Academic literature on the topic 'Hydrogen Bond Length'
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Journal articles on the topic "Hydrogen Bond Length"
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Ferraris, G., and G. Ivaldi. "Bond valence vs bond length in O...O hydrogen bonds." Acta Crystallographica Section B Structural Science 44, no. 4 (August 1, 1988): 341–44. http://dx.doi.org/10.1107/s0108768188001648.
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Chandler, Graham S., Magdalena Wajrak, and R. Nazim Khan. "Neutron diffraction structures of water in crystalline hydrates of metal salts." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 71, no. 3 (May 26, 2015): 275–84. http://dx.doi.org/10.1107/s2052520615005387.
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Neutron diffraction structures of water molecules in crystalline hydrates of metal salts have been collected from the literature up to December 2011. Statistical methods were used to investigate the influence on the water structures of the position and nature of hydrogen bond acceptors and cations coordinated to the water oxygen. For statistical modelling the data were pruned so that only structures with oxygen as hydrogen acceptors, single hydrogen bonds, and no more than two metals or hydrogens coordinated to the water oxygen were included. Multiple linear regression models were fitted with the water OH bond length and bond angle as response variables. Other variables describing the position and nature of the acceptors and ions coordinated to the waters were taken as explanatory variables. These variables were sufficient to give good models for the bond lengths and angles. There were sufficient structures involving coordinated Mg^{2+} or Cu^{2+} for a separate statistical modelling to be done for these cases.
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ZHANG, FANGFANG, and DONGFENG XUE. "CHEMICAL BONDING BEHAVIORS OF N—H⋯O HYDROGEN BONDS OF ${\rm{NH}}_4^ + \cdots {\rm{O}}$ SYSTEMS IN INORGANIC CRYSTALS." Modern Physics Letters B 23, no. 31n32 (December 30, 2009): 3943–50. http://dx.doi.org/10.1142/s0217984909022046.
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The original length d0 of N — H and H ⋯ O bonds in various inorganic [Formula: see text] systems was comprehensively studied from a chemical bond viewpoint. Two linear relationships between d0 and the average bond lengths of each [Formula: see text] system, d0, N - H , versus [Formula: see text] and d0, H ⋯ O versus [Formula: see text] were respectively established. It is indicated that d0 is affected by the crystalline environment evidently, therefore, the valence electron distribution of hydrogen atom which depends on the lengthening degree of the original bond length is strongly affected by the chemical environment of hydrogen atoms. The obtained valence electron distributions of hydrogen are in a good agreement with the bond valence sum rule, and their overall applicability to ammonium ion interactions was discussed.
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Корабельников, Д. В., and Ю. Н. Журавлев. "Структура и колебательные свойства гидратов оксианионных кристаллов из первых принципов." Физика твердого тела 60, no. 10 (2018): 2014. http://dx.doi.org/10.21883/ftt.2018.10.46533.072.
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AbstractStructural parameters and IR spectra of hydrates of lithium and sodium perchlorates, calcium sulfate hydrate (gypsum), and lithium nitrate hydrate are calculated ab initio using the density functional theory. The bond lengths in the water molecules are established as functions of length and energy of hydrogen bonds. The relationship between lengths of intra-anionic and hydrogen bonds is considered. The splitting of intramolecular vibrations of water is highlighted. The stretching vibration frequency of water is determined as a function of length and energy of hydrogen bonds. The combined (mixed) vibrations of anions and molecules of water with frequencies below 1400 cm^–1 are feasible as well.
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Olesen, Solveig Gaarn, and Steen Hammerum. "Redshift or Adduct Stabilization—A Computational Study of Hydrogen Bonding in Adducts of Protonated Carboxylic Acids." European Journal of Mass Spectrometry 15, no. 2 (April 2009): 239–48. http://dx.doi.org/10.1255/ejms.970.
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It is generally expected that the hydrogen bond strength in a D–H•••A adduct is predicted by the difference between the proton affinities (Δ PA) of D and A, measured by the adduct stabilization, and demonstrated by the infrared (IR) redshift of the D–H bond stretching vibrational frequency. These criteria do not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The Δ PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength.
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Stenfors, Brock A., Richard J. Staples, Shannon M. Biros, and Felix N. Ngassa. "Crystal structure of 1-[(4-methylbenzene)sulfonyl]pyrrolidine." Acta Crystallographica Section E Crystallographic Communications 76, no. 3 (February 28, 2020): 452–55. http://dx.doi.org/10.1107/s205698902000208x.
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The molecular structure of the title compound, C11H15NO2S, features a sulfonamide group with S=O bond lengths of 1.4357 (16) and 1.4349 (16) Å, an S—N bond length of 1.625 (2) Å, and an S—C bond length of 1.770 (2) Å. When viewing the molecule down the S—N bond, both N—C bonds of the pyrrolidine ring are oriented gauche to the S—C bond with torsion angles of −65.6 (2)° and 76.2 (2)°. The crystal structure features both intra- and intermolecular C—H...O hydrogen bonds, as well as intermolecular C—H...π and π–π interactions, leading to the formation of sheets parallel to the ac plane.
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Cornilescu, Gabriel, Benjamin E. Ramirez, M. Kirsten Frank, G. Marius Clore, Angela M. Gronenborn, and Ad Bax. "Correlation between3hJNC‘and Hydrogen Bond Length in Proteins." Journal of the American Chemical Society 121, no. 26 (July 1999): 6275–79. http://dx.doi.org/10.1021/ja9909024.
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Ueda, Takahiro, Shigenori Nagatomo, Hirotsugu Masui, Nobuo Nakamura, and Shigenobu Hayashi. "Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations." Zeitschrift für Naturforschung A 54, no. 6-7 (July 1, 1999): 437–42. http://dx.doi.org/10.1515/zna-1999-6-715.
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Abstract Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.
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XIONG, ZICHANG, JUN GAO, DONGJU ZHANG, and CHENGBU LIU. "HYDROGEN BOND NETWORK OF 1-ALKYL-3-METHYLIMIDAZOLIUM IONIC LIQUIDS: A NETWORK THEORY ANALYSIS." Journal of Theoretical and Computational Chemistry 11, no. 03 (June 2012): 587–98. http://dx.doi.org/10.1142/s0219633612500381.
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Hydrogen bond is a key factor in the determination of structures and properties of room-temperature ionic liquids. Connections of these hydrogen bonds form a network. In this work, we analyzed the hydrogen bond network of 1-alkyl-3-methylimidazolium ionic liquids using network theory. A two-dimensional view of the hydrogen bond network has been generated, the connection pattern shown that the average length of line shape connection is 2.44 to 2.77 for six 1-alkyl-3-methylimidazolium ionic liquids, and the connection patterns are different for short and long alkyl side chain length. The degree of each ion was calculated and analyzed. The nodes with zero degree were adopted to detect the boundary of the clusters in the ionic liquids, which have no hydrogen bond connected with neighbor ions. This work indicates that the network analysis method is useful for understanding and predicting the structure and function of RTILs.
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Tiritiris, Ioannis, Stefan Saur, and Willi Kantlehner. "Crystal structure of (ethoxyethylidene)dimethylazanium ethyl sulfate." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (November 7, 2015): o916. http://dx.doi.org/10.1107/s2056989015020678.
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In the title salt, C6H14NO+·C2H5SO4−, the C—N bond lengths in the cation are 1.2981 (14), 1.4658 (14) and 1.4707 (15) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.3157 (13) Å shows double-bond character, indicating charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H...O hydrogen bonds between H atoms of the cations and O atoms of neighbouring ethyl sulfate anions are present, generating a three-dimensional network.
Dissertations / Theses on the topic "Hydrogen Bond Length"
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Alessi, Dario <1990>. "Reviewing interactions between uranyl’s oxygen atom, hydrogen, p block elements, and their effects in uranium-oxygen bond length." Master's Degree Thesis, Università Ca' Foscari Venezia, 2020. http://hdl.handle.net/10579/18359.
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Thanks to the Cambridge Structural Database, in this thesis work has been selected several uranyl’s ion crystal structures, which share interactions between uranyl’s oxygen and block p elements, or hydrogen. These interactions belong to hydrogen bond, chalcogen and halogen bond or, in a more generic way, short contact interactions. In order to select the structures, the research fields were limited for certain elements to a value within their Van der Waals peak. It was evaluated the influence that these interactions provide to the uranyl’s ion bond length (U=Oyl) from two points of view: a) by considering the type of interacting element and b) by considering the type of donor atom in equatorial position. The data collected were also used to verify the existence of a trend that correlates the interaction length, or nature of equatorial ligands, to the uranyl’s bond length. A comparation between the IR and Raman data, provided by the original works, completes the overview. In conclusion, the main synthetic routes to achieve the structures analysed in this research were highlighted.
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Safsaf, Abdelaziz. "Etude structurale par diffraction des rayons x d'un phosphonate et de quelques hydroxydiphosphonates." Paris 13, 1989. http://www.theses.fr/1989PA132001.
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Pour les acides phosphoniques, diphosphoniques et diphosphonates organiques acides, la corrélation entre la longueur p-oh et la distance oh. . . O est linéaire. Les molécules d'éthanédiphosphonate-1,1 (hydroxy-1 "0,0,0',o'"-tetramethyl) et les molécules dérivées, possedent une relative flexibilité (corrélation linéaire entre l'angle p-c-p et le décalage des deux groupes acides phosphoniques)
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Kuo, Li-Hung, and 郭禮閎. "Effect of Lysine Side Chain Length at Non-Hydrogen Bonded Strand Positions on β-Hairpin Stability and Toward Introducing a Hydrogen Bond Surrogate at the N-Terminus of Rev Peptide on RNA Recognition." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/35294568871900306564.
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碩士國立臺灣大學
化學研究所
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There are many factors that contribute to protein folding and structure stability: intrinsic propensity of amino acids, side chain ion pairing interaction, hydrophobic effect, hydrogen bonding, van der Waals interaction. In this study, we focused on the effect of lysine side chain length on sheet propensity at a non-hydrogen bonded strand position in β-hairpin. The β-hairpin peptides HPTAlaXaa (Xaa= Dap, Dab, Orn, Lys) were designed with the side chain of Lys9 systematically shortened to investigate the effect of Lys side chain length on sheet propensity. The peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. All peptides were purified to 95% purity and were analyzed by 2D NMR experiments. Sequence specific assignment was performed. The hairpin structures were confirmed by chemical shift deviation, 3JHNα coupling constants,and NOE signals.The fraction folded and ΔG of peptides were derived by comparing the chemical shifts with the fully folded and unfolded reference peptides. The percent folding of HPTAlaXaa peptides with Lys analogs at the guest position followed the trend: HPTAlaDap ~ HPTAlaDab < HPTAlaOrn ~ HPTAlaLys, showing that the longer the Lys analogue side chain, the more stable the β-haiprin structure. The HIV Rev protein binds RRE RNA to regulate the transport of unspliced and spliced mRNA from the nucleus to the cytoplasm posttranscriptionally. The Rev peptide is a random-coil. However, the conformation of the Rev peptide changes to an α-helix while binding to RRE RNA. Hydrogen bond surrogate (HBS) is one of the several cross-linking systems for stabilizing an α-helix, using the covalent bond C=C-C-N to substitute the C=O…H-N (i, i+4) hydrogen bond in a short helix. In order to synthesize an HBS peptide, strategy for synthesis of dipeptides that contained an allyl group on the amino group was designed and refined. Two wild type Rev peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. The secondary structure of the two peptides was random-coil analyzed by circular dichroism spectroscopy. The binding specificity of the Rev peptides was determined by gel shift assay. The dissociation constants of the Rev peptides were similar to previous studies.
Book chapters on the topic "Hydrogen Bond Length"
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Kubelka, Jan, Petr Bour, R. A. Gangani D. Silva, Sean M. Decatur, and Timothy A. Keiderling. "Chirality in Peptide Vibrations: Ab Initio Computational Studies of Length, Solvation, Hydrogen Bond, Dipole Coupling, and Isotope Effects on Vibrational CD." In ACS Symposium Series, 50–64. Washington, DC: American Chemical Society, 2002. http://dx.doi.org/10.1021/bk-2002-0810.ch004.
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Libowitzky, Eugen. "Correlation of O-H Stretching Frequencies and O-H O Hydrogen Bond Lengths in Minerals." In Hydrogen Bond Research, 103–15. Vienna: Springer Vienna, 1999. http://dx.doi.org/10.1007/978-3-7091-6419-8_7.
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Kamal Kant Arya, Rajeshwar, Arun Kumar, Anchala Guglani, Dheeraj Bisht, and Deepak Kumar. "Chromene as Antioxidants." In The Role of Chromenes in Drug Discovery and Development, 215–24. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815124330123010012.
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Chromene is a heterocyclic compound that contains oxygen in its ring. It is widely obtained naturally from both animals and plants, and it is an integral part of alkaloids, tocopherol, anthocyanins, and flavonoids. The 2-oxo-2H-chromene is called coumarins, and coumarins have excellent antioxidant potential due to the presence of the phenol group, more than 1300 coumarins have been identified to date. The chromene scaffold in coumarins has the structural modification ability that makes it the structure of choice for medicinal purposes. Various medicines can be synthesized by using a chromene scaffold e.g. asthma, hypertension, antifungal, and antimicrobial. Chromene shows a good antioxidant potential that depends on its hydrogen ion.releasing capacity and stabilizes hydrogen with the help of a high resonating structure. The bond length between bonds also enhances the free radical scavenging function. In this chapter, we have discussed some chromene derivatives and their antioxidant potential, and the effect of cyclic structure on the antioxidant’s function.
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Bunker, Bruce C., and William H. Casey. "The Structure and Properties of Water." In The Aqueous Chemistry of Oxides. Oxford University Press, 2016. http://dx.doi.org/10.1093/oso/9780199384259.003.0008.
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Water is one of the most complex fluids on Earth. Even after intense study, there are many aspects regarding the structure, properties, and chemistry of water that are not well understood. In this chapter, we highlight the attributes of water that dictate many of the reactions that take place between water and oxides. We start with a single water molecule and progress to water clusters, then finally to extended liquid and solid phases. This chapter provides a baseline for evaluating what happens when water encounters simple ions, soluble oxide complexes called hydrolysis products, and extended oxide phases. The primary phenomenon highlighted in this chapter is hydrogen bonding. Hydrogen bonding dominates the structure and properties of water and influences many water–oxide interactions. A single water molecule has eight valence electrons around a central oxygen anion. These electrons are contained in four sp3-hybridized molecular orbitals arranged as lobes that extend from the oxygen in a tetrahedral geometry. Each orbital is occupied by two electrons. Two of the lobes are bonded to protons; the other two lobes are referred to as lone pairs of electrons. The H–O–H bond angle of 104.5° is close to the tetrahedral angle of 109.5°. The O–H bond length in a single water molecule is 0.96 Ǻ. It is important to recognize that this bond length is really a measure of the electron density associated with the oxygen lone pair bonded to the proton. This is because a proton is so incredibly small (with an ionic radius of only 1.3·10−5 Ǻ) that it makes no contribution to the net bond length. The entire water molecule has a hard sphere diameter of 2.9 Ǻ, which is fairly typical for an oxygen anion. This means the unoccupied lone pairs are distended relative to the protonated lone pairs, extending out to roughly 1.9 Ǻ. The unequal distribution of charges introduces a dipole within the water molecule that facilitates electrostatic interactions with other molecules.
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Coppens, Philip. "Chemical Bonding and the X-ray Scattering Formalism." In X-Ray Charge Densities and Chemical Bonding. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195098235.003.0005.
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The assumption that the atomic electron density is well described by the spherically averaged density of the isolated atom has been the basis of X-ray structure analysis since its inception. The independent-atom model (IAM) is indeed a very good approximation for the heavier atoms, for which the valence shell is a minor part of the total density, but is much less successful for the lighter atoms. The lightest atom, hydrogen, has no inner shells of electrons, so that the effect of bonding is relatively pronounced. Because of the overlap density in covalent X—H bonds (X = C, N, O), the mean of the hydrogen electron distribution is significantly displaced inwards into the bond. When a spherical IAM hydrogen scattering factor is used in a least-squares adjustment of the atomic “position,” the result will be biased because the centroid of the density associated with the H atom is shifted in the direction of the bond. The result is an apparent shortening of X—H bonds which is far beyond the precision of X-ray structure determination (Hanson et al. 1973). For sucrose, for example, the differences between X-ray and neutron bond lengths are 0.13 (1) Å averaged over 14 C—H bonds, and 0.18 (3) A averaged over eight O—H bonds (Hanson et al. 1973). The observed discrepancy between X-ray results and spectroscopic values was first explained in terms of the electron distribution in the 1950s by Cochran (1956) and Tomii (1958). That the bond density is also of significance for heavier atoms is evident from the occurrence of the spherical-atom forbidden (222) reflection of diamond and silicon, even at low temperatures where anharmonic thermal effects (see chapter 2) are negligible. The historical importance of the nonzero intensity of the diamond (222) reflection is illustrated by the following comment made by W. H. Bragg, in 1921: . . . Another point of interest is the existence of a small (222) reflection (in diamond). This has been looked for previously but without success. . . .
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Finney, John. "3. Water as ice(s)." In Water: A Very Short Introduction, 24–45. Oxford University Press, 2015. http://dx.doi.org/10.1093/actrade/9780198708728.003.0003.
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‘Water as ice(s)’ describes the sixteen known crystalline phases of ice, starting with normal ice, as well as a potential seventeenth phase called cubic ice, for which they may be evidence elsewhere in the universe. The different crystalline structures of ice are shown on a phase diagram that depicts how changes in pressure and temperature affect the structure of ice. The Bernal–Fowler rules of ice structures are also explained. Ordered arrangements of water molecules all show four-coordinated geometry, but water shows great molecular versatility under pressure: hydrogen bond lengths and OOO angles can vary when forming the high pressure ice structures.
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Dispinar, Derya. "Melt Quality Assessment." In Encyclopedia of Aluminum and Its Alloys. Boca Raton: CRC Press, 2019. http://dx.doi.org/10.1201/9781351045636-120052503.
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It is well known that the reaction of liquid aluminum with the moisture in the environment results in two products: aluminum oxide and hydrogen gas that dissolves in aluminum. Both of these products are considered to be detrimental to the properties of aluminum alloys. Therefore, test equipment has been developed to check the levels of these defects in the melt. Many of these involve expensive and consumable tools. In addition, an experienced personnel may be required to interpret the results. Nonetheless, aluminum oxide is harmless as long as it remains on the surface. The problem begins when this oxide is entrained into the liquid aluminum such as turbulence during transfer or mold filling in a non-optimized design. This can only happen by folding of the oxide. During this action, rough surface of the oxides comes in contact to form no bonds. These defects are known as bifilms that have certain characteristics. First, they act as cracks in the cast parts since they are oxides. It is important to note that aluminum oxide has thin amorphous oxide (known as young oxides) and thick crystalline oxide (γ-Al2O3) that may be formed in a casting operation. Second, almost zero force is required to open these bifilms due to the unbonded folded oxide skins. Thus, these defects can easily form porosity by unravelling during solidification shrinkage. On the other hand, the formation of porosity by hydrogen is practically impossible. Theoretically, hydrogen has high solubility in the liquid but it has significantly low solubility in solid aluminum. Thus, it is suspected that hydrogen is rejected from the solidification front to form hydrogen gas and porosity. However, the hydrogen atom has the smallest atomic radii and high diffusibility. Therefore, segregation of hydrogen in front of the growing solid is difficult. In addition, the energy required for hydrogen atoms to segregate and form hydrogen gas molecule is around 30,000 atm. Under these conditions, porosity formation by hydrogen is not likely to be achieved. Hydrogen probably stays in a supersaturated state or diffuses homogeneously through the cast part. The effect of hydrogen can only be seen when it can diffuse into the unbonded gap between the bifilms to open them up to aid the unravelling of bifilms to form porosity. This phenomenon can be easily detected by a very simple test called reduced pressure test. When a sample is solidified under vacuum, the bifilms start to open up. Since all porosity is formed by bifilms, the cross section of the sample solidified under vacuum can be analyzed by means of image analysis software. The sum of maximum length of pores can be measured as an indication of melt quality. Since bifilms are the most detrimental defects, this value is called “bifilm index” given in millimetres, which makes this test the only test that can quantify aluminum melt quality in such detail including both the effects of bifilms and hydrogen together. Several Al-Si alloys were used at various conditions: degassing with lance, ceramic diffusers, and graphite rotary has been compared. Gravity sand casting, die casting, and low-pressure die casting methods were evaluated. The effect of grain refiners and modifiers was studied. And the evolution of the bifilm index has been presented.
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White, Perrin C. "Genes and Hormones." In Textbook of Endocrine Physiology. Oxford University Press, 2011. http://dx.doi.org/10.1093/oso/9780199744121.003.0005.
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Much of the knowledge presented in the following chapters has been gained using molecular genetic techniques to analyze the structure, synthesis, regulation, and effects of hormones. This chapter provides an overview of some of the relevant techniques and associated concepts. To allow the reader to understand older experiments, we have tried to include techniques that are now of mainly historical interest as well as current concepts. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) consist of nucleotides . A nucleotide consists of a base , a sugar moiety (either deoxyribose or ribose), and a phosphate group. The sugars and phosphates alternate in the backbone of a nucleic acid strand. In general, there are four possible bases. In DNA, these are adenine ( A ), cytosine ( C ), guanine ( G ), and thymine ( T ). Adenine and guanine are purines , whereas cytosine and thymine are pyrimidines . The corresponding nucleotides are adenosine , cytidine , guanosine , and thymidine. In RNA, uracil (uridine) is substituted for thymine (thymidine). DNA is double stranded. Each strand has a direction because the deoxyribose molecules forming the backbone are asymmetrical, with the phosphate bonds linking each two sugar molecules going from the 3’ position of one to the 5’ position of the next. Thus, the 5’ position of a sugar molecule is free at one end (the 5’ end) of the strand, and the 3’ position is free at the other. The two strands of a DNA molecule run in opposite directions, so that the 5’ end of one strand is opposed to the 3’ end of the complementary strand. The DNA strands interact with each other through complementary (Watson-Crick) base pairing , in which A and T, or C and G, are paired through hydrogen bonds. Thus, the sequence of one DNA strand unambiguously determines the sequence of the complementary strand during DNA replication. The length of a DNA segment is typically given in bases or nucleotides (nt) or, if double stranded, base pairs (bp).
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Mark, James E., Harry R. Allcock, and Robert West. "Ferrocene-Based Polymers, and Additional Phosphorus- and Boron-Containing Polymers." In Inorganic Polymers. Oxford University Press, 2005. http://dx.doi.org/10.1093/oso/9780195131192.003.0010.
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Ferrocene is an inexpensive, stable molecule with an interesting and reversible electrochemistry. It is synthesized by the metal-hydrogen exchange reaction of cyclopentadiene with sodium followed by treatment of the resultant sodium cyclopentadienide anion with ferrous chloride. The high stability and electroactivity of the ferrocene molecule has prompted numerous attempts to incorporate it into polymer structures. So, too, has the inherent torsional freedom of the cyclopentadienyl groups around the iron atoms and their capacity to serve as swivel group sites. Polymerization attempts range from the addition reactions of vinylferrocene and its derivatives, to condensation reactions, ringopening polymerizations, and dendrimer assemblies. These will be considered in turn. Considerable effort in the 1970s by Pittman, George, Hayes, Korshak, and others was applied to exploring the addition polymerization of vinylferrocene to give organic polymers with pendent ferrocenyl side groups. This type of polymerization reaction has been attempted with the use of free radical, cationic, anionic, and Ziegler–Natta methods. For free radical polymerization reactions, the initiating radicals must be generated from azo-initiators because peroxides cause oxidation of the metal. In polymerizations of the type shown in reaction (2) the side group ferrocene units are the source of both the thermal stability of the product polymers and complications inherent in the free radical polymerization process. For example, electron donation from the iron atoms to a growing radical chain end can convert an active radical to an anion, which terminates the polymerization. The Fe+ center then rearranges to form a paramagnetic, ionically bound Fe(III) species. Ultimately this leads to extensive chain-transfer, limitation of the chain length, and formation of branched structures. This does not occur if the ferrocene unit is insulated from the vinyl group by a spacer unit, as in, because these monomers polymerize normally. For example, monomer gives polymers with Mn molecular weights as high as 250,000. However, the electron-transfer process outlined in reaction (2) has serious practical consequences in the free-radical polymerization of. First, directly or indirectly, it causes precipitation of the growing polymer chains until, at monomer to polymer conversions of 90% or more, all of the polymeric product is insoluble in most organic solvents.
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Dyall, Kenneth G., and Knut Faegri. "Relativistic Effects on Molecular Bonding and Structure." In Introduction to Relativistic Quantum Chemistry. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195140866.003.0030.
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Having covered much of the theory relevant to relativistic quantum chemistry, the logical next step would be to turn to the application of this theory in the calculation of chemical phenomena and in the interpretation of experimental data. We shy away from this task for the reason that research and development in the field have increased greatly over the past decades, and with the present level of activity, even doubling the volume of this book might not do justice to much of the excellent work being done in this field. Also, the present publication rates and tempo of developments would probably make much of our analysis obsolete or incomplete within a short time. Fortunately, the specialist literature has been reviewed quite frequently, and with the theoretical background from the previous sections of this work this wealth of information should be accessible to the reader. A good overview can be found in the volumes edited by Schwerdtfeger (2002, 2004). The bibliographies of Pyykkö (1986, 1993, 2000) should also be consulted to locate the relevant literature sources. There is, however, one area that we feel deserves some extra attention. This is the theory of bonding and structure in molecules. So far most of what we have presented could be regarded as pertaining as much to atomic physics as to quantum chemistry. Molecules have mainly appeared through the discussion of the molecular point groups and their treatment within the various schemes. Molecular orbital theory, valence bonding, and hybridization are concepts that are central to our understanding of molecular bonding and structure. In this final chapter, we therefore discuss how these concepts are influenced by relativity and what changes this might cause in the parameters we observe, such as valencies, bond lengths, vibrational frequencies, dissociation energies, and reaction barriers. Our concepts of molecules are based on our concepts of atoms. Molecular orbitals are conveniently viewed in terms of linear combinations of atomic orbitals. Thus, our understanding of relativistic effects on bonding should start with an understanding of the relativistic effects on atomic spinors. In chapter 7, we found that the mean radius of a hydrogenic spinor decreased due to relativistic effects.
Conference papers on the topic "Hydrogen Bond Length"
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Wang, Ying, and Youping Chen. "An Atomic Model of Cellulose Network in Wood Cell Wall." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-67603.
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Wood is composed of parallel columns of long hollow cells which are made up of layered composite of semi-crystalline cellulose fibrils embedded in an amorphous matrix of hemicellulose and lignin. The extraordinary mechanical performance of wood is believed to result from a molecular mechanism operated through hydrogen bond connection. However, the molecular interactions, the assembly method of cell-wall components, as well as the molecular mechanisms responsible for the deformation of wood, are not well understood yet. Progress in studying the superior mechanical properties of wood cell is severely hindered because of this fact. To overcome this barrier, the foremost step is to build up an atomic model of the native cellulose fibril network, which is the dominant polysaccharide in wood cell walls. Then, in this work, we proposed the atomic models to study the cellulose network which includes a single cellulose microfibril (MF), and a thin film which is built up by first secondary layers (S1) and second secondary layers (S2) composed of cellulose MF with periodic boundary conditions. Additionally, we investigated the length effect of the microfibril and compared the effect of explicit water solvent environment with the vacuum environment. Moreover, the spatial arrangements of these atomic models have been determined by molecular mechanics simulation (energy minimization). The hydrogen bond length of the crystalline part of the inner cellulose was evaluated using first principle calculation.
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McCoy, Anne, and Sotiris Xantheas. "EXPLORING THE RELATIONSHIPS BETWEEN ANHARMONICITY AND OH BOND LENGTHS IN HYDROGEN BONDED COMPLEXES." In 71st International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2016. http://dx.doi.org/10.15278/isms.2016.tj01.
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Geddes, V. A., G. V. Louie, G. D. Brayer, and R. T. A. MacGillivray. "MOLECULAR BASIS OF HEMOPHILIA B: IDENTIFICATION OF THE DEFECT IN FACTOR IX VANCOUVER." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643872.
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Factor IX Vancouver (fIX-V) is the cause of a moderate form of hemophilia B. An individual presenting with this disorder had 2.6% of normal procoagulant activity in his plasma but had 62% of the normal factor IX antigen level. Specific antibodies showed that fIX-V contains epitopes for both the heavy and light chains of factor IXa. To identify the defect involved, DNA was isolated from the lymphocytes of the male hemophiliac. Southern blot analysis using a full-length factor IX cDNA as a hybridization probe showed no gross differences between the fIX-V gene and the normal factor IX gene. The DNA from the hemophiliac was then partially digested with Sau3A and the resulting fragments (10-20kbp in size) were ligated into the BamHI site of λEMBL3. The DNA was then packaged into phage particles in vitro, and the recombinant phage were screened with the factor IX cDNA as a probe. Eight phage were isolated that contained overlapping DNA covering the complete gene for fIX-V. DNA sequence analysis of the protein-encoding regions, the intron/exon junctions and 5'-and 3'-flanking sequences revealed a single nucleotide change from the normal factor IX gene. The codon for amino acid 397 was changed from ATA (lie) to ACA (Thr). This mutation is in the catalytic domain of factor IXa and is novel amongst those hemophilia B mutations reported to date. Based on the known three dimensional structures of the pancreatic serine proteases, trypsin, elastase and chymotrypsin, models have been constructed for the structures of the catalytic domains of both the normal and Thr-397 mutant of factor IXa. These results suggest that the Thr-397 mutation may alter the conformation of the substrate binding region in the active site of factor IXa Vancouver through the formation of a hydrogen bond between the hydroxyl group of the Thr-397 side chain and the main chain carbonyl group of Trp-385. The postulated conformational change would lead to reduced binding affinity for the factor IXa substrate resulting in a reduction in the catalytic activity of fIXa-Vancouver.Supported in part by grants from the Medical Research Council of Canada (to GDB and RTAM).
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Wiseman, Samuel, Andrea Gruber, and James R. Dawson. "Flame Transfer Functions for Turbulent, Premixed, Ammonia-Hydrogen-Nitrogen-Air Flames." In ASME Turbo Expo 2022: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/gt2022-83298.
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Abstract Ammonia is a promising hydrogen and energy carrier but also a challenging fuel to use in gas turbines, due to its low flame speed, limited flammability range, and the production of NOx from fuel-bound nitrogen. Previous experimental and theoretical work has demonstrated that partially-dissociated ammonia (NH3/H2/N2 mixtures) can match many of the laminar flame properties of methane flames. Among the remaining concerns pertaining to the use of NH3/H2/N2 blends in gas turbines is their thermoacoustic behavior. This paper presents the first measurements of flame transfer functions (FTFs) for turbulent, premixed, NH3/H2/N2-air flames and compares them to CH4-air flames that have a similar unstretched laminar flame speed and adiabatic flame temperature. FTFs for NH3/H2/N2 blends were found to have a lower gain than CH4 FTFs at low frequencies. However, the cut-off frequency was found to be greater, due to a shorter flame length. The results suggest that NH3/H2/N2 blends may excite different thermoacoustic modes in gas turbines. In addition, the dependence of the flame response on forcing amplitude was measured for a forcing frequency of 650 Hz and the linearity of the NH3/H2/N2 flame response up to high forcing amplitudes suggests that particularly high-amplitude limit cycles may occur. For both CH4 flames and NH3/H2/N2 flames the confinement diameter was found to have a strong influence on peak gain values. The effect on the FTF phase was modest, except in the case of extreme confinement, where almost all of the flame is close to the wall, and in the case of a significant change in the flame stabilisation. Chemiluminescence resolved along the longitudinal direction shows a suppression of fluctuations when the flame first interacts with the wall followed by a subsequent recovery, but with a significant phase shift. Nevertheless, simple Strouhal number scalings based on the flame length and reactant bulk velocity at the dump plane result in a reasonable collapse of the FTF cut-off frequency and phase curves.
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Dzhimak, S. S., M. I. Drobotenko, A. A. Svidlo, and A. A. Elkina. "INFLUENCE OF THE 2H/1H ISOTOPE COMPOSITION OF A MEDIUM ON THE PROBABILITY OF BROKENING OF HYDROGEN BONDS BETWEEN BASE PAIRS IN A DNA MOLECULE." In NOVEL TECHNOLOGIES IN MEDICINE, BIOLOGY, PHARMACOLOGY AND ECOLOGY. Institute of information technology, 2022. http://dx.doi.org/10.47501/978-5-6044060-2-1.95-101.
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In this work, the role of single substitutions of protium for deuterium in the formation of bub-bles of open states is studied by mathematical modeling methods. It is shown that the proba-bility of formation of bubbles of a certain length (from 12 to 27 nucleotides) depends on the localization of the deuterium atom in the DNA molecule and may differ significantly from the probability of open states in general.
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Fazio, V. "Supercontraction of spider silks as a humidity-driven phase transition." In AIMETA 2022. Materials Research Forum LLC, 2023. http://dx.doi.org/10.21741/9781644902431-10.
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Abstract. Spider silks have been intensively studied among natural materials for their extreme mechanical properties such as very high strength, ultimate strain, and toughness. Another striking phenomenon characterizing spider silk, known as supercontraction, is a substantial contraction, up to a half of the initial length, occurring when an unconstrained silk thread is exposed to a wet environment. We propose a multiscale model that deduces the hygro-dependent macroscopic behaviour of the spider silks starting from the nano and micro-structure properties of the material. In particular, we describe the influence of humidity at the macromolecular scale by considering the moisture effects disrupting hydrogen-bonds and enabling the decrease of the natural (zero force) end-to-end chains length due to entropic effects. The main novelty of our theoretical approach is a description in the field of solid-solid phase transitions, with the system undergoing a transition driven by humidity from an unfolded, hard dry to a folded, soft wet configuration. Based on a statistical mechanical approach, we are able to describe the temperature dependence of the supercontraction effects and its cooperative properties quantitatively predicting the observed experimental behaviour.
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Rollins, Brandon C., Oliver J. Tarbard, Kenneth E. Bagnoli, and Ramgopal Thodla. "Fracture Toughness Behavior of Carbon Steels in Mildly Sour Waters." In ASME 2021 Pressure Vessels & Piping Conference. American Society of Mechanical Engineers, 2021. http://dx.doi.org/10.1115/pvp2021-63030.
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Abstract Corrosion and cracking of typical materials used in refinery equipment exposed to sour water has long been a concern for the industry [1]. The failure of an amine absorber tower in 1984 heightened the need to understand the performance of these materials in sour water encountered by the industry [2]. This phenomenon is often generically referred to as “wet H2S cracking”, though it includes various forms of damage. In the years following the absorber tower failure numerous studies were undertaken to understand the performance of typical pressure vessel steels exposed to sour water including fracture toughness testing in NACE A or NACE B solutions [3]. NACE A and B solutions are significantly more aggressive solutions (lower pH and higher Hydrogen Sulfide [H2S] concentration) than most common refinery sour waters. Due to the severity of the testing solution, the results are likely overly conservative and may lead to unrealistic integrity assessments of refinery vessels by applying API 579 Fitness for Service (FFS) assessments. Following the 1984 incident, most of the research carried out into sour water environments was targeted to material susceptibility and effects of sour water on new steel. Limited baseline data are available that quantify the effects of sour water on the mechanical properties on service aged or vintage materials. In fact, most data generated on the fracture toughness of steels in sour water has been undertaken for upstream projects, where the conditions are often more aggressive than in downstream applications. An ASME-API 579 Part 9 flaw analysis is required to be performed on wet H2S crack-like defects that fail an ASME-API 579 Part 7 Level 2 analysis [4]. To account for the loss in toughness associated with the presence of hydrogen embrittlement, lower bound crack arrest fracture toughness (KIR) is normally used as a lower bound estimate. Some wet H2S defects, such as Hydrogen Induced Cracking (HIC), require an API 579 Part 9 crack like flaw assessments even though they typically pass the Level 2 analysis. However, the FFS assessment is limited by the small tolerable crack lengths from API 579 Part 9 analysis due to the application of the lower bound KIR values. The use of lower bound KIR values is potentially overly conservative because it is a key input parameter into a crack like flaw assessment. Furthermore, the presence of H2S typically will cause subcritical crack growth due to the presence of hydrogen in the fracture process zone ahead of the crack tip. This can take place under constant load, or under fatigue. The latter issue is often evaluated for oil production facilities, particularly for offshore applications. In the downstream sector of the refining industry, the application of crack growth modelling is not normally applied due to the scarcity of applicable experimental data. As a result, either weld repair or protective coatings are typically used to prevent known tolerable flaw sizes from growing during future operation. To address such issues, a comprehensive test program was conducted to evaluate both the fracture toughness and subcritical crack growth properties of ex-service steels in mildly sour waters, which are more applicable to the downstream refining industry. The environmental severity was also explored by varying combinations of pH and H2S partial pressure. The main objective was to characterize the steel specimen performance in near neutral pH with high as well as low H2S concentrations.
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Jewel, Yead, Prashanta Dutta, and Jin Liu. "Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52337.
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Sugar (one of the critical nutrition elements for all life forms) transport across the cell membranes play essential roles in a wide range of living organism. One of the most important active transport (against the sugar concentration) mechanisms is facilitated by the transmembrane transporter proteins, such as the Escherichia coli lactose permease (LacY) proteins. Active transport of sugar molecules with LacY proteins requires a proton gradient and a sequence of complicated protein conformational changes. However, the exact molecular mechanisms and the protein structural information involved in the transport process are largely unknown. All atom atomistic simulations are able to provide full details but are limited to relative small length and time scales due to the computational cost. The protein conformational changes during sugar transport across LacY are large scale structural reorganization and inaccessible to all atom simulations. In this work, we investigate the molecular mechanisms and conformational changes during sugar transport using coarse-grained molecular dynamics (CGMD) simulations. In our coarse-grained force field, we follow the procedures developed by Han et al. [1, 2], in which the protein model is united-atom based and each heavy atom together with the attached hydrogen atoms is represented by one site, then the protein force filed is coupled with the MARTINI [3] water and lipid force fields. This hybrid force field takes the advantage of the efficiency of MARTINI force field for the environment (water and lipid), while retaining the detailed conformational information for the proteins. Specifically, we develop the new force fields for interactions between sugar molecules and protein by matching the potential of mean force between all-atom and coarse-grained models. Then we validate our force field by comparing the potential of mean force for a glucose interaction with a carbohydrate binding protein from our new force field, with the results from all atom simulations. After validation, we implement the force field for sugar transport across LacY proteins. Through our simulations we are able to capture the formation/breakage of the important hydrogen bonds and salt bridges, which are crucial to the overall conformational changes of LacY.
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Xu, Steven X., Douglas A. Scarth, Preeti Doddihal, and Paula Mosbrucker. "Feasibility of Developing a Risk-Informed Procedure to Define Pressure-Temperature Limits for Fracture Protection of Zr-Nb Pressure Tubes Under Heat-Up and Cool-Down Conditions." In ASME 2015 Pressure Vessels and Piping Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/pvp2015-46010.
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A fracture mechanics based calculation procedure is provided in the CSA Standard N285.8 to define pressure-temperature limits for fracture protection of CANDU Zr-Nb pressure tubes. The calculated pressure-temperature limits are used to construct a plant-specific operating envelope for pressure tubes under reactor heat-up and cool-down conditions. The current calculation procedure to define pressure-temperature limits for fracture protection is deterministic, and makes use of conservative inputs, including an axial through-wall crack of 20 mm in length, lower-bound fracture toughness, and a safety factor of 1.3 on the calculated critical internal pressure. The deterministic procedure is straightforward to use, and has a long history of successful applications of protecting pressure tubes from rupture. However, the deterministic procedure will potentially impose challenging operational constraints on pressure tubes at late life conditions, due to the predicted low fracture toughness of pressure tubes with high levels of hydrogen equivalent concentration. As an alternative, the CSA Standard N285.8 also permits probabilistic evaluation of fracture protection, which implies the acceptability of using risk-informed pressure-temperature limits for pressure tubes under reactor heat-up and cool-down conditions. The feasibility of developing a risk-informed procedure to define pressure-temperature limits for fracture protection of pressure tubes under heat-up and cool-down conditions is described in this paper. The intent is to use the risk-informed methodology to develop alternate pressure-temperature limits that allow more operational flexibility and still satisfy safety goals. The proposed risk-informed approach is consistent with risk-informed approaches that have been used in the U.S. nuclear industry.