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Using density functional theory, polyols were used as model ligands for Cu+/Cu2+ complexes to study the role of the hydrogen bond network on the metal binding affinity. In addition to the gas phase studies, the calculations were performed in 1‐decanol and DMSO solvents. The Cu2+ complexes were the most stable complexes with the highest bond dissociation energies (BDE). The presence of three H‐bonds in the first shell increased BDE values up to 17.99 and 57.07 kcal/mol for Cu+ and Cu2+ complexes in the gas phase, respectively, whereas the presence of another three H‐bonds in the second shell increased BDE values up to 7.27 and 24.35 kcal/mol for Cu+ and Cu2+ complexes in the gas phase, respectively. Therefore, this H‐bond network caused, for example, a more stable Cu+ complex with a formation constant of 1.4 × 1017 times. The natural bond orbital (NBO), atoms in molecules (AIM), and reduced density gradient (RDG) analyses showed that the intramolecular hydrogen bond network led to the enhancement of metal‐binding affinity. [ABSTRACT FROM AUTHOR]

This study has centered on potentially important enzyme‐ligand interaction currently not incorporated: stacked cation–π interaction between the guanidinium group of arginine 590 residues in the HMG‐CoA reductase active site and the 4‐fluorophenyl group of type II statins. The geometry of interaction between these planar groups has been considered based on the X‐ray crystallographic structures already available in the protein data bank (PDB) archive. Electronic interaction energies between this residue and statins have been acquired by M06 and MP2 methods. In addition, stacking interaction and hydrogen bonding as two important investigated interactions are verified through prominent analyses: (1) quantum theory of atoms in molecules (QTAIM) analysis; (2) plotting and quantitative molecular surface analyses such as electrostatic potential (ESP) analysis, Hirshfeld surface (HS) and Becke surface (BS) analyses; (3) visual study methods such as noncovalent interaction (NCI), independent gradient model (IGM) analyses; and (4) localized orbital locator integrated pi over plane (LOLIPOP) index. The results indicate the absolute binding energy for type II statins is overall more than for type I statins. [ABSTRACT FROM AUTHOR]

1-Aminophosphonates are valuable compounds with wide range of applications in biological and industry. Various reaction conditions and catalysts have been reported for the synthesis of 1-aminophosphonates via three-component (dialkyl phosphite + aldehyde + amine) or two-component reaction (dialkyl phosphite + imine). Here a solvent-free synthesis of 1-aminophosphonates under very mild reaction conditions is reported. The three-component condensation reactions of dialkyl phosphite, carbonyl compound, and an amine gave 1-aminophosphonates in good to excellent yields under solvent- and catalyst-free conditions at ambient temperature. Hydrophosphorylation of imines in the presence of dialkyl phosphite under the same conditions gave also 1-aminophosphonates in good to excellent yields. These results showed that the reaction needs no catalyst or solvent for activation. It seems a tautomeric form of dialkyl phosphite (as one of the components) catalyzed the reaction. The reaction yield decreased using any solvent. In addition, a novel method is reported for the synthesis of N -deprotected 1-aminophosphonates (analogues of 1-amino acids) from N -PMP 1-aminophosphonate in the presence of TCCA. To understand the activity of the dialkyl phosphite under solvent-free conditions, the DFT calculations have provided insight into the basis of this activity. [ABSTRACT FROM AUTHOR]

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 precisely predict the inhibition of PIM-1 kinase by the novel designed drugs and compare them with the recently synthesized chemotherapeutic drugs such as DBC (Table 1). All designed structures were optimized at the B3LYP/6-311++G(d,p) level. The designed structure UNK4 (Table 1) was the most similar structure to DBC in terms of volumes, areas, and electrostatic potential map to DBC. The results obtained in this research represented that UNK4, with the building blocks of amino acid and cyclic carbohydrates could be considered an alternative anticancer drug for DBC. [ABSTRACT FROM AUTHOR]

A thermodynamic cycle is used to carry out several proton affinity, as well as electron-binding measurements, which are then used to effectively and accurately measure the cycloalkane and cycloalkene carbon-hydrogen (C-H) bond dissociation energies in the gas phase. The results show that the normally cited bond energies for such cyclic hydrocarbons are much smaller than their actual values, while a vast difference is observed between the actual and calculated values of their bond strengths.

The heat of hydrogenation of phenylcyclobutadiene is determined via a thermodynamic cycle by carrying out gas-phase measurements on 1-phenylcyclobuten-3-yl cation. The results are compared to G3, G3(MP2), and B3LYP computations and represent the first experimental measurements of the energy of a monocyclic cyclobutadiene.

A linear relation between delta-H(super degree) (sub acid)(HX), EA[X(sub .)], and BDE(HX) is shown for specific classes of compounds and only one of these quantities is needed to determine the others. The intercepts obtained from plots of delta-H(super degree) (sub acid)(HX) vs EA[X(sub .)] provide bond energies which correspond to BDE(HX) when EA[X(sub .)] = 0.

The alpha,2-, alpha,3- and alpha,4-dehydrophenoxide anions are regiospecifically generated by collisional activation of o-, m-, and p-nitrobenzoate. The alpha,2 and alpha,4 isomers are synthesized by reacting o-benzyne radical anion with carbon dioxide and electron ionization of p-diazophenol.

Mechanistic and energetic aspects for the conversion of camphor to 5-exo-hydroxycamphor by the compound I iron-oxo species of cytochrome P450 are discussed from B3LYP DFT calculations. The reaction occurs in a two-step manner along the lines that the oxygen rebound mechanism suggests.

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 and N-protonated 2,5-dihydro-1H-pyrrole, (c) furan and N-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 the exo reaction pathway. The optimized structures of the transition states (TSs) and products, along with the Gibbs free energies of activation and reaction were calculated in the gas phase and dichloromethane by B3LYP/6-31G++(d,p) method. It was found that the exo adduct is the most kinetically and thermodynamically favored product for all of the DA reactions mentioned above. Moreover, the role of the HB in stabilizing the exo stereoisomer (and the corresponding TS) was much more pronounced for the reactions involving cationic species (cases b–d). In the end, a hypothetical synthetic method was proposed for obtaining exo-2-alkylbicyclo[2.2.1]heptanes. Our findings suggest that the HB can be employed as an effective interaction to control the stereoselectivity of DA reactions. [ABSTRACT FROM AUTHOR]

Ionic liquids, which are widely known as room temperature molten salts, have been the subject of much scientific debate for more than a decade. These compounds can be used as green solvents or even as additives in many reactions. Due to their noticeable conductivity, which is a function of the interaction energies existing between the ion pairs in ionic liquids, the synthesis and introduction of new families of these chemicals are of importance. The target of this paper is to design new carboxylate-based ionic liquids containing OH and CF3 groups. Our results indicate that the properties of these ILs are highly affected by the presence of OH and CF3 groups, in which OH stabilizes the negative charge of the anion via intramolecular hydrogen bonds and CF3 stabilizes it through the electron withdrawing effect. These groups decrease the binding energy between the anion and cation of the carboxylate-based ionic liquids and thus affect their physical properties such as melting point and density as well as their chemical properties. All calculations in this study were performed in the gas phase at the B3LYP/6-311++G(d,p) level. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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), critical point (CP) eigenvalues (atoms in molecules [AIM] analysis), and natural bond orbital (NBO) analysis including natural population analysis (NPA) and change of charge transfer energy (ΔECT). Our results show that in the presence of Au3 NC, BDEs of the NH and OH bonds increase in both ONHAu3 (1) and ONOHAu3 (2) compared with their free forms (ONH and ONOH, respectively). In other words, the tendency to dissociate these bonds and form their corresponding RNS (1′ and 2′) decreases in the presence of gold. This is exactly the opposite of what is observed for the OH bonds in HOHAu3 (3), HOOHAu3 (4), and their corresponding ROS (3′ and 4′). Therefore, we can conclude that gold shows a different behavior in the face of RNS compared with ROS where it is a better scavenger of ROS than RNS. [ABSTRACT FROM AUTHOR]

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 369 kcal.mol−1, indicating they are stronger acid than ethanol and 2‐propanol with the acidity values of 378.3 and 375.1 kcal.mol−1, respectively. This is related to the stabilization of the conjugate bases of these sugar through intramolecular H‐bonds, which were analyzed in this study using atoms in molecules (AIM) and natural bonding orbital (NBO) methods. AIM and NBO analyses indicate the presence of one bifurcated intramolecular H‐bond in the conjugate bases of L‐lyxose and L‐arabinose and two bifurcated H‐bonds in conjugate base of D‐ribose, whereas the conjugate bases of L‐fucose, L‐rhamnose, and D‐xylose present one normal intramolecular H‐bond. According to the topological parameters and charge transfer data, existence of normal and bifurcated intramolecular H‐bonds could greatly increase acidity of deoxy‐hexose sugars. The H‐bond strength in the conjugate bases of aldo‐pentose sugars is higher than that in the conjugate bases of methyl‐pentose sugars including CH3 group on C5, making aldo‐pentose sugars stronger acid than methyl‐pentose sugars. [ABSTRACT FROM AUTHOR]

Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules like carbohydrates, nucleic acids and proteins and have served as templates for proton transfer reactions. The computations in dimethyl sulfoxide on a series of polyols have shown that multiple hydrogen bonds to a single charged center have led to enhanced acidities and a new class of Bronsted acids is described.

A study is conducted, in which the enthalpies of formation of o-, m- and p-benzoquinone are determined by carrying out gas-phase ion energetic measurements, combustion calorimetry and phase-change determinations, and high-level quantum chemical computations. By combining the results obtained in thermodynamic cycles, the heats of hydrogenation and the heats of formation of o-, m- and p-benzoquinone are derived.

Bracketing and equilibrium techniques were used for examining the gas-phase acidity of 3,3-dimethylcyclopropene. The C-H bond energies of 3,3-dimethylcyclopropene differs by 26.1 plusmn 3.8 kcal mol(super -1).

Abstract: 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 critical points of hydrogen bonds and the interaction energy values was checked. [ABSTRACT FROM AUTHOR]

Abstract: 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 anchoring bond is responsible for the interaction of Au3 cluster and ROH (or RO•), its nature was interpreted by means of the quantum theory of atoms in molecules and the natural bond orbital. The results indicate that O–Au bond is stronger and has more covalent character in RO•–Au3 than in ROH–Au3. The interaction of Au3 cluster with RO• is 1.5 to 3 times more than that with ROH. As a result, gold cluster scavenging property appears more prominent than its free radical initiation activity. [ABSTRACT FROM AUTHOR]

Abstract: The free radical activity of lespedezacoumestan was investigated toward hydroxyl (˙OH) radical in polar and nonpolar media using density functional theory. Four reaction mechanisms including radical adduct formation, hydrogen atom transfer, sequential single electron‐proton transfer (SET‐PT), and sequential proton loss electron transfer were considered. The rate constants and branching ratio for all possible sites of reaction were calculated and reported for the first time. According to the obtained results, lespedezacoumestan reacts faster with ˙OH radical in aqueous solution than in nonpolar media. Also, lespedezacoumestan is an excellent ˙OH radical scavenger regardless of the environment polarity. [ABSTRACT FROM AUTHOR]