Cooperativity in noncovalent interactions

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Modulation of hydrogen bonding upon ion binding: insights into cooperativity

The impact due to the of presence of ions, such as Mg<SUP>2+</SUP>, Na<SUP>+</SUP>, H<SUP>+</SUP>, Cl<SUP>−</SUP>, and OH<SUP>−</SUP> on hydrogen bonded clusters of increasing size (water, formamide, and acetamide [n = 1–10]) in the context of associated cooperativity has been explored using density functinal theory (DFT) calculations. Sequential binding energies (SBE) rise on addition of monomer in case of parent clusters. SBE for ionic clusters are several times higher than that of parent clusters initially. This behavior is more dramatic on addition of either Mg<SUP>2+</SUP> or H<SUP>+</SUP> compared to other ions. Interestingly, SBE of both parent and ionic clusters approach nearly uniform values beyond n = 6 irrespective of kind of ion present in the cluster with the exception of magnesium

A theoretical study on interaction of cyclopentadienyl ligand with alkali and alkaline earth metals

Ab initio and density functional theory calculations are performed on half-sandwich (M-Cp) and sandwich (Cp-M-Cp) complexes of alkali and alkaline earth metals (M = Li, Na, K, Mg, and Ca) with cyclopentadienyl ligand (Cp). A comparison of dissociation energies demonstrates the ease of dissociation of the complex as ions in solvent phase and preference for dissociation as radicals in gas phase. Atoms in molecules analysis is used to characterize this cation−π interaction based on electron density values obtained at the cage critical point. The contribution of various components to the complex energy is estimated using reduced variational space analysis confirming maximum contribution from the coulomb exchange followed by contributions from polarization and charge transfer components of cyclopentadienyl ligand

Cation-π interaction: its role and relevance in chemistry, biology and material science

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Estimating the binding ability of onium ions with CO<SUB>2</SUB> and π systems: a computational investigation

Density functional theory (DFT) calculations have been employed on 165 complexes of onium ions (NH4+, PH4+, OH3+, SH3+) and methylated onium ions with CO2, aromatic (C6H6) and heteroaromatic (C5H5X, X = N, P; C4H5Y, Y = N, P; C4H4Z, Z = O, S) systems. The stability of CO2⋯onium, CO2⋯π and onium⋯π complexes was shown to be mediated through various noncovalent interactions such as hydrogen bonding, NH–π, PH–π, OH–π, SH–π, CH–π and π–π. We have discussed 17 complexes wherein the proton transfer occurs between the onium ion and the heteroaromatic system. The binding energy is found to decrease with increasing methyl substitution of the complexes containing onium ions. Binding energy components of all the noncovalent complexes were explored using localized molecular orbital energy decomposition analysis (LMO-EDA). The CO2⋯π complexes were primarily stabilized by the dispersion term followed by contributions from electrostatic and polarization components. In general, for onium ion complexes with CO2 or π systems, the electrostatic and polarization terms primarily contribute to stabilize the complex. As the number of methyl groups increases on the onium ion, the dispersion term is seen to have a key role in the stabilization of the complex. Quantum theory of atoms in molecules (QTAIM) analysis and charges based on natural population analysis (NPA) in various complexes have also been reported in order to determine the nature of noncovalent interactions in different complexes

Analyzing coordination preferences of Mg<SUP>2+</SUP> complexes: insights from computational and database study

Solvation of metal cations has attracted substantial interest on account of its functional importance in biological systems. In the present study, we undertake a comprehensive analysis of hydrated complexes of Mg<SUP>2+</SUP> with up to 20 water molecules using MP2/cc-pVTZ and density functional theory (DFT) calculations. The effect of first, second, and higher solvation shells on magnesium coordination has been systematically analyzed by considering Mg<SUP>2+</SUP>(H<SUB>2</SUB>O)n complexes. Numerous competing conformations for each of the metal ion complexes have been explored and the minima structures obtained were further analyzed. The study probes the relative preferences among various coordination numbers and unambiguously establishes that coordination number 6 is the most optimal choice. The relative abundance of Mg<SUP>2+</SUP> ion and its coordination with water and other ligands has been analyzed in the Protein Data Bank and Cambridge Structural Database. It is noted that the M–O distance and charge transfer to metal ion increase as the number of solvating water molecules increases. The computational studies are in excellent agreement with the experimental observations, and provide support to multiple coordinate site preferences for Mg<SUP>2+</SUP>

A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH<SUB>3</SUB>CONH<SUB>2</SUB>] (n = 1–15)

Insights into the formation of hydrogen bonded clusters are of outstanding importance and quantum chemical calculations play a pivotal role in achieving this understanding. Structure and energetic comparison of linear, circular and standard forms of (acetamide)n clusters (n = 1–15) at the B3LYP/D95** level of theory including empirical dispersion correction reveals significant cooperativity of hydrogen bonding and size dependent structural preference. A substantial amount of impact of BSSE is observed in these calculations as the cluster size increases irrespective of the kind of arrangement. The interaction energy per monomer increases from dimer to 15mer by 90% in the case of the circular arrangement, by 76% in the case of the linear arrangement and by 34% in the case of the standard arrangement respectively. The cooperativity in hydrogen bonding is also manifested by a regular decrease in average O⋯H and C–N bond distances, while average C=O and N–H bond lengths increase with increasing cluster size. Atoms-In-Molecules (AIM) analysis is used to characterize the nature of hydrogen bonding between the acetamide molecules in the cluster on the basis of electron density (ρ) values obtained at the bond critical point. An analysis of N–H bond stretching frequencies as a function of the cluster size shows a marked red shift as the cluster size increases from 1 to 15

First principles study and database analyses of structural preferences for sodium ion (Na<SUP>+</SUP>) solvation and coordination

Extensive computations were performed on aqueous clusters of monovalent sodium cation [Na<SUP>+</SUP>(H<SUB>2</SUB>O)n; (n = 1–20)] using MP2/cc-pVTZ and density functional theory. The structure, energy, and coordination number (CN) preference of a large number of competing conformations of different complexes have been explored. For complexes up to n = 12, the CN 4 is most preferred while 5, 6 CNs are favored in case of larger complexes containing up to 20 water molecules. These results are in very good agreement with experimental observations. The strength of hydrogen bonding among the waters coordinated to the Na<SUP>+</SUP> ion is found to play a major role in the stability of the complexes. The varying preferences for CN of Na<SUP>+</SUP> ion were explored by screening two important databases: Protein Databank and Cambridge Structural Database. A linear correlation is observed between the M (Metal)–O distance and the charge on metal ion in complex with the increase in CN of metal ion

Hydrogen bonded networks in formamide [HCONH<SUB>2</SUB>]<SUB>n</SUB> (n = 1 − 10) clusters: a computational exploration of preferred aggregation patterns

Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH2]n, (n = 1 − 10) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP)

Hydrogen bonding in water clusters and their ionized counterparts

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H<SUB>2</SUB>O)<SUB>n</SUB>, n = 2−20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts