Sharif Digital Repository

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our... 

The behaviour of solvatochromic absorbance probes (4-nitroaniline, 4-nitroanisole, and Reichardt's dye) within binary mixtures of polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (Triton X-100 or TX-100)/organic solvents (2-propanol, hexanol, butyl acetate, THF, toluene, and p-xylene) was extensively explored by using solvatochromism and the quantum theory of atoms in molecules (QTAIM). To be more precise, the polarity parameters, ET N, and Kamlet-Taft parameters, such as the hydrogen bond donor ability (HBD) (α), hydrogen bond acceptor ability (HBA) (β), and dipolarity/polarizability (π∗), have been investigated in selected mixtures at 298 K. All binary mixtures exhibit complex... 

Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au3 cluster on RO• vs its impacts on RO-H bond dissociation enthalpy, at B3LYP/ LACVP+* level (RH, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). In the presence of Au3 cluster, bond dissociation enthalpy of O-H bond and the spin density at the RO• oxygen are reduced dramatically. These are clear evidences for both the Au3 facilitation of the RO-H bond breakage and its scavenging of RO• radical. Since O-Au anchoring... 

In this study, the structural and electronic properties of a carbohydrate-based (6-amino-6-deoxy hexopyranose [ADHP]) ionic liquid were explored. The interactions among 3 anions (BF4 ¯, PF6 ¯, and ClO4 ¯) and ADHP as cation were investigated at B3LYP/6-311++G(d,p) level. Based on the calculated interaction energy, it was found that PF6 ¯ anion has the highest interaction energy with ADHP. It was found that the hydrogen bonds play an important role in the interaction of ion pairs. The nature of hydrogen bonds in the optimized ion pars was analyzed by using natural bond orbital analysis and the quantum theory of atoms in molecules. The linear relationship between electron density at the bond... 

Anticancer character of gold cluster has been indicated through its free radical scavenging properties. This is in contrast to its free radical promoting ability suggested by other workers. Here, we address this controversy by probing the stabilizing effects of Au3 cluster on RO• vs its impacts on RO–H bond dissociation enthalpy, at B3LYP/ LACVP+* level (R═H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). In the presence of Au3 cluster, bond dissociation enthalpy of O–H bond and the spin density at the RO• oxygen are reduced dramatically. These are clear evidences for both the Au3 facilitation of the RO–H bond breakage and its scavenging of RO• radical. Since O–Au... 

In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H 2 O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy-1,4-benzoquinone. Noncovalent interaction reduced density gradient (NCI-RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm... 

The unusual monosaccharaides such as deoxy-hexose sugars, including methyl-pentose and aldo-pentose, are promising and important sugars in life science. However, little research on H-bond interactions in these systems has been reported. The aldo-pentose has a proton instead of the CH2OH group on C5; conversely, methyl-pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H-bonds on acidity of CH3-pentose sugars (L-fucose and L-rhamnose) and aldo-pentose sugars (D-xylose, L-lyxose, D-ribose, and L-arabinose) using B3LYP/6-311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy-hexose were found to be from 343 to... 

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd  

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd  

In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),... 

In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),... 

Various thermodynamic and structural properties of amino acid ionic liquids (AAILs), comprising 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C 2 OHmim] + ) cation mixed with Glycinate [Gly], Serinate [Ser], Alaninate [Ala], and Prolinate [Pro] AA anions are explored using molecular dynamic (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis. In general, the simulated thermodynamic results are in good agreement with the reported experimental data. Structural dependence of vdW- and electrostatic energies of AAILs is [Pro] > [Ala] > [Ser] > [Gly] and [Gly] > [Ala] > [Pro] > [Ser], respectively. The similar trend of electrostatic energies is found for their interaction... 

Herein, we report the synthesis, characterization and combined structural and full computational analysis of noncovalent interactions in a new hydrazine ligand and its two chlorido- and endo-nitrito-rhenium(I) tricarbonyl complexes. The analysis of crystal structures has been accompanied by comprehensive computational studies of the noncovalent interactions utilizing the quantum theory of atoms in molecules (QTAIM), natural bond orbitals (NBO), independent gradient model (IGM), and electron localization function (ELF) to shed light on the nature of the interactions. On the other hand, comprehensive energy decomposition analysis (EDA) by extended transition state coupled with natural orbitals... 

In this work, the intramolecular H-bonds in galactose were studied using DFT at the B3LYP/6–311++G (d,p) levels of theory, atoms in molecules (AIM), and natural bond orbital (NBO). AIM and NBO analysis revealed a cooperative network of trifurcated, bifurcated, and normal H-bonds for the conjugate bases of open galactse (O-Gal). While for the conjugate base of the cyclic form of galactose, we identified bifurcated and normal H-bonds, which may highlight a crucial feature of the biological activity of a whole class of natural sugars. The O-H…O bonds are categorized as mostly electrostatic, strong H-bonds and more favorable, whereas for multiple interactions involving C=O…H, C-H…O and C-H…H-C... 

In this study, two types of ionic liquids (ILs) based on 1 butyl 3 methylimidazolium [Bmim]+ and butyltrimethylammonium [Btma]+ cations, paired to tetrafluoroborate [BF4], hexafluorophosphate [PF6], dicyanamide [DCA], and bis(trifluoromethylsilfonyl)imide [Tf2N] anions, were chosen as adsorbates to investigate the influence of cation and anion type on the adsorption of ILs on the graphene surface. The adsorption process on the graphene surface (circumcoronene) was studied using M06 2X/cc pVDZ level of theory. Empirical dispersion correction (D3) was also added to the M06 2X functional to investigate the effects of dispersion on the binding energy values. The graphene···IL configurations,... 

In this study, drastic influence of the intramolecular cation-π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation-π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation-π interaction of ammonium with aromatic ring. These cation-π interactions strongly influence the basicity of amines. Natural bond orbital (NBO)...