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At least 19 recordsLinked to original sources
PubMed2002

Carbon [bond] hydrogen bond activation by titanium imido complexes. Computational evidence for the role of alkane adducts in selective C [bond] H activation.

This paper reports calculations that probe the role of R (hydrocarbon) and R' (ligand substituent) effects on the reaction coordinate for C [bond] H activation: Ti(OR')(2)(=NR') + RH --> adduct --> transition state --> (OR')(2)Ti(N(H)R')(R). Compounds with R = H, Me, Et, Vy, cPr, Ph, Cy, Bz, and cubyl are studied using quantum (R' = H, SiH(3), SiMe(3)) and classical (R' = Si(t)Bu(3)) techniques. Calculated geometries are in excellent agreement with data for experimental models. There is little variability in the calculated molecular structure of the reactants, products, and most interestingly, transition states as R and R' are changed. Structural flexibility is greatest in the adducts Ti(OR')(2)(=NR')...HR. Despite the small structural changes observed for Ti(OR')(2)(double bond] NR') with different R', significant changes are manifested in calculated electronic properties (the Mulliken charge on Ti becomes more positive and the Ti [double bond] N bond order decreases with larger R'), changes that should facilitate C [bond] H activation. Substantial steric modification of the alkane complex is expected from R [bond] R' interactions, given the magnitude of Delta G(add) and the conformational flexibility of the adduct. Molecular mechanics simulations of Ti(OSi(t)Bu(3))(2)([double bond] NSi(t)Bu(3))...isopentane adducts yield an energy ordering as a function of the rank of the C [bond] H bond coordinated to Ti that is consistent with experimental selectivity patterns. Calculated elimination barriers compare very favorably with experiment; larger SiH(3) and TMS ligand substituents generally yield better agreement with experiment, evidence that the modeling of the major contributions to the elimination barrier (N [bond] H and C [bond] H bond making) is ostensibly correct. Calculations indicate that weakening the C [bond] H bond of the hydrocarbon yields a more strongly bound adduct. Combining the different conclusions, the present computational research points to the adduct, specifically the structure and energetics of the substrate/Ti-imido interaction, as the main factor in determining the selectivity of hydrocarbon (R) C [bond] H activation.

Journal Article↗
PubMed2001

A C-H...O=C hydrogen bond? Intramolecular hydrogen bonding in a novel semirubin.

(4Z)-8-(5-Carboxypentyl)-9-butyl-2,3-diethyl-dipyrrin-1-one (1), a new analogue of xanthobilirubic acid, (4Z)-8-(carboxyethyl)-2,7,9-dimethyl-3-ethyl-dipyrrin-1-one, was synthesized in four steps from the known 2,3-diethyl-dipyrrin-1-one. Whereas xanthobilirubic acid (which is a model for one-half of bilirubin, the yellow pigment of jaundice) and its homologues with hexanoic and longer acid chains at C-8 engage only in intermolecular hydrogen bonding, 1 is found to engage in intramolecular hydrogen bonding. In CDCl(3) solution, dipyrrinone 1 adopts an anti-Z conformation, and its hexanoic acid COOH is hydrogen-bonded to the lactam H-N-C=O and to the pyrrole C(7)-H but not to the pyrrole NH. The latter constitutes an example of a hydrogen bond of the type C-H...O=C, weak and detected typically in crystals. Dipyrrinone 1 is found by vapor pressure osmometry to be monomeric in CHCl(3), but its methyl ester (2) tends toward being dimeric, like that of methyl xanthobilirubinate, which is dimeric.

Bilirubin↗
PubMed1978

Specific configurations of hydrogen bonding. I. Hydrogen bonding and conformational preferences of N-acylamino-acids, peptides and derivatives.

From a reexamination of the X-ray studies of the crystal structures of 27 N-acylamino acids, peptides and their derivatives and 30 linear peptides, it is concluded that specific formation of short intermolecular hydrogen bonds (2,5 to 2.6 A) from the carboxyl OH to the N-acyl oxygen is an important feature for N-acylamino acids. For N-acyl-N-amides, the formation of hydrogen bonds 2.7 to 2.9A long between N(acyl-H...O(amide) is strongly preferred. The dihedral angle delta between the N-acyl and carboxyl groups or adjacent amide groups shows a preference for values near 20 degrees or 90 degrees for N-acylamino acids and 90 degrees for N-acyl-N-amides.

Amino Acids↗
PubMed2001

Noncovalent Synthesis Using Hydrogen Bonding.

Hydrogen bonds are like human beings in the sense that they exhibit typical grouplike behavior. As an individual they are feeble, easy to break, and sometimes hard to detect. However, when acting together they become much stronger and lean on each other. This phenomenon, which in scientific terms is called cooperativity, is based on the fact that "1+1 is more than 2". By using this principle, chemists have developed a wide variety of chemically stable structures that are based on the reversible formation of multiple hydrogen bonds. More than 20 years of fundamental studies on these phenomena have gradually developed into a new discipline within the field of organic synthesis, and is nowadays called "noncovalent synthesis". This review describes noncovalent synthesis based on the reversible formation of multiple hydrogen bonds. Starting with a thorough description of what the "hydrogen bond" really is, it guides the reader through a variety of bimolecular and higher order assemblies and exemplifies the general principles that determine their stability. Special focus is given to reversible capsules based on hydrogen-bonding interactions that exhibit interesting encapsulation phenomena. Furthermore, the role of hydrogen-bond formation in self-replicating processes is actively discussed, and finally the review briefly summarizes the development of novel materials (nanotubes, liquid crystals, polymers, etc.) and principles (dynamic libraries) that recently have emanated from this intriguing field of research.

Journal Article↗
PubMed2005

Probing the low-barrier hydrogen bond in hydrogen maleate in the gas phase: a photoelectron spectroscopy and ab initio study.

The strength of the low-barrier hydrogen bond in hydrogen maleate in the gas phase was investigated by low-temperature photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of maleic and fumaric acid monoanions (cis-/trans-HO(2)CCH=CHCO(2)(-)) were obtained at low temperatures and at 193 nm photon energy. Vibrational structure was observed for trans-HO(2)CCH=CHCO(2)(-) due to the OCO bending modes; however, cis-HO(2)CCH=CHCO(2)(-) yielded a broad and featureless spectrum. The electron binding energy of cis-HO(2)CCH=CHCO(2)(-) is about 1 eV blue-shifted relative to trans-HO(2)CCH=CHCO(2)(-) due to the formation of intramolecular hydrogen bond in the cis-isomer. Theoretical calculations (CCSD(T)/ aug-cc-pVTZ and B3LYP/aug-cc-pVTZ) were carried out to estimate the strength of the intramolecular hydrogen bond in cis-HO(2)CCH=CHCO(2)(-). Combining experimental and theoretical calculations yields an estimate of 21.5 +/- 2.0 kcal/mol for the intramolecular hydrogen bond strength in hydrogen maleate.

Chemical Phenomena↗
PubMed1985

Studies on hydrogen bonds. Part V--Hydrogen bonding in energy minimization studies of peptides.

An energy term, representing the N-H...O type of hydrogen bond, which is a function of the hydrogen bond length (R) and angle (theta) has been introduced in an energy minimization program, taking into consideration its interpolation with the non-bonded energy for borderline values of R and theta. The details of the mathematical formulation of the derivatives of the hydrogen bond function as applicable to the energy minimization have been given. The minimization technique has been applied to hydrogen bonded two and three linked peptide units (gamma-turns and beta-turns), and having Gly, Ala and Pro side chains. Some of the conformational highlights of the resulting minimum energy conformations are a) the occurrence of the expected 4----1 hydrogen bond in all of the burn-turn tripeptide sequences and b) the presence of an additional 3----1 hydrogen bond in some of the type I and II tripeptides with the hydrogen bonding scheme in such type I beta-turns occurring in a bifurcated form. These and other conformational features have been discussed in the light of experimental evidence and theoretical predictions of other workers.

Chemical Phenomena↗
PubMed2003

Computational evidence for methyl-donated hydrogen bonds and hydrogen-bond networking in 1,2-ethanediol-dimethyl sulfoxide.

The 1:1 complex of 1,2-ethanediol with dimethyl sulfoxide was studied using density functional theory. A network of three hydrogen bonds holds the complex together, including two in which each methyl group donates to the same hydroxyl oxygen. Four lines of evidence support the existence of methyl-donated hydrogen bonds. The interaction energy is 36 +/- 5 kJ/mol using Becke's three parameter hybrid theory with the 1991 nonlocal correlation functional of Perdew and Wang, and a moderately large basis set (B3PW91/6-311++G**//B3PW91/6-31+G**). To determine the energy of each hydrogen bond, a relaxed potential energy scan was performed in a smaller basis set to break the weaker hydrogen bonds by forced systematic rotation of the methyl groups. Two cross-checking analyses show cooperative effects that cause individual hydrogen bond energies in the network to be nonadditive. When one methyl hydrogen bond is broken, the remaining interactions stabilize the complex by storing an additional 2-3 kJ/mol. With all hydrogen bonds intact, the O[bond]H...O[bond]S hydrogen bond contributes 26 +/- 2 kJ/mol stability, and each weak methyl bond stores 5 +/- 2 kJ/mol.

Journal Article↗
PubMed2002

(3h)J((15)N-(31)P) spin-spin coupling constants across N[bond]H....O[bond]P hydrogen bonds.

Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been performed to evaluate three-bond (15)N-(31)P coupling constants ((3h)J(N[bond]P)) across N[bond]H....O[bond]P hydrogen bonds in model cationic and anionic complexes including NH(4)(+):OPH, NH(4)(+):OPH(3), NH(3):(-)O(2)PH(2), NFH(2):(-)O(2)PH(2), and NF(2)H:(-)O(2)PH(2). Three-bond coupling constants can be appreciable when the phosphorus is P(V), but are negligible with P(III). (3h)J(N[bond]P) values in complexes with cyclic or open structures are less than 1 Hz, a consequence of the nonlinear arrangement of N, H, O, and P atoms. For complexes with these structures, (3h)J(N[bond]P) may not be experimentally measurable. In contrast, complexes in which the N, H, O, and P atoms are collinear or nearly collinear have larger values of (3h)J(N[bond]P), even though the N[bond]P distances are longer than N[bond]P distances in cyclic and open structures. In linear complexes, (3h)J(N[bond]P) is dominated by the Fermi-contact term, which is distance dependent. Therefore, N[bond]P (and hydrogen-bonding N[bond]O) distances in these complexes can be determined from experimentally measured (15)N-(31)P coupling constants.

Journal Article↗
PubMed2004

Hydrogen-bonding cooperativity: using an intramolecular hydrogen bond to design a carbohydrate derivative with a cooperative hydrogen-bond donor centre.

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.

Journal Article↗
PubMed2000

Substituent effects on two-center three-electron bonds and hydrogen bonds involving unsaturated organic functional groups and an ammonia radical cation--the resonance contribution

A theoretical investigation of the substituent effects on the two-center, three-electron (2c-3e) bond involved between unsaturated functional groups and an amine nitrogen is presented. The competitive hydrogen-bonded complexes are also studied. In both cases, the bond energies are found to be in the range of 20-30 kcal mol(-1). The variation of these energies is discussed with respect to the electron-donating effect of the substitutents, as well as with respect to the alpha-bonded atom of the organic functional group (O, S, NH). For the 2c-3e bonds, the results are discussed on the basis of the differences of the ionization potential (delta IP) of the separated fragments and can be rationalized through the valence bond theory. For the hydrogen bonds, the substituent influence is discussed by using the differences of the proton affinities (delta PA) of the substrates. The resonating nature of the hydrogen bond in these cationic systems is investigated and is found to account for most of the binding energy. Marcus theory is compared with the proposed resonating model.

Journal Article↗
PubMed2002

Magnitudes and chemical consequences of R(3)N(+)-C-H...O[double bond]C hydrogen bonding.

The magnitude of the stabilizing interaction between an aliphatic C[bond]H bond attached to an ammonium nitrogen and a carbonyl oxygen was evaluated by ab initio calculations at the MP2/6-311++G** level of theory. Attractive R(3)N(+)-C-H...O[double bond]C interactions play an important role in supramolecular recognition and various types of stereoselective catalysis. Our calculations show that R(3)N(+)-C-H...O[double bond]C is the strongest hydrogen bond of the C-H...O type known to date. Such hydrogen bonds remain as stabilizing interactions even in water for amide acceptors.

Acetates↗
PubMed2002

Study of the nature of improper blue-shifting hydrogen bonding and standard hydrogen bonding in the X3CH...OH2 and XH...OH2 complexes (X = F, Cl, Br, I): A correlated Ab initio study.

Weak hydrogen bonding was studied in the XH...OH2 and X3CH...OH2 complexes (X = F, Cl, Br, I) using the correlated MP2 ab initio method with relativistic Stuttgart/Dresden pseudopotentials and basis set (SDD). The accuracy of the method was tested for selected nonrelativistic complexes by performing MP2 calculations with all-electron basis sets (6-311G** and TZVPP). The characteristics of bonding in the hydrogen halide complexes correspond to the standard H-bonding (an elongation of the X-H bond and red shift of its stretch frequency), whereas those in the X3CH...OH2 complexes (X = F, Cl) are typical of improper blue-shifting H-bonding (a contraction of the CH bond and blue shift of the respective stretch frequency). A natural bond orbital analysis revealed some important differences between both classes of complexes: a) the electron density transfer (EDT) in the former complexes is considerably larger than that in the latter complexes: b) the EDT in the former complexes is almost completely directed to the sigma*-antibonding orbital of the XH bond, which causes a weakening of this bond, its elongation, and a concomitant decrease of the XH stretch frequency. In the latter complexes, only a small portion of the EDT goes to the sigma*-antibonding orbital of the CH bond of the proton donor and a larger part is transferred to the remote (nonparticipating) part of the proton donor. As a consequence, the structural reorganization of the proton donor occurred, leading to the contraction of the C-H bond. The fact that a small red shift of the C-H stretch frequency was found in bromoform-water and iodoform-water complexes was explained by the competition of both the above-mentioned mechanisms with dominating passage of electron density to the sigma*-antibonding orbital of the C-H bond. For an explanation of all the geometric features of both types of complexes, it is however necessary to consider both charge transfer and electrostatic effects. The electrostatic effects fail sometimes to interpret the geometry changes in the proton donor.

Journal Article↗
PubMed2004

LZnX complexes of tripodal ligands with intramolecular RN-H hydrogen bonding groups: structural implications of a hydrogen bonding cavity, and of X/R in the hydrogen bonding geometry/strength.

Tripodal ligands N(CH2Py)3-n(CH2Py-6-NHR)n(R=H, n=1-3 L1-3, n=0 tpa; R=CH2tBu, n=1-3 L'1-3) are used to investigate the effect of different hydrogen bonding microenvironments on structural features of their LZnX complexes (X=Cl-, NO3-, OH-). The X-ray structures of [(L2)Zn(Cl)](BPh4)2.0.5(H2O.CH3CN), [(L3)Zn(Cl)](BPh4)3.CH3CN, [(L'1)Zn(Cl)](BPh4) 1', [(L'2)Zn(Cl)](BPh4)2'.CH3OH, and [(L'3)Zn(Cl)](BPh4)3' have been determined and exhibit trigonal bipyramidal geometries with intramolecular (internal) N-HCl-Zn hydrogen bonds. The structure of [(L'2)Zn(ONO2)]NO3 4'.H2O with two internal N-HO-Zn hydrogen bonds has also been determined. The axial Zn-Cl distance lengthens from 2.275 A in [(tpa)Zn(Cl)](BPh4) to 2.280-2.347 A in 1-3, 1'-3'. Notably, the average Zn-N(py) distance is also progressively lengthened from 2.069 A in [(tpa)Zn(Cl)](BPh4) to 2.159 and 2.182 A in the triply hydrogen bonding cavity of 3 and 3', respectively. Lengthening of the Zn-Cl and Zn-N(py) bonds is accompanied by a progressive shortening of the trans Zn-N bond from 2.271 A in [(tpa)Zn(Cl)](BPh4) to 2.115 A in 3 (2.113 A in 3'). As a result of the triply hydrogen bonding microenvironment the Zn-Cl and Zn-N(py) distances of 3 are at the upper end of the range observed for axial Zn-Cl bonds, whereas the axial Zn-N distance is one of shortest among N4 ligands that induce a trigonal bipyramidal geometry. Despite the rigidity of these tripodal ligands, the geometry of the intramolecular RN-HX-Zn hydrogen bonds (X=Cl-, OH-, NO3-) is strongly dependent on the nature of X, however, on average, similar for R=H, CH2tBu.

Journal Article↗
PubMed2006

Comparative study of weak interactions in molecular crystals: H-H bonds vs hydrogen bonds.

The crystal structures of tetraphenylphosphonium squarate, bianthrone, and bis(benzophenone)azine are shown to contain a variety of C-H(delta+)...(delta+)H-C interactions, as well as a variety of C-H...O and C-H...C(pi) interactions. Each of these molecules possesses interactions that can possibly be characterized as either H-H bonds or weak hydrogen bonds based on the first four criteria proposed by Koch and Popelier. These interactions have been completely characterized topologically after the multipole refinement of the structures. It appears that weak interactions of the form C-H(delta+)...(delta+)H-C possess certain correlations between the various properties of the electron density at the bond critical points. The coexistence of the three types of interactions makes it possible to establish similarities and differences in the correlations of these weak interactions. This all leads to a better understanding of H-H interactions and how they fit into the hierarchy of weak interactions.

Journal Article↗
PubMed2002

Hydrogen bonding in nitroaniline analogues: hydrogen-bonded sheets in 2-amino-4,6-dimethoxy-5-nitropyrimidine and pi-stacked hydrogen-bonded sheets in 4-amino-2,6-dimethoxy-5-nitropyrimidine.

In 2-amino-4,6-dimethoxy-5-nitropyrimidine, C(6)H(8)N(4)O(4), the molecules are linked by one N-H...N and one N-H...O hydrogen bond to form sheets built from alternating R(2)(2)(8) and R(6)(6)(32) rings. In isomeric 4-amino-2,6-dimethoxy-5-nitropyrimidine, C(6)H(8)N(4)O(4), which crystallizes with Z' = 2 in P-1, the two independent molecules are linked into a dimer by two independent N-H...N hydrogen bonds. These dimers are linked into sheets by a combination of two-centre C-H...O and three-centre C-H...(O)(2) hydrogen bonds, and the sheets are further linked by two independent aromatic pi-pi-stacking interactions to form a three-dimensional structure.

Journal Article↗
PubMed2006

Ab initio study of hydrogen bonding and proton transfer in 3:1 FH:NH3 and FH:collidine complexes: structures and one- and two-bond coupling constants across hydrogen bonds.

Ab initio EOM-CCSD calculations have been performed on 3:1 FH:NH3 complexes at their own optimized MP2/6-31+G(d,p) geometries and at the optimized geometries in the hydrogen-bonding regions of corresponding 3:1 FH:collidine complexes. The isolated gas-phase equilibrium 3:1 FH:NH3 complex has an open structure with a proton-shared Fa-Ha-N hydrogen bond, while the isolated equilibrium 3:1 FH:collidine complex has a perpendicular structure with an Fa-Ha-N hydrogen bond that is on the ion-pair side of proton-shared. The Fa-N coupling constant ((2h)J(Fa-N)) for the equilibrium 3:1 FH:NH3 complex is large and negative, consistent with a proton-shared Fa-Ha-N hydrogen bond; (2h)JFb-Fa is positive, reflecting a short Fb-Fa distance and partial proton transfer from Fb to Fa across the Fb-Hb-Fa hydrogen bond. In contrast, (2h)JFa-N has a smaller absolute value and (2h)JFb-Fa is greater for the 3:1 FH:NH3 complex at the equilibrium 3:1 FH:collidine geometry, consistent with the structural characteristics of the Fa-Ha-N and Fb-Hb-Fa hydrogen bonds. Coupling constants computed at proton-transferred 3:1 FH:collidine perpendicular geometries are consistent with experimental coupling constants for the 3:1 FH:collidine complex in solution and indicate that the role of the solvent is to promote further proton transfer from Fa to N across the Fa-Ha-N hydrogen bond, and from Fb to Fa across the two equivalent Fb-Hb-Fa hydrogen bonds. The best correlations between experimental and computed coupling constants are found for complexes with perpendicular proton-transferred structures, one having the optimized geometry of a 3:1 FH:collidine complex at an Fa-Ha distance of 1.80 A, and the other at the optimized 3:1 FH:collidine geometry with distances derived from the experimental coupling constants. These calculations provide support for the proposed perpendicular structure of the 3:1 FH:collidine complex as the structure which exists in solution.

Hydrogen Bonding↗