Crystal Engineering: Strategies and Architectures

1997 ◽  
Vol 53 (4) ◽  
pp. 569-586 ◽  
Author(s):  
C. B. Aakeröy
Keyword(s):  
Molecular Structure ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Structural Data ◽  
Building Blocks ◽  
Intermolecular Forces ◽  
Design Strategies ◽  
Playing Field ◽  
Molecular Building Blocks

The area broadly described as crystal engineering is currently expanding at a brisk pace. Imaginative schemes for supramolecular synthesis, and correlations between molecular structure, crystal packing and physical properties are presented in the literature with increasing regularity. In practice, crystal engineering can be many different things; synthesis, statistical analysis of structural data, ab initio calculations etc. Consequently, we have been provided with a new playing field where chemists from traditionally unconnected parts of the spectrum have exchanged ideas, defined goals and made creative contributions to further progress not only in crystal engineering, but also in other disciplines of chemistry. Crystal engineering is delineated by the nature and structural consequences of intermolecular forces, and the way in which such interactions are utilized for controlling the assembly of molecular building blocks into infinite architectures. Although it is important to acknowledge that a crystal structure is the result of a subtle balance between a multitude of non-covalent forces, this article will focus on design strategies based upon the hydrogen bond and will present a range of approaches that have relied on the directionality and selectivity of such interactions in the synthesis of predictable one-, two- and three-dimensional motifs.

Quantitative analysis of solid-state diversity in trifluoromethylated phenylhydrazones

2017 ◽  
Vol 73 (5) ◽  
pp. 781-793 ◽  
Author(s):  
Dhananjay Dey ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Closed Shell ◽  
Building Blocks ◽  
High Dispersion ◽  
Scanning Calorimetry ◽  
Dispersion Energy ◽  
Molecular Building Blocks ◽  
Electrostatic Contribution

The cooperative roles of various structural motifs associated with the presence of different intermolecular interactions in the formation of molecular crystals are investigated in a series of trifluoromethylated phenylhydrazones. Out of the six compounds analysed, two exhibit three-dimensional structural similarities with geometrically equivalent building blocks, while a third exists as two polymorphic forms crystallized from ethanol solutions at low temperature (277 K) and room temperature (298 K), respectively. The compounds were characterizedviasingle-crystal and powder X-ray diffraction techniques and differential scanning calorimetry. In the absence of any strong hydrogen bonding, the supramolecular constructs are primarily stabilizedviamolecular pairs with a high dispersion-energy contribution, due to the presence of molecular stacking along the molecular backbone along with C—H...π interactions in the solid state, in preference to an electrostatic contribution. The interaction energies for the most stabilizing molecular building blocks are in the range −29 to −43 kJ mol−1. In addition, weak N—H...F, C—H...F and N—H...C interactions and F...F, F...C, F...N and C...N contacts act as secondary motifs, providing additional stability to the crystal packing. The overall molecular arrangements are carefully analysed in terms of their nature and energetics, and the roles of different molecular pairs towards the crystal structure are delineated. A topological study using the quantum theory of atoms in molecules was used to characterize all the atomic interactions in the solid state. It established the presence of (3, −1) bond critical points and the closed-shell nature of all the interactions.

scholarly journals Towards computer-guided tuning of the crystal packing of porous organic cages

2014 ◽  
Vol 70 (a1) ◽  
pp. C667-C667
Author(s):  
Angeles Pulido ◽  
Ming Liu ◽  
Paul Reiss ◽  
Anna Slater ◽  
Sam Chong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Molecular Sieves ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Aromatic Aldehydes ◽  
Lattice Energy ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Computational Techniques

Among microporous materials, there has been an increasing recent interest in porous organic cage (POC) crystals, which can display permanent intrinsic (molecular) and extrinsic (crystal network) porosity. These materials can be used as molecular sieves for gas separation and potential applications as enzyme mimics have been suggested since they exhibit structural response toward guest molecules[1]. Small structural modifications of the initial building blocks of the porous organic molecules can lead to quite different molecular assembly[1]. Moreover, the crystal packing of POCs is based on weak molecular interactions and is less predictable that other porous materials such as MOFs or zeolites.[2] In this contribution, we show that computational techniques -molecular conformational searches and crystal structure prediction- can be successfully used to understand POC crystal packing preferences. Computational results will be presented for a series of closely related tetrahedral imine- and amine-linked porous molecules, formed by [4+6] condensation of aromatic aldehydes and cyclohexyl linked diamines. While the basic cage is known to have one strongly preferred crystal structure, the presence of small alkyl groups on the POC modifies its crystal packing preferences, leading to extensive polymorphism. Calculations were able to successfully identify these trends as well as to predict the structures obtained experimentally, demonstrating the potential for computational pre-screening in the design of POCs within targeted crystal structures. Moreover, the need of accurate molecular (ab initio calculations) and crystal (based on atom-atom potential lattice energy minimization) modelling for computer-guided crystal engineering will be discussed.

Self-Assembly of Proteins into Three-Dimensional Structures Using Bio-Conjugation

2014 ◽  
Vol 1663 ◽  
Author(s):  
Garima Thakur ◽  
Kovur Prashanthi ◽  
Thomas Thundat
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Gold Surface ◽  
Building Blocks ◽  
Growth Conditions ◽  
Base Layer ◽  
Chemical Structures ◽  
Molecular Building Blocks ◽  
Ring Structures ◽  
Self Assembled

ABSTRACTSelf–assembly of molecular building blocks provides an interesting route to produce well-defined chemical structures. Tailoring the functionalities on the building blocks and controlling the time of self-assembly could control the properties as well as the structure of the resultant patterns. Spontaneous self-assembly of biomolecules can generate bio-interfaces for myriad of potential applications. Here we report self-assembled patterning of human serum albumin (HSA) protein in to ring structures on a polyethylene glycol (PEG) modified gold surface. The structure of the self-assembled protein molecules and kinetics of structure formation entirely revolved around controlling the nucleation of the base layer. The formation of different sizes of ring patterns is attributed to growth conditions of the PEG islands for bio-conjugation. These assemblies might be beneficial in forming structurally ordered architectures of active proteins such as HSA or other globular proteins.

scholarly journals Crystal structures of 2-aminopyridine citric acid salts: C5H7N2 +·C6H7O7 − and 3C5H7N2 +·C6H5O7 3−

2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Almost All

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.

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.

scholarly journals Making crystals with a purpose; a journey in crystal engineering at the University of Bologna

IUCrJ ◽  
2017 ◽  
Vol 4 (4) ◽  
pp. 369-379 ◽  
Author(s):  
Dario Braga ◽  
Fabrizia Grepioni ◽  
Lucia Maini ◽  
Simone d'Agostino
Keyword(s):  
Charge Distribution ◽  
Functional Groups ◽  
Crystal Engineering ◽  
Building Blocks ◽  
Mixed Crystals ◽  
The Other ◽  
Molecular Building Blocks ◽  
The One ◽  
The University ◽  
Conceptual Relationship

The conceptual relationship between crystal reactivity, stability and metastability, solubility and morphology on the one hand and shape, charge distribution, chirality and distribution of functional groups over the molecular surfaces on the other hand is discussed,viaa number of examples coming from three decades of research in the field of crystal engineering at the University of Bologna. The bottom-up preparation of mixed crystals, co-crystals and photoreactive materials starting from molecular building blocks across the borders of organic, organometallic and metalorganic chemistry is recounted.

scholarly journals New Ag(I) Coordination Complexes Based on Bis(1-isoquinolinecarboxamide)ethane.

2014 ◽  
Vol 70 (a1) ◽  
pp. C665-C665
Author(s):  
Nicole Parra ◽  
Julio Belmar ◽  
Claudio Jiménez ◽  
Jorge Pasán ◽  
Catalina Ruiz-Pérez
Keyword(s):  
Crystal Engineering ◽  
Rational Design ◽  
Crystal Packing ◽  
Functional Materials ◽  
Coordination Complexes ◽  
Intermolecular Forces ◽  
Research Area ◽  
Molecular Structures ◽  
Gauche Conformation ◽  
Design And Synthesis

Crystal Engineering is an interdisciplinary research area that involves chemists, physicists, biologists and materials scientists.1It is an important field inside Supramolecular Chemistry which has been considered as a new form of synthesis, named Supramolecular Synthesis.2It is known that important properties in molecular solids are closely related with the way that molecules are aggregated in the condensed phase. Consequently, the ability to control the molecular association in the crystal packing could offer control over specific properties and potential applications. Because of that, the main goal of Crystal Engineering is the rational design and synthesis of functional materials using the nature of the intermolecular forces as a toolkit. Our strategy is the systematic study of non-covalent forces in homologous series.3In this work our interest is focused on the study of crystal packing of two homologous ligands N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (1) and N,N'-dimethyl-N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (2) and their Ag(I) coordination complexes. The compound 1 consists of two isoquinoline rings and one ethylene bridge linked by amide functional groups. Compound 2 is the result of the N-methylation of 1. The main difference in the molecular structures is that while 1 present a gauche conformation in the 1,2-ethanediamine bridge (600) 2 present a staggered conformation (1800). Curiously, in spite of this fact, the Ag(I) complexes in both cases present a small torsion angle of 4501-Ag(I) and 6502-Ag(I). These orientations allow the torsion of the isoquinoline moiety and the formation of homonuclear 0D coordination complexes, over the 1D coordination polymer expected. The main intermolecular interaction in 1 is the amide-to-amide hydrogen bond that is replaced by a weak CH··O interaction in 2 On the other hand, both Ag(I) complexes use the nitrate counteranion to build a chain using NH··O(nitrate) in 1 and CH(quinoline)··O(nitrate) in 2.Acknowledgment: Grant DIUC 212.023.049-1.0

Three-dimensional Nanorobotic Manipulations of Carbon Nanotubes

2002 ◽  
Vol 14 (3) ◽  
pp. 245-252 ◽  
Author(s):  
Lixin Dong ◽  
◽  
Fumihito Arai ◽  
Toshio Fukuda ◽  
◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Flexural Rigidity ◽  
Three Dimensional ◽  
Building Blocks ◽  
Intermolecular Forces ◽  
Multiwalled Carbon ◽  
Atomic Force ◽  
Manipulation System ◽  
Afm Cantilever ◽  
End Effectors

A nanorobotic manipulation system with 10 degreesof-freedom (DOFs) is presented and applied in 3-D manipulation of carbon nanotubes (CNTs) by controlling intermolecular forces. Manipulators are actuated with PicomotorsTM (New Focus Inc.) for coarse motions and PZTs for fine ones, and operated inside a scanning electronic microscope (SEM). Resolutions of manipulators are better than 30nm (linear) and 2mrad (rotary) for coarse motions, and within nanoorder for fine ones. Atomic force microscope (AFM) cantilevers are used as end-effectors, and van der Waals forces between them and objects are controlled by applying dielectrophoresis. Individual multiwalled carbon nanotubes (MWNTs) have been picked up on an AFM cantilever, placed between two cantilevers, and bent between a cantilever and sample substrate. As basic building blocks for more complex nanostructures and devices, CNT-junctions are constructed. A cross-junction was constructed with two MWNTs (∼ø40nm × 6μm and ∼ø50nm ö 7μm), and a T-junction was made of two MWNTs (∼ø40nm × 3μm and ∼ø50nm × 2μm). A kink junction is formed by bending an MWNT (∼ø40nm × 6μm) over its elastic limit for 20 times. Force measurements are performed and the flexural rigidity and Young's Modulus of an ∼ø30nm ∼7μm MWNT are estimated in situ to be 8.641 × 10-20Nm2 and 2.17TPa. Such manipulations are essential for both the property characterization of CNTs and the fabrication of functional nanosystems.

Parameterization of the close packing of molecules in the unit cell

2004 ◽  
Vol 60 (6) ◽  
pp. 725-733 ◽  
Author(s):  
Elna Pidcock ◽  
W. D. Sam Motherwell
Keyword(s):  
Molecular Orientation ◽  
Crystal Packing ◽  
Building Blocks ◽  
Close Packing ◽  
Unit Cell ◽  
Box Model ◽  
Molecular Building Blocks ◽  
Molecular Dimension ◽  
Cell Dimensions ◽  
Unit Cells

The box model of crystal packing describes unit cells in terms of a limited number of arrangements, or packing patterns, of molecular building blocks. Cell dimensions have been shown to relate to molecular dimensions in a systematic way. The distributions of pattern coefficients (cell length/molecular dimension) for thousands of structures belonging to P21/c, P\bar 1, P212121, P21 and C2/c are presented and are shown to be entirely consistent with the box model of crystal packing. Contributions to the form of the histograms from molecular orientation and molecular overlap are discussed. Gaussian fitting of the histograms has led to the parameterization of close packing within the unit cell and it is shown that molecular crystal structures are very similar to one another at a fundamental level.

scholarly journals A Strong Link Between Organic Chemistry and Chemical Crystallography Started a Century Ago

2019 ◽  
Vol 92 (2) ◽  
pp. 315-321
Author(s):  
Biserka Kojić-Prodić ◽  
Krešimir Molčanov
Keyword(s):  
Organic Chemistry ◽  
Crystal Engineering ◽  
Materials Science ◽  
Structural Data ◽  
Intermolecular Forces ◽  
Molecular Structures ◽  
X Rays ◽  
Molecular Architecture ◽  
X Ray ◽  
Chemical Crystallography

The article sheds light on some historical crossings of organic chemistry and chemical crystallography. It connects past and present bringing into the focus Prof. Kata Mlinarić-Majerski’s research. An impact of structural chemistry on organic synthesis and reactivity is shown. X-ray structure analysis was established as a unique method to determine the composition and architecture of synthetic and natural organic molecules, already in the second decade of the last century; some of historical and scientific milestones are shown. Numerous controversies were solved, when intriguing molecular structures had been determined and the nature of chemical bond was clarified. An absolute structure (chirality) determination using an anomalous dispersion of X-rays was an important step forward, particularly in pharmaceutical industry. Structural data provided by X-ray crystallography, stored by Cambridge Structural Data Centre have been of great impact on many areas of science. They are closely related to intra- and intermolecular forces and structure/function correlations directing us to synthesis of compounds with designed properties. The developments of supramolecular chemistry, crystal engineering, materials science, and most of all of molecular machines have been assisted by chemical crystallography. The essay does not aim to review the complete scientific opus of Prof. K. Mlinarić-Majerski but it is focused on some of the highlights of her research. The interdisciplinary approach in her research is related to the use of X-ray structural analysis to define molecular architecture, conformational chirality, conformational isomerism, and get insight into reaction paths, interactions governing molecular assembling, and to recognise chemical properties of new compounds. In these researches the X-ray crystallographers were involved.

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