阿魏酸分子结构和振动光谱的理论研究

阿魏酸是一种有效的天然油脂抗氧化剂.采用密度泛函理论(DFT) B3LYP方法和从头算HF两种方法,在6-311++G**基组水平上对阿魏酸分子的几何结构进行全优化,得到其几何结构参数,进一步计算得到阿魏酸的红外和拉曼振动光谱.计算结果表明,采用B3LYP和HF 2种方法优化得到的几何结构及频率值是一致的,对在B3LYP方法下计算得到的红外和拉曼振动频率进行合理的理论归属并与SDBS数据库实验数据进行比较,发现计算得到的红外和拉曼振动频率与实验测定结果符合较好.阿魏酸分子结构和振动光谱的研究,为研究阿魏酸及其衍生物的化学结构与生理活性之间的构效关系提供依据.     

On the molecular structure of HOOO

The molecular structure of trans, planar hydridotrioxygen (HOOO) has been examined by means of isotopic spectroscopy using Fourier transform microwave as well as microwave-millimeter-wave double resonance techniques, and high-level coupled cluster quantum-chemical calculations. Although this weakly bound molecule is readily observed in an electrical discharge of H(2)O and O(2) heavily diluted in an inert buffer gas, we find that HOOO can be produced with somewhat higher abundance using H(2) and O(2) as precursor gases. Using equal mixtures of normal and (18)O(2), it has been possible to detect three new isotopic species, H(18)OOO, HO(18)O(18)O, and H(18)O(18)O(18)O. Detection of these species and not others provides compelling evidence that the dominant route to HOOO formation in our discharge is via the reaction OH + O(2) → HOOO. By combining derived rotational constants with those for normal HOOO and DOOO, it has been possible to determine a fully experimental (r(0)) structure for this radical, in which all of the structural parameters (the three bond lengths and two angles) have been varied. This best-fit structure possesses a longer central O-O bond (1.684 A?), in agreement with earlier work, a markedly shorter O-H bond distance (0.913 A?), and a more acute [angle]HOO angle (92.4°) when compared to equilibrium (r(e)) structures obtained from quantum-chemical calculations. To better understand the origin of these discrepancies, vibrational corrections have been obtained from coupled-cluster calculations. An empirical equilibrium (r(e) (emp)) structure, derived from the experimental rotational constants and theoretical vibrational corrections, gives only somewhat better agreement with the calculated equilibrium structure and large residual inertial defects, suggesting that still higher order vibrational corrections (i.e., γ terms) are needed to properly describe large-amplitude motion in HOOO. Owing to the high abundance of this oxygen-chain radical in our discharge expansion, a very wide spectral survey for other oxygen-bearing species has been undertaken between 6 and 25 GHz. Only about 50% of the observed lines have been assigned to known hydrogen-oxygen molecules or complexes, suggesting that a rich, unexplored oxygen chemistry awaits detection and characterization. Somewhat surprisingly, we find no evidence in our expansion for rotational transitions of cis HOOO or from low-lying vibrationally excited states of trans HOOO under conditions which optimize its ground state lines.     

On the molecular structure of cycloheptadiene

Molecular mechanics calculations on cycloheptadiene indicate that the molecule has a structure which undergoes a wide pseudorotational motion between two C₁ forms, and a C₁ form, and this structure is in equilibrium with the C₂ form. It is shown that this equilibrium mixture is consistent with all of the available experimental data.     

On the applicability of elastic network normal modes in small-molecule docking

Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.     

Elastic network normal modes provide a basis for protein structure refinement

It is well recognized that thermal motions of atoms in the protein native state, the fluctuations about the minimum of the global free energy, are well reproduced by the simple elastic network models (ENMs) such as the anisotropic network model (ANM). Elastic network models represent protein dynamics as vibrations of a network of nodes (usually represented by positions of the heavy atoms or by the C(α) atoms only for coarse-grained representations) in which the spatially close nodes are connected by harmonic springs. These models provide a reliable representation of the fluctuational dynamics of proteins and RNA, and explain various conformational changes in protein structures including those important for ligand binding. In the present paper, we study the problem of protein structure refinement by analyzing thermal motions of proteins in non-native states. We represent the conformational space close to the native state by a set of decoys generated by the I-TASSER protein structure prediction server utilizing template-free modeling. The protein substates are selected by hierarchical structure clustering. The main finding is that thermal motions for some substates, overlap significantly with the deformations necessary to reach the native state. Additionally, more mobile residues yield higher overlaps with the required deformations than do the less mobile ones. These findings suggest that structural refinement of poorly resolved protein models can be significantly enhanced by reduction of the conformational space to the motions imposed by the dominant normal modes.     

Electron-proton effect and the structure of excited molecular complexes

The essence of the electron-proton effect is clarified by the example of donor-acceptor complexes. It is shown that this effect plays a universal role in accelerating dark and photochemical processes due to interaction between electron and proton excitations.     

CNDO/2 molecular orbital studies on the electronic structure and conformational modes of 4-amino-tetrolic acid

4-aminotetrolic acid and its zwitterion have been studied using the CNDO/2 method. The molecular electronic structures, dipole moments and barriers to internal rotation are discussed. A simple procedure to overcome difficulties. encountered with the calculations on the zwitterionic form is described.     

Quantum chemical study on the configurations of encapsulated metal ions and the molecular vibration modes in endohedral dimetallofullerene La2@C80

The configuration of La ions of La(2)@C(80) in the [80]fullerene cage was investigated by use of quantum chemical calculations. We found that the D(3)(d)() configuration is the global minimum in total energy, being more stable by 1.9 kcal/mol than the D(2)(h)() configuration, which has been considered to be the most stable. The potential energy surface calculation clarified that La ions travel between 10 equivalent D(3)(d)() positions through D(2)(h)() positions and consequently form pentagonal dodecahedral trajectory, which is in good agreement with the previous synchrotron radiation structural study. The experimental and theoretical investigation of the Raman spectrum revealed that the symmetry of molecular vibration is dramatically reduced simply by encapsulation of two La ions, and resulting vibrational modes were successfully assigned. The Raman peak at 163 cm(-)(1) was interpreted as the in-phase synchronously coupled mode of the [80]fullerene cage elongation and the La-La stretching, rather than a conventional and naive assignment as a metal-to-cage vibration mode.     

The effect of molecular structure on the chiral random grain boundary phase

A chiral random grain boundary (RGB) phase was recently observed in a hockey-stick biphenyl-substituted 1,3,4-oxadiazole derivative. In the RGB phase, achiral molecules self-assemble into randomly oriented blocks of chiral smectic layers and the motif of the unique microstructure is attributed to the similarity of hockey-stick molecules both to bent-core and to rod-like molecules. In order to explore the effect of molecular structure on the RGB phase in detail, we systematically change the molecular design. When the flexible tail decreases, the high-temperature Smectic A (SmA) phase is replaced by a nematic phase, showing a phase sequence of Iso-N-SmA-RGB-Cryst in 2-(4-dodecyloxyphenyl)-5-biphenyl-1,3,4-oxadiazole. However, when we replace the 1,3,4-oxadiazole group by the 1,3,4-thiadiazole group, the bending angle increases in the 1,3,4-thiadiazole derivatives and the RGB phase disappears. Or when the length of the arm becomes short in naphthalene-substituted 1,3,4-oxadiazole, these molecules exhibited only normal rod-like molecules’ mesomorphism. These results will provide deep insights on the relationship of molecular structure and mesophase structural property.     

On the molecular electron structure of three phosphinine-containing macrocycles

A broad set of structural models and theoretical methods has been successfully used for studying both the molecular electron structure of the silacalix[3]phosphinine and the changes of the macrocycle core under the conditions that frequently correspond to its complexes with metals. The macrocycle core of the silacalix[3]phosphinine and its neutral derivatives are strongly deviated from the main molecular plane. The phosphorous electron lone pairs and the pi-cloud of the phosphinine units give the main contribution to the electron valence structure in the silacalix[3]phosphinine and also in its both oxidized and reduced derivatives. Although the electron lone pairs of the P atoms tend to be strongly repulsive, they are either totally or partially extended above all the fragment of the phosphorous atoms depending on geometrical factors or even strongly coupled with the pi-cloud of the phosphinine units. Electronic processes that take away part of the electron density from the macrocyle favor both its planar configuration and the asymmetric distribution of the valence electrons in the silacalix[3]phosphinine and its derivatives. The limit condition to this effect is the appearance of a new in-plane sigma molecular orbital between the P atoms of two neighboring phosphinine units.     

Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.     

Memory effect of the molecular topology of lamellar polyethylene on the strain-induced fibrillar structure

The fibrillar structure that develops upon drawing of semi-crystalline polymers has been investigated at room temperature by means of in situ SAXS for a series of ethylene copolymers crystallized through various thermal treatments. The long period of the microfibrils for any given material proved to be only dependent on the experimental conditions of the drawing. This suggested the occurrence of a destruction and reconstruction of the semi-crystalline structure via fragmentation accompanied with melting–recrystallization. However, the diameter of the microfibrils proved to keep the memory of the lamellar microstructure via a correlation with the content of interphase at the crystal-amorphous boundary. A physical explanation is proposed for these apparently antagonist findings. The memory of the lamellar semi-crystalline microstructure is completely erased in the microfibrils owing to the melting–recrystallization process. In contrast, the diameter of the fibrils keeps the memory of the chain topology to which a major role is ascribed in the strain-induced fragmentation of the crystalline lamellae.     

The spectrum of vibration modes in soft opals

Numerous vibrational modes of spherical submicrometer particles in fabricated soft opals are experimentally detected by Brillouin light scattering and theoretically identified by their spherical harmonics by means of single-phonon scattering-cross-section calculations. The particle size polydispersity is reflected in the line shape of the low-frequency modes, whereas lattice vibrations are probably responsible for the observed overdamped transverse mode.     

Charge effect of the cation on the structure and the molecular mobility of polymer electrolytes

A study of the thermal and mechanical characteristics of polyethylene oxide-Fe(SCN)₃ complexes shows the existence of structures which can be described by considering a crystalline phase of pure polyethelene oxide (PEO) and an amorphous phase of PEO with dissolved salt. Increasing salt contents decrease the content of crystals, favoring the formation of complexes with a high degree of noncrystallinity as a result of strong polymersalt interactions which tend to enhance the distortion degree of the polymeric skeleton. The microscopic homogeneity of the complexes is also confirmed by the presence in the thermal and mechanical spectra of single glass transitions, which shift to higher temperatures with increasing salt content. Two molecular relaxations are present in the mechanical behavior of these systems, the γ-and the α_a-processes at low and high temperatures, respectively, and show a relaxation strength which increases with decreasing degree of crystallinity of the polymer up to a X ～ 0.10 molar fraction. Both relaxations exhibit a marked nonexponentiality which has been well accounted for in terms of a gaussian distribution of relaxation times for the γ-process and of the Kolrausch-Williams-Watt exponential function for the α_a-process. In the glassy region, the elastic modulus E' reveals a linear temperature dependence which has been interpreted as arising from the anharmonicity of vibrational modes. Increasing noncrystallinity of the system gives rise to an increase of the anharmonicity parameter, which has been ascribed to the influence of the “free volume” in determining the thermal expansivity. ©1995 John Wiley & Sons, Inc.