What a difference a decade makes: progress in ab initio studies of the hydrogen bond

Proton Transfer in a Bare Superacid-Amine Complex: A Microwave and Computational Study of Trimethylammonium Triflate

The complex formed from trimethylamine ((CH₃)₃N) and trifluoromethanesulfonic acid (triflic acid, CF₃SO₃H) has been observed by Fourier transform microwave spectroscopy in a supersonic jet. Spectroscopic data, most notably ¹⁴N nuclear quadrupole coupling constants, are combined with computational results at several levels of theory to unambiguously demonstrate complete or near-complete proton transfer from the triflic acid to the trimethylamine upon complexation. Thus, the system is best regarded as a trimethylammonium triflate ion pair in the gas phase. The formation of an isolated ion pair in a 1:1 complex of a Brønsted acid and base is unusual and likely arises due to the strong acidity of triflic acid. Simple energetic arguments based on proton affinities and the Coulomb interaction energy can be used to rationalize this result.

Computational study of acylphloroglucinols: an investigation with many branches

Acylphloroglucinols (ACPLs) are a broad class of compounds structurally derived from phloroglucinol and characterised by the presence of a CRO group. They are interesting for their biological activities and their potentialities as lead compounds in drug development. The current review considers a series of works which, altogether, sum up to a systematic computational study of ACPLs in vacuo and in three solvents – chloroform, acetonitrile and water. An initial set of studies, focusing on ACPLs as a class and utilising an adequately representative selection of molecules, identified patterns in the conformational preferences and molecular properties of ACPLs, which appear valid for the whole class or for specific subclasses such as monomeric ACPLs, dimeric ACPLs, ACPLs with substituents containing C=C double bonds, etc. The validity of the identified patterns was further verified through the study of additional and significantly different ACPL molecules, as well as other molecular structures containing ACPL units. Furthermore, the computational study of ACPLs proved interesting for the insights into the factors stabilising their conformers, first of all intramolecular hydrogen bonding, which plays dominant roles in determining conformational preferences and energetics. The current review outlines the objectives, approaches and main results of these studies. The obtained information may be relevant for further studies aimed at a better understanding of the molecular bases of the biological activities of ACPLs.

Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study

This concomitant experimental and theoretical study provides a definitive EOS for α-glycine up to the record pressure of 50 GPa.

Experimental and theoretical studies on the corrosion inhibition of mild steel by some sulphonamides in aqueous HCl

Corrosion inhibition studies of mild steel in aqueous HCl by some sulphonamides have been investigated using weight loss, potentiodynamic polarization (PDP), Electrochemical Impedance Spectroscopy (EIS) and Density Functional Theory (DFT).

Computational study of interactions and nuclear magnetic shielding constants in linear chains of formamide clusters

We investigated the energetic, structural, dielectric, and nuclear magnetic shielding properties of linear n-formamide clusters, with n up to 6, to quantitatively characterize cooperative effects in model biological systems. The geometries of the complexes were optimized at the MP2 and DFT/B3LYP levels by using the pc-2 and pc-3 basis sets, while the nuclear magnetic shielding constants were calculated by employing pcS-n type basis sets, which have been optimized specifically for density functional calculations of these properties. The interaction energies show the cooperative effect, which favors the successive addition of monomers. In addition, by analyzing structural changes in the intermolecular C=O, C-N and hydrogen O⋯H bonds, as well as in the average dipole moments as cluster size increases, we found that the cooperative interaction far exceeds that expected for electrostatic interactions. Such non-pairwise-additive effects are also reflected in the changes of the nuclear magnetic shielding constants. In particular, the negativity of O shielding decreases around 23% from the monomer to the 6-formamide chain. It is possible to note the decrease in the shielding of H and in the deshielding of O as a result of their hydrogen bonding. However, the results obtained show that these variations in the extremes of formamide chains tend to zero, and the respective shielding values tend to stabilize as the number of monomers increases in the chain. Also, the cooperative effect increases in the middle of the chains, by decreasing the shielding for all atoms except that of O, which decreases its deshielding. These results could serve to guide improvements in current conventional models for simulating hydrogen bonded systems.

Quantifying the role of water in protein-carbohydrate interactions

Water-mediated interactions play a key role in carbohydrate-lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d) level in which either a methanol molecule was bound to the conserved water (liganded state) or in which a water molecule replaces the methanol (unliganded state). Not surprisingly, the binding of a water to clusters containing charged amino acid side chains was more favorable by 1.55 to 7.23 kcal/mol than that for the binding of a water to the corresponding pure water clusters. In contrast, the binding energy of water to clusters containing polar-uncharged amino acid side chains ranged from 4.35 kcal/mol less favorable to 4.72 kcal/mol more favorable than for binding to the analogous pure water clusters. The overall trend for the binding of methanol versus water, in any of the clusters, favored methanol by an average value of 1.05 kcal/mol. To extend these studies to a complex between a protein (Concanavalin A) and its carbohydrate ligand, a cluster was examined that contained the side chains of three key amino acids, namely asparagine, aspartate, and arginine, as well as a key water molecule, arranged as in the X-ray diffraction structure of Con A. Again, using methanol as a model for the endogenous carbohydrate ligand, energies of -5.94 kcal/mol and -5.70 kcal/mol were obtained for the binding of methanol and water, respectively, to the Con A-water cluster. The extent to which cooperativity enhanced the binding energies has been quantified in terms of nonadditive three-body contributions. In general, the binding of water or methanol to neutral dimers formed cooperative clusters; in contrast, the cooperativity in charged clusters depended on the overall geometry as well as the charge.

Theoretical studies of the solvent effect on the conformation of the HO-C-C-X (X = F, NH2, NO2) moiety with competing intra- and intermolecular hydrogen bonds

Theoretical calculations up to the ab initio IEF-PCM/CCSD(T)/CBS//IEF-PCM/B3LYP/6-311++G** and IEF-PCM/B97D/aug-cc-pvtz levels have been performed for 2X-ethanol and 2X-phenol systems with X = F, NH(2), NO(2) in chloroform and aqueous solution. The calculated relative free energies by means of the IEF-PCM continuum dielectric method do not differ very much at the DFT and ab initio levels. Application of explicit solvent models and the FEP/MC method for determining relative solvation free energies causes, however, large deviations in the predicted equilibrium compositions, although the predominant conformation for the solute is generally in agreement with that from the corresponding IEF-PCM calculations. Existence of an intramolecular hydrogen bond (HB structure) for species with the HO-C-C-X moiety is preferred compared with a conformation when the hydrogen bond is disrupted (NoHB) for the considered F- and NO(2)-substituted molecules both in chloroform and aqueous solution. For 2NH(2)-ethanol, the HB structure is predominant in chloroform, whereas the 93:7 ratio for the OCCN trans/gauche species was obtained in aqueous solution. 2NH(2)-phenol exhibits a subtle equilibrium of the HB and NoHB conformations in both solvents. Potential of mean force calculations predict about a 10% solute association for the trans 2NH(2)-ethanol solute even in the fairly dilute 0.22 molar solution, whereas direct MC simulations do not support the maintenance of a doubly hydrogen-bonded dimer. Aqueous solution characteristics, as coordination numbers and numbers of strongly bound water molecules to the solute at T = 298 K and p = 1 atm, correspond reasonably to the derived molecular structures.

Vibrational spectroscopic studies of N,N'-dimethylpropyleneurea-water system: affected solvent spectra and factor analysis

FT-IR spectra of N,N'-dimethylpropyleneurea (DMPU)-water system have been measured in the 4000-500 cm(-1) range by Attenuated Total Reflectance (ATR) technique in the entire composition range. The hydration of DMPU in diluted aqueous solutions has been additionally studied with transmission FT-IR spectroscopy of isotopically diluted HDO in H(2)O, used as a probe of solute hydration. The spectra have been analysed with the quantitative version of the difference spectra method that leads to isolation of the spectrum of solvent affected by the presence of the solute. DMPU-affected HDO spectra provide information about the energetic state of water molecules in the hydration shell, while affected H(2)O spectra additionally reflect the structural state of the water hydrogen bond network. The CO stretching band of DMPU has been used to obtain also the H(2)O-affected DMPU spectrum. The affected H(2)O and DMPU spectra have been determined in infinite dilution approximation, as well as for increasing concentrations of the solute. These results are confronted with factor analysis of ATR spectra, which shows the presence of three well-defined intermolecular complexes in the studied system. Presumable structures of these complexes have been proposed on the basis of Density Functional Theory (DFT) calculations of optimal cluster geometries.

Geometry and spectral properties of the protonated homodimer of pyridine in the liquid and solid states. A combined NMR, X-ray diffraction and inelastic neutron scattering study

The structure and spectral signatures of the protonated homodimer of pyridine in its complex with a poorly coordinating anion have been studied in solution in CDF(3)/CDClF(2) down to 120 K and in a single crystal. In both phases, the hydrogen bond is asymmetric. In the solution, the proton is involved in a fast reversible transfer that determines the multiplicity of NMR signals and the sign of the primary H/D isotope effect of --0.95 ppm. The proton resonates at 21.73 ppm that is above any value reported in the past and is indicative of a very short hydrogen bond. By combining X-ray diffraction analysis with model computations, the position of the proton in the crystal has been defined as d(N-H) = 1.123 Å and d(H···N) = 1.532 Å. The same distances have been estimated using a (15)N NMR correlation. The frequency of the protonic out-of-plane bending mode is 822 cm(-1) in agreement with Novak's correlation.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Prediction of macroscopic properties of protic ionic liquids by ab initio calculations

We have systematically investigated combinations of anions and cations in a number of protic ionic liquids based on alkylamines and used ab initio methods to gain insight into the parameters determining their liquid range and their conductivity. A simple, almost linear, relation of the experimentally determined melting temperature with the calculated volume of the anion forming the ionic liquid is found, whereas the dependence of the melting temperature with increasing cation volume goes through a minimum for relatively short side chain length. On the basis of the present results, we propose a strategy to predict the nature of protic ionic liquids in terms of low vapor pressure and conductivity. Comparisons with previously reported strategies for prediction of melting temperatures for aprotic ionic liquids are also made.

Structure of the Jet-Cooled 1-Naphthol Dimer Studied by IR Dip Spectroscopy: Cooperation between the π−π Interaction and the Hydrogen Bonding

The structure of a jet-cooled 1-naphthol (1-NpOH) dimer was investigated by using resonant-enhanced two-photon ionization (R2PI) and ion-detected infrared (IR) dip spectroscopy. A geometrical optimization and a frequency calculation in (1-NpOH)2 were also performed at the MP2/cc-pVDZ level. Stable isomers in the MP2/cc-pVDZ calculation were classified into a structure dominated only by the pi-pi interaction and structures formed by cooperation between the pi-pi interaction and hydrogen bonding. On the basis of a comparison between the observed and calculated IR spectra, the geometry of (1-NpOH)2 was concluded to be a pi-pi stacking structure supported by hydrogen bonding.

Does the A·T or G·C Base-Pair Possess Enhanced Stability? Quantifying the Effects of CH···O Interactions and Secondary Interactions on Base-Pair Stability Using a Phenomenological Analysis and ab Initio Calculations

An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.

Low-barrier hydrogen bond between phosphate and the amide group in phosphopeptide

As the conversion between the monoionic (1) and diionic (2) form of the phosphate occurs, the phosphorylated peptides or proteins can not only cause the formation of a hydrogen bond between the phosphate group and the amide group but also change the strength of the hydrogen bond to form low-barrier hydrogen bonds (LBHBs). This reversible protonation of the phosphate group, which changes both the electrostatic properties of the phosphate group and the strength of the hydrogen bond, provides a possible mechanism in regulating protein function.

Ab Initio Study of Hydrogen Bonding and Proton Transfer in 3:1 FH:NH3 and FH:Collidine Complexes: Structures and One- and Two-Bond Coupling Constants across Hydrogen Bonds

Ab initio EOM-CCSD calculations have been performed on 3:1 FH:NH3 complexes at their own optimized MP2/6-31+G(d,p) geometries and at the optimized geometries in the hydrogen-bonding regions of corresponding 3:1 FH:collidine complexes. The isolated gas-phase equilibrium 3:1 FH:NH3 complex has an open structure with a proton-shared Fa-Ha-N hydrogen bond, while the isolated equilibrium 3:1 FH:collidine complex has a perpendicular structure with an Fa-Ha-N hydrogen bond that is on the ion-pair side of proton-shared. The Fa-N coupling constant ((2h)J(Fa-N)) for the equilibrium 3:1 FH:NH3 complex is large and negative, consistent with a proton-shared Fa-Ha-N hydrogen bond; (2h)JFb-Fa is positive, reflecting a short Fb-Fa distance and partial proton transfer from Fb to Fa across the Fb-Hb-Fa hydrogen bond. In contrast, (2h)JFa-N has a smaller absolute value and (2h)JFb-Fa is greater for the 3:1 FH:NH3 complex at the equilibrium 3:1 FH:collidine geometry, consistent with the structural characteristics of the Fa-Ha-N and Fb-Hb-Fa hydrogen bonds. Coupling constants computed at proton-transferred 3:1 FH:collidine perpendicular geometries are consistent with experimental coupling constants for the 3:1 FH:collidine complex in solution and indicate that the role of the solvent is to promote further proton transfer from Fa to N across the Fa-Ha-N hydrogen bond, and from Fb to Fa across the two equivalent Fb-Hb-Fa hydrogen bonds. The best correlations between experimental and computed coupling constants are found for complexes with perpendicular proton-transferred structures, one having the optimized geometry of a 3:1 FH:collidine complex at an Fa-Ha distance of 1.80 A, and the other at the optimized 3:1 FH:collidine geometry with distances derived from the experimental coupling constants. These calculations provide support for the proposed perpendicular structure of the 3:1 FH:collidine complex as the structure which exists in solution.

Pentachlorocyclopropane/Base Complexes: Matrix Isolation Infrared Spectroscopic and Density Functional Study of C−H- - -N Hydrogen Bonds

Hydrogen-bonded complexes of pentachlorocyclopropane with the bases acetonitrile, ammonia, monomethylamine, and dimethylamine have been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton of pentachlorocyclopropane (Pccp) to the electron donor (N) of the base was evidenced by red shifts of the CH stretching mode. These shifts, which range from 22 to 170 cm(-1), increase in the order CH3CN, NH3, (CH3)NH2, and (CH3)2NH. Density functional theory (DFT) calculations at the B3LYP level agree well with experiment and support the formation of 1:1 complexes of Pccp/base. Distinct changes were observed in ring modes as well as CCl and CCl2 modes. The hydrogen bond energy of the complexes varies from 2.95 to 4.22 kcal/mol and is stronger than our previously studied bromocyclopropane-ammonia complex (2.35 kcal/mol, MP2).

Cooperativity and Proton Transfer in Hydrogen-Bonded Triads

Ab initio MP2/6-311+G(3df,2pd) and MP2/aug-cc-pVTZ calculations have been carried out to investigate the structures and properties of AHXHYH(3) (A=F, Cl; X=F, Cl; Y=N, P) hydrogen-bonded complexes. Significant cooperative effects are observed in the XHYH3 dyads in the triads due to the presence of the polar near-neighbor AH. These effects are greater when the polar partner is HF, which is a better proton donor than HCl. Structural changes, red shifts of proton-donor stretching frequencies, nonadditive interaction energies, and electron density redistributions unambiguously demonstrate that the X--HY hydrogen bond (HB) is stronger in the triads than in the corresponding dyads, while the X--H bond of the proton donor becomes weaker. Even more pronounced cooperative effects are observed in the AHXH dyads due to the presence of the YH3 partner. These effects are weaker in complexes having PH3 rather than NH3 as the proton acceptor, since NH3 is a stronger base. Cooperativity also enhances the proton-donating ability of the YH3 moiety, with the result that all complexes except FHFHPH3 are cyclic. Cooperativity, together with the ease of breaking the Cl--H bond in ClHClHNH3 and FHClHNH3, leads to proton transfer (PT), so that these two complexes are better described as approaching hydrogen-bonded ClHCl- x +HNH3 and FHCl- x +HNH3 ion pairs.

Clusters of glycolic acid with three to six water molecules

Semiempirical, ab initio, and density functional theory calculations are used to locate many low-energy minima on the potential energy surfaces of the CH2OHCOOH-(H2O)n complexes with n = 3,4,5,6. In the clusters with three, four, and five water molecules, the lowest-energy structure consists of a (H2O)n complex, not necessarily of lowest energy, hydrogen bonded to the carboxylic group of the glycolic acid. The lowest-energy structure for n = 6 is similar except that the water hexamer is hydrogen bonded to both the carboxylic and alpha-hydroxyl groups of the acid. In all the lowest-energy clusters, the intramolecular hydrogen bond remains intact in the glycolic acid.