Sharif Digital Repository

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... 

PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to... 

We have studied the intramolecular H-bonds existing in cyclic and open forms of glucose using B3LYP/6-311++G(d,p) level, AIM, and NBO methods. The theoretical results indicated that based on acidity values, (ΔHacid), glucose in the open form is more acidic than cyclic form. The acidity values for open and cyclic glucose (332 and 338 kcal/mol) exhibit significantly lower values (i.e., stronger acid) than the reported acidity values for α-/ß-anomers of D-glucopyranose and simple alcohols. Because their conjugate bases are more stabilized through trifurcated and bifurcated intramolecular H-bonds. AIM analysis showed normal H-bonds in the conjugate bases of open glucose (O-Glc), bifurcated, and... 

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)... 

Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution (H2O, DMSO, and CH 3CN) phase. Polarized continuum model was applied to calculate pKa values of alkyl sulfonic acids and polyolalkyl sulfonic acids. A comparison between acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution phase indicates that the acidity strength of polyolalkyl sulfonic acids enhances with the increase of the cooperativity effect of intramolecular hydrogen bonds in polyolalkyl sulfonic acids. Natural bond orbital and quantum theory of atoms in molecules... 

In the present density functional theory study, we have compared intrinsic properties of non-natural nucleobases (acA, acG, acC, and acT nucleobases) such as proton affinities, gas phase acidities, tautomerization, and hydrogen-bonding properties with those in normal Watson-Crick nucleobases (A, G, C, T nucleobases). The hydrogen-bonding interactions in non-natural and Watson-Crick base pairs were studied at B3LYP/6-311++G (d,p) level regarding their geometries, energies, and topological features of the electron density. The quantum theory of atoms-in-molecule (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in base pairs. The... 

In this study, ionic liquids formed between 1-ethyl-3-methylimidazolium cation ([emim]+) and alkyltrifluoroborate ([RBF3]-, R = n-CmH2m+1 (m = 1-5)) anions have been investigated theoretically. The interactions between the cation and anions have also been calculated at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory. The calculated interaction energies were found to decrease in magnitude with the increase of side-chain length in anions. The results of energy decomposition analysis (EDA) show that the interaction of these anions with [emim]+ cation is electrostatic in the nature and the side chain length in the anions has an important effect on the contribution of ΔEelect term. The... 

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... 

The cation radicals of DNA constituents generated by the ionizing radiation initiate the alteration of the bases, which is one main type of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break, and it is important to identify the cation radical formation at particular atomic site in these molecules so that the major pathway for the nucleic acid damage may be trapped. In the present study, we explored theoretically energetic, structural, and electronic properties of the possible radicals formed via proton atom abstraction at various sites of sugar part of deoxycytidine cation radical by employing density functional theory at... 

The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA.... 

Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the... 

Different strategies are employed in designing strong and selective anion receptors but stereoelectronic effects have been largely ignored. In this work, the stereo configuration of a non-interacting ether is found to have a large impact of more than two orders of magnitude on the binding of a rigid diol with tetrabutylammonium chloride in acetonitrile-d3. A favorable carbon-oxygen dipole and an intramolecular C-H⋯OH hydrogen bond in an equatorially substituted ether is found to be energetically more important than a stabilizing hydrogen bond in the corresponding axially oriented alcohol. IR spectroscopy is also used to probe the structures of the bound complexes and several binding motifs... 

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... 

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... 

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were... 

In this article, we report the computational examination of the impact of hydrogen bonding (HB) on the stereoselectivity of a series of Diels-Alder (DA) reactions. Four different types of diene/dienophile couples were studied including (a) cyclopenta-2,4-dien-1-ol and heteroatom-substituted cyclopentenes, (b) substituted cyclopentadienes andN-protonated 2,5-dihydro-1H-pyrrole, (c) furan andN-protonated 5-azabicyclo[2.1.1]hex-2-ene, and (d)N-protonated cyclopenta-2,4-dien-1-amine and α,β-unsaturated carbonyl compounds. These systems were designed such that the HB can only exist in theexoreaction pathway. The optimized structures of the transition states (TSs) and products, along with the... 

The pKa value for protonated forms of different benzo-substituted quinuclidines in aqueous solution has been calculated using DFT methods (MP2//B3LYP, B3LYP and M06-2X) and 6-311++G(d,p) basis set and are compared with corresponding experimental values. The results were obtained from different theoretical methods so close to the corresponding experimental values but the best agreement were achieved with B3LYP/6-311+G(d,p) level of theory. The average error was found to be less than 1.6pKa unit. Relative pKa values were computed for each protonated benzo-substituted quinuclidine using quinuclidine as a reference. Solvation was included in the calculations in all used different methods using... 

Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the... 

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... 

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...