Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.     

Phase transitions,conformational lability,and intermolecular interactions in alkoxycyanobiphenyls

Vibrational spectroscopy methods (IR absorption, Raman scattering, calculations) were used to study changes in molecular structures of alkoxycyanobiphenyls during phase transitions. The spectra were measured in the 33–3500 cm⁻¹ region at temperatures of 100–450 K. The temperature dependences of the IR bands that correspond to the noncharacteristic vibrations of molecular fragments between the phenyl rings and the alkyl radicals point to the conformational polymorphism of these molecules. An analysis of the Raman bands corresponding to the characteristic vibrations of the C−H bonds of alkyl radicals [q(CH)], the C−H and C−C bonds of phenyl rings [q(CH) and Q(CC)], and the CN bonds of the cyano groups [Q(CN)] suggests significant intermolecular interactions. The conformational lability and intermolecular interactions are associated with differences in molecular packing in the substances of this homologous series. Saratov State University. Institute of Solid State Physics, Rostov State University. Institute of Physics, Uzbekistan Academy of Sciences. Samarkand State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 5, pp. 814–822, September–October, 1995. Translated by I. Izvekova     

Intramolecular S···O chalcogen bond in thioindirubin

Results of X-ray diffraction study and quantum-chemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C–H···O and S···O interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (σ-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C–S bonds. One of these σ-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of σ-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using “Atoms in Molecules” (AIM) theory. Energies of the C–H···O hydrogen bond and the S···O σ-hole bond derived from AIM and NBO theories are very close.     

Explorations of the nature of the coupling interactions between vitamin C and methylglyoxal: a DFT study

As the first step toward understanding the augment role of vitamin C (Vc) for the anticancer effect of methylglyoxal (MG), the nature of the coupling interactions between Vc and MG has been systematically investigated at the B3LYP/6-311++G** level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The possible stable complexes have been located on their potential energy surface (PES). Most of them are characterized by one or two intermolecular H-bonds with the binding energies varying from −11.1 to −2.0 kcal/mol. AIM analyses suggest that all the intermolecular H-bonds have been predominated by the electrostatic interaction. A good linear correlation between the intermolecular H-bond distance and the electron density as well as its Laplacian at the bond critical point of the intermolecular H-bond has been observed. Depending on the selected coupling modes between Vc and MG, the origin of the blue-shifts of the stretching vibrational frequencies of different C–H bonds has been elucidated. Additionally, the inherent reason for the positive role of Vc in the anticancer process for MG has been verified through the investigation of the one-electron oxidation behaviors of the most stable complex.     

Modelling of carbohydrate–aromatic interactions: <Emphasis Type="Italic">ab initio </Emphasis>energetics and force field performance

Summary Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate–aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from −2.8 to −12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree–Fock method (interaction energies from +1.0 to −6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.     

Theoretical study on the CH3NgF species

Geometrical parameters, harmonic vibrational frequencies, atomic charge distributions, bonding character, and relative stability of the CH₃NgF (Ng = He, Ar, Kr, or Xe) species were investigated at the MP2 level of theory. CH₃HeF was also predicted stable at the CCSD(T) level. All the four CH₃NgF species have C _3v symmetry. Ng–F bond lengths of the CH₃NgF species are all longer than those of the corresponding HNgF species. The calculated infrared intensities of the C–Ng and Ng–F stretching vibrations are much larger than those of the other vibrations, which is advantageous for the experimental spectroscopic identification of the species. The atoms in molecules (AIM) topological analysis indicated that the three Ng–F (Ng = He, Ar, or Kr) bonds are dominated by electrostatic interaction whereas the two C–Ng (Ng = Ar or Kr) bonds are dominated by covalent interaction. In contrast, the bond length analysis seems to indicate that both the Ng–F and C–Ng bonds are dominated by covalent interaction. According to the MP2 calculations, CH₃HeF and CH₃ArF are higher in energy than the dissociation limits CH₃ + He + F and CH₃ + Ar + F by 15.10 and 2.64 kcal/mol whereas CH₃KrF and CH₃XeF are lower in energy than CH₃ + Kr + F and CH₃ + Xe + F by 16.80 and 38.44 kcal/mol, respectively.     

Supramolecular systems based on the melamine salt of bis(hydroxymethyl)phosphinic acid (melafen) dihydrate and surfactants

Bis(hydroxymethyl)phosphinic acid and melamine were shown by FTIR and UV spectroscopy to form the salt (melafen), whose cations and anions involving water molecules can be joined into supramolecular structures due to electrostatic interactions and hydrogen bonds. The conductometry, dielcometric titration, and dynamic light scattering methods showed that melafen in water and chloroform in a concentration range of 10⁻¹⁰–10⁻⁴ mol L⁻¹ involving the solvent structures exist as supramolecular polymeric nanostructures, whose size and properties change nonlinearly depending on the melafen concentration. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1207–1214, June, 2008.     

Ab initio MO study of ethylene insertion into the Sm–C bond of H2SiCp2SmCH3

Ethylene insertion into the Sm–C bond of H₂SiCp₂SmCH₃, a model reaction of an olefin polymerization propagation step, has been studied by ab initio molecular orbital methods. The small electronegativity of the Sm atom makes the Sm–C bond ionic, the methyl group being negatively charged by −0.75. The reaction passes through a loose ethylene complex with a binding energy of 15 kcal/mol and then a tight four-centered transition state with an agostic interaction between the Sm atom and one of the methyl CH bonds. A small activation energy of 14 kcal/mol is required to pass through this transition state, indicating that this is an easy reaction. Compared with the reactions with group 4 cationic silylene-bridged metallocenes the activation energy is higher and the reaction is less exothermic. The origin of these differences is discussed. The results of molecular mechanics calculations on regio- and stereoselectivities in the insertion reaction of propylene are also reported. Received: 13 July 1998 / Accepted: 28 August 1998 / Published online: 2 November 1998     

Hydration and protonation ofO-vinylacetoxime in the gas phase: anab initio study

Ab initio HF/6–31G^* calculations ofO-vinylacetoxime monohydrates and cations were performed. Each conformer forms two stable H-complexes with participation of N and O atoms. The former have planar heavy-atom skeletons, whereas the water molecule in the latter is located above the plane of the proton-acceptor complex. The complexes stabilized by N...HO and O...HO bonds have different dipole moments and frequencies of the OH stretching vibrations. The most energetically favorable cation is formed by adding a proton to the C_β atom of the vinyl group ofO-vinylacetoxime. Theap,ap-conformer (ap is antiperiplanar) of this cation is 6.5 and 34.9 kcal mol⁻¹ more stable than the onium cations with the NH⁺ and OH⁺ fragments, respectively, and is characterized by polarization and appreciable lengthening of the N−O and C=C bonds. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 597–600, April, 2000.     

Nature and physical origin of CH/pi interaction: significant difference from conventional hydrogen bonds

Recently reported high-level ab initio calculations and gas phase spectroscopic measurements show that the nature of CH/pi interactions is considerably different from conventional hydrogen bonds, although the CH/pi interactions were often regarded as the weakest class of hydrogen bonds. The major source of attraction in the CH/pi interaction is the dispersion interaction and the electrostatic contribution is small, while the electrostatic interaction is mainly responsible for the attraction in the conventional hydrogen bonds. The nature of the "typical" CH/pi interactions is similar to that of van der Waals interactions, if some exceptional "activated" CH/pi interactions of highly acidic C-H bonds are excluded. Shifts of C-H vibrational frequencies and electronic spectra also support the similarity. The hydrogen bond is important in controlling structures of molecular assemblies, since the hydrogen bond is sufficiently strong and directional due to the large electrostatic contribution. On the other hand, the directionality of the "typical" CH/pi interaction is very weak. Although the "typical" CH/pi interaction is often regarded as an important interaction in controlling the structures of molecular assemblies as in the cases of conventional hydrogen bonds, the importance of the "typical" CH/pi interactions is questionable.     

Ab initio and DFT theory studies of interaction of thymine with formaldehyde

In this article, the interaction of formaldehyde (FA) with thymine is theoretically investigated by computational chemistry methods. The optimization geometries and vibrational frequencies of FA, thymine and three complexes between thymine and FA have been calculated by using the density functional theory and ab initio methods at the B3LYP/6-311G(d, p) and MP2/6-311G(d, p) levels. The NBO and AIM methods are used to analyse interaction as well. Conformers (A), (B) and (C) are cyclic structures with C–H***O and N–H***O hydrogen bonds on a common plane. The corrected complex interaction energies of cyclic structures (A), (B) and (C) at MP2/6-311G(d, p) levels are −38.41, −26.94 and −26.01 kJ/mol, respectively. The order of stability is (A) > (B) > (C).     

Crystallographic evidence for intramolecular C−H...O interactions in principal nucleosides. Refinement of the crystal structure of thymidine

An analysis of crystallographic data for the major nucleosides has shown that their molecules (except for guanosine) exhibit specific intramolecular C−H...O interactions, which are weak hydrogen bonds. In purine nucleosides these interactions are rare and rather weak. For pyrimidine nucleosides, in addition to the previously known intramolecular interaction C₆−H₆...O_5′, we have revealed the intramolecular interactions C_1′−H_1′...O₂ and C₆−H₆...O_1′. The three interactions make approximately equal contributions to the stabilization of the anti-conformation in pyrimidine nucleosides and make this conformation prevailing. To enhance the reliability of the results of studying the C−H...O interactions in thymidine, we performed an additional, more exact, X-ray diffraction analysis of the substance. Institute of Physiologically Active Substances, Russian Academy of Sciences, Chernogolovka. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 1, pp. 178–184, January–February, 1995. Translated by I. Izvekova     

The role of carbonyl and thiocarbonyl groups in the conformational isomerism of haloacetones and halothioacetones

The presumable, but not well-known parallelism between carbonyl and thiocarbonyl groups as electron acceptors in conformational analysis is reported. Our theoretical investigation was carried out for model compounds, namely mono-haloacetones and mono-halothioacetones. Furthermore, the donor ability of C–H and C–halo bonds has been evaluated on the basis of natural bond orbital (NBO) analysis and orbital levels calculations, and the conformational isomerism discussed in terms of classical and hyperconjugative interactions. It has been found that the conformational behavior of the titled compounds is strongly dependent on the π donor/acceptor behavior, which differs substantially between C=O and C=S systems, as well as on the steric/electrostatic and non-Lewis-type interactions involving the series of halogens.     

Germyl mesolytic dissociations in the allylgermane and penta- 2,4-dienylgermane radical anions. A theoretical study

In two stable structures have a trigonal bipyramidal arrangement around Ge, with the extra electron in equatorial (tbp eq) or axial (tbp ax) position. In only tbp ax is found, while a second structure with a tetrahedral germyl group has the extra electron on the conjugated π system. C−Ge bond cleavage yields allyl/ pentadienyl radicals plus germide. Both dissociation reactions require 4–6 kcal mol⁻¹, less than the analogous C and Si systems (ca. 30 and 14 kcal mol⁻¹, respectively). Fragmentation is dramatically activated with respect to homolysis in the corresponding neutrals. The wavefunction is dominated by one single configuration at all distances, in contrast to homolytic cleavage, in which two configurations are important. C−Ge bond dissociation is at variance also with heterolysis, due to spin recoupling of one of the C−Ge bond electrons with the originally unpaired electron. Contribution to the Fernando Bernardi Memorial Issue.     

Hydroxyl orientations in cellobiose and other polyhydroxyl compounds: modeling versus experiment

Theoretical and experimental gas-phase studies of carbohydrates show that their hydroxyl groups are located in homodromic partial rings that resemble cooperative hydrogen bonds, albeit with long H…O distances and small O–H…O angles. On the other hand, anecdotal experience with disaccharide crystal structures suggested that these clockwise ‘c’ or counter-clockwise (reverse ‘r’) sequences are not prevalent in the crystalline state. The situation was clarified with quantum mechanics calculations in vacuum and in continuum solvation, as well as Atoms-In-Molecules analyses. From the experimental side, the Cambridge Structural Database was searched. Geometric criteria for these sequences were developed. A criterion based on 120° ranges of hydroxyl orientations accepted 4% of sequences as having ‘c,c’ or ‘r,r’ orientations instead of the 7% expected based on chance. Criteria based on an O–H…O angle > 90° and a 90° lower limit of the absolute value of the H–O–C…H improper torsion accepted 7.0% of the 358 sequences as ‘c,c’ or ‘r,r’. Highly variable orientation of the hydroxyl groups in crystals was seen to depend mostly on strong inter-residue or intermolecular hydrogen bonds. That lack of specific orientation in general for the crystal structures was supported by the solvated calculations that showed very little variation in the energy when one of the hydroxyl groups in 1,2-dihydroxycyclohexane was rotated. The vacuum calculations found the energy to vary with rotation by more than 4 kcal/mol, confirming the gas-phase experiments and calculations on more complicated molecules. Molecules examined in some detail include scyllo inositol and native and methylated cellobiose.     

Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH<Subscript>2</Subscript>···Y

Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y··· H₂CZ (Z = O, S, Se) and Y···H₂CZ₂ (Z = F, Cl, Br) (Y = Cl⁻, Br⁻) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y···H-C, and that the interaction energies and blue shifts are large, the energy of each Y···H-C H-bond is 15–27 kJ/mol, and Δr(CH) = −0.1 − −0.5 pm and Δv(CH) = 30 − 80 cm⁻¹. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hyperconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of electron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.     

Molecular Structure and Conformational Composition of 1-[(Methylthio)methyl]-2-nitrobenzene (MTMNB): A Theoretical and Experimental Study

The conformational composition of gaseous MTMNB and the molecular structures of the rotational forms have been studied by electron diffraction at 130^∘C aided by results from ab initio and density functional theory calculations. The conformational potential energy surface has been investigated by using the B3LYP/6-31G(d,p) method. As a result, six minimum-energy conformers have been identified. Geometries of all conformers were optimized using MP2/6-31G(d,p), B3LYP/6-31G(d,p), and B3LYP/cc-pVTZ methods. These calculations resulted in accurate geometries, relative energies, and harmonic vibrational frequencies for all conformers. The B3LYP/cc-pVTZ energies were then used to calculate the Boltzmann distribution of conformers. The best fit of the electron diffraction data to calculated values was obtained for the six conformer model, in agreement with the theoretical predictions. Average parameter values (r_a in angstroms, angle α in degrees, and estimated total errors given in parentheses) weighted for the mixture of six conformers are r(C–C) = 1.507(5), r(C–C)_{ring, av} = 1.397(3), r(C–S)_av = 1.814(4), r(C–N) = 1.495(4), r(N–O)_av = 1.223(3), ∠(C–C–C)_ring = 116.0–122.5, ∠ C6–C4–C7 = 118.2(4), ∠ C–C–S = 113.6(6), ∠ C–S–C = 98.5(12), ∠ N–C–C4 = 121.9(3), ∠(O–N–C)_av = 116.8(3), ∠ O–N–O = 127.0(4). Torsional angles could not be refined. Theoretical B3LYP/cc-pVTZ torsional angles for the rotation about C–N bond, φ_C−N, were found to be 30.5–36.5^∘ for different conformers. As to internal rotation about C–C and C–S bonds, values of φ_C−C = 68–118^∘ and φ_C−S = 66–71^∘ were obtained for the three most stable conformers with gauche orientation with respect to these bonds. Some conclusions of this work were presented in a short communication in Russ. J. Phys. Chem. 2005, 79, 1701.     

Ab initio study of the cooperativity between NH···N and NH···C hydrogen bonds in H3N–HNC–HNC complex

Ab initio calculations at the MP2/aug-cc-pVTZ level have been performed to study the cooperativity of hydrogen bonds in homoclusters (HNC–HNC–HNC and HNC–HNC–HNC–HNC) and heteroclusters (H₃N–HNC–HNC and H₃N–HNC–HNC–HNC). The cooperative energies in the HNC–HNC–HNC and H₃N–HNC–HNC trimers are –2.05 and –2.56 kcal/mol, respectively. The result shows that the cooperativity in the heterotrimer is larger than that in the homotrimer. A similar result also happens in the tetramers. The energy decomposition scheme indicates that orbital interaction is a major contribution to the cooperative energy of N···HN hydrogen bond, whereas the electrostatic and orbital interactions to that of C···HN hydrogen bond. The effect of HNC chain length on the strength of N···HN hydrogen bond has also been considered at the MP2/aug-cc-pVDZ level. It is indicated that the interaction energy of N···HN hydrogen bond trends to be a fixed value when the HNC number tends to be infinite, and the strength of N···HN hydrogen bond is regulated mainly through the electrostatic and polarization interactions although the charge transfer interaction also has an effect on it.     

Local dipole interactions induce helicity of (<Emphasis Type="Italic">S</Emphasis>)-2-butyl-<Emphasis Type="Italic">N</Emphasis>-(1,8-naphthaloyl)-2-aminobenzoate molecules containing 1,8-naphthalimide rings utilized as a column building blocks: X-ray and quantum mechanical studies

In the crystal of triclinic symmetry the title compound contains four independent molecules, which differ in the conformation of the aliphatic carbon chain (T, G ⁺and G ⁻) and in the helicity (M or P) of the N-(1,8-naphthaloyl)-2-aminobenzoate (NAB) unit. Quantum chemical MP2 calculations showed that isolated molecules favor helicity of NAB bichromophores most likely due to attractive interactions between local dipoles formed along carbonyl bonds, such that the helical arrangement of O=C–C–C–N–C=O fragments is stabilized by intramolecular interactions between terminal anti-parallel local carbonyl dipoles. In the crystal structure, columnar stacking of the anti-parallel 1,8-naphalimide rings is observed. In a column the neighboring NAB units display opposite helicity.     

Direct ab initio MD study on the hydrogen abstraction reaction of triplet state acetone from methanol molecule

Solvent re-orientation process of triplet acetone/methanol complex and intermolecular hydrogen atom abstraction reaction on the triplet state energy surface, (CH₃)₂C=O (T₁) + CH₃OH → (CH₃)₂C–OH + CH₂OH in gas phase, have been investigated by means of density functional theory (DFT) and direct ab initio molecular dynamics (MD) methods. The static DFT calculation of hydrogen abstraction reaction at the T₁ state showed that the transition state is 16.4 and 30.9 kcal/mol lower than the energy levels of S₁ and S₂ states, respectively, and 9.2 kcal/mol higher than the bottom of T₁ state. The product state, (CH₃)₂C–OH⋯CH₂OH, is 8.4 kcal/mol lower in energy than the level of T₁ state. The direct ab initio MD calculation showed that the product is rapidly formed within 150 fs and the separated products (CH₃)₂C–OH + CH₂OH were formed. The mechanism of reaction dynamics of the triplet acetone/methanol complex was discussed on the basis of theoretical results.