Related questions Question fcbe8. How do the two strands of DNA stay together? Question How many atoms can hydrogen bond with carbon? How does hydrogen bonding affect vapor pressure? How does hydrogen bonding affect the boiling point of water? How does hydrogen bonding affect the melting point? When one molecule hydrogen bonds through two or more sites with another molecule, a ring structure known as a chelate is formed. Chelating compounds are useful for removing or mobilizing molecules and atoms such as metals.
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The RAHB discovery prompted new studies on strong H-bonds, finally leading to a general H-bond classification in six classes, called the six chem. These studies attested to the covalent nature of the strong H-bond showing, by a formal valence-bond treatment, that weak H-bonds are basically electrostatic while stronger ones are mixts.
At this limit, the strong and sym. In this Account, this hypothesis is reconsidered by using a new instrument, the pKaslide rule, a bar chart that reports in sep. Allowing the two scales to shift so to bring selected donor and acceptor mols. Reliability of pKa slide rule predictions has been verified by extensive comparison with two classical sources of H-bond strengths: i the gas-phase dissocn.
The results attest that the pKa slide rule provides a reliable soln. The hydrogen bond is the most important of all directional intermol. It is operative in detg. Research into hydrogen bonds experienced a stagnant period in the s but re-opened around , and has been in rapid development since then.
In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. Within this range, the nature of the interaction is not const. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state.
In this review, a coherent survey is given on all these matters. Sigala, Paul A. Hydrogen bonds profoundly influence the architecture and activity of biol. Deep appreciation of hydrogen bond contributions to biomol. Here we directly test the structural basis of model II. Neutron crystallog. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after assocn.
These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biol. Acta Crystallogr. B: Struct. Quantum Chem. Substituent effects on the phys. Substituents alter the phys. Several quantum chem. All of these latter parameters yielded correlation coeffs. BMC Chem. Quantum mechanics QM calculations and fundamental equations that account for substituent effects may provide insight into these important properties.
PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains. RESULTS: These studies revealed that: 1 different semiempirical QM methods yield similar results for the electronic effects of side chain groups, 2 polarizability, which reflects molecular deformability, represents steric factors in electronic terms, and 3 inductive effects contribute to the propensity of an amino acid for alpha-helices.
Gross, Kevin C. Historically, Hammett consts. Taking the exptl. Among the calcd. The aniline mol. Substituents on the Ph ring alter this out-of-plane angle as well as other mol. Among the mol. Of several measures of at. This latter result suggests that the natural charge, rather than either the Mulliken or electrostatic charges, may be the preferred charge descriptor for correlation purposes.
The isotopic fractionation factors of homo- and heteroconjugate complexes reach a min. Both biphenolates and bicarboxylates generate such fractionation factors. The electronic spectra of the nitrobiphenolates require that these substances be mixts. O center, so their lowest allowed vibrational levels appear to fall above the central max.
Many properties of these substances are modeled with simple, quartic-quadratic potential functions. A heteroconjugate complex is predicted and obsd. The fractionation factors of strongly unsym. The potentials of heteroconjugates can be modeled with quartic-cubic-quadratic functions. Nature Publishing Group. The energetic contributions of hydrogen bonding to protein folding are still unclear, despite more than 70 years of study.
This is due partly to the difficulty of extg. Herein, we test the hypothesis that hydrogen bond strengths depend on the polarity of their microenvironment, with stronger hydrogen bonds forming in nonpolar surroundings. Double-mutant cycle anal. Such large coupling energies between hydrogen bond strengths and local polarity suggest that the context dependence of hydrogen bond strengths must be accounted for in any comprehensive account of the forces responsible for protein folding.
Biochemistry 41 , — , DOI: Here the authors examine the principles underlying the catalytic efficiency of KSI by computer simulations using the empirical valence bond method in combination with mol. The simulations reproduce available kinetic and structural data very well and allow the authors to examine several features of the catalytic mechanism in detail.
The crit. H-bond between Tyr 16 and the intermediate is found to be a normal ionic H-bond with the preferred proton location on the tyrosine residue. The possibility of an active site water mol. The existence of such a water mol. Enzyme catalysis and hydrogen bonding were discussed. National Academy of Sciences. The rubredoxin from Clostridium pasteurianum CpRd provides an excellent system for investigating how protein sequence modulates the redn. The length or strength of each hydrogen bond was inferred from the magnitude of electron spin delocalized across the hydrogen bond from the iron atom onto the nitrogen.
The aggregate lengths of these six hydrogen bonds are shorter in both oxidn. Differences in aggregate hydrogen bonding upon redn. Sequence effects on the redn. Methods Enzymol. FEBS J. Blackwell Publishing Ltd. Short H-bonds SHBs are present in many chem. It is well known that these SHBs are found in the active site of enzymes and aid enzyme catalysis.
This study aimed to systematically characterize all SHBs from a nonredundant dataset of protein structures. The study revealed that SHBs are commonly found in proteins and are widely present in different regions of the protein chain, such as the backbone or side-chain, and in different secondary structural regions such as helixes, strands, and turns. The frequency of occurrence of donors and acceptors from the charged side-chains as well as from the neutral backbone atoms was equally high.
This suggested that SHBs in proteins occur either due to increased strength or due to geometrical constraints and this was illustrated from several examples. Thus, this anal. The donor-acceptor specificities of SHBs and their role in stabilizing protein tertiary structure are some of the highlights of this investigation. In the interest of continuity, earlier work is quoted when it relates to that published during this period. Academic Press. This article considers two questions about string H-bonding.
Do strong H-bonds occur in org. Should the strongly basic properties of proton sponge mols. These questions are debatable and it is the purpose of this article to consider the currently available evidence bearing on them and to define the terms of the debate.
The effects of steric compression were also discussed. Tetrahedron 57 , — , DOI: Elsevier Science Ltd. Progressive incorporation of electron-withdrawing substituents into the arom. Induction of this unique linkage correlates with a 1. According to NMR evidence, this is attained for 3-chloronitrosalicylic acid.
We present addnl. Hydrogen cis-cyclohexane 1,2-dicarboxylate, displays low-field 1H NMR signals in aprotic solvents at The LBHB in hydrogen 2,2-dimethylmalonate is further characterized by the observation of a pos. Low-field 1H NMR signals are not obsd. These compds. Internally strained dicarboxylic acid monoanions also display low field 1H NMR signals in aq. Dalton Trans.
Royal Society of Chemistry. The distribution of distances from atoms of a particular element E to a probe atom X oxygen in most cases , both bonded and intermol. In general, the distribution is characterized by a max.
The anal. PLoS Biol. A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis.
Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole.
The binding of substituted phenolates of constant molecular shape but increasing pK a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0. This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
H-bonds play major roles in biol. Nonetheless, H-bonded protons are not typically obsd. Here, the authors report the NMR detection of the H--bonded protons donated by Tyr and Glu to the chromophore O atom in the active site of the bacterial photoreceptor, photoactive yellow protein PYP. The authors used the NMR resonances for these H-bonds to probe their conformational properties and ability to rear-range in response to nearby electronic perturbation.
The detection of geometric isotope effects transmitted between the Tyr and Glu H-bonds provided strong evidence for robust coupling of their equil. The incorporation of a modified chromophore contg. Thus, these results elucidate fundamental properties of H-bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of H-bonds obsd. Predictive estimates of E. A: Found. Descriptive statistics and predictive estimates of E.
An intermol. This function was then applied to the crystal lattice energy and H bonding calcns. The nature of these intermol.
The effects of crystal forces on mol. Nature , — , DOI: A spatial freedom factor was applied to the statistical anal. The donor and acceptor groups were aliph. OH groups in polyalcs. Assuming that the optimum H bond is linear the correction factor depends on the OH The cor.
Because living organisms are in const. Here, the authors focus specifically on the conformational changes that occur in proteins and how studying these protein dynamics may provide insights into enzymic catalysis.
Advances in integrating techniques such as x-ray crystallog. For proteins amenable to at. Concurrently, there is an increasing need for using perturbations to test predictive models of dynamics-function relations. In DHFR, mutations that alter the ability of the active site to sample productive higher energy states on the millisecond time scale reduce the rate of hydride transfer significantly. Recently identified rescue mutations restore function, but the mechanism by which they do so remains unclear.
The exact role of any changes in the dynamics remains an open question. For CypA, a network of side-chains that exchange between 2 conformations is crit.
Mutations that lock the network in one state also reduce catalytic activity. A further understanding of enzyme dynamics of well-studied enzymes such as DHFR and CypA will lead to improvement in ability to modulate the functions of computationally designed enzymes and large macromol. In designed enzymes, directed evolution expts. Detailed x-ray studies suggest that these mutations likely limit the conformational space explored by residues in the active site.
For proteins where at. Understanding the conformational dynamics of larger systems such as protein machines will likely become more accessible and provide new opportunities to rationally modulate protein function. The phys. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chem. This Perspective highlights recent exptl.
The data necessitate a reformulation of the dominant textbook definition of biol. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site.
The available model also suggests a phys. We conclude by addressing the often conflicting interface between computational and exptl. Annual Reviews Inc. Since the discovery of enzymes as biol. Nevertheless, there is no universally accepted comprehensive description.
Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an abs. Site-directed mutagenesis has emerged as an enormously powerful approach to probe enzymic catalysis, illuminating many basic features of enzyme function and behavior.
The emphasis of site-directed mutagenesis on the role of individual residues has also, inadvertently, limited exptl. The 1st part of this review highlights the structural and functional interconnectivity central to enzymic catalysis.
In the 2nd part, the authors discuss the features of enzymes that distinguish them from simple chem. These are presented in conceptual models that, while simplified, help illustrate the vast amt. In the last section, the authors highlight the mol. The promise of advancing and integrating cutting edge conceptual, exptl. FResearch 3 , 94 , DOI: The movement to bring datasets into the scholarly record as first class research products validated, preserved, cited, and credited has been inching forward for some time, but now the pace is quickening.
As data publication venues proliferate, significant debate continues over formats, processes, and terminology. Here, we present an overview of data publication initiatives underway and the current conversation, highlighting points of consensus and issues still in contention. Data publication implementations differ in a variety of factors, including the kind of documentation, the location of the documentation relative to the data, and how the data is validated.
Publishers may present data as supplemental material to a journal article, with a descriptive "data paper," or independently. Complicating the situation, different initiatives and communities use the same terms to refer to distinct but overlapping concepts. For instance, the term published means that the data is publicly available and citable to virtually everyone, but it may or may not imply that the data has been peer-reviewed.
In turn, what is meant by data peer review is far from defined; standards and processes encompass the full range employed in reviewing the literature, plus some novel variations. Basic data citation is a point of consensus, but the general agreement on the core elements of a dataset citation frays if the data is dynamic or part of a larger set. Even as data publication is being defined, some are looking past publication to other metaphors, notably "data as software," for solutions to the more stubborn problems.
Public Library of Science. Despite widespread support from policy makers, funding agencies, and scientific journals, academic researchers rarely make their research data available to others. At the same time, data sharing in research is attributed a vast potential for scientific progress.
It allows the reproducibility of study results and the reuse of old data for new research questions. Based on a systematic review of 98 scholarly papers and an empirical survey among secondary data users, we develop a conceptual framework that explains the process of data sharing from the primary researcher's point of view.
We show that this process can be divided into six descriptive categories: Data donor, research organization, research community, norms, data infrastructure, and data recipients. Drawing from our findings, we discuss theor.
We conclude that research data cannot be regarded as knowledge commons, but research policies that better incentivise data sharing are needed to improve the quality of research results and foster scientific progress. Trends Ecol. Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers - data accessibility, discovery, re-use, preservation and, particularly, data sharing.
Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data but are not satisfied with long-term data preservation.
These properties explain why ice floats on water, and how goldfish can survive at the bottom of a frozen pond over the winter. The presence of hydrogen bonds also makes water molecules more 'sticky' or in scientific terms cohesive and adhesive.
The small charges on the water molecules allows them to stick together which is why water has a 'skin' that small insects can walk on, and also explains why water can be sucked up a straw so easily.
It's not just straws either, plants draw water up from their roots to the top of the highest leaves without any kind of pumping mechanism. They rely on the ability of water to form a thin unbroken tube, all the way up the length of the trunk. Hydrogen bonds are a great example of why I love the 'chemistry' part of biochemistry so much.
From the tiny world of the nucleus and the principles of intercellular forces the properties of larger and complex organisms can be built up. From the tiny elecrogen-low nucleus of hydrogen we get an explanation how plants get water to the leaves, and how fish survive over winter.
I find that amazing! The views expressed are those of the author s and are not necessarily those of Scientific American. A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs.
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