Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.     

The nature of base stacking: a Monte Carlo study

To elucidate the physical origin of the preference of nucleic acid bases for stacking over hydrogen bonding in water, Monte Carlo simulations were performed starting from Watson?CCrick structures of the adenine?Cthymine, adenine?Curacil and guanine?Ccytosine base pairs, as well as from the Hoogsteen adenine?Cthymine base pair, in clusters comprising 400 and 800 water molecules. The simulations employed a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. All simulations reached stacked structures, confirming that such structures are preferred over the hydrogen-bonded Watson?CCrick and Hoogsteen base pairs. The Monte Carlo simulations show the complete transition from hydrogen-bonded base pairs to stacked structures in the Monte Carlo framework. Analysis of the average energies shows that the preference of stacked over hydrogen-bonded structures is due to the increased water?Cbase interaction in these structures. This is corroborated by the increased number of water?Cbase hydrogen bonds in the stacked structures.     

Effects of vibrational,averaging on structures and order parameters of difluorobenzenes in various oriented media

The previously reported structures of the difluorobenzenes obtained from partially oriented NMR spectra have been corrected for harmonic vibrational motions. Possible effects arising from pseudo-dipolar couplings have also been investigated. The vibrationally corrected structures are frequently outside of the experimental errors of the uncorrected structures. The vibrational corrections are found to decrease the range in the distance ratios resulting from the use of various solvent systems.     

Artificial β‐Double Helices from Achiral γ‐Peptides

Double helices are not common in polypeptides and proteins except in the peptide antibiotic gramicidin A and analogous l,d ‐peptides. In contrast to natural polypeptides, remarkable β‐double‐helical structures from achiral γ‐peptides built from α,β‐unsaturated γ‐amino acids have been observed. The crystal structures suggest that they adopted parallel β‐double helical structures and these structures are stabilized by the interstrand backbone amide H‐bonds. Furthermore, both NMR spectroscopy and fluorescence studies support the existence of double‐helical conformations in solution. Although a variety of folded architectures featuring distinct H‐bonds have been discovered from the β‐ and γ‐peptide foldamers, this is the first report to show that achiral γ‐peptides can spontaneously intertwine into β‐double helical structures.     

Substructure isomorphism matrix

A substructure isomorphism matrix n x p contains binary elements describing which of the given p query structures (substructures) are part of the given n target structures (molecular structures). Such a matrix can be used to investigate the diversity of the target structures and allows the characterization and comparison of structural libraries. A quadratic substructure isomorphism matrix n x n is obtained if the same structures are used as molecular structures and as substructures; this matrix contains full information about the topological hierarchy of the n structures. A hierarchical arrangement of chemical structures is useful for the evaluation of results obtained from searches in structure databases.     

Structures and rearrangements of LiCl clusters

Molecular dynamics simulations are used to investigate the low-temperature structures and temperature-driven rearrangements of (LiCl)n clusters, with n ranging from 3 to 500. It is found that for n < or = 32 expanded, ring-based structures are energetically more stable than cubic (rocksalt) forms at low temperature. For n > or = 108, the cubic structures are lower in energy, but as the clusters are heated rearrangements to expanded structures occur well below the melting temperature. Hexagonal (LiCl)3 rings are a distinguishing feature of the expanded, ring-based structures. Highly asymmetric ion sizes are essential for the formation of the expanded structures. Similar transitions from more-ordered to less-ordered solid states are not found for corresponding (KCl)n clusters, which remain in the cubic structure until they melt.     

Demonstrating accuracy of the already proposed protocol for structure elucidation of cyclodextrin inclusion complexes by validation using quantitative ROESY analysis

In this study, we attempt to ascertain the accuracy of the structures determined using our previously developed method and hence the accuracy of our method. In the present report, we have taken the guest molecule cetirizine (CTZ) and the host molecules are α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD). Structures with good accuracy were elucidated using a productive fusion of experimental and computational methods. We performed molecular mechanics studies (MM) in light of experimental ROESY studies, followed by molecular dynamics studies (MD). The results from these studies were analyzed using quantitative ROESY analysis to determine the final accurate structures of the complexes. The accuracy of these structures was tested using density functional theory (DFT) that is an accurate method for structure determination. DFT studies were carried out using the functionals B3LYP and M06L with def-TZVP basis set and similarly quantitative ROESY analysis was performed for the obtained structures. The ROESY intensities of the structures obtained from MM and MD studies, were compared with ROESY intensities of the structures obtained from DFT studies. Calculated ROESY intensities of the structures obtained from B3LYP functional are comparable, with intensities of structures obtained from MM and MD studies, but M06L functional showed poor results. In addition to the accuracy of MM and MD studies, low computational cost and less time input make it good method for structural studies for CD inclusion complexes.

     

A benchtop method for the fabrication and patterning of nanoscale structures on polymers

A benchtop method for the facile production of nanoscale metal structures on polymers is demonstrated. This approach allows for the design and patterning of a wide range of metallic structures on inexpensive polymer surfaces, affording the fabrication of nanoscaled platforms for use in the design of sensors, actuators, and disposable electronic and photonic devices. Numerous structures, from simple nanowires to multilayered metallic gratings, are demonstrated, with sizes ranging from microns to the nanoscale. The process involves molding a malleable metal film deposited on a rigid substrate such as mica, by the compression of a plastic polymer stamp with the desired pattern against the metal film. While under compression, an etchant is then used to modify the metal. Upon separation of the stamp from the support, micro- to nanoscaled metallic structures are found on the stamp and/or on the substrate. The sizes of the structures formed depend on the sizes of the features on the stamp but can be fine-tuned by about 4-fold through variations in both pressure and duration of etching. Also, depending on the processing, multiple dimension metallic structures can be obtained simultaneously in a single stamping procedure. The metallic structures formed on the stamp can also be subsequently transferred to another surface allowing for the construction of multilayered materials such as band gap gratings or the application of electrical contacts. Using this approach, fabrication of both simple and complex micro- to nanoscaled structures can be accomplished by most any researcher as even the grating structure of commercial compact disks may be used as stamps, eliminating the requirement of expensive lithographic processes to form simple structures.     

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.     

Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures

The ability to discriminate native structures from computer-generated misfolded ones is key to predicting the three-dimensional structure of a protein from its amino acid sequence. Here we describe an assessment of semiempirical methods for discriminating native protein structures from decoy models. The discrimination of decoys entails an analysis of a large number of protein structures, and provides a large-scale validation of quantum mechanical methods and their ability to accurately model proteins. We combine our analysis of semiempirical methods with a comparison of an AMBER force field to discriminate decoys in conjunction with a continuum solvent model. Protein decoys provide a rigorous and reliable benchmark for the evaluation of scoring functions, not only in their ability to accurately identify native structures but also to be computationally tractable to sample a large set of non-native models.     

Theoretical infrared spectrum of the ethanol hexamer

The hydrogen bond network of ethanol clusters is among the most complex hydrogen bond networks of molecular clusters. One of the reasons of its complexity arises from the number of possible ethanol monomers (there are three isoenergetic isomers of the ethanol monomer). This leads to difficulties in the exploration of potential energy surfaces (PESs) of ethanol clusters. In this work, we have explored the PES of the ethanol hexamer at the MP2/aug-cc-pVDZ level of theory. We have provided structures and their relative stability at 0 K and for temperatures ranging from 20 to 400 K in the gas phase. These structures are used to compute the theoretical infrared (IR) spectrum of the ethanol hexamer at the MP2/aug-cc-pVDZ level of theory. As a result, 98 different structures have been investigated, and six isomers are reported to be the most isoenergetically stable structures of the ethanol hexamer. These isomers are folded cyclic structures in which the stability is enhanced by the implication of CH⋯O interactions. Our investigations show that the PES of the ethanol hexamer is very flat, yielding several isoenergetic structures. Furthermore, we have noted that several isomers contribute to the population of the ethanol hexamer at high temperatures. As far as the IR spectroscopic study is concerned, we have found that the IR spectra of the most stable structures are in good agreement with the experiment. Considering this agreement, these structures are used to assign the experimental peaks in the CH-stretching region. We concluded that the stability of the structures of the ethanol hexamer is related both to OH⋯O hydrogen bonds and CH⋯O interactions. Overall, we have found that the IR spectrum of the ethanol hexamer, calculated from the contribution of all the possible stable structures weighted by their probability, excellently reproduce the experimental spectrum of the ethanol hexamer.     

Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops

A method has been developed for minimizing the energy of a polypeptide with rigid geometry while keeping all disulfide loops closed exactly. Exact closure of disulfide loops implies that some dihedral angles become implicit functions of the remaining dihedral angles in the polypeptide; the efficacy of the method is related to the manner in which the implicitly defined dihedral angles are chosen. The method has been used to find minimum-energy conformations of bovine pancreatic trypsin inhibitor, ribonuclease A, crambin, the defensin HNP3 dimer, and ω-conotoxin. For the first two proteins, the starting conformations for energy minimization had been derived previously from crystal structures using pseudopotentials to keep the disulfide loops almost closed. Starting conformations for the remaining three proteins were derived from their crystal or NMR structures by similar procedures. In all cases, the energy-minimized structures had a significantly and, in some cases, substantially, lower energy than the starting structures. The RMS deviations between the exactly closed energy- minimized structures and the crystal or NMR structures from which they were derived ranged from 0.9 Å to 1.9 Å, suggesting that the computed structures can serve as “regularized” native structures for these proteins. The energy of a ribonuclease derivative lacking the 65–72 disulfide bridge was minimized using the procedure; the result showed that this derivative has a low-energy structure with a conformation very close to that of native ribonuclease, and is consistent with its postulated role in the folding of ribonuclease. These results offer strong support for the validity of the rigid-geometry model in the studies of the conformational energy of proteins. © 1997 by John Wiley & Sons, Inc.     

Review of structures in low-energy bremsstrahlung: Classical and quantum descriptions

A brief review of recent advances in studying structures in energy dependence of the bremsstrahlung cross sections for low incident electron energies is presented. Examples of structures are given in both classical and quantum formalisms. It is shown that the origin of the structures can be formulated as a lack of contribution to the radiation from electrons with certain angular momenta at certain energies. In quantum mechanics the lack of contribution to the total cross section from certain electron angular momenta is due to zeroes in corresponding dipole matrix elements. In classical mechanics summation over angular momentum is replaced by integration and structures are due to suppressed or enhanced contribution from certain intervals of angular momentum. A survey of the known properties of the matrix elements’ zeroes is given.     

Ti-Al系金属间化合物的价电子结构分析

1　引言ＴｉＡｌ系金属间化合物因具有良好的高温性能与很低的密度在未来航空航天及兵工等方面有着美好的应用前景,但由于极低的室温脆性使其真正投入商用仍很困难.脆性一直是材料科学所关注的问题,这些年来虽在这方面做了大量工作,但大多研究仍停留在实验规律上[1].为深入理解脆性,从物理机理特别是化学键本质上探讨已势在必行.近年来已有人[2]从电子结构或电荷密度分布来解释ＴｉＡｌ的脆性本质,也有人[3]从价电子结构来分析Ｔｉ3Ａｌ的强韧性,但就整个ＴｉＡｌ系金属间化合物的全面分析而言,这些工作还缺乏系统性.固体与分子经验电子理论…     

DNA triangles and self-assembled hexagonal tilings

We have designed and constructed DNA complexes in the form of triangles. We have created hexagonal planar tilings from these triangles via self-assembly. Unlike previously reported structures self-assembled from DNA, our structures appear to involve bending of double helices. Bending helices may be a useful design option in the creation of self-assembled DNA structures. It has been suggested that DNA self-assembly may lead to novel materials and efficient computational devices.     

硅氧团簇(SiO2)nO2H4的密度泛函理论研究

提出硅氧团簇(SiO2)nO2H4的两种新构型: 基于笼状结构和环状结构的构型, 并与链状构型相比较, 用密度泛函理论的B3LYP方法在6-31G(d)基组水平上计算了三种构型n=2～22(n取偶数)的几何结构、平均结合能、能隙以及能量的二次差分. 分析计算结果发现, 笼状构型不但在n=4和8处存在幻数团簇(实验上已经观察到), 而且预测在n=14处也存在类似的幻数团簇; 此外, 与(SiO2)n团簇不同的是, (SiO2)nO2H4团簇的环状构型的稳定性从n=4开始大于链状构型, 意味着水的加成对硅氧团簇的稳定性有着重要的影响.     

Annual variation of the angular distribution of the UV beneath public shade structures

Local governments provide many shade structures at parks and sporting ovals for public use. However, the question remains of how effective are public shade structures at reducing biologically effective UV radiation throughout the year? Broadband measurements of the angular distribution of scattered UV beneath three specific public shade structures was conducted for relatively clear skies and for a solar zenith angle (SZA) ranging from 13 degrees to 76 degrees. The ultraviolet protection factors (UPF) for the shade structures ranged from 18.3 to 1.5 for an increasing SZA. Measurements showed that the horizontal plane received the highest SUV levels from the SZA of 28 degrees to 75 degrees, 42 degrees to 76 degrees, and 50 degrees to 76 degrees for the small, medium and large structures, respectively. This was due to the angle of the sun causing the shade created by the shade structure to be outside the structure. For the small shade structure, the measurements directed to the west were the highest levels in the shade after approximately 28 degrees. For the medium and large shade structures, the measurements directed to the west and south were the highest levels in the shade after roughly 42 degrees and 50 degrees, respectively.     

柔软的球状和长方体状氧化硅中空结构的制备研究

采用自组装形成的芘纳米结构作为模板,成功地制备了柔软的球状和长方体状氧化硅中空结构.当不同量的芘在十六烷基三甲基溴化铵(CTAB)溶液中自组装时,产生的自组装结构展现出明显的从球状到长方体状的形貌变化.这些结构被用作氧化硅前驱体溶胶-凝胶反应的模板,获得了球状和长方体状氧化硅/芘复合结构.通过乙醇除去模板后,生成了柔软的球状(直径约为400nm)和长方体状(长为0.5—2.5μm)的氧化硅中空结构.这些结果展现了采用有机纳米结构作为模板来合成无机中空结构的优势:合成简便、结构多样以及结构形貌的灵活可控.     

氨甲酰基硅烷与硝酮的反应及产物的互变异构

氨甲酰基硅烷可以与硝酮反应, 合成α-(N′-甲基-Ｎ′-三甲基硅氧基)氨基-N,N-二甲基苯乙酰胺(5). 经研究发现, 该产物具有互变异构现象, 提出了这一互变异构体的结构, 并通过1H NMR谱在不同温度(55～－30 ℃)下的数据, 证实了指定结构的存在: 在55 ℃时, 呈现结构(5)的形式; 而在－30 ℃时, 呈现结构(8)的形式, 它们互变的中间体结构则在55～－30 ℃之间随温度的变化而变化.     

De novo glycan structural identification from mass spectra using tree merging strategy

MotivationGlycans are large molecules with specific tree structures. Glycans play important roles in a great variety of biological processes. These roles are primarily determined by the fine details of their structures, making glycan structural identification highly desirable. Mass spectrometry (MS) has become the major technology for elucidation of glycan structures. Most de novo approaches to glycan structural identification from mass spectra fall into three categories: enumerating followed by filtering approaches, heuristic and dynamic programming-based approaches. The former suffers from its low efficiency while the latter two suffer from the possibility of missing the actual glycan structures. Thus, how to reliably and efficiently identify glycan structures from mass spectra still remains challenging.ResultsIn this study we propose an efficient and reliable approach to glycan structure identification using tree merging strategy. Briefly, for each MS peak, our approach first calculated monosaccharide composition of its corresponding fragment ion, and then built a constraint that forces these monosaccharides to be directly connected in the underlying glycan tree structure. According to these connecting constraints, we next merged constituting monosaccharides of the glycan into a complete structure step by step. During this process, the intermediate structures were represented as subtrees, which were merged iteratively until a complete tree structure was generated. Finally the generated complete structures were ranked according to their compatibility to the input mass spectra. Unlike the traditional enumerating followed by filtering strategy, our approach performed deisomorphism to remove isomorphic subtrees, and ruled out invalid structures that violates the connection constraints at each tree merging step, thus significantly increasing efficiency. In addition, all complete structures satisfying the connection constraints were enumerated without any missing structure. Over a test set of 10 N-glycan standards, our approach accomplished structural identification in minutes and gave the manually-validated structure first three highest score. We further successfully applied our approach to profiling and subsequent structure assignment of glycans released from glycoprotein mAb, which was in perfect agreement with previous studies and CE analysis.