Fizik Bölümü / Department of Physics
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Publication Alzheimer Hastalığı Tedavisinde Etkili Cyclo(Phe-Phe) Dipeptidinin Konformasyon Analizi(Yüzüncü Yıl Üniversitesi Fen Bilimleri Enstitüsü, 2021) Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİMCyclo(Phe-Phe) dipeptidi Alzheimer hastalığı tedavisinde etkili bir dipeptitdir. Bu çalışmada Cyclo(Phe-Phe) dipeptidinin 3-Boyutlu yapısı teorik konformasyon analizi (TKA) metodu ile belirlenmiştir. Konformasyon analizinde, Ramachandran haritalarından yararlanılarak ve yan-zincir dihedral açıları (χ) yardımıyla tüm olası konformasyonlar belirlenmiştir. Bu haritalar kullanılarak programa girilen başlangıç dihedral açılarla, konformasyon analizi sonunda hesaplanan dihedral açılar karşılaştırmalı olarak verilerek tablolaştırılmıştır. Hesaplama sonucunda dipeptidin en kararlı beş konformasyonunun toplam enerjileri ve toplam enerjilerine katkı sağlayan van der Waals, elektrostatik, hidrojen bağ ve torsiyon enerjileri ayrı ayrı hesaplanmıştır. Ek olarak, en minimum enerjili konformasyon Gaussian03 programı ile DFT metodu kullanılarak optimize edilmiştir. Belirlenen optimize geometri ile konformasyon analizi sonrasında elde edilen geometri karşılaştırılmıştır.Publication Benchmarking the Anisotropy of Nitroxyl Radical Solvation With IR Spectroscopy(The Royal Society of Chemistry, 2024) Bras, Elisa M.; Zimmermann, Charlotte; FAUSTO, RUI; Suhm, Martin A.Two simple nitroxyl radicals, di-tert-butyl nitroxyl (DTBN) and 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) are solvated by one or two water, methanol, tert-butyl alcohol or phenol molecules. The resulting low temperature IR spectra of the vacuum-isolated microsolvates in the OH stretching range are assigned based on harmonic DFT predictions for closed shell solvent dimers and trimers and their offset from experiment, to minimise theory-guided assignment bias. Systematic conformational preferences for the first and second solvent molecule are observed, depending on the conformational rigidity of the radical. These assignments are collected into an experimental benchmark data set and used to assess the spectral predicting power of different DFT approaches. The goal is to find inexpensive computational methods which provide reliable spectral predictions for this poorly explored class of microsolvates.Publication Crystallization Kinetics: Relationship Between Crystal Morphology and the Cooling Rate-Applications for Different Geological Materials(MDPI, 2023-01-24) Aysal, Namık; Kurt, Yiğit; ILDIZ, GÜLCE ÖĞRÜÇ; Öztürk, Hüseyin; Yeşiltaş, Mehmet; Laçin, Davut; Öngen, Sinan; Nikitin, Timur; FAUSTO, RUICrystal morphology is controlled by several physicochemical parameters such as the temperature, pressure, cooling rate, nucleation, diffusion, volatile composition, and viscosity. The development of different crystal morphologies is observed as a function of the cooling rate in many different rock types (i.e., glassy volcanic rocks, and archeometallurgical slags). Crystallization is a two-stage kinetic process that begins with the formation of a nucleus and then continues with the accumulation of ions on it. The shapes of the crystals depend on the degree of undercooling (& UDelta;T), and euhedral crystals, having characteristic forms that reflect their crystallographic internal structure, that grow just below their liquidus temperature. In this study, crystal morphologies in different minerals (e.g., quartz, sanidine, olivine, pyroxene, magnetite, etc.) that had developed in silicic volcanic rocks (spherulites) and slags from ancient mining were investigated and characterized using optical microscopy, X-ray diffraction, and Fourier-transform infrared (FTIR), Raman, and scanning electron microscope-energy dispersive X-ray fluorescence (SEM-EDX) spectroscopic techniques. Depending on the increase in the cooling rate, quartz, feldspar, olivine, pyroxene, and magnetite minerals were found to crystallize in subhedral, skeletal, dendritic, spherical, bow-tie and fibrous forms in glassy volcanic rocks and archeometallurgical slags.Publication Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi(Süleyman Demirel Üniversitesi, 2021) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etkigösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozinaminoasitlerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analiziyapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenenkonformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimlerve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplamenerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkılarıayrı ayrı hesaplanmıştır. Konformasyon analizi ile belirlenen en kararlı konformer,Gaussian03 programı kullanılarak, DFT (Density Functional Teory), B3LYPfonksiyoneli ve 6-31++G(d,p) baz seti ile optimize edilmiş ve optimize yapınıntemel titreşim dalga sayıları aynı teori düzeyinde hesaplanmıştır. Ayrıca, IRşiddetleri, Raman aktiviteleri, potansiyel enerji dağılımları MOLVIB programıkullanılarak saptanmış, Simirra programı ile ölçeklendirilmiş Raman aktiviteleri,Raman şiddetlerine dönüştürülmüştür. Ek olarak bu dipeptidin dimerik formuoluşturulmuş ve DFT/B3LYP/6-31G(d,p) teori düzeyinde optimize edilerek halkayapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarakverilmiştir. Dimerik yapının oluşumunda rol oynayan moleküller arası hidrojenbağları belirlenmiştir.Publication Di-Alkyl Adipates as New Phase Change Material for Low Temperature Energy Storage(Springer/Plenum Publishers, 2023) Sequeira, Maria C. M.; Nogueira, Bernardo A.; Caetano, Fernando J. P.; Diogo, Herminio P.; Fareleira, Joao M. N. A.; FAUSTO, RUIThis work is a contribution to the thermal characterization of a selected binary system of two di-n-alkyl adipates that can be used as phase change material for thermal energy storage at low temperatures. The construction of the solid-liquid phase diagram using differential scanning calorimetry (DSC), complemented with Raman Spectroscopy studies for the system composed by diethyl and dibutyl adipates is presented. The solidus and liquidus equilibrium temperatures were determined by DSC for the pure components and 30 binary mixtures at selected molar compositions were used to construct the corresponding solid-liquid phase diagram. The binary system of diethyl and dibutyl adipates presents eutectic behaviour at low temperatures. The eutectic temperature was found at 240.46 K, and the eutectic composition was determined to occur at the molar fraction xdibutyl = 0.46. Additionally, the system shows a polymorphic transition, characteristic of dibutyl adipate, occurring at ca. 238 K, confirmed by optical microscopy. To the best of our knowledge, no reference to the phase diagram of the present system could be found in the literature. Raman spectroscopy was essential to complement the construction of the phase equilibrium diagram, enabling the identification of the solid and liquid phases of the system. Finally, the liquidus curve of the phase diagram was also successfully predicted using a suitable fitting equation, being the root mean square deviation of the data from the correlation equal to 0.54 K. In addition, this fitting operation enabled a correct prediction of the eutectic composition of the system.Publication Evaluation of Anti-Cancer and Anti-Covid-19 Properties of Cationic Pentapeptide Glu-Gln-Arg-Pro-Arg, From Rice Bran Protein and Its D-Isomer Analogs Through Molecular Docking Simulations(Elsevier Science Inc., 2021) Gasymov, Oktay K.; Çelik, Sefa; Ağaeva, Gülşen; AKYÜZ, SEVİM; Keçel-Gündüz, Serda; Qocayev, Niftali M.; Özel, Ayşen E.; Ağaeva, Ülker; Bakhishova, Matanat; Aliyev, Jamil A.Bioactive peptides derived from food proteins are becoming increasingly popular due to the growing awareness of their health-promoting properties. The structure and mechanism of anti-cancer action of pentapeptide GluGln-Arg-Pro-Arg (EQRPR) derived from a rice bran protein are not known. Theoretical and experimental methods were employed to fill this gap. The conformation analysis of the EQRPR pentapeptide was performed first and the obtained lowest energy conformer was optimized. The experimental structural data obtained by FTIR and CD spectroscopies agree well with the theoretical results. D-isomer introduced one-by-one to each position and all D-isomers of the peptide were also examined for its possible anti-proteolytic and activity enhancement properties. The molecular docking revealed avid binding of the pentapeptide to the integrins alpha(5)beta(1) and alpha(IIb)beta(3), with K-d values of 90 nM and 180 nM, respectively. Moreover, the EQRPR and its D-isomers showed strong binding affinities to apo-and holo-forms of M-pro, spike glycoprotein, ACE2, and dACE2. The predicted results indicate that the pentapeptide may significantly inhibit SARS-CoV-2 infection. Thus, the peptide has the potential to be the leading molecule in the drug discovery process as having multifunctional with diverse biological activities.Publication Fourier Transform Infrared Spectroscopy Based Complementary Diagnosis Tool for Autism Spectrum Disorder in Children and Adolescents(MDPI, 2020) ILDIZ, GÜLCE ÖĞRÜÇ; Bayari, Sevgi; Karadağ, Ahmet; Kaygısız, Ersin; Fausto, RuiAutism spectrum disorder (ASD) is a neurodevelopmental disorder that begins early in life and continues lifelong with strong personal and societal implications. It affects about 1%-2% of the children population in the world. The absence of auxiliary methods that can complement the clinical evaluation of ASD increases the probability of false identification of the disorder, especially in the case of very young children. In this study, analytical models for auxiliary diagnosis of ASD in children and adolescents, based on the analysis of patients' blood serum ATR-FTIR (Attenuated Total Reflectance-Fourier Transform Infrared) spectra, were developed. The models use chemometrics (either Principal Component Analysis (PCA) or Partial Least Squares Discriminant Analysis (PLS-DA)) methods, with the infrared spectra being the X-predictor variables. The two developed models exhibit excellent classification performance for samples of ASD individuals vs. healthy controls. Interestingly, the simplest, unsupervised PCA-based model results to have a global performance identical to the more demanding, supervised (PLS-DA)-based model. The developed PCA-based model thus appears as the more economical alternative one for use in the clinical environment. Hierarchical clustering analysis performed on the full set of samples was also successful in discriminating the two groups.Publication Graphene-Assisted Chemical Stabilization of Liquid Metal Nano Droplets for Liquid Metal Based Energy Storage(Wiley, 2024) Sanati, Afsaneh L.; Nikitin, Timur; FAUSTO, RUI; Majidi, Carmel; Tavakoli, MahmoudEnergy storage devices with liquid-metal electrodes have attracted interest in recent years due to their potential for mechanical resilience, self-healing, dendrite-free operation, and fast reaction kinetics. Gallium alloys like Eutectic Gallium Indium (EGaIn) are appealing due to their low melting point and high theoretical specific capacity. However, EGaIn electrodes are unstable in highly alkaline electrolytes due to Gallium oxide dissolution. In this letter, this bottleneck is addressed by introducing chemically stable films in which nanoscale droplets of EGaIn are coated with trace amounts of graphene oxide (GO). It is demonstrated that a GO to EGaIn weight ratio as low as 0.01 provides enough protection for a thin film formed by GO@EGaIn nanocomposite against significantly acidic or alkaline environments (pH 1-14). It is shown that GO coating significantly enhances the surface stability in such environments, thus improving the energy storage capacity by over 10x. Microstructural analysis confirms GO@EGaIn composite stability and enhanced electrochemical performance. Utilizing this, a thin-film supercapacitor is fabricated. Results indicate that when coating the EGaIn with GO to EGaIn ratio of 0.001, the areal capacitance improves by 10 times, reaching 20.02 mF cm(-2). This breakthrough paves the way for advanced liquid metal-based thin-film electrodes, promising significant improvements in energy storage applications.Publication Interactions Mechanism of Commonly Used Drugs for the Treatment of COVID-19(Bulletin of the Chemical Society of Ethiopia, 2020) Çelik, Sefa; Demirağ, A. Demet; Özel, Ayşen E.; AKYÜZ, SEVİMIn this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (M-P(ro)) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 M-P(ro) and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of MP' system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 M-P(ro) and spike glycoprotein can play an important role for the treatment of COVID-19.Publication Micro-Raman Spectroscopy and X-ray Diffraction Analyses of the Core and Shell Compartments of an Iron-Rich Fulgurite(MDPI, 2022) KARADAĞ, AHMET; Kaygısız, Ersin; Nikitin, Timur; Öngen, Sinan; ILDIZ, GÜLCE ÖĞRÜÇ; Aysal, Namık; Yılmaz, Ayberk; Fausto, RuiFulgurites are naturally occurring structures that are formed when lightning discharges reach the ground. In this investigation, the mineralogical compositions of core and shell compartments of a rare, iron-rich fulgurite from the Mongolian Gobi Desert were investigated by X-ray diffraction and micro-Raman spectroscopy. The interpretation of the Raman data was helped by chemometric analysis, using both multivariate curve resolution (MCR) and principal component analysis (PCA), which allowed for the fast identification of the minerals present in each region of the fulgurite. In the core of the fulgurite, quartz, microcline, albite, hematite, and barite were first identified based on the Raman spectroscopy and chemometrics analyses. In contrast, in the shell compartment of the fulgurite, the detected minerals were quartz, a mixture of the K-feldspars orthoclase and microcline, albite, hematite, and goethite. The Raman spectroscopy results were confirmed by X-ray diffraction analysis of powdered samples of the two fulgurite regions, and are consistent with infrared spectroscopy data, being also in agreement with the petrographic analysis of the fulgurite, including scanning electron microscopy with backscattering electrons (SEM-BSE) and scanning electron microscopy with energy dispersive X-ray (SEM-EDX) data. The observed differences in the mineralogical composition of the core and shell regions of the studied fulgurite can be explained by taking into account the effects of both the diffusion of the melted material to the periphery of the fulgurite following the lightning and the faster cooling at the external shell region, together with the differential properties of the various minerals. The heavier materials diffused slower, leading to the concentration in the core of the fulgurite of the iron and barium containing minerals, hematite, and barite. They first underwent subsequent partial transformation into goethite due to meteoric water within the shell of the fulgurite. The faster cooling of the shell region kinetically trapped orthoclase, while the slower cooling in the core area allowed for the extensive formation of microcline, a lower temperature polymorph of orthoclase, thus justifying the prevalence of microcline in the core and a mixture of the two polymorphs in the shell. The total amount of the K-feldspars decreases only slightly in the shell, while quartz and albite appeared in somewhat larger amounts in this compartment of the fulgurite. On the other hand, at the surface of the fulgurite, barite could not be stabilized due to sulfate lost (in the form of SO2 plus O-2 gaseous products). The conjugation of the performed Raman spectroscopy experiments with the chemometrics analysis (PCA and, in particular, MCR analyses) was shown to allow for the fast identification of the minerals present in the two compartments (shell and core) of the sample. This way, the XRD experiments could be done while knowing in advance the minerals that were present in the samples, strongly facilitating the data analysis, which for compositionally complex samples, such as that studied in the present investigation, would have been very much challenging, if possible.Publication Molecular Docking Analysis of Used Drugs for the Treatment of Cancer(Süleyman Demirel Üniversitesi, 2021) Demirbağ, Aliye Demet; Çelik, Sefa; AKYÜZ, SEVİM; Özel, AysenIn this study, the lowest energy molecular structures were determined by conformational analysis of six drugs commonly used in cancer treatment, in order to use as initial data for docking simulations. Using the AutoDock Vina software, the interaction mechanisms of the 6 FDA approved drugs (Pemetrexed, Irinotecan, Tamoxifen, Gemcitabine, Topotecan and Temozolomide) with DNA were investigated. In addition, MM/PB(GB)SA calculations for the drug-DNA structures under investigation have been performed. The calculated binding affinities and binding free energies of interactions were showed the stability of the structures. It has been found that the active site where these molecules interact with DNA is the same and that their various interactions, primarily hydrogen bond, play an important role in this stability of the structures. Furthermore, the pharmacophoric features of the investigated molecules were determined.The aim of the work is to deeply investigate the binding properties of the title drugs with DNA.Publication Nanoscale Study of the Polar and Electronic Properties of a Molecular Erbium(III) Complex Observed via Scanning Probe Microscopy(MDPI, 2023) Ivanov, Maxim; Grempka, Arkadiusz; Buryakov, Arseniy; Nikitin, Timur; Justino, Licinia L. G.; FAUSTO, RUI; Vilarinho, Paula M.; Paixao, Jose A.We successfully synthesized millimeter-sized single crystals of the molecular erbium(III) complex Er(acac)(3)(cphen), where acac = acetylacetonate and cphen = 5-chloro-1,10-phenanthroline. The novelty of this work stems from the exhaustive examination of the polar and electronic properties of the obtained samples at the macro-, micro-, and nanoscale levels. The single crystal X-ray diffraction method demonstrates the monoclinic (noncentrosymmetric space group P2(1)) crystallographic structure of the synthesized samples and scanning electron microscopy exhibits the terrace-ledge morphology of the surface in erbium(III) crystals. By using the piezoelectric force microscopy mode, the origin of the polar properties and the hyperpolarizability in the synthesized samples were assigned to the internal domain structure framed by the characteristic terrace-ledge topography. The direct piezoelectric coefficient (similar to d33) was found to be intensely dependent on the local area and was measured in the range of 4-8 pm/V. A nanoscale study using the kelvin probe force and capacitance force (dC/dz) microscopy modes exposed the effect of the Er ions clustering in the erbium(III) complex. The PFM method applied solely to the Er ion revealed the corresponding direct piezoelectric coefficient (similar to d33) of about 4 pm/V. Given the maximum piezoelectric coefficient in the erbium(III) complex at 8 pm/V, we highlight the significant importance of the spatial coordination between the lanthanide ion and the ligands. The polar coordination between the lanthanide ion and the nitrogen and oxygen atoms was also corroborated by Raman spectroscopy supported by the density functional theory calculations. The obtained results can be of paramount importance for the application of molecular erbium(III) complex crystals in low-magnitude magnetic or electric field devices, which would reduce the energy consumption and speed up the processing switching in nonvolatile memory devices.Publication Phenylpropiolic Acid Isolated in Cryogenic Nitrogen and Xenon Matrices: NIR and UV-Induced Study(AIP Publishing, 2023) Lopes S.; Nikitin T.; FAUSTO, RUIPhenylpropiolic acid (C6H5C≡CCOOH, PPA) isolated in nitrogen and xenon cryogenic matrices was studied by infrared spectroscopy. The experimental studies were complemented by a series of quantum chemical calculations carried out at the density functional theory (B3LYP) and MP2 levels of theory (with different basis sets). The calculations predicted the existence of two planar PPA conformers, differing in the arrangement of the carboxylic group. The higher-energy trans-PPA conformer has a negligible population in the gas phase at room temperature and was prepared in situ in the N2 cryomatrix through vibrationally-induced rotamerization of the lower-energy cis-PPA conformer, achieved using selective narrowband infrared excitation of the OH stretching coordinate of the latter species. Broadband UV (λ > 235 nm) irradiation of matrix-isolated cis-PPA was also undertaken, leading to the observation of cis-PPA → trans-PPA isomerization. No other UV-induced photoreactions were observed. The in situ generated trans-PPA conformer was found to decay back to cis-PPA in the dark by tunneling, and its lifetimes under different experimental conditions were determined. The assignment of the infrared spectra of both conformers is presented, considerably extending the vibrational information available on this molecule.Publication PLS-DA Model for the Evaluation of Attention Deficit and Hyperactivity Disorder in Children and Adolescents through Blood Serum FTIR Spectra(MDPI, 2021) ILDIZ, GÜLCE ÖĞRÜÇ; KARADAĞ, AHMET; Kaygısız, Ersin; Fausto, RuiAttention deficit and hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorders of childhood. It affects similar to 10% of the world's population of children, and about 30-50% of those diagnosed in childhood continue to show ADHD symptoms later, with 2-5% of adults having the condition. Current diagnosis of ADHD is based on the clinical evaluation of the patient, and on interviews performed by clinicians with parents and teachers of the children, which, together with the fact that it shares common symptoms and frequent comorbidities with other neurodevelopmental disorders, makes the accurate and timely diagnosis of the disorder a difficult task. Despite the large effort to identify reliable biomarkers that can be used in a clinical environment to support clinical diagnosis, this goal has never been achieved hitherto. In the present study, infrared spectroscopy was used together with multivariate statistical methods (hierarchical clustering and partial least-squares discriminant analysis) to develop a model based on the spectra of blood serum samples that is able to distinguish ADHD patients from healthy individuals. The developed model used an approach where the whole infrared spectrum (in the 3700-900 cm(-1) range) was taken as a holistic imprint of the biochemical blood serum environment (spectroscopic biomarker), overcoming the need for the search of any particular chemical substance associated with the disorder (molecular biomarker). The developed model is based on a sensitive and reliable technique, which is cheap and fast, thus appearing promising to use as a complementary diagnostic tool in the clinical environment.Publication Recycling Ophthalmic Lens Wastewater in a Circular Economy Context: A Case Study with Microalgae Integration(MDPI, 2024) FAUSTO, RUIWater pollution poses a global threat to ecosystems and human health and is driven by the presence of various contaminants in wastewater, including nano- and microplastics. Despite the magnitude of this problem, the majority of global wastewater is released untreated into water bodies. To combat this issue, a multi-strategy approach is needed. This study explores a circular economy-based solution for treating emerging pollutants, particularly wastewater from ophthalmic spectacle lens production. Our approach integrates solid waste materials into polymeric and cement matrices while also utilising wastewater for microalgae cultivation. This innovative strategy focuses on biomass generation and economic valorisation. By adopting a circular economy model, we aim to transform environmental pollutants from wastewater into valuable organic products. A key component of our approach is the utilisation of microalgae, specifically Nannochloropsis sp., known for its high lipid content and resilience. This microalgae species serves as a promising biobased feedstock, supporting the production of innovative biobased products, such as biopolymers, for ophthalmic lens manufacturing. Our interdisciplinary approach combines microalgae technology, analytical chemistry, cement production, and polymer processing to develop a sustainable circular economy model that not only addresses environmental concerns, but also offers economic benefits. This study underscores the potential of harnessing high-value products from waste streams and underscores the importance of circular economy principles in tackling pollution and resource challenges.Publication Sandwich-Type Double-Layer Piezoelectric Nanogenerators Based on One- and Two-Dimensional ZnO Nanostructures With Improved Output Performance(Nature Research, 2023) Fakhri, Parisa; Eaianli, Naeimeh; Bagherzadeh, Roohollah; Jaleh, Babak; Kashfi, Mohammad; FAUSTO, RUIPiezoelectric nanogenerators (PENGs) have attracted great interest owing to their broad range application in environmental mechanical energy harvesting to power small electronic devices. In this study, novel flexible and high-performance double-layer sandwich-type PENGs based on one-dimensional (1-D) and two-dimensional (2-D) zinc oxide (ZnO) nanostructures and Ni foam as the middle layer have been developed. The morphology and structure of 1- and 2-D ZnO nanostructures have been studied by scanning electron microscopy (SEM) and X-ray diffraction (XRD). To investigate the effect of structural design on the piezoelectric performance, single-layer PENGs were also fabricated. The piezoelectric output of all prepared PENGs were evaluated under different human impacts at various forces and frequencies. The double-layer designed PENGs showed a two times larger voltage output compared to the single-layer PENGs, and the use of Ni foam as middle-layer and of 2-D ZnO nanosheets (compared to 1-D nanorods) was also found to increase the performance of the designed PENGs. The working mechanism of the prepared PENGs is also discussed. The design of nanogenerators as double-layer sandwich structures instead of two integrated single-layer devices reduces the overall preparation time and processing steps and enhances their output performance, thus opening the gate for widening their practical applications.Publication Solid-Liquid Phase Equilibrium: Alkane Systems for Low-Temperature Energy Storage(Springer/Plenum Publishers, 2024) Sequeira, Maria C. M.; Nogueira, Bernardo A.; Caetano, Fernando J. P.; Diogo, Herminio P.; Fareleira, Joao M. N. A.; FAUSTO, RUIThe thermal characterization of two binary systems of n-alkanes that can be used as Phase Change Materials (PCMs) for thermal energy storage at low temperatures is reported in this work. The construction of the solid-liquid binary phase diagrams was achieved using differential scanning calorimetry (DSC) and Raman spectroscopy. The solidus and liquidus equilibrium temperatures were determined using DSC for thirty-nine different samples, three for the pure n-alkanes and the remaining for binary mixtures at selected molar compositions and used to acquire the corresponding solid-liquid phase diagrams. The two binary systems of n-octane/n-decane (C8/C10) and n-decane/n-dodecane (C10/C12) are characterized by a eutectic behavior at low temperatures. The eutectic temperature for the system C8/C10 was found at 211.95 K and the eutectic composition appeared at the molar fraction xoctane = 0.87. For the system C10/C12, the eutectic temperature was found at 237.85 K, and the eutectic composition appeared for the molar fraction xdecane = 0.78. This work aims to fulfill the lack of available data in the existing literature, considering the potential application of these systems for low-temperature thermal energy storage. Raman spectroscopy was used to complement the DSC data for the construction of the solid-liquid phase equilibrium diagrams, enabling the identification of the solid and liquid phases of the system. Additionally, the liquidus curve of the phase diagram was successfully described using a modified freezing point depression curve as fitting equation, the absolute root mean square deviation for the data correlation of the C8/C10 and C10/C12 systems being 2.56 K and 1.22 K, respectively. Ultimately, the fitting procedure also enabled a good prediction of the eutectic point for both studied systems.Publication Structural Aspects of the Ortho Chloro- and Fluoro- Substituted Benzoic Acids: Implications on Chemical Properties(MDPI, 2020) ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, RuiThis article presents a detailed comprehensive investigation of the ortho fluoro- and chloro- substituted benzoic acids both, as isolated molecules and in the crystalline phase. Quantum chemical calculations performed within the density functional theory (DFT) formalism are used to investigate the potential energy landscapes of the molecules, taking into special consideration the effects of the interactions between the carboxylic group and the ortho halogen substituents, as well as the nature of these later on the structure and properties of the investigated systems. The structures of the relevant conformers of the molecules are discussed in comparative terms, and used to rationalize experimental data obtained for the compounds in the gas phase and isolated in low-temperature inert matrices. The UV-induced photofragmentation reactions of two of the compounds isolated in cryogenic inert matrices were studied as illustrative cases. The structures of the crystals reported previously in the literature are revisited and discussed also in a comparative basis. Particular emphasis is given to the analysis of the intermolecular interactions in the different crystals, using Hirshfeld surface analysis, the CE-B3LYP energy decomposition model and the HOMA index, and to their correlation with thermodynamic data.Publication Structure, Vibrational Spectra, and Cryogenic MatrixPhotochemistry of 6-Bromopyridine-2-Carbaldehyde: From the Single Molecule of the Compound to the Neat Crystalline Material(MDPI, 2023) Brito, Anna Luiza B.; Lopes, Susy; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui6-Bromopyridine-2-carbaldehyde (abbreviated as BPCA) is used both as a building block in supramolecular chemistry and as a ligand for transition metal catalysts and luminescent complexes. In this study, the structure and vibrational spectra of BPCA were investigated in both the room temperature neat crystalline phase and for the compound isolated in cryogenic Ar, Kr and Xe matrices. The experimental studies were complemented by quantum chemical DFT(B3LYP)/6-311++G(d,p) calculations. For the crystalline compound, infrared and Raman spectra were obtained and interpreted. Comparison of the obtained infrared spectrum of the crystal with those obtained for the isolated molecules of BPCA in the studied cryomatrices helped to conclude that the intermolecular interactions in the crystal do not significantly perturb the intramolecular vibrational potential. Structural analysis further supports the existence of weak coupling between the intermolecular interactions and the structure of the constituting molecular units in crystalline state. The intermolecular interactions in the BPCA crystal were also evaluated by means of Hirshfeld analysis, which revealed that the most important interactions are weak and of the (HN)-N- horizontal ellipsis , (HO)-O- horizontal ellipsis , (HH)-H- horizontal ellipsis , (HBr)-Br- horizontal ellipsis and (BrBr)-Br- horizontal ellipsis types. The conformer of BPCA present in the crystal was found to correspond to the most stable form of the isolated molecule (trans), which bears stabilizing C-(HO)-O- horizontal ellipsis =C and C(=O)(HN)-N- horizontal ellipsis interactions. This conformer was shown to be the single conformer present in the as-deposited cryogenic matrices prepared from the room temperature gaseous compound. Broadband UV irradiation of matrix-isolated BPCA (lambda >= 235 nm) resulted in the conversion of the trans conformer into the higher-energy cis conformer, where repulsive C-(HH)-H- horizontal ellipsis -C(=O) and C=(OLPLPN)-N- horizontal ellipsis (where LP designates a lone electron pair) interactions are present, and decarbonylation of the compound with formation of 2-bromopyridine (plus CO). The decarbonylation reaction was found to be more efficient in the more polarizable Xe matrix, indicating stabilization of the radicals initially formed upon breaking of the C-C(HO) and C-H (aldehyde) bonds in this medium, and testifying the occurrence of the decarbonylation reaction with involvement of radical species. TD-DFT calculations were used to access the nature of the excited states associated with the observed UV-induced reactions. As a whole, this study provides fundamental data to understand the physicochemical behavior of the compound, bridging the properties of the isolated molecule to those of the neat crystalline com-pound. Such information is of fundamental importance for the understanding of the role of BPCA in supramolecular chemistry and to potentiate its applications in synthesis and as a ligand for transition metal catalysts and luminescent complexes.Publication Synthesis, Antimicrobial Activity, Molecular Docking and ADMET Study of a Caprolactam-Glycine Cluster(Taylor & Francis Inc., 2021) Çelik, Sefa; Albayrak, Ali Tuğrul; AKYÜZ, SEVİM; Özel, Ayşen E.; Sığırcı, Belgi DirenDensity functional theory calculations were performed with DFT method using both b3lyp/6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gram-negative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process. Communicated by Ramaswamy H. Sarm