Molecular Mechanics: The Cross-conjugated Carbonyl Group in Heterocyclic Compounds. 1. Parameterisation (MM2) of the >C=O Bond

A new type of carbon atom has been included in the MM2 force field when it is part of a carbonyl group cross-conjugated in a heterocyclic molecule. This carbon atom is fully included in the π system calculation. New stretching parameters for the C=O bond have been estimated by a statistical process from X-ray molecular structures recorded in the Cambridge Structural Database System. The proposed parameters have been found appropriate for compounds in which the atoms adjacent to the carbonyl are a carbon and a heteroatom i.e. mainly for the α-pyrone ring and the conjugated "lactams". They are inappropriate for carbonates and oxazo-ones but should be valid for quinones provided that they are not involved in a charge transfer complex. The mean unsigned deviation for 111 bond lengths (89 cyclic molecules) is 0.01Å but the maximum deviation can reach ± 0.03Å. Part of the observed dispersion could be the result of the variation of the effective dielectric constant D from one crystal to another.     

Molecular mechanics:the cross-conjugated carbonyl group in heterocyclic compounds. 3. Parameterisation (MM2) of the adjacent C=C bond: evaluation tests

In the MM2 force field, the definition of a new type of carbon (carbonyl atom, when it is cross-conjugated) has led to the reestimation of the mechanical parameters of the adjacent C(O)-O and C(O)-N bonds in fully-conjugated cyclic compouds: !-pyrones, '-lactones, and conjugated "lactams". New parameters, based on the study of 97 bonds, are presented here for the similar adjacent C(O)-C bond in the same compounds. Comparison of calculated bond lengths to experimental X-ray bond lengths shows that, statistically, the results are substantially improved but the dispersion remains large. Full optimisation of the molecules concerned shows that in some cases the errors accumulate on the C(O)-O bond which is more sensitive to errors in the evaluation of its own ? bond order. The origins of the discrepancies are discussed. Using caffeine as a test molecule, the MM2 method with the parameters proposed here, appears less acurate than the ab initio and DFT methods (both with 6-31G**basis) but still better than the semi-empirical methods (AM1-PM3).     

The structures of solvated methylmercury(II) chlolade,bromide and iodide in pyridine solution; Implications for aqueous solution

The structures of solvated methylmercury(II) halides in pyridine solution were determined by a large angle X-ray scattering technique. Near-linear CH₃HgX (X = Cl, Br and I) species solvated by two weakly-coordinated pyridine molecules are indirectly interpreted. Additional mercury-pyridine interactions, through van der Waals forces, are found at the sum of the van der Waals radii. The HgX bond distances in the methylmercury(II) halides are found to be 2.325(8), 2.480(3) and 2.649(3) Å for chloride, bromide and iodide, respectively. The HgC bond distances are assumed to be ∼2.08 Å. This interaction is indicated in the radial distribution functions. The bond distance between mercury and the two solvating pyridine molecules is ∼2.8 Å, e.g., 2.84(2) Å in methylmercury(II) bromide. The additional mercury interactions with roughly two pyridine molecules at the sum of van der Waals radii are revealed at around 3.15 Å. Comparison between Raman stretching vibrations and the solvated structures of methylmercury(II) complexes found in various solvents indicates a lower limit in solvent donor property for the formation of solvate bonds to mercury for the methylmercury(II) halides.     

Density functional and Møller–Plesset studies of cyclobutanone⋯HF and ⋯HCl complexes

The molecular structure (hydrogen bonding, bond distances and angles), dipole moment and vibrational spectroscopic data [vibrational frequencies, IR and vibrational circular dichroism (VCD)] of cyclobutanone?HX (X?=?F, Cl) complexes were calculated using density functional theory (DFT) and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6–311G, 6–311G^**, 6–311 + + G^**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2 and B3LYP levels with basis sets including diffuse functions. Surface potential energy calculations were carried out with scanning HCl and HF near the oxygen atom. The nonlinear hydrogen bonds of 1.81 Å and 175° for HCl and 1.71 Å and 161° for HF were calculated. In these complexes the C=O and H–X bonds participating in the hydrogen bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and the band assignments reported are in excellent agreement with experimental IR spectra. The C=O stretching vibrational frequencies of the complexes show red shifts with respect to cyclobutanone.     

Crystal Structure and Conformation of 8-(2-Hydroxyethylamino) and 8-(Pyrrolidin-1-yl) Adenosines

In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 2₁; a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) Å, β = 92.261(1)°, V = 707.10(3) ų, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of N–H·O type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) Å, β = 103.254(2)°, V = 1524.4(2) ų, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of O–H·N type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.     

Packing analysis of carbohydrates and polysaccharides. V. Crystal structures of two polymorphs of pachyman triacetate

The crystal structures of two polymorphic forms of pachyman triacetate, the fully acetylated derivative of a naturally occuring β-(1 → 3)-D -glucan, were determined by a combination of stereochemical and x-ray diffraction analysis. The two polymorphs could be obtained depending on the temperature and the degree of stretching of film specimens of the substance: polymorph I resulted from stretching 25–50% at 125°C and polymorph II resulted from further stretching to 300% at 215°C. Both polymorphs had previously been shown to have sixfold helical chain conformations, but of unequal pitch. Subsequent detailed structure refinement performed with bond lengths, bond angles, conformational angles, and helix-packing parameters as refinement variables, and the simultaneous minimization of packing and conformational energy and the crystallographic R-factor as refinement criteria, resulted in a complete determination of the two crystal structures. Pachyman triacetate I was found to be a right-handed helix packing with antiparallel polarity and space group P2₁2₁2₁ symmetry (unit-cell parameters a = 11.0, b = 19.0, c (fiber repeat) = 22.38 Å). The acetate groups were nearly planar and the O(2) and O(4) acetates were oriented in such a fashion that the carbonyl double-bond nearly eclipsed the corresponding C—H bond of the ring. The O(6) was in the tg position and its acetate was oriented in such a fashion that the bond sequence C(6)—O(6)—C(6C)—C(6M) was nearly trans-planar, with the carbonyl double-bond bisecting the tetrahedral angle formed by C(6) and its two hydrogens. The final R = 0.221. Pachyman triacetate II was similarly found to be a right-handed helix, but packing as a 50:50 mixture of parallel and antiparallel polarities (unit-cell parameters a = 11.49, b = 20.13, c (fiber repeat) = 18.6 Å). The acetate positions in pachyman triacetate II were substantially the same as in pachyman triacetate I. The final R for the 50:50 mixture was 0.234. Probable reasons for the change in packing polarities are discussed, as are the difficulties encountered in the structure refinement of acetate derivatives.     

Metal complexes of virus inhibitors. Part III. Coordination properties of 1-n-propyl-2-α-hydroxybenzylbenzimidazole and the X-ray crystal structure of Ni(C17H18N2O)2(C17H17N2O)1(ClO4)1

Complexes are described of Cobalt(II) and Nickel- (II) salts with the title ligand L. The X-ray crystal structure is described of NiL₂L′₁(ClO₄)₁. One ligand molecule (L′) in this complex is deprotonated and the structure involves strongly hydrogen bonded dimers with OHO bonds = 2.56 Å and 2.62 Å and a NiNi bond = 4.77 Å. The corresponding Cobalt complex is thought to be similar but no other compounds containing L′ were obtained.     

A density functional theory analysis for the adsorption of the amine group on graphene and boron nitride nanosheets

In this paper first principles total energy calculations to study the adsorption of amine group (NH₂) on graphene (G) and boron nitride (hBN) nanosheets are developed; the density functional theory, within the local density approximation and Perdew-Wang functional was employed. The sheets were modeled with a sufficiently proved C_nH_m-like cluster with armchair edge. The optimized geometry was obtained following the minimum energy criterion, searching on four positions for each nanosheet: perpendicular to the carbon atom, on the hexagon, inside the hexagon and on the bridge C–C, for the G-amine interaction; and, perpendicular to the B, perpendicular to the N, on the hexagon, and inside the hexagon, for the hBN-amine interaction. A physisorption, with amine parallel to the C–C–C bond with a distance graphene-amine of 2.56 Å, was found. For the case of BN a B–N bond, with bond length equal to 1.56 Å, was found; the amine lies perpendicular to the nanosheet. When the graphene is doped with B and Al atoms a chemisorption with B–N (1.57 Å) and Al–N (1.78 Å) bonds is observed; the bond angle in the amine group is also incremented, 5.5° and 8.1°, respectively. In the presence of point defects (monovacancies) of B in the hBN-amine and C in the G-amine, there exists chemisorption, increasing the reactivity of the sheets.     

The molecular structures of pyridine-chromiumpentacarbonyl and bis(pyridine)-chromiumtetracarbonyl

The structures of pyridinechromiumpentacarbonyl, (1), and bis(pyridine)chromiumtetracarbonyl,(2) have been determined. (1) crystallizes in the space group Pbam with a = 15.289(3) Å, b = 19.276(5) Å and c = 7.677(6) Å. (2) crystallizes in the space group P$\text{1}$ with a = 7.365(2) Å, b = 8.136(2) Å, c = 13.491(4) Å, α = 89.49(2)°, β = 88.89(2)°, and γ = 63.09(2)°. The structures refined to R_w values of 0.020 and 0.034 for (1) and (2), respectively. In both cases the pyridine rings are planar and stagger the cis CrCO bonds. A comparison of the structural results from these two compounds to piperidinechromiumpentacarbonyl and Cr(CO)₆ seems to indicate that the pyridine ligand is a weaker σ-donor and stronger π-acceptor than the saturated analog, piperidine.     

Raman spectroscopic study of polycrystalline mono- and polyunsaturated 1-eicosanoyl-d(39)-2-eicosenoyl-sn-glycero-3-phosphocholines: bilayer lipid clustering and acyl chain order and disorder characteristics

Polycrystalline lipid samples of a series of mono- and polyunsaturated, double bond positional isomers of 1-eicosanoyl-d(39)-2-eicosenoyl-sn-glycero-3-phosphocholines [C(20-d(39)):C(20:1 Delta(j))PC, with j = 5, 8, 11, or 13; C(20-d(39)):C(20:2 Delta(11,14))PC; and C(20-d(39)):C(20:3 Delta(11, 14,17))PC] were investigated using vibrational Raman spectroscopy to assess the acyl chain packing order-disorder characteristics and putative bilayer cluster formation of the isotopically differentiated acyl chains. Perdeuteration of specifically the saturated sn-1 acyl chains for these bilayer systems enables each chain's intra- and intermolecular conformational and organizational properties to be evaluated separately. Various saturated chain methylene CD(2) and carbon-carbon (C&bond;C) stretching mode peak height intensity ratios and line width parameters for the polycrystalline samples demonstrate a high degree of sn-1 chain order that is unaffected by either the double bond placement or number of unsaturated bonds within the sn-2 chain. In contrast, the unsaturated sn-2 chain spectral signatures reflect increasing acyl chain conformational disorder as either the cis double bond is generally repositioned toward the chain terminus or the number of double bonds increases from one to three. The lipid bilayer chain packing differences observed between the sn-1 and sn-2 chains of this series of monounsaturated and polyunsaturated 20 carbon chain lipids suggest the existence of laterally distributed microdomains predicated on the formation of highly ordered, saturated sn-1 chain clusters.     

Computational study on C−H…π interactions of acetylene with benzene, 1,3,5-trifluorobenzene and coronene

Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C?H^…π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals that the C?H^...π interaction complex where acetylene located above to the center of benzene ring (classical T-shaped) is the lowest energy structure. This structure is twice more stable than the configuration characterized by H atom of benzene interacting with the π-cloud of acetylene. The binding energy of 2.91 kcal/mol calculated at the M06-2X/6-311+G(d,p) level for the lowest energy configuration (1A) is in very good agreement with the experimental binding energy of 2.7?±?0.2 kcal/mol for benzene-acetylene complex. Interestingly, the C?H^...π interaction of acetylene above to the center of the aromatic ring is not the lowest energy configuration for 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. The lowest energy configuration (2A) for the former complex possesses both C?H^...π interaction and C?H^...F hydrogen bond, while the lowest energy structure for the coronene-acetylene complex involves both π-π and C?H^...π interactions. C?H stretching vibrational frequencies and the frequency shifts are reported and analyzed for all of the configurations. We observed red-shift of the vibrational frequency for the stretching mode of the C-H bond that interacts with the π-cloud. Acetylene in the lowest-energy structures of the complexes exhibits significant red-shift of the C?H stretching frequency and change in intensity of the corresponding vibrational frequency, compared to bare acetylene. We have examined the molecular electrostatic potential on the surfaces of benzene, 1,3,5-trifluorobenzene, coronene and acetylene to explain the binding strengths of various complexes studied here.     

A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues

Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: approximately 1759-1776 cm(-1) for zero, approximately 1733-1749 cm(-1) for one, and 1703-1710 cm(-1) for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins.     

Theoretical investigations on the hydrogen bonding of nitrile isomers with H2O,HF, NH3 and H2S

The hydrogen bonds formed by the interaction of nitriles with water, hydrogen fluoride, ammonia and hydrogen sulphide have been studied using B3LYP and second-order Møller–Plesset perturbation (MP2) methods and 6-311+ + G(d,p) basis set. The energies and structures of 80 hydrogen-bonded complexes between nitriles and small molecules were examined systematically using B3LYP and MP2 procedure. Categorisation of the hydrogen bonds involved in the various complexes led to an ordering of hydrogen bond donor and acceptor abilities for some functional groups. The interaction energies have been corrected for the basis set superposition error using Boy's counterpoise correction method. The Morokuma energy decomposition analysis reveals that the strong interactions are due to the attractive contributions from the electrostatic (ES), polarisation (PL) and charge transfer (CT) components. The topological parameters, electron density and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital (NBO) analysis has also been performed to study the CT from proton acceptor to the antibonding orbital of the H–Y bond in the proton donor part of complexes. The frequency analysis of C–H…Y bond in the complexes indicates the blue-shifting nature largely in case of sp² hybridised carbon atom.     

Molecular Mechanics Studies of Molybdenum Disulphide Catalysts Parameterisation of Molybdenum and Sulphur

Abstract

A method for the parameterisation of molybdenum disulphide is presented which reproduces the crystal structure accurately. The method involves calculating parameters such that there is no net force contribution from any individual term of the potential on any atom. Ideal bond lengths and bond angles are taken from the X-ray crystal structure; stretching and bending force constants are calculated from a combination of spectroscopic data and quantum mechanics calculations, whereby the energy function with bond length or bond angle is calculated and fitted with an harmonic potential. For the non-bonded Lennard-Jones parameters, the dispersion coefficient C was calculated by an interpolation of existing published parameters using a multiple regression and then the crystal energy was minimised with respect to the van der Waals radius r₀ using a fixed crystal fragment.

These parameters were tested for various models of the hexagonal and rhombohedral forms of MoS₂. RMS fits between structures minimised with molecular mechanics and experimental models ranged from 0.006 Å to 0.012 Å.     

Crystal packing driven by metal-ligand interactions, hydrogen bonds, π-π stacking and anion-π stacking

Two polymeric copper(II) compounds have been synthesized with the ligand bis(pyrimidin-2yl)amine (dipm), by means of coordination bonds, Watson-Crick type hydrogen bond interactions and π-π stacking. Both supramolecules hold the same cationic building block, namely [Cu(dipm)₂(H₂O)₂]²⁺. However, their crystal structure significantly differs and this variation apparently arises from the nature of the anion which induces dissimilar crystal packings. The crystal growth is driven by several synergistic intermolecular interactions, i.e., coordination and hydrogen bonds, π-π and anion-π stacks.     

β-Turn conformations in crystal structures of model peptides containing α,α-Di-n-propylglycine and α,α-Di-n-butylglycine

The crystal state conformations of three peptides containing the α,α-dialkylated residues. α,α-di-n-propylglycine (Dpg) and α,α-di-n-butylglycine (Dbg), have been established by x-ray diffraction. Boc-Ala-Dpg-Alu-OMe (I) and Boc-Ala-Dbg-Ala-OMe (III) adopt distorted type II β-turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: ? = 66.2°, ψ = 19.3°; III: ? = 66.5°. ψ = 21.1°) deviate appreciably from ideal values for the i + 2 residue in a type II β-turn. In both peptides the observed (N…O) distances between the Boc CO and Ala (3) NH groups are far too long (1: 3.44 Å: III: 3.63 Å) for an intramolecular 4 → 1 hydrogen bond. Boc-Ala-Dpg-Ata-NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules HA and HB adopt consecutive β-turn (type III-III in HA and type III-I in IIB) or incipient 3₁₀-helical structures, stabilized by two intramolecular 4 → 1 hydrogen bonds. In all four molecules the bond angle N-C^α-C′ (τ) at the Dxg residues are ≥ 110°. The observation of conformational angles in the helical region of ?,ψ space at these residues is consistent with theoretical predictions. © 1995 John Wiley & Sons, Inc.     

Theoretical π-π* absorption and circular dichroic spectra of helical poly(L-proline) forms I and II

Absorption and CD spectra of the π-π* transition near 200 nm are calculated for helical (Pro)_n I and II (n = 6, 10) using the dipole interaction model, including interactions among all atoms, with optical parameters obtained from previous studies of related molecules. Calculated spectra for (Ala)_n and (Pro)_n in the same conformation show marked differences. The spectra for (Pro)_n are sensitive to side-chain structure but are found to agree reasonably well with exeriment for forms I and II when the side-chain C? C bond length is set at 1.54 Å, with structural data otherwise obtained from x-ray diffraction studies.     

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts. II. IR spectral studies.

The IR spectra of crystalline cytidine (Cyd), ethenocytidine (epsilon Cyd), and their hydrochlorides (Cyd-Hcl and epsilon CyD-HCl) have been analyzed to determine the spectroscopic manifestations of the structural differences that were previously established for these nucleosides from X-ray studies. O,N-Deuteration of the samples turned out to be a successful approach to obtaining interpretable spectra. The analysis was carried out in three frequency ranges: (i) The 2600-1900 cm-1 range originating from the vO-D and VN-D vibrations. All intermolecular hydrogen bonds could be recognized here. The positions of the individual vO-D (vN-D) bands were correlated with the geometrical delta HB parameters presenting the strengths of hydrogen bonds in which these groups act as donors (ii) The 1750-1500 cm-1 region originating from the stretching vibrations of double bonds. All absorption bands in this region were interpreted in terms of electronic structures of the base fragments. (iii) The region of the C-H stretching vibrations of the base fragments (3200-3000 cm-1) and sugar moieties (3000-2800 cm-1). The Csp2-H vibrations also reflect the electronic structures of the base fragments, whereas the vCsp-H frequencies seem to be sensitive to etheno-bridging and to the presence of an intramolecular C6-H...05' hydrogen bond.     

Identification of the C=O stretching vibrations of FMN and peptide backbone by 13C-labeling of the LOV2 domain of Adiantum phytochrome3

Phototropin, a blue-light photoreceptor in plants, has two FMN-binding domains named LOV1 and LOV2. We previously observed temperature-dependent FTIR spectral changes in the C=O stretching region (amide-I vibrational region of the peptide backbone) for the LOV2 domain of Adiantum phytochrome3 (phy3-LOV2), suggesting progressive structural changes in the protein moiety (Iwata, T., Nozaki, D., Tokutomi, S., Kagawa, T., Wada, M., and Kandori, H. (2003) Biochemistry 42, 8183-8191). Because FMN also possesses two C=O groups, in this article, we aimed at assigning C=O stretching vibrations of the FMN and protein by using 13C-labeling. We assigned the C(4)=O and C(2)=O stretching vibrations of FMN by using [4,10a-13C2] and [2-13C] FMNs, respectively, whereas C=O stretching vibrations of amide-I were assigned by using 13C-labeling of protein. We found that both C(4)=O and C(2)=O stretching vibrations shift to higher frequencies upon the formation of S390 at 77-295 K, suggesting that the hydrogen bonds of the C=O groups are weakened by adduct formation. Adduct formation presumably relocates the FMN chromophore apart from its hydrogen-bonding donors. Temperature-dependent amide-I bands are unequivocally assigned by separating the chromophore bands. The hydrogen bond of the peptide backbone in the loop region is weakened upon S390 formation at low temperatures, while being strengthened at room temperature. The hydrogen bond of the peptide backbone in the alpha-helix is weakened regardless of temperature. On the other hand, structural perturbation of the beta-sheet is observed only at room temperature, where the hydrogen bond is strengthened. Light-signal transduction by phy3-LOV2 must be achieved by the progressive protein structural changes initiated by the adduct formation of the FMN.     

Harmonic force field for nitro compounds

Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).