Theoretical investigations on structure, electrostatics potentials and vibrational frequencies of Li+ - CH3- O- (CH2- CH2- O)n- CH3 (n=3-7) conformers

Electronic structure, charge distributions and vibrational characteristics of CH₃ O(CH₂ CH₂ O) _n CH₃ (n=3-7) have been derived using the ab initio Hartree Fock and density functional calculations. For tri- to hexaglymes the lowest energy conformers have trans- conformation around the C-C and C-O bonds of the backbone. For heptaglyme (n=7 in the series), however, gauche-conformation around the C-C bonds renders more stability to the conformer and turns out to be 10.1 kJ mol ⁻¹ lower in energy relative to the conformer having trans-orientation around the C-C and C-O bonds. The molecular electrostatic potential topographical investigations reveal deeper minima for the ether oxygen in conformers having the gauche conformation around the C-C bonds over those for the trans- conformers. A change from trans- to gauche-conformation around the C-C bonds of the lowest energy conformer of heptaglyme engenders a triplet of intense bands ∼1,150 cm ⁻¹ in the vibrational spectra. Theoretical calculations predict that Li ⁺ binds strongly to the heptaglyme conformer in the above series. The frequency shifts in the vibrational spectra of CH₃O(CH₂CH₂O) _n CH₃- Li⁺ (n=3-7) conformers have been discussed     

5‐Ethynyl‐2′‐deoxycytidine: a DNA building block with a `clickable' side chain

The title compound [systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐ethynylpyrimidin‐2(1H)‐one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N‐glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I‐1) and −151.4 (1)° for conformer (I‐2), both in the anti range. The sugar residue of (I‐1) shows a C2′‐endo envelope conformation (²E, S‐type), with P = 164.7 (1)° and τ_m = 36.9 (1)°, while (I‐2) shows a major C3′‐exo sugar pucker (C3′‐exo‐C2′‐endo, ₃T², S‐type), with P = 189.2 (1)° and τ_m = 33.3 (1)°. Both conformers participate in the formation of a layered three‐dimensional crystal structure with a chain‐like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.     

Reactivity of C<Subscript>3</Subscript>-C<Subscript>8</Subscript> alkanes with nitronium ions in sulfuric acid

We have determined the parameters of the Arrhenius equation (E, log A) for reactions between \textNO₂⁺ {\text{NO}}_2^{+} ions and C₃-C₈ alkanes in HNO₃–93 wt.% H₂SO₄ solutions at 277–353 K, and we have also estimated the activation parameters E _j , log A _j for secondary and tertiary C—H bonds of these alkanes. We show that the following compensation relations are satisfied: E = 2.3R βlog A + C with isokinetic temperature β = 360 ± 65 K, and also E _j =2.3Rβ _j log A _j  + C _j , for secondary C—H bonds, β₂ =300 ± 60, and for tertiary C—H bonds, β₃ =310 ± 50.     

Crystal structure of Li(H<Subscript>2</Subscript>O)<Subscript>3</Subscript>[GaEdta]

The ethylenediaminetetraacetate complex Li(H₂O)₃[Ga(Edta)] was synthesized and its crystal structure composed of octahedral (Ga(Edta)⁻ anions connected to the Li(H₂O)₃⁺ ion through the oxygen atom was studied. Five of the six hydrogen atoms of water molecules are involved in weak hydrogen bonds with the oxygen atoms of four Ga(Edta)⁻ complexes, the complex anion is hydrogen-bonded to five water molecules. In addition, shortened contacts C(221)–H(22A)…O(112) between the Ga(Edta)⁻ anions were found. As a result, the molecular packing in the crystal is determined by the three-dimensional lace of hydrogen bonds. The results are compared with published data for the lithium salts of Bi(III), Sb(III), Fe(III), Ni(II), and Hg(II) ethylenediaminetetraacetates.     

Crystallization process analysis for Se<Subscript>0.95</Subscript>In<Subscript>0.05</Subscript> and Se<Subscript>0.90</Subscript>In<Subscript>0.10</Subscript> chalcogenide glasses using the contemporary isoconversional models

Carrying out crystallization studies for both Se_0.95In_0.05 and Se_0.90In_0.10 chalcogenide glasses under non-isothermal conditions at different heating rates, it was realized that a rate controlling process occurs where random nucleation of one- to two-dimensional growth is accompanied with the introduction of up to 10 at% In into glassy Se matrix. The crystallization kinetics together with its dimensionality has been studied using the four currently used isoconversional models (Kissinger–Akahira–Sunose, Ozawa–Flynn–Wall, Tang, and Starink). The activation energy of crystallization (E _c) has been determined using these indicated four models where a satisfactory concurrence is achieved. The value of E _c shows a decrease while increasing both the In-content as well as the extent of crystallization.     

High-resolution photofragment translational spectroscopy for the UV photodissociation of C<Subscript>2</Subscript>H<Subscript>5</Subscript>I

The photodissociation of ethyl iodide at 279.71, 281.73, 304.02 and 304.67 nm has been studied on our new mini-photofragment translational spectrometer with a total flight path of only 5 cm. Some vibrational peaks are firstly resolved in the TOF spectra of I*(2P1/2) and I(2P3/2) channels. These vibrational peaks are assigned to the excitation states (v2 = 0, 1, 2,…) of the umbrella mode (v2, 540 cm-1) of the photofragment C2H5, and the distribution of the vibrational states is obtained. The dissociation energy has been determined to be D0(C-I)=2.314 ±0.03 eV. The energy partitioning of the available energy (Eavl=ET Eint=ET EV,R) calculated from our experimental data (-E)int/Eavl= 22.1% at 281.73 nm, 22.4% at 304.02 nm for the I* channel, and (-E)int/Eavl = 25.2% at 279.71 nm, 25.9% at 304.67 nm for the I channel, seem to be more reliable.     

Fluorine Substitution Effects on Flexibility and Tunneling Pathways: The Rotational Spectrum of 2‐Fluorobenzylamine

The effect of ring fluorination on the structural and dynamical properties of the flexible model molecule 2‐fluorobenzylamine has been studied by rotational spectroscopy in free‐jet expansion and quantum chemical methods. The complete potential energy surface originating from the flexibility of the aminic side chain has been calculated at the B3LYP/6‐311++G** level of theory and the stable geometries were also characterized with MP2/6‐311++G**. The rotational spectra show the presence of two of the predicted four stable conformers: the global minimum (I), in which the side chain’s dihedral angle with the phenyl plane is almost perpendicular, is stabilized by an intramolecular hydrogen bond between the fluorine atom and one hydrogen of the aminic group; and a second conformer II (E_II?E_I≈5 kJ mol^?1) in which the dihedral angle is smaller and the amino group points towards the aromatic ortho hydrogen atom. This conformation is characterized by a tunneling motion between two equivalent positions of the amino group with respect to the phenyl plane, which splits the rotational transition. The ortho fluorination increases, with respect to benzylamine, the tunneling splitting of this motion by four orders of magnitude. The motion is analyzed with a one‐dimensional flexible model, which allows estimation of the energy barrier for the transition state as approximately 8.0 kJ mol^?1.     

6,6′‐Dimethoxygossypolone

6,6′‐Dimethoxygossypolone (systematic name: 7,7′‐dihydroxy‐5,5′‐diisopropyl‐6,6′‐dimethoxy‐3,3′‐dimethyl‐1,1′,4,4′‐tetraoxo‐2,2′‐binaphthalene‐8,8′‐dicarbaldehyde), C₃₂H₃₀O₁₀, is a dimeric molecule formed by oxidation of 6,6′‐dimethoxygossypol. When crystallized from acetone, 6,6′‐dimethoxygossypolone has monoclinic (P2₁/c) symmetry, and there are two molecules within the asymmetric unit. Of the four independent quinoid rings, three display flattened boat conformations and one displays a flattened chair/half‐chair conformation. The angles between the planes of the two bridged naphthoquinone structures are fairly acute, with values of about 68 and 69°. The structure has several intramolecular O—H...O and C—H...O hydrogen bonds and several weak intermolecular C—H...O hydrogen bonds, but no intermolecular O—H...O hydrogen bonds.     

Loop problem in proteins: Developments on Monte Carlo simulated annealing approach

Calculations of loop segments in bovine pancreatic trypsin inhibitor starting from random conformations are more efficient, reproducible, and reliable due to several program enhancements. Monte Carlo simulated annealing (MCSA) calculations of a five-residue α-helix N-terminus segment (H5) and β-strand segment (B5) in this study are compared to the corresponding loop calculations in our previous study. Characteristics of the calculations are: the lowest final total energy conformations (LECs) are within 5 kcal/mol; the average backbone deviations of the computed segments from the native X-ray conformations are 0.43 ± 0.15 Å for H5 and 0.68 ± 0.20 Å for B5; and all the native backbone-backbone hydrogen bonds (H bonds) are present in the best LECs. Compared to the previous study, the H5 and B5 calculations are about 3 and 24 times more efficient, respectively. In the analysis of the best H5 simulated annealing run, backbone-backbone H bonds appear between RT = 4 and 70 kcal/mol, where RT is the Boltzmann temperature factor. H bonds that involve side chains appear in the RT = 1–10 kcal/mol range. Program enhancements implemented are varying main chain versus side chain dihedral angle selection rate, varying ϕ/ψ and χ₁/χ₂ dihedral angles in pairs, the use of main chain and side chain rotamer libraries, and varying the location of the segment origin. © 1996 by John Wiley & Sons, Inc.     

Conformational Analysis of Planar Enol Rotamers of 2,4-Pentanedione: an Ab Initio Study

All conformations among different planar enol conformers (rotamers) of 2,4-pentanedione were studied by means of the Hartree-Fock method using the STO-3G** basis set. The calculations were carried out with the Gaussian-98 program. For each conformation, stationary points with the highest energy on the energy curve were found graphically. Several conformations have low energy barriers and correspond to rotations around single bonds. They describe the spatial motion of only one (in most cases, hydrogen) atom or a small molecular fragment. All low energy barriers are in the interval 13-59 kJ·mol^-1. As would be expected, the lowest energy barrier is exhibited by the conformation that leads to the formation of an enol rotamer having an intramolecular H-bond (so-called -shaped form). On the other hand, conformations in which rotation around a bond leads to a break of the intramolecular hydrogen bond have the highest energy barriers. Conformations in which rotation occurs around the double bond have high energy barriers. The influence of the solvents CHCl₃ and CH₃CN on the intramolecular H-bond has also been studied by means of IPCM at the HF/6-31G** level.     

DFT study of α-maltose: influence of hydroxyl orientations on the glycosidic bond

The result of DFT geometry optimization of 68 unique α-maltose conformers at the B3LYP/6-311++G** level of theory is described. Particular attention is paid to the hydroxyl group rotational positions and their influence on the glycosidic bond dihedral angles. The orientation of lone pair electrons across the bridging hydrogen bonds are implicated in directing the glycosidic dihedral angles with for example, conformers gg-gg and gt-gt, having different minimum energy conformations for the clockwise (c) and the reverse clockwise (r) forms. Conformers tg-gg, gg-tg, tg-tg, gt-gg, and gg-gt were studied, to understand the intermediate glycosidic bond conformations. The conformation, tg-gg-c, was found to be the lowest energy structure. When the hydroxyl groups on each glucose residue were made to point in opposite directions, i.e., c/r and r/c, the optimized structures were found to have high relative energies. Several optimized ‘kink’ structures were found around (, ψ_H) ∼(−40°, −40°), the lowest relative energy conformation being ∼3 kcal/mol. “Kink” conformations are observed in crystalline CA-10 and CA-14mers. Band-flip conformations, also observed in X-ray structures of CA-26 fragments, were studied with the lowest energy α-maltose conformations ∼4.0 kcal/mol above the global energy minimum. Several trends in geometry resulting from hydroxyl rotamer directions are described. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.     

A 2′‐deoxycytidine long‐linker click adduct forming two conformers in the asymmetric unit

The title compound {systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐[6‐(1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl)hex‐1‐ynyl]pyrimidin‐2(1H)‐one}, C₂₄H₂₈N₆O₄, shows two conformations in the crystalline state, viz. (I‐1) and (I‐2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N‐glycosylic bonds of both conformers adopt similar anti conformations, with χ = −168.02 (12)° for conformer (I‐1) and χ = −159.08 (12)° for conformer (I‐2). The sugar residue of (I‐1) shows an N‐type (C3′‐endo) conformation, with P = 33.1 (2)° and τ_m = 29.5 (1)°, while the conformation of the 2′‐deoxyribofuranosyl group of (I‐2) is S‐type (C3′‐exo), with P = 204.5 (2)° and τ_m = 33.8 (1)°. Both conformers participate in hydrogen‐bond formation and exhibit identical patterns resulting in three‐dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N—H...N, N—H... O, O—H...N and O—H...O).     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

Folding Lattice HP Model of Proteins Using the Bond‐Fluctuation Model

In this paper, we find ‘good’ amino acid sequences that fold to a desired “target” structure as a ground state conformation of lowest accessible free energy using the modified bond‐fluctuation lattice model. In our protein lattice model, bond lengths are set to vary between one and √2 in three dimensions. Our results agree well with the native state energies E_N. Comparisons with the “putative native state” (PNS) energy E_PNS and the “hydrophobic zippers” (HZ) energy E_HZ are made. For every sequence, the global energy minimum is found to have multiple degeneracy of conformations, which is the same result as for the constraint‐based hydrophobic core construction (CHCC) method. The interior conformations of the ground states are also discussed.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

Synthesis and characterization of new sulfone‐derivatized phenylenevinylene‐based conjugated copolymers with evolving energy levels and gaps

A new series of stable, processable, and chain end functionalizable sulfone‐derivatized phenylenevinylene‐based conjugated polymers (SFPVs) containing different donor type comonomers have been synthesized and characterized. The polymer main chains are consisted of a sulfone‐phenylene electron accepting unit coupled with an electron donating unit which is derived from one of the dialdehyde comonomers based on benzene, thiophene, and pyrrole (with or without alkoxy side chains). The optical energy gaps (E_g) of the new polymers (in solvent) are in a range of 1.9–2.3 eV, with the lowest energy gap obtained from the polymer containing pyrrole as the donor unit. By using a combination of strong donor unit (such as pyrrole) and a relatively weak but stable acceptor unit (sulfone‐substituted benzene), E_g of the conjugated polymers can be tailored to below 2 eV, while the vinylene bonds on the polymer main chain are still chemically stable to survive strong basic conditions as compared with the S,S‐dioxo‐thiophene‐based PTV polymers developed earlier for potential supra‐molecular block copolymer systems. The lowest energy gap P(Pyrrole‐SFPV) exhibited 10 times better photoelectric power conversion efficiency than P(TV‐SFPV). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Raman spectroscopic study of the hydration of short-chain poly(oxyethylene)s C <Subscript>1</Subscript>E<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>C <Subscript>1</Subscript> (<Emphasis Type="Italic">n</Emphasis>=1−4)

The hypothesis that the degree of hydration of poly(oxyethylene) (POE) in aqueous solution depends on the mole ratio of water molecules to ether oxygen atoms in the molecule has been verified by studying the isotropic Raman spectra in the O−H stretching region for four short-chain POEs (C ₁E _n C ₁ withn=1−4). Excellent coincidence of the O−H stretching Raman band for all four POEs studied in the range of mole ratio H₂O/O _ether from 25 to 0.6 was observed, thus confirming the assumption stated above. A conclusion that all ether oxygen atoms in the POE molecule participate in hydrogen bonding with water molecules has been made.     

Molecular dynamics of (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone in solution studied by NMR spectroscopy

The formation of hydrogen bonds and the molecular dynamics for molecules (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone, (E)-4-bromoacetophenone thiosemicarbazone have been investigated in solution using NMR. The results confirm the formation of different O-H…O type intramolecular hydrogen bonds in the oxime molecule. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined.     

Synthesis and structure of the polymeric complex [Ag<Subscript>2</Subscript>(Ph<Subscript>3</Subscript>P)<Subscript>2</Subscript>B<Subscript>10</Subscript>H<Subscript>10</Subscript>]<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>

A method for the synthesis of the silver(I) complex with the closo-decaborate anion and triphenylphosphine [Ag₂(Ph₃P)₂B₁₀H₁₀] _n was developed and the structure of this complex was studied. The polymeric chain of the complex is formed with participation of Ag(I) atoms, which coordinate the B₁₀H₁₀²⁻ anions through the apical (B(1)–B(2), B(9)–B(10)) and equatorial (B(3)–B(6), B(5)–B(8)) edges, the metalligand bonding occurring through three-center two-electron bonds (MHB). The P atoms of two triphenylphosphine molecules are also incorporated in the inner coordination sphere of the metal: the CN of the silver atom is 4 + 1.