad systems in zinc(II) enzymes. The lattice water molecules in complex (2) play a critical role in the formation of a three-dimensional hydrogen-bonded molecular architecture.

Associations of squaric acid and its anions as multiform building blocks of hydrogen-bonded molecular crystals

2001 ◽  
Vol 57 (6) ◽  
pp. 859-865 ◽  
Author(s):  
Gastone Gilli ◽  
Valerio Bertolasi ◽  
Paola Gilli ◽  
Valeria Ferretti
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Negative Charge ◽  
Three Dimensional ◽  
Molecular Crystals ◽  
Building Blocks ◽  
Squaric Acid ◽  
Orthosilicic Acid ◽  
Molecular Plane ◽  
Dimensional Crystal

Squaric acid, H2C4O4 (H2SQ), is a completely flat diprotic acid that can crystallize as such, as well as in three different anionic forms, i.e. H2SQ·HSQ−, HSQ− and SQ2−. Its interest for crystal engineering studies arises from three notable factors: (i) its ability of donating and accepting hydrogen bonds strictly confined to the molecular plane; (ii) the remarkable strength of the O—H...O bonds it may form with itself which are either of resonance-assisted (RAHB) or negative-charge-assisted [(−)CAHB] types; (iii) the ease with which it may donate a proton to an aromatic base which, in turn, back-links to the anion by strong low-barrier N—H+...O1/2− charge-assisted hydrogen bonds. Analysis of all the structures so far known shows that, while H2SQ can only crystallize in an extended RAHB-linked planar arrangement and SQ2− tends to behave much as a monomeric dianion, the monoanion HSQ− displays a number of different supramolecular patterns that are classifiable as β-chains, α-chains, α-dimers and α-tetramers. Partial protonation of these motifs leads to H2SQ·HSQ− anions whose supramolecular patterns include ribbons of dimerized β-chains and chains of emiprotonated α-dimers. The topological similarities between the three-dimensional crystal chemistry of orthosilicic acid, H4SiO4, and the two-dimensional one of squaric acid, H2C4O4, are finally stressed.

Theoretical Modeling of the N-H and N-D Stretching Bands of Hydrogen-Bonded 1-Methylthymine Crystal and Its Deuterated Form

2006 ◽  
Vol 2 (4) ◽  
pp. 205-219
Author(s):  
Marek Boczar ◽  
Łukasz Boda ◽  
Marek J. Wójcik
Keyword(s):  
Hydrogen Bonds ◽  
High Frequency ◽  
Molecular Crystals ◽  
Low Frequency ◽  
Unit Cell ◽  
Fermi Resonance ◽  
Bending Vibrations ◽  
Theoretical Simulation ◽  
Stretching Vibrations ◽  
Centrosymmetric Dimers

Theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N•••O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within an unit cell and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the νs stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model.

scholarly journals Hydrogen bonds in molecular crystals alanine and tyrosine: NBO analysis

2020 ◽  
Vol 64 (10) ◽  
pp. 1-6
Author(s):  
Tatiana G. Volkova ◽  
◽  
Iroda Mamirjon kizi Abdukhalimova ◽  
Irina O. Talanova ◽  
◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Molecular Crystals ◽  
Dft Method ◽  
Nbo Analysis ◽  
Chemical Modeling ◽  
Theoretical Concepts ◽  
Oh Groups ◽  
The Third

At present, the theoretical concepts of the hydrogen bond (H-bond) in condensed media, for example, in living systems, biomolecules, are not fully solved. Quantum chemical modeling is used as one of the methods for studying the nature and determining the strength of the H-bond. In this paper, we continue to study the system of hydrogen bonds in molecular crystals of alanine and tyrosine. The dimers of these amino acids were modeled using the DFT method using the B97D functional with bases 6-31++G**. In the framework of NBO analysis, the stabilization energies of the formed hydrogen bond and the value of the transferred charge are calculated. It is shown that in alanine dimers, the main factor affecting the h-bond stabilization energy is the geometric parameters and, first of all, (N-H...O). The binding σ-orbital of the hydrogen bond is the result of the interaction of a hybrid NBO of the lone electron pairs of an oxygen atom and a loosening σ*-NBO N−H bond. The nature of bond formation in all three cases is the same, and the charge transfer value is greater than the value of the bond criterion, which indicates the presence of hydrogen bonds in all analyzed alanine systems. In tyrosine dimers, two H-bonds are formed that are similar in nature, as well as in geometric and energy parameters. The third H-bond is very weak, and the amount of charge transfer indicates its absence. The main interaction between the molecules in the third tyrosine dimer is the H-bond between the –СОО− and –OH groups. It was found that the scheme of formation of hydrogen bonds in molecular crystals of tyrosine is somewhat different from that of alanine.

Sulfonamide Molecular Crystals: Structure, Sublimation Thermodynamic Characteristics, Molecular Packing, Hydrogen Bonds Networks

2013 ◽  
Vol 13 (9) ◽  
pp. 4002-4016 ◽  
Author(s):  
German L. Perlovich ◽  
Alex M. Ryzhakov ◽  
Valery V. Tkachev ◽  
Lars Kr. Hansen ◽  
Oleg A. Raevsky
Keyword(s):  
Hydrogen Bonds ◽  
Molecular Crystals ◽  
Thermodynamic Characteristics ◽  
Molecular Packing

Conformational analysis: crystallographic, molecular mechanics and quantum chemical studies of C—H...O hydrogen bonding in the flexible bis(nosylate) derivative of catechol

2004 ◽  
Vol 60 (5) ◽  
pp. 598-608 ◽  
Author(s):  
Orde Quentin Munro ◽  
Lynette Mariah
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Lattice ◽  
Molecular Mechanics ◽  
Quantum Chemical ◽  
Critical Role ◽  
Crystalline Solid ◽  
Molecular Architecture ◽  
X Ray ◽  
Hydrogen Bonded

The single-crystal X-ray diffraction analysis of 2-{[(4-nitrophenoxy)sulfonyl]oxy}phenyl 4-nitrophenyl sulfate (4) reveals that an interesting intermolecular or extended structure (a one-dimensional hydrogen-bonded polymer) is formed because of pairs of intermolecular (aryl)C—H...O(nitro) hydrogen bonds between the C 2 symmetry monomer units. The axis of the hydrogen-bonded polymer runs co-linear with the [101] face diagonal of the monoclinic unit cell. Molecular mechanics calculations using a modified version of the MM+ force field and a random conformational search algorithm have been used to locate the important low-energy in vacuo conformations of (4). The MM-calculated conformation of (4) that most closely matches the X-ray structure lies some 26.5 kJ mol−1 higher in energy than the global minimum-energy conformation, consistent with the notion that the crystallographically observed molecular architecture of (4) is a local energy minimum in the absence of its crystal lattice environment. Since the X-ray conformation of (4) was correctly calculated only when all of the neighbouring molecules in the crystal lattice were included in the simulation, hydrogen bonding and other non-bonded interactions in the crystal lattice clearly dictate the experimentally observed conformation of (4). Quantum chemical calculations (AM1 method) confirm the critical role played by the intermolecular (aryl)C—H...O(nitro) hydrogen bonds in controlling the crystallographically observed conformation of (4) and show that self-recognition in this system by hydrogen bonding is favoured on electrostatic grounds. Collectively, the molecular simulations suggest that because the lowest-energy molecular conformation of (4) does not permit the formation of an extended hydrogen-bonded `supramolecular' structure, it is not the preferred conformation in the crystalline solid state.

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