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Hydrogen Bonding

Korbinian Liebl, Martin Zacharias
The sequence dependent structure and flexibility of the DNA double helix is of key importance for gene expression and DNA packing and it can be modulated by DNA modifications. The presence of a C5'-methyl group in thymine or the frequent C5'-methylated-cytosine affects the DNA fine structure, however, the underlying mechanism and steric origins have remained largely unexplained. Employing Molecular Dynamics free energy simulations that allow switching on or off interactions with the methyl groups in several DNA sequences, we systematically identified the physical origin of the coupling between methyl groups and DNA backbone fine structure...
December 12, 2018: Nucleic Acids Research
Hui Yang, Xian-Ying Duan, Jia-Jia Lai, Yan Zhao, Xin-Jun Wang, Mei-Lin Wei
Cocrystals and isomers, two well-known unique concepts in supramolecular chemistry, are rarely put together until now. For the first time, we report three unprecedented and interesting cocrystals of twin isomers of coordination polymers (CPs) in situ formed by typical Keggin anions and Cu(II)-4,4'-bis(hydroxymethyl)-2,2'-bipyridine (Cu(II)-H2 L) complex moieties. In cocrystals 1-3, the Cu(II)-H2 L complex moieties are quadrisupported on Keggin-type anions through W(Mo)-Ot-Cu-Ot-W(Mo) (Ot is the terminal O atom) links in the crystal to form two twin ionic/neutral CPs with a fixed chemical stoichiometry...
December 12, 2018: Inorganic Chemistry
A-Reza Nekoei, Morteza Vatanparast
Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
Latévi M Lawson Daku
We report a detailed ab initio molecular dynamics (AIMD) study of the structural and vibrational properties of aqueous [Fe(tpy)2]2+ (tpy = 2,2':6',2''-ter-pyridine) in the low-spin (LS) and high-spin (HS) states, which extends our previous work on aqueous [Fe(bpy)3]2+ (bpy = 2,2'-bipyridine) [L. M. Lawson Daku and A. Hauser, J. Phys. Chem. Lett., 2010, 1, 1830-1835; L. M. Lawson Daku, Phys. Chem. Chem. Phys., 2018, 20, 6236-6253]. Upon the LS → HS change of states, the axial and distal Fe-N bonds of aqueous [Fe(tpy)2]2+ are predicted to lengthen by 0...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
Ali H Tayeb, Mehdi Tajvidi
Cellulose nanofibrils (CNFs) are able to form strong oxygen-barrier films suitable for food packaging but lack the needed water resistance in comparison to plastics. Desired water barrier quality can be achieved by applying mineral additives within the nanofibrils network. In current contribution, a sustainable hybrid system with improved water-barrier function is proposed by incorporating colloidal montmorillonite nano-clay (MMT) and two crosslinking agents namely; polyamidoamine epichlorohydrin (PAE) and Acrodur® thermoset acrylic resin (ACR) into CNF interfaces...
December 12, 2018: ACS Applied Materials & Interfaces
Naoto Sato, Kazuma Tochigi, Yoshiyuki Kuroda, Hiroaki Wada, Atsushi Shimojima, Kazuyuki Kuroda
The controlled assembly of molecular building blocks enables the rational design of nanomaterials. In this study, two types of cage-type oligosiloxanes with double-three ring (D3R) structures are modified with dimethylsilanol groups to form supramolecular assemblies. One is the siloxane cage derived from Si(OEt)4 (denoted as the Q6 cage), and the other is the organosiloxane cage derived from (EtO)3Si-CH2-Si(OEt)3 (denoted as the T6 cage). The syntheses of the silanol-modified cages are performed in two steps: (i) dimethylsilylation of the corner Si-O- groups on the Q6 and T6 cages to introduce Si-H groups and (ii) subsequent oxidation of the Si-H groups to Si-OH groups...
December 12, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Leonid B Krivdin
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates...
October 2018: Progress in Nuclear Magnetic Resonance Spectroscopy
Longgang Jia, Wenjuan Wang, Jingcheng Sang, Wei Wei, Wenping Zhao, Fuping Lu, Fufeng Liu
Aggregation of amyloid β peptide (Aβ) is closely associated with the occurrence and development of Alzheimer's disease (AD). Reproducible and detailed studies on the aggregation kinetics and structure of various aggregates have been conducted using recombinant Aβ peptides. While the His6 tag is commonly used in the purification of recombinant proteins due to its great simplicity and affinity, there is little information on the aggregation of His6-tagged Aβ and its corresponding cytotoxicity. Moreover, it is also unclear whether there is an effect of the His6-tag on the amyloidogenicity and cytotoxicity of recombinant Aβ1-42...
December 11, 2018: ACS Chemical Neuroscience
Hongwei Ren, Xue Wang, Shaohan Lian, You Zhang, Erhong Duan
Deep eutectic solvents (DES) are generally composed of two or three cheap and safe components that are associated with each other via hydrogen bonds. The formation Caprolactam (CPL)-tetraalkyl ammonium halide (TAAX) DES and its hydrate were investigated using React IR. TAAX was introduced to CPL in the molten state at 353.15 K, the intermolecular H-N-C=O⋯H-N-C=O hydrogen bonds (CPL dimer) transfer to X- ⋯H-N-C=O (CPL-TAAX DES). When water was added to CPL-TAAX DES, intermolecular X- ⋯H-N-C=O⋯H-O-H hydrogen bonds appeared, and CPL-TAAX DES hydrate was formed...
December 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Jinxing Wang, Jidong Liang, Li Sun, Sha Gao
Biomass washout from high-speed anaerobic suspended bed bio-reactors is still a challenge to their stable operation. Preserving active biomass to efficiently retain biomass in the reactor is one of the solutions to this problem. Herein, two carriers (polyvinyl alcohol/chitosan (PVA/CS) and PVA/CS/Fe gel beads) were prepared using the cross-linking method. The fourier transform infrared (FTIR) and 13 C nuclear magnetic resonance (13 C NMR) analyses showed that PVA/CS gel beads formed mainly through hydrogen-bonds (NH2 OH- )...
December 3, 2018: Chemosphere
V Divya, V L Pushpa, K B Manoj
Designing of new potential specific inhibitors for CDK4 is very important in cancer therapy. The imperative features that can inhibit CDK4 were identified and refined by docking under standard precision mode, extra precision mode, extra precision mode with core-constraints and induced fit using extra precision protocol. Statistically significant correlation was observed when docking experiments in the extra precision mode carried out by applying core constraints in the ligand molecule which forms two specific hydrogen bonds with Val96 of CDK4...
December 8, 2018: Chemical Biology & Drug Design
Yu Deng, Da Tang, Qiu-Ru Wang, Sheng Huang, Li-Zhi Fu, Cheng-Hong Li
To develop new antibiotics owning a special mechanism, we used the molecular assembly method to synthesize a series of novel pleuromutilin derivatives containing a cinnamic acid scaffold at the C-14 side chain. We evaluated their antibacterial activity and used in silico molecular docking to study their binding mode with the target. The structure-activity relationship (SAR) study suggested that compounds with NO2 (13e), OH (13u), and NH2 (13y) appeared more active (0.0625-2 µg/mL) in vitro against several penicillin-resistant Gram-positive bacteria and the position of the substituent on the benzene ring would affect the activity...
December 7, 2018: Archiv der Pharmazie
Kazuki Fujii, Koichi Mitsudo, Hiroki Mandai, Toshinobu Korenaga, Seiji Suga
We developed an efficient enantioselective acyl migration reaction of furanyl carbonates to construct all-carbon quaternary stereogenic centers. In some cases, the reactions required only 0.05 mol % (minimum 500 ppm order) of catalyst and showed a high TOF value (3,640 h-1). Multigram-scale reactions (10 grams) also proceeded with high enantioselectivity (>99:1 er) in quantitative yield. The catalyst was robust and easily recovered in 98% yield, and could be recycled in the same reaction without a loss of catalytic activity or enantioselectivity...
December 7, 2018: Chemistry: a European Journal
Lin-Ling Yu, Zi-Fen Luo, Ying-Ying Zhang, Shi-Chuan Wu, Cao Yang, Jian-Hua Cheng
The presence of tetracycline antibiotics (TCS) in the water and wastewater has raised growing concern due to its potential environmental impacts; thus, their removal is of high importance. In this study, a novel aluminum-based MOF/graphite oxide (Al-MOF/GO) granule was prepared as an adsorbent for the removal of TCS including oxytetracycline (OTC) and chlortetracycline (CTC). The adsorbent was characterized via XRD, FTIR, BET, SEM, and XPS methods. The granules exhibited similar crystal structure and some new mesopores appearing compared to the parent Al-MOF/GO powder...
December 8, 2018: Environmental Science and Pollution Research International
Lining Zhao, Wansong Zong, Hao Zhang, Rutao Liu
The toxic mechanism of cadmium-quantum dot (Cd-QDs) to organisms is still debating. In this paper, it was found that Cd-QDs could induce adverse effects to kidney by entering into cells in a time and dose manner and disturbing the redox balance in vivo. As a selenium containing protein, glutathione peroxidase3 (Gpx3) plays a crucial role in maintaining the balance of redox system. The decrease of Gpx3 activity might be related to the imbalance of redox system. Similar to the animal results, it was demonstrated that Gpx3 activity is also inhibited by Cd-QDs in vitro...
December 10, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
Ryohei Yamakado, Haruna Ishibashi, Yukari Motoyoshi, Nobuhiro Yasuda, Hiromitsu Maeda
α-Aryl-substituted dipyrrolylquinoxalines were synthesized and were converted to deprotonated forms stabilized by intramolecular hydrogen bonding, providing π-electronic anions, which act as building units of ion-pairing assemblies in combination with countercations.
December 11, 2018: Chemical Communications: Chem Comm
Muhammed Shah Miran, Mahfuzul Hoque, Tomohiro Yasuda, Seiji Tsuzuki, Kazuhide Ueno, Masayoshi Watanabe
In order to identify the key factor governing the transport properties and extent of proton transfer in protic ionic liquids (PILs), a series of PILs were prepared by simple neutralisation of a super-strong acid, bis(trifluoromethanesulfonyl)amide acid (H[NTf2]), with a range of amines comprising diverse structures, including secondary and tertiary amines. The bulk physicochemical properties of the resulting PILs with a wide variation in the ΔpKa values of the constituent acid and protonated bases were compared to those of previously reported PILs derived from a super-strong base, 1,8-diazabicyclo[5...
December 10, 2018: Physical Chemistry Chemical Physics: PCCP
Daniel C Elton, Michelle Fritz, Marivi Fernández-Serra
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy...
December 10, 2018: Physical Chemistry Chemical Physics: PCCP
Aleksandr V Zhuravlev, Oleg V Vetrovoy, Elena V Savvateeva-Popova
Kynurenines, the products of tryptophan oxidative degradation, are involved in multiple neuropathologies, such as Huntington's chorea, Parkinson's disease, senile dementia, etc. The major cause for hydroxykynurenines's neurotoxicity is the oxidative stress induced by the reactive oxygen species (ROS), the by-products of L-3-hydroxykynurenine (L-3HOK) and 3-hydroxyanthranilic acid (3HAA) oxidative self-dimerization. 2-aminophenol (2AP), a structural precursor of L-3HOK and 3HAA, undergoes the oxidative conjugation to form 2-aminophenoxazinone...
December 10, 2018: PLoS Computational Biology
Manuel Bañó-Polo, Carlos Baeza-Delgado, Silvia Tamborero, Anthony Hazel, Brayan Grau, IngMarie Nilsson, Paul Whitley, James C Gumbart, Gunnar von Heijne, Ismael Mingarro
Integral membrane proteins are assembled into the ER membrane via a continuous ribosome-translocon channel. The hydrophobicity and thickness of the core of the membrane bilayer leads to the expectation that transmembrane (TM) segments minimize the cost of harbouring polar polypeptide backbones by adopting a regular pattern of hydrogen bonds to form α-helices before integration. Co-translational folding of nascent chains into an α-helical conformation in the ribosomal tunnel has been demonstrated previously, but the features governing this folding are not well understood...
December 7, 2018: Nature Communications
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