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Special Issue "Intramolecular Hydrogen Bonding"

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Synthesis".

Deadline for manuscript submissions: closed (30 June 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Ronald K. Castellano

Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
Website | E-Mail
Fax: +1 352 846 0296
Interests: aromatic interactions; bio-inspired electronic materials; donor-acceptor interactions; hydrogen bonding; noncovalent interactions; organic light emitting devices; organic synthesis; photophysical properties; organic photovoltaics; pi-conjugated materials; self-assembly; supramolecular chemistry; synthesis of multifunctional molecules

Special Issue Information

Dear Colleagues,

Intramolecular hydrogen bonds play critical structure- and function-serving roles in biological and synthetic molecular systems. In many cases, the interactions are strong enough to influence molecular and supramolecular structure over long time scales and in diverse solvent or solid-state environments. Classic examples come from biological and biomimetic (e.g., self-folding) molecules that rely on intramolecular hydrogen bonds in water to stabilize the functional secondary and tertiary structure. In other settings, they subtly affect conformational dynamics or competing transition state energetics. The utility of these interactions in catalysis, particularly organocatalysis, continues to gain appreciation among synthetic practitioners. With respect to the photophysical properties and electronic structures of molecules, intramolecular hydrogen bonds are now used routinely to enforce the planarization of π-conjugated materials and enjoy an important role in excited state intramolecular proton transfer processes and associated photochromic, thermochromic, and sensing applications. For supramolecular chemists, these interactions underpin a standard strategy to “preorganize” hosts for guest binding. Our ability to rationally deploy intramolecular hydrogen bonds in molecular design is linked to how well they are fundamentally understood. Along these lines, significant advances have been made over recent years to delineate the energetic and spectroscopic features of the interactions through experimental and theoretical methods. Research papers dealing with all aspects of intramolecular hydrogen bonding, from theory to experiment, and from physical characterization to synthetic application, are welcomed for inclusion into this Special Issue of Molecules. Review articles, particularly those emphasizing the unique structural or functional aspects of intramolecular hydrogen bonding, are also encouraged.

Prof. Dr. Ronald K. Castellano
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed Open Access monthly journal published by MDPI.

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Keywords

  • biomolecular structure
  • catalysis
  • conformation
  • crystal engineering
  • excited state intramolecular proton transfer
  • host-guest complexes
  • intramolecular hydrogen bonding
  • low-barrier hydrogen bonds
  • peptidomimetics
  • photophysical properties
  • resonance-assisted hydrogen bonding
  • sensors
  • spectroscopic characterization of intramolecular hydrogen bonds
  • supramolecular chemistry
  • tautomerism
  • theoretical investigation of intramolecular hydrogen bonds
  • unconventional hydrogen bonds

Published Papers (10 papers)

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Editorial

Jump to: Research, Review

Open AccessEditorial Special Issue: Intramolecular Hydrogen Bonding
Molecules 2014, 19(10), 15783-15785; doi:10.3390/molecules191015783
Received: 26 September 2014 / Revised: 27 September 2014 / Accepted: 27 September 2014 / Published: 29 September 2014
Cited by 3 | PDF Full-text (610 KB) | HTML Full-text | XML Full-text
Abstract
Intramolecular hydrogen bonds play critical structure- and function-serving roles in biological and synthetic molecular systems. This special issue, through eight contributions, showcases the prominence of these non-covalent interactions within several scientific disciplines, and in various structural contexts and environments. Reported, for example, are
[...] Read more.
Intramolecular hydrogen bonds play critical structure- and function-serving roles in biological and synthetic molecular systems. This special issue, through eight contributions, showcases the prominence of these non-covalent interactions within several scientific disciplines, and in various structural contexts and environments. Reported, for example, are the consequences of intramolecular hydrogen bonds on the structures of molecules that show biological activity, for biological mechanisms, and for the conformational switching of functional synthetic molecules. Also showcased in the contributions are the state-of-the-art experimental and theoretical methods available for the characterization of intramolecular hydrogen bonds, which critically report on their strengths, geometries, and spectroscopic signatures in the gas, solid, and solution phases. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)

Research

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Open AccessArticle Solid State Structure and Solution Thermodynamics of Three-Centered Hydrogen Bonds (O∙∙∙H∙∙∙O) Using N-(2-Benzoyl-phenyl) Oxalyl Derivatives as Model Compounds
Molecules 2014, 19(9), 14446-14460; doi:10.3390/molecules190914446
Received: 27 August 2014 / Accepted: 9 September 2014 / Published: 12 September 2014
Cited by 4 | PDF Full-text (1724 KB) | HTML Full-text | XML Full-text
Abstract
Intramolecular hydrogen bond (HB) formation was analyzed in the model compounds N-(2-benzoylphenyl)acetamide, N-(2-benzoylphenyl)oxalamate and N1,N2-bis(2-benzoylphenyl)oxalamide. The formation of three-center hydrogen bonds in oxalyl derivatives was demonstrated in the solid state by the X-ray diffraction analysis of
[...] Read more.
Intramolecular hydrogen bond (HB) formation was analyzed in the model compounds N-(2-benzoylphenyl)acetamide, N-(2-benzoylphenyl)oxalamate and N1,N2-bis(2-benzoylphenyl)oxalamide. The formation of three-center hydrogen bonds in oxalyl derivatives was demonstrated in the solid state by the X-ray diffraction analysis of the geometric parameters associated with the molecular structures. The solvent effect on the chemical shift of H6 [δH6(DMSO-d6)–δH6(CDCl3)] and Δδ(ΝΗ)/ΔT measurements, in DMSO-d6 as solvent, have been used to establish the energetics associated with intramolecular hydrogen bonding. Two center intramolecular HB is not allowed in N-(2-benzoylphenyl)acetamide either in the solid state or in DMSO-d6 solution because of the unfavorable steric effects of the o-benzoyl group. The estimated Δ and Δ values for the hydrogen bonding disruption by DMSO-d6 of 28.3(0.1) kJ·mol−1 and 69.1(0.4) J·mol−1·K−1 for oxalamide, are in agreement with intramolecular three-center hydrogen bonding in solution. In the solid, the benzoyl group contributes to develop 1-D and 2-D crystal networks, through C–H∙∙∙A (A = O, π) and dipolar C=O∙∙∙A (A = CO, π) interactions, in oxalyl derivatives. To the best of our knowledge, this is the first example where three-center hydrogen bond is claimed to overcome steric constraints. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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Open AccessArticle On the Nature of the Transition State Characterizing Gated Molecular Encapsulations
Molecules 2014, 19(9), 14292-14303; doi:10.3390/molecules190914292
Received: 17 July 2014 / Revised: 21 August 2014 / Accepted: 28 August 2014 / Published: 11 September 2014
Cited by 1 | PDF Full-text (1369 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Gated molecular encapsulations, with baskets of type 1, are postulated to occur by the mechanism in which solvent molecule penetrates the inner space of 1, through one of its apertures, while the residing guest simultaneously departs the cavity. In the transition
[...] Read more.
Gated molecular encapsulations, with baskets of type 1, are postulated to occur by the mechanism in which solvent molecule penetrates the inner space of 1, through one of its apertures, while the residing guest simultaneously departs the cavity. In the transition state of the exchange, three pyridine-based gates are proposed to assume an open position with both incoming solvent and departing guest molecules interacting with the concave surface of the host. The More O’Ferrall-Jencks diagram and linear free energy relationships (LFERs) suggest a more advanced departure of the guest when bigger solvents partake in the displacement. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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Open AccessArticle Elucidation of the Relationships between H-Bonding Patterns and Excited State Dynamics in Cyclovalone
Molecules 2014, 19(9), 13282-13304; doi:10.3390/molecules190913282
Received: 7 July 2014 / Revised: 8 August 2014 / Accepted: 20 August 2014 / Published: 28 August 2014
Cited by 5 | PDF Full-text (2177 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should
[...] Read more.
Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should produce an enhanced phototoxicity. Indeed, although curcumin exhibits photosensitized antibacterial activity, this compound is characterized by very fast excited-state dynamics which limit its efficacy as a photosensitizer. In previous works we showed that the main non-radiative decay pathway of keto-enolic curcuminoids is through excited-state transfer of the enolic proton to the keto-oxygen. Another effective deactivation pathway involves an intermolecular charge transfer mechanism occurring at the phenyl rings, made possible by intramolecular H-bonding between the methoxy and the hydroxyl substituent. In this paper we present UV-Vis and IR absorption spectra data with the aim of elucidating the intramolecular charge distribution of this compound and its solvation patterns in different environments, with particular focus on solute-solvent H-bonding features. Moreover, we discuss steady state and time-resolved fluorescence data that aim at characterizing the excited-state dynamics of cyclovalone, and we compare its decay photophysics to that of curcumin. Finally, because during the characterization procedures we found evidence of very fast photodegradation of cyclovalone, its photostability in four organic solvents was studied by HPLC and the corresponding relative degradation rates were calculated. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
Open AccessArticle Conjugates of 1'-Aminoferrocene-1-carboxylic Acid and Proline: Synthesis, Conformational Analysis and Biological Evaluation
Molecules 2014, 19(8), 12852-12880; doi:10.3390/molecules190812852
Received: 1 July 2014 / Revised: 12 August 2014 / Accepted: 13 August 2014 / Published: 21 August 2014
Cited by 3 | PDF Full-text (2104 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Our previous studies showed that alteration of dipeptides Y-Fca-Ala-OMe (III) into Y-Ala-Fca-OMe (IV) (Y = Ac, Boc; Fca = 1'-aminoferrocene-1-carboxylic acid) significantly influenced their conformational space. The novel bioconjugates Y-Fca-Pro-OMe (1, Y = Ac; 2, Y
[...] Read more.
Our previous studies showed that alteration of dipeptides Y-Fca-Ala-OMe (III) into Y-Ala-Fca-OMe (IV) (Y = Ac, Boc; Fca = 1'-aminoferrocene-1-carboxylic acid) significantly influenced their conformational space. The novel bioconjugates Y-Fca-Pro-OMe (1, Y = Ac; 2, Y = Boc) and Y-Pro-Fca-OMe (3, Y = Boc; 4, Y = Ac) have been prepared in order to investigate the influence of proline, a well-known turn-inducer, on the conformational properties of small organometallic peptides with an exchanged constituent amino acid sequences. For this purpose, peptides 14 were subjected to detailed spectroscopic analysis (IR, NMR, CD spectroscopy) in solution. The conformation of peptide 3 in the solid state was determined. Furthermore, the ability of the prepared conjugates to inhibit the growth of estrogen receptor-responsive MCF-7 mammary carcinoma cells and HeLa cervical carcinoma cells was tested. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
Open AccessArticle Roles of Intramolecular and Intermolecular Hydrogen Bonding in a Three-Water-Assisted Mechanism of Succinimide Formation from Aspartic Acid Residues
Molecules 2014, 19(8), 11440-11452; doi:10.3390/molecules190811440
Received: 23 June 2014 / Revised: 20 July 2014 / Accepted: 23 July 2014 / Published: 4 August 2014
Cited by 5 | PDF Full-text (1567 KB) | HTML Full-text | XML Full-text
Abstract
Aspartic acid (Asp) residues in peptides and proteins are prone to isomerization to the β-form and racemization via a five-membered succinimide intermediate. These nonenzymatic reactions have relevance to aging and age-related diseases. In this paper, we report a three water molecule-assisted, six-step mechanism
[...] Read more.
Aspartic acid (Asp) residues in peptides and proteins are prone to isomerization to the β-form and racemization via a five-membered succinimide intermediate. These nonenzymatic reactions have relevance to aging and age-related diseases. In this paper, we report a three water molecule-assisted, six-step mechanism for the formation of succinimide from Asp residues found by density functional theory calculations. The first two steps constitute a stepwise iminolization of the C-terminal amide group. This iminolization involves a quintuple proton transfer along intramolecular and intermolecular hydrogen bonds formed by the C-terminal amide group, the side-chain carboxyl group, and the three water molecules. After a conformational change (which breaks the intramolecular hydrogen bond involving the iminol nitrogen) and a reorganization of water molecules, the iminol nitrogen nucleophilically attacks the carboxyl carbon of the Asp side chain to form a five-membered ring. This cyclization is accompanied by a triple proton transfer involving two water molecules, so that a gem-diol tetrahedral intermediate is formed. The last step is dehydration of the gem-diol group catalyzed by one water molecule, and this is the rate-determining step. The calculated overall activation barrier (26.7 kcal mol−1) agrees well with an experimental activation energy. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
Open AccessArticle Redox-Dependent Conformational Switching of Diphenylacetylenes
Molecules 2014, 19(8), 11316-11332; doi:10.3390/molecules190811316
Received: 28 April 2014 / Revised: 23 July 2014 / Accepted: 24 July 2014 / Published: 31 July 2014
Cited by 5 | PDF Full-text (2047 KB) | HTML Full-text | XML Full-text
Abstract
Herein we describe the design and synthesis of a redox-dependent single-molecule switch. Appending a ferrocene unit to a diphenylacetylene scaffold gives a redox-sensitive handle, which undergoes reversible one-electron oxidation, as demonstrated by cyclic voltammetry analysis. 1H-NMR spectroscopy of the partially oxidized switch
[...] Read more.
Herein we describe the design and synthesis of a redox-dependent single-molecule switch. Appending a ferrocene unit to a diphenylacetylene scaffold gives a redox-sensitive handle, which undergoes reversible one-electron oxidation, as demonstrated by cyclic voltammetry analysis. 1H-NMR spectroscopy of the partially oxidized switch and control compounds suggests that oxidation to the ferrocenium cation induces a change in hydrogen bonding interactions that results in a conformational switch. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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Open AccessArticle Intramolecular Hydrogen Bond in Biologically Active o-Carbonyl Hydroquinones
Molecules 2014, 19(7), 9354-9368; doi:10.3390/molecules19079354
Received: 9 May 2014 / Revised: 18 June 2014 / Accepted: 27 June 2014 / Published: 3 July 2014
Cited by 10 | PDF Full-text (1081 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and
[...] Read more.
Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LPàσ* interactions for IHBs, O1O2-H2 and the delocalization LPàπ* for O2-C2 = Cα(β). For the O1O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2àπ* C2 = Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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Review

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Open AccessReview Isotope Effects on Chemical Shifts in the Study of Intramolecular Hydrogen Bonds
Molecules 2015, 20(2), 2405-2424; doi:10.3390/molecules20022405
Received: 4 December 2014 / Revised: 17 December 2014 / Accepted: 5 January 2015 / Published: 30 January 2015
Cited by 4 | PDF Full-text (1360 KB) | HTML Full-text | XML Full-text
Abstract
The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” and
[...] Read more.
The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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Open AccessReview 1H-NMR as a Structural and Analytical Tool of Intra- and Intermolecular Hydrogen Bonds of Phenol-Containing Natural Products and Model Compounds
Molecules 2014, 19(9), 13643-13682; doi:10.3390/molecules190913643
Received: 30 June 2014 / Revised: 20 August 2014 / Accepted: 21 August 2014 / Published: 2 September 2014
Cited by 16 | PDF Full-text (7867 KB) | XML Full-text
Abstract
Experimental parameters that influence the resolution of 1H-NMR phenol OH signals are critically evaluated with emphasis on the effects of pH, temperature and nature of the solvents. Extremely sharp peaks (Δν1/2 ≤ 2 Hz) can be obtained under optimized experimental conditions
[...] Read more.
Experimental parameters that influence the resolution of 1H-NMR phenol OH signals are critically evaluated with emphasis on the effects of pH, temperature and nature of the solvents. Extremely sharp peaks (Δν1/2 ≤ 2 Hz) can be obtained under optimized experimental conditions which allow the application of 1H-13C HMBC-NMR experiments to reveal long range coupling constants of hydroxyl protons and, thus, to provide unequivocal assignment of the OH signals even in cases of complex polyphenol natural products. Intramolecular and intermolecular hydrogen bonds have a very significant effect on 1H OH chemical shifts which cover a region from 4.5 up to 19 ppm. Solvent effects on –OH proton chemical shifts, temperature coefficients (Δδ/ΔT), OH diffusion coefficients, and nJ(13C, O1H) coupling constants are evaluated as indicators of hydrogen bonding and solvation state of phenol –OH groups. Accurate 1H chemical shifts of the OH groups can be calculated using a combination of DFT and discrete solute-solvent hydrogen bond interaction at relatively inexpensive levels of theory, namely, DFT/B3LYP/6-311++G (2d,p). Excellent correlations between experimental 1H chemical shifts and those calculated at the ab initio level can provide a method of primary interest in order to obtain structural and conformational description of solute-solvent interactions at a molecular level. The use of the high resolution phenol hydroxyl group 1H-NMR spectral region provides a general method for the analysis of complex plant extracts without the need for the isolation of the individual components. Full article
(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)
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