Investigating cation binding properties of crown ethers with DFT methods

Benzopiran kumarinleri doğal bitkilerden sentezlenen ve pek çok özellik gösteren önemli bileşiklerdir. Bu moleküller, kromofor özelliklerinden dolayı en çok boya kimyasında kullanılmaktadırlar. Kuvvetli oksijen köprüleri içeren bu makro halkalı bileşikler, alkali ve toprak alkali metaller ile (+) yüklü kompleksler oluşturmaktadırlar. Pedersen, yüksek seçiciliği olan taç eter moleküllerin keşfi ve kullanımı ile ilgili olarak yaptığı çalışmalardan ötürü 1987 Nobel Kimya ödülünü almıştır. Kumarin türevlerinin optik özellikleri ile makro halkalı taç eterlerin katyon bağlama özelliklerini bir araya getirerek uygulama alanlarını genişletmek üzere Tiftikçi ve Erk tarafından bir seri molekül sentezlenmiştir (Tiftikçi ve Erk,2004). Literatüre son yıllarda kazandırılan bu moleküllerin elektronik ve optik özelliklerinin bilinmesi daha sonra yapılacak olan sentezlere de ışık tutacaktır. Bu özelliklerin teorik yöntemlerle anlaşılmasına yönelik yapılan bu çalışmada ayrıca kumarin halkasının makro halkaya bağlanma pozisyonuna, kumarin halkası üzerindeki sübstitüsyona, makro halka büyüklüğüne ve katyonun büyüklüğüne bağlı olarak moleküllerin UV soğurma spektrumlarındaki ve katyon bağlama enerjilerindeki değişiklikler de incelenmiştir. Bağlanma enerjileri ya da moleküllerin iyon seçiciliği Li+, Na+, ve K+ iyonları için Yoğunluk Fonksiyoneli Teorisi (YFT) yöntemiyle B3LYP/6-31g(d) seviyesinde gaz fazında, su ve asetonitril için ortamın dielektrik sabiti değiştirilerek çözücü ortamında hesaplanmıştır. Elde edilen sonuçlar mevcut olan deneysel sonuçlarla karşılaştırılmıştır. Katyonlu ve katyonsuz moleküllerin 0 Kelvin’deki gaz fazı ve çözücüye göre düzeltilmiş elektronik enerjileri, sıfır enerjisi göz önüne alınarak hesaplanmıştır. Katyon bağlama reaksiyonunun entalpisi ve serbest enerjisi ise baz fonksiyonundan gelen hatalara göre düzeltilerek rapor edilmiştir. Bağlanma enerjilerinin daha yüksek bazda tekrarlanan hesaplarla baz fonksiyonuna bağlı olarak nasıl değiştiği incelenmiştir. Anahtar Kelimeler: Kumarin, Taç Eterler, DFT, BSSE.The coumarins of benzopyran are important compounds which are synthesized from natural plants and have a good number of features. These molecules are mostly used at dye chemistry-because of their chromophoric features. Macrocyclic ether molecules which are known as good cation binding compounds, are first discovered in 1967 by Charles J. Pedersen who won 1/3 of the Chemistry Nobel Prize for the development and use of molecules with structure-specific interactions of high selectivity These molecules contain strong oxygen bridges and have a tendency to form positively charged complexes with alkaline and soil alkaline metals in solution. Being aware of the electronic and optical features of these molecules, which have been shown recent literatures, will illuminate the forthcoming syntheses. To bring optical features of the coumarin derivatives and the cation binding features of macrocyclic crown ethers together, a series of new molecules are synthesized by Tiftikçi and Erk to expand the application areas of both type of molecules (Tiftikçi; Erk, 2004). In this study which is done to understand these features with theoretical methods, the binding position of the coumarin to the macrocyclic,  the substitution on the coumarin, the magnitude of macrocyclic and according to the magnitude of the cation, the changes on the UV absorption spectrums of molecules and the cation binding energy are also analyzed. The energy of binding or the ion selectivity of the molecules are calculated with the following methods; for Li+, Na+, ve K+ ions with the method of DFT (Density Functional Theory) at the B3LYP/6-31g(d) level at gas phase, for water and asetonitril, by changing the constant dielectric at the solvent medium. The outcomes which are yield are compared with the existing experimental outcomes. The gas phase at the 0 Kelvin of the molecules with and without cations and their corrected electronic energy according to the solvent are calculated by regarding the zero energy. Also, the enthalpies and free energy of the cation binding reaction are reported by correcting according to the errors coming from the base function (BSSE). Depending on the base function, how the binding energies change with repeated calculations at a higher base is examined. In this study cationic recognition of the computerized form of crown ethers, which were synthesized before, has been investigated. For that reason optimization of the molecules has been carried out. Geometries of the studied molecules optimized using Density Functional Theory method (Devlin vd, 1994,1996) B3LYP (Becke 3 Parameter Lee-Yang-Parr) functional (Lee vd, 1998), and 6-31g(d) bases functional. Using optimized molecules with Time Dependent Density Functional Theory methods Exited states were optimized. Using exited states values which were computed by TDDFT method, UV graphics drawn with a computer software written in Fortran. The attained values are normalized to 1 and graphs are plotted according to wave lengths. UV spectra peaks are analyzed to find source and reasons of the peak it could happen is investigated (Erk vd., 1998). To investigate interactions with Na+ cation, BSSE correlation energy method used for calculation of reaction energies. To investigate effect of solvent water and asetonitril used as solvent. Reaction energies of water and asetonitril were also calculated. Attained results are compared with the experimental results. To confirm optimized geometries, experimental X-ray results of   18crown6 Na+ molecules compared with results of the study. There is a concordant between experimental X-Ray data and theoretical optimized geometry. So the method applied in this study has been chosen correctly for those molecules?. For studies carried out in asetonitril, when UV peaks are compared with experimental data, it has been understood that there is accommodation between them. With comparing experimental and theoretical data It has been tried to proof the correctness of the applied methods. These evidences could be used in further studies as basis. The UV absorption is shifted to visible region when coumarin ring is added to alone crown ethers. For that reason the optical properties of crown ethers can be investigated. Moreover if coumarin rings are added to aromatic groups like phenyl, the maximum UV peaks are shifted to red region. If more functional groups are added to the crown ether ring, the cation binding energy of the crown ether will decrease. For that reason cation binding also decreases. Keywords: Coumarin, Crown Ethers, DFT, COMPASS, BSSE

YFT ile halkalaşma reaksiyon mekanizmalarının incelenmesi

Over the past decade there has been a growing interest in the use of carbonyl ylides that were simply generated by addition of carbene or carbenoids onto the oxygen atom of a carbonyl group. Only a few ylides have been isolated and their existence in reactions have been verified indirectly. Thus, computational studies serve as a strong tool to explain the  reaction mechanisms. The reactions of α,-unsaturated carbonyl ylides have attracted considerable attention as they provide a challenging route for the synthesis of  dihydrofuran derivatives. The reactions of a few carbenes with cis E-enones gave rise to dihydrofuran intermediates, probably via 6-electrocyclization of the corresponding conjugated carbonylylide. Anac and Sezer have shown that the reaction of α,-unsaturated ketones with dimethyl diazomalonat (dmdm) in the presence of copper acetylacetonate (C(acac)2) give dihydrofuran type products while α,-unsaturated aldehydes give 1,3-dioksol derivatives. They also reported that the substituents of both enone and diazocarbonyl components had a beneficial influence on the reaction rate and favored the dihydrofuran formation. In this study, Cu(acac)2 catalyzed cycloaddition  reaction of dmdm  with 6,6-dimethyl-2-methylenebicyclo[3.1.1]heptan-3-on (P), a strained and cisoid-fixed bicyclic α,-conjugated enone, was studied to elucidate the preference of the reaction route leading to 1,3-dioxole type of products although, dihydrofuran derivatives were also the expected outcomes of the reaction. It was a surprising result since it was contrary to previous reports on other ketones which yielded dihydrofuran type of products. Geometry optimizations of  reactants, products and the transition states were carried out by Density Functional Theory (DFT) method with empirically parametrized hybrid functional B3LYP at 6-31G* level. Calculations were performed by using Gaussian 03 software package. The equilibrium structures have been characterized by the lack of imaginary vibrations whereas transition states have been characterized by the presence of exactly one imaginary vibration belonging to the reaction coordinate and also verified by the IRC (Intrinsic Reaction Coordinate) analysis. The single-point electronic energies were corrected to Gibbs free energies at 298.15 Kº and 1 atm based on the unscaled harmonic frequencies obtained with the 6-31G* basis sets. The partial charges on the atoms were calculated by the Natural Bond Orbital (NBO) analysis. The reaction of dmdm with Cu(acac)2 gives copper(I) carbene complex. The calculations showed that the copper(I) carbene complex is a stable and chiral complex in which the carbene carbon is sp2 hybridized. This complex can also be considered as a Fischer type carbene because of the double bond character of Cu-C4 bond which is a result of the strong  and  interactions between them. Reaction of carbene complex with P can yield the ylide intermediate in one of the two possible geometries, namely E and Z, depending on the orientation of the substrate. We have shown that with the concerted mechanism, E-ylide would only give the 1,3-dioxole, whereas the dihydrofuran derivative would be the only product that can be obtained from the Z-ylide. In the latter mechanism, the olefinic C1=C2 double bond must lose its olefinic character and rotate so as to bring the reacting centers close to each other for an efficient overlap. The reacting center, C4 is at the center of two ester groups that have an extended delocalization, thus it will resist pyramidilization as it undergoes reaction. Additionally, ester groups will cause steric hindrance in the vicinity of reacting centers. These geometric hindrances that make the reaction difficult, cause an increase in the reaction barrier. On the other hand, the transition state in 1,3-dioxole formation is very early which results in a low barrier for the reaction. The reacting centers are oriented in a very favorable geometry for an efficient overlap in cyclization to a 1,3-dioxole product. Cyclization in 1,3-dioxole transition state geometries is not hindered by steric or pyramidilization effects. Thus, cyclization to 1,3-dioxole products does not require a dramatic change in the overall geometry of the reactant, which results in a much lower barrier. In conclusion, the reaction mechanisms leading to different products greatly depend on the conformations of copper-stabilized carbonyl ylides, which are treated as reactants in our calculations. The conformational effects and donor-acceptor type stabilizations between the catalyst and the carbonyl ylide observed in the reactants and the transition state geometries seem to be the main reasons for the favored 1,3-dioxole formation reaction. Keywords: DFT, reaction mechanisims, carbonyl ylides. Oksijenli beş üyeli heterosiklik yapılar 1,3-dioksol ve dihidrofuran bileşikleri gibi doğal ve bioaktif özelliklerinden dolayı önemli bileşiklerdir. Bu sebeple, bu bileşiklerin tek aşamada yüksek verimle sentezlenmeleri önemlidir. Bu çalışmada 6,6-dimetil-2-metilenbisiklo[3.1.1]heptan-3-on bileşiğinin bakır(II) asetilasetonat katalizörü varlığında dimetil diazomalonat ile reaksiyonuna ait olası tüm mekanizalar Yoğunluk Fonksiyoneli Teorisi (DFT) ile incelenmiştir. Bu reaksiyonlar için kabul gören mekanizma Doyle tarafından önerilmiştir ve bu mekanizma incelenen reaksiyon için uygulanmıştır. Hesaplamar sonucu, dihidrofuran ve 1,3-dioksol türevlerinin reaksiyon mekanizmalarının, reaktif moleküllerin konformasyonuna bağlı olduğu sonucuna varılmıştır. Cu atomu 1,3-dioksol oluşumu reaksiyonunun geçiş aşamalarını geri bağ ile kararlı hale getirmektedir. 1,3-dioksol oluşumu geçiş aşamaları birer erken geçiş aşaması şeklinde tanımlanabilmektedir. Bunun sebebi, geçiş aşamaları ile E yilidlerin geometrilerinin birbirlerine büyük oranda benzemesidir. Öte yandan, dihidrofuran geçiş aşamalarında  C-C çift bağının uzayarak kapanmanın meydana gelmesi için gerekli geometriye ulaşabilmek için çift bağ etrafında dönmesi ve karben karbonuna yaklaşması gerekmektedir. Bakır atomu ise karben karbonuyla olan koordinasyonunu kaybetmek zorundadır ve karben karbonu, kendisine bağlı ester grupları ile piramidal bir geometriye ulaşmalıdır. Ester gruplarının karben karbonuyla sübstitüsyonu sonucu karben karbonunun elektron yoğunluğu ester grupları tarafından delokalizedir. Tüm bu geometrik ve elektronik etkiler sebebiyle dihidrofuran reaksiyonu 1,3-dioksol kapanmasına oranla büyük bir aktivasyon bariyeri gerektirmektdir. Yapılan hesaplamalara göre 6,6-dimetil-2-metilenbisiklo[3.1.1]heptan-3-on molekülünün tercihli kapanma ürünü 1,3-dioksol türevleridir. Anahtar Kelimeler: YFT, reaksiyon mekanizması, karbonil yilid

Pattern formation of two-dimensional model phospholipid molecules by molecular dynamics simulation.

Ph.D. - Doctoral Progra

The role of diisocyanate and soft segment on the intersegmental interactions in urethane and urea based segmented copolymers: A DFT study

Structures and intersegmental interactions in segmented thermoplastic copolymers were studied by density functional theory (DFT) method at B3LYP and M06-2X/6-31g(d,p) levels. Hard segments were chosen to be highly polar urethane and urea groups with various diisocyanate groups. Soft segments were represented by flexible polymers with a wide range of polarity such as poly(epsilon-caprolactone) (PCL), poly(1,6-hexyl 1,2-ethyl carbonate) (PHEC), polytetramethylene oxide (PTMO), polydimethylsiloxane (PDMS), polyisobutylene (PIB) and polybutadiene (PBu). It was observed that the structural properties such as symmetry and planarity of the diisocyanate groups of the hard segments as well as the miscibility between the hard and soft segments played an important role on the packing of the hard segments and thus, on the phase behavior of copolymers. According to the experimental studies in the literature, these systems have always displayed phase separated morphologies. The calculated interaction energies here revealed that the phase separation is inevitable since the self interactions of the urea/urethane blocks were stronger than their interactions with the soft blocks due to the H-bonding. The control of the size and the shape of the micro phase domains in these materials is very important especially for their biotechnological applications and it can be achieved by varying the type and weight percentage of the soft segments as well as symmetry and planarity of the diisocyanate groups as shown in this work

MORPHOLOGICAL PROPERTIES OF PYRROLE AND PHENYLENE ROD-COIL DIBLOCK COPOLYMERS BY DISSIPATIVE PARTICLE DYNAMICS

Poly (para-phenylene)s (PPP) and polypyrroles (PPy) are important members of the conducting polymers. Rod-coil type diblock copolymers formed by coupling of PPP and PPy rigid blocks with polycaprolactone (PCL), polystyrene (PS) and polymethylmethacrylate (PMMA) coil blocks were modeled and morphological properties have been studied by a coarse grained simulation method at the mesoscale. Geometry optimizations and the atomic charge calculations were done quantum mechanically to obtain the input parameters for the mesoscale dynamics simulations. The accurate mixing energies and the Flory-Huggins interaction parameters between the monomers of polymers were calculated and used to study the phase behaviors and the morphologies of the copolymers as a function of type and weight percentages of the blocks by Dissipative Particle Dynamics (DPD) simulations. We showed that the methodology employed took into account not only the interaction parameter and chain length of the blocks but also the chemical structure of the polymers and it could be used to produce the phase diagram of the copolymers which has importance for the industrial applications of such materials. Among the studied copolymers, the most suitable one for thin layer applications was predicted to be PPP-b-PCL in which PPP forms lamellar and cylindrical phases in the PCL matrix if amount of PPP rod block is below 50 wt%

A comparative study on the efficiencies of polyethylene compatibilizers by using theoretical methods

Functionalization of polyethylene chains by grafting of polar groups onto backbones is the most versatile way for preparing polyethylene based compatibilizers (PECs). In this work, a series of theoretical studies were performed to analyze the structure, adhesion and mixing behaviors of PECs. The effect of grafting different polar groups such as acrylic acid (AA), glycidyl methacrylate (GMA), maleic anhydride (MAH) and itaconic acid (IA) on the structure and cohesive properties of polyethylene chains were studied by Molecular Dynamics simulations. The mixing behavior of grafted polyethylenes with some commodity polymers such as polyetylene teraphthalate (PET), polyamide 6 (Nylon6), polyvinyl acetate (PVA) and polylactide (PLA) as well as with starch (ST) and starch acetate (STac) were investigated quantitatively by determining accurate interaction parameters using the modified Flory-Huggins Theory. We showed that the polar groups are the most reactive sites and they bind the chemically incompatible polymers by enabling the stronger interactions at the interfacial region

Multiscale Modeling of the Morphology and Properties of Segmented Silicone-Urea Copolymers

Molecular dynamics and mesoscale dynamics simulation techniques were used to investigate the effect of hydrogen bonding on the microphase separation, morphology and various physicochemical properties of segmented silicone-urea copolymers. Model silicone-urea copolymers investigated were based on the stoichiometric combinations of alpha,omega-aminopropyl terminated polydimethylsiloxane (PDMS) oligomers with number average molecular weights ranging from 700 to 15,000 g/mole and bis(4-isocyanatocyclohexyl)methane (HMDI). Urea hard segment contents of the copolymers, which were determined by the PDMS molecular weight, were in 1.7-34% by weight range. Since no chain extenders were used, urea hard segments in all copolymers were of uniform length. Simulation results clearly demonstrated the presence of very good microphase separation in all silicone-urea copolymers, even for the copolymer with 1.7% by weight hard segment content. Experimentally reported enhanced properties of these materials were shown to stem from strong hydrogen bond interactions which leads to the aggregation of urea hard segments and reinforcement of the PDMS

Theoretical approach to the structural, electronic, and morphological properties of poly(E >-caprolactone) grafted polypyrroles

Poly(E >-caprolactone) grafted polypyrroles (PPy-g-PCL) are an important member of hairy-rod copolymers which have many industrial applications. PPy-g-PCL cooligomers were studied for their electronic, structural and morphological properties by density functional theory (DFT), molecular dynamics and mesoscale dynamics simulation methods. The band gaps of the cooligomers were calculated at the B3LYP/6-31g(d,p) level by varying the grafting position of PCL group. UV spectra was studied by time-dependent DFT methods. The solubility parameters and interaction parameters between the PCL and PPy were calculated via molecular dynamics simulations. The morphological behaviors were studied by the molecular dynamics and dissipative particle dynamics (DPD) methods to understand the role of rigidity of polypyrrole backbone, the chain lengths of PPy and PCL and the incompatibility of the polymers on the formation of layered phase domains observed experimentally for high weight percentages of PCL side chains