The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)???HMX???FA (formamide), HMX???HMX???H2O and HMX???HMX???HMX complexes involving the chair and chair–chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6–31++G(d,p):PM3) and ONIOM2 (M06-2X/6–31++G(d,p):PM3) methods. The solvent effect of FA or H2O on the cooperativity effect in HMX???HMX???HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX???HMX???HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX???HMX???HMX.
In order to reveal the mechanism of drug action and design of DNA/RNA-targeted drugs containing aromatic rings, the cooperativity effects between the intermolecular π???π and H-bonding interactions in curcumin(drug)???cytosine(DNA/RNA base)???H2O were investigated by the B3LYP-D3 and MP2(full) methods with the 6–311++G(2d,p) basis set. The π???π interaction plays an important role in stabilizing the linear ternary complexes with the cooperativity effects, and the cyclic structures suffer the anticooperativity effects. The cooperativity or anticooperativity effects are notable, which could lead to a possible significant change in drug activity. The hydration is essentially the cooperativity or anticooperativity effect. These results were confirmed by the atoms in molecules (AIM), reduced density gradient (RDG), and surface electrostatic potentials analyses. The cyclic complexes are more stable, from which it can be deduced that the drug always links with the DNA/RNA base and H2O by the π???π or H-bonding interactions, and only in this way can the drug activity be shown. Therefore, the designed DNA/RNA-targeted drugs should possess a certain number of hydrophilic groups in contact with the DNA/RNA base and H2O to reconcile drug activity by the cooperativity effect between the π???π and H-bonding interactions, as is in agreement with many of the drugs in use.
Quantum chemical calculations were performed to investigate the stability of the ternary complexes BeH2···XMH3···NH3 (X?=?F, Cl, and Br; M?=?C, Si, and Ge) and the corresponding binary complexes at the atomic level. Our results reveal that the stability of the XMH3···BeH2 complexes is mainly due to both a strong beryllium bond and a weak tetrel–hydride interaction, while the XMH3···NH3 complexes are stabilized by a tetrel bond. The beryllium bond with a halogen atom as the electron donor has many features in common with a beryllium bond with an O or N atom as the electron donor, although they do exhibit some different characteristics. The stability of the XMH3···NH3 complex is dominated by the electrostatic interaction, while the orbital interaction also makes an important contribution. Interestingly, as the identities of the X and M atoms are varied, the strength of the tetrel bond fluctuates in an irregular manner, which can explained by changes in electrostatic potentials and orbital interactions. In the ternary systems, both the beryllium bond and the tetrel bond are enhanced, which is mainly ascribed to increased electrostatic potentials on the corresponding atoms and charge transfer. In particular, when compared to the strengths of the tetrel and beryllium bonds in the binary systems, in the ternary systems the tetrel bond is enhanced to a greater degree than the beryllium bond.
Utilizing first-principles calculations, we studied the electronic and optical properties of C24, C12X6Y6, and X12Y12 fullerenes (X?=?B, Al; Y?=?N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C24 may be tuned by doping, and the B12N12 fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices. They could also be used in solar cells and LEDs due to their low reflectivities.
To explore the adsorption mechanism of NO, NH3, N2 on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N2 physisorption, and N2 is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH3 physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.
Magnetic shielding constants for an isolated fullerene C60, cucurbituril CB[9], and the host-guest complex C60@CB[9] were calculated as a function of separation of the monomers. Our results in the gas phase and water indicate a significant variation of the magnetic properties for all atoms of the monomers in the complex and after liberation of fullerene C60 from the interior of the CB[9] cavity. The interaction between the two monomers results in a charge transfer that collaborates with a redistribution of electron density to deshield the monomers.
High-level ab initio calculations on the complexes between noble gas atoms (He, Ne, Ar, Kr, and Xe) and dihalogen molecules (F2, Cl2, Br2, and I2) reveal trends, both in interaction energies and the energy difference between the linear and T-shaped structures, that can be explained well in terms of dispersion interactions enhanced by polar flattening of the halogens. The partial discrepancies with experimental findings are discussed.
This work is focused on the donor properties of cobalt-exchanged cationic sites in zeolites. It is based on cluster and periodic density functional theory modeling for relevant {[Co(II)(NH3)n]–NO} adducts, where Co(II) means a cobalt cation embedded either in a periodic model of chabasite (CHA) zeolite or in model clusters. NO stretching frequencies were derived from MD trajectories and compared to harmonic values from cluster calculations. By relating calculated NO frequencies to experimental FTIR spectra, it was shown that the forms of {Co(II)-NO} adducts comprising three or four ammonia co-ligands dominate the spectrum taken in ammonia-saturation conditions while forms with two NH3 ligands prevail under intermediate ammonia saturation. Finally, this work confirms the critical dependence of Co(II) activation ability towards NO upon the center donor properties, reinforced by ligation of strong donor ammonia ligands. However, strongly bound ligands appear also to compete with interaction of the center with the electron-rich framework, and a balance must be observed to maintain optimal activation ability.
Graphical abstract A snapshot from MD trajectory showing a fragment of periodic framework with twoCo(II)–NO centers, bound to one framework oxygen and strongly coordinating three ammonia ligands with four others forming the second coordination sphere
An accurate comparison of the interaction of furan, pyrrole, and thiophene with different gaseous analytes is vital not only for understanding the sensing mechanism of corresponding polymers but also for rational design of new materials. In the present study, DFT calculations at (M05-2X/Aug-cc-PVDZ) have been performed to investigate the interaction behavior of furan, pyrrole, and thiophene (as models for their corresponding polymers) with different analytes (NH3, CO2, CO, N2H4, HCN, H2O2, H2S, CH4, CH3OH, SO2, SO3, H2O). The interaction of heterocycles with analytes is illustrated by changes in geometric, energetic, and electronic properties. SAPT calculations were performed for energy decomposition analysis to study the contribution of non-covalent components of the total interaction energy for each complex. Analysis of energetic and electronic properties reveals that all heterocycles are highly sensitive to SO3. The results suggest that sensing ability of polypyrrole is higher than polyfuran and polythiophene for all analytes.
Relativistic density functional theory finds that two isomers of a diuranium(III) complex of a polypyrrolic macrocycle (H4L) feature active sites on uranium moieties, allowing for their potential application in activating industrially and economically important small molecules. To address this, a series of adducts [(X)nU2(L)](2–m)+ (X?=?THF, I? and HI; n?=?1 and 2; m?=?0, 1 and 2) have been examined. The coordination from X to the exposed uranium(s) changes the general geometry and electronic structure slightly. Thermodynamic calculations reveal that iodine termination is energetically favored over THF/HI coordination.
Graphical abstract Scalar and spin-orbit coupling relativistic DFT calculation reveals that the active sites on the uranium moieties of [U2(L)]2+ lead to formation of adducts [(THF)nU2(L)]2+, [InU2(L)](2–n)+ and [(HI)nU2(L)]2+ (n?=?1 and 2). Coordination to the exposed uranium(s) changes geometrical and electronic properties slightly, but iodine termination is the most energetically favored.
The interaction of external water molecules with hydrated pyrrole-2-carboxaldehyde PCL/(H2O)n complexes was investigated. The work was supported by both theoretical [DFT/TD-DFT methods using 6-311G++(d,p) basis set in the ground (S0) and excited (S1, S2, S3)states] and experimental [UV-Vis, FTIR and Raman] verification. The focus of the present work was on the weak intermolecular O–H?O, N–H?O–H hydrogen bonded interaction (IerHB) between PCL and external water molecules, and the influence of increasing the number of water molecules to form hydrated PCL/(H2O)n complexes. Effects were observed on different vibrational normal modes and on electronic transition levels. A hydrogen-bonded network of water induces a shift to higher energy in certain normal modes of PCL to form stable PCL/(H2O)n complexes by lowering the barrier energy. Potential energy distribution (PED) analysis indicates a significant charge transfer from PCL to water by creating a water bridge. Hydrogen bonding effects account for the substantial red shift and broadness in νNH, νCO vibrational modes. Water rearrangement turns out to be the main driving force for hydrated complex formation.
Density functional theory (DFT) calculations were carried out to explore the geometric, spectroscopic, and electronic properties of three magic silver clusters Agn (n?=?8, 18, and 20) in detail. The computed results show that the global minima of these clusters are compact, near-spherical structures, while other low-lying isomers exhibit oblate or prolate shapes. Vertical ionization energies for the low-lying isomers were also computed and assigned with respect to available experimental values. Although several isomers were predicted to have similar energies, their electronic and vibrational signatures were quite distinctive, meaning that they could be used as fingerprint signals to distinguish between isomers. In addition, the electronic structures of these systems were explored using the phenomenological shell model. Calculations for the coinage metal clusters M20 (M?=?Cu, Ag, Au) indicated that the structures and properties of the Ag cluster are similar to those of the Cu cluster in that both Cu20 and Ag20 prefer a compact structure whereas Au20 prefers to adopt a tetrahedral form.
In this article, we explore the capacity of formed Schiff base complexes to trap metal atoms or ions, using their aromatic ends. The intrinsic geometry of each complex defines the process of substitution. Two cases were studied; one involving a trans Schiff base complex and the other considering how a salen ligand, with nickel systems traps chromium. We also assessed the nature of the new bonds and the frontier molecular orbitals.
The effect of alkali metal oxides MnO (M?=?Li, Na, K; n?=?2, 3, 4) on the geometric, electronic, and linear and nonlinear optical properties of the Mg12O12 nanocage was investigated by density-functional-based methods. According to the computational results, these alkali metal oxides are adsorbed on the Mg12O12 nanocage because this adsorption reduces its energy gap. The static first hyperpolarizability (β0) of the nanocage is dramatically increased in the presence of the alkali metal oxides, with the greatest increase seen in the presence of the superalkalis (i.e., M3O; M?=?Li, Na, and K). The highest first hyperpolarizability (β0?≈?600,000 a.u.) was calculated for K3O@Mg12O12, which was considerably more than that for Mg12O12. The thermodynamic properties and relative stabilities of these inorganic compounds are discussed.
The dual role of the ionic liquid 1-butyl-3-methyl-imidazolium trifluoroacetic acid ([C4mim]TFA) as an extractant for thiophene (TH) and a catalyst for the oxidation of TH was explored at the molecular level by performing density functional theory (DFT) calculations. The calculated interaction energies demonstrated why [C4mim]TFA is a better extractant for thiophene sulfone (THO2) than for TH. Two pathways were proposed for the oxidation of TH to THO2 with [C4mim]TFA acting as a catalyst. In the dominant pathway, a peracid is formed which then oxidizes TH to the sulfoxide and sulfones. The presence of [C4mim]TFA was found to greatly reduce the barrier to the oxidative desulfurization (ODS) of TH using H2O2 as an oxidant.
Nine minima were found on the intermolecular potential energy surface for the ternary system HNO3(CH3OH)2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO3…(CH3OH)2. The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO3…(CH3OH)2, meaning that it cannot be neglected in simulations in which the pair-additive potential is applied.
In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors.
A dispersion correction is introduced and tested for MNDO. The shift in electron density caused by the interaction between oscillating dipoles in the London picture of dispersion is mimicked by adding a small r?7-dependent attractive nucleus–electron potential to the core Hamiltonian. This potential results in a shift in electron density similar to that used by Feynman to explain dispersion. The resulting parameterized self-consistent and inherently multicenter treatment (MNDO-F) gives good results for CHNO compounds that do not exhibit hydrogen bonds, which MNDO cannot reproduce. This “Feynman” dispersion correction is also applicable to Hartree–Fock and density functional theory.
This paper inquires the C60 capabilities to contain radio-iodide (131I2) molecules. The encapsulation conditions are investigated applying first principles method to simulate with geometric optimizations and molecular dynamics at 310 K and atmospheric pressure. We find that the n131I2@C60 system, where n?=?1, 2, 3…, is stable if the content does not exceed three molecules of radio-iodide. The application of density functional theory allows us to determine that, the nanocapsules content limit is related with the amount of charge that is transferred from the iodine 131I2 molecules to the carbon atoms in the fullerene surface. The Mulliken population analysis reveals that the excess of charge increases the repulsive forces between atoms and the bond length average in the C60 structure. The weakened bonds easily break and will critically damage the encapsulation properties. Additionally, we test the interaction nanocapsules with different amounts of radioactive iodine diatomic molecules content with calcium atoms, and find that only the fullerene containing one radioactive iodine diatomic molecule was able to interact with up to nine atoms of calcium without disrupting or cracking. Other fullerenes with two and three radio iodine diatomic molecules cannot resist the interaction with a single calcium atom without cracking or being broken.
The local and condensed Fukui functions as well as the principle of hard and soft acids and bases were used to study the addition of free radicals to the exocyclic and endocyclic double bonds of seven monocyclic monoterpenes of formula C10H16. The results obtained showed that, in general, the most reactive double bond was the one with the most substituents on the double-bonded carbon atoms, and that the reaction of a double bond with an electrophile is a soft–soft interaction. The effects of substituents on the double-bonded carbon atoms and the stabilization of the monoterpenes were interpreted by invoking hyperconjugated structures, which led us to propose a simple rule: the larger the value of the Fukui function for the double bond, the greater the hyperconjugative stabilization and the susceptibility of the double bond to electrophilic attack. In general, our results are in good accordance with relevant experimental and theoretical results published in the literature.
