This article is dedicated to the memory of Dr. F. H. Allen and the 50th anniversary of the Cambridge Crystallographic Data Centre (CCDC); the world-renowned centre for deposition and control of ...crystallographic data including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. The mission exposed at the web site (http://www.ccdc.cam.ac.uk) is clearly stated: “The Cambridge Crystallographic Data Centre (CCDC) is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high quality information, software and services.” The Cambridge Structural Database (CSD), one among the first established electronic databases, nowadays is one of the most significant crystallographic databases in the world. In the International Year of Crystallography 2014, the CSD announced in December over 750,000 deposited structures. The use of the extensive and rapidly growing database needs support of sophisticated and efficient software for checking, searching, analysing, and visualising structural data. The seminal role of the CSD in researches related to crystallography, chemistry, materials science, solid state physics and chemistry, (bio)technology, life sciences, and pharmacology is widely known. The important issues of the CCDC are the accuracy of deposited data and development of software for checking the data. Therefore, the Crystallographic Information File (CIF) is introduced as the standard text file format for representing crystallographic information. Among the most important software for users is ConQuest, which enables searching all the CSD information fields, and the web implementation WebCSD software. Mercury is available for visualisation of crystal structures and crystal morphology including intra- and intermolecular interactions with graph-set notations of hydrogen bonds, and analysis of geometrical parameters. The CCDC gives even more options to the users developing sophisticated software such as GOLD, IsoStar and SuperStar, DASH, and extensive knowledge electronic libraries such as Mogul and Relibase. The CCDC released the new facility – Mercury’s Solid Form module. Such demanding projects require a highly competent team of experts with a scientific approach based on the long tradition in crystallography, modelling and informatics. The Cambridge Structural Database and diversified software and searching engines are useful tools in research and teaching. The use of electronic media and computer graphics makes “data mining” very efficient and useful, but also aesthetically appealing due to the molecular architecture. One can expect even more advanced approaches using cloud computing and ‘Big Data’ management; merging data from related databases will enable to recognize hidden molecular and crystal properties and information that could bring new important knowledge. Since 1985, the CSD has been available to users in Croatia. The use of the CSD in Croatia is illustrated by a few examples performed and published by the presenting authors and colleagues.
Stogodišnjica rendgenske kristalografije Kojić-Prodić, B; Molčanov, K
Kemija u industriji; časopis kemičara i tehnologa Jugoslavije,
07/2013, Volume:
62, Issue:
7-8
Journal Article
Peer reviewed
Open access
The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them.
W. L. Bragg
Stogodišnjica rendgenske kristalografije veže se uz prvi pokus difrakcije ...rendgenskih zraka koji su s kristalom modre galice izveli njemački fizičari W. Friedrich i P. Knipping prema ideji i teorijskom predviđanju M. von Lauea 1912. Matematička formulacija pojave, kao i temeljne postavke znanosti o građi kristala - kristalografije, u to vrijeme vezane uz mineralogiju, pogodovale su razvitku metode za određivanje geometrijske strukture tvari na atomnoj razini. Već su 1913. otac i sin Bragg započeli stvarati temelje za primjenu rendgenske difrakcije u određivanju kristalnih struktura jednostavnih molekula. Povijesni primjeri određivanja struktura od kuhinjske soli do složenih, za život bitnih, (makro)molekula, kao globularnih proteina hemoglobina i mioglobina, DNA, vitamina B12, te novog otkrića ribozima, ilustriraju razvojni put rendgenske strukturne analize. Otkriće trodimenzijskih struktura tih molekula metodom rendgenske difrakcije pokrenulo je nove znanstvene discipline poput molekularne biofizike, molekularne genetike, strukturne molekularne biologije, bioanorganske kao i organometalne kemije i niza drugih disciplina. Otkriće i razvoj rendgenske kristalografije revolucioniralo je naše spoznaje u svim područjima prirodnih znanosti: fizici, kemiji, biologiji, geološkim znanostima i znanosti o materijalima. Znanstvena javnost prepoznala je ta temeljna znanstvena postignuća (uključujući i otkriće X-zraka) dodijelivši Nobelove nagrade tridesetdevetorici znanstvenika i dvjema znanstvenicama. Eksplozivan razvoj znanosti i tehnologije tijekom 20. i 21. stoljeća temelji se na spoznajama o detaljnoj trodimenzijskoj građi molekula i njome predviđenih i objašnjenih fizičkih, kemijskih, bioloških i farmakoloških svojstava molekula. Jedan od svježih primjera, koji je bilo teško predvidjeti, uspješna je i nedovršena priča o grafenima, koja puni naslovnice vodećih znanstvenih časopisa kao što su Science, Nature, Nature Materials, Nature Nanotechnology, Nature Chemistry i Nature Physics. Suvremena kristalografska istraživanja pokrivaju široko područje znanosti i veoma su inovativna, te nije uputno predviđati u kojim će se smjerovima nastaviti razvijati.
Bis(LeuOH) (1 a), bis(ValOH) (2 a) and bis(PhgOH) (5 a) (Phg denotes (R)‐phenylglycine) oxalyl amides are efficient low molecular weight organic gelators of various organic solvents and their ...mixtures as well as water, water/DMSO, and water/DMF mixtures. The organisational motifs in aqueous gels are dominated primarily by lipophilic interactions while those in organic solvents are formed by intermolecular hydrogen bonding. Most of the gels are thermoreversible and stable for many months. However, 2 a forms unstable gels with organic solvents which upon ageing transform into variety of crystalline shapes. For some 1 a/alcohol gels, a linear correlation between alcohol dielectric constants (ε) and gel melting temperatures (Tg) was found. The 1H NMR and FTIR spectroscopic investigations of selected gels reveal the existence of temperature dependent network assembly/dissolution equilibrium. In the 1H NMR spectra of gels only the molecules dissolved in entrapped solvent could be observed. By using an internal standard, the concentration of dissolved gelator molecules could be determined. In FTIR spectra, the bands corresponding to network assembled and dissolved gelator molecules are simultaneously present. This enabled determination of the Kgel values by using both methods. From the plots of ln Kgel versus 1/T, the ΔHgel values of selected gels have been determined (−ΔHgel in 10–36 kJ mol−1 range) and found to be strongly solvent dependent. The ΔHgel values determined by 1H NMR and FTIR spectroscopy are in excellent agreement. Crystal structures of 2 a and rac‐5 a show the presence of organisational motifs and intermolecular interactions in agreement with those in gel fibres elucidated by spectroscopic methods.
Bis(LeuOH) (1 a), bis(ValOH) (2 a) i bis(PhgOH) (5 a) (Phg označava (R)‐fenilglicin) oksal amidi su efikasni gelatori male molekulske mase koji geliraju različita organska otapala, njihove smjese kao i vodu te smjese voda/DMSO i voda/DMF. Njihovo uređenje u hidro‐ gelskim mrežama prvenstveno određuju međumolekulske lipofilne interakcije dok je uređenje u organskim gelovima određeno tvorbom međumolekulskih vodikovih veza. Gelovi su većinom termoreverzibilni i stabilni kroz više mjeseci. Međutim, 2 a tvori nestabilne gelove s organskim otapalima koji starenjem prelaze u različite kristalne oblike. Za gelove nekih nižih alkohola s 1 a utvrđeno je da postoji linearna međuovisnost dielektrične konstante (ε) alkohola i temperaturne točke taljenja gela (Tg). Proučavanje gelova 1H NMR i FTIR spektroskopijom otkriva temperaturno ovisnu ravnotežu između gelske mreže i otopine gelatora u gelskoj tekućini. NMR spektar gela odgovara samo molekulama gelatora otopljenim u gelskoj tekućini; upotrebom unutarnjeg standarda može se odrediti njegova koncentracija. U FTIR spektrima gela prisutne su istovremeno vrpce gelatora organiziranog u gelskoj mreži i vrpce gelatora otopljenog u gelskoj tekućini. Ovo omogućava određivanje Kgel NMR i FTIR metodama. Iz linearne ovisnosti ln Kgel o 1/T određene su ΔHgel vrijednosti nekih gelova (−ΔHgel u rasponu od 10–36 kJ mol−1) koje značajno ovise o otapalu. Vrijednosti za ΔHgel dobivene NMR i FTIR metodama se potpuno slažu. Kristalne strukture 2 a i rac‐5 a određene rentgenskom strukturnom analizom pokazuju motive uređenja i intermolekulske interakcije slične onima u gelskim nitima koje su utvrđene spektroskopskim metodama.
Stable gels can be obtained from water and organic solvents with bis(amino acid) oxalyl amides. In aqueous systems lipophilic interactions and lateral hydrogen bonding dominate their self‐organisation into gel fibres as depicted here. In organic‐solvent gels intermolecular hydrogen bonding governs the self‐organisation. Gels were studied by 1H NMR, FTIR, TEM, SEM and single crystal X‐ray analysis.
Prikaz je posvećen uspomeni na dr. F. H. Allena i obilježavanju 50-godišnjice The Cambridge Crystallographic Data Centre (CCDC), svjetski poznatog centra, koji pohranjuje i provjerava kristalografske ...podatke, uključujući koordinate atoma koje određuju trodimenzijsku strukturu organskih molekula i metalnih kompleksa s organskim ligandima. Misija institucije istaknuta na njezinim web-stranicama je jasna: “Centar za kristalografske podatke u Cambridgeu (CCDC) potpomaže napredak kemije i kristalografije za sveopću dobrobit pružajući kvalitetne informacije, softver i podršku.” Baza strukturnih podataka u Cambridgeu (CSD), jedna je od prvih elektroničkih i najznačajnijih baza u svijetu. U Međunarodnoj godini kristalografije 2014., u prosincu, Centar je obznanio 750.000. pohranjenu strukturu. Upotreba opsežne baze podataka, koja se brzo povećava, zahtijeva podršku u dobro osmišljenom i učinkovitom softveru za provjeru, pretraživanje, analizu i vizualizaciju strukturnih podataka. Prestižna je uloga te baze u istraživanjima povezanim s kristalografijom, kemijom, znanošću o materijalima, fizikom i kemijom krutog stanja, (bio)tehnologijom, znanošću o životu, te farmakologijom, posebno u oblikovanju lijekova. CCDC posvećuje posebnu pažnju točnosti pohranjenih podataka i razvoju softvera za tu namjenu (CIF). Jedan od najvažnijih softvera za korisnike je ConQuest, koji omogućava pretraživanje svih informacija u bazi CSD-a, te njegovo postavljanje na mreži u interaktivnom obliku pod imenom WebCSD. Za vizualizaciju kristalnih struktura i morfologije kristala, uključujući analizu intramolekularnih i intermolekularnih interakcija te topološke oznake vodikovih veza, kao i svih geometrijskih podataka, na raspolaganju je Mercury. Centar (CCDC) pruža još veće mogućnosti korisnicima razvijajući kompleksne softvere poput GOLD, IsoStar i SuperStar te DASH, kao i opsežne elektroničke biblioteke poput Mogula i Relibase. CCDC je pružio novu mogućnost korištenjem Mercuryjeva modula Solid Form. Takvi složeni i zahtjevni projekti mogu se ostvarivati samo s veoma kvalitetnim timom stručnjaka sa znanstvenim pristupom, temeljeći se na dugogodišnjoj tradiciji u kristalografiji, modeliranju i informatici. Sama baza, raznolik softver i alati za pretraživanje afirmirali su se u istraživanju, nastavi i stručnoj izobrazbi. Primjena elektroničkih medija i računalne grafike čini “data mining” učinkovitima i korisnima, ali i estetski privlačnim zbog molekularne arhitekture. Možemo očekivati još više unapređenja zbog uporabe “računarstva u oblacima” (cloud computing) i rukovanja opsežnim podacima (Big Data); umrežavanje podataka iz srodnih baza pomoći će da prepoznamo sakrivena svojstva molekula i kristala i informacija koje mogu otkriti nove važne spoznaje. Od 1985. Strukturna baza podataka u Cambridgeu (CSD) dostupna je korisnicima u Hrvatskoj. Upotreba te baze u Hrvatskoj ilustrirana je s nekoliko primjera autora ovog prikaza i nekih korisnika.
Prikaz o kiralnosti posvećen je 100. godišnjici rođenja Nobelovca Vladimira Preloga i predstojećoj 160. godišnjici Pasteurovog otkrića kiralnosti soli vinske kiseline. Pojavu kiralnosti u prirodi ...prepoznali su umjetnici i graditelji koristeći je u svojim djelima što je ilustrirano primjerima u uvodu. Napretkom znanosti kroz povijest do danas šire se spoznaje o kiralnosti i gotovo je nemoguće obuhvatiti sve njezine aspekte i primjene. Opisana su ključna povijesna otkrića vezana uz pojavu zakretanja ravnine polariziranog svjetla kao posljedicu kiralnosti te otkrića Pasteura i lorda Kelvina. Kiralnost se susreće u fizici elementarnih čestica kao i u svim područjima kemije: analitičkoj i organskoj kemiji, kemiji prirodnih spojeva, medicinskoj i farmaceutskoj kemiji, biokemiji i biotehnologiji, kao i molekularnoj biologiji. Kratko je opisano širenje spoznaja o kiralnosti i fizikalne osnove molekularne kiralnosti. Sustavno su definirane: geometrijska, topološka i konformacijska
kiralnost. Povezanost simetrije i kiralnosti dolazi do izražaja i u kristalografiji. Kako je rendgenska strukturna analiza metoda kojom se jednoznačno određuje molekularna arhitektura, neosporno je da se pri tome utvrđuje i apsolutna konfiguracija molekula Bijvoetovim pristupom. Sažeto su opisane dvije metode za određivanje apsolutne konfiguracije: metoda rendgenske difrakcije i kružnog dikroizma. U skladu s obilježavanjem značajnog jubileja, prikaz je orijentiran na ulogu kiralnosti u (stereo)kemiji. To je u skladu s E. L. Elielovim pristupom koji stereokemiju smatra načinom
gledanja na kemiju, a ne granom kemije. Taj pristup omogućava sagledavanje različitih aspekata kiralnosti i usuglašavanje postojećih nepotpunih definicija o kiralnosti molekula, što zacijelo otvara nove primjene. Budućnost nam nudi da više saznamo o kiralnosti u službi komunikacije molekula koje upravljaju našim životnim procesima. U tijeku su eksperimenti priprave raznorodnih dinamičkih kiralnih supramolekula iz akiralnih molekula i predstoji istražiti kako se to korisno može upotrijebiti. Istraživanje izotopne kiralnosti kvantno-kemijskim metodama omogućit će razumijevanje odstupanja od zakona pariteta i rasvijetliti fizikalne osnovice molekularne kiralnosti.
The 100th Anniversary of X-Ray Crystallography Kojić-Prodić, B.; Molčanov, K.
Kemija u industriji; časopis kemičara i tehnologa Jugoslavije,
07/2013, Volume:
62, Issue:
7-08
Journal Article
Peer reviewed
Open access
The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them.W. L. BraggThe 100th anniversary of X-ray crystallography dates back to the first ...X-ray diffraction experiment on a crystal of copper sulphate pentahydrate. Max von Laue designed the theoretical background of the experiment, which was performed by German physicists W. Friedrich and P. Knipping in 1912. At that time, the mathematical formulation of the phenomenon and the fundamental concepts of crystallography were subjects of mineralogy. Altogether, they facilitated the development of methods for determination of the structure of matter at the atomic level. In 1913, father and son Bragg started to develop X-ray structure analysis for determination of crystal structures of simple molecules. Historic examples of structure determination starting from rock salt to complex, biologically important (macro)molecules, such as globular proteins haemoglobin and myoglobin, DNA, vitamin B12 and the recent discovery of ribozyme, illustrate the development of X-ray structural analysis. The determination of 3D structures of these molecules by X-ray diffraction had opened new areas of scientific research, such as molecular biophysics, molecular genetics, structural molecular biology, bioinorganic chemistry, organometallic chemistry, and many others. The discovery and development of X-ray crystallography revolutionised our understanding of natural sciences – physics, chemistry, biology, and also science of materials. The scientific community recognised these fundamental achievements (including the discovery of X-rays) by awarding twenty-eight Nobel prizes to thirty-nine men and two women. The explosive growth of science and technology in the 20th and 21st centuries had been founded on the detailed knowledge of the three-dimensional structure of molecules, which was the basis for explaining and predicting the physical, chemical, biological and pharmacological properties of molecules. A most recent and striking example is the still unfinished story of graphenes, occupying the front pages of leading scientific journals, such as Science, Nature, Nature Materials, Nature Nanotechnology, Nature Chemistry and Nature Physics. Contemporary crystallographic research covers numerous scientific domains, and it is a very innovative area of science. Who would dare to be a prophet and foresee future findings?
Four new chiral bis(amino alcohol)oxalamides (1–4: amino alcohol=leucinol, valinol, phenylglycinol, and phenylalaninol, respectively) have been prepared as low‐molecular‐weight organic gelators. ...Their gelation properties towards various organic solvents and mixtures were determined and these were then compared to related bis(amino acid) oxalamide gelators. Spectroscopic (FTIR, 1H NMR) and X‐ray diffraction studies revealed that the primary organization motif of (S,S)‐1 and racemate 1 (rac‐1) in lipophilic solvents involved the formation of inverse bilayers. The X‐ray crystal structure of (S,S)‐1 also shows this type of bilayer organization. The crystal structure of rac‐2 reveals meso bilayers of hydrogen‐bonded aggregates. Within the bilayers formed, the gelator molecules are connected by cooperative hydrogen bonding between oxalamide units and OH groups, while the interbilayer interactions are realized through lipophilic interactions between the iBu groups of leucinol. Oxalamide meso‐1 lacks any gelation ability and crystallizes in monolayers. In dichloromethane rac‐1 forms an unstable gel; this is prone to crystallization as a result of the formation of symmetrical meso bilayers. In contrast, in aromatic solvents rac‐1 forms stable gels; this indicates that enantiomeric bilayers are formed. Oxalamide rac‐1 is capable of gelling a volume of toluene three times larger than (S,S)‐1. A tranmission electron microscopy investigation of rac‐1 and (S,S)‐1 toluene gels reveals the presence of thinner fibers in the former gel, and, hence, a more compact network that is capable of immobilizing a larger volume of the solvent. The self‐assembly of these types of gelator molecules into bilayers and subsequent formation of fibrous aggregates can be explained by considering the strength and direction of aggregate forces (supramolecular vectors) in three‐dimensional space.
To gel or not to gel: Chiral bis(amino alcohol) oxalamides 1–4 (amino alcohol=leucinol, valinol, phenylglycinol, and phenylalaninol, respectively, shown here schematically) represent new and efficient low‐molecular‐weight organic gelators of lipophilic organic solvents. Spectroscopic and crystallographic investigations, which took into consideration the strength and direction of supramolecular vectors in three‐dimensional space, indicated that these gelators self‐assemble into bilayers and fibrous aggregates. Gelator stereochemistry (racemate, pure enatiomer, meso stereomer) and its influence on gelation properties are discussed.
A method for the preparation of new solvated clusters of the composition M6Br12(H2O)6HgBr2X2 · 12H2O (MNb, Ta; XCl, Br, I) is given. The cubic crystals of Nb6Br12(H2O)6HgBr4 · 12H2O 1 and ...Ta6Br12(H2O)6HgBr4 · 12H2O 2 were characterized by the X‐ray structure analysis: 1: cubic, space group Fd3m, a = 21.0072(6) Å, Z = 8, R = 0.051 (Rw = 0.066); 2: cubic, space group Fd3m, a = 20.9698(1) Å, Z = 8, R = 0.038 (Rw = 0.050). 1 and 2 contain octahedral cluster cation M6Br12(H2O)62+ and tetrahedrally arranged HgBr42− anion. The MM bond distances are 2.949(1) Å for 1 and 2.9000(8) Å for 2. The HgBr bond distances in HgBr42− anion are 2.614(2) Å in 1 and 2.622(2) Å in 2. The crystal packing patterns of the isostructural clusters 1 and 2 involve the three‐dimensional hydrogen bond network; the crystalline water molecules act as donors of hydrogen to the bromine atoms of the cluster and HgBr42− units, whereas the coordinated water molecules form hydrogen bonds to the crystalline water molecules. Nb6Br12(H2O)6HgBr4 · 12H2O is diamagnetic and semiconducting with the activation energy, Ea = 0.20 eV.
Reaktionen von Hexanuclearen Niob‐ und Tantal‐Halogenid‐Clustern mit Quecksilber(II)‐Halogeniden. I. Synthese und Struktur der halbleitenden Verbindungen M6Br12(H2O)6HgBr4 · 12H2O, MNb, Ta
Die Darstellung der neuen Clusterverbindungen M6Br12(H2O)6HgBr2X2 · 12H2O (MNb, Ta; XCl, Br, I) wird beschrieben. Für Nb6Br12(H2O)6HgBr4 · 12H2O 1 und Ta6Br12(H2O)6HgBr4 · 12H2O 2 wurden die Strukturen röntgenographisch aus Einkristallen bestimmt: 1: kubisch, Raumgruppe Fd3m, a = 21.0072(6) Å, Z = 8, R = 0.051 (Rw = 0.066); 2: kubisch, Raumgruppe Fd3m, a = 20.9698(1) Å, Z = 8, R = 0.038 (Rw = 0.050). 1 und 2 enthalten ein oktaedrisches M6Br12(H2O)62+‐Cluster‐Kation und ein tetraedrisches HgBr42−‐Anion. Die MM‐Abstände betragen 2.949(1) Å für 1 und 2.9000(8) Å für 2 und die HgBr‐Abstände 2.614(2) Å in 1 und 2.622(2) Å in 2. Die Kristallstrukturen der isotypen Clusterverbindungen 1 und 2 können mit einem dreidimensionalen Netz von H‐Brücken beschrieben werden; die Kristallwassermoleküle sind Donatoren von Wasserstoffatomen zu den Bromatomen der Cluster‐Kationen und zu HgBr42−‐Anionen. Die koordinierten Wassermoleküle bilden Wasserstoffbrücken zu den Kristall‐wassermolekülen. Nb6Br12(H2O)6HgBr4 · 12H2O ist diamagnetisch und halbleitend mit der Aktivierungsenergie, Ea = 0.20 eV.
Almost hundred years old concepts on hydrogen bonding are brought into light to be compared to the contemporary views and theories. The first findings were based on qualitative grounds and relied ...upon observations of simple experiments and very much on human imagination. It is a challenge to contrast the old and new views and to see if they could be verified or revised. Over the last decades there has been tremendous development of methods for structure elucidation and many hydrogen bonded molecular structures were determined and deposited in structural data bases. The structural aspect of hydrogen bond in the solid state is well defined. However, the knowledge of hydrogen bonded structures in the liquid state is still limited. Studies on hydrogen bond dynamics, which are in progress, with new experimental methods will help to better understand processes in solutions. In many systems the functioning of hydrogen bonding at atomic level has been still an enigma. In biological reactions the proton transfer is a key issue of acid-base enzyme catalysis and ribozymic function, transport reactions such as "water wires" functioning through the membrane protein channels and photosynthetic reaction centres. The paramount example for the unique role of the proton in specificity and rates is the storage life's genetic information: hydrogen bonds define the complementarities of G with C and A with T whereas the hydrogen transfer controls the genetic mutations. Ultra-fast time-resolved spectroscopies of hydrogen bonds and proton-transfer processes accompanied by very sophisticated theoretical frameworks such as multidimensional quantum dynamics and combined quantum mechanics/molecular mechanics are offering new insights into functioning of hydrogen bond.
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