230 research outputs found
Molecules and molecular crystals
No full textChapter 8: Molecules and molecular crystals (G. Gilli and P. Gilli);
INDEX:
8.1 Chemistry and X-ray crystallography 592;
8.1.1 Crystal and molecular structure 592;
8.1.2 The growth of structural information 594;
8.2 The nature of molecular crystals 595;
8.2.1 Intermolecular forces 595;
8.2.2 Thermodynamics of molecular crystals 616;
8.2.3 Free and lattice energy of a crystal from atom–atom potentials 619;
8.2.4 Polymorphism 622;
8.2.5 The prediction of crystal structures 623;
8.3 Elements of classical stereochemistry 627;
8.3.1 Structure: constitution, configuration, and conformation 627;
8.3.2 Isomerism 629;
8.3.3 Ring conformations 634;
8.4 Molecular structure and chemical bond 642;
8.4.1 Introduction 642;
8.4.2 Quantum-mechanical methods 643;
8.4.3 Qualitative bonding theories 645;
8.4.4 The VSEPR theory 647;
8.4.5 The VB theory 649;
8.4.6 Molecular mechanics (MM) 651;
8.4.7 Molecular mechanics, force fields, and molecular simulation (MS) 654 ;
8.5 Molecular hermeneutics: the interpretation of molecular structures 657;
8.5.1 Correlation methods in structural analysis 657;
8.5.2 Some three-centre–four-electron linear systems 659;
8.5.3 Nucleophilic addition to organometallic compound 661;
8.5.4 Nucleophilic addition to the carbonyl group 662;
8.5.5 Conformational rearrangements by structure-correlation methods 664;
8.5.6 Evidence for resonance-assisted H-bond (RAHB) by structure-correlation methods 669;
References 67
Noncovalent Interactions in Crystals
No full textNoncovalent Interactions in Crystals (P. Gilli and G. Gilli); in: Supramolecular Chemistry: from Molecules to Nanomaterials (J.W. Steed and P.A. Gale eds.) - Volume 6: Supramolecular Materials Chemistry
ABSTRACT:
The over 500 000 structures collected in current crystallographic databases represent the greatest archive of noncovalent molecular interactions ever conceived by man. Their analysis provides an invaluable basis for understanding these interactions in the crystalline state and for transferring this knowledge to gas phase and condensed phases, such as pure liquids or solutions in polar and nonpolar solvents. This chapter is intended to review the different classes of noncovalent interactions and to supply the mathematical background for their description.
For the sake of clarity, the treatment distinguishes between physical and chemical interactions. Physical interactions are considered essentially independent of molecular constitution and deriving from (i) van der Waals forces (atomic repulsion/exchange and attraction/dispersion terms); (ii) electrostatic multipolar forces (mostly monopolar and dipolar terms); and (iii) hydrophobic forces, a kind of interaction that develops in crystal clathrates and water solutions. Conversely, interactions of chemical nature are strictly related to the physicochemical properties of molecules with particular concern for (iv) groups that are either Bronsted acids (proton donors, D–H) or Bronsted bases (proton acceptors, :A) and may interact by forming D–H· · ·:A hydrogen bonds and (v) groups that are either Lewis bases (electron donors, D:) or Lewis acids (electron acceptors, :A) and may interact by forming D:-->A electron donor–acceptor (EDA) or charge-transfer (CT) interactions.
Special emphasis is given to interactions that play a determinant structure-directing role in molecular interaction and recognition phenomena, such as hydrogen and halogen bonding.
INDEX:
1 Introduction;
1.1 The birth of structural chemistry;
2 A Chemical Classification of Crystals;
2.1 Chemical forces in crystals;
2.2 Metallic crystals;
2.3 Covalent crystals;
2.4 Ionic crystals;
2.5 Molecular crystals;
3 Nonbonded Forces in Molecular Crystals. A Classification;
4 Mostly Physical Intermolecular Forces in Crystals;
4.1 vdW nonbonded forces;
4.2 Electrostatic multipolar forces;
4.3 Hydrophobic forces;
5 Mostly Chemical Intermolecular Forces in Crystals;
5.1 Charge-transfer (CT) or electron donor–acceptor (EDA) interactions;
5.2 Hydrogen bond (H-bond);
6 Conclusions;
Reference
RESONANCE-ASSISTED HYDROGEN-BONDING .3. FORMATION OF INTERMOLECULAR HYDROGEN-BONDED CHAINS IN CRYSTALS OF BETA-DIKETONE ENOLS AND ITS RELEVANCE TO MOLECULAR ASSOCIATION
No full textThe beta-diketone enol (or enolone) HO-C=C-C=O fragment produced by enolization of beta-diketones is known to form strong intramolecular O-H...O hydrogen bonds where the decrease of the O...O contact distance (up to 2.40 angstrom) is correlated with the increased pi-delocalization of the O-C=C-C=O heteroconjugated system, the phenomenon has been interpreted by the resonance-assisted hydrogen-bonding (RAHB) model [Gilli, Bellucci, Ferretti & Bertolasi (1989). J. Am. Chem. Soc. 111. 1023-1028; Bertolasi, Gilli, Ferretti & Gilli (1991). J. Am. Chem. Soc. 113, 4917-4925]. When the intramolecular hydrogen bond is forbidden for steric reasons, molecules crystallize by forming hydrogen-bonded infinite chains of pi-delocalized enolone fragments (resonant beta-chains), i.e. they are hybrids of the canonical forms -OH...O=C-C=C-OH...O=C- =+OH...-O-C=C-C=+OH...-O-C=. The occurrence of beta-chains in 14 crystals of enolone (2-en-3-ol-1-one) and eight of enediolone (2-en-2,3-diol-1-one) derivatives has been studied. The beta-chains were found to have the following properties: (i) O...O distances depend on the enediolone substituents and range from 2.69 angstrom in beta-ketoesters to 2.46 angstrom in beta-diketones; (iii) calculated hydrogen-bond energies are in the range 20-66 kJ mol-1; (iii) a strict intercorrelation between hydrogen-bond strengthening and pi-system delocalization is observed, in complete agreement with the RAHB model proposed previously. Beta-Chain morphologies are analyzed with the aim of determining crystal-engineering rules for the production of solid materials where systems of polar beta-chains can induce ferroelectric and second harmonic generation properties. The RAHB concept is generalized to other heteroconjugated systems such as carboxylic acids, amides, enamines (RN=CR-NHR) and enaminones (O=CR-CR=CR-NHR), and its possible relevance in biological processes such as base coupling in DNA and folding of proteins is briefly discussed
Evidence for Intramolecular N-H...O Resonance-Asssisted Hydrogen Bonding in Beta-Enaminones and Related Heterodienes. A Combined Crystal-Structures, IR and NMR Spectroscopic, and Quantum-Mechanical Investigation
No full textThe resonance-assisted hydrogen bond (RAHB) is a model of synergistic interplay between pi -delocalization and hydrogen-bond (H-bond) strengthening originally introduced (Gilli, G.; Bellucci, F.; Ferretti, V.; Bertolasi, V. J. Am. Chem. Sec. 1989, 111, 1023; Bertolasi, V.; Gilli, P.; Ferretti, V.1 Gilli, G. J. Aln. Chem. Sec. 1991, 113, 4917) for explaining the abnormally strong intramolecular O-H...O bonds formed by the ...O=C-C=C-OH... beta -enolone fragment I which are typical of B-diketone enols. The applicability of this model to the intramolecular N-H...O hydrogen bonds formed by a number of heteroconjugated systems (...O=C-C=C-NH..., beta -enaminones II; O=C-C=N-NH..., ketohydrazones III; and ...O=N-C=C-NH..., nitrosoenamines IV) is investigated. The X-ray crystal structures of five molecules which close a six-membered ring by an intramolecular N-H...O bond through the resonant ...O=X-C=X-NH... (X = C, N) fragments II-IV are compared to those of two other molecules closing the same ring through the nonresonant ...O=C-C-C-NH... beta -aminone moiety V. Experimental findings are complemented by a CSD (Cambridge Structural Database) search of all compounds forming intramolecular N-H...O bonds through the molecular fragments II-V and by a comprehensive analysis of the IR v(NH) stretching frequencies and H-1 NMR delta (NH) chemical shifts available for compounds of these classes of known crystal structure. It is shown that all the descriptors of H-bond strength [d(N...O) shorthening, decrease of v(NH), increase of delta (NH), and increase of pi -delocalization within the heteroconjugated fragment] are mutually intercorrelated according to RAHB rules, which can then account for the strength of heteronuclear N-H...O bonds in II-IV as well as for that of the homonuclear O-H...O bonds in I. Heteronuclear N-H...O bonds appear, however, to have distinctive features. In particular, their strength turns out to be partially hampered by the proton affinity difference (BPA) between the N and O atoms, so that very strong H-bonds (2.65 greater than or equal to d(N...O) greater than or equal to 2.48 Angstrom, 3200 greater than or equal to v(NH) greater than or equal to 2340 cm(-1), 13 less than or equal to delta (NH) less than or equal to 18 ppm) can occur only when the pi -delocalization of the heterodienic moiety is associated with proper electron-attracting substituents which are able to decrease this Delta PA by increasing the NH acidity. Moreover, at variance with strong O-H...O RAHBs, whose protons are mostly found in nearly symmetrical positions, even the strongest N-H...O RAHBs are highly dissymmetric, despite the very similar changes undergone by both IR and H-1 NMR spectra in O-H...O and N-H...O H-bonded systems. Specificities of heteronuclear H-bonds are shown to be interpretable by the electrostatic-covalent H-bond model (ECHBM) which was previously developed for the homonuclear case (Gilli, P.; Bertolasi, V.; Ferretti, V.; Gilli, C. J. Am. Chem. Sec. 1994, 116, 909). The conclusions drawn are corroborated by extended DFT quantum-mechanical calculations at the B3LYP/6-31+G(d,p)B3LYP/6-31+G(d,p) level of theory and by full geometry optimization carried out on 27 variously substituted heterodienes II-IV and nonresonant beta -aminones v. calculations allow the estimation of H-bond energies that are found to be approximately 2.75 kcal mol(-1) for nonresonant V and 5.22, 6.12, and 7.03 kcal mol(-1) for unsubstituted resonant II, III, and IV, respectively
Hydrogen bond models and theories: The dual hydrogen bond model and its consequences
No full textThe H-bond can be reinterpreted starting from the dual H-bond model, for which any D–H···:A bond is not a bond donated by D–H to :A but rather consists of two bonds formed by the central proton with two adjacent acceptors. Analogously, the H-bond energy, E(HB), is not the D–H···:A dissociation energy but the smaller of two bond-dissociation energies, D0(D–H) and D0(H–A), by which −D: and :A are competitively bound to the proton. If one is stronger, the other is weaker, and weak the overall H-bond will be. Strong bonds occur when ΔD0 = D0(D–H) − D0(H–A) = 0 or, in terms of affinity for the proton (pa), when Δpa = pa(D−) − pa(A) = 0. H-bond properties are then function of two variables, pa(D−) and pa(A), or better of their linear combinations, Σpa = pa(D−) + pa(A) and Δpa = pa(D−) − pa(A), having respective meanings of mean donor/acceptor electronegativity and of energy difference, ΔrE, between tautomeric D–H···:A and (−)D:···H–A(+) forms. Two cases are studied. The case: ‘Σpa variable for Δpa = 0’ leads to quantitative relationships between D/A electronegativity and maximum energy, E(HB,MAX), achievable for each D/A electronegativity class, EC(D,A). The case: ‘Δpa variable for Σpa = constant’ leads to formulate three different but inter-consistent H-bond theories which are separately discussed. The last one, which is called ‘pKa equalization principle’ and where Δpa values are empirically estimated from the acid–base dissociation constants in water as ΔpKa = pKAH(D–H) − pKBH+(A–H+), is shown to be a powerful method of large applicability for predicting the H-bond strengths from thermodynamic parameters
The Nature of the Hydrogen Bond: Outline of a Comprehensive Hydrogen Bond Theory
No full textHydrogen bond (H-bond) effects are known: it makes sea water liquid, joins cellulose microfibrils in trees, shapes DNA into genes and polypeptide chains into wool, hair, muscles or enzymes. Its true nature is less known and we may still wonder why O-H...O bond energies range from less than 1 to more than 30 kcal/mol without apparent reason. This H-bond puzzle is re-examined here from its very beginning and presented as an inclusive compilation of experimental H-bond energies andgeometries.New concepts emerge from this analysis: new classes of systematically strong H-bonds (CAHBs and RAHBs: ch
Evidence for Resonance-Assisted Hydrogen Bonding. 2.1Intercorrelation between Crystal Structure and Spectroscopic Parameters in Eight Intramolecularly Hydrogen Bonded 1,3-Diary 1–1,3-propanedione Enols
No full textCrystal structure analysis of eight 1,3-diaryl-1,3-propanedione enols has been accomplished with the aim of investigating in more detail the intramolecular hydrogen bond formed by the H-C=C-C=O fragment characterizing beta-diketone enols; structural data were correlated with spectroscopic parameters, that is IR nu(OH) stretching frequencies and H-1 NMR chemical shifts of the enolic proton. Present experimental data show that this hydrogen bond is characterized by the following interrelated features: (i) very short O- -O distances (2.432-2.554 angstrom); (ii) strong delocalization in the heteroconjugated fragment; (iii) lengthening of the O-H bond (to 1.20 angstrom); (iv) lowering of the nu(OH) frequencies (2566-2675 cm-1) and downfield shift of the enolic proton resonance (15.3-17.0 ppm). The data can bc interpreted by (and are in support of) the RAHB (resonance assisted hydrogen bond) model previously suggested (Gilli, G.; Bellucci, F.; Ferretti, V.; Bertolasi, V. J. Am. Chem. Soc. 1989, 111, 1023) for explaining the unusual features the hydrogen bond displays in these compounds. It is shown that the model is able to interpret fine structural details such as the general weakening of the intramolecular hydrogen bond caused by electron-donating 1,3-substituents or additional hydrogen bonds accepted by the carbonyl and the preference displayed by the proton for dwelling on the carbonyl oxygen having the smaller negative charge induced both by the nature of 1,3-substituents or by intermolecular hydrogen bonds or short contacts
Out-of-plane deformation pathways of the R(X=)C-NR2 fragment present in amides, thioamides, amidines, enamines, and anilines. A concerted study making use of structural data, molecular mechanics, and ab initio calculations
No full textThe R(X=)C-NR(1)R(2) (R(1), R(2) = alkyl groups) fragment is present in many classes of molecules and assumes, usually, a planar conformation owing to the C-N partial double-bond character. It can undergo,however, a cis-trans isomerization process by rotation around the C-N bond and concomitant nitrogen pyramidalization. In a previous paper (Gilli, G.; Bertolasi, V.; Bellucci, F.; Ferretti, V. J. Am. Chem. Sec. 1986, 108, 2420) the isomerization pathway was mapped by the use of some 90 crystal structures containing the fragment of interest, and a semiempirical potential giving the total energy of the fragment during its deformation was proposed. In the present work the previous sample of crystal structures is updated to the current state of the crystallographic databases; the observed geometries are compared with the out-of-plane deformation energy maps obtained by ab initio SCF calculations at the 4-31G level for sample molecules (thioformamide, formamide, formamidine, vinylamine, and aniline) representative of the five chemical classes investigated. It is shown that the originally proposed potential is validated by this analysis and that the values of the energetic barriers involved in the reaction, evaluated from the ab initio energy maps, are in good agreement with the available experimental data. It is found, moreover, that there is a specific class of compounds (o- and p-nitroanilines and polyconjugated enamines and amidines) which deviate from the general behavior. The crystal structures of two of these compounds are reported, and possible reasons for the discrepancies discussed
Progetto PRIN biennale: 'Legami ad Idrogeno Intelligenti in Natura e nei Materiali Funzionali'
No full textLa caratteristica peculiare del LI è che la sua forza non può essere direttamente valutata dalla natura degli atomi interagenti come dimostrato, per esempio, dal legame O-H..O che è noto variare la sua energia di legame nell'incredibile intervallo 0.2-31 kcal/mol. Il maggior contributo dato dal nostro gruppo in questo campo riguarda la scoperta che l’energia del LI può essere prevista a livello semiquantitativo mediante l'uso dei 'chemical leitmotifs' (CL), che sono i cinque motivi molecolari in grado di dar origine a legami forti (quattro casi) o di forza modetrata (un caso), tutti gli altri casi di LI essendo deboli. Questi cinque motivi sono stati indicati dagli acronimi (+/-)CAHB, (-)CAHB, (+)CAHB, RAHB e PAHB (CAHB = charge-assisted, RAHB = resonance-assisted, PAHB= polarization-assisted HB; (+)= positive, (-)= negative).
L'identificazione dei cinque CL ci ha permesso di mettere a punto un nuovo metodo di indagine capace di prevedere la forza dei LI che si formeranno sulla base delle sole caratteristiche strutturali delle molecole che partecipano all’associazione. Questa aumentata capacità di previsione rappresenta un sensibile vantaggio nella progettazione mirata di cristalli molecolari aventi specifiche proprietà fisiche (ingegneria cristallina) e nell'interpretazione delle complesse strutture biomacromolecolari e, in generale, offre la possibilità di identificare i modi più efficaci di interazione e riconoscimento molecolare 'su un foglio di carta ', vale a dire da un disegno schematico dei frammenti molecolari interagenti.
Questo nuovo strumento di indagine è stato da noi utilizzato per analizzare diversi sistemi molecolari e biomolecolari campione dove si ipotizzava che LI forti fossero coinvolti nel meccanismo d'azione di particolare fenomeni chimici (reattività, tautomeria, riconoscimento, meccanismi dei materiali funzionali,..) o biochimici (catalisi enzimatica, fenomeni di trasporto, binding recettoriale,..). Un’analisi preliminare ha stabilito che lo spettro dei fenomeni coinvolti è molto vasto, potendo includere la tautomeria cheto-enolica, le proprietà bistato dei cristalli ferroelettrici, il trasferimento protonico allo stato eccitato, la formazione di αlfa-eliche, l'accoppiamento delle basi nel DNA, la catalisi enzimatica nella chetosteroide-isomerasi e nelle proteasi a serina ed aspartico, oltre che la formazione di LI forti nei minerali e la trasmissione protonica in acqua e nei canali transmembrana della gramicidina A e delle acquaporine. Nell’ambito del presente progetto, questi LI particolarmente forti che, a causa della loro forza intrinseca, sono capaci di svolgere funzioni di controllo in sistemi complessi sono stati chiamati 'LI funzionali', perché capaci di svolgere un ruolo funzionale, o 'LI intelligenti (smart HB)', perché, visti dall’esterno, appaiono agire in modo intelligente
Modern Hydrogen Bonding Theory
No full textThe H-bond was discovered in 1920 by W.M. Latimer and W.H. Rodebush [1] with the collaboration of M.L Huggins [2], three young men working in the laboratory of G.N. Lewis who gave of it a definition based on the Lewis electron-dot formalism which appears to be quite lucid and accurate even in modern terms. By the time that L. Pauling wrote his famous book “The Nature of the Chemical Bond” (1939-1940) [3], the H-bond had received complete systematization within the scheme of the newly developing VB theory, including the distinction between weak electrostatic and strong covalent H-bonds which was successively given VB theoretical dignity by Coulson and Danielsson (1954) [4]. This line of thought was accepted during the 1957 Ljubljana Conference [5] (the first H-bond meeting) and in “The Hydrogen Bond” by Pimentel and McClellan (1960) [6] (the first H-bond book).
This unified approach did not survive the division of sciences in more specialized branches occurred in the post-war period. The accumulation of ever new thermodynamic, spectroscopic and structural data, together with the underlying battle between VB and MO methods, lead to a period of general confusion, summarized in the Hopfinger’s (1973) statement “The only one definite fact about H-bonds is that there does not appear to be any definite rules which govern their geometry” [7]. It became clear, however, that the main point of the discussion was centered on the H-bond nature itself, that is on whether the H-bond was electrostatic, covalent, or both, a subject on which the most imaginative positions became allowed.
In 1991, Jeffrey and Saenger published “Hydrogen Bonding in Biological Structures” [8] where, for the first time, the most reliance is placed on the restricted number of accurate neutron structures and, in their absence, on carefully selected X-rays ones. This marks a turning point in H-bond studies: we accept the idea that our previous theories may be in error because based on insufficiently accurate experimental data, suspend temporarily any judgment on them, and start again to collect the widest and most reliable set of H-bond data from which to infer the true nature of the H-bond and then to lay sound foundations for any further theoretical advance. In the last 15 years, this novel data-oriented method of dealing with the H-bond problem has involved many researchers worldwide who, taking advantage of the existing crystallographic (CSD) [9] and thermodynamic (NIST) databases, have produced substantial changes in our way of considering the H-bond phenomenon. These changes will be the object of the present lecture
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