The hydration structure of sodium glycinate (Na+GL?) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na+GL?]β is more than 30 kJ mol?1 higher than [Na+GL?]α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na+GL?]?(H2O)8 were derived from [Na+GL?]β instead of [Na+GL?]α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na+GL?]β is more stable than [Na+GL?]α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X?=?O1, O2, N) in the low-energy conformers, Na+GL? will be dissociated as Na+ and GL? in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na+GL? will provide a physical explanation for the weakening Na-O1 interaction.
The B3LYP/6–31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li+, Na+, K+) and divalent (Mg2+) metal counterions in interaction with the charged PO2? group, on the geometrical and vibrational characteristics of the DNA fragments of 3′,5′-dDSMP, represented by four conformers (g+g+, g+t, g?g? and g?t). All complexes were optimized through two solvation models [the explicit model (6H2O) and the hybrid model (6H2O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li+, Na+, K+, Mg2+) always remain in the bisector plane of the O1–P–O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li+, Na+) deviate from the bisector plane, while the largest counterions (K+ and Mg2+) always remain in the same plane. On the other hand, the present calculations reveal that the g+g+ conformer is the most stable in the presence of monovalent counterions, while conformers g+t and g?t are the most stable in the presence of the divalent counterion Mg2+. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4′-C3′-O3′-PO?2-O5′-C5′-C4′ segment of all complexes of the g?g? conformer in 6H2O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g+g+ conformer in the presence of the monovalent counterion and of g?t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H2O/Continuum for the g+g+ conformer and experimental value measured in an aqueous solution of the DMP-Na+ complex, is <1.07% for the PO2? (asymmetric and symmetric) stretching modes and <2.03% for the O5′-C5′ and O3′-C3′ stretching modes.
Since the thermal stabilities of ionic liquids (ILs) are of significance for their application, an amine-functionalized IL 1,2-dimethyl-(3-aminoethyl) imidazolium tetrafluoroborate [aEMMIM][BF4] was chosen to study thermal decomposition mechanisms via the methods of FT-IR, 1H NMR, TGA, TGA-MS and density functional theory (DFT) calculations. Theoretical and experimental results indicated that amine-functionalization reduces the thermal stability of [aEMMIM][BF4] compared to its non-functionalized counterpart. Moreover, we found that [aEMMIM][BF4] follows a unimolecular nucleophilic substitution (SN1) decomposition (98.8 %), whereas the bimolecular nucleophilic substitution (SN2) decomposition (1.2 %) is unfavorable. The SN1 and SN2 reactions were fully optimized at B3LYP/6-311++G(d,p) level, and the energies of reactant (R), intermediates (IM), transition state (TS) and product (P) were obtained and analyzed by reaction mechanism. The energy of the intermediate is higher than that of the reactants by 18.92 kJ mol?1, and the energy of the TS is higher than that of the IM by 155.23 kJ mol?1. This result indicates that the IM are also more stable than the P2 product, thus the reaction is endothermic. The chemical nature of the covalent and hydrogen bonds was analyzed by vibrational modes analysis (VMA), nature bond orbital (NBO) and the theory of atoms in molecules (AIM).
Graphical Abstract Proposed thermal decomposition of [aEMMIM][BF4] via unimolecular ( SN1) and bimolecular( SN2) nucleophilic substitution mechanisms. The electrostatic potential surface (ESP) of the transition state illustrates that hydrogen bonds are generated when [BF4]? is close to [aEMMIM]+, and SN1 decomposition is much favorable than SN2 decomposition.
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 perfectly planar Al13+ cluster (CI) and a quasi-planar Al13+ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.
The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC3H4N2+; X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH3)3SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC3H4N2+ to form the σ-hole and π-hole interactions in the bimolecular complexes (CH3)3SiY?·?·?·?XC3H4N2+ and (CH3)3SiY?·?·?·?C3(X)H4N2+(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors. The electrostatic energy is the main contribution in the formation of both kinds of interactions, it has linear relations with the VS,max values of σ-hole and the V′S,max values of π-hole. Both the σ-hole and π-hole interactions belong to the closed-shell and noncovalent interactions. The π-hole interactions are stronger than the σ-hole interactions. For the π-hole interactions, the contribution percents of the dispersion energies are somewhat greater than those of the σ-hole interactions, while it is contrary for the polarization energy.
The mechanistic details of N-heterocyclic olefin-catalyzed formation of cyclic carbonate from CO2 and propargylic alcohols were investigated by DFT calculations. Six mechanisms, four for the formation of five-membered cyclic carbonate (M-A, M-B, M-B’ and M-C), and two for six-membered cyclic carbonate (M-D and M-E), were fully investigated. The energy profiles in dichloromethane showed that M-B is the predominant reaction with the lowest barrier of 31.99 kcal mol?1, while M-C and M-D may be kinetically competitive to M-B. The very high activation energy of 45.37 kcal mol-1, 57.07 kcal mol-1 and 59.61 kcal mol?1 for M-A, M-B’ and M-E, respectively, suggest that they are of lesser importance in the overall mechanism.
Graphical abstract Formations of five-membered ring product and six-membered ring product are kinetically competitive, but five-membered ring product is thermodynamically more preferable.
The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The preferred structures are combined to monovalent (Li+, Na+, and K+) cations and further fully optimized, and an isoenergetic map corresponding to the complex (MG2?, 2Na+) was performed. Then, the reactivity of MG complexes with mono- and bivalent cations was studied using the global nucleophilic index. The position selectivity was also predicted using the local nucleophilic indices. It was demonstrated that experimental trends of relative reactivity and regioselectivity of the complexes are correctly predicted using these empirical indices of reactivity.
New ionic liquids (ILs) involving increasing numbers of organic and inorganic ions are continuously being reported. We recently developed a new force field; in the present work, we applied that force field to investigate the structural properties of a few novel imidazolium-based ILs in aqueous mixtures via molecular dynamics (MD) simulations. Using cluster analysis, radial distribution functions, and spatial distribution functions, we argue that organic ions (imidazolium, deprotonated alanine, deprotonated methionine, deprotonated tryptophan) are well dispersed in aqueous media, irrespective of the IL content. Aqueous dispersions exhibit desirable properties for chemical engineering. The ILs exist as ion pairs in relatively dilute aqueous mixtures (10 mol%), while more concentrated mixtures feature a certain amount of larger ionic aggregates.
Designing and synthesizing novel electron-donor polymers with the high photovoltaic performances has remained a major challenge and hot issue in organic electronics. In this work, the exciton-dissociation (kdis) and charge-recombination (krec) rates for the PC61BM-PTDPPSe system as a promising polymer-based solar cell candidate have been theoretically investigated by means of density functional theory (DFT) calculations coupled with the non-adiabatic Marcus charge transfer model. Moreover, a series of regression analysis has been carried out to explore the rational structure–property relationship. Results reveal that the PC61BM-PTDPPSe system possesses the large open-circuit voltage (0.77 V), middle-sized exiton binding energy (0.457 eV), and relatively small reorganization energies in exciton-dissociation (0.273 eV) and charge-recombination (0.530 eV) processes. With the Marcus model, the kdis, krec, and the radiative decay rate (ks), are estimated to be 3.167×1011 s?1, 3.767×1010 s?1, and 7.930×108 s?1 respectively in the PC61BM-PTDPPSe interface. Comparably, the kdis is as 1～3 orders of magnitude larger than the krec and the ks, which indicates a fast and efficient photoinduced exciton-dissociation process in the PC61BM-PTDPPSe interface.
Graphical Abstract PTDPPSe is predicted to be a promising electron donor polymer, and the PC61BM-PTDPPSe system is worthy of further device research by experiments.
A two-layer ONIOM study on the hydrodesulfurization mechanism of thiophene in H-FAU and M-FAU (M?=?Li+, Na+, and K+) has been carried out. The calculated results reveal that in H-FAU, for a unimolecular mechanism, the rate-determining step is hydrogenation of alkoxide intermediate. The assistance of H2O and H2S molecules does not reduce the difficulty of the C-S bond cracking step more effectively. A bimolecular hydrodesulfurization mechanism is more favorable due to the lower activation barriers. The rate-determining step is the formation of 2-methylthiophene, not the C-S bond cracking of thiophene. Moreover, the ring opening of thiophene is much easier to occur than the desulfurization step. A careful analysis of energetics indicates that H2S, propene, and methyl thiophene are the major products for the hydrodesulfurization process of thiophene over H-FAU zeolite, in good agreement with experimental findings. In M-FAU zeolites, both unimolecular and bimolecular cracking processes are difficult to occur because of the high energy barriers. Compared to the case on H-FAU, the metal cations on M-FAU increase the difficulty of occurrence of bimolecular polymerization and subsequent C-S bond cracking steps.
Graphical abstract Hydrodesulfurization process of thiophene can take place in H-FAU zeolite. Two different mechanisms, unimolecular and bimolecular ones, have been proposed and evaluated in detail. The bimolecular mechanism is more favorable due to lower activation barrier as described in the picture above. Our calculated data indicate that H2S, propene, and methylthiophene are the major products, in good agreement with experimental observations. The effect of metal cations on the reaction mechanism is also investigated in this work.
A mechanistic investigation using Becke3LYP density functional theory (DFT) was carried out on the palladium-catalyzed amidition of bromobenzene and tBu-isocyanide. The whole catalytic cycle consists of five steps: oxidative addition, migratory insertion, anion exchange, reductive elimination, and hydrogen migration. The rate-determining step is oxidative addition, with a small Gibbs free energy of 14.6 kcal mol?1. In the migratory insertion step, tBu-isocyanide provides an important source of carboxy and amino groups to establish the amide group. For anion exchange, path 1a is suggested as the most favorable pathway with the help of the base, and water provides a source of oxygen which is perfectly in line with experimental observations. Finally, in the hydrogen migration step, we illustrate that the six-membered ring path is energetically favored due to the assisting influence of water. In addition, our calculations indicate that using dimethyl sulfoxide as a solvent does not change the rate-determining step.
The selectivity of phosphoryl P(O)R3, sulfoxide S(O)R2, and carbonyl C(O)R2 (R?=?NH2, CH3, OH, and F) derivatives with lanthanide cations (La3+, Eu3+, Lu3+) was studied by density functional theory calculations. Theoretical approaches were also used to investigate energy and the nature of metal–ligand interaction in the model complexes. Atoms in molecules and natural bond orbital (NBO) analyses were accomplished to understand the electronic structure of ligands, L, and the related complexes, L–Ln3+. NBO analysis demonstrated that the negative charge on phosphoryl, carbonyl, and sulfoxide oxygen (OP, OC, and OS) has maximum and minimum values when the connected –R groups are –NH2 and –F. The metal–ligand distance declines as, –F?>?–OH?>?–CH3?>?–NH2. Charge density at the bond critical point and on the lanthanide cation in the L–Ln3+ complexes varies in the order –F?<?–OH?<?–CH3?<?–NH2, due to greater ligand to metal charge transfer, which is well explained by energy decomposition analysis. It was also illustrated that E(2) values of Lp(N)?→?σ*(Y–N) vary in the order P=O ? S=O ? C=O and the related values of Lp(N)?→?σ*(Y=O) change as C=O ? S=O ? P=O in (NH2)nYO ligands (Y?=?P, C, and S). Trends in the L–Ln3+ CP–corrected bond energies are in good accordance with the optimized OY?Ln distances. It seems that, comparing the three types of ligands studied, NH2–substituted are the better coordination ligands.
Graphical Abstract Density functional theory (B3LYP) calculations were used to compare structural, electronic and energy aspects of lanthanide (La, Eu, Lu) complexes of phosphine derivatives with those of carbonyls and sulfoxides in which the R– groups connected to the P=O, C=O and S=O are –NH2, –CH3, –OH and –F.
Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen, H2, with various poly-aromatic hydrocarbons (PAHs) as a model system for graphene were carried out to accurately describe the physisorption phenomenon. The binding energies corrected for the basis set superposition error, ΔEbind(BSSE), were obtained using the optimized geometries at the MP2 level with a large basis set and were compared with the single point binding energies, denoted as ΔEbind(BSSE-s), using large basis sets on the geometries optimized at the small basis sets, such as SVP and TZVP. The calculations showed that the ΔEbind(BSSE-s) values were similar to those at the MP2 level with the large basis sets. The binding strength increased gradually with increasing size of the PAHs. The ΔEbind(BSSE-s) for an infinite graphene sheet was estimated to be ?1.70 kcal mol?1 using the non-linear curve fitting method. The present work could be expected to provide more useful and reliable information on H2 physisorption.
Graphical abstract Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen with various poly-aromatic hydrocarbons as a model system for graphene indicate that the perpendicular type A is the most favorable and the binding energy on an infinite graphene sheet is estimated to be ?1.70 kcal mol?1.
The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol?1) reactive toward hydroxylation.
Figure The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21 G level, and in some cases at the B3LYP/6-31 G* level, and the energy associated with the attachment of the OH substituent was determined.
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.
Efficient design of ionic compounds requires a systematic understanding of cation–anion interactions. Weakening of electrostatic attraction is essential to increase the liquid range of the ionic compound and decrease its melting point. Here, we report simulations of the closest-approach cation–anion distances in a variety of ion pairs containing the tetrakis(pentafluorophenyl)borate (TFPB–) anion. Small alkali cations (Li+, Na+) penetrate the TFPB– core, whereas K+ and larger organic cations do not. In the latter case, the shortest possible distance from the cations to the boron atom of TFPB– ranges from 0.50 nm to 0.63 nm. TFPB– was shown to be substantially rigid, providing a steric hindrance to thermodynamically efficient cation–anion coordination. Our results prove that TFPB– is more efficient for electrostatic charge confinement than the tetraoctylammonium cation, whereas the perfluorophenyl group is more efficient than linear alkyl chains. These simulations will motivate development of TFPB–-based ionic liquids with low phase transition points.
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.
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 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.
