What Is the Covalency of Hydrogen Bonding?

We report quantifying the strengths of different types of hydrogen bonds in hydrogen-bond networks (HBNs) via measurement of the adiabatic electron detachment energy of the conjugate base of a small covalent polyol model compound (i.e., (HOCH2CH2CH(OH)CH2)2CHOH) in the gas phase and the pKa of the corresponding acid in DMSO. The latter result reveals that the hydrogen bonds to the charged center and those that are one solvation shell further away (i.e., primary and secondary) provide 5.3 and 2.5 pKa units of stabilization per hydrogen bond in DMSO. Computations indicate that these energies increase to 8.4 and 3.9 pKa units in benzene and that the total stabilizations are 16 (DMSO) and 25 (benzene) pKa units. Calculations on a larger linear heptaol (i.e., (HOCH2CH2CH(OH)CH2CH(OH)CH2)2CHOH) reveal that the terminal hydroxyl groups each contribute 0.6 pKa units of stabilization in DMSO and 1.1 pKa units in benzene. All of these results taken together indicate that the presence of a charged center can provide a powerful energetic driving force for enzyme catalysis and conformational changes such as in protein folding due to multiple hydrogen bonds in a HBN.

Hydrogen bond interactions in small covalent model compounds (i.e., deprotonated polyhydroxy alcohols) were measured by negative ion photoelectron spectroscopy. The experimentally determined vertical and adiabatic electron detachment energies for (HOCH(2)CH(2))(2)CHO(-)(2a), (HOCH(2)CH(2))(3)CO(-) (3a), and (HOCH(2)CH(2)CH(OH)CH(2))(3)CO(-) (4a)reveal that hydrogen-bonded networks can provide enormous stabilizations and that a single charge center not only can be stabilized by up to three hydrogen bonds but also can increase the interaction energy between noncharged OH groups by 5.8 kcal mol(-1) or more per hydrogen bond. This can lead to pK(a) values that are very different from those in water and can provide some of the impetus for catalytic processes.

A combination of surface-enhanced Raman spectroscopy (SERS), surface-enhanced infrared spectroscopy (SEIRA), and density functional theory (DFT) calculations are used to study the adsorption and thin film growth of isoniazid (an antimicrobial used to treat tuberculosis) on silver nanostructures (SNS). It is known that an isoniazid crystal takes on a C1 configuration where one of the hydrogens at the end of the hydrozyl group (−NH-NH2) form an intramolecular hydrogen bond with the only oxygen atom. DFT calculations involving combinations of isoniazid dimers, trimers, and tetramers are used to model and interpret the Raman spectrum of isoniazid powder. The DFT calculations highlight the importance of accurately modeling hydrogen-bonding interactions between adjacent hydrozyl groups as well as interactions involving the ring nitrogen and the hydrozyl group. SERS, SEIRA, and DFT calculations involving isoniazid dimers and four-metal silver clusters reveal that isoniazid takes on a T conformation in a monolayer adsorbed on SNS where the hydrozyl group is rotated around a single bond so that the −NH2 is oriented down with respect to the oxygen atom. Further evidence from the SEIRA and DFT calculations illustrate that the multilayer of isoniazid deposited from acetone maintains a geometry similar to the T conformation. In addition to the polar solvent acetone, n-heptane, a solvent with nonpolar bonds, is used to study the interactions of isoniazid with the SNS. These studies reveal that isoniazid has a stronger affinity for SNS when using n-heptane as the deposition solvent. An increase in attraction between isoniazid and the SNS is probably accomplished by changing the angle of interaction of the NH2 and −NH groups with respect to the SNS. It is believed that a lower level of solvation occurs when using n-heptane as a deposition solvent, which allows for increased isoniazid attraction to the SNS.

Protein-Lipid Interactions and their Relation to the Physical-Chemical Stability of Concentrated Milk. A Review1,2

The use of water as a solvent for carrying out organic reactions was nonexistent till about the middle of the 20th century. In view of the environmental concerns caused by pollution of organic solvents, chemists all over the world have been trying to carry out organic reactions in aqueous phase. The advantage of using water as a solvent is its cost, safety (it is non-inflammable, and is devoid of any carcinogenic effects) and simple operation. Water has the highest value for specific heat of all substances. It’s unique enthalpic and entropic properties has led the chemists to use it as a solvent in organic reactions. Water has an abnormally low volatility because its molecules are associated with each other by means of hydrogen bonds. In fact, the H bonding is the main reason why covalent compounds have low solubility in water. Ionic material become hydrated and polar materials take part in the hydrogen bonding, so they are soluble.

Introductory Biology courses typically introduce the structure and function of biomolecules such as proteins and nucleic acids. To understand biomolecules fully, students require knowledge of fundamental chemistry concepts such as covalent bonding, intermolecular interactions and hydrophilicity/hydrophobicity (1).&nbsp;Students enter our large (&gt;400 student) course with a notoriously limited conceptual grasp of basic chemistry principles.&nbsp;Our lesson is an activity designed on the principles of POGIL (<a href="https://pogil.org/">Process Oriented Guided Inquiry Learning</a>).&nbsp;In 50 minutes, students build their own definitions of the following: polar vs. non-polar covalent bonds, hydrophilicity/hydrophobicity and the nature of hydrogen bonding based simply on the relative electronegativities of oxygen, nitrogen, carbon and hydrogen.&nbsp;We find that this exercise improves students&rsquo; understanding of these chemical concepts. Since adopting this activity, students have been better able to understand biomolecular structures and predict interactions between molecules. <em>Primary image:</em>&nbsp;Hydrogen Bond.&nbsp;Possible hydrogen bond interaction that can form between two simple organic molecules.

The aim of this study is to determine prospective chemistry teachers' creative comparisons about the basic concepts of inter- and intramolecular forces, and to uncover the relationship between these creative comparisons and prospective teachers' conceptual understanding. Based on a phenomenological research method, this study was conducted with 101 prospective chemistry teachers studying in the Chemistry Education Department at a state university in Turkey in the academic year 2011–2012. The research made use of two data collection instruments, a creative comparison questionnaire and semi-structured interviews. The concepts of “non-polar covalent bonds, dipole–dipole force, hydrogen bonds, ionic bonds, covalent bonds, polar covalent bonds, and van der Waals force” were set out in the creative comparison questionnaire and the prospective teachers were asked to complete the sentences about these concepts (example: ionic bond is like .......... because ...........). Content analysis techniques were employed in the analysis of the creative comparisons set out in the questionnaire. The analysis of the data revealed that the prospective teachers generally developed their creative comparisons based on the formation and strength of the different bonds and that they also had alternative conceptions, particularly regarding the formation of covalent bonds, hydrogen bonds, and the van der Waals force. Semi-structured interviews were conducted in order to learn more about this and obtain detailed information about the level of understanding of the prospective teachers. Twelve prospective teachers were selected for the interviews on the basis of the creative comparisons they had developed in the creative comparison questionnaire. The analysis of the interviews showed that the level of conceptual understanding of the prospective teachers was not tightly linked to the complexity of their creative comparisons. However, it was seen that the creative comparisons submitted by the prospective teachers could be used to infer their conceptual understanding. Also, these creative comparisons could be helpful in determining what the prospective teachers' alternative conceptions were.

Описан метод трехпараметрической характеристики селективности газохроматографических неподвижных фаз, который базируется на представлении энергии межмолекулярного взаимодействия вкладами неполярных, полярных сил и водородных связей. Все параметры, используемые в математических выражениях, имеют физический смысл, переносимы и не требуют проведения дополнительных экспериментов. Характеристики неподвижных фаз могут быть рассчитаны как из экспериментальных данных по хроматографическому удерживанию, так и a priori, по известной структурной формуле фазы. Описаны оба способа и проведен расчет параметров для ряда веществ. Полученные разными способами характеристики селективности неподвижных фаз согласуются между собой. Рассматривается также основанная на трехпараметрической модели концепция выбора неподвижной фазы для разделения близких веществ.

Poly(4-hydroxystyrene) (PHS) molecules in solid films are connected to each other through polar and nonpolar molecular interaction and hydrogen bonds. Although the dissociation of phenolic hydroxyl groups plays a major role in the dissolution of PHS films in tetramethylammonium hydroxide (TMAH) aqueous developer, it is important to clarify the effects of other interactions. In this study, we investigated the dissolution dynamics of partially protected PHS in organic developer by a quartz crystal microbalance method to deepen the fundamental understanding of the dissolution dynamics of chemically amplified resists. The dissolution dynamics in the solvents, in which the phenolic hydroxyl groups are hardly dissociated, was measured. In a 50 vol% methanol aqueous developer, a large swelling was observed. By decreasing the polarity of the developer, the dissolution dynamics was significantly changed. In the hexyl acetate, the dissolution kinetics of PHS films became similar to that in TMAH aqueous developer although the dissolution mechanism is different.

A model for the interaction between neutral molecules in amorphous isotropic environment is considered. The intermolecular interaction energy contains three independent groups of quantities describing non-polar forces, polar forces, and hydrogen bonds. Respectively, each of the forces is represented by its own molecular descriptor: generalized charge, dipole moment, and two numbers showing the ability of the molecule to be the donor or the acceptor of the H-bond. The H-bond contribution to the total energy of intermolecular interaction is described as a product of some quantum-mechanical threshold value and the probability of correct arrangement of interacting molecules. The accuracy of the model is verified by applying it to the estimations of the energies of dimers composed of water, alcohol, and carbon acid molecules. The accuracy and convenience of the model are evidently manifested in a priori calculations of the vaporization heat of water, alcohols, and carbon acids.

Understanding basic chemical concepts, including bonding, polar and nonpolar molecules, and hydrogen bonds is difficult for many biology students, who often have minimal chemistry backgrounds. The concept of electronegativity is introduced at the beginning of the chemical foundations part of a biology course as a central integrative concept. By using the electronegativity concept and an associated line graph, students gain an understanding of why ionic and covalent bonds form and which atoms form them, why atoms form polar and nonpolar covalent bonds, and what chemical groups can form hydrogen bonds. Positive student reviews indicate that this is an effective method for introducing chemical principles.

Crystal structure at 1.95 å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition

The proposed model of intermolecular interactions contains three independent groups of quantities describing non-polar forces, polar forces, and hydrogen bonds. The contribution of hydrogen bonding to the total energy of intermolecular interaction is represented as a product of some quantum-mechanical threshold value and the probability of molecular arrangement that makes this bonding possible. Two characteristics, “polarity” and “hydrophilicity”, distinguishing polar and non-polar species, are introduced. Along with the generalized charge, these characteristics are independent arguments of the three-parameter model for liquid phases used in chromatography. The model is applied to describe the interaction of polar molecules in the gas phase with liquid polyethylenee glycol (PEG). Theoretical dependences of PEG polarity and hydrophilicity on the polymer′s molecular mass are derived. The graph of these dependences plotted in “polarity–hydrophilicity” coordinates agrees well chromatography data for characteristics of PEGs used as stationary phases.

Aqueous solutions of poly(N-isopropyl acrylamide) show a lower critical solution temperature. The thermodynamic properties of the system have been evaluated from the phase diagram and the heat absorbed during phase separation and the phenomenon is ascribed to be primarily due to an entropy effect. From viscosity, sedimentation, and light-scattering studies of solutions close to conditions of phase separation, it appears that aggregation due to formation of nonpolar and intermolecular hydrogen bonds is important. In addition, a weakening of the ordering effect of the water-amide hydrogen bonds as the temperature is raised contributes to the stability of the two-phase system.

A nonpolar bond to hydrogen vs. lone pair: Incorporation of HPO32− and SeEO32− into a lead perrhenate framework