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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]

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]

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]

Polyols were used as model ligands for Mg2+, Ca2+, and Zn2+ complexes to study the role of the hydrogen bond network on the metal binding affinity and modulation of successive pKa values using density functional theory. The results confirm that the acidity of polyols dramatically increases upon metal complexation in the order Zn2+ ＞ Mg2+ ＞ Ca2+. For example, the three H-site positions in the hydroxyl groups of the heptaol, bound to Zn2+, are 11.2, 29.9, and 30.9 pKa units (in methanol) more acidic than those of pure heptaol. This acidity enhancement leads to making polyols as good ligands toward complexation. For instance, the formation constants of the heptaol in the presence of Zn2+, Mg2+, and Ca2+ in methanol were 5.67 × 1071, 6.46 × 1066, and 1.26 × 1053 times lower than those in its third deprotonation state, respectively. The natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and reduced density gradient (RDG) analyses show that the intramolecular hydrogen bond network and increment of carbon chain length lead to the enhancement of metal binding affinity. These findings can be used for the manipulation of ligands and metal cations in designing metalloproteins. [ABSTRACT FROM AUTHOR]

In this work, the antioxidant ability of fisetin was explored toward hydroxyl (•OH) radical in aqueous and lipid solution using density functional level of theory. Different reaction mechanisms have been studied: hydrogen atom transfer, single electron transfer followed by proton transfer, and radical adduct formation, and sequential proton loss electron transfer. Rate constants for all possible reaction sites have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different channels of reaction are reported for the first time. Results show that the reactivity of fisetin toward hydroxyl (•OH) radical takes place almost exclusively by radical adduct formation regardless of the polarity of the environment. Also, the single-electron transfer process seems to be thermodynamically unfavorable in both media. [ABSTRACT FROM AUTHOR]

The α-C-H bond dissociation energy (BDE) of phenylcyclopropane (1) was experimentally determined using Hess' law. An equilibrium acidity determination of 1 afforded ΔH°acid = 389.1 ± 0.8 kcal mol-1, and isotopic labeling established that the α-position of the three-membered ring is the favored deprotonation site. Interestingly, the structure of the base proved to be a key factor in correctly determining the proper ionization site (i.e., secondary amide ions are needed, and primary ones and OH- lead to incorrect conclusions since they scramble the deuterium label). An experimental measurement of the electron affinity of 1-phenylcyclopropyl radical (EA = 17.5 ± 2.8 kcal mol-1) was combined with the ionization energy of hydrogen (313.6 kcal mol-1) to afford BDE = 93.0 ± 2.9 kcal mol-1. This enabled the effect of the phenyl substituent to be evaluated and compared to other situations where it is attached to an sp³- or sp²-hybridized carbon center. M06-2X, CCSD(T), G4, and W1BD computations were also carried out, and a revised C-H BDE for cyclopropane of 108.9 ± 1.0 kcal mol-1 is recommended. [ABSTRACT FROM AUTHOR]

For the first time, the mechanism of Fischer esterification between acetic acid and ethanol over silica-functionalized propylsulfonic acid (silica-propyl-SO 3 H) catalyst was explored by means of computational modeling techniques. For this purpose, 6-edge-atom cage-like cluster comprising Si–O–Si sequences has been selected to represent the surface of the catalyst. The results indicate that the reaction goes through concerted transition states. In all optimized structures no proton (H + ) transfer occurs from catalyst to the substrates and the role of the catalyst is via the activation of the substrates through the formation of strong hydrogen bonds (H-bonds). Furthermore, the energetic diagram demonstrates that the activation energies of forward (esterification) and reverse (ester hydrolysis) reactions only differ by 0.3 kcal/mol. The quantum theory of atoms in molecules (QTAIM) analysis was performed to investigate the nature of H-bonds. Another mechanism in which the catalyst has been acted as the Brønsted acid/base was also provided for this reaction. [ABSTRACT FROM AUTHOR]

Computational investigations on the gas phase S N 2 reactions of X ions ( X - = OH - , F - , Cl - , Br - , and I - ) with fluoroethane and 2-fluoroethanol (β-hydroxyl ethyl fluoride) were performed by using MPW1K, M06 and CCSD(T) methods with a range of basis sets including 66-311++G ∗∗ , TZVP, aug-cc-pVDZ and SDD. To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis and Bader’s quantum theory of atoms in molecules (QTAIM). In our calculations, we took into account two possible pathways for these reactions, i.e. S N 2 reactions of 2-fluoroethanol. In path( i ), β-hydroxyl group participates in hydrogen bonding (H-bonding) with fluoride ion as leaving group in transition state. However, in path( ii ), transition state includes H-bonding between hydroxyl group and nucleophile X − . Results indicate that in comparison with the absence of β-OH substituent i.e. reactions of fluoroethane, the activation barrier decreases in path( i ), but increases in path( ii ). The progress of each pathway depends on H-bonding character of nucleophile and leaving group. In addition, for X - = Cl - we compared β-OH group effect in the gas phase with its effect in dimethyl sulfoxide (DMSO). [ABSTRACT FROM AUTHOR]

• Acidity enhancement of bioorganic compounds. • Hydrogen bonding effects on acidity of bioorganic molecules. • Stability of the conjugate base via H-bond network. Density functional theory method and B3LYP/6-31+G(d) level of theory were used to predict the acidity of barbiturates and their corresponding metabolites in the gas and solution phase (H 2 O). Polarized continuum model was applied to calculate p K a values of barbiturates and metabolites. A comparison between acidity of barbiturates and metabolites in the gas and solution phase indicates that the acidity strength of barbiturates enhances with the increase of intramolecular hydrogen bonds in metabolites. This acidity can increase to 9.47 kcal/mol in gas phase and 2.73 p K a units in solution phase for a typical metabolite of barbiturate due to the effect of intramolecular hydrogen bonds. Also, linear correlation between gas phase acidity (ΔG acid) and solution phase (p K a) was obtained and can be used for p K a prediction of metabolites in solution phase. [ABSTRACT FROM AUTHOR]

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 (H2O, 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 intramolecular hydrogen bonding effect on acidity. Quantum theory of atoms in molecules (QTAIM) was also used to study the nature of hydrogen bonds. QTAIM results showed that the intramolecular hydrogen bonds in these structures are electrostatic (closed‐shell) interactions in nature. In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy‐1,4‐benzoquinone derivatives are explored by using ab initio and density functional theory (DFT) calculations. It was found that remote hydrogen bonding could play a surprisingly role in increasing the acidity of hydroxy‐1,4‐benzoquinone. [ABSTRACT FROM AUTHOR]