Sharif Digital Repository

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... 

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),... 

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  

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... 

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... 

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... 

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, 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,... 

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

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... 

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M3 clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M3 clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H⋯M and O-H⋯M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next... 

Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare... 

The reaction pathway (including the transition state) of ethylene addition to permanganate (MnO4-) in the presence of ethylene glycol (EG) has been qualitatively and quantitatively studied by means of B3LYP/6-311++G* theoretical analysis. Interestingly, by cluster formation of the EG with permanganate, oxidation reaction becomes thermodynamically and kinetically more favorable. The influences of electron-withdrawing as well as electron-donating substituents were also explored. Results of the quantum theory of atoms in molecules and natural bond orbital analyses revealed that [3 + 2] addition reaction of alkenes in the presence of EG as hydrogen bonding donor to MnO4- becomes more exothermic.... 

The optimized minimum-energy geometries of different macrocyclic amines and their protonated structures were determined by using ab initio and density functional theory (DFT) calculations. All the gas phase optimizations and energy calculations were performed at the DFT/B3LYP/6-311++G(d,p) level of theory. The HF/6-31 + G(d,p) level was used for all single point calculations in the solution phase. Geometry optimizations indicate that the most stable structures are stabilized by intramolecular hydrogen bonds. The proton affinity (PA) of macrocyclic amines is controlled by the strength of intramolecular hydrogen bonds of macrocyclic amines. These hydrogen bonds strongly influence the basicity...