Sharif Digital Repository

The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F-, Cl-, and CN-) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the... 

A method for two dimensional position finding of stationary targets whose bearing measurements suffers from indeterminable bias and random noise has been proposed. The algorithm uses convex optimization to minimize an error function which has been calculated based on circular as well as linear loci of error. Taking into account a number of observations, certain modifications have been applied to the initial crude method so as to arrive at a faster, more accurate method. Simulation results of the method illustrate up to 30% increase in accuracy compared with the well-known least square filter  

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

Interactions of α-D-glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM-B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α-D-glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M.H-O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy... 

The unique plasmonic character of silver and gold nanoparticles has a wide range of applications, and tailoring this property by changing electronic and geometric structures has received a great deal of attention. Herein, we study the role of the quantum properties in controlling the plasmonic excitations of gold and silver atomic chains and rods. The influence of relativistic effects, scalar as well as spin-orbit, on the intensity and energy of plasmonic excitations is investigated. The intensity quenching and the red shift of energy in the presence of relativistic effects are introduced via the appearance of d orbitals directly in optical excitations in addition to the screening of... 

The primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives... 

We study the quantum plasmonic features of gold and silver nanoparticles using TD-DFT+TB, a new density functional theory approach to the calculation of excited states, which combines a full DFT ground state with tight-binding approximations in the linear response calculation. In this framework, the optical properties of closed-shell Ag, Au and bimetallic Ag-Au nanoparticles with tetrahedral symmetry (with 20, 56, 120, and 165 atoms) and icosahedral structure (with 13, 55, and 147 atoms) were obtained and compared to full linear response time-dependent density functional theory (TD-DFT) as a reference and also to time-dependent density functional based tight binding (TD-DFTB) as a low-cost... 

A cooperative space-frequency (SF) coded orthogonal frequency division multiplexing system is considered and its performance over quasi-static frequency-selective Rayleigh fading channels is evaluated. An expression for exact outage error probability is derived and its tight closed-form lower bound is presented. The tightness of the lower bound is demonstrated through Monte Carlo simulation. Asymptotic analysis indicates that the proposed protocol achieves full spatial and frequency diversities available in the cooperative communication system. The theoretical analysis of the proposed SF coded cooperation protocol is further confirmed by computer simulation using a previously introduced SF... 

Metal nanoclusters can be synthesized in various sizes and shapes and are typically protected with ligands to stabilize them. These ligands can also be used to tune the plasmonic properties of the clusters as the absorption spectrum of a protected cluster can be significantly altered compared to the bare cluster. In this paper, we computationally investigate the influence of thiolate ligands on the plasmonic intensity for silver, gold and alloy clusters. Using time-dependent density functional theory with tight-binding approximations, TD-DFT+TB, we show that this level of theory can reproduce the broad experimental spectra of Au144(SR)60 and Ag53Au91(SR)60 (R = CH3) compounds with... 

The binuclear cyclometalated complexes [Pt2Me 2(ppy)2(μ-dppm)], 1a, and [Pt2Me 2(bhq)2(μ-dppm)], 1b, in which ppy = 2-phenylpyridyl, bhq = benzo{h}quinoline and dppm = bis(diphenylphosphino)methane, were synthesized by the reaction of [PtMe(SMe2)(ppy)] or [PtMe(SMe 2)(bhq)] with 1/2 equiv of dppm at room temperature, respectively. Complexes 1a and 1b were fully characterized by multinuclear (1H, 31P, 13C, and 195Pt) NMR spectroscopy and were further identified by single crystal X-ray structure determination. A comparison of the intramolecular Pt-Pt and π-π interactions in complexes 1a and 1b has been made on the basis of data on crystal structures and wave functions analysis. The binuclear... 

From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects directed clinical tests towards optimizing safe utilization strategies. The noble metal nanoparticles (NP) are promising materials with antiviral and antibacterial properties that can deliver the drug to the target agent, thereby reducing the side effects. In this work, we applied both the quantum mechanical and classical atomistic molecular dynamics approaches to demonstrate the adsorption properties of HCQ/CQ on Ag, Au, AgAu, and Pt... 

Traditionally, the frequency spectrum is licensed to users by government agencies in a fixed manner where the licensee has exclusive right to access the allocated band. However, with increasing demand for the spectrum and scarcity of vacant bands, a spectrum policy reform seems inevitable. Meanwhile, recent measurements suggest the possibility of sharing spectrum among different parties subject to interference-protection constraints. In order to enable access to an unused licensed spectrum, a secondary user has to monitor licensed bands and opportunistically transmit whenever no primary signal is detected. Spectrum-sharing between a primary licensee and a group of secondary users has been... 

Naphthalimide derivatives provide highly versatile self-assembled systems and aggregated forms with fascinating emission properties that make them potential candidates for many applications such as bioimaging and sensing. Although various aggregated species of naphthalimide derivatives have been well documented, little is known about the correlation between their structure and photophysical properties. Here the preparation of a series of tetrameric naphthalimide molecules in which naphthalimide units are linked by bis-N-heterocyclic carbene complexes of coinage metals is described. An in-depth structural investigation into these tetramers has been carried out in solution and the solid state... 

Chiral recognition has long been a challenging issue to deal with in biological systems, drug design and food authentication. Implementing nanoparticle-based probes with intrinsic or induced chirality in this field has addressed several issues concerning sensitivity, reliability, rapidness and the cost of chiral sensing platforms. Yet, research into chiral nanoprobes that can be used for visual monitoring of chiral substances is still in its infancy. As part of this study, a visual chiral recognition platform has been developed in which a combination of blue-emitting carbon dots (BCDs) and mercaptopropionic acid-capped CdTe quantum dots (MPA-QDs) with inherent chiroptical activity were... 

To improve our understanding of the chemistry of actinide complexes and to spur their development in the field of actinide markers, two new uranium complexes were synthesized using 8-hydroxyquinoline and 5,7-dichloro-8-hydroxyquinoline. The prepared complexes were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, ultraviolet− visible spectroscopy, elemental analysis, and single-crystal X-ray diffraction. The impact of the electron-withdrawing group of the ligand on the photoluminescence spectra of the complexes in solution and in the solid state was scrutinized. The bandgap of the complexes was calculated using the density functional theory (DFT) method to... 

Herein we describe the synthesis and characterization of the first platinum(IV) metal-organic cage [(Me3PtIV)8(byp)12](OTf)8 (2), in which the organometallic moieties trimethylplatinum(IV) (PtMe3) occupied the corners of a cubane structure and 4,4′-bipyridine ligands used as linkers. The first-principles density functional theory calculations showed that the highest occupied molecular orbitals were localized on the PtMe3 moieties, while the lowest unoccupied molecular orbitals were distributed on the organic linkers. © 2021 American Chemical Society  

Herein we describe the synthesis and characterization of the first platinum(IV) metal-organic cage [(Me3PtIV)8(byp)12](OTf)8 (2), in which the organometallic moieties trimethylplatinum(IV) (PtMe3) occupied the corners of a cubane structure and 4,4′-bipyridine ligands used as linkers. The first-principles density functional theory calculations showed that the highest occupied molecular orbitals were localized on the PtMe3 moieties, while the lowest unoccupied molecular orbitals were distributed on the organic linkers. © 2021 American Chemical Society  

Coinage metal clusters are of great importance for a wide range of scientific fields, ranging from microscopy to catalysis. Despite their clear fundamental and technological importance, the experimental structural determination of copper clusters has attracted little attention. We fill this gap by elucidating the structure of cationic copper clusters through infrared (IR) photodissociation spectroscopy of Cu n + -Ar m complexes. Structures of Cu n + (n = 3-10) are unambiguously assigned based on the comparison of experimental IR spectra in the 70-280 cm -1 spectral range with spectra calculated using density functional theory. Whereas Cu 3 + and Cu 4 + are planar, starting from n = 5, Cu n +... 

In this paper, we analyze the performance of a nonlinear two-photon-absorption (TPA) receiver and compare its performance with that of a single-photon-absorption (SPA) receiver in the context of spectral-phase-encoded optical code-division multiple access (CDMA) technique. The performances for the above systems are evaluated for two different transmission scenarios, namely, asynchronous and slot-level synchronous transmitters. Performance evaluation includes different sources of degradation such as multiple-access interference, noise due to optical amplification, shot noise, and thermal noise. In obtaining the performance, the mean and variance of the received signal in each of the above... 

In this paper, the authors study the performance of a two-photon absorption (TPA) receiver in a typical communication system employing an optical amplifier. For the study, the authors develop a comprehensive performance analysis, taking into account noises due to an optical amplifier, shot noise, and thermal noise, using Gaussian approximation technique. In evaluating the performance of the system using this technique, the mean and the variance of the received signal will be derived. Comparing the results of receivers using the TPA process with that of a typical single-photon absorption (SPA) structure leads the authors to conclude that TPA receivers can be used when the speed of the...