Spin-polarized first-principles total-energy calculations have been performed to investigate the possible chain reaction of acetylene molecules mediated by hydrogen abstraction on hydrogenated hexagonal boron nitride monolayers. Calculations have been done within the periodic density functional theory (DFT), employing the PBE exchange correlation potential, with van der Waals corrections (vdW-DF). Reactions at two different sites have been considered: hydrogen vacancies on top of boron and on top of nitrogen atoms. As previously calculated, at the intermediate state of the reaction, when the acetylene molecule is attached to the surface, the adsorption energy is of the order of ?0.82 eV and ?0.20 eV (measured with respect to the energy of the non interacting molecule-substrate system) for adsorption on top of boron and nitrogen atoms, respectively. After the hydrogen abstraction takes place, the system gains additional energy, resulting in adsorption energies of ?1.52 eV and ?1.30 eV, respectively. These results suggest that the chain reaction is energetically favorable. The calculated minimum energy path (MEP) for hydrogen abstraction shows very small energy barriers of the order of 5 meV and 22 meV for the reaction on top of boron and nitrogen atoms, respectively. Finally, the density of states (DOS) evolution study helps to understand the chain reaction mechanism.
We present a theoretical study on the detailed mechanism and kinetics of the H+HCN →H+HNC process. The potential energy surface was calculated at the complete basis set quantum chemical method, CBS-QB3. The vibrational frequencies and geometries for four isomers (H2CN, cis-HCNH, trans-HCNH, CNH2), and seven saddle points (TSn where n = 1 ? 7) are very important and must be considered during the process of formation of the HNC in the reaction were calculated at the B3LYP/6-311G(2d,d,p) level, within CBS-QB3 method. Three different pathways (PW1, PW2, and PW3) were analyzed and the results from the potential energy surface calculations were used to solve the master equation. The results were employed to calculate the thermal rate constant and pathways branching ratio of the title reaction over the temperature range of 300 up to 3000 K. The rate constants for reaction H + HCN → H + HNC were fitted by the modified Arrhenius expressions. Our calculations indicate that the formation of the HNC preferentially occurs via formation of cis–HCNH, the fitted expression is kPW2(T) = 9.98 × 10?22T2.41 exp(?7.62 kcal.mol?1/RT) while the predicted overall rate constant kOverall(T) = 9.45 × 10?21T2.15 exp(?8.56 kcal.mol?1/RT) in cm3 molecule?1s?1.
Graphical Abstract (a) Potential energy surface, (b) thermal rate constants as a function of temperature and (c) the branching ratios (%) of PW1, PW2, PW3 pathways involved in rm H + HCN → H + HNC process.
Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen–halogen contacts and hydrogen bonds (I?N, I?F, I?I, F?F, I?H and F?H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of ?9.58 kcal mol?1 and ?7.10 kcal mol?1 observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen–halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures.
Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.
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.
Mechanisms for the activation of water, ammonia, and other small molecules by the PCcarbeneP nickel pincer complex were studied computationally with the aid of density functional theory. The calculation results indicate that the strongly donating, nucleophilic carbene center can engage in a variety of heterolytic splitting of E?H (E=H, C, N, O) bonds, some of which are reversible. The cleavage of E?H bonds across the Ni=C bond represents a new mode of bond activation by ligand cooperativity in nickel pincer complex. On the basis of the calculations, we also demonstrate that reversible H2 activation across the Ir=C bond via the PCcarbeneP iridium pincer complex was observed in the experiments, while other E?H (E=C, N, O) bonds were not activated. Our calculations are in good agreement with experimental observations and could provide new insights into ligand cooperativity in nickel pincer complexes.
Density functional theory (DFT) calculations are performed to study the hydrogen-bonding in the DMSO-water and DMF-water complexes. Quantitative molecular electrostatic potential (MESP) and atoms-in-molecules (AIM) analysis are applied to quantify the relative complexation of DMSO and DMF with water molecules. The interaction energy of DMSO with water molecules was higher than in DMF-water complexes. The existence of cooperativity effect helps in the strong complex formation. A linear dependence was observed between the hydrogen bond energies EHB, and the total electron densities in the BCP’s of microsolvated complexes which supports the existence of cooperativity effect for the complexation process. Due to the stronger DMSO/DMF and water interaction, the water molecules in the formed complexes have a different structure than the isolated water clusters. NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex.
Graphical abstract NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex.
MP2/aug-cc-pVTZ calculations were performed for complexes linked by hydrogen bonds. Three types of proton donating species were taken into account: H2O, CCl3H, and H3O+. These calculations are supported by the natural bond orbital (NBO) method and the quantum theory of atoms in molecules (QTAIM) approach. Numerous correlations between parameters of H-bonded systems were found. The most important are those which show the response of the system on the H-bond formation; for example, the increase of polarization of the A-H bond correlates with the strength of the hydrogen bond. Similar relationships were found for the σ-hole bonds while the π-hole bonds do not follow the trends known for the hydrogen bonds.
The evolution of structural properties, thermodynamics and averaged (dynamic) total hardness values as a function of the composition of binary water–organic solvents, was rationalized in view of the intermolecular interactions. The organic solvents considered were ethanol, acetonitrile, and isopropanol at 0.25, 0.5, 0.75, and 1 mass fractions, and the results were obtained using molecular dynamics simulations. The site-to-site radial distribution functions reveal a well-defined peak for the first coordination shell in all solvents. A characteristic peak of the second coordination shell exists in aqueous mixtures of acetonitrile, whereas in the water–alcohol solvents, a second peak develops with the increase in alcohol content. From the computed coordination numbers, averaged hydrogen bonds and their lifetimes, we found that water mixed with acetonitrile largely preserves its structural features and promotes the acetonitrile structuring. Both the water and alcohol structures in their mixtures are disturbed and form hydrogen bonds between molecules of different kinds. The dynamic hardness values are obtained as the average over the total hardness values of 1200 snapshots per solvent type, extracted from the equilibrium dynamics. The dynamic hardness profile has a non-linear evolution with the liquid compositions, similarly to the thermodynamic properties of these non-ideal solvents.
Graphical abstract Computed dynamic total hardness, as a function of the cosolvent mass fraction for water–ethanol (EtOH), water–isopropanol (2PrOH) and water–acetonitrile (AN)
The anti-hypertensive drugs amlodipine, atenolol and lisinopril, in ordinary and PEGylated forms, with different combined-ratios, were studied by molecular dynamics simulations using GROMACS software. Twenty simulation systems were designed to evaluate the interactions of drug mixtures with a dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane, in the presence of water molecules. In the course of simulations, various properties of the systems were investigated, including drug location, diffusion and mass distribution in the membrane; drug orientation; the lipid chain disorder as a result of drug penetration into the DMPC membrane; the number of hydrogen bonds; and drug surface area. According to the results obtained, combined drugs penetrate deeper into the DMPC lipid bilayer membrane, and the lipid chains remain ordered. Also, the combined PEGylated drugs, at a combination ratio of 1:1:1, enhance drug penetration into the DMPC membrane, reduce drug agglomeration, orient the drug in a proper angle for easy penetration into the membrane, and decrease undesirable lipotoxicity due to distorted membrane self-assembly and thickness.
An experimentally determined structure for human CYP2J2—a member of the cytochrome P450 family with significant and diverse roles across a number of tissues—does not yet exist. Our understanding of how CYP2J2 accommodates its cognate substrates and how it might be inhibited by other ligands thus relies on our ability to computationally predict such interactions using modelling techniques. In this study we present a computational investigation of the binding of arachidonic acid (AA) to CYP2J2 using homology modelling, induced fit docking (IFD) and molecular dynamics (MD) simulations. Our study reveals a catalytically competent binding mode for AA that is distinct from a recently published study that followed a different computational pipeline. Our proposed binding mode for AA is supported by crystal structures of complexes of related enzymes to inhibitors, and evolutionary conservation of a residue whose role appears essential for placing AA in the right site for catalysis.
Graphical Abstract Arachidonic acid docked in the active site of CYP2J2 assumes a catalytically competent binding mode stabilised by hydrogen bonds to Arg117
Protonation in the two-electron/two-proton reduction processes of 2,6-dichlorophenolindophenolate (DCIP) is investigated combining density functional theory (DFT) and molecular dynamics (MD) methods. DCIP (anion), DCIP?– (radical anion), and DCIP2? (dianion) are considered, including the electronic structure analysis from the prospective of quantum theory of atoms and molecules (QTAIM). It is shown that oxygen on the indophenolate moiety and nitrogen are the first and/or the second proton acceptor sites and their energetic order depends on the total charge of the system. MD simulations of differently charged species interacting with the solvent molecules have been performed for methanol, water, and oxonium cation (H3O+). Methanol and water molecules are found to form only hydrogen bonds with the solute irrespective of its charge. The calculated pKa values show that the imino group of DCIPH? is a weaker acid than water. While in the case of DCIP (and DCIP?–) plus oxonium cation, proton transfer from the solvent to the solute was evidenced for both aforementioned acceptor sites. In addition, MD simulations of bulks containing 15 and 43 molecules of water around the DCIP molecule have been performed, revealing the formation of 2–4 hydrogen bonds.
Graphical Abstract 2,6-Dichlorophenolindophenolate interacts with solvent molecules (water, oxonium cation and methanol). Hydrogen transfer and electronic structure are studied by DFT and molecular dynamics methods
A new compound based on the D-π-A concept, where D = dimethylamino-phenyl and A = naphthoic acid, separated by an imine motif, was designed, synthesized and characterized. The spectral, energetics, and structural characteristics of the compound were studied thoroughly theoretically by density functional theory (DFT) in the gas and aqueous phases and experimentally (steady-state absorption) in aqueous media with various degrees of polarity and hydrogen bonding ability. This compound shows high sensitivity to the polarity, basicity and proton affinity of the environment. Based on DFT, TD-DFT and NBO analysis, the compound exists in the ground-state with both intermolecular and intramolecular hydrogen bond conformations in association with the –COOH, with latter isomer calculated to be more stable. Furthermore, structural changes via intermolecular solute–solvent interactions, dictate electronic modifications and spectral changes.
Hydrogen molecule adsorption on frameworks consisting of alkaline earth metal atoms (Be, Mg, or Ca) in LTL zeolite was investigated via density functional theory. A 24T zeolite cluster model was used in this study. HOMO and LUMO energy, chemical potential, chemical hardness, electronegativity, adsorption energy, and adsorption enthalpy values were calculated. The Mg-LTL and Ca-LTL clusters were found to have much lower chemical potentials and adsorption energies than those of the Be-LTL cluster. Additionally, the calculations indicated that the Mg-LTL and Ca-LTL clusters are softer (considering their lower chemical hardness values) and more chemically reactive than the Be-LTL cluster. The calculated hydrogen adsorption enthalpies were ?14.7 and ?9.4 kJ/mol for the Mg-LTL and Ca-LTL clusters, respectively, which are significantly larger than the enthalpy of liquefaction for the hydrogen molecule. These results imply that the Mg-LTL and Ca-LTL zeolite structures are promising cryoadsorbents for hydrogen storage.
Graphical abstract Hydrogen adsorption was theoretically investigated on Be-, Ca- and Mg-LTL clusters. Ca- and Mg-LTL zeolites are potential cryoadsorbent materials for hydrogen storage.
Second group metal dimers can replace the carbon atom in benzene to form metallabenzene (C5H6M2) compounds. These complexes possess some aromatic character and promising hydrogen adsorption properties. In this study, we investigated the aromatic character of these compounds using aromaticity indices and molecular orbital analysis. To determine the nature of interactions between hydrogen and the metallic center, variation-perturbational decomposition of interaction energy was applied together with ETS-NOCV analysis. The results obtained suggest that the aromatic character comes from three π orbitals located mainly on the C5H5? fragment. The high hydrogen adsorption energy (up to 6.5 kcal mol?1) results from two types of interaction. In C5H6Be2, adsorption is controlled by interactions between the empty metal orbital and the σ orbital of the hydrogen molecule (Kubas interaction) together with corresponding back-donation interactions. Other C5H6M2 compounds adsorb H2 due to Kubas interactions enhanced by H2–π interactions.
Using density functional theory, we explored the termination process of Si (100)-2?×?1 reconstructed surface mechanistically through the dehydrogenation of small molecules, considering methyl amine and methanol as terminating reagents. At first, both the terminating reagents form two types of adduct through adsorption on the Si (100)-2?×?1 surface, one in chemisorption mode and the other via physisorption, from which the dehydrogenation process is initiated. By analyzing the activation barriers, it was observed that termination of the Si-surface through the dehydrogenation is kinetically almost equally feasible using either reagent. We further examined in detail the mechanism for each termination process by analyzing geometrical parameters and natural population analysis charges. From bonding evaluation, it is evident that hydrogen abstraction from adsorbates on the Si-surface is asymmetric in nature, where one hydrogen is abstracted as hydride by the electrophilic surface Si and the other hydrogen is abstracted as proton by the neucleophilic surface Si. Moreover, it was also observed that hydride transfer from adsorbate to the Si-surface occurs first followed by proton transfer. Overall, our theoretical interpretation provides a mechanistic understanding of the Si (100)-2?×?1 reconstructed surface termination by amine and alcohol that will further motivate researchers to design different types of decorated semiconductor devices.
Graphical Abstract Surface termination process of Si(100)-2×1 through formation of non-polar Si–H bonds via dehydrogenation of methylamine and methanol as terminating reagents
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.
The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value Lмах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules.
The factors that explain the competition between intramolecular NO linkage photoisomerization and NO photorelease in five ruthenium nitrosyl complexes were investigated. By applying DFT-based methods, it was possible to characterize the ground states and lowest triplet potential energy surfaces of these species, and to establish that both photoisomerization and photorelease processes can occur in the lowest triplet state of each species. This work highlights the crucial role of the sideways-bonded isomer, a metastable state also known as the MS2 isomer, in the photochemical loss of NO, while the results obtained also indicate that the population of the triplet state of this isomer is compulsory for both processes and show how photoisomerization and photorelease interfere.
Detailed electrostatic potential (ESP) analyses were performed to compare the directionality of halogen bonds with those of hydrogen bonds and lithium bonds. To do this, the interactions of HOOOH with the molecules XF (X?=?Cl, Br, H, Li) were investigated. For each molecule, the percentage of the van der Waals (vdW) molecular surface that intersected with the ESP surface was used to roughly quantify the directionality of the halogen/hydrogen/lithium bond associated with the molecule. The size of the region of intersection was found to increase in the following order: ClF?<?BrF?<?HF?<?LiF. The maximum ESP in the region of intersection, VS, max, was observed to become more positive according to the sequence ClF?<?BrF?<?HF?<?LiF. For ClF and BrF, the positive electrostatic potential was concentrated in a very small region of the vdW molecular surface. On the other hand, for HF and LiF, the positive electrostatic potential was more diffusely scattered across the vdW surface than for ClF and BrF. Also, the optimized geometries of the dipolymers HOOOH···?XF (X?=?Cl, Br, H, Li) indicated that halogen bonds are more directional than hydrogen bonds and lithium bonds, consistent with the results of ESP analyses.
Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391–5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100–200 pN range, consistent with published experimental estimates.
