1GS3: Contribution of a Low-Barrier Hydrogen Bond to Catalysis by Delta-5-3-Ketosteroid Isomerase is not Extremely High Compared to that of an Ordinary Hydrogen Bond. Low-Barrier Hydrogen Bond of Pi Ksi
Attempts have been made earlier to determine structures of HIV-1 and simian immunodeficiency virus (SIV) PRs complexed with substrate oligopeptides (10, 12). In these attempts, the crystals of the complex were prepared by using the method of cocrystallization, in the hope that crystal formation preceded product release. However, in the crystals obtained, HIV-1 PR was found to be complexed with only the N-terminal (P) product peptide, whereas SIV PR was found to be complexed with a C-terminal (Q) product peptide. No structures with both products bound simultaneously were obtained (12). Through careful superpositions of the two product complexes, these authors have concluded that unacceptably close separations between scissile carbon and nitrogen atoms (1.3-2.2 Å) preclude the presence of both products in the active site during cocrystallization. In contrast, we have attempted to prepare the complex by the soaking method. Because, as has been shown here, soaking does not result in cleavage of the ...
Introduction] Cooperative binding by proteins to DNA results in higher sequence specificity as well as greater sensitivity to concentration changes. We recently reported cooperative binding of two oligonucleotides at abutting sites by triple helix formation on double helical DNA. However, the enhanced binding observed was modest (a factor of 3.5) and likely due to favorable basestacking interactions between adjacent oligonucleotides and/or induced conformational changes propagated to adjacent binding sites. Thus, the issue arises whether cooperativity in oligonucleotide-directed triple helix formation can be enhanced by the addition of discrete dimerization domains. We report here the binding properties of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and bind neighboring sites on double helical DNA by triple helix formation. ...
hort hydrogen bonds are present in many chemical and biological sys-tems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to system-atically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and are widely present in different regions of the protein chain, such as the backbone or side chain, and in different secondary structural regions such as helices, strands and turns. ... ...
Those of us who are evaluating hydrogen futures need to become aware of the significant progress in new hydrogen energy research, which could revolutionize our energy picture in short order, once the necessary science and engineering are done. A sophisticated scenario for a hydrogen economy would include at least two eventualities: one is a "baseline" scenario which includes the tried-and-true hydrogen chemistry of internal combustion and fuel cells, as discussed in this Congress. The second brings into consideration new hydrogen energy and other new energy technologies, which could take the world by storm within a decade or two. As we conceptualize and begin to build solar-hydrogen systems, we would also want to increase our support of new hydrogen energy research which could lead to commercially viable units within years. Why should we do this? We need to keep our options open until such time we can make a more rational decisions about our energy future. On the one hand, we want to move into ...
A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen. An electronegative atom such as fluorine, oxygen, or nitrogen is a hydrogen bond acceptor, regardless of whether it is bonded to a hydrogen atom or not. An example of a hydrogen bond donor is ethanol, which has a hydrogen bonded to oxygen; an example of a hydrogen bond acceptor which does not have a hydrogen atom bonded to it is the oxygen atom on diethyl ether. Carbon can also participate in hydrogen bonding, especially when the carbon atom is bound to several electronegative atoms, as is the case in chloroform, CHCl3. The electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the atom with a positive partial charge. Because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, nevertheless represents a large charge ...
Get this from a library! Planar-Chiral Hydrogen-Bond Donor Catalysts : Synthesis, Application and Structural Analysis.. [Jakob Schneider]
Crystal structure of the title compound is orthorhombic, Pbca, a=7.8689(2)Å, b=9.6519(3)Å, c=31.3579(9)Å. The structure was solved by direct methods and refined by a full-matrix least squares procedure to final R (all)=0.0682 for 2853 unique diffractions merged from 24459 measured at 183(2)K. The molecule is formed by two planar moieties joined through an atom of sulphur. The short intramolecular O...O contact is 2.430(2)Å, the intramolecular hydrogen bond is slightly asymmetric. Theoretical ab initio calculations done at B3LYP/SVP and ONIOM(MP2/SVP:B3LYP/SVP) levels showed that the experimental geometry of pentanedione pseudoring is close to the geometry corresponding to a transition state on the asymmetric potential energy curve. Calculated energy difference between two minima is only 4.72 kJ/mol and the energy barrier 6.02 kJ/mol, which agrees well to ~6.6kJ/mol found in microwave spectroscopic study of malonaldehyde.
Green fluorescent protein (GFP) is a luminescent protein with a central chromophore and is used in biological imaging. By modifying the chromophore itself or the protein environment, the photophysical properties can be fine-tuned, yet until recently this has not been well understood. However, Lars Andersen (Aarhus University) and his group have developed a laser-action spectroscopy technique to enable the chromophore to be studied in a vacuum. This has revealed that a single hydrogen bond initiated a 0.5eV shift in the absorption spectrum of the GFP chromophore and highlights the importance of understanding the biophysics of chromophores and how this can help in the development of new colour chromophores.. ...
We demonstrate in a combined two-color pump-probe and quantum dynamical study that population of the O-H stretching oscillator of a medium-strong intramolecular hydrogen bond is redistributed along th
The chemistry of acrolein and crotonaldehyde-derived propano-deoxyguanosine (γ-OH-PdG and α-CH3-γ-OH-PdG) adducts was monitored in the 5´-CpG-3´ sequence within a dodecamer duplex by NMR spectroscopy, in situ, using a series of site-specific 13C- and 15N-edited experiments. One striking phenomenon was the formation of an interstrand DNA cross-link, predominantly a carbinolamine. The cross-link existed in equilibrium with the non-crosslinked aldehyde and its geminal diol hydrate. The ratio of aldehyde/diol increased at higher temperatures. The effects of the pH and complementary bases were examined. Molecular modeling suggested that the carbinolamine linkage should be capable of maintaining Watson-Crick hydrogen bonds at both of the tandem C•G base pairs. In contrast, dehydration of the carbinolamine cross-link to an imine (Schiff base) cross-link, or cyclization of the latter to form a pyrimidopurinone cross-link, was predicted to require disruption of Watson-Crick hydrogen bonds at one ...
(15)N and (1)H Solid-State NMR Investigation of a Canonical Low-Barrier Hydrogen-Bond Compound: 1,8-bis(dimethylamino) Naphthalene. (15)N and (1)H
As a means of making chitosan more useful in biotechnological applications, it was hydrolyzed using pepsin, chitosanase and α-amylase. The enzymolysis behavior of these enzymes was further systematically studied for its effectiveness in the production of low-molecular-weight chitosans (LMWCs) and other derivatives. The study showed that these enzymes depend on ion hydronium (H3O+), thus on pH with a pH dependence fitting R2 value of 0.99. In y = 1.484[H^+] + 0.114, the equation of pH dependence, when [H^+] increases by one, y (k_0/k_m) increases by 1.484. From the temperature dependence study, the activation energy (Ea) and pre-exponential factor (A) were almost identical for two of the enzymes, but a considerable difference was observed in comparison with the third enzyme. Chitosanase and pepsin had nearly identical Ea, but α-amylase was significantly lower. This serves as evidence that the hydrolysis reaction of α-amylase relies on low-barrier hydrogen bonds (LBHBs), which explains its low Ea in
Iron oxyhydroxide (FeOOH) mineral plays an important role in a variety of atmospheric, terrestrial and technological settings. Molecular resolution of reactions involving these minerals is thereby required to develop a fundamental understanding of their contributions in processes taking place in the atmosphere, Earths upper crust as well as the hydrosphere. This study resolves interactions involving four different types of synthetic FeOOH particles with distinct and well-defined surfaces, namely lath- and rod-shaped lepidocrocite (γ), goethite (α) and akaganéite (β). The surface and bulk reactivities of these particles are controlled by their distinct structures. When exposed to ambient atmospheric or aqueous conditions their surfaces are populated with different types of (hydr)oxo functional groups acting as reaction centers. These sites consist of hydroxyl groups that can be singly- (≡FeOH, -OH), doubly- (≡Fe2OH, μ-OH), or triply-coordinated (≡Fe3OH, μ3-OH) with underlying Fe ...
The coupling of hydrogen bonds is central to structures and functions of biological systems. Hydrogen bond coupling in sodium dihydrogen triacetate (SDHTA) is investigated as a model for the hydrogen bonded systems of the type O-H...O. The twodimensional potential energy surface is derived from the full-dimensional one by selecting the relevant vibrational modes of the hydrogen bonds. The potential energy surfaces in terms of normal modes describing the anharmonic motion in the vicinity of the equilibrium geometry of SDHTA are calculated for the different species, namely, HH, HD, DH, and DD isotopomers. The ground state wave functions and their relation to the hydrogen bond structural parameters are discussed. It has been found that the hydrogen bonds in SDHTA are uncoupled, that is elongation of the deuterated hydrogen bond does not affect the non-deuterated one ...
For the first time, a group of scientists from University of California, San Diego in United States has quantitatively measured the strength of hydrogen bonds between two complex molecules. They also observed an abnormal trend regarding the bond strength in the absence and presence of electron transfer. This work contributes to the understanding of how the hydrogen bond strength changes, an important point that reveals the way biological systems function.. Hydrogen bonds are a type of electrostatic attraction between hydrogen atoms and certain highly electronegative atoms including N, O and F. These bonds help to bind individual water molecules together and keep water as liquid at room temperature, a critical condition for the origin of life.. The researchers, led by Prof. Kubiak, picked two ruthenium-based complexes joined by hydrogen bonds as their studying platform. As shown in Figure 1, the two-molecule system has three states depending on whether the ends are charged or not: the neutral ...
Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecules three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server ...
Translatory and torsional vibrations of the molecules. Using melamine for an example, the elastic properties of the intermolecular hydrogen bonds are demonstrated. Using the thermally induced vibrations at 60 and 300 K it is shown, that they are the mechanical storage means of the specific heat of the melamine crystal.
In the case of DB32W (Fig. 2b), molecules 1 and 2 interact via a strong N4-H4B⋯N1 hydrogen bond (I) in the asymmetric unit with the stabilization energy of −11.2 kcal mol−1 (57% electrostatic contribution and 43% dispersion contribution). Molecule 2 interacts with the water molecule present in the asymmetric unit via a O1W-H1W⋯N3 hydrogen bond (IV; −6.5 kcal mol−1). Fig. 3b shows the molecular arrangement in the hydrate form down the ab plane. Here, the primary structural motifs involving short and highly directional strong hydrogen bonds generate different types of cyclic tetrameric (R1 and R2) and hexameric (R3 and R4) synthons (Desiraju and co-workers21 have discussed about the tetrameric and hexameric supramolecular synthons associated with a strong N-H⋯O hydrogen bond for aniline-phenol co-crystals). In this case, all the cyclic rings are interconnected with each other. Two symmetry independent molecules (1 and 2) and one water molecule form a molecular chain via the strong ...
Hydrogen bonds are much weaker than chemical bonds, but stronger than intermolecular van der Waals interactions ,,. ,, With this study, [AA] have opened up new ways to identify three-dimensional molecules such as nucleic acids or polymers via observation of hydrogen atoms ,,. Hydrogen bonds directly detected for the first time. May 12, 2017 https://m.phys.org/news/2017-05-hydrogen-bonds.html. Shigeki Kawai, Tomohiko Nishiuchi, et al. Direct quantitative measurement of the C═O⋅⋅⋅H-C bond by atomic force microscopy. Science Advances. 12 May 2017:Vol. 3, no. 5, e1603258 DOI: 10.1126/sciadv.1603258. http://advances.sciencemag.org/content/3/5/e1603258. ...
Abstract Various physicochemical factors influence DNA replication fidelity. Since it is now known that Watson-Crick hydrogen bonds are not necessary for efficient and selective replication of a base pair by DNA polymerase enzymes, a number of alternative physical factors have been examined to explain the efficiency of these enzymes. Among these factors are minor groove hydrogen bonding, base stacking, solvation, and steric effects. We discuss the concept of active site tightness in DNA polymerases, and consider how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair. A high level of active site tightness is expected to lead to higher fidelity relative to proteins with looser active sites. We review the current data on what parts and dimensions of active sites are most affected by size and shape, based on data with modified nucleotides that have been examined as polymerase substrates. We also discuss recent data on nucleotide analogs displaying ...
Alstom and Eversholt Rail have unveiled the design of a new hydrogen train for the UK market. The train, codenamed Breeze, will be a conversion of existing Class 321 trains, reengineering some of the UKs most reliable rolling stock. These trains could run across the UK as early as 2022....
Alstom and rolling stock operating company Eversholt Rail have unveiled the design of a new hydrogen train codenamed Breeze for the UK
The report was presented and discussed at the event Delivering the Hydrogen Economy, to showcase several hydrogen projects that position the North West as pioneers in this technology.. Ed Syson, chief safety and strategy officer at Cadent, said: "We carried out this study because there is an obvious desire and enthusiasm in the North West to think big and take a lead in finding low-cost ways to cut emissions. Industry and policy makers can now be assured that HyNet can deliver the bulk volume of hydrogen needed in the North West, via a pipeline network. Distributing it this way cuts the costs considerably and means hydrogen can complement electricity and advanced biofuels as an attractive option for future fuel.". At the event INOVYN, a wholly owned subsidiary of INEOS, also announced plans for a study into the potential for grid-scale storage of bulk hydrogen in salt caverns in mid Cheshire. Large-scale, low-cost hydrogen storage is essential to the deployment of hydrogen into the gas grid. A ...
The fact that the oxygen end of a water molecule is negatively charged and the hydrogen end positively charged means that the hydrogens of one water molecule attract the oxygen of its neighbor and vice versa. This is because unlike charges attract. This largely electrostatic attraction is called a hydrogen bond and is important in determining many important properties of water that make it such an important liquid for living things. Water can also form this type of bond with other polar molecules or ions such as hydrogen or sodium ions. Further, hydrogen bonds can occurr within and between other molecules. For instance, the two strands of a DNA molecule are held together by hydrogen bonds. Hygrogen bonding between water molecules and the amino acids of proteins are involved in maintaining the proteins proper shape ...
The Schellman motif is a widely observed helix terminating structural motif in proteins, which is generated when the C-terminus residue adopts a left-handed helical (aL) conformation. The resulting hydrogen-bonding pattern involves the formation of an intramolecular 6 - 1 interaction. This helix terminating motif is readily mimicked in synthetic helical peptides by placing an achiral residue at the penultimate position of the sequence. Thus far, the Schellman motif has been characterized crystallographically only in peptide helices of length 7 residues or greater. The structure of the hexapeptide Boc-Pro-Aib-Gly-Leu-Aib-Leu-OMe in crystals reveal a short helical stretch terminated by a Schellman motif, with the formation of 6 - 1 C-terminus hydrogen bond. The crystals are in the space group P212121 with a = 18.155(3) Å, b = 18.864(8) Å, c 5 11.834(4) Å, and Z = 4 . The final R1 and wR2 values are 7.68 and 14.6%, respectively , for 1524 observed reflections [Fo ,- 3(Fo)]. A 6 - 1 hydrogen bond ...
The donor and acceptor groups found in biological structures which form O - H ··· O bonds are given in Box 6.1. The C - OH ⋯ O hydrogen bonds are the primary intermolecular cohesive force between the...
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The structural features of the compounds presented in the solid state correlate strongly with those found in solution. For example, stereoisomer characterisation [(E)- or (Z)-] and the presence of intramolecular hydrogen bonding are confirmed by both techniques although the X-ray study reveals extended intermolecular hydrogen bonding, which is not observed in solution-based techniques (1H NMR). The predominant motif in the crystal structures is that of intermolecular hydrogen bonding (N-H…O=C) between the 1H-indol-2(3H)-one units. This motif is maintained in the one structure that contains a hydrogen-bonding hydrate molecule. However, one structure, methyl 3-(1-methylethylidene)-2-oxo-2,3-dihydro-1H-indole-1-carboxylate, a carbamate analogue lacking an N-H bond, displays no intermolecular hydrogen bonding.. ...
When an imbalance of electrical charge occurs within a molecule, the molecule is said to be polar or to exhibit polarity - in which case one end has a positive charge and the other has a negative charge (just like a magnet).. A polar molecule acts a little like an atom in need of an electron. Its positively charged end is attracted to negatively charged things around it - most commonly the negatively charged sides of other polar molecules.. The most common example of hydrogen bonding involves water molecules. This figure illustrates how the covalent bond between oxygen and hydrogen creates an electrical imbalance in water molecules and how, as a result, the negative end of one water molecule is attracted to the positive ends of another water molecule forming hydrogen bonds.. Hydrogen bonds are weak compared to covalent and ionic bonds, but these weak bonds play an important role in the environment and in living things. Theyre important in forming DNA chains, and they give liquid water some ...
These results show the dynamical nature of the quenching process; i.e. the quenching is due to the excited state interaction of AC with the amine. The mean value of the quenching constant obtained from Stern-Volmer plots of the steady-state and time-resolved fluorescence data, 5x1010 M-1 s-1, is similar to those of the quenching constants, kq, reported in Table 1 for the AC-DMF and AC-DMA systems. These quenching constants are, on the other hand, of the order of magnitude expected for a difussion controlled process in cyclohexane. Conversely, the changes observed in the absorption and fluorescence spectra of AC in cyclohexane upon the addition of methylethylcetone entirely resemble those produced by the amides.. On the basis of the above results, we conclude that, in the ground state, the pyrrolic NH group of AC interacts preferently with the carbonyl groups of the amides, but, in the excited state, the hydrogen-bonding interactions take place through the lone electron pair of the nitrogen atoms ...
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Step by Step Replication The DNA chains unwind and divide at the replication fork. The protein DNA Helicase moves along the DNA breaking the weak hydrogen bonds between the nitrogen bases. DNA Polymerase binds to the separated strands of DNA and assembles new nucleotides in a complimentary chain Covalent bonds hold the phosphates and sugars together. Hydrogen bonds hold the nitrogen bases together.
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Sugar molecules such as the one here are coated on the surface of many human pathogens. We are attempting to increase the protein-sugar binding interactions by extending a specific loop region of this protein. Please build upon this region, and extend it to make additional hydrogen bond interactions with the sugar. The best Foldit designs will then be used to generate potential pathogen capture reagents. Please read the blogpost for more info and if you are new to Foldit, make sure you have completed Intro Puzzle 5-2, and 7-1 through 7-4 before trying this puzzle ...
Introduction. Levels of Protein Structure Proteins are a group of organic compounds whose molecules consist of carbon, oxygen, nitrogen and sometimes sulphur atoms. They are condensation polymers of amino acids. Each amino acid carries two functional groups ( an amino group - NH and a carboxyl group - COOH.) These two functional groups are attached to a alpha-carbon along with hydrogen and the R group. The R group differs from amino acid to amino acid. Amino acids can be joined together by condensation. A hydrogen atom is removed from the amino group of one amino acid and this combines with an - OH group removed from the carboxylic acid of the other, forming a molecule of water. This is called a dipeptide bond. ...read more. Middle. or to fold into sheets (beta pleated sheet). The secondary structure of proteins occurs due to the formation of hydrogen bond in the polypeptide. It is the hydrogen bond which keeps the particular shape of the polypeptide chain. These hydrogen bonds are present ...
Thus when water molecules are close together, their positive and negative regions are attracted to the oppositely-charged regions of nearby molecules. The force of attraction, shown here as a dotted line, is called a hydrogen bond. Each water molecule is hydrogen bonded to four others. The hydrogen bonds that form between water molecules account for some of the essential - and unique - properties of water. ...
The nucleophilic reactivity of fluoride ion is altered in the presence of hydrogen-bond donors, including alcohols. Relatively little is known about the coordination involved; to rectify this, the X-ray structures of fourteen novel fluoride-alcohol complexes with tetrabutylammonium as the counterion have bee
Blockage of the interactions between immunologic checkpoint protein PD-1 and its ligand PD-L1 showed efficacy for cancer treatment. X-ray structures have captured static conformational snapshots of PD-1 and revealed that the CC loop adopts an open conformation in the apo-protein but turns into a closed form and interacts with PD-L1 in the complex. This structural heterogeneity brings difficulties to the structure-based drug discovery targeting PD-1. To gain insight into the role of the CC loop in molecular recognition, we have undertaken a comparative study between the open and closed conformations in apo-PD-1 and the PD-1/PD-L1 complex using molecular dynamics simulations. Results show that the moderate stability of intramolecular hydrogen bonds between SER71 and THR120 allows the CC loop to sample both the open and closed states in apo-PD-1. Binding of PD-L1 accelerates the open-to-closed switch and locks the loop in the closed state by four newly formed intermolecular... Read more ...
Cell fate is governed by combinatorial actions of transcriptional regulators assembling into multiprotein complexes. However, the molecular details of how these complexes form are poorly understood. One such complex, which contains the basic-helix-loop-helix heterodimer SCL:E47 and bridging proteins LMO2:LDB1, critically regulates hematopoiesis and induces Tcell leukemia. Here, we report the crystal structure of (SCL:E47) bHLH :LMO2:LDB1 LID bound to DNA, providing a molecular account of the network of interactions assembling this complex. This reveals an unexpected role for LMO2. Upon binding to SCL, LMO2 induces new hydrogen bonds in SCL:E47, thereby strengthening heterodimer formation. This imposes a rotation movement onto E47 that weakens the heterodimer:DNA interaction, shifting the main DNA-binding activity onto additional protein partners. Along with biochemical analyses, this illustrates, at an atomic level, how hematopoietic-specific SCL sequesters ubiquitous E47 and associated cofactors and
Hydrogen bonds range from the very strong, comparable with covalent bonds, to the very weak, comparable with van der Waals forces. Most hydrogen bonds are weak attractions with a binding strength about one-tenth of that of a normal covalent bond. Nevertheless, they are very important. Without them, all wooden structures would collapse, cement would crumble, oceans would vaporize, and all living things would disintegrate into inanimate matter.
The Smad family of proteins mediates transforming growth factor-beta signaling from cell membrane to the nucleus. In the nucleus, Smads serve as transcription factors by directly binding to specific DNA sequences and regulating the expression of ligand-response genes. A previous structural analysis, at 2.8-A resolution, revealed a novel DNA-binding mode for the Smad MH1 domain but did not allow accurate assignment of the fines features of protein-DNA interactions. The crystal structure of a Smad3 MH1 domain bound to a palindromic DNA sequence, determined at 2.4-A resolution, reveals a surprisingly important role for water molecules. The asymmetric placement of the DNA-binding motif (a conserved 11-residue beta-hairpin) in the major groove of DNA is buttressed by seven well ordered water molecules. These water molecules make specific hydrogen bonds to the DNA bases, the DNA phosphate backbones, and several critical Smad3 residues. In addition, the MH1 domain is found to contain a bound zinc atom ...
The rate constants for the reaction of dia zo diphenylmethane with 2-substituted cyclohex-1-enylcarboxylic acids, determined in butan-1-ol, 2-methylpropan-1-ol and ethylene glycol, together with the rate constants determined previously in methanol, ethanol, propan-1-ol and propan-2-ol, are correlated using the total solvatochromic equation, of the form log k = A o + sp* + aa + bb, the two parameter model log k = Ao + sp*+ aa and the single parameter model log k = Ao + bb, where p*, b and a represent the solvent dipolarity/polarizability, solvent hydrogen bond acceptor basicity and hydrogen bond donor acidity, respectively. The results obtained for 2-substituted cyclohex-1-enylcarboxylic acids are compared to the results for 2-subsituted benzoic acids under the same experimental conditions. ...
Success in evolution depends critically upon the ability of organisms to adapt, a property that is also true for the proteins that contribute to the fitness of an organism. Successful protein evolution is enhanced by mutational pathways that generate a wide range of physicochemical mechanisms to adaptation. In an earlier study, we used a weak-link method to favor changes to an essential but maladapted protein, adenylate kinase (AK), within a microbial population. Six AK mutants (a single mutant followed by five double mutants) had success within the population, revealing a diverse range of adaptive strategies that included changes in nonpolar packing, protein folding dynamics, and formation of new hydrogen bonds and electrostatic networks. The first mutation, AK(BSUB) Q199R, was essential in defining the structural context that facilitated subsequent mutations as revealed by a considerable mutational epistasis and, in one case, a very strong dependence upon the order of mutations. Namely, ...
Current polymorphism studies are being carried out using one of the following three alternatives: atom-atom potentials, DFT (Density Functional Theory) calculations and ad-hoc potentials. However, all of them have serious disadvantatges. 1) with software that uses atom-atom potentials: Advantages: fast and capable of working with large molecules. Disadvantages: the blind tests carried out by the Cambridge Crystallographic Data Centre are giving a 50% maximum success in the predictions. 2) with software based on DFT calculations: Advantages: good results Disadvantages: they are computationally very slow, so they are only used for very simple molecules compared with drug molecules. In addition, they have errors predicting van der Waals interactions and weak hydrogen bridges if not corrected empirically. 3) with software using ad hoc potentials for each molecule obtained from systematic exploration of the surface potential of intermolecular interactions: Advantages: efficient and faster.
The title compound, C15H12N2O2S, crystallizes in the ortho-rhom-bic space group Pna21, with two mol-ecules in the asymmetric unit (Z′ = 2). Each mol-ecule consists of a 2-hy-droxy Schiff base moiety linked through a spacer to a 2-amino-benzo-thia-zole moiety. Each mol-ecule contains an intra-molecular hydrogen bond between the -OH group and imine N atom, forming a six-membered ring. The two independent molecules are linked by a pair of C-H⋯O hydrogen bonds, forming dimers with an R 2 2(20) ring motif. These dimers are further lined into sheets in the ab plane by weak inter-molecular C-H⋯N inter-actions. The structure was refined as an inversion ...
Pressure-induced changes in 3hJNC′ scalar couplings through hydrogen bonds were investigated in the immunoglobulin binding domain of streptococcal protein G. 1H, 15N and 13C triple-resonance NMR spect
The polypeptide chain of a protein seldom forms just a random coil. Remember that proteins have either a chemical (enzymes) or structural function to fulfill. High specificity requires an intricate arrangement of 3-dimensional interactions and therefore a defined conformation of the polypeptide chain. In fact, some neurodegenerative diseases like Huntingtons may be related to random coil formation in certain proteins. The two most common secondary structure arrangements are the right-handed a-helix and the b-sheet, which can be connected into a larger tertiary structure (or fold) by turns and loops of a variety of types. These two secondary structure elements satisfy a strong hydrogen bond network within the geometric constraints of the bond angles w, j and f . The b-sheets can be formed by parallel or, most common, antiparallel arrangement of individual b-strands. ...
The substitution of the three essential purines in SL2 RNA with bases in which hydrogen bond donors and acceptors are replaced with aliphatic groups and with bases in which hydrogen bond donors and acceptors are placed incorrectly on the base has enabled us to compare the positive contributions of correct functional groups with the negative contributions of incorrectly placed functional groups to the binding specificity of the U1A protein. These comparisons have suggested that specific recognition of essential purines by the U1A protein varies from primarily discrimination against non-cognate bases for A1 to direct contributions of the base functional groups for G4. The base modifications introduced in these experiments are likely to not only eliminate and introduce individual interactions that either destabilize or stabilize the complex, but to affect other interactions in the complex that are energetically coupled with the modified base. Cooperative networks of interactions involving both ...
The title compound, (I), complements N-{4-[(benzenesulfonyl)amino]butyl}benzenesulfonamide, C16H20N2O4S2 (Linden & Bienz, 1999), (II), with a propyl chain in (I) replacing the butyl chain in (II).. In (I) (Fig. 1), the dihedral angle between the aromatic rings is 71.8 (2)°. The conformation of the central N-C-C-C-N chain linking the two S atoms can be described as gauche-gauche in terms of the N1-C7-C8-C9 and C7-C8-C9-N2 torsion angles of 72.5 (5) and 65.7 (5)°, respectively. Both N atoms in (I) are clearly in pyramidal coordination geometries, implying that the lone pairs on the N atoms are not conjugated with their adjacent benzene sulfonyl groups. A similar situation was observed in (II).. In the crystal of (I), the molecules are linked by N-H···O hydrogen bonds (Table 1). Considered separately, the N1 bond leads to [010] C(8) chains and the N2 bond generates [100] C(4) chains. Both the acceptor O atoms are part of the same (atom S2) sulfonyl group: it is perhaps notable that these O ...
Utilizing several different trialkylarsine oxides and substituted pyridine N-oxides as a hydrogen bond acceptors in tri-substituted guanidines we designed several very basic superbases possessing intramo-lecular hydrogen bonds (IHB-superbases), with proton affinity in the gas phase that comes very close to that of paradigmatic P4-tBu Schwesinger superbase and with pKa in acetonitrile up to 36 units.. ...
Hyundais newly announced Nexo fuel-cell EV (FCEV) was listed as one of the top products in the auomotive space in 2018 at the recent Consumer Electronic Show.
In the title compound, [Mn(C10H7N6)2(H2O)4]2H2O, the Mn2+ lies on a twofold rotation axis and is six-coordinated by two N atoms from your water OH?O and OH?N hydrogen bonds and poor C stacking inter-actions between the benzene rings [minimum ring centroid separation = 3. Cheng (2011 ?). An independent determination of the title structure is usually reported by Wang (2012 ?). Experimental ? Crystal data ? [Mn(C10H7N6)2(H2O)4]2H2O = 585.47 Monoclinic, = 19.1342 (18) ? = 13.2100 (4) ? = 13.3280 (13) ? = 131.056 (2) = 882531-87-5 2540.3 (4) ?3 = 4 Mo = 294 K 0.80 0.11 0.10 mm Data collection ? Rigaku/MSC Mercury CCD Rabbit Polyclonal to E2F6 diffractometer Absorption correction: multi-scan (> 2(= 1.31 2239 reflections 196 parameters 512 restraints H-atom parameters constrained max = 0.34 e ??3 min = ?0.55 e ??3 Data collection: (Rigaku/MSC, 1998) ?; cell refinement: 882531-87-5 (Rigaku/MSC, 2002 ?); program(s) used to solve structure: (Sheldrick, 2008 ?); program(s) used to refine structure: ...
The title compound is an important organic intermediate which has been used to synthesis the antineoplastic drug Cediranib. The drug has shown promising activity against diseases which include lung and breast cancer (Folkman, 1996).. The molecular structure of the title molecule is shown in Fig. 1. The bond lengths (Allen et al., 1987) and angles are within normal ranges. In the molecule the two aromatic rings (C1-C6) and (C8-C13) are almost normal to one another with a dihedral angle of 85.81 (10) °.. In the crystal, molecules are linked by C-H···O hydrogen bonds forming chains propagating along the b axis direction (Table 1 and Fig. 2). There are also C-H···π interactions present (Table 1) linking the chains to form two-dimensional networks lying parallel to (102).. ...
I have been trying two main recipes on this puzzle. Both are supposed to keep improving the score, but both have sometimes let the score drop while running. One of them has ended several times in an unusual manner, saying "User cancelled....." each time. I have also seen a higher score reported on the Group and Soloist Scoreboards than my Recipe Output, auto- and quicksaves, and Undo Graph have given. When I have tried to reset to this higher score, I could not do so. I may have seen this high score flash on the screen and then quickly disappear a few times in the little window that lists your Score, Rank, and Filter Score.. If you want more details, please send me a Foldit private message.. ...
The types of intermolecular forces present in ammonia, or NH3, are hydrogen bonds. The hydrogen bonds are many magnitudes stronger than other intermolecular forces in NH3; therefore, when examining...
Interaction map of inhibitor 6: hydrogen‐bonding network to structural water molecules in addition to direct hydrogen bonding to Thr 224, Thr 226 and Met
The well-ordered cross β-strand structure found in amyloid aggregates is stabilized by many different side chain interactions, including hydrophobic interactions, electrostatic charge and the intrinsic propensity to form β-sheet structures. In addition to the side chains, backbone interactions are important because of the regular hydrogen-bonding pattern. β-Sheet breaking peptide analogs, such as ...
The side chain of serine can form a hydrogen bond with the side chain of which of the following amino acids? threonine asparigine Can someone expla...
1EP4: Binding of the second generation non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding.
Part of the hydrogen bonding network, the hydrogen bonded interactions are showing as dashed lines. [symmetry codes: (I) -1+x, y, z; (II) 1-x, -y, 2-z; (III) 2-
According to Autocar in the UK, a new hydrogen fuel cell-powered city car will be unveiled next week. The car has been designed over the last three years
Ive been spending a lot of time lately looking at solutions for automated business processes that are based on the online, low-barrier, and highly collaborative worlds of SaaS and Web 2.0. Primarily, this is part of my exploration of using Web 2.0 in the enterprise, sometimes called Enterprise 2.0, but which we call Enterprise Web 2.0 here.
eng] The interplay between two important non-covalent interactions involving aromatic rings is studied by means of ab initio calculations (MP2/6-31++G**). They demonstrate that synergetic effects are present in complexes where cation-p and hydrogen bonding interactions coexist. These synergetic effects have been studied using the atoms-in-molecules theory and the Molecular Interaction Potential with polarization partition scheme ...
a chemical bond consisting of a hydrogen atom between two electronegative atoms (e.g., oxygen or nitrogen) with one side be a covalent bond and the other being an ionic bond. ...
This interactive activity helps learners visualize the role of electrons in the formation of ionic and covalent chemical bonds. Students explore different types of chemical bonds by first viewing a single hydrogen atom in an electric field model.…
i want to fing out why ice float on the water. everybody know the electron is negative and proton is positive.when 2 hydrogen covalently bonded with
Understanding the way that proteins and other biological molecules operate means digging deeply -- examining not only their structures, but also seein
In the essentially planar title mol-ecule, C(10)H(9)BrN(4)S, the C=N double bond is in a trans configuration. In the crystal structure, the S atom acts as a hydrogen-bond acceptor for the aromatic NH, aliphatic NH and terminal NH(2) groups of three symmetry-related mol-ecules, forming a weak hydrogen-bonded layer structure.. ...
Hydrogen bonds hold DNA strands together. Nitrogenous bases are between these two strands that link together in a specific manner with different types of hydrogen...
The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space groupP21(#4) witha= 17.538 34(5),b= 8.326 89(2),c= 7.261 11(2) Å,β= 98.7999(2)°,V= 1047.929(4) Å3, andZ= 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in thebc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O-H···O hydrogen bonds. Several C-H···O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™as entry 00-064-1501. ...
TY - JOUR. T1 - Unprecedented four-way-output molecular response system based on biphenyl-2,2′-diyldiacridiniums. T2 - induction of axial chirality through intramolecular hydrogen bonds between chiral amide groups. AU - Suzuki, Takanori. AU - Ohta, Kenji. AU - Nehira, Tatsuo. AU - Higuchi, Hiroki. AU - Ohta, Eisuke. AU - Kawai, Hidetoshi. AU - Fujiwara, Kenshu. PY - 2008/1/28. Y1 - 2008/1/28. N2 - Upon the attachment of N-(R)-2-phenylethylamide moieties to the acridinium units of the title dication, intramolecular hydrogen bonds induce a diastereomeric preference in terms of axial chirality (70% de at -40 °C in CH2Cl2). Thus, external stimuli induce not only UV-vis and fluorescence spectra changes but also changes in the CD and fluorescence-detected CD (FDCD) spectra, realizing unprecedented four-way-output molecular response systems.. AB - Upon the attachment of N-(R)-2-phenylethylamide moieties to the acridinium units of the title dication, intramolecular hydrogen bonds induce a ...
Its hard to find anything that is "always" true in chemistry, but Id bet that within a series of molecules where the only variable is the number of $\ce{OH}$ groups, your statement is generally true, so I basically agree with your position. Your analysis and examples are also good. As you pointed out, it is about intermolecular forces. Specifically, molecules with hydroxyl groups can form intermolecular hydrogen bonds (see first picture below). These hydrogen bonds cause the molecules to "stick" together and act as if they had a higher molecular weight. Sugars have many hydroxyl groups that give rise to many intermolecular hydrogen bonds and cause sugars to flow in a slow, syrupy manner.. ...
The conversion of cholesterol to pregnenolone is a physiologically essential process which initiates with two sequential hydroxylation processes catalyzed by cytochrome P450 side-chain cleavage enzyme (P450SCC). Extensive efforts have been exerted; however, the mechanistic details remain obscure. In this work, we employed the dispersion-corrected density functional theoretical (DFT-D) calculations to investigate the mechanistic details of such hydroxylation processes. Calculated results reveal that the active intermediate Compound I (CpdI) of P450SCC hydroxylates cholesterol efficiently, which coincides with previous spectrometric observations. The hydrogen bond effect of water molecule within the active site lowers the energy barrier significantly. Intriguingly, the adjacent hydrogen bond (H-bond) between the hydroxyl group of the substrate and the oxo group of CpdI in the second hydroxylation affects the H-abstraction significantly. Such H-bond was weakened during the C-H bond activation ...
Three new hydrogen filling stations opened in California within the span of one week, bringing the total to 39. The new stations are in Palo Alto, at LAX (Los Angeles International Airport), and in the Sacramento area. The Citrus Heights hydrogen station, the 37th retail hydrogen station in California, is...
A hydrogen bond (often informally abbreviated H-bond) is a partial intermolecular bonding interaction between a lone pair on an electron rich donor atom, particularly the second-row elements nitrogen (N), oxygen (O), or fluorine (F), and the antibonding orbital of a bond between hydrogen (H) and a more electronegative atom or group.[4] Such an interacting system is generally denoted Dn-H···Ac, where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The use of three centered dots for the hydrogen bond is specifically recommended by the IUPAC.[5] While hydrogen bonding has both covalent and electrostatic contributions, and the degrees to which they contribute are currently debated, the present evidence strongly implies that the primary contribution is covalent.[6] Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule).[7][8][9][10] Depending on the nature of ...
Textbook solution for Chemistry & Chemical Reactivity 9th Edition John C. Kotz Chapter 11 Problem 8PS. We have step-by-step solutions for your textbooks written by Bartleby experts!
We know what a hydrogen bond is, so now we apply it to the freezing of water. When the molecules of water are still a liquid, they are free-moving and make/break hydrogen bonds very easily and frequently. The molecules can slip in and out at close proximity due to its high energy. But when the temperature drops, the molecules lose energy, slow down, and keep their hydrogen bonds for longer. Soon enough, at 4° C, the hydrogen bonds start altering the layout of the molecules. A single water molecule can only form a maximum of four hydrogen bonds with its neighboring molecules. At 4° C and below, a molecule will "keep" its bonds and lock into a crystalline lattice with its four neighbors. Then the molecules are at "arms length" so to speak and there are less molecules in a given space; the density is now lower ...
A symmetric hydrogen bond is a special type of hydrogen bond in which the proton is spaced exactly halfway between two identical atoms. The strength of the bond to each of those atoms is equal. It is an example of a 3-center 4-electron bond. This type of bond is much stronger than "normal" hydrogen bonds, in fact, its strength is comparable to a covalent bond. It is seen in ice at high pressure, and also in the solid phase of many anhydrous acids such as hydrofluoric acid and formic acid at high pressure. It is also seen in the ion [F-H-F]−. Much has been done to explain the symmetric hydrogen bond quantum-mechanically, as it seems to violate the duet rule for the first shell: The proton is effectively surrounded by four electrons. Because of this problem, some consider it to be an ionic bond. ...
In the title compound, C18H22N2O4S2, the 2H-chromene ring system is essentially planar (r.m.s. deviation = 0.012 A ° ). The molecular conformation is stabilized by a C-H� � �O hydrogen bond. In the crystal, N-H� � �S and C-H� � �O hydrogen bonds occur, the former enclosing an R2 2(22) ring motif, and lead to the formation of a two-dimensional slab-like network lying parallel to (101). �-� interactions are observed between inversion-related aromatic rings [shortest centroid-centroid distance = 3.6300 (11) A ° ].. ...
Hydrogen is the simplest element. Each atom of hydrogen has only one proton. Hydrogen is also the most plentiful gas in the universe. Stars like the sun consist primarily of hydrogen.. The sun is essentially a giant ball of hydrogen and helium gases. In the suns core, hydrogen atoms combine to form helium atoms. This process-called fusion-gives off radiant energy.. The radiant energy from the sun gives earth light and helps plants grow. Radiant energy is stored as chemical energy in fossil fuels. Most of the energy that people use today originally came from the suns radiant energy.. Hydrogen as a gas (H2) is not found by itself on earth. Hydrogen gas is found only in compound form with other elements. Hydrogen combined with oxygen is water (H2O). Hydrogen combined with carbon forms different compounds like methane (CH4), coal, and petroleum. Hydrogen is found in all growing things and is an abundant element in the earths crust.. Hydrogen has the highest energy content of any common fuel by ...
terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H group. Based on this, eight types of secondary structure are assigned. The 310 helix, α helix and π helix have symbols G, H and I and are recognized by having a repetitive sequence of hydrogen bonds in which the residues are three, four, or five residues apart respectively. Two types of beta sheet structures exist; a beta bridge has symbol B while longer sets of hydrogen bonds and beta bulges have symbol E. T is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (where the angle between ...
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.
Two distinct isomers for the binary complex between phenylacetylene and methylamine were observed. The first complex is characterized by the presence of a C-H center dot center dot center dot N hydrogen bond between the acetylenic C-H group and the N atom of methylamine. In the second complex the N-H group of methylamine interacts with the pi electron density of the benzene ring accompanied by a peripheral interaction between the methyl C-H group and the pi electron density of the C C bond. Stabilization energies and Gibbs free energies at the complete basis set (CBS) limit of the coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] suggest that while the C-H center dot center dot center dot N hydrogen bonded complex is the global minimum, the N-H center dot center dot center dot pi hydrogen bonded complex is a high energy local minimum. The formation of the N-H center dot center dot center dot pi complex could be related to kinetic trapping or higher ...
Intramolecular hydrogen bonding in alpha-phenylcinnamic acids and their heteroatom-containing derivatives studied by ab initio quantum chemical methods. (deposited 2013. Jan. 25. 11:24) [Ezt látja] ...
Although lamivudine and emtricitabine, two L-deoxycytidine analogs, have been widely used as antiviral drugs for years, it is structrually unknown how they are bound and incoproated by any DNA polymerases or reverse transcriptases. To fill the void, we solved 12 high resolution ternary crystal structures of human DNA polymerase lambda, DNA, and L-dCTP or the triphosphates of lamivudine and emtricitabine. The structures of these 12 ternary complexes reveal that relative to natural D-dCTP in the canonical ternary structure, these L-nucleotides all have their ribose rotated by 180°. Among the four ternary complexes with a specific L-nucleotide in each asymmetric unit, two are similar and show that the L-nucleotide forms three Watson-Crick hydrogen bonds while in the remaining two similar ternary complexes, the L-nucleotide surprisingly interacts with the side chain of a conserved active site residue R517 through one or two hydrogen bonds. Our mutagenic and kinetic studies further demonstrate that ...
Polyethylene glycol (PEG) is a unique polymer material with enormous applicability in many industrial and scientific fields. Here, its use as macromolecular crowder to mimic the cellular environment in vitro is the focus of the present study. We show that femtosecond mid-IR pump-probe spectroscopy using three different IR probes, HDO, HN3, and azido-derivatized crowder, provides complete and stereoscopic information on water structure and dynamics in the cytoplasm-like macromolecular crowding environment. Our experimental results suggest two distinct subpopulations of water molecules: those that interact with other water molecules and those that are part of a hydration shell of crowder on its surface. Interestingly, water dynamics even in highly crowded environment remains bulk-like in spite of significant perturbation to the tetrahedral H-bonding network of water molecules. That is possible because of the formation of water aggregates (pools) even in water-deficient PEGDME-water solutions. In ...
Gelatin is a protein, made from the hydrolysis of collagen, a protein that makes up about a third of all mammalian tissue. Collagen is what makes up much of the connective tissue, tendons, and the protein part of bones. Hydrolysis in proteins is the process of adding a molecule of water to break the bonds between some of the amino acids, thereby making the protein chains smaller. Collagen forms a triple helix, where three chains of connected amino acids form weak hydrogen bonds between the double bonded oxygen atoms and the hydrogen atoms attached to the adjacent chains nitrogens. The three chains then twist together like three cords in a rope. In gelatin, when the triple helices are heated in water, they open up, and some of the hydrolyzed ends fray out to tangle with other ropes, and water is trapped in the strands. The result is a gel, a wiggly semi-solid mass. ...
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A system for producing, dispensing, using and monitoring a hydrogen enriched fuel includes a producing system configured to produce the hydrogen enriched fuel, a vehicle having an engine configured to use the hydrogen enriched fuel, and a dispensing system configured to store and dispense the hydrogen enriched fuel into the vehicle. The system also includes a fuel delivery system on the vehicle configured to deliver the hydrogen enriched fuel to the engine, and a control system configured to control the producing system and to monitor the use of the hydrogen enriched fuel by the vehicle. A method includes the steps of producing hydrogen gas and a hydrocarbon fuel, blending the hydrogen gas and the hydrocarbon fuel into the hydrogen enriched fuel, using the hydrogen enriched fuel in the engine, and tracking emissions during the producing step and during the using step.
DNA is made of the sugar Deoxyribose, and is an acid. The "rungs" of the molecule are made of a phosphate group linked to a deoxyribose sugar which are linked to one of four nitrogenous bases: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). A fits with T and C fits with G and vice versa. The bases are linked by weak Hydrogen bonds so it can easily replicate. When it replicates, the molecule unwinds, and an enzyme called DNA Polymerase moves down the bonds and "unzips" it. Then another strand comes and fits with correct corresponding base. This happens in the Cells nulceus. The molecule replicates when the cell divides. Thats DNA basics for you. Also, to extract DNA, the lower the temp., the better perserved DNA stays when the cell gets dissolved. ...
# 2006 International Union of Crystallography All rights reserved In the crystal structure of the title compound, C16H18N2O2, the indole moiety is nearly planar. The two carbonyl groups are almost perpendicular, with a torsion angle of 105.7 (4) , and the single C-C bond linking the two carbonyl groups is 1.515 (5) Å in length. The molecules are linked together by N-H O intermolecular hydrogen bonds.
Air Products has announced plans to construct a new 180-mile long pipeline connecting its existing Louisiana and Texas hydrogen pipeline systems, creating the worlds largest hydrogen plant and pipeline supply network.
The U.S. Department of Energy has awarded $7 million to projects expected to advance the development of hydrogen fuel cell systems for variously sized vehicles.
Irish drugs and alcohol research, data, policy and sources of evidence on prevention, treatment, rehabilitation, crime and consequences.
For the study different datasets were considered i.e the Drugs( taken from drug bank and KEGG drugs),Metabolites(HMDB, HumanCYC, BiGG),Toxic( DSSTox, FDA Carcinogeneticity, ITER, Super Tox icity), Natural Products(ZINC NP database),Leads(BIONET, Maybridge),NCI and CHEMBL.From the compounds duplicates entries ,organic ions, metal ions are removed and also corrupted or missing structure are removed. After all the filtering process the data was clustered in Pipleline pilot "Clara" program using ECFP_4 or FCFP_4 fingerprints. Physicochemical analysis was done using clutering with respect to the Lipinski properties: molecular weight, the number of hydrogen bond acceptors, AlogP (a hydrophobicity measure) and the number of hydrogen bond donors and other descriptors such as the molecular polar surface area, Molecular solubility, number of rings, number of rotatable bonds. A scaffold analysis was also done and also the results are analysed. ...
Researchers from the University of Basels Swiss Nanoscience Institute network have reported the results in the journal Science Advances, phys.org wrote.. Hydrogen is the most common element in the universe and is an integral part of almost all organic compounds.. Molecules and sections of macromolecules are connected to one another via hydrogen atoms, an interaction known as hydrogen bonding.. These interactions play an important role in nature, because they are responsible for specific properties of proteins or nucleic acids and, for example, also ensure that water has a high boiling temperature.. To date, it has not been possible to conduct a spectroscopic or electron microscopic analysis of hydrogen and the hydrogen bonds in single molecules, and investigations using atomic force microscopy have also not yielded any clear results.. Dr. Shigeki Kawai, from Professor Ernst Meyers team at the Swiss Nanoscience Institute and the Department of Physics at the University of Basel, has now ...
We synthesized the new supramolecular host molecules 7 and 13 based on functionalized resorcarenes bearing Kemps triacid. Conformations in solution have been investigated and the influence of intra-and intermolecular hydrogen bonds from the triacid was shown by low temperature and DOSY NMR experiments. The results of host 7 are supported by DFT calculations. The binding behaviour of 7 towards different 2-amino pyridincs in chloroform has been investigated by NMR titrations. The association constants reach from K 207 M-1 for 2-amino-5-cyano pyridine to K=1551 M-1 for 2-amino-4-methyl pyridine. The association constants of the formed complexes of 7 with 2-amino pyridines were compared with those of the simple host systems 14 and 15 in order to evaluate the influence of the attached resorcarene host. (c) 2008 Elsevier Ltd. All rights reserved ...
Qorianka Kilcher with her new Honda FCX Clarity hydrogen-powered car. Photo: Honda Qorianka Kilcher Gets a New Honda FCX Clarity Hydrogen Car Green actress Qorianka Kilcher, know for her role of Pocahontas, has been driving a first generation Honda
STM image simultaneously acquired for H2O and D2O dimers (size: 5.5×5.5 nm^2, 2.4×2.0 nm^2). The dimer is characterized by the bi-stable fluctuating image. The dimer consists of hydrogen-bond donor and acceptor molecules. The fluctuating image results from the interchange of the donor and acceptor, in which the roles of their molecules are exchanged. Interestingly, the STM image of the dimer shows drastic change upon substitution with D2O. It suggests that the interchange process involves quantum tunneling. The image was obtained at 24 mV sample bias and 0.5 nA tunneling current at 6 K ...