40-Godišnjica institucije Cambridge Crystallographic Data Centre posvećene pohranjivanju podataka o molekularnim i kristalnim strukturama -

The article is dedicated to 40th anniversary of The Cambridge Crystallographic Data Centre (CCDC), the world-known centre (http://www.ccdc.cam.ac.uk) responsible 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. Cambride Structural Database (CSD), one among the first established electronic databases, nowadays is the most significant crystallographic database in the world. CSD has about 400,000 deposited structures. The use of the extensive database, which is growing rapidly, needs support of efficient and sophisticated software for searching, analysing and visualising structural data. The seminal role of CSD in the research related to crystallography, chemistry, material sciences, solid state physics and chemistry, life sciences, pharmacology, and in particular in drug design, has been documented in more than 1300 scientific papers. The important issues of CCDC are the accuracy of deposited data and development of software that enables a wide variety of applications. Such demanding project requires higly competent team of experts; thus the article brings into focus the scientific approach of the team based on the long tradition in crystallography, modelling and informatics. The article is not dedicated to 40th anniversary of the centre only, but it also reveals how Cambridge Structural Database can be used in the research and teaching. The use of electronic media and computer graphics makes data mining" very efficient and useful but also esthetically appealing due to the molecular architecture. At the Rudjer Bošković Institute, Zagreb, Croatia there is The National Affiliated Centre of Cambridge Crystallographic Data Centre responsible for communication and dissemination of CSD in Croatia, Slovenia and Macedonia. The use of CSD is illustrated by two examples performed and published by the presenting authors: a) the analysis of the less-common hydrogen bonds with the ester oxygen atom as a proton acceptor, and b) topological analysis of tubular assemblies of macrocyclic polythianes extensively described in the references 24 and 28

Identification and Characterization of Alkaline Uranyl(2 +) Phosphates

The spontaneous precipitation in the systems U02(N03)2- -MOH-HaP04--H20 and U02(N03)2-MNOa-H3P04- H20 (M = = Li, Na, K, Rb, Cs) is examined. The formation of alkaline- uranyl(2+) phosphates polyhydrates is detected: M[U02P04] · · n H20 (n = 4 for M = Li, n = 3 for M = Na, K, Rb and n = 2.5 for M =Cs). The X-ray powder patterns of these compounds are determined and compared with that of H30[U02P04] · 3 H20. A close structural relation within this series is observed. The size of the alkaline ionic species in the particular compound affects the content of crystalline water in the unit cell

Spontaneous Precipitation in the System Uranyl(2+ )nitrate Potassium Hydroxide - Phosphoric Acid - Water

The precipitation system U02(NOs)2-KOH-H3P04-H20 (at 298 K) aged for 1 day and for 30 days is examined ([U02(NOs)2] = = 1 · 10-a mol dm-3, [KOH] varied from 1 · 10-6 to 6 · 10-1 mol dm-3, [H3P04] from 2 · 10-4 to 6 · 10-1 mol dm-3 and 1.5 <pH< 11.5). The precipitation and phase boundaries are determined. The solid phases U02HP04 · 4 H20(s) and (U02)s(P04)2 · 8 H20 are stable at [KOH] < 1 · 10-3 mol dm-3, 1.5 <pH < 4.0. Uranates precipitate at pH > 9.5. The stability region of KU02P04 · 3 H20(s) is found at high concentrations of KOH and H3P04. X-ray diffraction pattern of this compound is given. According to the precipitation boundary after 30 days (equilibrium conditions) the solubility product of KU02P04 · 3 H20 is determined: log ([K+] · · [U022+] [P043-]) = -- 26.28 (at I =0 mol dm-3)

50-Godišnjica Cambridge Structural Database i 30-godišnjica uporabe u Hrvatskoj

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.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

40th Anniversary of The Cambridge Crystallographic Data Centre Dedicated to Deposition of Data Related to Crystal and Molecular Structures, "Cambridge Structural Database"

U 2005. obilježila se 40-godišnjica postojanja i rada svjetski poznatog centra Cambridge Crystallographic Data Centre (CCDC), čija je temeljna svrha prikupljanje, provjera i čuvanje kristalografskih podataka koji uz bibliografske podatke sadrže i koordinate atoma i iona koji određuju trodimenzionalnu strukturu molekula u kristalu. Cambridge Structural Database (CSD), jedna od prvih elektroničkih baza podataka, najveća je i najznačajnija baza kristalografskih podataka na svijetu s gotovo 400.000 pohranjenih struktura. Upotrebu opsežne baze podataka, koja se stalno povećava, nužno prati i razvoj učinkovitih računalnih programa za pretraživanje, analizu i obradu te vizualizaciju. Ključna uloga CSD-a u istraživanjima vezanim uz kristalografiju, kemiju, znanosti o materijalima, fiziku i kemiju čvrstog stanja, znanosti o životu, farmakologiju, posebice u dizajnu lijekova, dokumentirana je u opsežnoj znanstvenoj literaturi. Izuzetna pažnja posvećuje se točnosti pohranjenih podataka i razvoju programske podrške koja omogućuje široku lepezu primjene. Složen i zahtjevan projekt može ostvarivati samo kompetentan tim stručnjaka, a neki zanimljivi podaci ukazuju na strogo znanstven pristup i tradiciju. Namjera ovog prikaza nije samo obilježavanje jubileja već se želi ukazati na velik broj mogućnosti korištenja baze u istraživanjima i nastavi. Upotreba elektroničkih medija i računalne grafike čini "data mining" ne samo učinkovitim i korisnim, već vizuelno estetskim doživljajem, koji nam pruža arhitektura molekula. Na Institutu "Ruđer Bošković" već 20 godina uspješno djeluje nekad jugoslavenski, a sada hrvatski nacionalni centar za suradnju sa CCDC-om, koji je i danas odgovoran za akademske korisnike u Hrvatskoj, Sloveniji i Makedoniji omogućavajući im pristup bazi i pratećim računalnim programima. Upotreba baze u istraživanju prikazana je i vlastitim rezultatima na studiju esterskog kisika kao akceptora protona u nastajanju vodikove veze te topološke analize tubularnih ansambala makrocikličkih politiana.The article is dedicated to 40th anniversary of The Cambridge Crystallographic Data Centre (CCDC), the world-known centre (http://www.ccdc.cam.ac.uk) responsible 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. Cambride Structural Database (CSD), one among the first established electronic databases, nowadays is the most significant crystallographic database in the world. CSD has about 400,000 deposited structures. The use of the extensive database, which is growing rapidly, needs support of efficient and sophisticated software for searching, analysing and visualising structural data. The seminal role of CSD in the research related to crystallography, chemistry, material sciences, solid state physics and chemistry, life sciences, pharmacology, and in particular in drug design, has been documented in more than 1300 scientific papers. The important issues of CCDC are the accuracy of deposited data and development of software that enables a wide variety of applications. Such demanding project requires higly competent team of experts; thus the article brings into focus the scientific approach of the team based on the long tradition in crystallography, modelling and informatics. The article is not dedicated to 40th anniversary of the centre only, but it also reveals how Cambridge Structural Database can be used in the research and teaching. The use of electronic media and computer graphics makes data mining" very efficient and useful but also esthetically appealing due to the molecular architecture. At the Rudjer Bošković Institute, Zagreb, Croatia there is The National Affiliated Centre of Cambridge Crystallographic Data Centre responsible for communication and dissemination of CSD in Croatia, Slovenia and Macedonia

Preparation and Characterization of Some Sodium-, Rubidium-, Cesium- and Ammonium-Oxodiperoxooxalato-Molybdates (VI) and Tungstates (VI)

Potassium derivatives of oxodiperoxooxalato- molybdates and tungstates: were prepared before1>2 studied by infrared Raman3 and X-ray methods4•5 .The crystal structure of corresponding molybdate with literature survey was published recently4

Chirality - The forthcoming 160th Anniversary of Pasteur\u27s Discovery

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 presented review on chirality is dedicated to the centennial birth anniversary of Nobel laureate Vladimir Prelog and 160 years of Pasteur\u27s discovery of chirality on tartrates. Chirality has been recognized in nature by artists and architects, who have used it for decorations and basic constructions, as shown in the Introduction. The progress of science through history has enabled the gathering of knowledge on chirality and its many ways of application. The key historical discoveries about the rotation of polarized light as a consequence of molecular chirality and findings of Pasteur and Lord Kelvin are described. Chirality can be found in physics of elementary particles and in many fields of chemistry: analytical and organic chemistry, chemistry of natural compounds, medicinal and pharmaceutical chemistry, biochemistry and biotechnology, and molecular biology. The development of knowledge about chirality and its physical background are briefly described. Definitions for geometrical, topological, and conformational chirality are given accompanied by numerous examples of molecules exhibiting such features. The relations between symmetry and chirality in crystallography are exposed. X-ray crystallography is a method of choice for unambiguous determination of molecular architecture, including the absolute configuration of the molecule using Bijvoet\u27s approach. Two methods of determination of absolute configuration by X-ray diffraction and circular dichroism are briefly discussed. To mark two significant jubilees, the essay is dedicated to the role of chirality in stereochemistry. Stereochemistry is not a branch of chemistry but rather a view at chemistry, as considered by E. L. Eliel; this approach is respected in the essay presented. This very approach leads to various aspects of chirality and brings to the consistency of many definitions. The future will bring us knowledge on the role of chirality in communications among molecules, which guide our life processes. The synthesis of various dynamically chiral supramolecules from achiral molecules and preparations of conjugated homochiral polymers will offer new types of biosensors, artificial enzymes and some sophisticated materials. The research of isotopic chirality by quantum-chemical methods reveals some parity-violating effects and shed more light on the physical bases of molecular chirality

The 100th Anniversary of X-Ray Crystallography

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.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 The 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? </div