Stacking (chemistry)

Image:Molybdenite-3D-balls.png

Metal dichalcogenides have the formula ME₂, where M = a transition metal and E = S, Se, Te.Wells, A.F. (1984) Structural Inorganic Chemistry, Oxford: Clarendon Press. {{ISBN|0-19-855370-6}}. In terms of their electronic structures, these compounds are usually viewed as derivatives of M⁴⁺. They adopt stacked structures, which is relevant to their ability to undergo intercalation, e.g. by lithium, and their lubricating properties. The corresponding diselenides and even ditellurides are known, e.g., TiSe₂, MoSe₂, and WSe₂.

{{Anchor|TTF-TCNQ}}

File:SegStackEdgeOnHMTFCQ.jpg/TCNQ charge transfer salt, highlighting the segregated stacking.{{cite journal|author1=D. Chasseau|author2=G. Comberton|author3=J. Gaultier|author4=C. Hauw|journal=Acta Crystallographica Section B|title=Réexamen de la structure du complexe hexaméthylène-tétrathiafulvalène-tétracyanoquinodiméthane|year=1978| volume=34|issue=2|page=689|doi=10.1107/S0567740878003830|doi-access=|bibcode=1978AcCrB..34..689C }}]]

A combination of tetracyanoquinodimethane (TCNQ) and tetrathiafulvalene (TTF) forms a strong charge-transfer complex referred to as TTF-TCNQ.{{cite journal |author1=P. W. Anderson |author2=P. A. Lee |author3=M. Saitoh | journal = Solid State Communications | volume = 13 | year = 1973 | pages = 595–598 | doi = 10.1016/S0038-1098(73)80020-1 | title = Remarks on giant conductivity in TTF-TCNQ |issue=5 | bibcode=1973SSCom..13..595A}} The solid shows almost metallic electrical conductance. In a TTF-TCNQ crystal, TTF and TCNQ molecules are arranged independently in separate parallel-aligned stacks, and an electron transfer occurs from donor (TTF) to acceptor (TCNQ) stacks.{{cite journal |doi=10.1021/acs.jchemed.5b00340|title=Opposites Attract: Organic Charge Transfer Salts |year=2015 |last1=Van De Wouw |first1=Heidi L. |last2=Chamorro |first2=Juan |last3=Quintero |first3=Michael |last4=Klausen |first4=Rebekka S. |journal=Journal of Chemical Education |volume=92 |issue=12 |pages=2134–2139 |bibcode=2015JChEd..92.2134V }}

File:Graphite-layers-side-3D-balls.png

Graphite consists of stacked sheets of covalently bonded carbon.{{cite book |last1=Delhaes |first1=Pierre |chapter=Polymorphism of carbon |editor-last1=Delhaes |editor-first1=Pierre |title=Graphite and precursors |date=2000 |publisher=Gordon & Breach |isbn=9789056992286|pages=1–24}}{{cite book |last1=Pierson |first1=Hugh O. |title=Handbook of carbon, graphite, diamond, and fullerenes : properties, processing, and applications |date=2012 |publisher=Noyes Publications |isbn=9780815517399 |pages=40–41}} The individual layers are called graphene. In each layer, each carbon atom is bonded to three other atoms forming a continuous layer of sp² bonded carbon hexagons, like a honeycomb lattice with a bond length of 0.142 nm, and the distance between planes is 0.335 nm.{{cite book |title= Graphite and Precursors |author= Delhaes, P. |publisher= CRC Press |year= 2001 |url= https://books.google.com/books?id=7p2pgNOWPbEC&pg=PA146 |isbn= 978-90-5699-228-6}} Bonding between layers is relatively weak van der Waals bonds, which allows the graphene-like layers to be easily separated and to glide past each other.{{cite journal |last1=Chung |first1=D. D. L. |title=Review Graphite |journal=Journal of Materials Science |date=2002 |volume=37 |issue=8 |pages=1475–1489 |doi=10.1023/A:1014915307738 |s2cid=189839788 }} Electrical conductivity perpendicular to the layers is consequently about 1000 times lower.{{Cite book |last=Pierson |first=Hugh O. |url=https://www.worldcat.org/oclc/49708274 |title=Handbook of carbon, graphite, diamond, and fullerenes : properties, processing, and applications |date=1993 |publisher=Noyes Publications |isbn=0-8155-1739-4 |location=Park Ridge, N.J. |oclc=49708274}}

Linear chain compounds are materials composed of stacked arrays of metal-metal bonded molecules or ions. Such materials exhibit anisotropic electrical conductivity.{{cite journal |author1=Bera, J. K. |author2=Dunbar, K. R. |journal= Angew. Chem. Int. Ed. |year= 2002 |volume= 41 |issue= 23 |pages= 4453–4457 |title= Chain Compounds Based on Transition Metal Backbones: New Life for an Old Topic |doi= 10.1002/1521-3773(20021202)41:23<4453::AID-ANIE4453>3.0.CO;2-1 |pmid=12458505}} One example is {{chem2|Rh(acac)(CO)2}} (acac = acetylacetonate, which stack with {{chem2|Rh***Rh}} distances of about 326 pm.{{cite journal|title=Refinement of the crystal structure of acetylacetonatodicarbonylrhodium(I)|last1=Huq|first1=Fazlul|last2=Skapski|first2=Andrzej C.|journal=J. Cryst. Mol. Struct.|year=1974|volume=4|issue=6|pages=411–418|doi=10.1007/BF01220097|s2cid=96977904}} Classic examples include Krogmann's salt and Magnus's green salt.

File:ACABRH02.png ({{chem2|Rh(acac)(CO)2}}) showing the "stacking" of the individual planar units through {{chem2|Rh***Rh}} interactions.|140px]]

{{main|Pi-stacking}}

π–π stacking is a noncovalent interaction between the pi bonds of aromatic rings.{{March6th|page=114}} Such "sandwich interactions" are however generally electrostatically repulsive. What is more commonly observed are either a staggered stacking (parallel displaced) or pi-teeing (perpendicular T-shaped) interaction both of which are electrostatic attractive.{{cite book | vauthors = Lewis M, Bagwill C, Hardebeck L, Wireduaah S |chapter=Modern Computational Approaches to Understanding Interactions of Aromatics | veditors = Johnson DW, Hof F |title=Aromatic Interactions: Frontiers in Knowledge and Application |date=2016 |publisher=Royal Society of Chemistry |location=England |isbn=978-1-78262-662-6 |pages=1–17 | chapter-url = https://books.google.com/books?id=CmwoDwAAQBAJ&pg=PA1 }} For example, the most commonly observed interactions between aromatic rings of amino acid residues in proteins is a staggered stacked followed by a perpendicular orientation. Sandwiched orientations are relatively rare.{{cite journal | vauthors = McGaughey GB, Gagné M, Rappé AK | title = pi-Stacking interactions. Alive and well in proteins | journal = The Journal of Biological Chemistry | volume = 273 | issue = 25 | pages = 15458–63 | date = June 1998 | pmid = 9624131 | doi = 10.1074/jbc.273.25.15458 | doi-access = free }} Pi stacking is repulsive as it places carbon atoms with partial negative charges from one ring on top of other partial negatively charged carbon atoms from the second ring and hydrogen atoms with partial positive charges on top of other hydrogen atoms that likewise carry partial positive charges.{{Cite journal| vauthors = Martinez CR, Iverson BL |date=2012|title=Rethinking the term "pi-stacking"|url=http://xlink.rsc.org/?DOI=c2sc20045g|journal=Chemical Science|language=en|volume=3|issue=7|pages=2191|doi=10.1039/c2sc20045g|issn=2041-6520|hdl=2152/41033|s2cid=95789541 |hdl-access=free}}

File:24 fig. 2.png

π–π interactions play a role in supramolecular chemistry, specifically the synthesis of catenane. The major challenge for the synthesis of catenane is to interlock molecules in a controlled fashion. Attractive π–π interactions exist between electron-rich benzene derivatives and electron-poor pyridinium rings.{{cite journal | vauthors = Ashton PR, Goodnow TT, Kaifer AE, Reddington MV, Slawin AM, Spencer N, Stoddart JF, Vicent C, Williams DJ |display-authors=6 |title=A [2] Catenane Made to Order |journal=J. Angew. Chem. Int. Ed. |year=1989 |volume=28 |issue=10 |pages=1396–1399 |doi=10.1002/anie.198913961 }} [2]Catanene was synthesized by treating bis(pyridinium) (A), bisparaphenylene-34-crown-10 (B), and 1, 4-bis(bromomethyl)benzene (C) (Fig. 2). The π–π interaction between A and B directed the formation of an interlocked template intermediate that was further cyclized by substitution reaction with compound C to generate the [2]catenane product.

• Noncovalent interaction
• Dispersion (chemistry)
• Cation–pi interaction
• Intercalation (biochemistry)
• Intercalation (chemistry)

{{reflist}}

• {{cite journal | vauthors = Luo R, Gilson HS, Potter MJ, Gilson MK | title = The physical basis of nucleic acid base stacking in water | journal = Biophysical Journal | volume = 80 | issue = 1 | pages = 140–148 | date = January 2001 | pmid = 11159389 | pmc = 1301220 | doi = 10.1016/S0006-3495(01)76001-8 | bibcode = 2001BpJ....80..140L }}
• [http://www.scs.illinois.edu/denmark/wp-content/uploads/gp/2011/gm-2011-1_18.pdf Larry Wolf (2011): π-π (π-Stacking) interactions: origin and modulation]

{{Chemical bonds}}

Category:Organic chemistry

Category:Chemical bonding

Category:Supramolecular chemistry