How Short Can the H···H Intermolecular Contact Be? New Findings that Reveal the Covalent Nature of Extremely Strong Interactions

Hydration of [Formula: see text]aminobenzoic acid: structures and non-covalent bondings of aminobenzoic acid-water clusters

CONTEXT

Micro-hydration of the aminobenzoic acid is essential to understand its interaction with surrounding water molecules. Understanding the micro-hydration of the aminobenzoic acid is also essential to study its remediation from wastewater. Therefore, we explored the potential energy surfaces (PESs) of the para-aminobenzoic acid-water clusters, ABW[Formula: see text], [Formula: see text], to study the microsolvation of the aminobenzoic acid in water. In addition, we performed a quantum theory of atoms in molecules (QTAIM) analysis to identify the nature of non-covalent bondings in the aminobenzoic acid-water clusters. Furthermore, temperature effects on the stability of the located isomers have been examined. The located structures have been used to calculate the hydration free energy and the hydration enthalpy of the aminobenzoic acid using the cluster continuum solvation model. The hydration free energy and the hydration enthalpy of the aminobenzoic acid at room temperature are evaluated to be -7.0 kcal/mol and -18.1 kcal/mol, respectively. The hydration enthalpy is in perfect agreement with a previous experimental estimate. Besides, temperature effects on the calculated hydration enthalpy and free energy are reported. Finally, we calculated the gas phase binding energies of the most stable structures of the ABW[Formula: see text] clusters using twelve functionals of density functional theory (DFT), including empirical dispersion. The DFT functionals are benchmarked against the DLPNO-CCSD(T)/CBS. We have found that the three most suitable DFT functionals are classified in the following order: PW6B95D3 > MN15 > [Formula: see text]B97XD. Therefore, the PW6B95D3 functional is recommended for further study of the aminobenzoic acid-water clusters and similar systems.

METHODS

The exploration started with classical molecular dynamics simulations followed by complete optimization at the PW6B95D3/def2-TZVP level of theory. Optimizations are performed using Gaussian 16 suite of codes. QTAIM analysis is performed using the AIMAll program.

Structures of DMSO clusters and quantum cluster equilibrium (QCE)

Dimethylsulfoxide (DMSO) clusters are crucial for understanding processes in liquid DMSO. Despite its importance, DMSO clusters have received negligible attention due to the complexity of their potential energy surfaces (PESs). In this work, we explored the PESs of the DMSO clusters from dimer to decamer, starting with classical molecular dynamics, followed by full optimizations at the PW6B95-D3/def2-TZVP level of theory. In addition, the binding energies, the binding enthalpy per DMSO, and the quantum theory of atoms in molecules (QTAIM) analysis of the most stable isomers are reported. Temperature effects on the stability of the isomers have also been assessed. After thoroughly exploring the PESs of the DMSO clusters, 159 configurations have been used to apply the quantum cluster equilibrium (QCE) theory to liquid DMSO. The quantum cluster equilibrium theory has been applied to determine the liquid properties of DMSO from DMSO clusters. Thus, using the QCE, the population of the liquid DMSO, its infrared spectrum, and some thermodynamic properties of the liquid DMSO are predicted. The QCE results show that the population of the liquid DMSO is mainly dominated by the DMSO dimer and decamer, with the contribution in trace of the DMSO monomer, trimer, tetramer, pentamer, and octamer. More interestingly, the predicted infrared spectrum of liquid DMSO is in qualitative agreement with the experiment.

Adsorption of some cationic dyes onto two models of graphene oxide

CONTEXT

The search for highly efficient adsorbent materials remains a significant requirement in the field of adsorption for wastewater treatment. Computational study can highly contribute to the identification of efficient material. In this work, we propose a computational approach to study the adsorption of four cationic basic dyes, basic blue 26 (BB26), basic green 1 (BG1), basic yellow 2 (BY2), and basic red 1 (BR1), onto two models of graphene oxide as adsorbents. The main objectives of this study are the assessment of the adsorption capacity of the graphene oxide towards basic dyes and the evaluation of the environmental and temperature effects on the adsorption capacity. Quantum theory of atoms in molecules (QTAIM) analysis has been used to understand the interactions between the dyes and graphene oxides. In addition, adsorption free energies of the dyes onto graphene oxides are calculated in gas and solvent phases for temperatures varying from 200 to 400 K. As a result, the adsorption free energy varies linearly depending on the temperature, highlighting the importance of temperature effects in the adsorption processes. Furthermore, the results indicate that the environment (through the solvation) considerably affects the calculated adsorption free energies. Overall, the results show that the two models of graphene oxide used in this work are efficient for removing dyes from wastewater.

METHODS

We have optimized the complexes formed by the interaction of dyes with graphene oxides at the PW6B95-D3/def2-SVP level of theory. The SMD solvation model realizes the implicit solvation, and water is used as the solvent. Calculations are performed using the Gaussian 16 suite of program. QTAIM analysis is performed using the AIMAll program. Gibbs free energies as function of temperature are calculated using the TEMPO program.

Effect of isopropyl side chain branching and different anions on electronic structure, vibrational spectra, and hydrogen bonding of isopropyl-imidazolium-based ionic liquids: Experimental and theoretical investigations

In the present work, four branched methylated, 1,2-dimethyl-3-isopropyl-imidazolium (i-[C₃Dmim⁺]) and protonated,1-methyl-3-isopropyl-imidazolium (i-[C₃mim⁺])-based ionic liquids (ILs) with varying anion (Br^-, BF₄^-, PF₆^-, and NTf₂^-) were synthesized and investigated by NMR, infrared (IR) and Raman spectroscopy. Based on infrared and Raman spectroscopy, complete vibrational assignments have been performed. The IR and Raman analysis revealed that the vibrational spectra are virtually unaffected upon methylation, while significant frequency changes were observed by changing anion. Furthermore, to determine the electronic structure, energetic stability, and vibrational properties of these i-[C₃Dmim]Y, i-[C₃mim]Y (Y = Br, BF₄, PF₆, and NTf₂) ion pairs, quantum chemical calculations including the dispersion correction method are performed both on single ions and on ionic couples. The calculated electron density was analyzed to expose non-covalent intra- and interionic interactions by the quantum theory of atoms in molecules (AIM) and interpreted in terms of both anion dependence and type of interaction. Computational results suggest that for all ionic couples the most energetically stable configuration is obtained with the anions located close to the C2 position of the imidazolium cation. However, in the case of i-[C₃mim]NTf₂ and i-[C₃Dmim]BF₄, similar energies were obtained in configurations 2 and 3 where the anion is located above the imidazolium ring. For i-[C₃mim]Br a stronger hydrogen bond is predicted than for other studied ILs. Calculations indicate that a red shift of the CH stretching bands should occur due to hydrogen bonding; indeed, such displacement of bands is experimentally observed.

Pseudo-resonance structures in chiral alcohols and amines and their possible aggregation states

We now report that some chiral compounds, like alcohols, which are not sterically hindered atropisomers nor epimer mixtures, exhibit two sets of simultaneous NMR spectra in CDCl3. Some other chiral alcohols also simultaneously exhibit two different NMR spectra in the solid state because two different conformers, A and B had different sizes because their corresponding bond lengths and angles are different. These structures were confirmed in the same solid state by X-ray. We designate these as pseudo-resonance for a compound exhibiting several different corresponding lengths that simultaneously coexist in the solid state or liquid state. Variable-temperature NMR, 2D NMR methods, X-ray, neutron diffraction, IR, photo-luminesce (PL) and other methods were explored to study whether new aggregation states caused these heretofore unknown pseudo-resonance structures. Finally, eleven chiral alcohols or diols were found to co-exist in pseudo-resonance structures by X-ray crystallography in a search of the CDS database.

Structures, binding energies and non-covalent interactions of furan clusters

Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.

Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis

Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and ¹H-chemical shifts [δ(¹H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on ¹J(N-H), ¹J(O-H), ^2hJ(O-N), and δ(¹H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on ^2hJ(N-O) under the proton transfer process was investigated. ^2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(¹H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as ¹J(N-H) (¹J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of ^2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of ^2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.

Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations

The intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs (Nu-Nu') is elucidated with QTAIM dual functional analysis (QTAIM-DFA). Perturbed structures generated using coordinates derived from the compliance constants (C ii ) are employed for QTAIM-DFA. The method is called CIV. Two, three, or four HBs are detected for Nu-Nu'. Each HB in Nu-Nu' is predicted to have the nature of CT-TBP (trigonal bipyramidal adduct formation through charge transfer (CT)), CT-MC (molecular complex formation through CT), or t-HBwc (typical HB with covalency), while the vdW nature is predicted for the C-H⋯X interactions, for example. Energies for the formation of the pairs (ΔE) are linearly correlated with the total values of C ii -1 in Nu-Nu'. The total C ii -1 values are obtained by summing each C ii -1 value, similarly to the case of Ohm's law for the parallel connection in the electric resistance. The total ΔE value for a nucleobase pair could be fractionalized to each HB, based on each C ii -1 value. The perturbed structures generated with CIV are very close to those generated with the partial optimization method, when the changes in the interaction distances are very small. The results provide useful insights for better understanding DNA processes, although they are highly enzymatic.

Preparation of an Amorphous Cross-Linked Binder for Silicon Anodes

An amorphous cross-linked binder is prepared from abundant and low-cost sodium alginate and carboxymethyl cellulose by protonation and mixing and is used to improve the electrochemical performance of silicon anodes in lithium-ion batteries. The amorphous cross-linked structure, formed by intermolecular hydrogen bonding between the functional groups in the two polymers, effectively enhances the flexibility and strength of the binder, resulting in strong adhesion between the binder and other components in the silicon anodes. Furthermore, the binder tolerates large volume changes and reduces the pulverization of silicon during the charge-discharge process. The hydrogen bonding in the binder helps to maintain the anode integrity during the volume change, leading to an excellent cycling stability and superior rate capability with a capacity of 1863 mAh g^-1 at 500 mA g^-1 after 150 cycles.

Intrinsic Dynamic Nature of Neutral Hydrogen Bonds Elucidated with QTAIM Dual Functional Analysis: Role of the Compliance Force Constants and QTAIM-DFA Parameters in Stability

The dynamic and static nature of various neutral hydrogen bonds (nHBs) is elucidated with quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA). The perturbed structures generated by using the coordinates derived from the compliance force constants (Cij ) of internal vibrations are employed for QTAIM-DFA. The method is called CIV. The dynamic nature of CIV is described as the "intrinsic dynamic nature", as the coordinates are invariant to the choice of the coordinate system. nHBs are, for example, predicted to be van der Waals (H2Se-✶-HSeH; ✶=bond critical point), t-HBnc (typical-HBs with no covalency: HI-✶-HI), t-HBwc (t-HBs with covalency: H2C=O-✶-HI), CT-MC [molecular complex formation through charge transfer (CT): H2C=O-✶-HF], and CT-TBP (trigonal bipyramidal adduct formation through CT: H3N-✶-HI) in nature. The results with CIV were the same as those with POM in the calculation errors, for which the perturbed structures were generated by partial optimization, and the interaction distances in question were fixed suitably in POM. The highly excellent applicability of CIV for QTAIM-DFA was demonstrated for the various nHBs, as well as for the standard interactions previously reported. The stability of the HBs, evaluated by ΔE, is well correlated with Cij (ΔE×Cij =constant value of -165.64), and the QTAIM parameters, although a few deviations were detected.

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study

In the present work, the influence of Cu⁺ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu⁺ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu⁺ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu⁺ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

Two pathways of proton transfer reaction to (triphos)Cu(η(1)-BH4) via a dihydrogen bond [triphos = 1,1,1-tris(diphenylphosphinomethyl)ethane]

The interaction of the η(1)-tetrahydroborate copper(i) complex (triphos)Cu(η(1)-BH4) () with proton donors [CF3CH2OH (TFE), (CF3)2CHOH (HFIP), (CF3)3COH (PFTB), PhOH, p-NO2C6H4OH (PNP), p-NO2C6H4N[double bond, length as m-dash]NC6H4OH (PNAP), CF3OH] was a subject of a combined IR spectroscopic and theoretical investigation. Spectral (Δν) and thermodynamic (ΔH) parameters of dihydrogen bond (DHB) formation were determined experimentally. The terminal hydride ligand (characterized by the basicity factor Ej(BH) = 0.87 ± 0.01) is found to be a site of proton transfer which begins with nucleophilic substitution of BH4(-) by the alcohol oxygen atom on the copper center (BH pathway). The activation barrier computed for (CF3)2CHOH in CH2Cl2 - ΔG = 20.6 kcal mol(-1) - is in good agreement with the experimental value (ΔG = 20.0 kcal mol(-1)). An abnormal dependence of the reaction rate on the proton donor strength found experimentally in dichloromethane is explained computationally on the basis of the variation of the structural and energetic details of this process with the proton donor strength. In the second reaction mechanism found (CuH pathway), DHB complexes with the initial ROH coordination to the bridging hydride lead to B-Hbr bond cleavage with BH3 elimination. "Copper assistance" via the CuO interaction is not involved. This mechanism can be evoked to explain the occurrence of proton transfer in coordinating solvents.

Super-strong and tough poly(vinyl alcohol)/poly(acrylic acid) hydrogels reinforced by hydrogen bonding

Super-strong and tough poly(vinyl alcohol)/poly(acrylic acid) hydrogels based on hydrogen bonding are prepared by the strategy of immersing and cold-drawing.

Multicenter (FX)n/NH₃ Halogen Bonds (X = Cl, Br and n = 1-5). QTAIM Descriptors of the Strength of the X∙∙∙N Interaction

In the present work an in depth deep electronic study of multicenter XBs (FX)_n/NH₃ (X = Cl, Br and n = 1–5) is conducted. The ways in which X∙∙∙X lateral contacts affect the electrostatic or covalent nature of the X∙∙∙N interactions are explored at the CCSD(T)/aug-cc-pVTZ level and in the framework of the quantum theory of atoms in molecules (QTAIM). Calculations show that relatively strong XBs have been found with interaction energies lying between −41 and −90 kJ mol⁻¹ for chlorine complexes, and between −56 and −113 kJ mol⁻¹ for bromine complexes. QTAIM parameters reveal that in these complexes: (i) local (kinetics and potential) energy densities measure the ability that the system has to concentrate electron charge density at the intermolecular X∙∙∙N region; (ii) the delocalization indices [δ(A,B)] and the exchange contribution [V_EX(X,N)] of the interacting quantum atoms (IQA) scheme, could constitute a quantitative measure of the covalence of these molecular interactions; (iii) both classical electrostatic and quantum exchange show high values, indicating that strong ionic and covalent contributions are not mutually exclusive.

A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding

Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm^-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.

Linear Four-Chalcogen Interactions in Radical Cationic and Dicationic Dimers of 1,5-(Dichalcogena)canes: Nature of the Interactions Elucidated by QTAIM Dual Functional Analysis with QC Calculations

The dynamic and static nature of extended hypervalent interactions of the ^BE···^AE···^AE···^BE type are elucidated for four center-seven electron interactions (4c-7e) in the radical cationic dimers (1·⁺) and 4c-6e in the dicationic dimers (1²⁺) of 1,5-(dichalcogena)canes (2: ^AE(CH₂CH₂CH₂)₂^BE: ^AE, ^BE = S, Se, Te, and O). The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied for the analysis. Total electron energy densities H_b(r_c) are plotted versus H_b(r_c) - V_b(r_c)/2 [= (ℏ²/8m)∇²ρ_b(r_c)] at bond critical points (BCPs) of the interactions, where V_b(r_c) values show potential energy densities at BCPs. Data from the fully optimized structures correspond to the static nature of the interactions. Those from the perturbed structures around the fully optimized ones are also plotted, in addition to those of the fully optimized ones, which represent the dynamic nature of interactions. The ^BE···^AE-^AE···^BE interactions in 1²⁺ are stronger than the corresponding ones in 1·⁺, respectively. On the one hand, for 1²⁺ with ^AE, ^BE = S, Se, and Te, ^AE···^AE are all classified by the shared shell interactions and predicted to have the weak covalent nature, except for those in 1a²⁺ (^AE = ^BE = S) and 1d²⁺ (^AE = ^BE = Se), which have the nature of regular closed shell (r-CS)/trigonal bipyramidal adduct formation through charge transfer (CT-TBP). On the other hand, ^AE···^BE are predicted to have the nature of r-CS/molecular complex formation through charge transfer for 1a²⁺, 1b²⁺ (^AE = Se; ^BE = S), and 1d²⁺ or r-CS/CT-TBP for 1c²⁺ (^AE = Te; ^BE = S), 1e²⁺ (^AE = Te; ^BE = Se), and 1f²⁺ (^AE = ^BE = Te). The ^BE···^AE-^AE···^BE interactions in 1·⁺ and 1²⁺ are well-analyzed by applying QTAIM-DFA.

Dihydrogen intermolecular contacts in group 13 compounds: H⋯H or E⋯H (E = B, Al, Ga) interactions?

A theoretical analysis rationalises the energetics and topology of B–H⋯H–B and B–H⋯B short contacts present in the crystal structures of many borane derivatives.

Formation of β-cyclodextrin complexes in an anhydrous environment

The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host-guest complexes and shows that hydrophobic interactions play a secondary role in this case. Graphical abstract The formation of complexes of β-cyclodextrin with selected n-alkanes, polyaromatics, and organic acids in an anhydrous environment is studied by differential scanning calorimetry, IR spectroscopy, and molecular modeling. The results obtained confirm the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds and give a new perspective on the mechanism of formation of host-guest complexes.

Adsorption of Hydrogen Molecules on Carbon Nanotubes Using Quantum Chemistry and Molecular Dynamics

Physisorption and storage of molecular hydrogen on single-walled carbon nanotube (SWCNT) of various diameters and chiralities are studied by means of classical molecular dynamics (MD) simulations and a force field validated using DFT-D2 and CCSD(T) calculations. A nonrigid carbon nanotube model is implemented with stretching (C-C) and valence angle potentials (C-C-C) formulated as Morse and Harmonic cosine potentials, respectively. Our results evidence that the standard Lennard-Jones potential fails to describe the H2-H2 binding energies. Therefore, our simulations make use of a potential that contains two-body term with parameters obtained from fitting CCSD(T)/CBS binding energies. From our MD simulations, we have analyzed the interaction energies, radial distribution functions, gravimetric densities (% wt), and the distances of the adsorbed H2 layers to the three zigzag type of nanotubes (5,0), (10,0), and (15,0) at 100 and 300 K.

Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations

In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.

The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspective

Resonance Assisted Hydrogen Bonds (RAHBs) are particularly strong H-Bonds (HBs) which are relevant in several fields of chemistry. The traditional explanation for the occurrence of these HBs is built on mesomeric structures evocative of electron delocalisation in the system. Nonetheless, there are several theoretical studies which have found no evidence of such electron delocalisation. We considered the origin of RAHBs by employing Quantum Chemical Topology tools, more specifically, the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms energy partition. Our results indicate that the π-conjugated bonds allow for a larger adjustment of electron density throughout the H-bonded system as compared with non-conjugated carbonyl molecules. This rearrangement of charge distribution is a response to the electric field due to the H atom involved in the hydrogen bonding of the considered compounds. As opposed to the usual description of RAHB interactions, these HBs lead to a larger electron localisation in the system, and concomitantly to larger QTAIM charges which in turn lead to stronger electrostatic, polarization and charge transfer components of the interaction. Overall, the results presented here offer a new perspective on the cause of strengthening of these important interactions.

Hydrogen and Dihydrogen Bonds in the Reactions of Metal Hydrides

The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed.

Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study

In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein–ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein–ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component.

A Palladium-Catalyzed Carbonylation Approach to Eight-Membered Lactam Derivatives with Antitumor Activity

The reactivity of 2-(2-alkynylphenoxy)anilines under PdI2 /KI-catalyzed oxidative carbonylation conditions has been studied. Although a different reaction pathway could have been operating, N-palladation followed by CO insertion was the favored pathway with all substrates tested, including those containing an internal or terminal triple bond. This led to the formation of a carbamoylpalladium species, the fate of which, as predicted by theoretical calculations, strongly depended on the nature of the substituent on the triple bond. In particular, 8-endo-dig cyclization preferentially occurred when the triple bond was terminal, leading to the formation of carbonylated ζ-lactam derivatives, the structures of which have been confirmed by XRD analysis. These novel medium-sized heterocyclic compounds showed antitumor activity against both estrogen receptor-positive (MCF-7) and triple negative (MDA-MB-231) breast cancer cell lines. In particular, ζ-lactam 3 j' may represent a novel and promising antitumor agent because biological tests clearly demonstrate that this compound significantly reduces cell viability and motility in both MCF-7 and MDA-MB-231 breast cancer cell lines, without affecting normal breast epithelial cell viability.

Complexes of carborane acids linked by strong hydrogen bonds: acidity scales

Scales based on DFT results of calculations and on the topological QTAIM parameters are introduced and discussed to order the species analyzed here by acidity; in particular, carborane acids are analyzed and the theoretical results are compared with experimental results.

The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

Dihydrogen bond intermediated alcoholysis of dimethylamine-borane in nonaqueous media

Dimethylamine-borane (DMAB) acid/base properties, its dihydrogen-bonded (DHB) complexes and proton transfer reaction in nonaqueous media were investigated both experimentally (IR, UV/vis, NMR, and X-ray) and theoretically (DFT, NBO, QTAIM, and NCI). The effects of DMAB concentration, solvents polarity and temperature on the degree of DMAB self-association are shown and the enthalpy of association is determined experimentally for the first time (-ΔH°assoc = 1.5-2.3 kcal/mol). The first case of "improper" (blue-shifting) NH···F hydrogen bonds was observed in fluorobenzene and perfluorobenzene solutions. It was shown that hydrogen-bonded complexes are the intermediates of proton transfer from alcohols and phenols to DMAB. The reaction mechanism was examined computationally taking into account the coordinating properties of the reaction media. The values of the rate constants of proton transfer from HFIP to DMAB in acetone were determined experimentally [(7.9 ± 0.1) × 10(-4) to (1.6 ± 0.1) × 10(-3) mol(-1)·s(-1)] at 270-310 K. Computed activation barrier of this reaction ΔG(‡theor)298 K(acetone) = 23.8 kcal/mol is in good agreement with the experimental value of the activation free energy ΔG(‡exp)270 K = 21.1 kcal/mol.