Quantum mechanics studies of cellobiose conformations

2006 ◽  
Vol 84 (4) ◽  
pp. 603-612 ◽  
Author(s):  
Alfred D French ◽  
Glenn P Johnson

Three regions of the conformation space that describes the relative orientations of the two glucose residues of cellobiose were analyzed with quantum mechanics. A central region, in which most crystal structures are found, was covered by a 9 × 9 grid of 20° increments of the linkage torsion angles ϕ and ψ. Besides these 81 constrained minimizations, we studied two central subregions and two regions at the edges of our maps of complete ϕ,ψ space with unconstrained minimization, for a total of 85 target geometries. HF/6-31G(d) and single-point HF/6-311+G(d) calculations were used to find the lowest energies for each geometry. B3LYP/6-31G+G(d) and single point B3LYP/6-11+G(d) calculations were also used for all unconstrained minimizations. For each target, 181 starting geometries were tried (155 for the unconstrained targets). Numerous different starting geometries resulted in the lowest energies for the various target structures. The starting geometries came from five different sets that were based on molecular mechanics energies. Although all five sets contributed to the adiabatic map, use of any single set resulted in discrepancies of 3–7 kcal/mol (1 cal = 4.184 J) with the final map. For most of the targets, the starting geometry that gave the lowest energy depended on the basis set and whether the HF or B3LYP method was used. However, each of the above four calculations gave the same overall lowest energy structure that was found previously by Strati et al. This global minimum, stabilized by highly cooperative hydrogen bonds, is in a region that is essentially not populated by crystal structures. HF/6-31G(d) energy contours of the mapped central region were compatible with the observed crystal structures. Observed structures that lacked O3···O5′ hydrogen bonds were about 1 kcal/mol above the map's minimum, and observed structures that have a pseudo twofold screw axis ranged from about 0.4 to 1.0 kcal/mol. The HF/6-311+G(d) map accommodated the observed structures nearly as well.Key words: cellulose, carbohydrate, conformation, energy, flexibility, folding, helix, shape.

2013 ◽  
Vol 634-638 ◽  
pp. 15-19
Author(s):  
Yan Zhi Liu ◽  
Yan Liu ◽  
Kun Yuan ◽  
Yuan Cheng Zhu

The recognition mechanism of the urea-based non-involving fluorine (A) and involving fluorine (B) derivation receptors for the chlorine anion (Cl-) was discussed by using the density function B3LYP method. The results showed that recognition mechanism was performed by using four coordination weak bonds, which include two N-H…Cl hydrogen bonds and two C-I…Cl halogen bonds. The calculated interaction energies (ΔECP) with basis set super-position error (BSSE) correction of the two systems are -121.78 and -179.71 kJ•mol-1, respectively. So, the urea-based involving fluorine derivation receptor (B) presents the better recognition capable for the Cl-. Natural bond orbital theory (NBO) analysis has been used to investigate the electronic behavior and property of the N-H…Cl hydrogen bonds and two blue-shift C-I…Cl halogen bonds in the A…Cl- and B…Cl- recognition systems, respectively.


2012 ◽  
Vol 10 (2) ◽  
pp. 395-406 ◽  
Author(s):  
U. Başköse ◽  
Sevgi Bayarı ◽  
Semran Sağlam ◽  
Hacı Özışık

AbstractThe conformational analysis of rasagiline [N-propargyl-1(R)-aminoindan] was performed by the density functional theory (DFT) B3LYP method using the 6–31++G (d,p) basis set. A single point energy calculations based on the B3LYP optimized geometries were also performed at MP2/6-31++G (d, p) level. The vibrational frequencies of the most stable conformer of rasagiline was calculated at the B3LYP level and vibrational assignments were made for normal modes on the basis of scaled quantum mechanical force field (SQM) method. The influence of mesylate and ethanedisulfonate salts on the geometry of rasagiline free base and its normal modes are also discussed.


2019 ◽  
Vol 16 (9) ◽  
pp. 705-717
Author(s):  
Mehrnoosh Khaleghian ◽  
Fatemeh Azarakhshi

In the present research, B45H36N45 Born Nitride (9,9) nanotube (BNNT) and Al45H36N45 Aluminum nitride (9,9) nanotube (AlNNT) have been studied, both having the same length of 5 angstroms. The main reason for choosing boron nitride nanotubes is their interesting properties compared with carbon nanotubes. For example, resistance to oxidation at high temperatures, chemical and thermal stability higher rather than carbon nanotubes and conductivity in these nanotubes, unlike carbon nanotubes, does not depend on the type of nanotube chirality. The method used in this study is the density functional theory (DFT) at Becke3, Lee-Yang-Parr (B3LYP) method and 6-31G* basis set for all the calculations. At first, the samples were simulated and then the optimized structure was obtained using Gaussian 09 software. The structural parameters of each nanotube were determined in 5 layers. Frequency calculations in order to extract the thermodynamic parameters and natural bond orbital (NBO) calculations have been performed to evaluate the electron density and electrostatic environment of different layers, energy levels and related parameters, such as ionization energy and electronic energy, bond gap energy and the share of hybrid orbitals of different layers.


2021 ◽  
Vol 5 (1) ◽  
pp. 5
Author(s):  
Evgeny V. Nazarchuk ◽  
Dmitri O. Charkin ◽  
Oleg I. Siidra

Three new uranyl sulfates, [pyH](H3O)[(UO2)3(SO4)4(H2O)2] (1), [pyH]2[(UO2)6(SO4)7(H2O)] (2), and [pyH]2[(UO2)2(SO4)3] (3), were produced upon hydrothermal treatment and successive isothermal evaporation. 1 is monoclinic, P21/c, a = 14.3640(13), b = 10.0910(9), c = 18.8690(17) Å, β = 107.795(2), V = 2604.2(4) Å3, R1 = 0.038; 2 is orthorhombic, C2221, a = 10.1992(8), b = 18.5215(14), c = 22.7187(17) Å, V = 4291.7(6) Å3, R1 = 0.030; 3 is orthorhombic, Pccn, a = 9.7998(8), b = 10.0768(8), c = 20.947(2) Å, V = 2068.5(3) Å3, R1 = 0.055. In the structures of 1 and 2, the uranium polyhedra and SO4 tetrahedra share vertices to form ∞3[(UO2)3(SO4)4(H2O)2]2− and ∞3[(UO2)6(SO4)7(H2O)]2− frameworks featuring channels (12.2 × 6.7 Å in 1 and 12.9 × 6.5 Å in 2), which are occupied by pyridinium cations. The structure of 3 is comprised of ∞2[(UO2)2(SO4)3]2− layers linked by hydrogen bonds donated by pyridinium cations. The compounds 1–3 are formed during recrystallization processes, in which the evaporation of mother liquor leads to a stepwise loss of hydration water.


2007 ◽  
Vol 62 (12) ◽  
pp. 711-715 ◽  
Author(s):  
Ahmad Seif ◽  
Mahmoud Mirzaei ◽  
Mehran Aghaie ◽  
Asadollah Boshra

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.


Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3294 ◽  
Author(s):  
Sławomir J. Grabowski

The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction.


2014 ◽  
Vol 70 (10) ◽  
pp. o1085-o1086
Author(s):  
Mathias O. Senge ◽  
Hans-Georg Eckhardt

In the title compound, C44H37BN4O2, the dihedral angle between the plane of the porphyrin macrocycle ring system [r.m.s. deviation = 0.159 (1) Å] and those of three phenyl rings are 66.11 (4), 74.75 (4) and 57.00 (4)°. The conformational distortion is characterized by a mixture of ruffled, saddle and in-plane distortion modes. In the crystal, the porphyrin molecules are linked by C—H...π interactions into supramolecular chains running along thea-axis direction. A pair of bifurcated N—H...(N,N) hydrogen bonds occur across the central region of the macrocycle.


Author(s):  
Zhe An ◽  
Jing Gao ◽  
William T. A. Harrison

The syntheses and crystal structures of 0.25-aqua(benzene-1,4-dicarboxylato-κ2O,O′)bis(sparfloxacin-κ2O,O′)manganese(II) dihydrate, [Mn(C8H4O4)(C19H22F2N4O3)2(H2O)0.25]·2H2O or [Mn(bdc)(Hspar)2(H2O)0.25]·2H2O, (I), and bis(sparfloxacin-κ2O,O′)copper(II) benzene-1,4-dicarboxylate dihydrate, [Cu(C19H22F2N4O3)2](C8H4O4)·2H2O or [Cu(Hspar)2](bdc)·2H2O, (II), are reported (Hspar = sparfloxacin and bdc = benzene-1,4-dicarboxylate). The Mn2+ion in (I) is coordinated by twoO,O′-bidentate Hspar neutral molecules (which exist as zwitterions) and anO,O′-bidentate bdc dianion to generate a distorted MnO6trigonal prism. A very long bond [2.580 (12) Å] from the Mn2+ion to a 0.25-occupied water molecule projects through a square face of the prism. In (II), the Cu2+ion lies on a crystallographic inversion centre and a CuO4square-planar geometry arises from its coordination by twoO,O′-bidentate Hspar molecules. The bdc dianion acts as a counter-ion to the cationic complex and does not bond to the metal ion. The Hspar ligands in both (I) and (II) feature intramolecular N—H...O hydrogen bonds, which closeS(6) rings. In the crystals of both (I) and (II), the components are linked by N—H...O, O—H...O and C—H...O hydrogen bonds, generating three-dimensional networks.


Author(s):  
Amila M. Abeysekera ◽  
Boris B. Averkiev ◽  
Pierre Le Magueres ◽  
Christer B. Aakeröy

The roles played by halogen bonds and hydrogen bonds in the crystal structures of N-(pyridin-2-yl)amides were evaluated and rationalised in the context of calculated molecular electrostatic potentials.


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