Open-chain Structure Research Articles

The Structure of Liquid Methanol

A combination of density functional calculations of molecular clusters with a quantum cluster equilibrium (QCE) model provides evidence that liquid methanol is dominated by cyclic and/or lasso structures. Only cluster populations including these structures fit the measured thermodynamic and spectroscopic properties, such as heat of vaporization, heat capacity, NMR chemical shifts, and quadrupole coupling constants. On the other hand, cluster populations comprising open-chain structures fail to reach the experimental values: the heat of vaporization is about 10 kJ mol(-1) too low, and the proton chemical shift is insufficiently downfield-shifted by about 1 ppm.

(2R,3S,4R)-1,2,4,5-Tetraacetoxy-3-methoxypentyl acetate

The title compound, C16H24O11, formed by acetolysis of a d-xylo­furan­ose derivative, has an open-chain structure adopting a hindered conformation in the solid state.

Neutron scattering study of the H-bond network in amorphous N-methylformamide

Original investigations of structural properties in noncrystalline solid N-methylformamide (HCONHCH(3)) are presented in this paper. After description of the sample preparation, the elastic neutron scattering formalism is applied to deduce the coherent scattering cross section for amorphous N-methylformamide. The contribution of each possible monomer (cis or trans) is computed and the corresponding distinct structure factor is deduced. Our measurements clearly show that the hydrogen-bond network occurs in amorphous N-methylformamide between C=O and N-H groups. The experimental spectra are consistent with an open-chain structure similar to the one existing in the crystalline form. The more probable clusters that have been identified in the liquid are also examined.

A theoretical study of the structures and stabilities of N4O2 isomers

Five N4O2 isomers and their possible decomposition pathways were investigated with Møller–Plesset perturbation theory (MP2) and density functional theory (DFT). The most stable isomer is the open-chain C2v structure, which has not been reported before. For all five N4O2 isomers, dissociation energies and eight transition states were studied in the present paper. The open-chain isomer 1 and the planar (C2h) isomer 3 could be potential candidates for high energy density materials (HEDM) due to their large dissociation energy and moderate dissociation barrier.

Base invariance of the manipulability index

The manipulability index suggested by Yoshikava is an important tool for the design of mechanisms and their control. It represents a quantitative measure of the functionality and the ability for realizing some tasks or groups of tasks. This index is some kind of performance measure and should be taken into consideration in the design phase of a mechanism and also in the design of control algorithms.In this paper two important properties of the manipulability index are investigated. The first part of the present work demonstrates that manipulability of a mechanism is independent of task space coordinates. In the second part, a proof of the independency of the manipulability index on the first DOF is given.This invariance is important for simplification of the mechanism's Jacobian matrix and gives excellent insight into the dependences of configuration space coordinates on this index. Moreover, it proves that the manipulability index is determined only by relative positions of the mechanism itself and by the mechanism's geometry.Finally, the properties of the manipulability index are illustrated by some examples for fundamental open kinematical chain structures.

An ab initio conformational study on 2,3-dihydrobilin-1,19(21H,24H)-dione, a model compound for open-chain tetrapyrroles

The molecule 2,3-dihydrobilin-1,19(21H,24H)-dione (DHB) was studied as a model of the fully conjugated linear open-chain tetrapyrroles phycocyanobilin (PCB), phycoerythrobilin (PEB) and phytochrome (PC) as well as biliverdin (BV) and bilirubin (BR). The rotations around the single bonds of the exocyclic methine bridges were investigated for all possible cis and trans, E and Z isomers of DHB. The geometries and energies of conformers were investigated with semiempirical and ab initio methods using AM1 and RHF/3-21G levels of theory. Results indicate that geometries with a central syn– cis configuration are preferred to other conformations around the central methine bridge. Four lowest energy conformations stabilized by hydrogen bonding and favorable geometric arrangements minimizing steric strain were predicted. This model elucidated the trends and identified variables associated with tetrapyrrole conformation and energy and thus may serve as a preliminary basis for studying other open-chain tetrapyrrole structures.

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate Kinase: Evidence for Recognition of an Open Chain Substrate

2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T. thermophilus protein ( TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 Å and 3.2 Å, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger α/β domain and a smaller β-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 Å. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the γ-phosphate of ATP to the 5′-hydroxyl group of KDG.

Synthesis of 2‐(1‐Alkoxyvinyl)oxazolidines by Condensation of 2‐Alkoxypropenals with 2‐Aminoalkanols and Ring—Chain Tautomerism of the Products.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Infrared Photodissociation Spectroscopy of Protonated Formic Acid and Acetic Acid Clusters

Infrared photodissociation spectra of protonated formic acid clusters, H+·(HCOOH)n (n = 2−5), are measured in the 3000−3700 cm-1 region. Density functional theory calculation is applied to H+·(HCOOH)n (n = 2−5). Geometry optimization of H+·(HCOOH)n (n = 2−5) indicates that stable forms of these clusters are open-chain structures with free OH groups at both ends. In the infrared photodissociation spectra of the n = 2 and n = 3 species, there are two sharp bands in the range of 3400−3700 cm-1. The lower- and higher-frequency bands of them are attributed to the free OH stretching vibrations of the peripheral COOH groups in the E and Z conformations, respectively. The intensity of the higher-frequency band, relative to that of the lower-frequency band, decreases from n = 2 to n = 3. The n = 4 and n = 5 ions exhibit only one sharp band in the same region. This band is assigned to the free OH stretching vibrations of the end COOH groups in the E conformation; the n = 4 and n = 5 ions have the peripheral COOH groups only in the E conformation. We observe infrared photodissociation spectra of H+·(HCOOH)n (n = 6, 7) in the 3500−3600 cm-1 region. The absence of any free OH band for n = 7 shows that both ends of chain structures of n = 7 are terminated by cyclic dimers. Infrared photodissociation spectra of H+·(CH3COOH)n (n = 2−5) are also examined in the 3000−3700 cm-1 region. Resemblance of the spectra of H+·(CH3COOH)n to those of H+·(HCOOH)n suggests that the acetic acid clusters have structures that are similar to those of the formic acid clusters; the intermolecular network is formed only by the COOH groups.

Synthesis of 2-(1-Alkoxyvinyl)oxazolidines by Condensation of 2-Alkoxypropenals with 2-Aminoalkanols and Ring-Chain Tautomerism of the Products

Reactions of 2-alkoxypropenals with 2-aminoalkanols afforded tautomeric mixtures of previously unknown 2-(1-alkoxyvinyl)oxazolidines and imino alcohols. The condensation takes 2 h at room temperature (89-100%) or 1-5 min under microwave irradiation. The tautomeric equilibrium shifts toward the open-chain structure with increase in the solvent polarity (CDCl3, CD2OD, DMSO-d6, D2O) and temperature. The presence of substituents in the oxazolidine ring raises the stability of the cyclic tautomer.

Novel porphyrin–quinazoline conjugates via the Diels–Alder reaction

Novel derivatives of meso-tetraphenylporphyrin with appended quinazoline moieties were synthesized, via the Diels–Alder reaction, between a 4-(porphyrinyl)pyrimidine ortho-quinodimethane and 1,4-benzoquinone, 1,4-naphthoquinone and N-( p-nitrophenyl)maleimide. The structure of one bis adduct was established by X-ray crystallography and mass spectrometry. We have unequivocally confirmed that the 2:1 adducts obtained from the reaction of pyrimidine-fused 3-sulfolenes with N-arylmaleimides have an open-chain structure and not a cyclooctapyrimidine structure, as previously published.

Structures and stability of N13 cluster

Quantum chemical studies for the nine N13 isomers with low spin were carried out at the UHF/6-31G*, UB3LYP/6-31G* and UMP2/6-311G* levels of theory. The most stable N13 isomer is structure 1 with C2v symmetry, which contains two separated pentazole rings connected by three nitrogen atoms. The results show that structures 1, 2, 3, 4 and 5 which are composed of the pentazole ring are more stable than the open chain structure 6 and structures 8 and 9 which contain the four- and six-membered rings. This suggests that the pentazole ring is a fundamental stable structural unit, which is applicable not only for the even-numbered nitrogen clusters, but also for the large odd-numbered clusters.

Theoretical Study of the Reaction of HCl with C3H2+: A Possible Source of Carbon−Chlorine Compounds in Space

A theoretical study of the (ClC 3 H 3 ) + species has been carried out. Two different models, G2 and QCISD(T) at the B3LYP geometries, have been employed. Our calculations predict that the global minimum is an open-chain isomer ClHCCCH 2 +( 2 A), whereas five different open-chain structures are also quite stable, lying about 5.9-13.1 kcal/mol above the ground state. The lowest-lying cyclic isomer, with a three-membered carbon ring, lies about 18.3 kcal/mol higher in energy. These theoretical results allow the development of thermodynamic arguments about the reaction pathways of the process HCI + C 3 H 2 +. For the reaction of HCl with CCCH 2 +, formation of different chlorine-carbon compounds is exothermic and there are several mechanisms leading to these species that are barrier-free. However, production of carbocation compounds (cyclopropenyl cation, c-C 3 H 3 +, and propargyl cation, l-C 3 H 3 +) could be competitive with the formation of chlorine-carbon species. The predicted dominant channels for the reaction with both HCCCH + and c-C 3 H 2 + isomers are l-C 3 H 3 + and c-C 3 H 3 +, respectively. Therefore, only the reaction of HCl with the CCCH 2 + isomer seems to be a possible source of chlorine-carbon compounds in space.

Antibacterial activity of quinolone–Macrocycle conjugates

Novel quinolone–macrocycle conjugates displayed submicromolar antibacterial activity against Escherichia coli and Staphylococcus aureus bacterial strains. An analogous open-chain structure was not active at 100 μM against the same pathogenic strains.

A computer-aided quantum chemical study of the N(15)(-) cluster.

Ab initio (RHF, MP2) and Density Functional Theory (DFT) methods have been used to examine six isomers of the N15m cluster with the 6-31+G* basis set. Different from the known odd-numbered anionic N7m, N9m, and N11m clusters, in which the open-chain structures are the most stable species, the most stable N15m isomer is structure 1 (C1), which may be considered as a complex between the fragments cyclic N5m (D5h) and staggered N10 (D2d). The decomposition pathways of structure 2 (CS), containing two aromatic N5 rings connected by a N5 chain, and the open-chain structure 3 (C2v) were studied at the B3LYP/6-31+G* level of theory. Relative energies were refined at the level of B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G*+ZPE (B3LYP/6-31+G*). The barriers for N2 and N5m (D5h) fission reactions for structure 2 are predicted to be 18.2 and 14.2 kcal x mol(-1), respectively. The corresponding N2+N3m fission barrier for structure 3 is predicted to be 11.2 kcal x mol(-1). Supplementary material is available for this article if you access the article at http://dx.doi.org/10.1007/s00894-003-0118-0. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Structure 1 of the N15m cluster, showing bond distances in A and bond angles in degrees

Triple equilibrium in N'-aryl-N-tosyldiazomalonimidolates, 1-tosyl-1,2,3-triazol-5-olates, and 1-aryl-1,2,3-triazol-5-olates

A series of 1-tosyl-substituted 4-arylcarbamoyl-1,2,3-triazol-2-olates, which can undergo rearrangement to isomeric 1-aryl-4-tosylcarbamoyl-1,2,3-triazol-5-olates and N-tosyl-N'-aryldiazomalonimidolates, were synthesized. An equilibrium between these compounds is observed in solutions in DMSO. The introduction of an electron-withdrawing substituent into the aryl residue increases the stability of the 1-tosyl-1,2,3-triazoles but reduces the stability of the 1-aryl-1,2,3-triazoles. π-Donating substituents increase the stability of the open-chain structure.

Structures and kinetic stability of N 7 cluster

Structures and kinetic stability of five N 7 isomers with low spin, including three isomers previously studied, were investigated by the second-order Møller–Plesset (MP2) theory and density functional theory (DFT) methods. Two open-chain structures with C S and C 2 (or C 2v) symmetry were predicted to be local minima on the N 7 potential energy surfaces, respectively. The previously reported C S-symmetric minimum consisting of a five-membered ring and a N 2 side chain was not found to be stable. The isomerization and decomposition pathways of the isomers were also investigated.

Structures and stabilities of C 3Cl 2 and C 3Cl 2+ isomers: a theoretical study

A theoretical study of the C 3Cl 2 and C 3Cl 2 + systems has been carried out. Predictions have been made for some of the molecular properties (geometries, dipole moments, and harmonic vibrational frequencies), which could help in their possible experimental detection. The nature of bonding in these isomers has been characterized by using Bader's topological analysis of the electronic charge density. According to our calculations, the lowest-lying C 3Cl 2 species is singlet dichlorocyclopropenylidene, with the singlet dichlorovinylidenecarbene and singlet and triplet dichloropropargylene lying about 13.3, 19.0 and 20.0 kcal/mol, respectively, higher in energy. In the case of C 3Cl 2 + isomers the global ground state is predicted to be an open-chain structure obtained from ionization of dichloropropargylene, but the cyclic isomer derived from dichlorocyclopropenylidene lies 10.1 kcal/mol higher in energy. It seems that both isomers could be accessible to experimental detection.

Water-Assisted Isomerization from Linear Propargylium (H2CCCH+) to Cyclopropenylium (c-C3H3+)

Calculations at the QCISD(T)/6-311+G(d,p)//B3LYP/6-31G(d) level indicate that the participation of water can effectively lower the isomerization barrier from linear propargylium (H2CCCH+) to cyclopropenylium (c-C3H3+). With the increase of the amount of H2O (nH2O, n = 1, 2, or 3) participating in the isomerization, the isomerization barrier decreases, and with three H2O molecules the isomerization becomes nearly barrierless. In contrast to previous studies on the catalytic effects of water on carbonyl systems and the reaction of H2O(g) with SO3(g), the so-called reactant and the catalyst do not associate into cyclic structures, but rather into open-chain structures. This work may be useful for further studies on the catalytic effect of other species having lone electronic pairs, such as H2S, NH3, and HF.

A Gaussian-3 study of N 7+ and N 7− isomers

A Gaussian-3 study is carried out to investigate the isomers of N 7 + and N 7 −. At MP2(FU)/6-31G(d) level, four N 7 +, and seven N 7 − isomers are identified. Of these 11 species, nine of them are reported for the first time. The most stable N 7 + isomer is 1 +, it has a ‘W-shape’ open-chain structure with C 2 v symmetry, while the most stable N 7 − isomer is 5 −, which is a weak N 2⋯N 5 − complex with C 1 symmetry. Natural bond orbital analysis suggests that the stability of some of the more stable isomers is enhanced by conjugation or hyperconjugation.