Energy Of Hydrogen Bond Formation Research Articles

The Evolution of Hydrogen Bond Network in Nafion via Molecular Dynamics Simulation

The hydrogen bond network (HBN) is of primary importance to the proton transport in Nafion. However, the evolution of the HBN in Nafion with water content and the underlying thermodynamics have not been revealed. In this study, the free energy of hydrogen bond formation is calculated based on an information-theoretic approach, indicating the formation of HBN in Nafion is a thermodynamically favorable process as the water content increases. In addition, the evolution of HBN in Nafion with water content including the topology and basic building blocks has been visualized and quantified by a ring statistics approach based on graph theory. Finally, the rearrangement dynamics and heterogeneity of HBN are also disclosed. This study provides a fundamental and comprehensive understanding of HBN in Nafion including the formation thermodynamics, topology, and rearrangement dynamics, which is useful for the design of high-performance proton exchange membranes.

Insights into the spontaneity of hydrogen bond formation between formic acid and phthalimide derivatives.

We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012. Our results indicate that the phthalimide derivatives that form hydrogen bond complexes most favorably, have in their structures only one C=O group and at least one NH group. On the other hand, the phthalimide derivatives predicted to form hydrogen bonds least favorably, possess in their structures two carbonyl groups, C=O, and no NH group. The ability to donate electrons and simultaneously receive one acidic hydrogen is the most important property related to the spontaneity of hydrogen bond formation. We further chose two cyclic compounds, phthalimide and isoindolin-1-one, in which to study the main changes in molecular, structural and spectroscopic properties as related to the formation of hydrogen bonds. Thus, the greatest ability of the isoindolin-1-one compound in forming hydrogen bonds is evidenced by the larger effect on the structural, vibrational, and chemical shifts properties associated with the O-H group. In summary, the electron-donating ability of the hydrogen bond acceptor emerged as the most important property differentiating the spontaneity of hydrogen bond formation in this group of complexes.

Residual water in polyvinyl alcohol

The state of sorbed water molecules in the matrix of polyvinyl alcohol is investigated via the methods of static sorption, DSC, TGA, IR Fourier spectroscopy, 1H NMR spectroscopy, and quantum-chemical simulation. It is shown that the sorption of water by polyvinyl alcohol characterized by an S-shaped isotherm is described by the double-sorption model. It is established that the low diffusion coefficients and extremely low rates of desorption processes observed in the range of low activities are determined by a shift of the equilibrium toward the formation of hydrogen-bonded complexes of water molecules with hydroxy groups of the polymer. A mechanism for the behavior of residual water in hydrophilic polymers is suggested. It implies that differences between polymers are determined only by the quantity of residual water immobilized in “traps” and the energy of hydrogen-bond formation.

Investigating hydrogen bonds in liquid ethylene glycol structure by means of molecular dynamics

Models of liquid ethylene glycol are built by means of molecular dynamics at temperatures ranging between 268 and 443 K, with 1000 molecules in rectangular parallelepiped basic cells. The dependences of structures of O-H…O hydrogen bonds on modeling time and temperature are analyzed. It is found that the hydrogen bonds emerge at different sites of a model, thus forming a hydrogen bonds network that is continuously rebuilt under the action of thermal fluctuations. The number of hydrogen bonds in the models is observed to decrease when the temperature is raised. The energy of hydrogen bond formation is found to be −20.0 ± 2.6 kJ mol−1, the average bond lifetime is 370 ps at 268 K and 147 ps at 323 K, and the activation energy of hydrogen bond rupture at these temperatures is ∼12.1 kJ mol−1. It is concluded that the data on the breaking of H-bonds at temperatures of 323 to 443 K can be explained by the molecules moving away from each other as a result of diffusive motion, accompanied by rearrangement of the hydrogen bonds network. The concentration of dimers in the models is shown to be rather low, while the average energy of forming a dimer from two ethylene glycol molecules is −35.4 kJ mol−1.

170 GMPC model and the helix–coil transition in biopolymers

The Hamiltonian of the generalized model of polypeptide chain (GMPC) is introduced to describe the system in which the conformations are correlated over some dimensional range Δ. The Hamiltonian does not contain any parameter designed especially for helix–coil transition and uses pure molecular microscopic parameters (the energy of hydrogen bond formation, reduced partition function of repeated unit, the number of repeated units fixed by one hydrogen bond, the flexibility of chain, the energies of interaction between the repeated units and the solvent molecules) (Badasyan et al., 2005, 2004). We evaluate the partition function using transfer-matrix approach. We describe the influence of solvent interaction with biopolymer, both with competing and noncompeting for hydrogen bond formation ways. On handling the problem of solvent influence on helix–coil transition, we obtained dependence on energy of solvent–macromolecule interaction, how solvents change correlation length, transition temperature, and interval. We obtained that two type interaction of solvent results in low temperature coil–helix transition, which we connect with cold denaturation. A consistent inclusion of osmotic pressure effects in a description of helix–coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition (Badasyan et al., 2012). We also took into account two biopolymers’ side-by-side interactions. In the case of effective repulsion; the shape of the melting curve is two-phase with high and wide correlation length in a plateau on denaturation curve (Badasyan et al., 2009). We also took into account structural heterogeneity of biopolymers using constrained annealing approximation (Serva & Paladin, 1993).

The energy of the intramolecular hydrogen bond in chloro-substituted N-methyl-salicylidene imines

The energetic effects of the conformational rearrangement of eight Schiff bases, differently chloro-substituted, are discussed on the basis of the results of B3LYP/6-31+G(d,p) calculations. The proton transfer tautomers as well as “open”-non-hydrogen-bonded forms were considered. It was found, that the hydrogen-bonded forms have the lowest energy, but the second most stable were the proton transfer states with an O…H N intramolecular hydrogen bond. The proton transfer in Schiff bases dominates in comparison to other conformational rearrangements. This is important for the understanding of thermochromic and photochromic properties of these molecules. By using a thermodynamic cycle, the steric effects connected with chelate ring formation are estimated to be up to 5 kcal/mol, much higher than in related Mannich bases (∼1 kcal/mol) which do not form resonance assisted hydrogen bonds. Accounting these effects the “real” value of the energy of hydrogen bond formation was estimated to be 15 kcal/mol which increases with growing number of chlorine atoms up to 16.5 kcal/mol for 4,5,6-trichloro substitution.

Semiquantal analysis of hydrogen bond

The semiquantal time-dependent Hartree (SQTDH) theory is applied to the coupled Morse and modified Lippincott-Schroeder (LS) model potentials of hydrogen bond. The structural correlation between the heavy atoms distance and the proton position, the geometric isotope effect, the energy of hydrogen bond formation, and the proton vibrational frequency shift are examined in a broad range of structural parameters. In particular, the geometric isotope effect is found to depend notably on the choice of the potential model, for which the LS potential gives the isotope shift of the heavy atoms distance in the range of 0.02-0.04 A, in quantitative agreement with the experimental findings from assortment of hydrogen bonding crystals. The fourth-order expansion approximation to the semiquantal extended potential was confirmed to be highly accurate in reproducing the full SQTDH results. The approximation is computationally efficient and flexible enough to be applied to general models of hydrogen bond.

Reactivity descriptors for the hydrogen bonding ability of pyridine bases

The hydrogen bonding interaction between pyridine bases and water was theoretically studied by applying density functional theory computations at the B3LYP/631G(d,p) level. The theoretically determined binding energies for the complexation process correlate well with the experimental solvatochromic parameters β for the respective bases. A very good linear relationship was also found between the evaluated binding energies of hydrogen bond formation and the respective electrostatic potential at nuclei (EPN) values at the pyridine nitrogen atom. It was found that the theoretical EPN values correlated linearly with the β constants and the quantities could be employed as alternative. It was concluded that the electrostatic potential at nuclei characterized quantitatively the reactivity of the studied molecules toward the hydrogen bond formation. EPN values could be applied as hydrogen bond descriptors in QSAR studies.

The Electrostatic Potential at Atomic Sites as a Reactivity Index in the Hydrogen Bond Formation

AbstractFor Abstract see ChemInform Abstract in Full Text.

Electrostatic potential at nuclei as a reactivity index in hydrogen bond formation. Complexes of ammonia with C–H, N–H and O–H proton donor molecules

In this study the use of molecular electrostatic potential at atomic sites as a reactivity descriptor for the process of hydrogen bonding is evaluated for a series of complexes involving different types of proton donor molecules and ammonia as a model proton acceptor. The compounds studied were: C 2H 4, CH 3CCH, CH 2CH–CCH, HCN, CH 3NH 2, (CH 3) 2NH, HNC, C 6H 5NH 2, cytosine, HCONHCH3, CH 3OH, C 2H 5OH, C 3H 7OH, C 6H 5OH, HCOOH and H 3CCOOH. Geometry optimisation and vibrational frequency calculations at the optimised geometry were performed for isolated monomers and hydrogen-bonded systems. Density functional theory computations at the B3LYP/6-31G(d,p) were employed. Linear dependence between the molecular electrostatic potential at the hydrogen atom in the isolated monomers and the energy of hydrogen bond formation is found. The results show that the electrostatic potential at atomic sites can be used as a reactivity descriptor for the ability different types of proton donor molecules to form hydrogen bonds.

The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation

The paper reviews results from computational studies by molecular orbital and density functional theories on several series of hydrogen bonded complexes. These studies aim at quantifying the reactivity of molecules for the complexation process. Excellent linear relationships are found between the electrostatic potential values at the sites of the electron donor and electron accepting atoms and the energy of hydrogen bond formation (Δ E). The series studied are: (a) complexes of R–CHO and R–CN molecules with hydrogen fluoride; (b) complexes of mono-substituted acetylene derivatives with ammonia; (c) (HCN) n hydrogen bonded cluster for n=2–7. All 22 studied complexes of carbonyl and nitrile compounds with hydrogen fluoride fall in the same dependence between the energy of hydrogen bond formation and the electrostatic potential at the atomic site of the carbonyl oxygen and nitrile nitrogen atoms, with linear regression correlation coefficient r=0.979. In the case of complexes of mono-substituted acetylene and diacetylene derivatives with NH 3, the correlation coefficient for the dependence between the electrostatic potential at the acidic hydrogen atom and Δ E equals 0.996. For the series of hydrogen bonded (HCN) n clusters, the correlation coefficient for the relationship between the electrostatic potential at the end nitrogen atom and Δ E is r=0.9996. Similarly, the analogous relationship with the electrostatic potential at the end hydrogen atom has a regression coefficient equal to 0.9994. The dependencies found are theoretically substantiated by applying the Morokuma energy decomposition scheme. The results show that the molecular electrostatic potential at atomic sites can be successfully used to predict the ability of molecules to form hydrogen bonds.

Electrostatic Potential at Atomic Sites as a Reactivity Descriptor for Hydrogen Bonding. Complexes of Monosubstituted Acetylenes and Ammonia

The applicability of molecular electrostatic potential values at atomic sites as a reactivity descriptor for the process of hydrogen bonding is assessed for a series of complexes involving acetylene and diacetylene derivatives as proton donors and ammonia as a model proton acceptor. The acetylenic compounds studied were of the type R−C⋮C−H, where R represents H, F, Cl, CH3, CH2F, CHF2, CF3, CH2Cl, CHCl2, CCl3, CN, H−C⋮C, F−C⋮C, Cl−C⋮C. Density functional theory computations at the B3LYP/6-31G(d,p) level were employed. An excellent linear relation between the molecular electrostatic potential at the acetylenic hydrogen atom in the isolated acetylenes with the energy of hydrogen-bond formation is found. It is concluded that the value of the electrostatic potential at the acidic hydrogen atomic site can be used as a reactivity descriptor for the hydrogen bonding ability of the molecules studied.

The linear relationship between Koopmans' and hydrogen bond energies for some simple carbonyl molecules

Recently Galabov and Bobadova-Parvanova have shown that the energy of hydrogen bond formation calculated at the HF/6-31G(d,p) level is highly correlated with the molecular electrostatic potential at the acceptor site for a number of simple carbonyl compounds. Here it is shown that the electrostatic potential can be replaced by Koopmans' energy. The correlation between this energy and the hydrogen bond formation energy is just as high as the one observed by Galabov and Bobadova-Parvanova. The Siegbahn simple potential relating Koopmans' energies and GAPT charges shows that the hydrogen bond energy is not simply correlated with the charge of the acceptor site because the charges on the neighboring atoms are also important in the hydrogen bonding process.

Aggregation in Dilute Solutions of 1-Hexanol in n-Hexane: A Monte Carlo Simulation Study

Configurational-bias Monte Carlo simulations in the isobaric−isothermal ensemble using the nonpolarizable TraPPE−UA (transferable potentials for phase equilibria−united-atom) force field were performed to study the aggregation of 1-hexanol in n-hexane. The spatial distribution of alcohols was sampled efficiently using special Monte Carlo moves. Analysis of the microscopic structures for 1, 3, and 5% solutions at a temperature of 298.15 K and a pressure of 101.3 kPa shows strong aggregation with a preference for tetramers and pentamers for all three concentrations. About half of these tetramers and pentamers are found in cyclic aggregates. The enthalpies for the formation of clusters of specific sizes were determined from simulations of a 3% solution at temperatures ranging from 298.15 to 328.15 K. The free energies and enthalpies of cluster formation show the large influences of hydrogen-bond cooperativity, which favors clusters larger than dimers, but a decreasing enthalpy gain and an increasing entropic penalty prevent the formation of very large clusters. These results have important implications for the thermodynamic modeling of hydrogen-bonding fluids, which commonly use a constant value for the free energy of hydrogen-bond formation. Overall agreement with Fourier transform infrared spectroscopic measurements on the extent of hydrogen bonding for the same mixtures is satisfactory.

Hydrogen-bonding classes in proteins and their contribution to the unfolding reaction.

This paper proposes to assess hydrogen-bonding contributions to the protein stability, using a set of model proteins for which both X-ray structures and calorimetric unfolding data are known. Pertinent thermodynamic quantities are first estimated according to a recent model of protein energetics based on the dissolution of alkyl amides. Then it is shown that the overall free energy of hydrogen-bond formation accounts for a hydrogen-bonding propensity close to helix-forming tendencies previously found for individual amino acids. This allows us to simulate the melting curve of an alanine-rich helical 50-mer with good precision. Thereafter, hydrogen-bonding enthalpies and entropies are expressed as linear combinations of backbone-backbone, backbone-side-chain, side-chain-backbone, and side-chain-side-chain donor-acceptor contributions. On this basis, each of the four components shows a different free energy versus temperature trend. It appears that structural preference for side-chain-side-chain hydrogen bonding plays a major role in stabilizing proteins at elevated temperatures.

Molecular electrostatic potential as reactivity index in hydrogen bond formation: an HF/6-31+G(d) study of hydrogen-bonded (HCN)n clusters, n=2,3,4,5,6,7

Ab initio molecular-orbital calculations of (HCN)n clusters for n=2,3,4,5,6,7 were performed following the procedure of King and Weinhold [B.F. King, F. Weinhold, J. Chem. Phys. 103 (1995) 333]. Geometry optimisation and vibrational frequency calculations at the optimised geometry were carried out at HF/6-31+G(d) level of theory. The calculations confirm the known linear relations between the energy of hydrogen bond formation (ΔE(n)) and: (1) the hydrogen bond length (rN⋯H(n−1)); (2) the change of the neighbouring C–H bond length (ΔrC–H(n)); and (3) its characteristic vibrational frequency shift (ΔνC–H(n)). An excellent linear dependence is found between the energy of hydrogen bond formation (ΔE(n)) and the molecular electrostatic potential at the end nitrogen atom (VN(n−1)). A perfect linear relation also exists between ΔE(n) and the molecular electrostatic potential at the end hydrogen atom (VH(n−1)). The results obtained confirm that the molecular electrostatic potential at atomic sites can be used as a reactivity index reflecting the ability of molecules to participate in hydrogen bonding.

Microscopical approach to the helix–coil transition in DNA

A model Hamiltonian for double-strand polynucleotides is suggested to describe the phenomenon of helix–coil transition. The Hamiltonian is constructed using solely the microscopical, pure physical quantities, characterizing the molecular chain, namely the energy of hydrogen-bond formation and the number of conformations of repeated unit. Realistic constraints are imposed on the conformations of chain in the case of loop formation. The advantage of the suggested approach is that the parameters of the model can be obtained from independent calculations or experiments. It is shown that with the approximation of neglecting the effect of large loops, the model of DNA is reduced to the generalized microscopical model of polypeptide chain.

Molecular Electrostatic Potential as Reactivity Index in Hydrogen Bonding: Ab Initio Molecular Orbital Study of Complexes of Nitrile and Carbonyl Compounds with Hydrogen Fluoride

Ab initio molecular orbital calculations at the HF/6-31+G(d,p) level were used to investigate the hydrogen bonding between hydrogen fluoride and two series of molecules, nitrile and carbonyl compounds of the type R−CN and R−CHO, respectively, where R= −H, −OH, −SH, −OCH3, −NH2, −NO2, −C⋮N, −F, −Cl, −CH3, and −CF3. Geometry optimization and vibrational frequency calculations at the optimized geometry were performed for isolated and hydrogen-bonded systems. The estimated energies of hydrogen-bond formation were corrected for zero-point vibrational energy and basis set superposition error (including the relaxation correction). Linear relations between the energy of hydrogen-bond formation (ΔE) and the H−F stretching frequency shift (ΔνHF) are obtained for the two series studied. Linear dependencies are also found between ΔE and the change of H−F bond length (ΔrHF). An excellent linear dependence is found between ΔER-CN and the ab initio calculated molecular electrostatic potential at the nitrile nitrogen (VN...

Ab Initio Molecular-Orbital Study of Hydrogen-Bonded Complexes of Carbonyl Aliphatic Compounds and Hydrogen Fluoride

Ab initio molecular-orbital calculations at the HF/6-31G(d,p) level were used to investigate the hydrogen bonding between open-chain aliphatic carbonyl compounds and hydrogen fluoride. The carbonyl compounds studied are H2CO, HCOOH, HCOSH, HCOOCH3, HCONH2, HCONO2, HCOCN, HCOF, HCOCl, HCOCH3, HCOCF3, CH3COOH, CH3COSH, CH3COOCH3, CH3CONH2, CH3CONO2, CH3COCN, CH3COF, CH3COCl, CH3COCH3, and CH3COCF3. Geometry optimization and vibrational-frequency and infrared-intensity calculations at the optimized geometry were performed for isolated and hydrogen-bonded systems. The estimated energies of hydrogen-bond formation were corrected for zero-point vibrational energy and basis-set superposition error. In agreement with expectations a linear relation (R = 0.994) between the energy of hydrogen-bond formation, ΔE, and the H−F stretching frequency shift, ΔνH-F, was obtained for the systems studied. A linear dependency was also found between ΔE and the change of H−F bond length, ΔrH-F (R = 0.994). Effective bond charges of the hydrogen bond, δO···H, for the series of compounds studied were evaluated from the theoretically derived dipole-moment derivatives. A satisfactory correlation (R = 0.938) between δO···H and the energy of hydrogen bond formation, ΔE, was obtained. The attempt to explain the differences in hydrogen-bond strength, ΔE, with the variation of the carbonyl oxygen atomic charges in the isolated molecules showed that neither Mulliken nor CHELPG and MK atomic charges can be successfully used for the purpose. However, the molecular electrostatic potential at the carbonyl oxygen in the isolated molecules, ΦO, correlates in a quite satisfactory manner (R = 0.979) with the energy of hydrogen-bond formation for the entire series of compounds. This result appears quite significant in view of its importance for understanding the mechanisms of intermolecular interactions leading to hydrogen bonding.

Interpretation of carbonyl stretching band intensities in the infrared spectra: an ab initio MO study

Ab initio MO calculations at HF/6-31G ** level have been used to investigate the variations in the carbonyl stretching band intensities in a series of 15 open-chain aliphatic carbonyl derivatives containing first-row elements (molecules of the type HCOX, CH 3COX and X 2CO, where X=–H, –CH 3, –OH, –OCH 3, –NH 2 and –F). Geometry optimisation and frequency and intensity calculations at the optimised geometry have been performed. Two types of local intensity parameters have been evaluated: (1) dipole moment derivatives with respect to CO bond stretching (∂ p/∂ r CO); and (2) effective charges of the CO bond ( δ CO). Atomic charges determined according to CHELPG scheme and the energy of hydrogen bond formation between hydrogen fluoride and the carbonyl oxygen have also been evaluated. Linear dependencies between effective bond charges ( δ CO) and carbonyl oxygen atomic charges, as well as between δ CO and the energy of hydrogen bond formation have been found. The relations obtained show that the derived local infrared intensity parameters can be used to characterise electric charge properties of the carbonyl bond.